title: P29-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 29


title: P37-T4

status: Public on Apr 17 2025

type: RNA

city: Valencia

first: Angela

middle: L.

last: Riffo-Campos

state: Valencia

address: Avda. Blasco Ibáñes, 17

department: Department of Biochemistry and Molecular Biology

country: Spain

institute: University of Valencia, and INCLIVA

hyb_protocol: The hybridization of the samples was carried out on SurePrint G3 Human Gene Expression v3 8x60K crystals (AMADID 72363).

scan_protocol: The scanning of the crystals after hybridization was carried out on the Agilent G2600D Scanner and finally the data was extracted with the Agilent Feature Extraction 12.0.3.2 program.

data_processing: The background correction was performed using the ”normexp” method implemented in the R "limma" package. Normalization of expression intensities was performed using the "normalizeBetweenArrays" function, by the "quantile" method of the "limma" package. Statistical analysis of the data was performed by adjusting a linear model for each gene using the "lmFit" function, the coefficients and standard errors are estimated using the "contrasts.fit" function, and finally the moderate t-statistics, the moderate F-statistic and the logarithmic probabilities of differential expression using the "ebayes" function of the R "limma" package.

molecule: total RNA

organism: Homo sapiens

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 37

label_protocol: The arrays were carried out following the Agilent protocol (One-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling).

extract_protocol: Manual extraction of RNA with the Qiagen RNeasy Mini Kit (ref: 74104). Once the RNA was obtained, quality controls were performed with measurements on the Nanodrop spectrophotometer (thermo Fisher) and on TapeStation (Agilent)

tag: tissue

value: Plasma

tag: group

value: Responders

tag: patient id


title: SCHW19_P9_

type: SRA

city: Boston

first: L. Nicolas

last: Gonzalez Castro

state: MA

address: 60 Fenwood Road

country: USA

institute: Mass General Brigham

description: Library name: SCHW19_P9

library_source: transcriptomic single cell

data_processing:
We processed sequencing data from raw reads to gene expression matrices as previously described (Tirosh et al., 2016). Brieﬂy, we used bcl2fastq to generate demultiplexed FASTQ ﬁles, and aligned the resulting paired-end scRNA-seq reads to the human transcriptome (hg19) using Bowtie (v0.12.7) (Langmead et al., 2009). We quantiﬁed gene expression levels from these alignments as transcripts-per-million (TPM) values by running RSEM (v1.2.19) in paired-end mode (Li and Dewey, 2011). We normalized the total transcripts per cell to one-hundred thousand (TP100K), as this is our estimated complexity of single-cell libraries prepared by SMART-Seq2 (Tirosh et al., 2016), and then log-transformed these values to report gene expression as E = ln(TP100K+1).
Assembly: hg19
Supplementary files format and content: SCHW_samples.mtx

source_name: Schwannoma

extract_protocol:
Fresh tumors were collected directly from the operating room at the time of surgery and presence of schwannoma was confirmed by frozen section. Tumors were mechanically and enzymatically dissociated using a papain-based tumor dissociation kit (Miltenyi Biotec). Tumor cells were blocked in 1% bovine serum albumin in Hanks buffered saline solution (BSA / HBSS). Tumors were first stained first with CD45- Vioblue direct antibody conjugate (clone REA747, Miltenyi Biotec) for 30 min at 4deg C. Cells were washed with cold PBS, and then re- suspended in 1mL of BSA / HBSS containing 1 mM calcein AM (Life Technologies) and 0.33 mM TO-PRO-3 iodide (Life Technologies) to co-stain for 30 min before sorting. CD45 negative cells were stained with calcein AM (Life Technologies) for viability and CD24-APC (human antibody, clone REA832, Miltenyi Biotec) and CD44-VioBlue (human antibody, clone REA690, Miltenyi Biotec) to sort subpopulations of viable non-immune cells. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter), 640nm (TO-PRO-3 or CD24-APC, 670/14 filter), and 405 nm (CD45-VioBlue or CD44-VioBlue, 450/50 filter) lasers. Standard, strict forward scatter height versus area criteria were used to discriminate doublets and gate only singleton cells. Viable single cells were identified as calcein AM positive and TO-PRO-3 negative. We sorted individual, viable, immune, and non-immune single cells into 96- well plates containing TCL buffer (QIAGEN) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80deg C prior to whole transcriptome amplification, library preparation and sequencing. Smart-seq2 whole transcriptome amplification, library construction, and sequencing were performed.
Single cell cDNA and sequencing libraries were prepared using the SMART-seq2 protocol (Picelli et al., 2014) with several adaptations. Agencourt RNAClean beads were used to purify RNA prior to oligo (dT) hybridization. RNase inhibitor was added to the dT annealing step at 1U/ml. Trehalose (1M) was used instead of water to make up the reaction volume. For the reverse transcription step, Maxima RNaseH-minus RT (200 U/ml) was used as the RT enzyme at 2U/ml. MgCl2 was added at 0.01M and DTT was omitted from the reaction. Trehalose (1M) was used to stabilize the reaction rather than betaine. The RT step was performed at 50 C for 90 minutes followed by 85 C for 5 minutes. In the PCR pre-ampliﬁcation step, an ISPCR primer was used at 0.2 mM and PCR was per-formed for 21 cycles. PCR puriﬁcation was performed using AMpure XP beads at 0.8X. Libraries were tagmented and enriched with dual indexes using Illumina Nextera XT Library Prep kits. Libraries from 384 or 768 cells with unique indexes were pooled together and sequenced at 2pM on an Illumina Nextseq 500 sequencer, yielding paired-end 38 base pair reads (Tirosh et al., 2016).

value: Schwannoma

tag: tissue type

value: tumor


title: SCHW19_P4_

description: Library name: SCHW19_P4


title: dTAG-SPT5-HCT116, ChIP_NELFC, muR1_Rep2

city: NYC

first: Rui

last: Sun

state: New York

address: 1425 Madison

institute: Icahn school of medicine at Mount Sinai

description: Library name: ChIP-muR1-NELFC-Rep2

library_source: genomic

data_processing:
Reads were trimmed and filtered using TrimGalore (version 0.6.10) and aligned to the hg38 human genome (Ensembl) and other spike-in genomes with HISAT2 (version 2.2.1). PCR duplicates were removed using Picard Tools (version 3.1.1). Alignment files were converted to Bam files with Samtools (version 1.14) for the downstream analysis.
Bigwig files were generated in 10 bp bin through the BamCoverage function in Deeptools (version 3.5.1). Reads were normalized using CPM method and scaled based on the spike-in/intergenic region signal. The bigwig files of replicates in the experiment were averaged using wiggletools (version 1.2).
Assembly: hg38
Supplementary files format and content: bigwig files include RNAPII occupancy signals

molecule: genomic DNA

growth_protocol: dTAG-SPT5 HCT116 cells were cultured in McCoy’s 5A medium (Corning) supplemented with 10% Fetal Bovine Serum (FBS) (Gibco) and 1× Penicillin-Streptomycin (Corning) at 37°C and 5% CO2.

extract_protocol:
About 20 million HCT116 cells grown on the 150 mm dish were cross-linked with 1% formaldehyde for 10 min at room temperature. Cross-linking was quenched with 125 mM glycine for 5 min. Cells were collected with a cell lifter (Costar) in 2 ml ChIP nuclei fractionation buffer [50 mM HEPES (pH 7.5), 140 mM NaCl, 1 mM EDTA (pH 8.0), 10% Glycerol, 1% NP-40, 0.25% Triton X-100] with proteinase and phosphatase inhibitors and incubated on ice for 10 min. Cell nuclei were collected by centrifugation at 4 °C at 600 × g for 10 min and washed with wash buffer [10 mM Tris-HCl (pH 8.0), 200 mM NaCl, 1 mM EDTA (pH 8.0), 0.5 mM EGTA (pH 8.0)]. The pellets were lysed in 1.8 mL RIPA buffer with proteinase and phosphatase inhibitors and sheared by sonication in a Bioruptor (Diagenode) at high power, for 2× 20 min with cycles of 30 s ON and 30 s OFF. Lysates were clarified by centrifugation at 16,000 × g for 10 min at 4 °C. 600 μL pre-cleared lysates were incubated with 4 μg antibodies overnight at 4 °C with end-to-end rotation. 22 μL Protein G magnetic beads (New England Biolabs) were added to the tube on the second day and the samples were incubated for another 4 hours at 4 °C with end-to-end rotation. The beads were washed with RIPA buffer three times, IP wash buffer [100 mM Tris-HCl (pH 8.0), 500 mM lithium chloride, 1% NP-40, 1% sodium deoxycholate] three times and TE buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0)] twice. Reversal of cross-linking was done by incubating beads in the elution buffer [10 mM Tris-HCl (pH 8.0), 1 mM EDTA (pH 8.0), 1% SDS, 200mM NaCl, 0.8 U Proteinase K] at 55 °C with heated lid for 16 h. On the third day, 1 μg of RNase A was added and the samples were incubated at 37 °C for 30 min. DNA was purified by using DNA Cleanup Kit (5 μg) (New England Biolabs).
The purified DNA was used for qPCR and library preparation. Spike-In DNA (S. cerevisiae) (Cell Signaling Technology) were added to each sample and DNA libraries were prepared with NEBnext Ultra II DNA library kit (New England Biolabs).

treatment_protocol: 125 nM dTAGv-1 for 4 hours; 250 nM NVP2 for 1 hour in specified experiments

tag: cell line

tag: cell type

value: Human colon cancer cell line

tag: genetic modification

tag: genotype

tag: chip antibody

value: Cell Signaling Technology; Cat. # 12265

tag: treatment


title: dTAG-SPT5-HCT116, ChIP_NELFC, muR1_Rep1

description: Library name: ChIP-muR1-NELFC-Rep1


title: dTAG-SPT5-HCT116, ChIP_NELFC, muR2_Rep1

description: Library name: ChIP-muR2-NELFC-Rep1


title: SCHW19_P6_

description: Library name: SCHW19_P6


title: dTAG-SPT5-HCT116, ChIP_NELFC, WT_Rep1

description: Library name: ChIP-WT-NELFC-Rep1


title: SCHW19_CD45p_P2_

description: Library name: SCHW19_CD45p_P2


title: dTAG-SPT5-HCT116, ChIP_NELFC, muALL_Rep2

description: Library name: ChIP-muALL-NELFC-Rep2


title: dTAG-SPT5-HCT116, ChIP_NELFC, muR1R2_Rep1

description: Library name: ChIP-muR1R2-NELFC-Rep1


title: dTAG-SPT5-HCT116, ChIP_NELFC, muALL_Rep1

description: Library name: ChIP-muALL-NELFC-Rep1


title: dTAG-SPT5-HCT116, ChIP_NELFC, muR2_Rep2

description: Library name: ChIP-muR2-NELFC-Rep2


title: SCHW19_CD45p_P1_

description: Library name: SCHW19_CD45p_P1


title: P25-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 25


title: 127_10_I-snMultiOme—ATAC

city: New Haven

first: Naftali

last: Kaminski

state: CT

address: 300 Cedar Street

department: PCCSM

institute: Yale School of Medicine

description:
Library name: 127_10_ATAC
10X Multiome ATAC + Gene Expression

library_source: genomic single cell

data_processing:
fastq files were generated from basecalls using CellRanger’s mkfastq implementation
snRNAseq fastqs were trimmed for read2 contaminants with cutadapt
trimmed reads were mapped with the STARsolo implementation of STAR (version: ) to GRCh38 with gencode reference annotation release #
count data was cleaned and annotated in R using the Seurat package  (version: )
Assembly: GRCh38; GENCODE release 37
Supplementary files format and content: .rds files of R objects for the package Seurat (Seurat library version: ; SeuratObject library version: ). Each object includes the gene expression, cell metadata and graph layout coordinates for cells/nuclei described in the associated manuscript.

source_name: lung

extract_protocol:
Nuclei for snMultiOme and PCLS were extracted from frozen tissue using the 10X Genomics nuclei extraction kit, per the manufacturer’s instructions.
Library construction for 10X Genomics “3prime v3.1” assays and 10X Genomics “Multiome ATAC + Gene Expression” were each constructed with the manufacturer’s recommended protocol.

treatment_protocol: In vivo lung samples were inflated and frozen after collection. Ex vivo precision cut lung slice (PCLS) were exposed for 5 days to either PBS or a fibrotic cocktail of TGF-b, PDGFa/b,TNFa and LPA

value: lung

value: nuclei

tag: condition

value: IPF

tag: subject

tag: sample


title: SCHW19_CD45n_P8_

description: Library name: SCHW19_CD45n_P8


title: SCHW19_CD45n_P7_

description: Library name: SCHW19_CD45n_P7


title: P27-T3

source_name: Gene expression of non-responders after 15 days of spinal cord stimulator in patient 27

value: Non-responders


title: P8-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 8


title: P32-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 32


title: 319_42_I-snMultiOme—ATAC

description:
Library name: 319_42_ATAC
10X Multiome ATAC + Gene Expression


title: SCHW19_CD45n_P5_

description: Library name: SCHW19_CD45n_P5


title: P14-T3

source_name: Gene expression of responders after 15 days of spinal cord stimulator in patient 27


title: Triadimefon-120h_1µM_R3

city: Hannover

first: Matthias

middle: M

last: Wehr

address: Nikolai-Fuchs-Str. 1

country: Germany

institute: Fraunhofer ITEM

library_source: transcriptomic

data_processing:
Reads were trimmed using fastp (version 0.20.0).
Reads were aligned to reference genome with STAR (version 2.7.1a).
Reads were quantified with RSEM (version 1.3.1).
Quality control reports were generated on all step using MultiQC (version 1.11)
Assembly: Danio_rerio.GRCz11.104
Supplementary files format and content: raw reads are provided in compressed format with the file extension of .fastq.gz for both reads of the paired-end sequencing. Quantified reads as produced by RSEM are provided with file extension .genes.results and isoforms.results for the respective alignement target and level of detail.

organism: Danio rerio

source_name: whole embryo

growth_protocol: Embryos from the wild type AB line were obtained for the development of the study following zebrafish breading guideline SOPs from the facility. Synchronized embryos were supplied to the laboratory and kept at 28.5 °C in an incubator until they reached 2 hpf.

extract_protocol:
Embryos were transferred to 1.5 ml microfuge tubes (kept on ice), followed by the removal of as much liquid as possible, and the addition of 250 μl/tube of TRIzol reagent. Embryos were lysed with pellet pestles by performing 20 strokes until the tissue was checked to be sufficiently disrupted, to then flash frozen all the tubes in liquid nitrogen. Samples were stored at -80 ºC until shipped to the University of Liège for sequencing.
Illumina mRNA stranded ligation Kit

treatment_protocol: Before treating, unfertilized embryos were discarded under the stereoscope by visual inspection. Synchronized embryos were placed in 6 well plates (25 embryos per well) in 7992 μl of E3 medium using a Pasteur pipette. Then, 8 μl of the x1000 working solution (or pure DMSO in the case of vehicle control) were added and plates incubated at 28.5 ºC. All assays were conducted blinded by using only the internal identification code of the compounds.

value: whole embryo

tag: concentration

tag: replicate

tag: plate

tag: compound

value: Triadimefon

tag: timepoint

tag: developmental stage

value: Larval:Day 5

tag: no. of_embryos

tag: cas

tag: vehicle control

value: E3 medium + 0.1% DMSO

value: Wild Type AB


title: Triadimefon-120h_5µM_R3

tag: tissue


title: Larv PRE1_UP Repli1

city: Montpellier

first: Bernd

last: Schuettengruber

address: 141, rue de la cardonille

country: France

institute: Institute de Génétique Humaine

data_processing:
Hi-C data was processed using the schic2 pipeline (https://github.com/tanaylab/schic2). In brief, raw sequencing reads were mapped independently to the reference genome using Bowtie2 in local alignment mode. The uniquely mapped (MAPQ > 36) reads were translated into a pair of fragment-ends (fends) by associating each read with its downstream fend. PCR duplicates and reads mapping to the same restriction fragment were excluded.
Assembly: dm6
Supplementary files format and content: Each processed file represent pairwise information of the observed genome contacts in the form of a "misha" (https://github.com/tanaylab/misha) database entry and can be further analyzed using the "shaman" pipeline (https://github.com/tanaylab/shaman).

organism: Drosophila melanogaster

source_name: larval imaginal leg discs

growth_protocol: Drosophila Melanogaster flies grown at 25°C on standard medium

extract_protocol:
HiC was performed according the protocol of the EpiTect Hi-C Kit from Quiagen
Libraries were preapred according the protocol of the EpiTect Hi-C Kit from Quiagen

value: larval imaginal leg discs

value: Wild type


title: 319_6_I-snMultiOme—ATAC

description:
Library name: 319_6_ATAC
10X Multiome ATAC + Gene Expression

tag: cell type


title: 325_70_I-snMultiOme—ATAC

description:
Library name: 325_70_ATAC
10X Multiome ATAC + Gene Expression


title: Larv PRE1_UP Repli2

tag: genotype


title: 249_13_D-snMultiOme—ATAC

description:
Library name: 249_13_ATAC
10X Multiome ATAC + Gene Expression

value: control


title: SCHW19_CD45n_P2_

description: Library name: SCHW19_CD45n_P2

tag: tissue type


title: SCHW19_CD45n_P3_

description: Library name: SCHW19_CD45n_P3


title: 204_26_I-snMultiOme—ATAC

description:
Library name: 204_26_ATAC
10X Multiome ATAC + Gene Expression


title: 325_61_I-snMultiOme—ATAC

description:
Library name: 325_61_ATAC
10X Multiome ATAC + Gene Expression


title: 302_11_D-snMultiOme—ATAC

description:
Library name: 302_11_ATAC
10X Multiome ATAC + Gene Expression


title: P26-T0

source_name: Gene expression of responders before of spinal cord stimulator in patient 26

value: Plasma

tag: group

value: Responders

tag: patient id


title: Triadimefon-120h_0.2µM_R3

tag: treatment


title: P23-T3

source_name: Gene expression of non-responders after 15 days of spinal cord stimulator in patient 23


title: P21-T4

source_name: Gene expression of responders after 2 months of spinal cord stimulator in patient 21


title: Larv deltaPRE1 Repli2


title: 190_28_I-snMultiOme—ATAC

description:
Library name: 190_28_ATAC
10X Multiome ATAC + Gene Expression

tag: condition

tag: subject

tag: sample


title: Larv deltaPRE1 Repli1


title: SCHW19_CD45n_P1_

description: Library name: SCHW19_CD45n_P1

value: Schwannoma

value: tumor


title: Triadimefon-120h_5µM_R2

tag: concentration

tag: replicate

tag: plate


title: SCHW17_P2_

description: Library name: SCHW17_P2


title: Larv Double  Repli3


title: 222_68_D-snMultiOme—ATAC

description:
Library name: 222_68_ATAC
10X Multiome ATAC + Gene Expression


title: IR H151 48h 3

city: Los Angeles

first: Frank

last: Pajonk

state: CA

address: 10833 Le Conte Ave

institute: UC Los Angeles

description: Library name: IR_H151_48h_3

data_processing:
Novogene Standard RNA-Seq pipeline
Assembly: Homo_sapiens_hg38
Supplementary files format and content: count, fpkm

source_name: Glioblastoma

growth_protocol: HK-374 cells were grown in DMEM containing 10% FBS, 1% pen/strep media at 37°C in a 5% CO2 incubator. Cells were grown as monolayers and plated into 6-well plates at 40,000 cells per well.

extract_protocol:
Total RNA was isolated using Trizol reagent. The treated cells were lysed in 1 ml of Trizol reagent, rocked for 5 min to obtain a homogenous mixture and then transferred to RNAeasy mini kit (Qiagen) colimns for RNA isolation by following manufacturer's protocol.
The RNA sequencing library was generated using NEBNext® Ultra RNA Library Prep Kit (New England Biolabs) according to manufacturer’s protocols. The library concentration was quantified using a Qubit 3.0 fluorometer (Life Technologies), and then diluted to 1 ng/uL before checking insert size on an Agilent Technologies 2100 Bioanalyzer (Agilent Technologies; Waldbronn, Germany) and quantifying to greater accuracy by quantitative Q-PCR (library molarity >2 nM). The library was sequenced on Illumina NovaSeq6000 with an average of 20M reads per RNA sample.

treatment_protocol: 4 days after seeding the cells were irradiated with 4 Gy. Controls were sham irradiated. Before irradiation cells were treated with either H151 or DMSO.

value: Glioblastoma

tag: cell line

value: patient-derived


title: Triadimefon-120h_1µM_R2

tag: compound

tag: timepoint

tag: developmental stage

tag: no. of_embryos


title: Larv Double  Repli2

tag: tissue


title: Triadimefon-120h_0.2µM_R2

tag: cas

tag: vehicle control

tag: genotype


title: IR H151 48h 2

description: Library name: IR_H151_48h_2

tag: cell type


title: SCHW17_P15_

description: Library name: SCHW17_P15

tag: tissue type


title: Triadimefon-120h_0µM_R3

tag: treatment


title: dPPRerpl2/P19 PWB2 rep3 3 dpi

city: Strasbourg

first: Kamel

last: HAMMANI

address: 12 rue du general Zimmer

institute: CNRS

data_processing:
The quality of the reads was assessed with FastQC 0.12.1 and adapters were trimmed with Trim-galore 0.6.10. Sequences with a quality lower than 30, with more than 5 Ns or smaller than 20 bp after trimming were removed.
The remaining reads were mapped against the N. benthamiana chloroplast genome SRR7540368  supplemented with the dPPRrpl2 nucleotide sequence with HISAT2 2.2.1 using the -k 50 option and default parameters.
Mapped reads were counted with featureCounts 2.0.1 with options -O -M --minOverlap 5, to consider multimapped reads.
Differential expression analysis was done using the DESeq2 1.42.0 package.
Assembly: N. benthamiana chloroplast genome SRR7540368  supplemented with the dPPRrpl2 nucleotide sequence
Supplementary files format and content: tab-delimited text includes raw counts for each samples

organism: Nicotiana benthamiana

source_name: leaf

extract_protocol:
RNA were extracted by TRIzol and  treated by DNase Turbo
Firstly, ribosomal RNA was removed from total RNA, followed by ethanol precipitation. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. During the second strand cDNA synthesis, dUTPs were replaced with dTTPs in the reaction buffer. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

value: leaf

value: WT

value: 3 dpi


title: SCHW17_P14_

description: Library name: SCHW17_P14


title: IR H151 48h 1

description: Library name: IR_H151_48h_1


title: SCHW17_P13_

description: Library name: SCHW17_P13


title: Triadimefon-120h_5µM_R1

value: whole embryo


title: dPPRerpl2/P19 PWB2 rep2 3 dpi


title: IR 48h 2

description: Library name: IR_48h_2


title: Triadimefon-120h_1µM_R1

value: Triadimefon


title: IR 48h 3

description: Library name: IR_48h_3


title: IR 48h 1

description: Library name: IR_48h_1


title: SCHW17_P12_

description: Library name: SCHW17_P12


title: dPPRerpl2/P19 PWB2 rep1 2 dpi

value: 2 dpi


title: SCHW17_P11_

description: Library name: SCHW17_P11


title: Triadimefon-120h_0.2µM_R1

value: Larval:Day 5

value: E3 medium + 0.1% DMSO


title: P19 rep3 3dpi


title: P19 rep2 3 dpi


title: DMSO 48h 3

description: Library name: DMSO_48h_3


title: DMSO 48h 2

description: Library name: DMSO_48h_2


title: Triadimefon-48h_25µM_R3

value: Wild Type AB


title: SCHW16_P9_

description: Library name: SCHW16_P9


title: Triadimefon-120h_0µM_R1


title: SCHW16_P8_

description: Library name: SCHW16_P8


title: SCHW17_P16_

description: Library name: SCHW17_P16


title: P19 rep1 2 dpi


title: Larv Double  Repli1

value: larval imaginal leg discs

value: Wild type


title: Triadimefon-120h_0µM_R2


title: Triadimefon-48h_5µM_R3


title: mng_bap1_24

type: genomic

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

institute: University Hospital Heidelberg, Intitute of Pathology

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta

source_name: MNG BAP1

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: material

value: FFPE

tag: Sex

value: Female

tag: age

tag: disease state

tag: outcome


title: PM2.5_3, circRNA-seq

city: Beijing

last: Chen

address: No.10 Xitoutiao, You An Men

country: China

institute: Capital medical university

description:
Library name: S9
total RNA

data_processing:
Reads were mapped to the genome using STAR, and DCC was employed to identify and estimate circRNA expression
Differentially expressed genes were identified using the edgeR program.
Assembly: hg19
Supplementary files format and content: Excel Open XML Spreadsheet files include read count  for each Sample

source_name: HBE

extract_protocol:
RNA was harvested using the Hipure Total RNA Mini Kit.RNA quality and quantity was measured by using NanoDrop  and RNA Integrity was determined by Agilent 2100 bioanalyzer
Approximately 2 μg of total RNA was used to prepare the sequencing library with a KAPA RNA HyperPrep Kit with RiboErase for Illumina@ (Kapa Biosystems, Inc., Woburn, MA, USA) following the manufacturer’s recommendations. After a quality check with the Agilent Bioanalyzer 2100 system, paired-End (PE150) sequencing was performed on all samples.

tag: cell line

value: HBE

value: Human bronchial epithelial cell


title: SCHW16_P5_

description: Library name: SCHW16_P5

value: Schwannoma

value: tumor


title: PM2.5_2, circRNA-seq

description:
Library name: S8
total RNA


title: mng_bap1_32


title: SCHW16_P4_

description: Library name: SCHW16_P4


title: Triadimefon-48h_0.2µM_R3

tag: concentration

tag: replicate

tag: plate

tag: compound


title: SCHW16_P3_

description: Library name: SCHW16_P3

tag: tissue


title: PM2.5_1, circRNA-seq

description:
Library name: S7
total RNA


title: mng_bap1_23

value: progressive

value: alive


title: Triadimefon-48h_0µM_R3

tag: timepoint

tag: developmental stage

tag: no. of_embryos

tag: cas


title: SCHW16_P2_

description: Library name: SCHW16_P2

tag: tissue type


title: iGMPs scRNA-seq

city: Riverside

first: Reuben

last: Franklin

address: 3401 Watkins Drive

institute: University of California, Riverside

description: Library name: scRNA_UT_0H_Clone1

data_processing:
For scRNA-seq data analysis, we used kallisto | bustool (kb_python 0.27.3), with default parameters. Raw reads were pseudo-aligned using kb count from kallisto | bustool to a custom transcriptome generated using kb index from mm39 Gencode VM26 reference genome (genome sequence primary assembly and comprehensive gene annotation) with mouse and rodent consensus transposable elements (RepBase 25.05) and eGFP CDS. Generated gene expression matrixes for each individual sample.
Assembly: mm39
Supplementary files format and content: Plain text files contain a list of unqiue cell barcodes (cell_x_genes.barcodes.txt) and list of gene names (cellls_x_genes.genes.txt). Matrix file (.mtx) contains count matrix.

molecule: polyA RNA

organism: Mus musculus

source_name: Blood

growth_protocol: Immortalized granulocyte-macrophage progenitor-like cells with a GFP reporter at the Lyz2 locus and the ER-HOXA9 transgene (herein GMPs or HOXA9-iGMPs)32,33 were cultured in RPMI-1640 supplemented with 10% FBS, 100U mL-1 penicillin, 100 µg mL−1 streptomycin, 2mM L-alanyl-L-glutamine dipeptide and stem cell factor (SCF). Depending on the batch, media was made with 1-2% SCF-conditioned media from SCF-secreting Chinese hamster ovary cells (a gift from David Sykes). Concentrations for each batch were determined with functional testing, exploiting the strict SCF-dependence of iGMPs. β-Estradiol (E2) was added to a final concentration of 150 ng/mL for normal culture.

extract_protocol:
Cell suspension was collected and enriched for live cells by removing dead cells (Dead Cell Removal Kit, Miltenyi Biotec). Cell concentration and viablity were determined for each sample via automated cell counter (Countness II, Thermo Fisher Scientific) with Trypan blue staining (Trypan Blue solution, Sigma-Aldrich). The cell concentration was adjusted with cells resuspended at 1,000 cells per uL in DPBS (DPBS, Thermo Fisher Scientific) with 0.05% BSA (Ultrapure BSA, Thermo Fisher Scientific) for 10x Chromium GEM-X Single Cell 3' v4 scRNA-seq. Gel Bead-in-emulsion (GEM) generation and barcoding was peformed by University of California, Irvine Genomics, Research, and Technology Hub following 10X Chromium GEM-X Single Cell 3' Reagent Kits v4 User Guide.
Single live cells suspension with the concentration of 1,000 cells per uL were loaded onto 10X Genomics Chromium GEM-X Chips according to manufactor recommendations. Reverse transcription and library construction were performed with 10X Chromium GEM-X Single Cell 3' Reagent Kits v4 following manufacter user guide. Sequencing was performed on Illumina NovaSeq X Plus.

treatment_protocol: For LacO-shChaf1b expression (CAF-1 OFF condition), IPTG was added at a concentration of 500 µM to iGMPs cultured with E2. For tetO-shSupt6 expression (SPT6 OFF condition), cells were treated with DOX at 1 µg/mL.

value: Blood

tag: cell type

value: granulocyte-macrophage progenitor

tag: genotype

tag: treatment

value: Untreated


title: Control_3, circRNA-seq

description:
Library name: S3
total RNA

value: control


title: Triadimefon-48h_25µM_R2

value: whole embryo

value: Triadimefon

tag: vehicle control


title: SPT6 OFF 48 h scRNA-seq

description: Library name: scRNA_DOX_48H_Clone1

value: 1 ug/mL DOX 48 h


title: Triadimefon-48h_5µM_R2

value: E3 medium + 0.1% DMSO

value: Wild Type AB


title: Control_2, circRNA-seq

description:
Library name: S2
total RNA


title: SCHW16_P10_

description: Library name: SCHW16_P10

source_name: Schwannoma


title: CAF-1 OFF 48 h scRNA-seq

description: Library name: scRNA_IPTG_48H_Clone1

value: 500 uM IPTG 48 h


title: DMSO 48h 1

description: Library name: DMSO_48h_1

value: Glioblastoma

value: patient-derived


title: SCHW16_P1_

description: Library name: SCHW16_P1


title: circDNA2 KD_3, RNA-Seq

description:
Library name: C3
total RNA

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence
paired-end clean reads were aligned to the reference genome using hisat2 (v2.0.5)
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene
Raw reads were normalized by calculated FPKM value using Ballgown (2.10.0).
Differentially expressed genes (DEGs) between conditions were determined with absolute fold change >1.5 and with P < 0.05.
Assembly: hg19
Supplementary files format and content: Excel Open XML Spreadsheet files include FPKM values  for each Sample

extract_protocol:
RNA was harvested using Trizol reagent.RNA quality and quantity was measured by using NanoDrop and RNA Integrity was determined by Agilent 2100 bioanalyzer
1-2 µg of total RNA was selected from each sample for sequencing library construction. The total RNA was first enriched for mRNA using the NEB Next® Poly(A) mRNA Magnetic Isolation Module, and then the library was constructed using the KAPA Stranded RNA-Seq Library Prep Kit (Roche) based on the dUTP strand-specific library construction method.

value: HBE

value: Human bronchial epithelial cell

value: circDNA2 knockdown


title: Triadimefon-48h_1µM_R2


title: SCHW16_P7_

description: Library name: SCHW16_P7

value: Schwannoma

value: tumor


title: dPPRerpl2/P19 PMDC32 rep3 3dpi

value: leaf

value: WT

value: 3 dpi


title: Triadimefon-48h_0.2µM_R2


title: Triadimefon-48h_1µM_R3


title: dPPRerpl2/P19 PMDC32 rep2 3 dpi


title: dPPRerpl2/P19 PMDC32 rep1 2 dpi

value: 2 dpi


title: SCHW15_P3_

description: Library name: SCHW15_P3


title: circDNA2 KD_1, RNA-Seq

description:
Library name: C1
total RNA


title: Triadimefon-48h_0µM_R2

value: whole embryo


title: SCHW15_P1_

description: Library name: SCHW15_P1


title: Control_3, RNA-Seq

description:
Library name: T3
total RNA

value: control


title: circDNA2 KD_2, RNA-Seq

description:
Library name: C2
total RNA


title: small extracellular vesicle, active infection, sample 10

city: Philadelphia

first: Thea

last: Golden

state: PA

address: 421 Curie Blvd Room 1213

department: Obstetrics and Gynecology

institute: University of Pennsylvania

data_processing:
Placenta and BeWo cell transcriptome reads were aligned to GrCh38/hg38 reference genome using Spliced Transcripts Alignment to a Reference (STAR) software.  FeatureCounts were used to count the read number mapped to each gene.  Then RPMK of each gene was calculated based on the length of the gene and read count mapped to the gene.
EV transcriptome reads were aligned to hg19 reference gemone using RSEM
Assembly: Placenta/BeWo cells-GrCh38/hg38, EV- hg19
Supplementary files format and content: Placenta/BeWo cells- tab-delimited text file includes FPKM for each sample
Supplementary files format and content: EV- tab-delimited text file includes TPM for each sample

source_name: plasma-derived extracellular vesicles

extract_protocol:
RNA was isolated from placenta and BeWo cell samples with Qiagen RNEasy Plus Mini Kit (Cat#74134, Qiagen).  EV RNA was isolated by BCP co-incubation, followed by isopropanol precipitation and ethanol washing.
NEBNext Ultra RNA Library Prep Kit for Illumina was used to prepare libraries from RNA isolated from placenta biopsies and BeWo cells.  EV RNA libraries were prepared following the SMART-seq protocol.

value: plasma-derived extracellular vesicles

value: active infection SARS-CoV-2


title: SCHW15_P2_

description: Library name: SCHW15_P2


title: Triadimefon-48h_1µM_R1

value: Triadimefon

value: E3 medium + 0.1% DMSO

value: Wild Type AB


title: SCHW14_P8_

description: Library name: SCHW14_P8


title: Triadimefon-48h_5µM_R1


title: Triadimefon-48h_25µM_R1


title: Triadimefon-48h_0µM_R1


title: small extracellular vesicle, active infection, sample 7


title: Triadimefon-24h_25µM_R3


title: SCHW14_P2_

description: Library name: SCHW14_P2


title: CeD1

city: Urumqi

first: Tian

last: Shi

address: No. 91, Tianchi Road, Tianshan District, Urumqi, Xinjiang, China

institute: Department of Gastroenterology, People’s Hospital of Xinjiang Uygur Autonomous Region

description: Library name: CeD1

data_processing:
Raw reads were preprocessed by cellranger software (v.1.3.0). Sequencing data of each sample was analyzed using the count function of cellranger, and the sequencing data of different samples were identified by their barcodes.The sequencing data were aligned to reference genome sequence by hg38, and the expression levels of genes in every nucleus were obtained.
The batch effects between samples were eliminated by the aggr function of cellranger software (v.1.3.0).
Seurat software (v. 3.1.4) was used for initial quality control and mitochondrial gene elimination.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell.

source_name: mucous membrane of small intestine

extract_protocol:
Iodixanol gradient centrifugation was used for single nucleus isolation. A proper amount of single nuclei (~8,000) was added to the reverse transcription mixture, single cell 3' gel beads (combined with 10x barcode), and partitioning oil in the 10x Genomics Chromium™ Single Cell Controller before starting the GEM (Gel Bead-In-EMulsions) generation program. GEM generation, reverse transcription, cDNA amplification, and library construction were performed followed by the standard protocols of 10x genomics.
The library sequencing was performed in the Illumina Hiseq platform (Illumina, San Diego, CA, USA) under the 2 × 150-bp double-ended sequencing pattern to generate FastQ data.

value: mucous membrane of small intestine

tag: disease state

value: celiac disease


title: small extracellular vesicle, active infection, sample 9


title: Control_1, circRNA-seq

description:
Library name: S1
total RNA

value: HBE

value: Human bronchial epithelial cell


title: Control_2, RNA-Seq

description:
Library name: T2
total RNA


title: small extracellular vesicle, active infection, sample 5


title: small extracellular vesicle, active infection, sample 4


title: Ctrl3

description: Library name: Ctrl3


title: Triadimefon-24h_1µM_R3


title: SCHW14_P7_

description: Library name: SCHW14_P7

value: Schwannoma


title: small extracellular vesicle, active infection, sample 6


title: Triadimefon-48h_0.2µM_R1


title: CeD3

description: Library name: CeD3


title: Triadimefon-24h_0.2µM_R3


title: Triadimefon-24h_0µM_R3


title: Ctrl1

description: Library name: Ctrl1


title: small extracellular vesicle, active infection, sample 8


title: SCHW14_P5_

description: Library name: SCHW14_P5

value: tumor


title: Triadimefon-24h_5µM_R3


title: SCHW14_P3_

description: Library name: SCHW14_P3


title: hiMG, LPS arm, LPS6

city: Sacramento

first: Izumi

last: Maezawa

institute: University of California Davis Medical Center

data_processing:
Adapter sequences in the raw FASTQ files were trimmed using Trimmomatic (v0.39) (seed mismatches = 6, palindrome clip threshold = 30, simple clip threshold = 10, minimum adapter length = 2). Removes low-quality bases (<2) from the start and end of the reads. Minimum length after trimming is 55 bp.
The remaining reads were mapped to the human reference genome hg38 using HISAT2 (v2.2.1)
The gene counts were summarized by featureCounts (v2.0.1). Reads were counted from exon specifically. The minimum mapping quality score is 20. Only primary alignments were counted.
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files for the AβO and LPS arms separately

source_name: Human iPS Cell Line 26

extract_protocol:
Total RNA from cultured cells was extracted using RNeasy Plus Mini Kit (Qiagen).
cDNA library construction and Illumina sequencing were performed by NovoGene (Sacramento, CA, USA)

value: Human iPS Cell Line 26

value: Induced pluripotent stem cell (Episomal)

value: CD34+, ApoE3

value: LPS

tag: arm


title: Triadimefon-24h_25µM_R2

value: whole embryo


title: hiMG, LPS arm, LPS5

tag: cell line


title: SCHW14_P14_

description: Library name: SCHW14_P14


title: SCHW13_P7_

description: Library name: SCHW13_P7


title: hiMG, LPS arm, LPS3


title: Triadimefon-24h_0.2µM_R2

tag: concentration


title: Control_1, RNA-Seq

description:
Library name: T1
total RNA

value: control


title: small extracellular vesicle, active infection, sample 3

value: plasma-derived extracellular vesicles


title: small extracellular vesicle, active infection, sample 2

value: active infection SARS-CoV-2


title: SCHW13_P5_

description: Library name: SCHW13_P5


title: Ctrl2

description: Library name: Ctrl2


title: SCHW14_P15_

description: Library name: SCHW14_P15


title: SCHW14_P13_

description: Library name: SCHW14_P13


title: SCHW14_P11_

description: Library name: SCHW14_P11


title: hiMG, LPS arm, LPS2


title: small extracellular vesicle, recovered 3rd trimester, sample 6

value: recovered SARS-CoV-2 infection in the 3rd trimester


title: Triadimefon-24h_0µM_R2

tag: replicate

value: Triadimefon

value: E3 medium + 0.1% DMSO


title: Triadimefon-24h_1µM_R2

tag: plate

value: Wild Type AB


title: SCHW14_P12_

description: Library name: SCHW14_P12


title: small extracellular vesicle, active infection, sample 1


title: CeD2

description: Library name: CeD2

value: mucous membrane of small intestine

value: celiac disease


title: small extracellular vesicle, recovered 3rd trimester, sample 5


title: Triadimefon-24h_5µM_R2

tag: compound


title: small extracellular vesicle, recovered 3rd trimester, sample 9

tag: tissue


title: small extracellular vesicle, recovered 3rd trimester, sample 10


title: hiMG, LPS arm, Control6

value: Control/Mock


title: SCHW13_P2_

description: Library name: SCHW13_P2

value: Schwannoma


title: Triadimefon-24h_5µM_R1

tag: timepoint


title: Triadimefon-24h_1µM_R1

tag: developmental stage


title: small extracellular vesicle, recovered 3rd trimester, sample 7


title: hiMG, LPS arm, LPS4


title: small extracellular vesicle, recovered 3rd trimester, sample 8


title: hiMG, LPS arm, Control5


title: hiMG, LPS arm, LPS1


title: hiMG, LPS arm, Control4


title: SCHW13_P4_

description: Library name: SCHW13_P4

value: tumor


title: Triadimefon-24h_25µM_R1

tag: no. of_embryos


title: SCHW13_P3_

description: Library name: SCHW13_P3


title: SCHW13_P9_

description: Library name: SCHW13_P9


title: SCHW13_P13_

description: Library name: SCHW13_P13


title: hiMG, LPS arm, Control3

value: Human iPS Cell Line 26


title: Triadimefon-24h_0µM_R1

tag: cas


title: SCHW13_P12_

description: Library name: SCHW13_P12

tag: tissue type


title: small extracellular vesicle, recovered 3rd trimester, sample 4


title: hiMG, LPS arm, Control2

tag: cell type

value: Induced pluripotent stem cell (Episomal)


title: small extracellular vesicle, recovered 2nd trimester, sample 10

value: recovered SARS-CoV-2 infection in the 2nd trimester


title: SCHW13_P14_

description: Library name: SCHW13_P14


title: small extracellular vesicle, recovered 3rd trimester, sample 2


title: Triadimefon-24h_0.2µM_R1

tag: genotype


title: small extracellular vesicle, recovered 3rd trimester, sample 1

tag: treatment


title: small extracellular vesicle, recovered 2nd trimester, sample 9


title: hiMG, AβO arm, AβO6

value: CD34+, ApoE3

value: AβO


title: SCHW13_P11_

description: Library name: SCHW13_P11


title: small extracellular vesicle, recovered 2nd trimester, sample 8


title: hiMG, LPS arm, Control1

value: LPS


title: SCHW11_P8_

description: Library name: SCHW11_P8


title: Triadimefon-8h_0.2µM_R3

value: whole embryo

tag: vehicle control


title: Triadimefon-8h_5µM_R3


title: hiMG, AβO arm, AβO4


title: SCHW11_P7_

description: Library name: SCHW11_P7


title: small extracellular vesicle, recovered 3rd trimester, sample 3

value: plasma-derived extracellular vesicles


title: Triadimefon-8h_25µM_R3


title: SCHW11_P9_

description: Library name: SCHW11_P9


title: Triadimefon-8h_1µM_R3


title: hiMG, AβO arm, AβO5


title: hiMG, AβO arm, AβO2


title: SCHW13_P1_

description: Library name: SCHW13_P1


title: small extracellular vesicle, recovered 2nd trimester, sample 6


title: small extracellular vesicle, recovered 2nd trimester, sample 7


title: small extracellular vesicle, recovered 2nd trimester, sample 5


title: Triadimefon-8h_25µM_R2


title: Triadimefon-8h_0µM_R3


title: hiMG, AβO arm, AβO3


title: Triadimefon-8h_5µM_R2


title: SCHW11_P11_

description: Library name: SCHW11_P11


title: small extracellular vesicle, recovered 2nd trimester, sample 4


title: Triadimefon-8h_1µM_R2


title: SCHW11_P6_

description: Library name: SCHW11_P6


title: SCHW11_P5_

description: Library name: SCHW11_P5


title: Triadimefon-8h_0µM_R2


title: SCHW11_P4_

description: Library name: SCHW11_P4


title: small extracellular vesicle, recovered 2nd trimester, sample 1


title: small extracellular vesicle, recovered 2nd trimester, sample 3


title: small extracellular vesicle, recovered 1st trimester, sample 10

value: recovered SARS-CoV-2 infection in the 1st trimester


title: SCHW10_P9_

description: Library name: SCHW10_P9


title: hiMG, AβO arm, Control6


title: small extracellular vesicle, recovered 2nd trimester, sample 2


title: hiMG, AβO arm, AβO1


title: Triadimefon-8h_25µM_R1

value: Triadimefon


title: hiMG, AβO arm, Control5


title: Triadimefon-8h_5µM_R1

value: E3 medium + 0.1% DMSO


title: Triadimefon-8h_0.2µM_R2

value: Wild Type AB


title: hiMG, AβO arm, Control4


title: SCHW10_P8_

description: Library name: SCHW10_P8


title: hiMG, AβO arm, Control3


title: small extracellular vesicle, recovered 1st trimester, sample 9


title: SCHW10_P7_

description: Library name: SCHW10_P7


title: Triadimefon-8h_1µM_R1


title: hiMG, AβO arm, Control2


title: small extracellular vesicle, recovered 1st trimester, sample 8


title: Triadimefon-8h_0.2µM_R1


title: SCHW10_P13_

description: Library name: SCHW10_P13


title: small extracellular vesicle, recovered 1st trimester, sample 7


title: SCHW10_P12_

description: Library name: SCHW10_P12


title: small extracellular vesicle, recovered 1st trimester, sample 6


title: SCHW11_P10_

description: Library name: SCHW11_P10


title: SCHW10_P11_

description: Library name: SCHW10_P11


title: seedling, MOI5, 7dpi, rep3

city: Jülich

first: Sebastian

middle: Hermann

last: Erdrich

state: Nordrhein-Westfalen

address: Wilhelm-Johnen-Straße

department: Institute of Bio- and Geosciences

institute: Forschungszentrum Jülich

description: Library name: Sample27

data_processing:
read quality was assessed with the FastQC software v.0.11.9
Trimming Sequencing adapters and low-quality sequences using the Trimmomatic tool v. 0.39
Kallisto mapping against;  Arabidopsis thaliana genome (TAIR 10.0)
Kallisto mapping against;  against the other species (Xcc [NC_007086.1] and phage Seregon [ON189048.1])
Differential expression analysis was performed using DESeq2
Assembly: Refrence sequence of the respective organism was used for read alignement
Supplementary files format and content: Kallisto_RAW_counts_data_Arabidopsis.csv; Kallisto_RAW_counts_data_Xcc.csv; Kallisto_RAW_counts_data_Seregon.xlsx
Supplementary files format and content: tpm/counts

organism: Arabidopsis thaliana

source_name: whole plant

growth_protocol: Codition specific inocculation with microbes.

extract_protocol:
First  rRNA depletion for mRNA and long noncoding species (eukaryotic or bacteria).
Second Random primers were used for first- and second-strand synthesis of cDNA. The ends of the double-stranded cDNA are processed, sequencing adapters are added, and the fragments are amplified.

treatment_protocol: The obtained tissue was immediately frozen in liquid nitrogen and stored at −80 °C. Sampling occurred in triplicates at 0, 2 and 7 dpi. For nucleic acid extraction, the frozen tissue was ground in a ball mill (Retsch MM200, Retsch, Germany) with a 4-5 mm stainless steel beat. Total RNA extraction from the resulting tissue powder was performed using the Rneasy® Plant Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. To remove genomic DNA contamination, total RNA was incubated with DNAse I (Thermo Fisher Scientific, AM1906) for 15 min.

value: whole plant

value: inocculation with Xanthomonas camplestris strain 8004 and phage Seregon (MOI5) in 1/2 MS medium


title: SKOV-3_DDP-siKRT14

city: Guangzhou

first: Zequn

last: Liu

state: Guangdong

address: 9 Jinsui Road, Tianhe District

department: Department of Obstetrics

institute: Guangzhou Women and Children’s Medical Center, Guangzhou Medical University

description: SKOV-3_DDP-siKRT14_vs_SKOV-3_DDP-siNC.xls

data_processing:
The sequencing data（Raw data）underwent quality control using fastp (v2.0) to remove adapters, trim low-quality reads (score < 20), and discard reads with an N content exceeding 10%.
The resulting processed data is referred to as clean data. Clean reads were aligned to the reference genome using HISAT2 (v2.1.0), and alignment quality was assessed using RSeQC (v3.0.1).
Expression quantification was performed with StringTie, and significant differential genes were identified using DESeq2 (with replicates) or edgeR (without), based on criteria of |log2 Fold change| ≥ 1 and padj < 0.05.
Assembly: HISAT2 (v2.1.0)
Supplementary files format and content: EXCELfile includes FPKM for each Sample

extract_protocol:
MagZolTM Reagent
Library preparation simplifies with a kit combining double-strand synthesis, end repair, and dA-tailing. mRNA is enriched with VAHTS mRNA Capture Beads（Vazyme, China） , then fragmented, and used for double-stranded cDNA synthesis. The cDNA is then purified, and adapters are ligated. Libraries are quality-checked using the Agilent Bioanalyzer and Qubit.

value: cisplatin-resistant ovarian cancer cell line

value: WT

value: transfected with negative control siRNA (siNC)


title: small extracellular vesicle, recovered 1st trimester, sample 5


title: seedling, MOI5, 7dpi, rep2

description: Library name: Sample26


title: small extracellular vesicle, recovered 1st trimester, sample 4


title: A2780_DDP-siNC

value: KRT14 knockdown

value: transfected with small interfering RNA (siRNA) targeting KRT14 (siKRT14)


title: SCHW10_P10_

description: Library name: SCHW10_P10

value: Schwannoma

value: tumor


title: seedling, MOI5, 7dpi, rep1

description: Library name: Sample25


title: small extracellular vesicle, recovered 1st trimester, sample 3


title: seedling, Xcc, 7dpi, rep3

description: Library name: Sample24

value: inocculation with Xanthomonas camplestris strain 8004 in 1/2 MS medium


title: SCHW9_P7_

description: Library name: SCHW9_P7


title: small extracellular vesicle, recovered 1st trimester, sample 2


title: miR-643 mimic Transfected THP1 Cells Replicate 3

city: LUCKNOW

first: Bhupendra

middle: N

last: Singh

state: Please select

address: Janakipuram Sector 10

department: Molecular Microbiology & Immunology

country: India

institute: CSIR-CDRI

data_processing:
CASAVA Pipeline was used to convert BCL to FASTQ
Complete Data Analysis was done using NF-CORE RNASeq analysis pipeline
Assembly: GrCH38
Supplementary files format and content: Read Count Values

growth_protocol: THP-1 cells were maintained in RPMI supplemented with 10%  fetal bovine serum (FBS) and antibiotic in humified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested after 24 hr treatment of macrophages using Rneasy mini plus kit (Qiagene)
As per Illumina Recommended Protocol

treatment_protocol: Macrophage differentiation was induced by treatment of 24 hr post confluent cells with PMA before performing the experiment.

value: Macrophage


title: hiMG, AβO arm, Control1

value: Human iPS Cell Line 26

value: Induced pluripotent stem cell (Episomal)

value: CD34+, ApoE3

value: Control/Mock

value: AβO


title: SCHW9_P3_

description: Library name: SCHW9_P3

data_processing:
We processed sequencing data from raw reads to gene expression matrices as previously described (Tirosh et al., 2016). Brieﬂy, we used bcl2fastq to generate demultiplexed FASTQ ﬁles, and aligned the resulting paired-end scRNA-seq reads to the human transcriptome (hg19) using Bowtie (v0.12.7) (Langmead et al., 2009). We quantiﬁed gene expression levels from these alignments as transcripts-per-million (TPM) values by running RSEM (v1.2.19) in paired-end mode (Li and Dewey, 2011). We normalized the total transcripts per cell to one-hundred thousand (TP100K), as this is our estimated complexity of single-cell libraries prepared by SMART-Seq2 (Tirosh et al., 2016), and then log-transformed these values to report gene expression as E = ln(TP100K+1).
Assembly: hg19
Supplementary files format and content: SCHW_samples.mtx

extract_protocol:
Fresh tumors were collected directly from the operating room at the time of surgery and presence of schwannoma was confirmed by frozen section. Tumors were mechanically and enzymatically dissociated using a papain-based tumor dissociation kit (Miltenyi Biotec). Tumor cells were blocked in 1% bovine serum albumin in Hanks buffered saline solution (BSA / HBSS). Tumors were first stained first with CD45- Vioblue direct antibody conjugate (clone REA747, Miltenyi Biotec) for 30 min at 4deg C. Cells were washed with cold PBS, and then re- suspended in 1mL of BSA / HBSS containing 1 mM calcein AM (Life Technologies) and 0.33 mM TO-PRO-3 iodide (Life Technologies) to co-stain for 30 min before sorting. CD45 negative cells were stained with calcein AM (Life Technologies) for viability and CD24-APC (human antibody, clone REA832, Miltenyi Biotec) and CD44-VioBlue (human antibody, clone REA690, Miltenyi Biotec) to sort subpopulations of viable non-immune cells. Sorting was performed with the FACS Aria Fusion Special Order System (Becton Dickinson) using 488 nm (calcein AM, 530/30 filter), 640nm (TO-PRO-3 or CD24-APC, 670/14 filter), and 405 nm (CD45-VioBlue or CD44-VioBlue, 450/50 filter) lasers. Standard, strict forward scatter height versus area criteria were used to discriminate doublets and gate only singleton cells. Viable single cells were identified as calcein AM positive and TO-PRO-3 negative. We sorted individual, viable, immune, and non-immune single cells into 96- well plates containing TCL buffer (QIAGEN) with 1% beta-mercaptoethanol. Plates were frozen on dry ice immediately after sorting and stored at -80deg C prior to whole transcriptome amplification, library preparation and sequencing. Smart-seq2 whole transcriptome amplification, library construction, and sequencing were performed.
Single cell cDNA and sequencing libraries were prepared using the SMART-seq2 protocol (Picelli et al., 2014) with several adaptations. Agencourt RNAClean beads were used to purify RNA prior to oligo (dT) hybridization. RNase inhibitor was added to the dT annealing step at 1U/ml. Trehalose (1M) was used instead of water to make up the reaction volume. For the reverse transcription step, Maxima RNaseH-minus RT (200 U/ml) was used as the RT enzyme at 2U/ml. MgCl2 was added at 0.01M and DTT was omitted from the reaction. Trehalose (1M) was used to stabilize the reaction rather than betaine. The RT step was performed at 50 C for 90 minutes followed by 85 C for 5 minutes. In the PCR pre-ampliﬁcation step, an ISPCR primer was used at 0.2 mM and PCR was per-formed for 21 cycles. PCR puriﬁcation was performed using AMpure XP beads at 0.8X. Libraries were tagmented and enriched with dual indexes using Illumina Nextera XT Library Prep kits. Libraries from 384 or 768 cells with unique indexes were pooled together and sequenced at 2pM on an Illumina Nextseq 500 sequencer, yielding paired-end 38 base pair reads (Tirosh et al., 2016).


title: seedling, Xcc, 7dpi, rep2

description: Library name: Sample23


title: SCHW9_P1_

description: Library name: SCHW9_P1


title: miR-643 mimic Transfected THP1 Cells Replicate 2


title: miR-643 mimic Transfected THP1 Cells Replicate 1


title: SCHW7_P8_

description: Library name: SCHW7_P8


title: SKOV-3_DDP-siNC


title: seedling, Xcc, 7dpi, rep1

description: Library name: Sample22


title: Triadimefon-8h_0µM_R1

value: whole embryo

value: Triadimefon

value: E3 medium + 0.1% DMSO

value: Wild Type AB


title: Uninfected THP1 Cells Replicate 3


title: SCHW7_P5_

description: Library name: SCHW7_P5


title: small extracellular vesicle, control, sample 8

value: plasma-derived extracellular vesicles

value: control


title: seedling, phage, 7dpi, rep2

description: Library name: Sample20

value: whole plant

value: inocculation with Xanthomonas phage Seregon in 1/2 MS medium


title: Uninfected THP1 Cells Replicate 2


title: seedling, phage, 7dpi, rep3

description: Library name: Sample21


title: A2780_DDP-siKRT14

value: cisplatin-resistant ovarian cancer cell line

value: WT

value: transfected with negative control siRNA (siNC)


title: seedling, phage, 7dpi, rep1

description: Library name: Sample19


title: SCHW7_P3_

description: Library name: SCHW7_P3

value: Schwannoma

value: tumor


title: small extracellular vesicle, control, sample 6


title: Uninfected THP1 Cells Replicate 1

value: Macrophage


title: seedling, mock, 7dpi, rep3

description: Library name: Sample18

value: mock inocculation with 1/2 MS medium


title: SCHW7_P2_

description: Library name: SCHW7_P2


title: small extracellular vesicle, control, sample 7


title: small extracellular vesicle, recovered 1st trimester, sample 1

value: recovered SARS-CoV-2 infection in the 1st trimester


title: seedling, mock, 7dpi, rep2

description: Library name: Sample17


title: M.tb H37Rv Infected THP1 Cells Replicate 2


title: small extracellular vesicle, control, sample 4


title: small extracellular vesicle, control, sample 5


title: seedling, mock, 7dpi, rep1

description: Library name: Sample16


title: SCHW6_P9_

description: Library name: SCHW6_P9


title: M.tb H37Rv Infected THP1 Cells Replicate 1


title: SCHW7_P1_

description: Library name: SCHW7_P1


title: small extracellular vesicle, control, sample 3


title: seedling, MOI5, 2dpi, rep3

description: Library name: Sample15

value: inocculation with Xanthomonas camplestris strain 8004 and phage Seregon (MOI5) in 1/2 MS medium


title: SCHW6_P7_

description: Library name: SCHW6_P7


title: small extracellular vesicle, control, sample 9


title: T47D_DOX_positive_Rep3

city: Brookline

first: Ayako

last: Nakashoji

state: Massachusetts

address: 450 Brookline Avenue,, Dana Building, room 830

institute: Dana Farber Cancer Institute

data_processing:
Raw sequencing reads were aligned to the human genome (GRCh38.74) using STAR.
Raw feature counts were normalized and differential expression analysis using DESeq2.
Differential expression rank order was utilized for subsequent Gene Set Enrichment Analysis (GSEA), performed using the fgsea (v1.8.0) package in R.
Gene sets queried included those from the Hallmark Gene Sets available through the Molecular Signatures Database (MSigDB).
Assembly: hg38
Supplementary files format and content: fastq
Supplementary files format and content: comma separated value file include raw counts for each sample
Supplementary files format and content: comma separated value file include TPM for each sample
Supplementary files format and content: comma separated value file include differentially expressed genes between DOX minus and plus.

source_name: breast

growth_protocol: MCF7 and T47D cells (American Type Culture Collection (ATCC), Manassas, VA, USA) were cultured in MEM (Corning, Corning, NY, USA) or RPMI (Thermo Fisher Scientific, Waltham, MA,) media supplemented with 10% fetal bovine serum (FBS; GEMINI Bio-Products, West Sacramento, CA, USA) and Insulin.

extract_protocol:
Total RNA from cells cultured in triplicates was isolated using RNeasy Plus Mini Kit.
TruSeq Stranded mRNA (Illumina, San Diego, CA, USA) was used for library preparation.

treatment_protocol: MUC1shRNA (MISSION shRNA TRCN0000122938; Sigma, St. Louis, MO, USA)  was inserted into the pLKO-tet-puro vector (Plasmid #21915; Addgene, Cambridge, MA, USA) . Vector-transduced cells were selected for growth in 1–2 μg/ml puromycin. Cells were treated with 0.1% DMSO as the vehicle control or 500 ng/ml doxycycline (DOX; Millipore Sigma).

value: breast

value: Breast Cancer

value: DOX


title: small extracellular vesicle, control, sample 2


title: seedling, MOI5, 2dpi, rep2

description: Library name: Sample14


title: small extracellular vesicle, control, sample 1


title: SCHW6_P6_

city: Boston

last: Gonzalez Castro

institute: Mass General Brigham

description: Library name: SCHW6_P6


title: seedling, MOI5, 2dpi, rep1

description: Library name: Sample13


title: T47D_DOX_positive_Rep2


title: T47D_DOX_positive_Rep1


title: SCHW7_P4_

description: Library name: SCHW7_P4


title: M.tb H37Rv Infected THP1 Cells Replicate 3


title: SCHW6_P5_

description: Library name: SCHW6_P5


title: large extracellular vesicle, active infection, sample 10

value: active infection SARS-CoV-2


title: seedling, Xcc, 2dpi, rep3

description: Library name: Sample12

value: inocculation with Xanthomonas camplestris strain 8004 in 1/2 MS medium


title: T47D_DOX_negative_Rep3

value: DMSO


title: SCHW6_P3_

description: Library name: SCHW6_P3


title: large extracellular vesicle, active infection, sample 9

value: plasma-derived extracellular vesicles


title: seedling, Xcc, 2dpi, rep2

description: Library name: Sample11

value: whole plant


title: T47D_DOX_negative_Rep2


title: large extracellular vesicle, active infection, sample 8


title: seedling, Xcc, 2dpi, rep1

description: Library name: Sample10


title: SCHW6_P2_

description: Library name: SCHW6_P2


title: SCHW6_P10_

description: Library name: SCHW6_P10


title: large extracellular vesicle, active infection, sample 7


title: MCF7_DOX_positive_Rep2


title: MCF7_DOX_positive_Rep3


title: seedling, phage, 2dpi, rep3

description: Library name: Sample9

value: inocculation with Xanthomonas phage Seregon in 1/2 MS medium


title: large extracellular vesicle, active infection, sample 6


title: SCHW6_P1_

description: Library name: SCHW6_P1


title: SCHW5_P9_

description: Library name: SCHW5_P9


title: large extracellular vesicle, active infection, sample 5


title: seedling, phage, 2dpi, rep2

description: Library name: Sample8


title: seedling, phage, 2dpi, rep1

description: Library name: Sample7


title: MCF7_DOX_positive_Rep1


title: SCHW5_P8_

description: Library name: SCHW5_P8


title: SCHW5_P7_

description: Library name: SCHW5_P7


title: large extracellular vesicle, active infection, sample 4


title: MCF7_DOX_negative_Rep3


title: seedling, mock, 2dpi, rep3

description: Library name: Sample6


title: large extracellular vesicle, active infection, sample 3


title: seedling, mock, 2dpi, rep2

description: Library name: Sample5


title: MCF7_DOX_negative_Rep2


title: SCHW5_P6_

description: Library name: SCHW5_P6


title: seedling, mock, 2dpi, rep1

description: Library name: Sample4


title: large extracellular vesicle, active infection, sample 2


title: T47D_DOX_negative_Rep1


title: SCHW5_P5_

description: Library name: SCHW5_P5


title: MCF7_DOX_negative_Rep1


title: large extracellular vesicle, active infection, sample 1


title: seedling, mock, 0dpi, rep3

description: Library name: Sample3


title: SCHW5_P4_

description: Library name: SCHW5_P4


title: Hep3B-Hypoxia-3

city: Xi'an

first: Yufeng

last: Wang

address: 277 West Yanta Road, Xi'an, Shaanxi, P.R.China

institute: the first affiliated hospital of Xi'an Jiaotong university

data_processing:
Qubit 3.0 fluorescence quantification apparatus
Qsep400
Illumina NovaSeq6000,PE150
BMKCloud
Assembly: BMKCloud
Supplementary files format and content: tab-delimited text file included raw counts for each sample
Supplementary files format and content: tab-delimited text file included RPKM values for each sample

source_name: hepatocellular carcinoma

growth_protocol: Hep3B cells were maintained in incubator (37℃, 5% CO2), and cultured in DMEM (Gibco, Grand Island, NY, USA) supplemented with 10% FBS (Gibco, Grand Island, NY, USA) and 1% penicillin-streptomycin (Invitrogen, CA, USA)

extract_protocol:
Total RNA was isolated from the subclones using TRIzol (Invitrogen) and treated with deoxyribonuclease (Qiagen).1.3μg RNA was provided for sequencing.
RNA libraries were prepared using SMARTER  mRNA-seq Library Pre Kit.

treatment_protocol: Hep3B cells were exposed to 20% or 1% oxygen for 24 hours, then the total RNA was isolated for subsequent test.

value: hepatocellular carcinoma

value: cell line

value: WT

value: genetic modification


title: seedling, mock, 0dpi, rep2

description: Library name: Sample2


title: SCHW5_P10_

first: L. Nicolas

address: 60 Fenwood Road

description: Library name: SCHW5_P10

value: Schwannoma

value: tumor


title: large extracellular vesicle, recovered 3rd trimester, sample 10

value: recovered SARS-CoV-2 infection in the 3rd trimester


title: Hep3B-Hypoxia-1


title: SCHW5_P2_

description: Library name: SCHW5_P2


title: Hep3B-Hypoxia-2


title: large extracellular vesicle, recovered 3rd trimester, sample 9


title: Hep3B-Normoxia-2


title: Hep3B-Normoxia-3


title: AGS, siRBM8A, rep3

first: Hang

last: Peng

address: No. 256 Youyi West Road

institute: Shaanxi Provincial People’s Hospital

description:
Library name: AGS_siRBM8A_3
siRBM8A_1_3

data_processing:
Raw reads were processed with Fastp to remove adapters, low-quality bases (Phred score < 20), and short reads (< 50). Clean reads were aligned to the human reference genome GRCh38 using HISAT2 with parameters optimized for transcriptome analysis. Gene expression levels FPKM were quantified using StringTie.
Assembly: GRCh38
Supplementary files format and content: File format: Tab-delimited text (.xlsx). Columns: GeneID, siNC_1, siNC_2, siNC_3, siRBM8A_1, siRBM8A_2, siRBM8A_3, gene_name.

source_name: Stomach

growth_protocol: AGS cells were cultured in RPMI1640 medium supplemented with 10% fetal bovine serum (FBS), 100 U/mL penicillin, and 100 μg/mL streptomycin. Cells were maintained in a humidified incubator at 37°C with 5% CO₂. The medium was changed every 2 - 3 days, and cells were passaged when they reached approximately 80% confluence using 0.25% trypsin - EDTA solution.

extract_protocol:
Discard culture medium and wash cells twice with PBS. Add 1 mL TRIzol reagent per 6-well plate to lyse cells. Transfer lysate to RNase-free tubes and incubate at room temperature for 5 min. Add 0.2 mL chloroform, vortex for 15 sec, and incubate for 5 min. Centrifuge at 12,000 rpm for 15 min at 4°C. Transfer aqueous phase to a new tube, mix with 0.5 mL isopropanol, and incubate for 10 min. Centrifuge at 12,000 rpm for 10 min at 4°C. Wash RNA pellet with 1 mL 75% ethanol (prepared with DEPC-treated water). Centrifuge at 7,500 rpm for 5 min at 4°C. Air-dry RNA pellet for 5-10 min and dissolve in DEPC-treated water. RNA concentration and purity were measured using Nanodrop, and integrity was assessed via Agilent 2100 Bioanalyzer.
1. mRNA was enriched using poly-A selection with magnetic beads. 2. mRNA was fragmented to 200-300 bp. 3. Double-stranded cDNA was synthesized using reverse transcriptase. 4. End repair and A-tailing were performed. 5. Sequencing adapters were ligated. 6. Libraries were amplified via PCR and validated using Bioanalyzer.

treatment_protocol: Cells were divided into two groups: siNC and siRBM8A. Transfection was performed using Lipofectamine 2000 according to the manufacturer’s protocol. Cells were harvested 48 hours post-transfection for RNA extraction. Three biological replicates were included per group.

value: Stomach

value: AGS

value: Gastric adenocarcinoma cell

value: Wild type

tag: batch


title: SCHW5_P1_

description: Library name: SCHW5_P1


title: SCHW4_P8_

description: Library name: SCHW4_P8


title: AGS, siRBM8A, rep2

description:
Library name: AGS_siRBM8A_2
siRBM8A_1_2


title: seedling, mock, 0dpi, rep1

description: Library name: Sample1

value: mock inocculation with 1/2 MS medium


title: AGS, siRBM8A, rep1

description:
Library name: AGS_siRBM8A_1
siRBM8A_1_1


title: large extracellular vesicle, recovered 3rd trimester, sample 7


title: Hep3B-Normoxia-1


title: SCHW4_P7_

description: Library name: SCHW4_P7


title: large extracellular vesicle, recovered 3rd trimester, sample 5


title: AGS, siNC, rep3

description:
Library name: AGS_siNC_3
siNC_3

value: siNC


title: trophoblast cell line, active infection, sample 6

source_name: trophoblast cell line

value: trophoblast cell line

value: BeWo cell

value: B30 clone

value: exposure to plasma-derived EVs isolated from subject with an active infection


title: AGS, siNC, rep2

description:
Library name: AGS_siNC_2
siNC_2


title: large extracellular vesicle, recovered 3rd trimester, sample 4

value: plasma-derived extracellular vesicles


title: large extracellular vesicle, recovered 3rd trimester, sample 3


title: SCHW4_P5_

description: Library name: SCHW4_P5


title: AGS, siNC, rep1

description:
Library name: AGS_siNC_1
siNC_1


title: SCHW4_P6_

description: Library name: SCHW4_P6


title: 127_10_I-snMultiOme—geneExp

city: New Haven

first: Naftali

last: Kaminski

address: 300 Cedar Street

institute: Yale School of Medicine

description:
Library name: 127_10_RNA
10X Multiome ATAC + Gene Expression

data_processing:
fastq files were generated from basecalls using CellRanger’s mkfastq implementation
snRNAseq fastqs were trimmed for read2 contaminants with cutadapt
trimmed reads were mapped with the STARsolo implementation of STAR (version: ) to GRCh38 with gencode reference annotation release #
count data was cleaned and annotated in R using the Seurat package  (version: )
Assembly: GRCh38; GENCODE release 37
Supplementary files format and content: .rds files of R objects for the package Seurat (Seurat library version: ; SeuratObject library version: ). Each object includes the gene expression, cell metadata and graph layout coordinates for cells/nuclei described in the associated manuscript.

molecule: nuclear RNA

source_name: lung

extract_protocol:
Nuclei for snMultiOme and PCLS were extracted from frozen tissue using the 10X Genomics nuclei extraction kit, per the manufacturer’s instructions.
Library construction for 10X Genomics “3prime v3.1” assays and 10X Genomics “Multiome ATAC + Gene Expression” were each constructed with the manufacturer’s recommended protocol.

value: lung

value: nuclei

tag: condition

value: IPF

tag: subject

tag: sample


title: large extracellular vesicle, recovered 3rd trimester, sample 2


title: large extracellular vesicle, recovered 3rd trimester, sample 8


title: trophoblast cell line, active infection, sample 5

tag: cell line


title: SCHW4_P4_

description: Library name: SCHW4_P4

value: Schwannoma


title: SCHW4_P3_

description: Library name: SCHW4_P3

value: tumor


title: SCHW4_P2_

description: Library name: SCHW4_P2


title: large extracellular vesicle, recovered 2nd trimester, sample 10

value: recovered SARS-CoV-2 infection in the 2nd trimester


title: Trophoblast cell line, control, sample 6

value: exposure to plasma-derived EVs isolated from Control subject


title: trophoblast cell line, active infection, sample 2


title: trophoblast cell line, active infection, sample 1


title: 190_28_I-snMultiOme—geneExp

description:
Library name: 190_28_RNA
10X Multiome ATAC + Gene Expression


title: SCHW4_P1_

description: Library name: SCHW4_P1


title: large extracellular vesicle, recovered 3rd trimester, sample 1

value: recovered SARS-CoV-2 infection in the 3rd trimester


title: large extracellular vesicle, recovered 2nd trimester, sample 9


title: 319_42_I-snMultiOme—geneExp

description:
Library name: 319_42_RNA
10X Multiome ATAC + Gene Expression


title: large extracellular vesicle, recovered 3rd trimester, sample 6


title: Trophoblast cell line, control, sample 5


title: large extracellular vesicle, recovered 2nd trimester, sample 8


title: SCHW3_P2_

description: Library name: SCHW3_P2


title: SCHW3_P1_

description: Library name: SCHW3_P1


title: SCHW2_P9_

description: Library name: SCHW2_P9


title: 319_6_I-snMultiOme—geneExp

description:
Library name: 319_6_RNA
10X Multiome ATAC + Gene Expression


title: Trophoblast cell line, control, sample 4


title: trophoblast cell line, active infection, sample 4


title: 204_26_D-snMultiOme—geneExp

description:
Library name: 204_26_RNA
10X Multiome ATAC + Gene Expression


title: large extracellular vesicle, recovered 2nd trimester, sample 6


title: Trophoblast cell line, control, sample 3


title: 249_31_D-snMultiOme—geneExp

description:
Library name: 249_13_RNA
10X Multiome ATAC + Gene Expression

value: control


title: large extracellular vesicle, recovered 2nd trimester, sample 5


title: SCHW2_P8_

description: Library name: SCHW2_P8


title: trophoblast cell line, active infection, sample 3


title: 325_61_I-snMultiOme—geneExp

description:
Library name: 325_61_RNA
10X Multiome ATAC + Gene Expression


title: 325_70_I-snMultiOme—geneExp

description:
Library name: 325_70_RNA
10X Multiome ATAC + Gene Expression


title: SCHW2_P7_

description: Library name: SCHW2_P7


title: Trophoblast cell line, control, sample 2


title: 302_11_D-snMultiOme—geneExp

description:
Library name: 302_11_RNA
10X Multiome ATAC + Gene Expression


title: 222_68_D-snMultiOme—geneExp

description:
Library name: 222_68_RNA
10X Multiome ATAC + Gene Expression


title: large extracellular vesicle, recovered 2nd trimester, sample 2


title: 325_70_I-snRNA

description:
Library name: 325_70_I
10X 3prime v3.1


title: SCHW2_P6_

description: Library name: SCHW2_P6


title: Trophoblast cell line, control, sample 1


title: SCHW2_P5_

description: Library name: SCHW2_P5


title: SCHW2_P3_

description: Library name: SCHW2_P3


title: 325_61_I-snRNA

description:
Library name: 325_61_I
10X 3prime v3.1


title: large extracellular vesicle, recovered 2nd trimester, sample 7


title: large extracellular vesicle, recovered 2nd trimester, sample 3


title: Placenta, active infection, sample 4

source_name: placenta

value: placenta

value: active infection SARS-CoV-5


title: SCHW2_P12_

description: Library name: SCHW2_P12


title: Placenta, active infection, sample 1

value: active infection SARS-CoV-2


title: large extracellular vesicle, recovered 1st trimester, sample 10

value: recovered SARS-CoV-2 infection in the 1st trimester


title: Placenta, active infection, sample 2

value: active infection SARS-CoV-3


title: Placenta, active infection, sample 3

value: active infection SARS-CoV-4


title: 323_71_I-snRNA

description:
Library name: 323_71_Ib
10X 3prime v3.1


title: large extracellular vesicle, recovered 2nd trimester, sample 1


title: large extracellular vesicle, recovered 1st trimester, sample 9


title: 325_36_I-snRNA

description:
Library name: 325_36_I
10X 3prime v3.1


title: Placenta, recovered 3rd trimester, sample 4


title: SCHW2_P11_

description: Library name: SCHW2_P11


title: large extracellular vesicle, recovered 1st trimester, sample 8


title: SCHW2_P10_

description: Library name: SCHW2_P10


title: large extracellular vesicle, recovered 2nd trimester, sample 4


title: 323_42_I-snRNA

description:
Library name: 323_42_Ic
10X 3prime v3.1


title: SCHW2_P1_

description: Library name: SCHW2_P1


title: Placenta, recovered 3rd trimester, sample 3


title: Placenta, recovered 3rd trimester, sample 2


title: large extracellular vesicle, recovered 1st trimester, sample 7


title: SCHW001-P7_

description: Library name: SCHW001-P7


title: Placenta, recovered 3rd trimester, sample 1


title: SCHW001-P6_

description: Library name: SCHW001-P6


title: 319_6_I-snRNA

description:
Library name: 319_6_Ib
10X 3prime v3.1


title: SCHW001-P5_

description: Library name: SCHW001-P5


title: large extracellular vesicle, recovered 1st trimester, sample 5


title: large extracellular vesicle, recovered 1st trimester, sample 6


title: Placenta, recovered 2nd trimester, sample 4


title: large extracellular vesicle, recovered 1st trimester, sample 4


title: large extracellular vesicle, recovered 1st trimester, sample 3


title: 253_72_I-snRNA

description:
Library name: 253_72_Ib
10X 3prime v3.1


title: 319_42_I-snRNA

description:
Library name: 319_42_Ib
10X 3prime v3.1


title: large extracellular vesicle, recovered 1st trimester, sample 2


title: SCHW001-P2_

description: Library name: SCHW001-P2


title: 224_48_I-snRNA

description:
Library name: 224_48_Ib
10X 3prime v3.1


title: Placenta, recovered 2nd trimester, sample 1


title: 224_41_I-snRNA

description:
Library name: 224_41_I
10X 3prime v3.1


title: IgG WT clone2, replicate 1, day 70

city: NY

first: zhixiong

last: sun

state: NY

address: 3908 pardes building, NYSPI

department: Psychiatry

institute: Columbia University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for NextSeq 550 output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
Reads were aligned to the UCSC hg38 genome using Bowtie2 (version 2.2.6). Unmapped and multi-mapped reads were filtered using SAMtools (version 1.7)
the ENCODE hg38 blacklist regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz) and duplicate reads were filtered using Picard (version 1.126)
high-quality peaks were identified with MACS2 (v.2.2.7.1) with Irreproducible Discovery Rate (IDR) < 0.05
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&Tag

source_name: independent clone 2

growth_protocol: Forebrain organoids were maintained in medium supplemented with 10% fetal bovine serum (FBS),1% Matrigel and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were resuspended in 100 µL Dig-wash Buffer containing the appropriate primary antibody. Primary antibody incubation was performed on a nutator platform overnight at 4 °C. Cells were washed 3 times with Dig-wash Buffer followed by incubution with an appropriate secondary antibody at RT for 1 hour. Following 3 washes, cells were incubated with pA-Tn5 adapter complex at RT for 1 hour. Following another 3 washes, cells were resuspended in 200 µL Tagmentation buffer at 37 °C for 1 h and then subjected to the addition of 2.25 µL of 0.5 M EDTA, 2.75 µL of 10% SDS and 0.5 µL of 20 mg/mL Proteinase K to stop tagmentation. Cells were then incubated at 55 °C for 2 hours followed by 85 °C for 20 min to inactivate Proteinase K. Genomic DNA was extracted using the ChIP DNA Clean & Concentrator kit
Genomic DNA was subjected to 12-14 cycles of PCR amplification for library construction with barcoded i5 and i7 primers, using 25 µL NEBNext HiFi 2× PCR Master mix (NEB). Libraries were cleaned up using Ampure XP beads (Beckman Counter), then sequenced on Illumina NextSeq 550 sequencer with pair-end sequencing (Read1, 37 bp; Read2, 38 bp)

treatment_protocol: Forebrain organoids were transduced with the AAV-hSYN-GFP virus (Addgene, 105539-AAV1) at DIV55, to label neurons with GFP. Sorting of neurons labelled with GFP at DIV70 was conducted using a BD influx cell sorter in 1.5 ml tubes pre-coated with 10% FBS. Sorted neurons were then collected by centrifugation at 400g at 4°C for 10 min, followed by ice-cold PBS wash.

value: independent clone 2

value: Neurons

tag: chip antibody

value: IgG (Abcam, #ab37415)


title: large extracellular vesicle, recovered 1st trimester, sample 1

value: plasma-derived extracellular vesicles


title: 323_37_I-snRNA

description:
Library name: 323_37_Ib
10X 3prime v3.1

value: lung

value: nuclei

value: IPF


title: 319_49_I-snRNA

description:
Library name: 319_49_Ib
10X 3prime v3.1


title: SETD1A Frame-shift Mutant clone2, replicate 3, day 70

value: SETD1A (Abcam, #ab70378)


title: 204_48_I-snRNA

description:
Library name: 204_48_I
10X 3prime v3.1


title: large extracellular vesicle, control, sample 8


title: large extracellular vesicle, control, sample 6


title: SETD1A Frame-shift Mutant clone2, replicate 2, day 70


title: Placenta, recovered 1st trimester, sample 2


title: SETD1A Frame-shift Mutant clone2, replicate 1, day 70


title: 204_26_I-snRNA

description:
Library name: 204_26_I
10X 3prime v3.1


title: Placenta, recovered 2nd trimester, sample 3

value: recovered SARS-CoV-2 infection in the 2nd trimester


title: 204_75_I-snRNA

description:
Library name: 204_75_I
10X 3prime v3.1


title: SETD1A WT clone2, replicate 3, day 70


title: Placenta, recovered 2nd trimester, sample 2


title: Placenta, recovered 1st trimester, sample 1


title: large extracellular vesicle, control, sample 7


title: 190_56_I-snRNA

description:
Library name: 190_56_I
10X 3prime v3.1


title: IgG WT clone2, replicate 2, day 70


title: Placenta, Control, sample 5


title: Placenta, recovered 1st trimester, sample 3


title: large extracellular vesicle, control, sample 5


title: 190_59_I-snRNA

description:
Library name: 190_59_I
10X 3prime v3.1


title: SETD1A WT clone2, replicate 2, day 70


title: Placenta, Control, sample 3


title: Placenta, Control, sample 4


title: 190_28_I-snRNA

description:
Library name: 190_28_I
10X 3prime v3.1


title: Placenta, Control, sample 2


title: SETD1A WT clone1, replicate 3, day 70

source_name: independent clone 1

value: independent clone 1


title: SETD1A WT clone2, replicate 1, day 70


title: large extracellular vesicle, control, sample 2

value: control


title: large extracellular vesicle, control, sample 3


title: 127_26_I-snRNA

description:
Library name: 127_26_Ib
10X 3prime v3.1


title: Placenta, Control, sample 1

value: placenta


title: large extracellular vesicle, control, sample 4


title: 127_13_I-snRNA

description:
Library name: 127_13_I
10X 3prime v3.1


title: large extracellular vesicle, control, sample 1


title: SETD1A WT clone1, replicate 1, day 70


title: 182_27ac_Input

city: New York

first: Viviane

last: Tabar

address: Sloan-Kettering Cancer Ctr., 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

data_processing:
ChIP-seq sequencing reads were trimmed and filtered for quality (Q15) and adapter content using version 0.4.5 of TrimGalore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) and running cutadapt (v1.15) and FastQC (v0.11.5). Reads were aligned to human assembly hg38 with version 2.3.4.1 of bowtie2 (http://bowtie-bio.sourceforge.net/bowtie2/index.shtml) and were deduplicated using MarkDuplicates of Picard Tools (v2.16.0). To ascertain enriched regions, MACS2 (https://github.com/taoliu/MACS) was used with a p-value setting of 0.001 and scored against matched input as the control. The BEDTools suite v2.29.2 (http://bedtools.readthedocs.io) was used to create normalized read density profiles. A global peak atlas was created by first removing blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/ hg38.blacklist.bed.gz)
Assembly: hg38
Supplementary files format and content: BIGWIG (BW) file contains the coverage of DNA fragments every other 10bp of the genome

source_name: cell line

growth_protocol: Primary glioma samples from patients were harvested at the time of surgery then dissociated and cultured under N2 medium (DMEM/F12 catalog#11330032, Gibco) and supplied with N2 supplement (catalog#17502048, Gibco), B27 (NeuroCult™ SM1 Without Vitamin A, catalog#05731, Stemcell) and growth factors (Recombinant Human EGF Protein, catalog#236EG, R&D SYSTEMS and Recombinant Human FGF basic/FGF2/bFGF, catalog#233FB, R&D SYSTEMS). All the plates and dishes used for cell culture were pre-coated with Poly-L-ornithine hydrobromide (PO) (catalog#P3655, Millipore Sigma), Fibronectin (FN) (catalog# 356008, Fisher healthcare) and mLaminin I (catalog# 3400-010-02, R&D systems). Primary tumor derived cells between passage 5 and passage 25 were used in this study.

extract_protocol:
Cells were fixed with 1% formaldehyde (catalog#F8775, sigma) for 10 minutes at room temperature. The reaction was stopped by adding glycine to a final concentration of 125 mM. Cells were washed with PBS and lysed in cell lysis buffer (50mM Tris-HCl, pH 8.0, 100mM NaCl, 5mM EDTA, 0.5% SDS) containing 1X Protease Inhibitor Cocktail (catalog#A32955, ThermoFisher) for 10 minutes.  This was spun at 800x G at 4°C for 5 minutes and the cell pellet was resuspended in 0.5 ml of Nuclear Lysis Buffer (50mM Tris-HCl, pH 8.0, 10mM EDTA, 0.2% SDS). Lysates were sonicated to yield 200–500 bp DNA fragments and diluted with ChIP dilution buffer (16.7mM Tris-HCl, pH 8.0, 167mM NaCl, 1.2mM EDTA, 1.1% Triton-X100). 1:100 of anti-H3K27ac (catalog#8173; CST), anti-HMGN1 antibody (catalog#12734S; CST), or anti-menin antibody (catalog#A300-105A; Fisher Scientific) were added to the sample and gently mixed overnight at 4°C. 50 μL of Pierce™ ChIP-grade Protein A/G Magnetic Beads (catalog#26162; Thermo Fisher) were washed with ChIP dilution buffer and gently mixed with the sample for 2 hours. Beads were washed with low-salt wash buffer (20mM Tris-HCl, pH 8.0, 150mM NaCl, 2mM EDTA, 1% Triton-X100, 0.05% SDS), high-salt wash buffer (20mM Tris-HCl, pH 8.0, 500mM NaCl, 2mM EDTA, 1% Triton-X100, 0.05% SDS), LiCl wash buffer (10mM Tris-HCl, pH 8.0, 250mM LiCl, 1% NP-40, 1% Sodium Deoxycholate, 1 mM EDTA), and TE buffer pH 8.0 (catalog# AM9858; Thermo Fisher). Immunoprecipitated DNA was eluted with 100uL elution buffer (1% SDS, 100mM NaHCO3, 10mM DTT), added with 1ul proteinase K, incubated at 62°C for 2-8 hours with shaking. This was followed by an incubation at 95°C for 10 minutes followed by cooling and PCR purification. DNA was purified using the Macherey-Nagel NucleoSpin Gel and PCR Clean-up kit (catalog#NC0389462). Library preparation and sequence were performed by Integrated Genomics Operation (IGO) core facility at MSKCC.
Library was prepared using KAPA HTP library kit (KAPA biosystems).

treatment_protocol: MY-182 1uM treated for 3 days.

value: cell line

value: glioblastoma


title: KO_27ac_Input


title: 127_10_I-snRNA

description:
Library name: 127_10_Ib
10X 3prime v3.1


title: SETD1A WT clone1, replicate 2, day 70


title: 182_27ac_S2


title: 120_21_I-snRNA

description:
Library name: 120_21_Ib
10X 3prime v3.1


title: APPC_Pho_1_3

city: Changchun

first: Hugang

last: Zhang

address: Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, School of Life Sciences, Jilin University, Changchun

institute: Jilin University

description:
Library name: Sample9
Column name in raw_counts_ALL_Samples.txt: APPC_Pho_1_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
The indexed samples were clustered, and sequenced on an Illumina Novaseq platform to obtain 150 bp paired-end reads. Differential expression analysis was performed using the DESeq2 R package (version 1.16.1).
The obtained P-values were adjusted to control the false discovery rate (FDR) using the Benjamini and Hochberg’s approach. Genes identified by DESeq2 with an adjusted P-value < 0.05 and |log2(FoldChange)| ≥ 1 were considered as differentially expressed.
Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) was conducted by the clusterProfiler R package. Gene set enrichment analysis (GSEA) was applied to identify differentially expressed gene sets on the basis of KEGG database.
Ingenuity pathway analysis (IPA) was utilized to annotate pathways and biological functions, indicating activation (Z-score > 0) or inhibition (Z-score < 0).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

growth_protocol: The RAW264.7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was extracted using TRNzol Universal Reagent.
Sequencing libraries were prepared using the NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer's guidelines.

treatment_protocol: Cells were stimulated overnight using 0.1ug/mL LPS. Afterwards, the cells were transfected with APPC/pHO-1 nanocomplexes, irradiated with 808 nm NIR (2 W/cm2) for 5 min at 6 h of transfection, and continued to be cultured up to 48 h.

value: Mouse monocyte macrophage leukemia cells

value: WT


title: WT_27ac_Input

value: NO treatment


title: 120_107_I-snRNA–biolRep2

description:
Library name: 120_107_Ic
10X 3prime v3.1


title: APPC_Pho_1_1

description:
Library name: Sample7
Column name in raw_counts_ALL_Samples.txt: APPC_Pho_1_1


title: APPC_Pho_1_2

description:
Library name: Sample8
Column name in raw_counts_ALL_Samples.txt: APPC_Pho_1_2


title: 182_27ac_S1


title: 120_101_I-snRNA

description:
Library name: 120_101_Ib
10X 3prime v3.1


title: LPS_2

description:
Library name: Sample5
Column name in raw_counts_ALL_Samples.txt: LPS_2

value: LPS


title: KO_27ac_S2


title: LPS_3

description:
Library name: Sample6
Column name in raw_counts_ALL_Samples.txt: LPS_3


title: 120_107_I-snRNA–biolRep1

description:
Library name: 120_107_I
10X 3prime v3.1


title: LPS_1

description:
Library name: Sample4
Column name in raw_counts_ALL_Samples.txt: LPS_1


title: 94_68_D-snRNA

description:
Library name: 94_68_D
10X 3prime v3.1


title: Control_3

description:
Library name: Sample3
Column name in raw_counts_ALL_Samples.txt: Control_3


title: KO_27ac_S1


title: 94_124_D-snRNA

description:
Library name: 94_124_D
10X 3prime v3.1


title: Control_2

description:
Library name: Sample2
Column name in raw_counts_ALL_Samples.txt: Control_2


title: 94_113_D-snRNA

description:
Library name: 94_113_D
10X 3prime v3.1


title: Control_1

description:
Library name: Sample1
Column name in raw_counts_ALL_Samples.txt: Control_1


title: WT_27ac_S1


title: 62_70_D-snRNA

description:
Library name: 62_70_Db
10X 3prime v3.1


title: MSK_19 cell shHMGN1 rep1

data_processing:
Reads were aligned to the human genome build using STAR and analyzed by differential analysis of raw sequencing counts using edgeR (Bioconductor)62 to calculate fold change and FDR.
Assembly: hg19
Supplementary files format and content: tab-delimited text file with counts, logFC, p value and FDR

extract_protocol:
Total RNA from cell are extracted using Trizol
RNASeq_RiboDeplete

value: NO


title: 62_97_D-snRNA

description:
Library name: 62_97_Dc
10X 3prime v3.1


title: MV_PD1_604, scRNA

city: San Francisco

first: Aaron

last: Diaz

institute: UCSF

description:
Library name: MV_PD1_604_scRNA
Medulloblastoma PDX model

data_processing:
We use Cell Ranger v6.1.2 to align reads to mm10 mouse genome for scRNA libraries.
Downstream analysis is performed using Seurat v5.0.1 and applied custom scripts
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Fresh tissues were dissected in pre-warmed Hibernate A buffer (Gibco, 2283833) and enzymatically dissociated at 37 °C for 10 minutes using a pre-warmed collagenase-based lysis buffer, with additional mechanical disruption in a Dounce homogenizer. Live cells were subsequently isolated via flow cytometry using a SONY SH800 Cell Sorter equipped with a 100 μm nozzle.
Single-cell capture, reverse transcription, cell lysis, and library preparation were performed using the 10x Genomics platform, following the manufacturer’s protocol. Approximately 25,000 cells were loaded per capture. Libraries were sequenced on an Illumina NovaSeq using parameters recommended by 10x Genomics.

value: Brain

value: CSCG

value: Medulloblastoma

value: MV-NIS with anti-PD1


title: MV_PD1_602_2, scRNA

description:
Library name: MV_PD1_602_2_scRNA
Medulloblastoma PDX model


title: 62_27_D-snRNA

description:
Library name: 62_27_D
10X 3prime v3.1

value: lung

value: nuclei


title: MSK_19 cell MEN1_KO rep2


title: MV_PD1_601, scRNA

description:
Library name: MV_PD1_601_scRNA
Medulloblastoma PDX model


title: MV_PD1_602_1, scRNA

description:
Library name: MV_PD1_602_1_scRNA
Medulloblastoma PDX model


title: WT_27ac_S2


title: 304_50_D-snRNA

description:
Library name: 304_50_Db
10X 3prime v3.1


title: 304_71_D-snRNA

description:
Library name: 304_71_Db
10X 3prime v3.1


title: MSK_19 cell shHMGN1 rep2


title: MSK_19 cell WT rep2


title: 304_30_D-snRNA

description:
Library name: 304_30_Db
10X 3prime v3.1


title: MSK_19 cell WT rep1


title: MV_313, scRNA

description:
Library name: MV_313_scRNA
Medulloblastoma PDX model

value: MV-NIS


title: MV_312, scRNA

description:
Library name: MV_312_scRNA
Medulloblastoma PDX model


title: 302_16_D-snRNA

description:
Library name: 302_16_D
10X 3prime v3.1


title: MV_311, scRNA

description:
Library name: MV_311_scRNA
Medulloblastoma PDX model


title: Blastema_7dpa_rep1

city: Bar Harbor

first: Prayag

last: Murawala

state: ME

address: 159 Old Bar Harbor Rd, Bar Harbor, ME 04609

institute: MDI Biological Laboratory

description: Gene expression of Cherry+-sorted-CT cells 7 day post-amputation

hyb_protocol: Custom-designed 400K Agilent arrays (Name:Am400k_v2, Design ID: 084163, Design Format: 2x 400 K, Control Grid: IS-420288-2-v2_400kBY2_gx_eqc_20100210) were probed with 3.75 ug of cRNA per array according to the Agilent protocol.

scan_protocol: Scan was performed using the AgilentG3_GX_1Color Raw scan protocol

data_processing: Microarray data were imported and processed using limma v3.58.1 in R applying backgroud correction using the normexp method, quantile between array normalization, filtering out control and low-expressed probes, as well as probes assigned to multiple genes. Gene set over-representation analysis per cluster was performed with clusterprofile v4.10.01 and GO.db v3.18.0.

organism: Ambystoma mexicanum

source_name: Blastema 7dpa replicate 1

label_protocol: A custom Agilent 400K microarray (Agilent Technologies) was designed using the axolotl transcriptome assembly release 25 (https://www.axolotl-omics.org/assemblies, version Am_2.2). Three sense probes and one antisense probe were designed for each annotated transcript with known strandedness. For transcripts with unknown strandedness, which includes non-coding, partial, or novel sequences lacking homology to known proteins, three sense, and three antisense probes were generated, utilizing RNA-seq strandedness data to guide orientation. Additionally, 20,839 probes from a previously established EST and cDNA-based microarray (Knapp et al. 2013) were incorporated to ensure backward compatibility. Overall, the microarray used in this project comprises a total of 415,996 probes. Cy3-labeled cRNA probes were generated from 45 ng of purified total RNA using Agilent Low Input Quick Amp Gene Expression Labeling Kit (Agilent, 5190-2307).

growth_protocol: Axolotls were raised up to 9-cm long (from nouse to tail), and  were individually housed in 20% Holtfreter’s solution all the time.

extract_protocol: Tissue from the intact lower arm or from the blastema at different stages of regeneration (1, 3, 5, 7, 10, and 14 dpa), including tissue 2 mm behind the amputation plane, was collected and washed in 0.8x PBS buffer. Blastemas from 4-6 axolotls from the same clutch were pooled to collect a sufficient numbers of cells. Three biological replicates represent independently collected and processed samples from three separate animal batches.  Tissue was transferred into 1 ml of dissociation solution containing 0.35/ml of Liberase TM (Roche, 05401119001) and 100 U/ml of DNase1 (Roche, 04716728001) in 0.8x PBS. Tissue was dissected into small pieces using forceps and then rocked or pipetted for approximately 30 minutes at RT. The cell suspension was cooled on ice and filtered through a 70-µm filter before FACS-sorting. Cherry+ cells were sorted directly into the lysis buffer RLT (Qiagen, 79216). Total RNA from 150,000 to 250,000 cells per sample was purified using RNeasy mini kit (Qiagen, 74104) according to the manufacturer’s protocol.

treatment_protocol: Axolotls were anesthetized using 0.03% benzocaine (Sigma-Aldrich, E1501) diluted in 20% Holtfreter’s solution. Once the axolotls no longer responded to mechanical stimuli, they were transferred to a surgical plate under a stereoscope (Carl Zeiss Microscopy, Stemi DV4). The right forelimb was then amputated at the mid-zeugopod level, and any protruding bone was carefully trimmed using scissors to facilitate skin retraction and wound healing. Subsequently, axolotls were immediately transferred to fresh 20% Holtfreter’s solution to aid their recovery.

tag: gender

value: Unknown

value: FACS-sorted Cherry+ cells

value: 9-cm long axolotl

tag: strain


title: SK4-3

city: Wuhan

first: Dong

last: Chen

state: Hubei

address: 888 Gaoxin Avenue

institute: Nissi Biotech

data_processing:
FASTX-toolkit (version 0.0.14) to obtain high-quality reads. the short reads less than 16nt were also dropped.
The dataset containing the clean reads was aligned to the GRch38 genome by HISAT2 allowing one  mismatch.
FPKM calculation (fragments per kilobase of transcript per million fragments mapped)
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the ABLas pipeline.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: BHT101 cells

growth_protocol: The BHT101 cell line was purchased from Pricella (CL-0617, Pricella, Wuhan, China), validated by STR profiling, and tested negative for mycoplasma. The BHT101 cells were cultured in DMEM high sugar basic culture medium (PM150210, Pricella, Wuhan, China) with 10% fetal bovine serum (FBS), 100 µg/mL streptomycin, and 100 U/mL penicillin at 37℃ with 5% CO2.

extract_protocol:
Total RNA was extracted by the TRIZOL (Ambion).  The RNA was further purified with two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. The quality and quantity of the purified RNA were redetermined by measuring the absorbance at 260 nm/280 nm (A260/A280) using NanoPhotometer N50（IMPLEN）. The integrity of RNA was further verified by 1.0% agarose gel electrophoresis.
Total RNA was treated with RQ1 DNase (Promega) to remove DNA. The quality and quantity of the purified RNA were determined by measuring the absorbance at 260nm/280nm (A260/A280) using smartspec plus (BioRad). RNA integrity was further verified by 1.5% agarose gel electrophoresis. For each sample, 1 μg of total RNA was used for RNA-seq library preparation. mRNAs were captured by VAHTS mRNA capture Beads (N401, Vazyme, Nanjing, China). The purified RNA was treated with RQ1 DNase (Promega) to remove DNA before used for directional RNA-seq library preparation by VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina （NR605）. Polyadenylated mRNAs were purified and fragmented. Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Adaptor (N323). After purification of ligation product and size fractioning to 300-500bps, the ligated products were amplified and purified, quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

treatment_protocol: Plasmid transfection of BHT101 cells was performed using Lipofectamine 2000 (Invitrogen, Carlsbad, CA, USA) according to the manufacturer's protocol. The transfected cells were then harvested after 48h for RT-qPCR and following analysis.

value: BHT101 cells

value: SK4 overexpression in BHT101 cells


title: SK4-2


title: 302_144_D-snRNA

description:
Library name: 302_144_D
10X 3prime v3.1

tag: tissue

value: control


title: MV_310, scRNA

description:
Library name: MV_310_scRNA
Medulloblastoma PDX model


title: 302_11_D-snRNA

description:
Library name: 302_11_D
10X 3prime v3.1


title: SK4-1


title: Blastema_14dpa_rep1

description: Gene expression of Cherry+-sorted-CT cells 14 day post-amputation

source_name: Blastema 14dpa replicate 1

tag: developmental stage


title: MV_302, scRNA

description:
Library name: MV_302_scRNA
Medulloblastoma PDX model


title: Blastema_7dpa_rep3

source_name: Blastema 7dpa replicate 3


title: MSK_19 cell MEN1_KO rep1

value: cell line

value: glioblastoma