title: RNA_CD34_D14_Rescue

city: Hershey

first: Meghana

last: Matur

state: PA

address: 500 University Drive

institute: Penn State

data_processing:
Sequenced reads were trimmed, and quality filtered using cutadapt (http://cutadapt.readthedocs.io, version 1.2.0) program and aligned to the human (hg38) genome using TopHat (version 2.0) and Bowtie2. Count matrix was generated by FeatureCounts and differential expression analysis was performed using DEseq2. Differential expression analysis for erythroblasts was performed by NOI-seq. Pheatmap was used construct heatmap. Gene set enrichment analysis (GSEA) was performed with gene sets obtained from the Molecular Signatures Database. GO analysis of differentially expressed (greater than 2-fold) genes was generated using Database for Annotation, Visualization, and Integrated Discovery (DAVID) Bioinformatics Resources. Sequence reads have been deposited in the NCBI GEO under accession number.
Assembly: hg19
Supplementary files format and content: Tabular file of raw counts (output from featureCounts)

source_name: Primary cord blood CD34

extract_protocol:
RNA is extracted using Quick-RNA miniprep kit (ZYMO research) according to manufacturer’s protocol.
1ug of RNA which have high RIN value (more than 8) were used as input for RNA-seq library preparation. We used NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) for enrichment mRNA and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB) for library preparation according to manufacturer’s protocol.

value: Primary cord blood CD34

value: CD34+ with scramble ncRNA-a3 KD siRNA


title: RXMM_Mock1

status: Public on May 07 2025

type: SRA

city: Seattle

first: Sigal

middle: B

last: Kofman

email: sigalk@uw.edu, Kofmansb@gmail.com

state: Washington

address: 750 Republican St

department: Immunology

country: USA

institute: University of Washington

library_source: transcriptomic

data_processing:
Raw reads mapped to Mus_musculus.GRCm39.cdna.all.fa.gz using Kallisto. Quality of reads checked on FASTqc and Multiqc
Transcripts annotated using Ensembl database Mus musculus v 79.
Samples were filtered to exlude genes with counts per million = in 3 or more samples and log2 counts per million were subsequently normalized in EdgeR.
Assembly: Mus_musculus.GRCm39.cdna.all.fa.gz
Supplementary files format and content: Data provided are log2 counts per million, filtered and normalized in a TSV file

molecule: total RNA

organism: Mus musculus

source_name: Immortalized MEFs

extract_protocol:
Total RNA from cell cultures was isolated uisng a Macherey-Nagel Nucleospin RNA kit
Libraries were prepared using a Nextera XT library preparation kit

tag: cell type

value: Immortalized MEFs

tag: genotype

value: recombined RXMM

tag: treatment

value: Mock


title: RXMM_Mock6


title: Healthy control 6

type: genomic

city: Aachen

first: Wolfgang

last: Wagner

address: Pauwelsstrasse 20

department: Helmholtz Institute for Biomedical Engineering

country: Germany

institute: RWTH Aachen University

hyb_protocol: DNA was bisulfite converted, amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChips (Illumina)  according to the standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan)

data_processing: pOOBAH using sesame

label: Cy5 and Cy3

molecule: genomic DNA

organism: Homo sapiens

source_name: PBMC

label_protocol: Standard Illumina protocol

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifucation (Ficoll) of 28 patients diagnosed with PMF, 2 patients diagnosed with ET and 10 healthy donors.

extract_protocol: Genomic DNA was isolated using the QIAamp DNA Mini Kit.

tag: Sex

value: Male

tag: age

tag: mutation

value: CTRL

tag: tissue

value: PBMC


title: RXMM_Mock3


title: Healthy control 3


title: UR_RXMM_Mock6

value: unrecombined RXMM


title: RNA_CD34_D14_KD

molecule: polyA RNA

value: CD34+ with scramble ncRNA-a3 KD siRNA + Tal1


title: UR_RXMM_Mock5


title: RXMM_AP1_4hrs2

value: BB homodimerizer


title: UR_RXMM_Mock4


title: RNA_CD34_D14_WT

value: CD34+ with scramble siRNA


title: UR_RXMM_Mock3


title: RNA_CD34_D7_Rescue


title: MDA-MB-231, treated 24 h with RBCs from healthy donor 2

city: Santiago de Compostela

first: Clotilde

last: Costa

address: Travesia da Choupana sn

country: Spain

institute: FIDIS

data_processing:
nbinomWaldTest using DESeq2
Assembly: transcripts were assembled with StringTie
Supplementary files format and content: excel files each column includes data fro each sample

extract_protocol:
RNA was harvested using AllPrep DNA/RNA Mini kit (Qiagen, Hilden, Germany).
Truseq stranded total RNA Library with Ribo-Zero Globin

tag: cell line

value: trile negative breast cancer

value: primed with RBCs from healthy donor 2


title: UR_RXMM_Mock2


title: Healthy control 2


title: UR_RXMM_Mock1


title: Healthy control 1


title: Healthy control 7

value: Female


title: 30- ET MPL mutation

value: MPL

tag: allele burden


title: 29- ET MPL mutation


title: RIPK3_ZIKV_3_24hrs

source_name: Primary Cortical Neurons

value: Primary Cortical Neurons

value: RIPK3 knockout

value: Zika virus


title: RIPK3_ZIKV_2_24hrs


title: RIPK3_ZIKV_1_24hrs


title: RNA_CD34_D7_WT

value: Primary cord blood CD34


title: RIPK3_Mock_3_24hrs


title: RIPK3_Mock_2_24hrs


title: RNA_CD34_D7_KD


title: 28- Pre-PMF MPL mutation


title: Healthy control 4


title: RNA_CD34_D3_Rescue

value: CD34+ with scramble ncRNA-a3 KD siRNA


title: 27- PMF MPL mutation


title: B6J_ZIKV_3_24hrs

value: WT


title: B6J_ZIKV_2_24hrs


title: B6J_ZIKV_1_24hrs


title: RNA_CD34_D3_WT


title: 26- PMF MPL mutation

value: Male


title: B6J_Mock_3_24hrs

value: Mock


title: RNA_CD34_D0

value: Wild type


title: 25- PMF MPL mutation

value: PBMC


title: B6J_Mock_1_24hrs


title: 24- PMF MPL mutation


title: B6J_Mock_2_24hrs


title: RNA_K562_KD1

value: Erythro Leukemic

value: K562 with ncRNA-a3 KD (clone 1)


title: RXMX_BB_24hrs_6

source_name: Primary cortical neurons

value: Primary cortical neurons

value: BB homodimerizer


title: RNA_K562_KD2

value: K562 with ncRNA-a3 KD (clone 2)


title: RXMX_BB_24hrs_5


title: 23- PMF MPL mutation


title: RXMX_BB_24hrs_4


title: RXMX_BB_24hrs_3


title: RNA_CD34_D3_KD

value: CD34+ with scramble ncRNA-a3 KD siRNA + Tal1


title: RIPK3_Mock_1_24hrs


title: 22- PMF MPL mutation

value: MPL


title: RNA_K562_WT1

value: K562 with pLKO.1 empty


title: NGC_K562_KD2

library_source: genomic

data_processing:
Sequence reads were analyzed by Capcruncher/0.2.2. Interaction profiles were generated using capcruncher with the following parameters: input files with pair-end fastq.gz files, genome files with human genome (hg38) index, restriction enzyme option with NlaIII, binning parameters with BIN 1000.
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
Cell pellets were permeabilized with ice-cold buffer (10mM Tris pH8.0, 10mM NaCl, 0.2% IgepaI CA-630, 1x Protease inhibitor) for 20min on ice, then suspended in NlaIII enzymatic digestion buffer containing 0.3% SDS and incubated at 37 °C for 1 hour with shaking
Libraries were indexed with Illumina Truseq indexed sequencing adapters using NEBnext reagents (E6000 / E6040 / E7335 / E7500) for end repair, dA labelling, adaptor ligation, and PCR indexing following the manufactures instructions with the following exceptions: DNA clean up steps were performed with Ampure XP (Beckman Coulter #A63881) beads. Oligo capture was performed using KAPA Hyper Prep Kit. Captured DNA was sequenced


title: RXMX_BB_24hrs_2


title: NGC_K562_KD1


title: RXMX_BB_24hrs_1


title: 21- PMF MPL mutation


title: 20- PMF JAK2 mutation


title: RXMX_BB_4hrs_6


title: RXMX_BB_4hrs_5


title: RXMX_BB_4hrs_4


title: NGC_K562_WT


title: RXMX_BB_4hrs_3


title: RXMX_BB_4hrs_2


title: 19- PMF JAK2 mutation


title: RXMX_BB_4hrs_1


title: 18- PMF JAK2 mutation

value: Female


title: RXMX_Mock_6


title: RXMX_Mock_5


title: 17- PMF JAK2 mutation


title: CnR_K562_RnTAL1

data_processing:
Cut&Run data was analyzed using CUT&Tag data processing pipeline (https://www.protocols.io/view/cut-amp-tag-data-processing-and-analysis-tutorial-e6nvw93x7gmk/v1)(37)
Assembly: hg19
Supplementary files format and content: bigwig

extract_protocol:
PAG-MNase was added to digest protein bound chromatin targets and incubated at RT for 10 minutes. Fragmented chromatin was released by incubating bead-cell mixture at 37°C for 10 min. For Cut&Run.RNase permeabilized cells were incubated with antibody along with 5µL of RNaseA and mixture was incubated at 16°C for 6 hours prior fragmentation with pAG-MNase
DNA fragments were purified and libraries were prepared using NEB Ultra II kits (#E7370) and NEBNext Multiplex Oligos for Illumina (#E7335, #E7500)

treatment_protocol: Cut&Run was performed using EpiCypher’s CUTANA kit


title: RXMX_Mock_4


title: RXMX_Mock_3


title: CnR_K562_RnBRG1


title: RXMX_Mock_1


title: RXMX_Mock_2


title: CnR_K562_16p300


title: 14- PMF JAK2 mutation


title: 4T1_CTC1592_3

city: Pamplona

first: Elizabeth

last: Guruceaga

address: Pio XII 55

institute: CIMA

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm39 human assembly using STAR v2.7.9a with default parameters.
featureCounts v1.6.0 software and Gencode vM32 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions
Obtained gene counts were normalized using edgeR and voom function of limma
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include gene counts obtained with featureCounts for each sample.

growth_protocol: All cell lines were cultured in RPMI 1640 supplemented with 10 mmol/L HEPES, 1% GlutaMAX and 1 mmol/ sodium pyruvate, Thismedium was supplemented with 10%FBS.

extract_protocol:
RNA was extracted with standard TRiZOL method
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Isolated CTC-in were obtained as described in PMID: 35191482.

value: TNBC breast cancer


title: 4T1_CTC1592_1


title: 4T1_CTC1592_2


title: 4T1_CTC1589_2


title: CnR_K562_16TAL1


title: 13- PMF JAK2 mutation


title: CnR_K562_16BRG1


title: 4T1_CTC1589_3


title: 4T1_CTC1589_1


title: CnR_K562_Rnp300


title: CnR_K562_p300_KD2


title: 4T1_C_3


title: 12- PMF JAK2 mutation


title: CnR_K562_TAL1_KD2


title: 4T1_C_2


title: 11- PMF JAK2 mutation


title: 4T1_C_1


title: ANV5_CTC803_3


title: CnR_K562_BRG1_KD2


title: 10- PMF CALR mutation

value: CALR


title: 16- PMF JAK2 mutation


title: ANV5_CTC803_2


title: ANV5_CTC803_1


title: CnR_K562_p300_KD1


title: 9- PMF CALR mutation


title: 15- PMF JAK2 mutation


title: ANV5_CTC700_3


title: ANV5_CTC700_2


title: 8- PMF CALR mutation


title: CnR_K562_TAL1_KD1


title: ANV5_CTC700_1


title: ANV5_C_3


title: 7- PMF CALR mutation


title: ANV5_C_2


title: ANV5_C_1


title: CnR_K562_BRG1_KD1


title: 6- PMF CALR mutation


title: 5- PMF CALR mutation


title: 5M_Tim3_cKO.5XFAD_rep3

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger). The include_introns option was set as active so that intronic reads generated by pre-mRNA could be counted.
Raw FASTQ files were mapped to a custom reference package built using cellranger mkref (v2.0.2) based on mouse mm10 (GENCODE vM23/Ensembl 98) and human genes APP and PSEN1 (NCBI Reference Sequence NC_000021.9 and NC_000014.9).
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain cortex

extract_protocol:
Nuclei from frozen mouse brain were isolated according to the protocol described in a previous report. In brief, frozen mouse frontal cortex was thawed and mechanically dissociated in ST buffer (10mM Tris-HCL pH7.5, 146mM NaCl, 1mM CaCl2, 21mM MgCl2) with 0.49% CHAPS (Millipore). Single-nuclei suspensions were filtered using a 40 μm strainer, centrifuged at 500g for 5min, and resuspended in ST buffer supplemented with 0.01% BSA (Sigma).
Nuclear suspensions were counted using a hemocytometer. 10x Chromium Single Cell 3’ Reagent Kit v3 (10x Genomics) was used according to manufacturer's protocol. In brief, 11,000 nuclei were loaded on the Chromium Chip (10x Genomics) and processed in the Chromium Controller. Single-nuclei were partitioned into Gel Beads-in-emulsion (GEMs), followed by RNA reverse transcription with barcoding. Libraries were created by breaking GEMs and pooling barcoded fractions, cDNA amplification, fragmentation and attachment of sample index and adapter.

value: Brain cortex

tag: strain


title: 5M_5XFAD_rep3

description: 10x Genomics


title: CnR_K562_p300_WT


title: 5M_control_rep2

description: 10x Genomics


title: CnR_K562_TAL1_WT


title: 5M_5XFAD_rep2

description: 10x Genomics


title: 4- PMF CALR mutation


title: 5M_Tim3_cKO_rep2

description: 10x Genomics


title: 3- PMF CALR mutation


title: 5M_Tim3_cKO.5XFAD_rep2

description: 10x Genomics


title: CnR_K562_BRG1_WT


title: 5M_5XFAD_rep1

description: 10x Genomics


title: ATAC_K562_KD1

data_processing:
Sequenced reads were trimmed and filtered using cutadapt PCR duplicates were removed using Picard MarkDuplicates (version 2.0.1), mitochondrial reads were removed with samtools, and sequences underwent quality control by FastQ. Reads and were mapped to the human (hg19) or mouse (mm9) reference genome using Bowtie2 with default parameters. ENCODE blacklist regions were filtered. SAM files were converted to BAM files and sorted using Samtools. Peak calling was performed using MACS2 with parameters (-g mm -p 1e-9 –nolambda -f BAMPE –nomodel –shiftsize 100 --extsize 200). A bigWig file, including fragment or read coverages for control and experimental datasets, was generated with the bedGraphToBigWig program, (https://www.encodeproject.org/software/bedgraphtobigwig/). Sequencing tracks were viewed using the Integrated Genomic Viewer.
Assembly: hg19
Supplementary files format and content: Bigwig

extract_protocol:
The fragmented DNA was purified using the MinElute Kit (QIAGEN)
Fragments were simultaneously amplified and indexed in a PCR reaction with 2x NEBNext High-Fidelity PCR master Mix (NEB). Following purification with AMPure XP beads (Beckman Coulter # A63881)


title: ATAC_K562_KD2


title: ATAC_K562_WT


title: 5M_Tim3_cKO_rep1

description: 10x Genomics


title: 5M_Tim3_cKO.5XFAD_rep1

description: 10x Genomics


title: PBMCs,ALS,Sporadic,ALS35

city: Pavia

first: Francesca

last: Dragoni

state: Italy

address: Via Mondino, 2

country: Italy

institute: IRCCS Mondino Foundation

description: Library name: ALS35_PBMC

data_processing:
FastQ files were generated via Illumina bcl2fastq2 (Version 2.17.1.14 http://support.illumina.com/downloads/bcl2fastq-conversion-software-v217.html).
Quantification of miRNAs was done as described in the literature [13]. The workflow, including quality control filter, trimming of adapters, and reads mapping against miRNA precursors, is implemented in Docker4Seq package
Assembly: HG19
Supplementary files format and content: fastq.gz

source_name: Blood

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were prepared by centrifugation. Peripheral blood was layered (density=1.077) and centrifuged at 950g for 30 min. After isolation on a Ficoll-Histopaque layer (Sigma, Italy), cell viability was assayed by a trypan blue

extract_protocol:
Total RNA from PBMCs was isolated from PBMCs using Trizol® reagent. The specifications from the manufacturer were followed.
Libraries for miRNA sequencing have been prepared using the Small RNA-Seq Library Prep kit (Lexogen) according to the user manual. Sequencing steps have been carried out on the Illumina NextSeq 550.

value: Blood

value: Peripheral Blood Mononuclear Cells

tag: condition

value: Sporadic ALS


title: 1- PMF CALR mutation


title: PBMCs,ALS,Sporadic,ALS34

description: Library name: ALS34_PBMC


title: Condition T-CM, rep5

city: Bethesda

first: Stanley

last: Lipkowitz

state: MD

address: 10 Centre Drive

department: Women's Malignancies Branch

institute: NIH

data_processing:
Libraries were sequenced on NovaSeq 6000 using pair-end sequencing with 101 nt read length (2x101 cycle mode).
Reads were trimmed using CutAdapt v1.18
Trimmed reads were then aligned to the reference genome (hg38) using STAR 2.7.0f with the following option (--runThreadN 32   --genomeDir HG38   --readFilesIn R1.trim.fastq.gz   R2.trim.fastq.gz    --readFilesCommand zcat --limitSjdbInsertNsj 4000000 --outSAMtype BAM   SortedByCoordinate      --outSAMstrandField None --outSAMunmapped Within --outWigType None --outWigStrand Stranded --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3   --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq -      --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsProtrude 10   ConcordantPair --peOverlapNbasesMin 10 --sjdbFileChrStartEnd uniq.filtered.SJ.out.tab --sjdbGTFfile genes.gtf --quantMode TranscriptomeSAM GeneCounts).
GENCODE v30 GTF was used for annotation.
Assembly: hg38
Supplementary files format and content: comma-separated text file containing raw counts for each sample.

source_name: Whole Blood

extract_protocol:
The human neutrophils were isolated from whole blood using EasySep™ Direct Human Neutrophil Isolation Kit (STEM cell Technologies). RNA was extracted using Rneasy mini kit (Qiagen).
Library was prepared using Illumina® Stranded Total RNA Prep. Ligation was done with Ribo Zero-Plus.

treatment_protocol: Donor isolated neutrophils were incubated for 18h with 5% CO2 in 37 C, either in serum free RPMI media (SFM)/ SFM added suboptimal dose (45nM) TRAIL designated as SFM-T/ MDA MB-231 collected condition media (CM)/ T-CM. This T-CM is obtained by incubating MDA-MB-231 cells with 45 nM of TRAIL for 24 Hrs in serum free RPMI and then collecting the media for neutrophil assay.

value: Whole Blood

value: neutrophils

value: incubated 18h in T-CM (TRAIL- treated MDA-MB-231 condition media)


title: Time pt.24H, rep 3

data_processing:
Libraries were sequenced on NextSeq using pair-end sequencing with 76 nt read length (2x76 cycle mode).
Reads were trimmed using CutAdapt v1.18
Trimmed reads were then aligned to the reference genome (hg38) using STAR 2.7.0f with the following option (--runThreadN 32   --genomeDir HG38   --readFilesIn R1.trim.fastq.gz   R2.trim.fastq.gz    --readFilesCommand zcat --limitSjdbInsertNsj 4000000 --outSAMtype BAM   SortedByCoordinate      --outSAMstrandField None --outSAMunmapped Within --outWigType None --outWigStrand Stranded --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.3   --outFilterIntronMotifs RemoveNoncanonicalUnannotated --clip3pAdapterSeq -      --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --alignEndsProtrude 10   ConcordantPair --peOverlapNbasesMin 10 --sjdbFileChrStartEnd uniq.filtered.SJ.out.tab --sjdbGTFfile genes.gtf --quantMode TranscriptomeSAM GeneCounts).
Gencode v28 was used for annotation.
Assembly: hg38
Supplementary files format and content: comma-separated text file containing raw counts for each sample.

growth_protocol: MDA-MB-231 cells were cultured in RPMI with 10% serum (FBS) and antibiotic in humidified atmosphere with 5% Carbon dioxide at 37 C.

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen). 1.3ug of total RNA was used for preparing the library.
Library was prepared using Illumina TruSeq Stranded mRNA Library Prep for paired-end sequencing.

treatment_protocol: MDA MB 231 cells were treated with suboptimal dose of TRAIL (45 nM) for different time points like 0H, 1H, 3H, 6H, 12H, 24H, in triplicates followed by RNA isolation.

value: Mesenchymal Basal B

value: TRAIL treated


title: PBMCs,ALS,Sporadic,ALS33

description: Library name: ALS33_PBMC


title: PBMCs,ALS,Sporadic,ALS31

description: Library name: ALS31_PBMC


title: PBMCs,ALS,Sporadic,ALS32

description: Library name: ALS32_PBMC


title: Time pt.24H, rep 2


title: Condition T-CM, rep 4


title: PBMCs,ALS,Sporadic,ALS30

description: Library name: ALS30_PBMC


title: Condition T-CM, rep 3


title: PBMCs,ALS,Sporadic,ALS29

description: Library name: ALS29_PBMC


title: PBMCs,ALS,Sporadic,ALS28

description: Library name: ALS28_PBMC


title: Time pt.24H, rep 1


title: Condition T-CM, rep 2


title: PBMCs,ALS,Sporadic,ALS27

description: Library name: ALS27_PBMC


title: PBMCs,ALS,Sporadic,ALS26

description: Library name: ALS26_PBMC


title: Time pt.12H, rep 3


title: PBMCs,ALS,Sporadic,ALS25

description: Library name: ALS25_PBMC


title: Condition T-CM, rep 1


title: 2- PMF CALR mutation

value: Male

value: PBMC


title: PBMCs,ALS,Sporadic,ALS24

description: Library name: ALS24_PBMC


title: Condition CM, rep5

value: incubated 18h in CM (MDA-MB-231condition media)


title: Time pt.12H, rep 1


title: PBMCs,ALS,Sporadic,ALS23

description: Library name: ALS23_PBMC


title: PBMCs,ALS,Sporadic,ALS21

description: Library name: ALS21_PBMC


title: Condition CM, rep 4


title: Time pt.6H, rep 3


title: Condition CM, rep 3


title: PBMCs,ALS,Sporadic,ALS20

description: Library name: ALS20_PBMC


title: Time pt.6H, rep 2


title: Condition CM, rep 2


title: 5M_control_rep1

description: 10x Genomics


title: Time pt.6H, rep 1


title: PBMCs,ALS,Sporadic,ALS17

description: Library name: ALS17_PBMC


title: PBMCs,ALS,Sporadic,ALS18

description: Library name: ALS18_PBMC


title: PBMCs,ALS,Sporadic,ALS16

description: Library name: ALS16_PBMC


title: PBMCs,ALS,Sporadic,ALS13

description: Library name: ALS13_PBMC


title: PBMCs,ALS,Sporadic,ALS15

description: Library name: ALS15_PBMC


title: Time pt.3H, rep 3


title: PBMCs,ALS,Sporadic,ALS14

description: Library name: ALS14_PBMC


title: Time pt.3H, rep 2


title: Condition SFM-T, rep5

value: incubated 18h in SFM-T (TRAIL)


title: Time pt.12H, rep 2


title: PBMCs,ALS,Sporadic,ALS12

description: Library name: ALS12_PBMC


title: Condition SFM-T, rep 4


title: Time pt.3H, rep 1


title: PBMCs,ALS,Sporadic,ALS22

description: Library name: ALS22_PBMC


title: PBMCs,ALS,Sporadic,ALS11

description: Library name: ALS11_PBMC


title: Condition SFM-T, rep 3


title: Time pt.1H, rep 2


title: PBMCs,ALS,Sporadic,ALS19

description: Library name: ALS19_PBMC


title: Condition SFM-T, rep 2


title: PBMCs,HealthyControl,HC17

description: Library name: HC17_PBMC

value: Healthy Control


title: PBMCs,HealthyControl,HC15

description: Library name: HC15_PBMC


title: Condition CM, rep 1


title: PBMCs,HealthyControl,HC14

description: Library name: HC14_PBMC


title: Time pt. 0H, rep 3


title: PBMCs,HealthyControl,HC12

description: Library name: HC12_PBMC


title: Condition SFM, rep5

value: incubated 18h in SFM


title: Time pt. 0H, rep 2


title: PBMCs,HealthyControl,HC13

description: Library name: HC13_PBMC


title: PBMCs,HealthyControl,HC10

description: Library name: HC10_PBMC


title: Condition SFM, rep 4


title: Condition SFM, rep 3


title: LCL transformed under 1% O2 by EBV, replicate 2 RNA-seq

first: Rui

last: Guo

state: Massachusetts

address: 150 Harrison Ave.

department: School of Medicine

institute: Tufts University

description: Library name: 1__O2_LCL_rep2

data_processing:
For RNA-seq, adaptor-trimmed Illumina reads for each individual library were mapped back to the human GRCh37.83 transcriptome assembly using STAR2.5.2b 85. Feature Counts was used to estimate the number of reads mapped to each contig 86. Only transcripts with at least 5 cumulative mapping counts were used in this analysis. DESeq2 was used to evaluate differential expression (DE) 87. DESeq2 uses a negative binomial distribution to account for overdispersion in transcriptome datasets. It uses a conservative analysis that relies on a heuristic approach. Each DE analysis used pairwise comparison between the experimental and control groups. Differentially expressed genes were identified and a P-values < 0.05 and absolute fold change > 2 cutoff was used. Differentially expressed genes (DEGs) were subjected to Enrichr analysis which was employed to perform gene list-based gene set enrichment analysis on the selected gene subset. The algorithm used to calculate combined scores was described previously 88. P value and log2 fold change were generated with DESeq2 under default settings with Wald test and normal shrinkage, respectively.
For ChIP-seq, read quality was assessed using FastQC to ensure no biases such as GC skew or PCR artifacts. ChIP-seq reads were aligned to the human genome (hg19) using default settings using Bowtie2, except -k was set to 1, with a mappability rate of 94–98%. Peaks were called using MACS v2.1.074 with an FDR threshold of ≤ 0.99(Ref), followed by IDR analysis (v2.0.3) with an IDR threshold of ≤ 0.02, as recommended by the ENCODE consortium to ensure peak reproducibility. Peaks in blacklist regions were excluded from downstream analysis. Bigwig files were generated using deepTools v3.5.6.
Assembly: hg19
Supplementary files format and content: For RNA-seq, tab-delimited text files include Log2FoldChange value (21%_O2_LCL v.s. 1%_O2_LCL), p value and FDR corrected p value (padj). Separate tab-delimited text files are also provided for raw counts and normalized counts of genes, respectively
Supplementary files format and content: bigWig, narrowPeak (except for input sample)

source_name: B lymphocytes

growth_protocol: Purified naïve B cells were incubated with B95-8 EBV at a multiply of infection (MOI) of 0.1 for 1 hour at 37°C in a 5% CO₂ incubator to facilitate viral entry. Following infection, cells were washed with serum free RPMI-1640 medium and resuspended in complete culture medium (RPMI-1640 supplemented with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin, and 100 μg/mL streptomycin). To assess the impact of oxygen levels on EBV transformation, infected B cells were cultured under two distinct oxygen conditions: 1) normoxia (21% O₂): cells were maintained in a standard tissue culture incubator (ThermoFisher) at 37°C with 5% CO₂; 2) hypoxia (1% O₂): cells were placed in a hypoxia incubator (ThermoFisher) set to 1% O₂, 5% CO₂, and 94% N₂ at 37°C. Cells were cultured for 28 days, during which they proliferated and transformed into lymphoblastoid cell lines (LCLs). LCLs were passaged every 3–4 days by replacing 2/3 of the medium with fresh RPMI-1640 supplemented with 10% FBS to support cell growth.

extract_protocol:
For RNA extraction, total RNAs were subsequently isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination. For chromatin samples, sample was prepared using the iDeal ChIP-seq kit for Histones (C01010059, HILOGIC Diagenode) following the sonication using Diagenode Pico.
For RNA-seq library preparation, 500 ng total RNA was used for polyA mRNA-selection using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490, New England Biolabs, Inc.  Ipswich, MA), followed by library construction via NEBNext Ultra RNA Library Prep Kit for Illumina (#E7530, New England Biolabs, Inc., Ipswich, MA). For ChIP-seq libaray preparaion, DNA libraries were prepared using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S, NEB) and sequenced at the Tufts Genomics Core.

treatment_protocol: Primary B cells were transformed by EBV under 21% O2 or 1% O2 tension.

value: B lymphocytes

value: EBV transformed LCL

value: 1% Oxygen


title: LCL transformed under 1% O2 by EBV, replicate 1, RNA-seq

description: Library name: 1__O2_LCL_rep1


title: LCL transformed under 1% O2 by EBV, replicate 3, RNA-seq

description: Library name: 1__O2_LCL_rep3


title: Condition SFM, rep 2


title: PBMCs,HealthyControl,HC18

description: Library name: HC18_PBMC

value: Blood


title: PBMCs,HealthyControl,HC16

description: Library name: HC16_PBMC

value: Peripheral Blood Mononuclear Cells


title: LCL transformed under 21% O2 by EBV, replicate 2, RNA-seq

description: Library name: 21__O2_LCL_rep2

value: 21% Oxygen


title: Condition SFM, rep 1

value: Whole Blood


title: LCL transformed under 21% O2 by EBV, replicate 3, RNA-seq

description: Library name: 21__O2_LCL_rep3


title: LCL transformed under 21% O2 by EBV, replicate 1, RNA-seq

description: Library name: 21__O2_LCL_rep1


title: Time pt.1H, rep 1


title: Condition SFM-T, rep 1

value: neutrophils


title: K562_VPR_1136_D9_tRNA_D100_R2

city: NASHVILLE

first: Marisol

last: Ramirez

state: TENNESSEE

address: 2220 Pierce Avenue, 571 Preston Research Building

department: Center for Quantitative Sciences, Department of Biostatisticss

institute: Vanderbilt University Medical Center

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt v2.10
Reads were aligned to the Gencode GRCh38.p13 genome using STAR v2.7.8a. Gencode v38 gene annotations were provided to STAR to improve the accuracy of mapping.
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC v0.11.9
featureCounts v2.0.2 was used to count the number of mapped reads to each gene.
Assembly: Gencode GRCh38.p13
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: K562 cells were cultured and maintained in IMDM (Invitrogen 12440) with 10% FBS (Atlanta Biologicals S1155OH) and 1% pen/step (Invitrogen 15140122) in 5% CO2 and 37°C conditions.

extract_protocol:
Total RNA was obtain via extraction with the Zymo Research RNA Microprep Kit following manufacturer's protocol.
mRNA enrichment and cDNA library preparation was completed by the stranded mRNA (polyA-selected) library kit (Illumina) following manufacturer's protocol.

treatment_protocol: Doxycycline (Sigma Aldrich D9891) was used to induce the expression of dCas9-VPR by adding to the cell culture medium at a final concentration of 100ng/mL. Recombinant human IFN-alpha (Fisher Scientific cat.# 12100-1) was used to induce SAMD9 at a final concentration of 1000U/mL. Treatment duration was 24 hours for conditions treated with IFN and Doxy.

value: CML-lymphoblast

value: Doxy 100ng


title: PBMCs,HealthyControl,HC11

description: Library name: HC11_PBMC


title: LCL transformed under 1% O2 by EBV, replicate 1, H3K27AC, ChIP

description:
Library name: 1__O2_LCL_H3K27ac_rep1
H3K27ac ChIP


title: LCL transformed under 1% O2 by EBV, replicate 2, H3K4me3, ChIP

description:
Library name: 1__O2_LCL_H3K4me3_rep2
H3K4me3 ChIP


title: patient 4 OVK13

type: RNA

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

hyb_protocol: Hybridized for 16 h at 32 C with rotary shake (250 rpm). Hybridization buffer and washing protocol was followed by the protocol supplied by TORAY Industries, Inc..

scan_protocol: 3D-Gene Scanner ((Toray Industries Inc., Tokyo, Japan) was used for scanning. Images were quantified using Extraction(Toray Industries Inc., Tokyo, Japan).

data_processing: The raw data of each spot was normalized by substitution with a mean intensity of the background signal determined by all blank spots’ signal intensities of 95% confidence intervals.

source_name: ovarian cancer

label_protocol: Extracted total RNA was labeled with Cy5 using the 3D-Gene miRNA labeling kit (Toray Industries Inc., Tokyo, Japan).

growth_protocol: Vaginal discharge was collected by wiping the vaginal discharge with swabs. The collected swabs were soaked in 4 ml of phosphate-buffered saline (PBS) (FUJIFILM Wako Pure Chemical Corporation, Osaka, Japan). The solution was collected, including the liquid squeezed from the swab.

extract_protocol:
Exosomes were extracted using the SmartSEC HT EV Isolation System (System Biosciences, CA, USA) according to the manufacturer’s protocol. The extracted exosomes were stored at -80°C. Exosome solution was submitted to Kamakura Techno‒Science, Inc. (Kanagawa, Japan).
RNA samples were extracted using 3D-Gene extraction reagent from liquid sample(Toray Industries Inc., Tokyo, Japan).

treatment_protocol: They were centrifuged at 3,000 ×g for 15 min at 4°C and the supernatant was collected. Subsequently, centrifuged at 12,000 ×g for 15 min at 4°C and the supernatant was collected. The centrifuged samples were stored at -80°C until further use.

value: vaginal discharge

tag: brca status

value: negative

tag: hrd status

tag: histology

value: High-grade serous carcinoma

value: female

tag: Stage

tag: lymph node metastasis

value: positive


title: LCL transformed under 1% O2 by EBV, replicate 1, H3K4me3, ChIP

description:
Library name: 1__O2_LCL_H3K4me3_rep1
H3K4me3 ChIP


title: patient 3 OVK11


title: PBMCs,HealthyControl,HC9

description: Library name: HC9_PBMC

value: Healthy Control


title: LCL transformed under 1% O2 by EBV, replicate 2, INPUT

description:
Library name: 1__O2_LCL_INPUT_rep2
Input


title: LCL transformed under 1% O2 by EBV, replicate 1, INPUT

description:
Library name: 1__O2_LCL_INPUT_rep1
Input


title: K562_VPR_1136_D9_tRNA_NT_R2

value: No Treatment


title: patient 1 E9

source_name: benign gynecological disease

value: Mature cystic teratoma


title: Time pt. 0H, rep 1

value: Mesenchymal Basal B

value: TRAIL treated


title: LCL transformed under 21% O2 by EBV, replicate 2, H3K27ac, ChIP

description:
Library name: 21__O2_LCL_H3K27ac_rep2
H3K27ac ChIP

value: B lymphocytes

value: EBV transformed LCL


title: K562_VPR_1136_D9_tRNA_NT_R1


title: patient 2 N3

value: Leiomyoma


title: K562_VPR_D9_1136_D9_D2000_R2

value: Doxy 2000ng


title: atac_pachy_smarca5_ko1

city: New Haven

first: Bluma

middle: J

last: Lesch

state: CT

address: 333 Cedar Street

department: Genetics

institute: Yale University

description: Library name: atac_pachy_ko1

data_processing:
Adapter trimming was performed using Cutadapt (Martin, 2011). Trimmed reads were aligned to the mouse genome (mm10) using Bowtie2 in very sensitive mode (Langmead and Salzberg, 2012). Mitochondrial reads were removed by excluding any reads aligning to chrMT. Peak calling was performed using MACS2 with default parameters.
Assembly: mm10
Supplementary files format and content: scRNA-seq: index (.tsv), feature (.tsv), and matrix (.mtx) files
Supplementary files format and content: ATAC-seq: .bed files of peaks

source_name: sorted testicular cells

extract_protocol:
A polypropylene collection tube was coated with 3 ml Collection Buffer (20% FBS in 1X PBS) for 2 hours at RT with end-over-end mixing. Seminiferous tubules were mechanically isolated from the tunica and transferred to a 15ml conical tube containing 5ml Digestion Solution I [0.75 mg/ml collagenase type IV (Gibco, 17104-019) in Dulbecco’s modified Eagle’s media (DMEM, Gibco, 11965092) supplemented with 1:1000 with 1 mg/ml DNase I (StemCell Technologies, 07900)] warmed to 37 °C, followed by incubation at 37 °C for 10 mins with end-over-end rotation. 5ml of cold DMEM was added and tubules allowed to settle on ice. The supernatant was discarded and the tubules were washed again with 5ml cold DMEM to deplete Leydig cells. 5ml of DMEM was added followed by centrifugation at 500xg for 5 mins at 4°C. The supernatant was removed and 5ml of Digestion Solution II [Accutase (Gibco, A1110501) supplemented with 1 mg/ml DNase I at 1:1000 at room temperature)] was added to the tubules followed by incubation with end-over-end rotation for 10 mins at RT with gentle pipetting after 5 mins to disperse the tubules. 5ml of cold Complete Media (10% FBS in DMEM) was added and the sample was centrifuged at 500 xg for 5 mins at 4 °C. The cell pellet was then resuspended in 5 ml of cold Complete Medium, filtered through a 100 μm strainer, and the cell suspension was transferred to a fresh 15 ml conical tube and centrifuged at 500 xg for 5 mins at 4 °C.Cells were stained with Hoechst dye and isolated by flow cytometry based on 4C DNA content.  50,000 sorted pachytene or pachytene-like cells were processed for each ATAC-seq library using the Active Motif kit (53150) as per the manufacturer’s protocol.
50,000 sorted pachytene or pachytene-like cells were processed for each ATAC-seq library using the Active Motif kit (53150) as per the manufacturer’s protocol.

value: sorted testicular cells

value: pachytene spermatocytes

value: Smarca5 fl/delta; Ddx4-Cre+ (Smarca5 cKO)


title: atac_pachy_wt2

description: Library name: atac_pachy_wt2

value: wild type C57BL6


title: LCL transformed under 21% O2 by EBV, replicate 2, H3K4me3, ChIP

description:
Library name: 21__O2_LCL_H3K4me3_rep2
H3K4me3 ChIP

value: 21% Oxygen


title: LCL transformed under 21% O2 by EBV, replicate 1, H3K4me3, ChIP

description:
Library name: 21__O2_LCL_H3K4me3_rep1
H3K4me3 ChIP


title: atac_pachy_wt1

description: Library name: atac_pachy_wt1


title: LCL transformed under 1% O2 by EBV, replicate 2, H3K27AC, ChIP

description:
Library name: 1__O2_LCL_H3K27ac_rep2
H3K27ac ChIP

value: 1% Oxygen


title: LCL transformed under 21% O2 by EBV, replicate 1, INPUT

description:
Library name: 21__O2_LCL_INPUT_rep1
Input


title: smarca5_scRNAseq rep 2

description: Library name: KO_2

data_processing:
Raw count matrices were generated using CellRanger (10X Genomics) and imported to Seurat 4.1.0 (Hao et al., 2021) and combined into one Seurat object. Reads were filtered to exclude doublets (nCount_RNA < mean + one standard deviation), dead or dying cells (nFeature_RNA > mean – one standard deviation) or high mitochondrial content (present.mt < mean + standard deviation). This filtered subset was log normalized and scaled. A linear dimensional reduction was performed using principal component analysis (PCA). Clusters were identified at a resolution of 0.5, and the “RunUMAP()” function was used to further investigate the dataset.
Assembly: mm10
Supplementary files format and content: scRNA-seq: index (.tsv), feature (.tsv), and matrix (.mtx) files
Supplementary files format and content: ATAC-seq: .bed files of peaks

source_name: whole testis

extract_protocol:
A polypropylene collection tube was coated with 3 ml Collection Buffer (20% FBS in 1X PBS) for 2 hours at RT with end-over-end mixing. Seminiferous tubules were mechanically isolated from the tunica and transferred to a 15ml conical tube containing 5ml Digestion Solution I [0.75 mg/ml collagenase type IV (Gibco, 17104-019) in Dulbecco’s modified Eagle’s media (DMEM, Gibco, 11965092) supplemented with 1:1000 with 1 mg/ml DNase I (StemCell Technologies, 07900)] warmed to 37 °C, followed by incubation at 37 °C for 10 mins with end-over-end rotation. 5ml of cold DMEM was added and tubules allowed to settle on ice. The supernatant was discarded and the tubules were washed again with 5ml cold DMEM to deplete Leydig cells. 5ml of DMEM was added followed by centrifugation at 500xg for 5 mins at 4°C. The supernatant was removed and 5ml of Digestion Solution II [Accutase (Gibco, A1110501) supplemented with 1 mg/ml DNase I at 1:1000 at room temperature)] was added to the tubules followed by incubation with end-over-end rotation for 10 mins at RT with gentle pipetting after 5 mins to disperse the tubules. 5ml of cold Complete Media (10% FBS in DMEM) was added and the sample was centrifuged at 500 xg for 5 mins at 4 °C. The cell pellet was then resuspended in 5 ml of cold Complete Medium, filtered through a 100 μm strainer, and the cell suspension was transferred to a fresh 15 ml conical tube and centrifuged at 500 xg for 5 mins at 4 °C.15,000 dissociated testis cells were processed using a Chromium Next GEM Single Cell 3’ v3.1 kit (10X Genomics) and sequenced using an Illumina NovaSeq machine with 150 base pair paired-end reads at a depth of 250 million reads.
15,000 dissociated testis cells were processed using a Chromium Next GEM Single Cell 3’ v3.1 kit (10X Genomics) and sequenced using an Illumina NovaSeq machine with 150 base pair paired-end reads at a depth of 250 million reads.

value: whole testis

value: mixed testicular cells


title: K562_VPR_1136_D9_tRNA_D100_R1

value: CML-lymphoblast

value: Doxy 100ng


title: K562_VPR_D9_1136_D9_D2000_R1


title: atac_pachy_smarca5_ko2

description: Library name: atac_pachy_ko2


title: K562_VPR_D9_1136_D100_R2


title: HEK293T_miR34aWT_rep4

city: Solna

first: Emma

middle: R

last: Andersson

address: Solnavägen 9

department: Department of Cell and Molecular Biology

country: Sweden

institute: Karolinska Institute

data_processing:
Reads were aligned to the human genome assembly version GRCh38 using STAR (version 2.7.11a).
Reads were assigned to genes using featureCounts in the subread package (version 2.0.3).
Differential gene expression analysis on the raw counts was carried out using edgeR (version 3.42.4).
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file contains raw feature counts.

extract_protocol:
Total RNA was isolated with GeneJET RNA Purification Kit (Thermo Scientific, K0731). Additional cleanup of genomic DNA was carried out with RapidOut DNA Removal Kit (Thermo Scientific, K2981). The quality of the isolated RNA was checked on an Agilent 2100 BioAnalyzer with the RNA 6000 Nano Kit.
cDNA libraries were prepared with the TruSeq RNA Sample Preparation v2 kit (Illumina, RS-122-2001/RS-122-2002), according to the manufacturer's protocol.

value: transfected with miR-34a-WT duplex


title: HEK293T_miR34aWT_rep1


title: HEK293T_miR34aRS_rep3

value: transfected with miR-34a-RS duplex


title: T cell differentiation model, experiment 2 – day 4

city: minatoku toranomon

first: Tatsuma

last: Matsuda

address: tokyo

institute: toranomon hospital

description:
Library name: ex2_day4
10x Genomics

data_processing:
ASTQ files were aligned using the 103 Genomics CellRanger 6.0.0. pipeline to the mouse GRCm39 reference transcriptome to generate gene-expression count matrices with the ‘‘exclude the introns’’ option.
Assembly: GRCm39
Supplementary files format and content: separated barcode file and features file, matrix file

source_name: T cell diferentiation model

growth_protocol: Bone marrow (BM) cells from 3- to 4-month-old Rosa26-Cas9;Bcl2 transgenic mice were lineage-depleted using biotin-conjugated antibodies and magnetic separation. Progenitors were retrovirally transduced with sgRNA, cultured with cytokines, and co-cultured on OP9-DLL1 for T cell induction. After 6 days, cells were analyzed by flow cytometry using lineage and surface markers following Fc receptor blocking.

extract_protocol:
CD45⁺ Cas9-LPs, with or without Notch stimulation, were sorted using a FACSAria (BD) and resuspended in PBS supplemented with 0.5% BSA.
Single-cell RNA-seq libraries were generated using the 10× Genomics Chromium Single Cell 3′ Reagent Kit, following the manufacturer’s protocol. Cells were encapsulated into GEMs, reverse transcribed, barcoded with cell-specific barcodes and UMIs, and cDNA was purified, amplified, and quality-checked. Libraries were constructed through enzymatic fragmentation, adapter ligation, indexing PCR, and double-sided size selection. Sequencing was performed on an Illumina NovaSeq platform, and data were processed with Cell Ranger for alignment to the mm10 genome, UMI counting, and expression quantification.

value: T cell diferentiation model

value: male


title: T cell differentiation model, experiment 2 – day 10

description:
Library name: ex2_day10
10x Genomics


title: K562_VPR_D9_1136_D100_R1


title: T cell differentiation model, experiment 2 – day 2

description:
Library name: ex2_day2
10x Genomics


title: LCL transformed under 21% O2 by EBV, replicate 2, INPUT

description:
Library name: 21__O2_LCL_INPUT_rep2
Input

value: B lymphocytes

value: EBV transformed LCL


title: HEK293T_miR34aRS_rep1


title: HEK293T_miR34aRS_rep5


title: T cell differentiation model, experiment 2 – day 6

description:
Library name: ex2_day6
10x Genomics


title: K562_VPR_D9_1136_D9_NT_R2

value: No Treatment


title: HEK293T_AllStars_rep4

value: transfected with AllStars negative control siRNA (Qiagen)


title: HEK293T_miR34aWT_rep2


title: K562_1136_iso_IFN_R1

value: IFN


title: HEK293T_miR34aRS_rep2


title: T cell differentiation model, experiment 2 – 16hr

description:
Library name: ex2_16hr
10x Genomics


title: K562_VPR_D9_1136_D9_NT_R1


title: HEK293T_AllStars_rep2


title: HEK293T_AllStars_rep3


title: T cell differentiation model, experiment 2 – 8hr

description:
Library name: ex2_8hr
10x Genomics


title: K562_1136_iso_NoTx_R2


title: HEK293T_AllStars_rep1


title: HEK293T_miR34aWT_rep5


title: K562_1136_iso_NoTx_R1


title: T cell differentiation model, experiment 2 – 0hr

description:
Library name: ex2_0hr
10x Genomics


title: HEK293T_miR34aWT_rep3


title: K562_WT_VPR_D9_tRNA_D100_R2


title: K562_WT_VPR_D9_tRNA_D100_R1


title: T cell differentiation model, experiment 2 – 24hr

description:
Library name: ex2_24hr
10x Genomics


title: HEK293T_AllStars_rep5


title: T cell differentiation model, experiment 1 – day 7

description:
Library name: ex1_day7
10x Genomics


title: K562_WT_VPR_D9_tRNA_NT_R1


title: T cell differentiation model, experiment 1 – day 5

description:
Library name: ex1_day5
10x Genomics


title: Healthy control-1

city: Chengdu

first: Ming

last: Chen

state: Sichuan

address: No. 37, GuoXue Xiang, Chengdu, China

country: China

institute: West China Hospital of Sichuan University

description: Library name: HC1_L

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text fle includes raw counts for each Sample

source_name: left-sided colonic mucosal biopsy specimens

extract_protocol:
Total RNA was harvested using Trizol from colon tissues
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: HC


title: Remission ulcerative colitis patient-3

description: Library name: UC13_L

value: left-sided colonic mucosal biopsy specimens

value: UC


title: Healthy control-2

description: Library name: HC3_L


title: K562_WT_VPR_D9_D2000_R2

value: Doxy 2000ng


title: Healthy control-3

description: Library name: HC8_L


title: Remission ulcerative colitis patient-2

description: Library name: UC9_L


title: T cell differentiation model, experiment 1 – day 10

description:
Library name: ex1_day10
10x Genomics


title: T cell differentiation model, experiment 1 – day 3

description:
Library name: ex1_day3
10x Genomics


title: endometrial epithelial cells rep 5

city: Liverpool

first: Jamie

last: Soul

address: Crown St

department: ISMIB

country: United Kingdom

institute: University of Liverpool

hyb_protocol: A total of 600 ng (300 ng of both Cy3 and Cy5) of labelled cRNA was fragmented and following the addition of 2 x HiRPM hybridisation buffer, samples were loaded onto arrays and hybridised for 17 hours at 65 oC in an Agilent hybridisation oven (Agilent Technologies, Santa Clara, USA). Following hybridisation the arrays were washed using the Agilent Gene Expression Wash Buffer kit

scan_protocol: Scanned using the Agilent G2505C scanner with Agilent G3_GX_2colour settings (Agilent Technologies, Santa Clara, US).

data_processing: Data was extracted using Agilent Feature Extraction Software version 11.0.1.1. R was used for downstream processing. Background corrected using the “normexp” function, normalised within arrays using “vsn” and “loess” methods and normalised between arrays using the “Aquantile” method in limma.

source_name: SSEA-1- rep5

label_protocol: 40 ng RNA was used in the initial input and the Agilent Low Input Quick Amp Labelling Kit (Agilent Technologies, Santa Clara, US) was used for target preparation, using the Two-Colour Microarray-Based Gene Expression Analysis protocol, according to manufacturer’s instructions.

growth_protocol: Freshly harvested endometrial tissue was mechanically and enzymatically digested and cells were then subsequently filtered into stromal and epithelial fractions

extract_protocol: Total RNA was extracted using TRIzol® Plus RNA Purification System (Invitrogen Life Technologies, Paisley, UK) according to the manufacturer’s instructions.

treatment_protocol: The epithelial single-cell suspension was labelled with anti-SSEA1 (CD15) MicroBeads (#130-094-530, Miltenyi Biotec, UK) and magnetic bead sorting (MACS) sorted into SSEA-1 enriched and SSEA-1 depleted populations using MACS separation columns (MS columns, Miltenyi Biotec, UK) according to manufacturer’s instructions

value: endometrium

tag: donor

source_name: SSEA-1+ rep5

tag: tag


title: endometrial epithelial cells rep 1

source_name: SSEA-1- rep1

source_name: SSEA-1+ rep1


title: K562_WT_VPR_D9_D2000_R1

tag: cell type

tag: genotype


title: T cell differentiation model, experiment 1 – day 2

description:
Library name: ex1_day2
10x Genomics

tag: Sex


title: Active ulcerative colitis patient-3

description: Library name: UC14_L


title: K562_WT_VPR_D9_tRNA_NT_R2

tag: treatment


title: endometrial epithelial cells rep 8

source_name: SSEA-1- rep8

source_name: SSEA-1+ rep8


title: endometrial epithelial cells rep 7

source_name: SSEA-1- rep7

source_name: SSEA-1+ rep7


title: endometrial epithelial cells rep 3

source_name: SSEA-1- rep3

source_name: SSEA-1+ rep3


title: endometrial epithelial cells rep 2

source_name: SSEA-1- rep2

source_name: SSEA-1+ rep2


title: endometrial epithelial cells rep 6

source_name: SSEA-1- rep6

source_name: SSEA-1+ rep6


title: Active ulcerative colitis patient-1

description: Library name: UC1_L


title: Active ulcerative colitis patient-2

description: Library name: UC12_L


title: T cell differentiation model, experiment 1 – day 1

description:
Library name: ex1_day1
10x Genomics

tag: age


title: K562_WT_VPR_D9_Dox100_R1


title: K562_1136_iso_IFN_R2


title: T cell differentiation model, experiment 1 – day 0

description:
Library name: ex1_day0
10x Genomics

tag: tissue


title: Kidney organoids pooled library

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description: Library name: McCracken-KidOrganoid-Sept2024-20241021-FLEXv1-hg

data_processing:
Aligned using Cellranger v8.0.1
Assembly: GRCh38
Supplementary files format and content: Raw counts and metadata, tab-delimitted

source_name: kidney organoids derived from human pluripotent stem cells

growth_protocol: Ureteric bud (UB) and nephrogenic mesenchyme (NM) were generated as previously described. Kidney organoids were made by assembling 500,000 NM progenitors with 30-60 UB spheroids into dense aggregates plated on transwell filters.

extract_protocol:
Kidney organoids at different timepoints were dissociated using TrypLE Express for 15-30 minutes at 37deg, with intermittent trituration with a P1000 pipette until they were largely dissociated into a single cell suspension. The cells were washed with PBS + 0.04% bovine serum albumin and filtered through a cell strainer snap cap tube. The single cell suspension was fixed and stored using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics), according to manufacturer’s instructions.
Single cell libraries were generated from the multiplexed cell suspensions using the Chromium Flex Fixed RNA Kit, Human Transcriptome (v1, 16 reactions, 10X Genomics).

treatment_protocol: Organoids were profiled under standard conditions, as well as organoids with NOTCH inhibition (DAPT) from days 4-6 and organoids grown in collecting duct (CD) medium +/- A83, U0126, and XAV939 from days 10-14.

tag: cell line

value: H9 + iPSC72-3 (GFP)

value: kidney organoid

value: WT

value: Control, DAPT (days 4-6), CD Medium (days 10-14), CD Medium + AUX (days 10-14)


title: endometrial epithelial cells rep 4

source_name: SSEA-1- rep4

source_name: SSEA-1+ rep4


title: ZS392

city: Kunming

first: Yanjiao

last: Li

address: Puxin Road 2

institute: Kunming University

data_processing:
Illumina Casava software used for basecalling
(1) Remove adapter polluted reads (remove reads contain adapter more than 5bp. For paired-end sequencing, both reads will be filtered if either end is polluted) (2) Remove low-quality reads (low-quality reads refer to reads in which more than 15% bases with base calling quality Q≤19. For paired-end sequencing, both reads will be filtered if either end is low-quality). (3) Remove reads which contain N higher than 5% (For paired-end sequencing, both reads will be filtered if either end has N beyond the offset 5%).
Hisat2 v2.2.1 was used for building the genome index, and Clean Data was mapped to the reference genome(GRCh38.109) using Hisat2 v2.2.1.
Stringtie v 2.1.7 was used for transcriptome expression estimation. Reads Count for each gene in each sample was counted by python scripts.
Assembly: human NCBI genome build 38 (hg38)
Supplementary files format and content: "counts.csv" containes gene counts;"TPM.csv" contains gene TPM values.

source_name: skin

growth_protocol: Human fibroblast cells and  fibroblast-derived cells till 18 days were routinely maintained in high glucose DMEM (Gibco) with 10% fetal bovine serum(Excell),  bone mesenchymal stem cells  were cultured in MSC medium including low glucose DMEM(Gibco) with 8% fetal bovine serum(Excell).

extract_protocol:
A total amount of 1μg RNA per sample was used as input material for the RNA sample preparations. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Fibroblasts were treated by small molecule cocktail for 18 days,  and on day 18 denoted as induced osteoblast.

value: skin

value: induced osteoblasts


title: ZS740


title: ZS390


title: K562_WT_VPR_D9_NoTx_R2

value: CML-lymphoblast


title: K562_WT_iso_IFN_R2


title: Remission ulcerative colitis patient-1

description: Library name: UC8_L

source_name: left-sided colonic mucosal biopsy specimens


title: K562_WT_VPR_D9_Dox100_R2

value: Doxy 100ng


title: Mouse thymus tissue, replication 1

description:
Library name: thymus1
10x Genomics

source_name: mouse thymus tissue

value: mouse thymus tissue

value: male


title: K562_WT_VPR_D9_NoTx_R1

value: No Treatment


title: ZU30


title: ZU22


title: KO3

city: Indianapolis

first: Xiaocheng

middle: Charlie

last: Dong

state: IN

address: 635 Barnhill Dr, MS 1021D

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description: Library name: KO3

data_processing:
Base calling and quality scoreing were performed by Real-Time Analysis (RTA) v2 in Illumina NovaSeq 6000
The bcl2fastq2 Conversion software were used to convert base call (bcl) files to FASTQ files, and trim adapter sequence at the same time.
The reads were mapped to the mouse genome using STAR (v2.7.11a) RNA-seq aligner with the following parameter: “--outSAMmapqUnique 60”.
Uniquely mapped sequencing reads were assigned to mm10 genes using featureCounts (from subread v2.0.0).
Differential gene expression analysis was performed using the edgeR package (v3.40.2).
Assembly: mm10
Supplementary files format and content: raw count

source_name: liver

extract_protocol:
Total RNAs were isolated and purified from WT and Atg14 HepKO mouse liver tissue samples using an RNeasy Plus Mini Kit (Qiagen).
Libraries were prepared using a stranded mRNA Prep Kit.

value: liver

value: Atg14 hepatocyte-specific knockout (HepKO)


title: ZT839

value: fibroblast


title: K562_WT_iso_NoTx_R2


title: KO2

description: Library name: KO2


title: ZH78


title: K562_WT_iso_IFN_R1

value: IFN


title: K562_WT_iso_NoTx_R1


title: ZT833


title: ZT829


title: ZT840


title: ZT836


title: Mouse thymus tissue, replication 2

description:
Library name: thymus2
10x Genomics


title: WT3

description: Library name: WT3

value: wild-type


title: EV_5_H

city: Leiden

first: Danijela

last: Koppers-Lalic

address: Albinusdreef 2

department: Medical Oncology & Medical Microbiology

country: Netherlands

institute: Leiden University Medical Center

description: Extracellular vesicles

data_processing:
Pre-processing, indentification, alignemnt and quantification of small non-coding RNAs were performed by using sRNAbench (v2.0) from  sRNAtoolBox
Differential expression was perfomed by using sRNAde (v1.5.0) from sRNAtoolBox
Assembly: miRBase (v22), GtRNAdb (v21) and RNAcentral databases were used as reference databases for alignment of miRNAs, tRNAs and all other types of small non-coding RNAs (sncRNAs) respectively

source_name: Blood-Plasma

extract_protocol:
Blood Plasma was isolated following the ThromboSeq protocol (Best et al. 2019). Plasma vesicles were immunocaptured from plasma, based on their membrane surface markers (CD61, CD9, CD63 or CD81), following a protocol (Fortunato et al. 2022) using magnetic beads (MACS beads, Miltenyi Biotec). Total RNA isolation was perfomed by using TRIzol LS reagent user guide with some modifications. Quality check of the isolated RNA was done with Agilent Bioanalyzer.
RNA libraries for RNA-seq were prepared using (Bioo Scientific; cat no. NOVA-5132-05)

value: Blood-Plasma

tag: group

value: Healthy

value: Extracellular vesicles

value: IC with anti-CD9, CD63 or CD81


title: ZU31


title: GRB2_Input1

city: Urumqi

first: hongyu

last: li

state: xinjiang

address: Affiliated Cancer Hospital of Xinjiang Medical University

institute: xinjiang medical university

data_processing:
By matching reads to the genome using HISAT2, the comparison result of the duplicate was thrown out. Following that, we used Piranha and ABLIRC to do peak calls. The "ABLIRC" method was used to find the places where GRCh38 binds.How to perform a peak call: From the start of each chromosome, 5 bp was used as a window and a step. It stops being a peak when the total depth of the eight windows in a row is less than 4% and every gene has been randomly read 500 times.To do a significance analysis on the found peaks, the frequency of the deepest peak of each gene was added up. Any peaks with a maximum depth of at least 10 or a p-value less than 0.05 were thrown out.After that, differences in abundance were analyzed based on where these peaks were found, using the input data as a standard. To find the best combined peak, the IP abundance had to be more than four times the input abundance. This can be changed as a parameter. The peaks helped find the IP target genes, and the HOMER software was used to see how the IP protein bound to the genes.
Assembly: GRCh38
Supplementary files format and content: peak_info.txt

source_name: SK-BR-3 cells

extract_protocol:
Total RNA was extracted using TRIZOL.  1 μg of RNA for each sample was processed with RQ1 DNase to remove DNA. VAHTS mRNA capture beads were used to extract the mRNAs. Double-stranded cDNA was created from fragmented RNAs,After end repair and tailing,they were ligated to VAHTS RNA Multiplex Oligos Set 1 for Illumina. Prior to sequencing, the ligated products underwent amplification, purification, quantification, and storage at -80 °C. Strand-specific sequencing is possible because the second cDNA strand, which is designated with dUTP, is not amplified.
cDNA libraries were prepared with the KAPA RNA Hyper Prep Kit (KK8544, Roche, Shanghai China) according the manufacturer’s procedure. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina NovaSeq Xplus system for 150 nt paired-end sequencing.
fRIP-seq

value: SK-BR-3 cells

tag: fraction

value: Input


title: T cell differentiation model, experiment 1 – day 4

description:
Library name: ex1_day4
10x Genomics

source_name: T cell diferentiation model

value: T cell diferentiation model


title: KO1

description: Library name: KO1


title: GRB2_IP2

value: IP


title: GRB2_IP1


title: EV_4_H

description: Extracellular vesicles


title: WT1

description: Library name: WT1


title: GRB2 overexpressed  in SK-BR-3 cells, rep1

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped. After that, clean reads were aligned to the GRCh38 genome by HISAT2 (Kim, Langmead et al. 2015) allowing 4 mismatches. Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped) (Trapnell, Williams et al. 2010).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using TRIZOL.  1 μg of RNA for each sample was processed with RQ1 DNase to remove DNA. VAHTS mRNA capture beads were used to extract the mRNAs. Double-stranded cDNA was created from fragmented RNAs,After end repair and tailing,they were ligated to VAHTS RNA Multiplex Oligos Set 1 for Illumina. Prior to sequencing, the ligated products underwent amplification, purification, quantification, and storage at -80 °C. Strand-specific sequencing is possible because the second cDNA strand, which is designated with dUTP, is not amplified.
The Illumina Library Preparation Kit previously utilized it for the purpose of generating customized RNA-seq libraries

value: GRB2 overexpressed  in SK-BR-3 cells

value: GRB2 overexpression


title: GRB2 overexpressed  in SK-BR-3 cells, rep3


title: EV_3_H

description: Extracellular vesicles


title: GRB2 overexpressed  in SK-BR-3 cells, rep2


title: M1-mut-IL18-BCR

city: guangzhou

first: Fan

last: Zhen

address: No. 74, Zhongshan Er Road, Guangzhou, Guangdong, P. R. China

institute: Sun Yat-sen University

description: Library name: sample9

data_processing:
The final library pool was sequenced on the Illumina NovaSeq 6000 platform and the sequencing data were processed using the Cell Ranger software (10X Genomics).
cellranger (v5.0.1) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table. Seurat package (version: 3.1.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data. PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: mm10
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes.
Supplementary files format and content: The .csv file contains all VDJ data.

source_name: B16F10 tumor

growth_protocol: B16F10 cells were injected subcutaneously into the right abdomen of C57BL/6J mice and treated with M1 (1.5 × 107 PFU) or M1-mutIL-18 (1.5 × 107 PFU) when the tumour volume was approximately 200 mm3

extract_protocol:
Mice were euthanised on the third day after the last dose and CD45+ immune cells in tumors were isolated by immunomagnetic beads (130-110-618, Miltenyi Biotec). Biological replicates from n = 3 pooled mice were processed for each experimental condition and analyzed by scRNAseq and scTCR-seq.
RNA libraries were generated by 10xGenomics Single Cell 5’ RNA, VDJ Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: PBS, M1 and M1-mutIL-18 was injected through the tail vein for 5 consecutive days

value: B16F10 tumor

value: CD45+ immune cells

value: tissue

value: WT


title: EV_2_H

description: Extracellular vesicles


title: SK-BR-3 cells, rep3

value: control


title: WT2

description: Library name: WT2

value: liver


title: EV_6_C

description: Extracellular vesicles

value: NSCLC


title: SK-BR-3 cells, rep1


title: SK-BR-3 cells, rep2


title: EV_1_H

description: Extracellular vesicles

value: Blood-Plasma


title: 4M_5XFAD_rep7

first: The Gene Lay Institute of

last: Immunology and Inflammation

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

data_processing:
Bulk RNA-seq data were preprocessed on Google Cloud via Terra.Bio. The BCL files were converted to FASTQ format using bcl2fastq (v2.20.0.422).
The fastq files were aligned using STAR version 2.7.5a.
Picard MarkDuplicates was used to identify the duplicate reads.
RNA-SeQC 2 was used for assessing sequencing depth and mapping quality.
Raw counts and TPMs were computed using RSEM.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw count and TPM values for each sample

source_name: 4 months old Alzheimer diseased wild type mice

extract_protocol:
Microglia were sorted directly into ~10uL of TCL buffer (QIAGEN) containing 1% β-mercaptoethanol for RNA extraction.
Pre library construction, samples were thawed briefly at RT and ~10uL of each was transferred to a 96-well plate. The construction of the full-length RNA-seq libraries followed a modified SMART-Seq2 protocol81. After first strand cDNA synthesis and amplification, the cDNA was purified with a 0.7x single sided SPRI. The cDNA quantification of samples was done via a Qubit hsDNA assay (Thermo Fisher) and fragment size distribution was assessed with a BioAnalyzer HS dsDNA assay (Agilent). Each sample was normalized to 0.20ng/uL and then tagmented and indexed using the Nextera XT DNA library prep kit (Illumina). The individually barcoded libraries were then pooled and a final quality control was done on the BioAnalyzer (Agilent). The pool was normalized to 4nM, denatured using 0.2 N NaOh and 0.2 M Tris-HCL and diluted in HCL to prepare for sequencing. 1300uL of the final diluted pooled library was loaded for sequencing on a NextSeq 500/550. Paired end sequencing was performed using an Illumina 75 cycle Nextseq 500 high output V2 kit in accordance with Illumina protocol (Reads 38 cycles x2, Index 8 cycles x2). This process was repeated for repeat batches.

tag: mouse strain

value: Microglia

value: Female

tag: plate

tag: cohort

tag: sample collection_date


title: M1-mut-IL18-scRNA

description: Library name: sample7


title: GRB2_Input2


title: M1-BCR

description: Library name: sample6


title: M1-mut-IL18-TCR

description: Library name: sample8


title: 4M_5XFAD_rep5


title: 4M_5XFAD_rep6


title: EV_5_C

description: Extracellular vesicles

value: Extracellular vesicles

value: IC with anti-CD9, CD63 or CD81


title: 4M_5XFAD_rep4


title: M1-TCR

description: Library name: sample5


title: 4M_control_rep8

source_name: 4 months old wild type mice


title: 4M_control_rep7


title: EV_4_C

description: Extracellular vesicles


title: 4M_control_rep6


title: M1-scRNA

description: Library name: sample4


title: EV_3_C

description: Extracellular vesicles


title: 4M_control_rep5


title: 4M_5XFAD_rep3


title: PBS-BCR

description: Library name: sample3

value: PBS


title: 4M_5XFAD_rep2


title: PBS-TCR

description: Library name: sample2


title: 4M_control_rep4


title: EV_1_C

description: Extracellular vesicles


title: 4M_control_rep3


title: 4M_5XFAD_rep1


title: 7M control_rep4

source_name: 7 months old wild type mice


title: 7M control_rep3


title: IFNAR-/-IAV2_B16

city: Hangzhou

first: Yushi

last: Yao

state: Zhejiang

address: 866 Yu Hang Tang Road

institute: Zhejiang University

description: Library name: KO_IAV2B16

data_processing:
Raw RNA sequencing fastq format data were processed through in-house perl scripts and clean data were obtained by removing reads containing adapter or poly-N and low-quality reads from raw data. Reads were then mapped to mm10 RefSeq genes downloaded from the UCSC Table Browser using Hisat2(v2.0.5). FeatureCounts(v1.5.0-p3) was used to count the reads numbers mapped to each gene. And FPKM (expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) of each gene was calculated based on the length and reads count mapped to the gene.
Assembly: mm10
Supplementary files format and content: csv file inculde raw counts for each sample

source_name: Lung

extract_protocol:
A total of 400,000 purified AMs per replicate were pelleted and lysed in TRIzol reagent (Thermo Fisher, Waltham, MA) and cryopreserved at -80 °C, followed by RNA extraction.
RNA libraries for Rna-seq were prepared uding NEBNext UltraTM RNA Library Prep Kit (New England Biolabs, Ipswich, MA) following manufacturer’s recommendations.

value: Lung

value: Alveolar Macrophages

value: Lung Primary Macrophages

value: IFNAR KO


title: PD_6_H

description: Platelet-derived vesicles

value: Healthy

value: Platelet-derived vesicles

value: IC with anti-CD61


title: 4M_control_rep1

city: Boston


title: 7M_5XFAD_rep2

source_name: 7 months old Alzheimer diseased wild type mice


title: PBS-scRNA

description: Library name: sample1

value: B16F10 tumor

value: CD45+ immune cells

value: tissue

value: WT


title: 7M control_rep2

value: control


title: PD_5_H

description: Platelet-derived vesicles

value: Blood-Plasma


title: WT_IAV2_B16

description: Library name: WT_IAV3B16


title: 7M_5XFAD_rep1

value: Microglia

value: Female


title: 7M control_rep1


title: IFNAR-/-IAV1_B16

description: Library name: KO_IAV1B16


title: WT_IAV1_B16

description: Library name: WT_IAV1B16


title: 3M_Tim3.cKO_nonphago_rep5

source_name: non-phagocytosing microglia from 3 months old Tim3 conditional knock out mice

value: nonphago

value: Male


title: PD_4_H

description: Platelet-derived vesicles


title: EV_2_C

description: Extracellular vesicles

value: NSCLC

value: Extracellular vesicles

value: IC with anti-CD9, CD63 or CD81


title: WT_IAV3_B16

description: Library name: WT_IAV4B16

value: Lung

value: Alveolar Macrophages

value: Lung Primary Macrophages


title: PD_3_H

description: Platelet-derived vesicles

value: Healthy

value: Platelet-derived vesicles

value: IC with anti-CD61


title: WT_PBS3_B16

description: Library name: WT_PBS3B16


title: 3M_Tim3.cKO_nonphago_rep4


title: 3M_control_nonphago_rep8

source_name: non-phagocytosing microglia from 3 months old wild type mice


title: 3M_control_nonphago_rep7


title: 3M_control_nonphago_rep6


title: PD_2_H

description: Platelet-derived vesicles


title: WT_PBS2_B16

description: Library name: WT_PBS2B16


title: 4M_control_rep2


title: 3M_control_nonphago_rep4


title: 3M_control_nonphago_rep5


title: WT_PBS1_B16

description: Library name: WT_PBS1B16


title: PD_6_C

description: Platelet-derived vesicles


title: WT IAV-SP3

description: Library name: WT_IAV3Sp

value: SP


title: 3M_control_nonphago_rep1


title: PD_1_H

description: Platelet-derived vesicles


title: 3M_control_nonphago_rep2


title: PD_5_C

description: Platelet-derived vesicles


title: 3M_Tim3.cKO_nonphago_rep3


title: PD_4_C

description: Platelet-derived vesicles


title: 3M_control_nonphago_rep3


title: 3M_Tim3.cKO_phago_rep4

source_name: phagocytosing microglia from 3 months old Tim3 conditional knock out mice

value: phago


title: PD_7_H

description: Platelet-derived vesicles


title: PD_3_C

description: Platelet-derived vesicles


title: WT IAV-SP2

description: Library name: WT_IAV2Sp

value: WT


title: WT IAV-SP1

description: Library name: WT_IAV1Sp


title: WT-PBS-SP2

description: Library name: WT_PBS4Sp


title: 3M_Tim3.cKO_nonphago_rep2


title: 3M_control_phago_rep4

source_name: phagocytosing microglia from 3 months old wild type mice

value: control


title: 3M_control_phago_rep5

value: Microglia


title: 3M_Tim3.cKO_phago_rep3


title: WT-PBS-SP1

description: Library name: WT_PBS3Sp


title: PD_2_C

description: Platelet-derived vesicles

value: Blood-Plasma


title: 3M_control_phago_rep3


title: 3M_Tim3.cKO_nonphago_rep1

value: nonphago


title: PD_8_H

description: Platelet-derived vesicles


title: 3M_control_phago_rep2

value: Male


title: PD_1_C

description: Platelet-derived vesicles

value: NSCLC


title: IFNAR-/-IAV AMs3

description: Library name: IFNARko_PR8_3

value: IFNAR KO

value: IAV


title: 3M_Tim3.cKO_phago_rep2


title: IFNAR-/-IAV AMs2

description: Library name: IFNARko_PR8_2

value: Lung


title: 3M_control_phago_rep1


title: 3M_Tim3.cKO_phago_rep1


title: Mouse2_AAV

city: Heidelberg

first: Shubhada

last: Kulkarni

address: In Neuenheimer Feld 669

institute: UKHD

description:
Library name: Sample2
Chromium X series (exact version not available)

data_processing:
A custom database was created for detecting viral transcripts. This consisted of mouse genome/transcriptome version GRCm38_102 toegther with the virus YFP sequence . The viral sequence was added as a single-exon gene entry in the annotation GTF file. A custom reference for above database was created using cellranger mkref (version 8.0.1).
Read alignment to the custom database and further gene expression quantifcation was performed using 10x cellranger count function with default parameters. Further post-processing of snRNA-seq data was performed in Seurat version 5.1.0 in R  version 4.4.1. For creating Seurat object, min.cells was set to 100 and min.features was set to 1,000 to remove low quality features and variables. Clustering was performed using resolution parameter set to 0.5. Marker genes used for assining cell-types were obtained from Tabula Muris.
Assembly: GRCm38_102
Supplementary files format and content: 10X feature-barcode matrix

source_name: left venctricle

extract_protocol:
single nuclei and total RNA were isolated by standard Genewiz protocols.
RNA libraries were prepared for sequencing using standard Illumina protocols.
Chemistry version: Single Cell 3' v4

value: left ventricle

tag: strain

value: male


title: Blood, AOSD, Still1137

city: Leeds

first: Sinisa

last: Savic

address: St James's University Hospital

institute: University of Leeds

data_processing:
Data was trimmed and QC using Cutadapt and FastQC
Trimmed Data was aligned to hg38 using STAR
Duplicates were marked with Picard
Reads were quantified using Featurecounts
Count data was analyzed using DESeq2 and Enrichr
Assembly: GRCh38
Supplementary files format and content: Excel workbook file of raw gene counts for each sample

source_name: Blood

extract_protocol:
PAXgene Blood miRNA Kit
Eukaryotic mRNA PolyA enrichment

value: Blood

tag: disease state

value: AOSD


title: IFNAR-/-IAV AMs1

description: Library name: IFNARko_PR8_1

value: Alveolar Macrophages

value: Lung Primary Macrophages


title: Blood, AOSD, Still1203


title: H358 AMG

city: Nanjing, Jiangsu

first: Zehao

last: Pan

state: Please Select

address: Baiziting No.42

institute: Nanjing Medical University Affiliated Cancer Hospital

data_processing:
Raw FASTQ data were trimmed by Trimmomatic (v0.33), and paired end reads were aligned to a concatenated human andDrosophilagenome (hg38).
To creat ATAC-seq coverage plots, the locations of the mapped ATAC-seq reads were extended to 150bp to represent sequenced fragments, renormalized (to reads per million,rpm) and reformatted in the bigWig file format.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value <=0.01
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: cell line

growth_protocol: DMEM, 1640, 15% fetal bovine serum, 2mM glutamine, 1*penicillin/streptomycin. Cells were cultured at 37C at 5% CO2

extract_protocol:
100,000 SW1573 and H358 cells cells were used to isolate nuclei. Nuclei were incubated with tagmentation Master Mix at 37 °C for 30 minutes after lysing the cells in ice-cold ATAC Lysis Buffer and the DNA was purified with the DNA purification column.
PCR amplification of tagmented DNA was performed to make libraries with the appropriate indexed primers.

value: cell line

value: H358 cells

value: Human non-small cell lung cancer

value: KRASG12C mutant

value: Sotorasib


title: H358 AN

value: Sotorasib+Napabucasin


title: SW1573 AN

value: SW1573 cells


title: Blood, AOSD, Still1038


title: SW1573 AMG


title: IFNAR-/-PBS AMs2

description: Library name: IFNARko_Naive_2

value: PBS


title: H358 DMSO

value: DMSO


title: Blood, AOSD, Still814


title: SW1573 DMSO


title: Blood, AOSD, Still808


title: LN-229 cells, temozolomide 144 h, rep 3

city: Mainz

first: Christian

last: Schwarzenbach

address: Obere Zahlbacher Str. 67

department: Institute of Toxicology

institute: University medical center Mainz

description: Highoutput FC, 2x150 cycles

data_processing:
Data processing was carried out by the core facility genomics at the IMB Mainz, using NGSpipe2go
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR (2.7.3a)
Read count extraction and normalization were performed using the subread package
DGE analysis was based on DEseq2, FC filter of 1 and adjusted p-value of 0.01
Assembly: hg38
Supplementary files format and content: *.bw files include the processed data

growth_protocol: LN-229 glioblastoma cell line, obtained from LGC Standards (Wesel am Rhein, Germany) was cultivated in DMEM, 10% fetal bovine serum. Cells were cultured in a humid atmosphere at 37°C; 5% CO2.

extract_protocol:
RNA was iosolated using the NucleoSpin® RNA Kit (Macherey-Nagel, Düren, Germany). Libraries were prepared with a starting amount of 1000 ng and amplified in 10 PCR cycles
NGS library prep was performed with by the core facility genomics of the IMB Mainz, utilizing Illumina's TruSeq stranded mRNA LT Sample Prep Kit following TruSeqStrandedmRNAReferenceGuide (Oct.2017)

treatment_protocol: LN-229 cells were exposed 24 h after seeding with temozolomide [50 µM] or nothing by directly adding TMZ to the medium

value: glioblastoma cell line

tag: time of_exposure

value: temozolomide [50 µM]


title: IFNAR-/-PBS AMs1

description: Library name: IFNARko_Naive_1

value: Lung

value: IFNAR KO


title: LN-229 cells, temozolomide 144 h, rep 1

description: Highoutput FC, 2x150 cycles


title: LN-229 cells, temozolomide 48 h, rep 3

description: Highoutput FC, 2x150 cycles


title: Blood, AOSD, Still702

value: Blood


title: LN-229 cells, temozolomide 48 h, rep 2

description: Highoutput FC, 2x150 cycles


title: IFNAR-/-IAV AMs2

description: Library name: Sample 4

data_processing:
Raw ATAC-seq fastq files from paired-end sequencing were trimmed by using fastp (v0.19.11) followed by quality control using fastqc(v0.11.5).
Clean data were aligned to the GRCm38/mm10 reference genome using BWA(v0.7.12-r1039). Samtools(v1.11) was used to remove unmapped, unpaired and mitochondrial reads. PCR duplicates were removed by using Picard.
Peak calling was performed using MACS2(v2.1.2, -q 0.05 --call-summits --nomodel --shift -100 --extsize 200 --keep-dup all).
The number of reads in each peak was determined using DiffBind(v3.4).
Differentially accessible peaks were identified following DESeq2 normalization using an FDR cut-off <0.05.
Tracks were visualized using Integrative Genomics Viewer (v.2.3.77, Broad Institute).
Assembly: mm10
Supplementary files format and content: narrowPeak

extract_protocol:
50,000 AMs were washed with cold PBS and resuspend in cold lysis buffer(10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Detail protocol could be find in Curr Protoc Mol Biol. ; 109: 21.29.1–21.29.9. doi:10.1002/0471142727.mb2129s109.
Cell lysates were centrifuged at 500g for 10 min at 4℃ and nuclei were resuspended in 50 µL of transposition reaction mix (25 µL of TD buffer + 2.5 µL of Tn5 Transposase + 22.5 µL of nuclease-free water; Illumina, San Diego, CA) and incubated for 30 min at 37 °C. Transposed DNA fragments were purified by using a Qiagen Reaction MiniElute Kit (Qiagen, Hilden, Germany), barcoded with Nextera single indexes (New England Biolabs, Ipswich, MA), and amplified by PCR for 11 cycles using NEBNext High Fidelity 2× PCR Master Mix (New England Biolabs, Ipswich, MA). PCR products were purified using a PCR Purification Kit (Qiagen, Hilden, Germany) and amplified fragment size was verified on an Agilent 2100 Bioanalyzer system (Agilent, Santa Clara, CA). ATAC-seq libraries were quantified by quantitative PCR.

value: IAV


title: Blood, AOSD, Still703

value: AOSD


title: IFNAR-/-IAV AMs3

description: Library name: Sample 5

value: Alveolar Macrophages

value: Lung Primary Macrophages


title: Blood, AOSD, Still1485


title: Blood, AOSD, Still628


title: IFNAR-/-PBS AMs3

description: Library name: IFNARko_Naive_3


title: LN-229 cells, untreated control, rep 3

description: Highoutput FC, 2x150 cycles


title: LN-229 cells, temozolomide 48 h, rep 1

description: Highoutput FC, 2x150 cycles


title: LN-229 cells, untreated control, rep 2

description: Highoutput FC, 2x150 cycles


title: LN-229 cells, untreated control, rep 1

description: Highoutput FC, 2x150 cycles


title: IFNAR-/-PBS AMs2

description: Library name: Sample 2


title: IFNAR-/-IAV AMs1

description: Library name: Sample 3


title: Blood, AOSD, Still556


title: RH4.deg.4, rep 3

city: Cambridge

first: Charles

middle: Arthur

last: Whittaker

institute: Koch Institute

data_processing:
Illumina NextSeq 500 using v3 chemistry. NextSeq Control Software v4.0.2.7, RTA 2.11.3. BCL files were converted to fastq using bcl2qseq. Indexes were split using custom scripts allowing 1 mismatch.
RNA-seq data was used to quantify transcripts from the hg38 human assembly with the gencode version 43 annotation using the nf-core/rnaseq workflow revision 3.12.0 (Alexander Peltzer et al. 2024). The genomic target included the LexogenSIRVData spike-in reference. Gene level summaries were prepared from the star_salmon quantitation using tximport version 1.28.0.
Assembly: hg38 human assembly with gencode43 annotation and Lexogen SIRV spike-in transcrips.
Supplementary files format and content: 230925Koe_MOLT4_intCt.txt.gz is a tab-delimited text file of integer count data.
Supplementary files format and content: 230925Koe_MOLT4_l2tpm.txt.gz is a tab-delimited text file of TPM data transformed to log2 with a plus1 offset.
Supplementary files format and content: 230925Koe_PSN1_intCt.txt.gz is a tab-delimited text file of integer count data.
Supplementary files format and content: 230925Koe_PSN1_l2tpm.txt.gz is a tab-delimited text file of TPM data transformed to log2 with a plus1 offset.
Supplementary files format and content: 230925Koe_RH4_intCt.txt.gz is a tab-delimited text file of integer count data.
Supplementary files format and content: 230925Koe_RH4_l2tpm.txt.gz is a tab-delimited text file of TPM data transformed to log2 with a plus1 offset.

growth_protocol: Cell lines were maintained at 5% CO2 at 37oC. Cells were cultured  in RPMI 1640 (Thermo Fisher Scientific, 11875093) + 10% fatal bovine serum (FBS). Cell lines were tested intermittently throughout studies using MycoAlert Mycoplasma Detection Kit (Lonza, Cat#LT07-418), generally a few days after thawing and immediately before significant studies (e.g. Proteomics, RNA-seq experiments).

extract_protocol:
Follwing treatment, cells were immediately lysed in lysis buffer (from PerkinElmer’s chemagic RNA Tissue 360 H96, VD200615) supplemented with BME flash frozen and stored at -80c. After all biological replicates were collected, samples were thawed in deep 96-well plates. An equal amount (~30pg) of Lexogen’s ERCC spike-in mix (SIRV-3) were added at this point following manufacturer’s recommendations. The PerkinElmer’s Chemagic 360 was used for bead-based RNA extraction following manufacturer’s standard protocol.
RNA was quantified using an Agilent Fragment Analyzer, purified using 2X RNA SPRI beads, and 1ng of total RNA was used for Illumina library preparation. Libraries were prepared using a reduced volume version of SMART-seq2 performed on an SPT Mosquito HV using 10 cycles of amplification for cDNA generation and 16 cycles for library generation using NexteraXT (Illumina).

treatment_protocol: 1000 cells were seeded and treated with treated with KB-0742, KI-CDK9d-32, or DMSO and cultured to the appropriate endpoint (2, 4, or 8 hours after treatment)

value: rhabdomyosarcoma

tag: time

value: 4 hr


title: RH4.deg.4, rep 4

tag: cell type


title: RH4.inh.4, rep 3


title: RH4.veh.4, rep 3


title: LN-229 cells, temozolomide 144 h, rep 2

description: Highoutput FC, 2x150 cycles


title: Blood, AOSD, Still475


title: Blood, AOSD, Still625


title: RH4.deg.8, rep 4

value: 8 hr


title: PDS_ENT_NHS_TCR

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

description:
Library name: SCAF3597t_PDS_ENT_NHS
CD45+ cells, tumor, PDS0101+Entinostat+NHS-IL12, TCR enrichment

data_processing:
The cellular samples were loaded in the lanes according to the 10X Genomics 5’ v2 Single Cell User Guide with a single capture lane per sample targeting recovery of up to 6,000 cells per lane.
Cell partitioning completed successfully with uniform emulsion consistency for all samples, then Reverse transcription PCR was run.
All subsequent steps GEM recovery, cDNA generation, and quality control were performed as described in the 10X Genomics 5’ v2 Single Cell User Guide.
Libraries were prepared using the 10X validated automation platform, Chromium Connect.
Base calling was performed using RTA 3.4.4, demultiplexing was performed using cellranger v7.1.0 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v7.1.0 (STAR 2.7.2a).
Sequenced reads were aligned to the 10x provided mouse reference sequences (refdata-gex-mm10-2020-A for GEX and refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 for TCR).
Assembly: Mouse mm10 genome build, with annotation refdata-gex-mm10-2020-A for GEX and refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 for TCR
Supplementary files format and content: H5 (.h5) files provided for each RNA-seq sample produced by CellRanger.
Supplementary files format and content: CSV (.csv) files provided for each TCR-seq sample summarizing TCR-seq metadata produced by CellRanger.
Library strategy: TCR-Seq

source_name: tumor

growth_protocol: 5x10^4 TC1 tumor cells were implanted s.c. in the right flank of C57Bl/6 mice. The tumors were allowed to grow to approximately 50mm^3 before mice were randomizaed for treatment. Tumors were harvested for CD45+ cell isolation 10 days after treatment start.

extract_protocol:
For each treatment group, representative 100mg sections from three individual tumors were pooled and processed. Single cell suspensions were obtained using the mouse tumor dissociation kit (Miltenyi Biotec) and CD45+ cells were isolated with murine TIL isolation kit (Miltenyi Biotec), both according to the manufacturer’s instructions. Cell counts were determined with AOPI and isolated cells were resuspended in PBS+0.04% BSA at a concentration of 1.8E6 cells/mL. 200µL of each cell solution was provided.
Single-cell RNA sequencing with TCR sequencing was performed using 10X Genomics CellRanger v 7.1.0 according to 10X Genomics 5’ v2 Single Cell User Guide. Cell viability was assessed via LunaFx7 (Logos Biosystems) and was >90% for all samples. Sequenced reads were aligned to the 10x Genomics provided mouse reference sequences (refdata-gex-mm10-2020-A for GEX and refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 for TCR).

treatment_protocol: Mice were treated with PBS, NHS-IL12, PDS0101, Entionstat and all combinations.

value: tumor

value: 13-15 weeks

tag: host strain


title: RH4.deg.8, rep 3


title: Blood, AOSD, Still468


title: RH4.inh.8, rep 3


title: RH4.veh.8, rep 3


title: ENT_NHS_TCR

description:
Library name: SCAF3595t_ENT_NHS
CD45+ cells, tumor Entinostat+NHS-IL12, TCR enrichment


title: Blood, AOSD, Still386


title: RH4.inh.4, rep 4


title: Blood, AOSD, Still350


title: RH4.veh.4, rep 4


title: IFNAR-/-PBS AMs1

description: Library name: Sample 1

tag: genotype


title: ENT_TCR

description:
Library name: SCAF3593t_ENT
CD45+ cells, tumor, Entinostat, TCR enrichment

tag: treatment

value: Entinostat


title: Blood, AOSD, Still298


title: Blood, AOSD, Still283


title: RH4.deg.4, rep 2


title: PDS0101_TCR

description:
Library name: SCAF3592t_PDS0101
CD45+ cells, tumor, PDS0101, TCR enrichment

tag: age


title: NHS-IL12_TCR

description:
Library name: SCAF3591t_NHS-IL12
CD45+ cells, tumor, NHS-IL12, TCR enrichment

tag: tissue


title: PBS_Control_TCR

description:
Library name: SCAF3590t_PBS_Control
CD45+ cells, tumor, PBS control, TCR enrichment

value: PBS Control


title: Blood, AOSD, Still199


title: RH4.inh.4, rep 2

tag: cell line


title: Blood, AOSD, Still206


title: PDS_ENT_NHS_GEX

description:
Library name: SCAF3597_PDS_ENT_NHS
CD45+ cells, tumor, PDS0101+Entinostat+NHS-IL12

data_processing:
The cellular samples were loaded in the lanes according to the 10X Genomics 5’ v2 Single Cell User Guide with a single capture lane per sample targeting recovery of up to 6,000 cells per lane.
Cell partitioning completed successfully with uniform emulsion consistency for all samples, then Reverse transcription PCR was run.
All subsequent steps GEM recovery, cDNA generation, and quality control were performed as described in the 10X Genomics 5’ v2 Single Cell User Guide.
Libraries were prepared using the 10X validated automation platform, Chromium Connect.
Base calling was performed using RTA 3.4.4, demultiplexing was performed using cellranger v7.1.0 (Bcl2fastq 2.20.0), and alignment was performed using cellranger v7.1.0 (STAR 2.7.2a).
Sequenced reads were aligned to the 10x provided mouse reference sequences (refdata-gex-mm10-2020-A for GEX and refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 for TCR).
Assembly: Mouse mm10 genome build, with annotation refdata-gex-mm10-2020-A for GEX and refdata-cellranger-vdj-GRCm38-alts-ensembl-5.0.0 for TCR
Supplementary files format and content: H5 (.h5) files provided for each RNA-seq sample produced by CellRanger.
Supplementary files format and content: CSV (.csv) files provided for each TCR-seq sample summarizing TCR-seq metadata produced by CellRanger.


title: PDS_ENT_TCR

description:
Library name: SCAF3596t_PDS_ENT
CD45+ cells, tumor, PDS0101+Entinostat, TCR enrichment


title: Blood, AOSD, Still193


title: RH4.inh.8, rep 2


title: PDS_NHS_TCR

description:
Library name: SCAF3594t_PDS_NHS
CD45+ cells, tumor, PDS0101+NHS-IL12, TCR enrichment


title: PDS_ENT_GEX

description:
Library name: SCAF3596_PDS_ENT
CD45+ cells, tumor, PDS0101+Entinostat


title: RH4.deg.8, rep 2


title: Blood, AOSD, Still181


title: ENT_NHS_GEX

description:
Library name: SCAF3595_ENT_NHS
CD45+ cells, tumor Entinostat+NHS-IL12


title: TAB2_20220225_8_T-21_N5

city: Setagaya-ku

first: Nobumasa

last: Watanabe

state: Tokyo

address: 2-1-6 Kamikitazawa

institute: Tokyo Metropolitan Institute of Medical Science

hyb_protocol: 600ng of Cy3-labeled cRNA was fragmented using the Agilent Gene Expression Hybridization Kit and hybridized with a SurePrint G3 Human GE v3 8x60K Microarray (Agilent Technologies). Hybridizations were performed for 17 hours at 65ºC at 10 rpm in a rotating hybridization oven.

scan_protocol: The slides were scanned  immediately after washing on SureScan Microarray Scanner (Agilent Technologies) using one color scan setting for 8x60k array slides (Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: Data was obtained using the Agilent Feature Extraction software (v12.1.1.1) with set to default for all parameters.

source_name: temporal arterial biopsy

label_protocol: 200 ng of total RNA was amplified and labeled using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's protocol.

growth_protocol: fresh biopsy

extract_protocol: tissue homogenized with Tissue-Lyzer (Qiagen) in Trizol reagent and RNA extracted by RNeasy kit (Qiagen)

treatment_protocol: stored at 4°C in All-protect Solution (Qiagen)

value: temporal arterial biopsy

tag: gender

value: Male

tag: diagnosis

value: PAN


title: TAB2_20220225_5_T-18_G6

value: Female

value: GCA


title: TAB2_20220225_7_T-20_G8


title: Blood, AOSD, Still178

value: Blood


title: TAB2_20220225_3_S-4_G10


title: TAB2_20220225_2_S-3_G9


title: RH4.inh.8, rep 4


title: RH4.veh.4, rep 2

value: DMSO


title: PDS_NHS_GEX

description:
Library name: SCAF3594_PDS_NHS
CD45+ cells, tumor, PDS0101+NHS-IL12


title: RH4.veh.8, rep 4


title: Blood, AOSD, Still175

value: AOSD


title: ENT_GEX

description:
Library name: SCAF3593_ENT
CD45+ cells, tumor, Entinostat


title: RH4.deg.4, rep 1


title: Blood, AOSD, Still173


title: PDS0101_GEX

description:
Library name: SCAF3592_PDS0101
CD45+ cells, tumor, PDS0101


title: RH4.inh.4, rep 1


title: RH4.veh.8, rep 2


title: RH4.veh.4, rep 1


title: Blood, AOSD, Still158


title: Blood, AOSD, Still171


title: TAB2_20220225_6_T-19_G7


title: TAB2_20220225_1_S-2_N6

value: RA


title: TAB1_20191129_8_S-1_N4

value: PMR


title: TAB1_20191129_6_T-8_G4


title: Blood, Healthy Control, J

value: Healthy Control


title: TAB1_20191129_5_T-7_G3


title: RH4.deg.8, rep 1

value: rhabdomyosarcoma


title: RH4.inh.8, rep 1

value: 8 hr


title: Blood, Healthy Control, I


title: wild type control mice, scRNAseq

city: New Haven

first: Fu

last: Gao

address: 55 Prospect Street

institute: Yale University

description:
Library name: WT
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the cellranger-7.1.0.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: mitral valve

extract_protocol:
Single cells were processed using Chromium Controller (10X Genomics) according to the manufacturer’s protocol.
Library was performed according to the manufacturer’s instructions (scRNA seq 3’ v3 protocol, 10x Genomics).

value: mitral valve


title: TAB2_20220225_4_T-16_G5


title: NHS-IL12_GEX

description:
Library name: SCAF3591_NHS-IL12
CD45+ cells, tumor, NHS-IL12

value: tumor

value: 13-15 weeks


title: MPC cells, PTX resistance rep3

city: Shanghai

first: Wenshuai

last: Liu

state: Shanghai

address: Fenglin road 180

department: General Surgery

institute: Zhongshan Hospital Fudan University

description:
Library name: MPC-PTX3
PTX resistance rep3

data_processing:
The original data in FASTQ format (raw data) was generated from the sequencing platform. The fastp (0.22.0) was used to filter the raw date to get high quality sequence for further study.
Assembly: The reference genome and gene annotation files were downloaded from genome website.
Supplementary files format and content: tab-delimited text file includeds raw counts for each sample

source_name: MPC-PTX

growth_protocol: The MPC and MPC-PTX were maintained in RPMI 1640 medium (Gibco, 61870036) supplemented with 10% FBS (Gibco, A5669701) and 1% antibiotics (Gibco, 15070063). The cells were maintained in a humidified incubator with 5% CO2 at 37℃.

extract_protocol:
The concentration, quality and integrity of total RNA were determined using a NanoDrop spectrophotometer (Thermo Scientific). 3μg of RNA were used as input material for the RNA sequencing.
Firstly, mRNA was purified by using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in an Illumina proprietary fragmentation buffer. First and second strand cDNA was synthesized using random oligonucleotides with Super Script II and DNA Polymerase I with RNase H, respectively. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities and the enzymes were removed. After adenylation of the 3′ ends of the DNA fragments, Illumina PE adapter oligonucleotides were ligated to prepare for hybridization. To select cDNA fragments of the preferred 400-500 bp in length, the library fragments were purified using the AMPure XP system (Beckman Coulter,Beverly, CA, USA). DNA fragments with ligated adaptor molecules on both ends were selectively enriched using Illumina PCR Primer Cocktail in a 15 cycle PCR reaction. Products were purified (AMPure XP system) and quantified using the Agilent high sensitivity DNA assay on a Bioanalyzer 2100 system (Agilent).

treatment_protocol: The MPC-PTX cells received over 30 cycles of PTX treatment

value: MPC-PTX

value: mouse gastric adenocarcinoma

value: PTX treated over 30 cycles

tag: batch


title: TAB1_20191129_4_T-6_G2

value: temporal arterial biopsy

value: Male


title: MPC cells, PTX resistance rep1

description:
Library name: MPC-PTX1
PTX resistance rep1


title: Blood, Healthy Control, G


title: PSN1.deg.2, rep 4

value: pancreatic adenocarcinoma

value: 2 hr


title: PSN1.veh.2, rep 4

value: DMSO


title: TAB1_20191129_7_T-11_N3

value: Fever of unknown origin


title: PBS_Control_GEX

description:
Library name: SCAF3590_PBS_Control
CD45+ cells, tumor, PBS control

value: PBS Control