title: Lung,WT,saline

description:
male, BD mouse sample tag 10
male, BD mouse sample tag 8
male, BD mouse sample tag 9
WTsa_SampleTag10_mm_RSEC_MolsPerCell_MEX.zip
IgGblm_SampleTag08_mm_RSEC_MolsPerCell_MEX.zip
antiIL11blm_SampleTag09_mm_RSEC_MolsPerCell_MEX.zip
processed_seurat_antibody.rds
processed_seurat_antibody_AT_annotated.rds

value: saline


title: Kute4, T35, D70

status: Public on Aug 12 2024

type: SRA

city: London

first: Franziska

last: Denk

address: Guy's Campus

department: Wolfson SPaRC

country: United Kingdom

institute: King's College London

description:
T35_D70_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_timepoints.csv

library_source: transcriptomic

data_processing:
Reads were pseudo-aligned with kallisto version 0.50.1 to the human genome: Homo Sapiens GCRh38, kallisto index version 13. An average of 32M reads were sequenced per sample, of which an average of 28M reads were successfully aligned. See Supplementary Table 1 for alignment statistics for each sample.
Genes were considered to be expressed in our dataset if their Transcripts Per Million (TPM) value was equal to 1 or more in all samples of a given group.
Assembly: Homo Sapiens GCRh38
Supplementary files format and content: Supplementary_Table_1_Alignment_Stats alignment statitics for all samples
Supplementary files format and content: Supplementary_Table_2_TPM xlsx file containing TPM values for all samples, as well as differential expression tables for the different groups
Supplementary files format and content: genecounts_iSN_timepoints.csv  comma-separated value file including raw gene counts for timepoint experiment samples
Supplementary files format and content: genecounts_iSN_IS.csv  comma-separated value file including raw gene counts for inflammatory soup experiment samples

molecule: total RNA

organism: Homo sapiens

source_name: HPSI0714i-kute_4 (Kute4)

growth_protocol: Experiments were conducted with two iPSC lines derived from one healthy male and one healthy female human donor: HPSI0714i-kute_4 (Kute4), female origin, obtained via the Human Induced Pluripotent Stem Cell (HIPSCI) Initiative at King’s College London and UKBi013-A-GCamP6f (UKB), male origin. iPSCs were maintained on 6-well plates coated with vitronectin (StemCell Technologies, catalogue #100-0763) in Stemflex media (ThermoFisher, #A3349401) until 80% confluence. Cells were gently dissociated from wells using Versene (ThermoFisher, #15040066) for 4 mins at 37°C. Prior to differentiation, iPSCs were seeded on 6-well plates coated with Geltrex (ThermoFisher, #A1413302) and allowed to expand in Stemflex media to 60% confluence. At this point (day 1), the medium was changed to mouse embryonic fibroblast conditioned medium (MEF, Bio-Techne, #AR005) supplemented with 10ng/mL human recombinant FGF-2 (Miltenyi, #130-093-839). 24 hours later (day (D)0), differentiation was initiated according to the Chambers protocol [7]. Briefly, from D0-D3, KSR media (Knockout DMEM (ThermoFisher, #10829018), 15% knockout serum replacement (ThermoFisher, #10828010), 1% Glutamax (ThermoFisher, #35050038), 1% non-essential amino acids (ThermoFisher, #11140035), 100uM beta-mercaptoethanol (ThermoFisher, #31350010), 1% antibiotic/antimycotic (ThermoFisher, #15240096) was added and changed daily. From D0-D1, 10µM SB431542 (Bio-techne, #1614-10) and 100nM LDN 193189 (Bio-techne, #6053-10) (SMAD inhibitors) were added to media. From D2-D3, in addition to SMAD inhibitors, 3µM CHIR99021 (Bio-techne, catalogue #4423-10), 10µM SU5402 (Merck, #SML0443), 10µM DAPT (Bio-techne, #2634-10) were also added to media. From D4-D5, media composition was changed to 75% KSR media + 25% N2 media (Neurobasal medium (ThermoFisher, #21103049), 2% B27 supplement (ThermoFisher, #17504044), 1% N2 supplement (ThermoFisher, #17502048), 1% Glutamax, 1% antibiotic/antimycotic) with all 5 inhibitors included. From D6-7, media composition was changed to 50% KSR + 50% N2, and only 3µM CHIR99021, 10µM SU5402 and 10µM DAPT included. From D8-9, media composition was changed to 25% KSR + 75% N2, and only 3µM CHIR99021, 10µM SU5402 and 10µM DAPT included. On D10, media composition was changed to 100% N2, and only 3µM CHIR99021, 10µM SU5402 and 10µM DAPT included. On D11, immature neurons were dissociated from wells using TrypLE (ThermoFisher, #12604013) for 7 mins at 37°C. Neurons were replated to Geltrex-coated 13mm glass coverslips at a density of 75,000 cells/well. Neurons were matured and maintained in N2 media containing 25ng/mL human b-NGF (Peprotech, #450-01), 25ng/mL human NT3 (Peprotech, #450-03), 25ng/mL human GDNF (Peprotech, #450-10), 25ng/mL human BDNF (Peprotech, #450-02). From D11-D14, media also contained 10mM ROCKi (Enzo, #ALX-270-333-M005) and 3µM CHIR99021. Media was changed twice a week. To remove proliferating, non-neuronal cells, 1-2µM Cytosine beta-D-arabinofuranoside (AraC, SLS, #C1768-100MG) was added every other media change until non-neuronal cells were removed.    For sequencing, neurons were matured to different timepoints (30-70 days).

extract_protocol:
For each group, two coverslips from a 24-well plate of neurons were combined into 350 µL RLT buffer from the RNeasy Micro Plus kit (Qiagen, #74134), supplemented with 1% beta-mercaptoethanol (PanReac AppliChem, #A1108.0100). The samples were stored at -80 °C degrees, until batch-controlled RNA extraction, library preparation and sequencing. RNA was purified using the RNeasy Micro Plus kit (Qiagen, #74134) following manufacturer’s instructions. We quantified the RNA amount using a Qubit high sensitivity RNA assay (Invitrogen, #Q32851) and checked its quality using a Tapestation 4150 system (Agilent). All samples had a RIN value of more than 9.9.
Samples were processed at once within the same library preparation and multiplexed into the same Illumina sequencing lane (150bp, paired-end reads) by the service provider Novogene Sequencing. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: Two batch-controlled sequencing experiments were conducted, comparing iSNs at three different timepoints (day 29-30, day 50-53, day 69-70) and comparing day 60 neurons treated with modified-Inflammatory soup (control media with 100 ng/ml NGF (Peprotech, #450-01-100), 100 ng/ml TNF (Peprotech, #300-01A-100), 1 μM histamine (Sigma-Aldrich, #H7250), 1 μM bradykinin (Sigma-Aldrich, #B3259), 1 μM serotonin (Sigma-Aldrich, #H9523), 1 μM prostaglandin E2 (Bio-techne, #2296)) versus control media (N2 media without growth factors) for 24 hours.

tag: cell line

value: HPSI0714i-kute_4 (Kute4)

tag: cell type

value: iPSC

tag: differentation batch

tag: treatment

value: Day 70


title: SPD rep1

city: Zhongshan

first: Yilie

last: Liao

state: China

address: Tsuihang New District

country: China

institute: Zhongshan Institute for Drug Discovery

description:
SP1_2
Liver from mice fed with 25% protein chow diet for 3 weeks

data_processing:
Paired-end RNA-seq sequencing library was sequenced with the Illumina HiSeq xten/NovaSeq 6000 sequencer (2 × 150bp read length).
Raw paired end reads were trimmed and quality controlled by SeqPrep and Sickle.
Clean reads were separately aligned to reference genome with orientation mode using TopHat software.
Differential gene expression was determined by DESeq2.
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample
Supplementary files format and content: Excel file includes differential expression analysis results by DESeq2

organism: Mus musculus

source_name: Liver

growth_protocol: B6.Cg-Lepob/J (ob/ob) mice, 8-week-old, 12/12h light on/off, ad libum fed

extract_protocol:
Livers were dissected and snap-frozen in liquid nitrogen. Total RNA were extracted with TRIzol reagent, and genomic DNA was removed using DNase I (TaKara).
RNA library was prepared for sequencing using TruSeqTM RNA sample preparation kit from Illumina (San Diego, CA).

treatment_protocol: Mice were subjected to chow diet containing either standard (25% kcal) or low (5% kcal) dietary protein content for 3 weeks (n=6 for each group).

tag: strain

value: B6.Cg-Lepob/J (ob/ob)

tag: age

tag: tissue

value: Liver

tag: genotype

value: Lep-/-


title: Lung,KO, WT ,saline

city: Singapore

first: Benjamin

last: Ng

address: 8 College Road

country: Singapore

institute: Duke-National University of Singapore Medical School

description:
female, BD mouse sample tag 6
female, BD mouse sample tag 1
male, BD mouse sample tag 5
KOsaCre1_SampleTag06_mm_RSEC_MolsPerCell_MEX.zip
WTsaCre1_SampleTag05_mm_RSEC_MolsPerCell_MEX.zip
processed_seurat_annotated.rds
processed_seurat_AT_annotated.rds

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option. FASTQ files were demultiplexed using the unique sample-tags, trimmed, mapped and annotated using the BD Rhapsody™ Sequence Analysis Pipeline (Revision 2.0) on the Seven Bridges Genomics platform (accessed on June 2023).
Low-quality read pairs were removed based on read length, average base quality score, and highest single-base frequency. Filtered reads were aligned to the Mus musculus genome (GRCm39 assembly) using STAR v2.7.4a embedded in the pipeline and annotated using the mouse GENCODE release M31 GTF.
Reads with identical cell labels, identical unique molecular identifier (UMI) sequences, and identical genes were collapsed into a single raw molecule, followed by removing artefacts using recursive substitution error correction (RSEC) developed by BD Biosciences.
Assembly: mm39
Supplementary files format and content: matrix files and Seurat files

source_name: Lung

extract_protocol:
Lungs were perfused with cold sterile saline through the right ventricle. The lungs were then intratracheally inflated with 1.5 ml of Dispase 50 U/ml (Corning) followed by installation of 0.5 ml of 1% low melting agarose (BioRad) via the trachea. The lungs were excised and incubated on an orbital shaker for 45 min at room temperature. Each lobe was then minced into small pieces in DMEM (GIBCO) supplemented with 10% FBS (GIBCO) and 0.33 U/ml DNase I (Roche) and placed on the orbital shaker for an additional 10 minutes. The cells were then filtered through a 100 µm cell strainer and centrifuged at 400 g for 5 min at 4°C. The cell pellet was resuspended in ACK-buffer (GIBCO), incubated for 2 min on ice and then filtered through a 40 µm cell strainer. The cells were centrifuged at 400 g for 5 min at 4°C and resuspended in DPBS (GIBCO) supplemented with 5% FBS, and then stained with the following antibodies: EpCAM-BV785 (BioLegend #118245), CD45-APC (BioLegend, 103112), CD31-APC/Cy7 (BioLegend, 102534), I-A/I-E - AlexaFluor488 (MHC-II) (BioLegend, 107616) and 4’, 6-diamidino-2-phenylindole (DAPI) (Life Technologies, 62248) was used to eliminate dead cells. The cells were then sorted on the BD FACS Aria III system (BD Bioscience).
Single cell capturing was performed using the BD Rhapsody™ Express Single-Cell Analysis System (BD Biosciences). Libraries were generated using BD Rhapsody Whole Transcriptome Analysis (WTA) Amplification kit according to the manufacturer’s protocols.

treatment_protocol: Mice at 10-14 weeks of age were anesthetized by isoflurane inhalation and subsequently administered a single dose of bleomycin (Sigma-Aldrich) oropharyngeally at 0.75 U/kg body weight (for IL11EGFP reporter mice) or 1.5 U/kg body weight (for all other mouse strains) in a volume of saline not exceeding 50 µl per mouse. Uninjured control mice received equal volumes of saline oropharyngeally. Mice were sacrificed at indicated time points post-bleomycin administration and lungs were collected for downstream analysis. Therapeutic doses of monoclonal anti-IL11 (X203, Aldevron) or IgG control antibodies were injected intraperitoneally at 20 mg/kg starting from day 4 and subsequently on day 7 and day 10 post-bleomycin administration.

value: Lung

value: Il11ra1_KO, WT (multiplexed)


title: Kute4, T35, D30

description:
T35_D29_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_timepoints.csv

value: Day 30


title: HPEpiC, Untreated, Biol rep2, Tube2

data_processing:
Libraries were demultiplexed using bcl2fastq v2.19.0.316 with the --no-lane-splitting option.
Adapter sequences were then trimmed using trimmomatic v0.36 in paired end mode with the options MAXINFO:35:0.5 MINLEN:35
Trimmed reads were aligned to the Homo sapiens GRCh38 using STAR v.2.2.1 with the options --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 in paired end, single pass mode.
Only unique alignments were retained for counting. Counts were calculated at the gene level using the FeatureCounts module from subread v.1.5.1, with the options -O -s 2 -J -T 8 -p -R -G.
The combined transcript model annotation file was constructed using Ensembl hg38 and FANTOM5 hg38 as previously described (PMID: 35841888) and used as annotation to prepare STAR indexes and for FeatureCounts.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Count values for each sample

source_name: HPEpiC

growth_protocol: Human pulmonary alveolar epithelial cells (HPEpiC) were seeded at a density of 1.5e4 cells per well in 96-well CellCarrier plates (PerkinElmer) or 3e5 cells per well in 6 well tissue culture plates (Corning) and cultured in AEpiCM (ScienCell Research Laboratories).

extract_protocol:
Total RNA was isolated using RNeasy columns (Qiagen). 1.0 ug of total RNA with RQS > 9 was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded mRNA Library Prep kit (Illumina) following manufacturer's protocols.

treatment_protocol: The cells were cultured for 24 hours prior to being treated with: Human IL11 (UniProtKB:P20809, GenScript), human TGFβ1 (PHP143B, Bio-Rad)

value: HPEpiC

value: pulmonary alveolar epithelial cells

value: Untreated


title: UKB, T9, D30

description:
T9_D30_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_timepoints.csv

source_name: UKBi013-A-GCamP6f (UKB)

value: UKBi013-A-GCamP6f (UKB)


title: UKB, T9, D70

description:
T9_D69_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_timepoints.csv


title: HPEpiC, IL11-treated, Biol rep1, Tube1


title: Eos_with Cond2_B Cell FRC

first: Lalit

last: Dubey

address: Charterhouse Square

institute: QMUL

data_processing:
Sequencing data which is referred as raw reads or raw data, were subjected to quality control (QC) to determine whether the sequencing data is suitable for subsequent analysis. After quality control, the filtered clean reads were aligned to the reference sequence.
Sequencing data filtering was performed using a filtering software SOAPnuke developed by BGI independently for filtering. As per BGI guiedlines the folowing steps were performed which involved removal of the reads containing the adaptor(adaptor pollution), Removal of reads whose N content is greater than 5%; Removal of low-quality reads (we define reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20% as low-quality reads). The filtered "Clean Reads" were then saved in FASTQ format.
After getting clean reads, we used Hierarchical Indexing for Spliced Alignment of Transcripts (HISAT)  software for mapping RNA-seq reads
Sequence alignment software was used to align the clean reads after quality control to the reference genome, so that the gene or transcript expression in the sample can be quantified. At the same time, the overall analysis of the transcriptome sequencing was performed, including the randomness of the transcript.
The clean reads were alinged to the reference genes by using Bowtie2 to get the alignment result.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: Tab-delimited text files includes TPM count for each sample
Supplementary files format and content: Tab-delimited text files includes FPKM count for each sample

source_name: Bone Marrow Derived

growth_protocol: bone marrow cells were obtained from femurs and tibiae of WT C57BL/6 mice by flushing with complete RPMI 1640 media containing 10% heat inactivated foetal bovine serum (FBS) (Sigma-Aldrich, non-USA origin). Red blood cells were lysed using ACK lysis buffer, and 1 × 106 cells/mL were plated in RPMI-1640 medium containing 10% FBS, penicillin-streptomycin and further supplemented with stem cell factor (100 ng/ml), and FLT3Ligand (100 ng/ml) (both from Miltenyi Biotec) from culture days 0 to 4. Cultures were changed on day 4 to new complete RPMI 1640 medium containing recombinant murine IL-5 (10 ng/ml, Peprotech) and further fed with IL-5 every other day between days 10 to 14. Cells were collected on day 14 (typically containing more than 92% eosinophils), counted, and used for the co-culture experiment.

extract_protocol:
Total RNA from eosinophils isolated from the co-culture was extracted using the Rneasy UCP Micro Kit (Qiagen) according to the manufacturer’s instructions
Stranded mRNA Library construction procedure were used as per BGI guidelines which involved using Oligo dT Selection (mRNA enrichment) followed by RNA fragment and reverse transcription, end repair, add A and adaptor ligation, PCR amplification, Single strand separation and cyclization, DNA nanoball synthesis followed by sequencing on DNBSEQ (DNBSEQ Technology) platform

treatment_protocol: Experiments were performed in triplicate wells and eosinophils were pooled post stimulation/co-culture to create a single sample for RNAseq

value: Bone Marrow Derived

value: No

value: Eosinophils

value: WT

value: Co-culture


title: Lung,KO,blm

description:
female, BD mouse sample tag 7
female, BD mouse sample tag 4
KOblmCre1_SampleTag07_mm_RSEC_MolsPerCell_MEX.zip
KOblmCre2_SampleTag04_mm_RSEC_MolsPerCell_MEX.zip
processed_seurat_annotated.rds
processed_seurat_AT_annotated.rds

value: bleomycin


title: Eos_with Cond1_LTbR FRC


title: UKB, T8, D30

description:
T8_D30_2
Supplementary_Table_1_Alignment_Stats
Supplementary_Table_2_TPM
genecounts_iSN_timepoints.csv

value: iPSC


title: HPEpiC, Untreated, Biol rep1, Tube1


title: CD45+ leukocytes from ascites/peritoneal lavage (pooled from n=4 independent mice)

city: New York

first: Juan

last: Cubillos-Ruiz

state: NY

address: 1300 York Ave.

country: USA

institute: Weill Cornell Medicine

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline v5.0.0
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built mouse reference genome (mm10-2020-A) and to extract gene expression UMI counts matrix.
Genome_build: mm10
Supplementary_files_format_and_content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: peritoneal lavage

growth_protocol: ID8-Defb29/Vegf-A cells were cultured in vitro and injected 1.5M i.p. into C57BL/6 mice. Tissue sample was collected at day 25 after tumor implantation.

extract_protocol:
Target cell inputs of 10,000 cells were loaded into a Chromium Controller using Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics) according to manufacturer’s instructions. After generation of GEMs, cDNA synthesis and subsequent library preparation of all samples was completed using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 (10x Genomics) according to manufacturer’s instructions.
The 10X Libraries (Single Cell 3’ v3) were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (28 bp for read 1 and 90 bp for read 2).

tag: cancer model

tag: strain background


title: CUT&TAG_RelA_60min

status: Public on Aug 11 2024

city: Los Angeles

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

library_source: genomic

data_processing:
Demultiplexed reads were mapped to the NCBI37/mm9 genome using Hisat2.
Binding sites were identified using MACS2 peak calling (fdr < 0.01).
Binding sites were annotated to the closest gene (mm9).
Assembly: mm9
Supplementary files format and content: bedGraph files for each sample represent the strength of binding at each genomic location.

molecule: genomic DNA

source_name: iMPDMs

growth_protocol:
Bone marrow was extracted from the hip, femur, tibia, and fibula of wild-type (C57/B16) mice. Cells were differentiated for 6 days in cell culture using 8%  M-CSF conditioned media, before stimulation.
Immortalized myeloid progenitor-derived macrophages (iMPDMs) were prepared as previously described (Sheu et al., Cell Systems 2023).

extract_protocol:
Crosslinking conditions of 0-4mM DSG and 0-2.0% formaldehyde were used. Chromatin shearing was done using the Covaris M220. Immunoprecipitation was performed with either anti-RelA or anti-cRel antibodies.
Libraries were constructed using the Kapa LTP Library Preparation Kit according to manufacturer instructions.

treatment_protocol: Lipid A stimulation for 15 - 60mins.

value: iMPDMs

value: Wild-type (C57/B16)

value: 60mins Lipid A


title: PFA_Input

source_name: BMDM

value: BMDM

value: 1.0h Lipid A


title: CUT&TAG_RelA_15min

value: 15mins Lipid A


title: CUT&TAG_RelA_45min

value: 45mins Lipid A


title: RelA_2.0_PFA


title: RelA_1.0_PFA


title: cRel_0.5_PFA


title: RelA_0.5_PFA


title: cRel_0.0_PFA


title: cRel_2.0_PFA


title: DSG_Input


title: cRel_4mM_DSG


title: RelA_2mM_DSG


title: RelA_4mM_DSG


title: cRel_0mM_DSG


title: liver, 165d, mnr, male, MUN_LIV_81 [mnr_rna_seq_446]

city: Winston-Salem

first: Jeannie

last: Chan

state: NC

address: Medical Center Boulevard

department: Internal Medicine

institute: Wake Forest School of Medicine

data_processing:
Raw sequences were de-multiplexed using the Illumina Casava v1.8 software.
Prealignment QC was performed using Partek Flow. Sequence reads with Phred scores ≥ Q30 were retained.
Sequence reads were aligned against the olive baboon reference genome (Panu_3.0) using STAR 2.5.3a.
Aligned reads were quantified using an expectation-maximization algorithm in Partek Flow and annotated using the NCBI release 93 gene model.
Assembly: Panu_3.0, GCF_000264685.3
Supplementary files format and content: Matrix table of transcript counts before normalization for all genes in 56 samples.

organism: Papio anubis

source_name: liver

extract_protocol:
Liver tissue was snap-frozen in liquid nitrogen immediately after collection and stored at -80ºC until use. Total RNA was isolated using TRIzol reagent.
mRNA was purified from total RNA prior to cDNA synthesis. cDNA libraries were prepared using the mRNA-Seq Sample Preparation Kit (Illumina) according to the manufacturer's protocol.

treatment_protocol: Control dams were fed ad libitum throughout the study, while 30% feed reduction (based on feed consumed by controls at the same gestation stage and adujsted for body weight) started at 30 dG for MNR dams.

value: liver

tag: gender

value: male

tag: gestation days

value: mnr

tag: tissue id


title: liver, 165d, mnr, female, MUN_LIV_79 [mnr_rna_seq_444]

value: female


title: liver, 165d, mnr, male, MUN_LIV_82 [mnr_rna_seq_447]


title: cRel_1mM_DSG


title: liver, 165d, mnr, male, MUN_LIV_80 [mnr_rna_seq_445]


title: liver, 165d, mnr, male, MUN_LIV_83 [mnr_rna_seq_448]


title: liver, 165d, mnr, female, MUN_LIV_77 [mnr_rna_seq_442]


title: liver, 165d, mnr, female, MUN_LIV_76 [mnr_rna_seq_441]


title: HPEpiC, TGFβ1-treated, Biol rep1, Tube1

value: HPEpiC

value: pulmonary alveolar epithelial cells


title: liver, 165d, control, male, MUN_LIV_74 [mnr_rna_seq_439]

value: control


title: liver, 165d, control, male, MUN_LIV_75 [mnr_rna_seq_440]


title: Bulk ATAC, Control macrophages, sample 5

city: Brussels

first: Daliya

last: Kancheva

address: Laarbeeklaan 103, Building E

country: Belgium

institute: Vrije Universiteit Brussel - VIB

description:
ATAC: read1 contains cell barcode and UMI; read2 contains ATAC sequences
MF_control_5_bulk_ATAC

data_processing:
Raw data scRNAseq and Multiome  files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Bulk ATAC-seq data was aligned to the mouse genome using Bowtie2
Assembly: mm10
Supplementary files format and content: Compressed .tar.gz files containing raw UMI counts in Cellranger output format, details for the ADT antibodies, ATAC Bigwig (.bw) files, and comma-delimited text files including metadata per cell

extract_protocol: All methods listed in Musrati et al. Infection history imprints prolonged changes to the Kupffer Cell epigenome, transcriptome and function.

value: Liver

value: Flt3-Cre Rosa26-Yfp

value: treated with melarsoprol (2 weeks post treatment)

tag: library type

value: ATAC


title: liver, 165d, control, male, MUN_LIV_73 [mnr_rna_seq_438]


title: liver, 165d, control, female, MUN_LIV_71 [mnr_rna_seq_436]


title: liver, 165d, control, male, MUN_LIV_72 [mnr_rna_seq_437]


title: liver, 165d, control, female, MUN_LIV_70 [mnr_rna_seq_435]


title: liver, 165d, control, female, MUN_LIV_69 [mnr_rna_seq_434]


title: liver, 140d, mnr, female, MUN_LIV_64 [mnr_rna_seq_333]


title: liver, 140d, mnr, male, MUN_LIV_66 [mnr_rna_seq_335]


title: liver, 140d, mnr, female, MUN_LIV_62 [mnr_rna_seq_331]


title: liver, 140d, mnr, male, MUN_LIV_65 [mnr_rna_seq_334]


title: liver, 140d, control, male, MUN_LIV_60 [mnr_rna_seq_329]


title: liver, 140d, control, male, MUN_LIV_59 [mnr_rna_seq_328]


title: liver, 140d, control, female, MUN_LIV_58 [mnr_rna_seq_327]


title: liver, 140d, mnr, female, MUN_LIV_63 [mnr_rna_seq_332]


title: liver, 140d, control, female, MUN_LIV_57 [mnr_rna_seq_326]


title: liver, 165d, mnr, female, MUN_LIV_78 [mnr_rna_seq_443]


title: liver, 120d, mnr, female, MUN_LIV_52 [mnr_rna_seq_261]


title: liver, 120d, mnr, male, MUN_LIV_54 [mnr_rna_seq_263]


title: liver, 120d, mnr, female, MUN_LIV_51 [mnr_rna_seq_260]


title: liver, 120d, mnr, male, MUN_LIV_55 [mnr_rna_seq_264]


title: liver, 140d, control, female, MUN_LIV_56 [mnr_rna_seq_325]


title: liver, 120d, mnr, male, MUN_LIV_53 [mnr_rna_seq_262]


title: liver, 140d, mnr, male, MUN_LIV_67 [mnr_rna_seq_336]


title: liver, 120d, control, male, MUN_LIV_48 [mnr_rna_seq_257]


title: liver, 120d, control, male, MUN_LIV_47 [mnr_rna_seq_256]


title: liver, 120d, control, female, MUN_LIV_46 [mnr_rna_seq_255]


title: liver, 165d, control, female, MUN_LIV_68 [mnr_rna_seq_433]


title: liver, 120d, mnr, female, MUN_LIV_50 [mnr_rna_seq_259]


title: liver, 90d, mnr, male, MUN_LIV_42 [mnr_rna_seq_183]


title: liver, 120d, control, male, MUN_LIV_49 [mnr_rna_seq_258]


title: liver, 120d, control, female, MUN_LIV_45 [mnr_rna_seq_254]


title: liver, 90d, mnr, male, MUN_LIV_40 [mnr_rna_seq_181]


title: liver, 90d, mnr, female, MUN_LIV_39 [mnr_rna_seq_180]


title: liver, 90d, mnr, male, MUN_LIV_41 [mnr_rna_seq_182]


title: liver, 90d, mnr, female, MUN_LIV_38 [mnr_rna_seq_179]


title: liver, 120d, control, female, MUN_LIV_44 [mnr_rna_seq_253]


title: liver, 90d, mnr, female, MUN_LIV_36 [mnr_rna_seq_177]


title: liver, 90d, control, male, MUN_LIV_35 [mnr_rna_seq_176]


title: liver, 90d, control, male, MUN_LIV_34 [mnr_rna_seq_175]


title: liver, 90d, control, male, MUN_LIV_33 [mnr_rna_seq_174]


title: liver, 90d, control, male, MUN_LIV_32 [mnr_rna_seq_173]


title: liver, 90d, control, female, MUN_LIV_30 [mnr_rna_seq_171]


title: liver, 90d, control, female, MUN_LIV_28 [mnr_rna_seq_169]


title: RelA_0.0_PFA

value: Wild-type (C57/B16)


title: liver, 90d, control, female, MUN_LIV_29 [mnr_rna_seq_170]


title: cRel_1.0_PFA


title: liver, 140d, control, male, MUN_LIV_61 [mnr_rna_seq_330]


title: cRel_2mM_DSG


title: liver, 90d, mnr, male, MUN_LIV_43 [mnr_rna_seq_184]


title: RelA_1mM_DSG


title: RelA_0mM_DSG


title: T18, snucRNAseq

city: Boston

first: Srinivas

middle: Raghavan

last: Viswanathan

state: Massachusetts

address: 450 Brookline Avenue

institute: Dana-Farber Cancer Institute

description: 10x genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) Assembly: hg38
Assembly: hg38
Supplementary files format and content: All files are standard Cellranger output files https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/overview

molecule: nuclear RNA

source_name: Kidney

extract_protocol:
Nuclei isolation was performed as previously described (Slyper et al., 2020). Low-retention microcentrifuge tubes (Fisher Scientific, Hampton, NH, USA) were used throughout the procedure to minimize nuclei loss. Briefly, OCT-embedded tissue fragments were quickly thawed on wet ice to remove excess OCT, tissue was next mechanically dissociated by pipetting and homogenized in TST solution, filtered through a 30 um MACS SmartStrainer (Miltenyi Biotec, Germany), and pelleted by centrifugation for four minutes at 500g at 4C. The final nuclei pellet was resuspended in 150 ul of 10x Genomics Diluted Nuclei Buffer, and trypan blue-stained nuclei were counted by eye using INCYTO C-Chip Neubauer Improved Disposable Hemacytometers (VWR International Ltd., Radnor, PA, USA).
Chromium Next GEM Single Cell 3ʹ library according to manufactures instructions

value: Kidney


title: Mybpc3 Biallelic Differentiation Batch 1

city: Ann Arbor

first: Joshua

last: Meisner

state: MI

address: 1540 E. Hospital Drive

department: Pediatrics

institute: University of Michigan

data_processing:
Bcl2fastq2 Conversion Software (Illumina) was used to generate de-multiplexed Fastq files from Illumina NovaSeq 6000 reads
The reads were trimmed using Cutadapt v2.3(Martin, 2011).
The reads were evaluated with FastQC(Andrews, 2010)(v0.11.8) to determine quality of the data
Reads were mapped to the reference genome GRCh38 (ENSEMBL), using STAR v2.7.8a(Dobinet al., 2013)and assigned count estimates to genes with RSEM v1.3.3(Li and Dewey, 2011).
QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7(Ewelset al., 2016).
Assembly: GRCh38 (ENSEMBL)
Supplementary files format and content: tab delimited text file includes TPM counts per gene for each sample

molecule: polyA RNA

source_name: iPSC derived cardiomyocytes

growth_protocol: iPSCs were cultured in mTeSR Plus. Cardiomyocytes were differentiated using optimized WNT modulation. iPSC were differentiated in RPMI plus B27 supplement without insulin during day 0–2 (CHIR 4–6 µM and 0-1 mM activin A during first 24 h) followed by CDM3 media (without B27) with IWP4 5 µM during days 3–4. Retinol inhibitor (BMS 453, 1 µM) was included for days 3–6 to minimize atrial lineage differentiation. IPSC-CMs were maintained in CDM3 until spontaneous contractions. After spontaneous contractions were visible, cardiomyocytes were purified in CDM3-lactate using glucose-deprived, lactate-containing media on days 12–16 with RPMI without glutamine and cryopreserved. Purified, cryopreserved iPSC-CMs were thawed and replated as monolayers (400,000 cells/cm2) for 8 additional days (approximately day 24 post differentiation) on stiff PDMS membranes with growth factor reduced Matrigel. iPSC-CMs were maintained in CDM3-lactate media (4 days) and then oxidative phosphorylation promoting RPMI media (Ox-Phos) plus B27 supplement (4 days). Ox-Phos media, adapted from Correia et al. 2017, is based on glucose-free RPMI with B27 supplement and galactose, lactate, glutamax, and pyruvate at final media concentrations of 4, 4, 2, and 0.5 mM, respectively.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen)
Library prep and next-generation sequencing was carried out in the Advanced Genomics Core at the University of Michigan.

value: iPSC derived cardiomyocytes

value: cardiomyocyte

value: Mybpc3 biallelic


title: Mybpc3 Biallelic Differentiation Batch 3


title: liver, 90d, mnr, female, MUN_LIV_37 [mnr_rna_seq_178]


title: Patient_8_Week4_TIL_GEX

city: Pittsburgh

first: Anthony

middle: Richard

last: Cillo

state: PA

address: The Assembly, Room 4070C Bay 10, 5051 Centre Ave

department: Immunology

institute: University of Pittsburgh

data_processing:
Sequencing runs were demultiplexed using bcl2fastq (v2.20.0)
FASTQ files were aligned to GRCh38 using Cellranger count (v6.0.1).
For TCR reconstruction, FASTQ files from TCR specific libraries were used as input into CellRanger vdj.
For CITEseq, TotalSeq specific libaries were aligned using CITEseqCount (v1.4.3).
Feature barcodes matrices were read into Seurat (v4.0.5) to create an aggregrated object for downstream analysis. CD8+ T cell were identified and subset from this overall object for downstream analysis.
Assembly: GRCh38
Supplementary files format and content: *_GEX files are tar archives containing a directory with barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (i.e. the output from CellRanger count).
Supplementary files format and content: *_TCR files are tar archives containing a directory with filtered_contig_annotations.csv (i.e. the output from CellRanger vdj).
Supplementary files format and content: *_CITEseq files are tar archives containing a directory with umi counts for each TotalSeq barcode in the format of barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz (i.e. the output from CITEseqCount).

source_name: Tumor

extract_protocol:
Whole blood was collected by venipuncture into EDTA tubes. Peripheral blood mononuclear cells were isolated by Ficoll-Hypaque density gradient centrifugation. Tumor biopsies were collected into RPMI supplemented with 10% fetal bovine serum. Tumor tissue was mechanically disrupted and passed over a 100 micron filter. Live CD45+ cells were sorted from both blood and tumor specimens. Samples were collected at baseline, following four weeks of therapy, and at 12-16 weeks or upon evidence of disease progression.
Libraries were created using 10X Genomics 5' GEX and VDJ kits as per the manufacturer's instructions.

treatment_protocol: Patients with advanced melanoma received intravenous infusions of monotherapy with relatlimab (anti-LAG3; 160 mg), montherapy with nivolumab (anti-PD1; 480 mg) or the combination of relatlimab+nivolumab (480 mg + 160 mg, respectively) for a lead-in period of 4 weeks.

value: Tumor

tag: timepoint

value: Week 4

value: Live CD45+ immune cells

value: Gene expression

tag: disease stage

value: IV

tag: biological sex

value: relatlimab + nivolumab


title: Patient_8_Week4_TIL_TCR

value: TCR sequencing

value: female


title: Patient_32_TIL_Baseline_GEX

extract_protocol:
Whole blood was collected by venipuncture into EDTA tubes. Peripheral blood mononuclear cells were isolated by Ficoll-Hypaque density gradient centrifugation. Tumor biopsies were collected into RPMI supplemented with 10% fetal bovine serum. Tumor tissue was mechanically disrupted and passed over a 100 micron filter. Live CD45+ cells were sorted from both blood and tumor specimens. Samples were collected at baseline, following four weeks of therapy, and at 12 or 16 weeks or upon evidence of disease progression.
Libraries were created using 10X Genomics 5' GEX and VDJ kits as per the manufacturer's instructions.

value: Baseline

value: male

value: Nivo


title: Patient_8_Week4_PBMC_TCR

source_name: Blood

value: Blood


title: Mybpc3 Biallelic Differentiation Batch 2

tag: cell line


title: Patient_8_Week4_PBMC_GEX

tag: cell type


title: Patient_8_Week16_TIL_GEX

value: Week 16

value: relalimab+nivolumab


title: Patient_8_Week16_PBMC_GEX


title: Patient_8_Baseline_TIL_TCR


title: Patient_8_Baseline_TIL_GEX


title: liver, 90d, control, female, MUN_LIV_31 [mnr_rna_seq_172]

value: liver

value: control


title: Patient_8_Baseline_PBMC_GEX


title: Patient_7_Week4_TIL_TCR

value: nivolumab


title: Patient_7_Week4_PBMC_GEX


title: Patient_7_Baseline_TIL_TCR

value: Tumor


title: Patient_7_Week4_TIL_GEX

value: Week 4


title: Patient_8_Baseline_PBMC_TCR

value: Live CD45+ immune cells


title: Patient_7_Baseline_TIL_GEX

value: Gene expression


title: Patient_7_Baseline_PBMC_GEX

value: IV


title: Patient_6_Week4_TIL_GEX

value: relatlimab + nivolumab


title: Patient_6_Week4_TIL_TCR

value: TCR sequencing


title: Patient_6_Week4_PBMC_GEX


title: Patient_6_Week16_PBMC_TCR


title: Patient_6_Week16_PBMC_GEX


title: Patient_6_Baseline_TIL_TCR


title: UNC11-56

first: Joanne

last: Sordillo

state: MA

address: 181 Longwood Avenue

department: Channing Division of Network Medicine

institute: Mass General Brigham

data_processing:
Channing Snakemake RNASeq Pipeline
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Skewer
Trimmed sequence reads were aligned to GRCh38 using STAR
Read count extraction and normalization were performed using Rsubreads and normalized with DESeq
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with log normalized counts of mRNA

source_name: Bronchial epithelial cells

extract_protocol:
Extracted RNA was prepared using the Illumina TruSeq Stranded Total RNA Prep Kit
378 ng high quality total RNA (RIN > 7, OD260/280 > 1.75, OD260/230 > 1.75) was used in the Illumina TruSeq Stranded Total RNA Sample Prep Kit (Cat # RS-122-2201). ERCC Spike-in controls (Ambion, P/N 4456739) are added during the RNA normalization as a qualitative control. First rRNA is removed from the total RNA and the remaining RNA is purified, fragmented and primed. Next, the cleaved RNA fragments are reverse transcribed into first strand cDNA using reverse transcriptase and random primers. The RNA template is then removed and a replacement strand is synthesized generating double stranded cDNA. After purification, the result is blunt-ended cDNA. A single ‘A’ nucleotide is added to the 3’ ends of the cDNA to prevent them from ligating to one another during the adapter ligation reaction. In this next reaction, a single T nucleotide on the 3’ end of each adaptor allows for ligation of the adaptor to the cDNA. This is later used to hybridize the libraries to the flow cell and for de-multiplexing after sequencing is complete. A final PCR is then conducted to amplify and enrich those DNA fragments that have the adapter molecules on both ends. This process can be carried out manually, in the case of low sample number, or automated on the SciClone.  Libraries are QC’d by quantitation with picogreen, size analysis on an Agilent Bioanalyzer or Tapestation 2200 and qPCR quantitation against a standard curve.
The assay used carried out in one batch on a Sciclone liquid handling system using the Illumina TruSeq Stranded Total RNA prep (Cat RS-122-2201) with ERCC spikein controls.  Three pools of 20 libraries were created and each was launched onto a HiSeq 2500 rapid 75PE flow cell.

value: Bronchial epithelial cells


title: Patient_6_Baseline_PBMC_TCR

value: Baseline


title: UNC11-57


title: UNC11-59


title: Patient_6_Baseline_PBMC_GEX

value: male


title: UNC11-55


title: Patient_5_Week4_TIL_TCR

value: relatlimab


title: Patient_6_Baseline_TIL_GEX


title: Patient_5_Week4_PBMC_TCR

value: Blood


title: Patient_5_Week4_PBMC_GEX


title: UNC11-53


title: Patient_5_Baseline_TIL_TCR


title: Patient_7_Baseline_PBMC_TCR


title: UNC11-51


title: Patient_5_Baseline_TIL_GEX


title: Patient_5_Baseline_PBMC_GEX


title: Patient_5_Baseline_PBMC_TCR


title: Patient_4_Week4_TIL_TCR

value: female


title: UNCD4-49


title: Patient_6_Week4_PBMC_TCR


title: UNC11-58


title: UNCD4-48


title: Patient_4_Week4_TIL_GEX


title: UNC11-60


title: Patient_4_Week4_PBMC_TCR


title: UNCD4-47


title: UNCD4-46


title: Patient_4_Baseline_TIL_TCR


title: Patient_5_Week4_TIL_GEX


title: UNCD4-45


title: UNC11-54


title: Patient_4_Week4_PBMC_GEX


title: Patient_4_Baseline_TIL_GEX


title: UNCD4-44


title: UNCD4-43


title: Patient_3_Week4_TIL_TCR


title: UNCD4-41


title: UNCD4-50


title: Patient_3_Week4_PBMC_TCR


title: UNCD4-42


title: Patient_3_Week4_TIL_GEX


title: UNC20-40


title: UNC11-52


title: UNC20-38


title: UNC20-39


title: Patient_3_Patient_4_Baseline_PBMC_TCR

value: Patient


title: Patient_3_Baseline_TIL_TCR


title: Patient_3_4_Baseline_PBMC_GEX

value: unknown


title: Patient_3_Baseline_TIL_GEX


title: U19_RNA_seq_94_S94

data_processing:
Raw sequencing data were de-multiplexed using Illumina bcl2fastq.
Prealignment QC was performed, and sequence reads with Phred scores < Q30 were discarded.
Sequence reads were aligned against the olive baboon reference genome (Panu_3.0) using STAR 2.5.3.a.
Aligned reads were quantified using an expectation-maximization algorithm in Partek Flow and annotated using NCBI annotation (release 93).
Transcript counts were normalized by the Trimmed mean of M-values method prior to performing WGCNA.
Assembly: Panu_3.0, GCF_000264685.3
Supplementary files format and content: Matrix table of transcript counts before normalization for 34 samples.
Supplementary files format and content: Matrix table of transcript counts after normalization for 34 samples.

source_name: female, brain, animal ID=NLC_BPC_0006

extract_protocol:
Total RNA was extracted from frozen brain tissues using the Direct-zol RNA MiniPrep Plus kits.
Stranded RNA-Seq libraries were constructed from total RNA using the KAPA RNA HyperPrep Kit with RiboErase according to the manufacturer's protocol.

treatment_protocol: Baboons were fed normal monkey chow diet ad libitum and had free access to water. They were provided with veterinary care throughout their lives.

tag: Sex

value: brain

tag: animal id


title: Patient_3_Week4_PBMC_GEX

tag: treatment

value: nivolumab


title: Patient_3_4_Baseline_CITEseq

value: CITEseq


title: UNC20-37


title: Patient_2_Week4_TIL_TCR

value: Tumor

value: Week 4


title: UNC20-34


title: U19_RNA_seq_83_S83

source_name: female, brain, animal ID=NLC_BPC_0017

tag: age


title: Patient_2_Week4_PBMC_TCR

tag: tissue

value: Live CD45+ immune cells


title: Patient_2_Week4_PBMC_GEX

value: Gene expression

value: IV


title: UNC20-35


title: Patient_2_Week4_TIL_GEX

value: relatlimab + nivolumab


title: Patient_2_Baseline_PBMC_TIL_TCR

value: TCR sequencing


title: UNC20-36

value: Bronchial epithelial cells


title: U19_RNA_seq_82_S82

source_name: female, brain, animal ID=NLC_BPC_0043


title: Patient_2_Baseline_PBMC_TIL_GEX

value: Baseline

value: male


title: Patient_2_Baseline_CITEseq


title: UNC20-31


title: U19_RNA_seq_80_S80

source_name: female, brain, animal ID=NLC_BPC_0018


title: Patient_24_Week4_TIL_PBMC_GEX

value: IIID

value: relatlimab


title: U19_RNA_seq_71_S71

source_name: female, brain, animal ID=NLC_BPC_0019

value: female


title: UNCD3-30


title: Patient_24_Baseline_PBMC_TIL_TCR


title: Patient_24_Week4_PBMC_TIL_CITEseq


title: UNCD3-29


title: UNCD3-28


title: U19_RNA_seq_93_S93

source_name: female, brain, animal ID=NLC_BPC_0038


title: Patient_24_Baseline_PBMC_TIL_GEX


title: Patient_23_Week4_PBMC_TCR

value: Blood


title: Patient_23_Week4_PBMC_GEX


title: UNCD3-27


title: Patient_21_Week4_TIL_GEX

value: IIIB


title: Patient_22_Baseline_TIL_GEX

value: IIIC


title: U19_RNA_seq_68_S68

source_name: female, brain, animal ID=NLC_BPC_0011

value: brain


title: UNC20-33


title: U19_RNA_seq_69_S69

source_name: female, brain, animal ID=NLC_BPC_0016


title: Patient_21_Baseline_TIL_TCR

value: Tumor


title: UNCD3-26


title: UNC20-32


title: U19_RNA_seq_61R_S6

source_name: female, brain, animal ID=NLC_BPC_0041


title: Patient_24_Week4_PBMC_TIL_TCR

value: Week 4


title: Patient_21_Baseline_TIL_GEX

value: Live CD45+ immune cells


title: U19_RNA_seq_81_S81

source_name: female, brain, animal ID=NLC_BPC_0051


title: Patient_22_Baseline_TIL_TCR


title: Patient_21_Baseline_PBMC_GEX

value: Gene expression


title: UNCD3-25


title: U19_RNA_seq_70_S70

source_name: female, brain, animal ID=NLC_BPC_0042


title: Patient_21_Baseline_PBMC_TCR


title: U19_RNA_seq_60_S60

source_name: female, brain, animal ID=NLC_BPC_0065


title: Patient_24_Baseline_PBMC_TIL_CITEseq

value: CITEseq


title: UNCD3-23


title: U19_RNA_seq_58_S58

source_name: female, brain, animal ID=NLC_BPC_0031


title: UNCD3-22


title: U19_RNA_seq_56_S56

source_name: female, brain, animal ID=NLC_BPC_0009


title: U19_RNA_seq_59_S59

source_name: female, brain, animal ID=NLC_BPC_0013


title: Patient_20_Week16_TIL_GEX

source_name: Tumor

value: Week 16

value: IV

value: relalimab+nivolumab


title: UNCD3-24

source_name: Bronchial epithelial cells

value: Bronchial epithelial cells


title: UNCD2-20


title: Patient_19_Baseline_TIL_GEX

value: Baseline


title: Patient_20_Baseline_PBMC_TIL_CITEseq

value: male


title: UNCD2-19


title: Patient_19_Baseline_PBMC_GEX

source_name: Blood


title: U19_RNA_seq_46_S46

source_name: female, brain, animal ID=NLC_BPC_0023


title: Patient_1_Baseline_TIL_TCR

value: TCR sequencing


title: UNCD3-21


title: UNCD2-18


title: Patient_1_Baseline_PBMC_TCR


title: Patient_1_Baseline_PBMC_GEX


title: U19_RNA_seq_48_S48

source_name: female, brain, animal ID=NLC_BPC_0062

value: female


title: Patient_19_Baseline_PBMC_TCR

value: Blood


title: Patient_18_Week4_PBMC_TIL_TCR

value: nivolumab


title: Patient_1_Baseline_TIL_GEX


title: Patient_19_Baseline_TIL_TCR


title: U19_RNA_seq_44_S44

source_name: female, brain, animal ID=NLC_BPC_0024


title: U19_RNA_seq_57_S57

source_name: female, brain, animal ID=NLC_BPC_0028


title: Patient_18_Week4_PBMC_TIL_CITEseq


title: U19_RNA_seq_45_S45

source_name: female, brain, animal ID=NLC_BPC_0027


title: Patient_18_Baseline_PBMC_GEX


title: UNCD2-17


title: Patient_18_Week4_TIL_PBMC_GEX


title: UNCD2-16


title: Patient_20_Baseline_PBMC_TIL_GEX


title: UNCD2-14


title: Patient_17_Week4_TIL_TCR

value: relatlimab + nivolumab


title: Patient_17_Week4_PBMC_TCR


title: Patient_17_Week4_TIL_GEX


title: UNCD2-15


title: Patient_17_Week16_PBMC_GEX


title: U19_RNA_seq_26R_S13

source_name: female, brain, animal ID=NLC_BPC_0032

value: brain


title: U19_RNA_seq_32_S32

source_name: female, brain, animal ID=NLC_BPC_0025


title: Patient_17_Baseline_TIL_TCR

value: Tumor


title: RAW 264.7 cells C/D group;rep3

city: Shenyang

first: Ziyi

last: Feng

address: Puhe road

institute: China medical university

description: treat：GelMA/PEDOT:PSS+PLLA/PDA (dynamic)

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequencellow-guality sequence using CLC genomic benchwork (parameter- Quaity 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 faction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text fles include RPKM values for each Sample

source_name: Monocytes; macrophages

growth_protocol: The RAW264.7 cell line was static cultured in a constant temperature cell culture incubator at 37 °C utilizing RAW 264.7 cell-specific medium (TCM-C766，Hycyte, China).

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug oftotal RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit folowing manufacturer's protocols.

treatment_protocol: The in vivo dynamic environment was simulated using ultrasonic stimulation treatment. Low-frequency ultrasound (48 khz, 5 min) has been introduced into the culture system to explore the interaction of the cells and the CMH system in a dynamic environment. GelMA (static) group was named as Gel/S as control group and the GelMA/PEDOT:PSS+PLLA/PDA (dynamic) group as C/D.

value: Monocytes; macrophages

value: macrophages

value: GelMA/PEDOT:PSS+PLLA/PDA (dynamic)


title: RAW 264.7 cells C/D group;rep1


title: UNCD2-12


title: RAW 264.7 cells C/D group;rep2


title: RAW 264.7 cells，Gel/S group，rep3

description: control：GelMA (static)

value: GelMA (static)


title: U19_RNA_seq_24_S24

source_name: female, brain, animal ID=NLC_BPC_0030


title: UNCD2-11


title: RAW 264.7 cells，Gel/S group，rep1

description: control：GelMA (static)


title: UNC18-10


title: RAW 264.7 cells，Gel/S group，rep2

description: control：GelMA (static)


title: Patient_17_Baseline_TIL_GEX

value: Live CD45+ immune cells

value: Gene expression


title: U19_RNA_seq_36_S36

source_name: female, brain, animal ID=NLC_BPC_0064


title: U19_RNA_seq_23_S23

source_name: female, brain, animal ID=NLC_BPC_0021


title: U19_RNA_seq_22_S22

source_name: female, brain, animal ID=NLC_BPC_0010


title: U19_RNA_seq_34_S34

source_name: female, brain, animal ID=NLC_BPC_0020


title: Patient_17_Baseline_PBMC_TCR

value: IV


title: Patient_17_Baseline_PBMC_GEX


title: UNC18-9

value: Bronchial epithelial cells


title: UNCD2-13


title: UNC18-8


title: Patient_17_Week4_PBMC_GEX

value: Week 4


title: Mouse, L881+LA, LA-2

first: Jian Ming

last: Jiang

address: 10 Medical Drive, MD6

department: Cardiovascular Research Institute

institute: National University of SIngapore

data_processing:
Adapter read sequence and Poly-N sequence were trimmed, low quality reads were removed from raw fastq format using in-house perl script
Index reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count read numbers mapped to each gene, and FPKM (Fragments Per Kilobase of Transcript Sequence per Millions base pairs) of each gene was calculated based on length of gene and read counts mapped to gene.
StringTie v1.3.3b were used for Novel Transcripts prediction
Differential gene expression analysis was performed using DESeq2 R package (1.20.0)
Assembly: mm10
Supplementary files format and content: Tab-delimited files including Raw counts of each samples
Supplementary files format and content: Tab-delimited files including FPKM of each samples

source_name: Heart

extract_protocol:
Apex was isolated and immersed in RNA Later. RNA was extracted using Trizol and ~1ug of Total RNA was sent for RNA Library Preparation.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dUTP for directional library. Library was constructed using NEBNext Ultra II Directional RNA Library Prep Kit (Cat No. E7760).

value: Heart

tag: genotype

value: WT

value: Lmna shRNA+Lamin A (Batch LA)


title: Mouse, L881+LA, LA-3


title: U19_RNA_seq_14R_S12

source_name: female, brain, animal ID=NLC_BPC_0012

value: female


title: U19_RNA_seq_20_S20

source_name: female, brain, animal ID=NLC_BPC_0026


title: U19_RNA_seq_13R_S2

source_name: female, brain, animal ID=NLC_BPC_0015


title: Patient_16_Week4_PBMC_GEX

source_name: Blood

value: Blood

value: IIIB


title: Mouse, L881, LA-2

value: Lmna shRNA (Batch LA)


title: Patient_16_Week16_PBMC_GEX

value: Week 16

value: relalimab+nivolumab


title: UNC18-7

source_name: Bronchial epithelial cells


title: Mouse, L881+LA, LA-1


title: Patient_16_Baseline_TIL_TCR

source_name: Tumor

value: Tumor

value: Baseline

value: TCR sequencing


title: U19_RNA_seq_11_S11

source_name: female, brain, animal ID=NLC_BPC_0014

value: brain


title: Mouse, L881, LA-3


title: UNC18-6


title: Patient_15_Baseline_PBMC_TIL_TCR

value: Live CD45+ immune cells

value: unknown


title: Mouse, Control, LA-2

value: Control (Batch LA)


title: UNC18-5

value: Bronchial epithelial cells


title: Mouse, Control, LA-1

value: Heart


title: U19_RNA_seq_10_S10

source_name: female, brain, animal ID=NLC_BPC_0045


title: Patient_16_Baseline_TIL_GEX

value: Gene expression


title: Patient_16_Baseline_PBMC_TCR


title: Mouse, L881, LA-1

value: WT


title: UNC18-3


title: U19_RNA_seq_01R_S1

source_name: female, brain, animal ID=NLC_BPC_0029

value: female


title: U19_RNA_seq_02R_S11

source_name: female, brain, animal ID=NLC_BPC_0022


title: Patient_16_Baseline_PBMC_GEX

value: Blood


title: Mouse, Control, LA-3


title: UNC18-4


title: UNC18-2


title: Patient_14_Week4_PBMC_TIL_GEX

value: Week 4

value: IV

value: relatlimab


title: Patient_15_Baseline_PBMC_TIL_GEX


title: fls2, H2O treatment, TP 480m, Biorep3

city: Wien

first: Yan

last: Ma

address: Dr.-Bohr-Gasse 3

country: Austria

institute: Gregor Mendel Institute

data_processing:
The resulting library was used for cluster generation with the Illumina TruSeq SR Cluster Kit v4 reagents and sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents. The Illumina Pipeline Software version 2.20 was used to process sequencing data.
purity-filtered read trimming for adapters and low-quality sequences was done with Cutadapt (v. 1.8) and removal of reads matching ribosomal RNA sequences with fastq_screen (v. 0.11.1). Low complexity reads were filtered with reaper (v. 15-065).
Cleaned reads were aligned against A.thaliana TAIR10 genome using STAR (v. 2.5.3a) and read counts per gene locus were obtained with htseqcount (v. 0.9.1) using A. thaliana TAIR10 Ensembl 39 gene annotation. RSeQC (v. 2.3.7) was used to evaluate the quality of the data alignment.
Statistical analysis was performed for genes in R (3.5.3). Genes with low counts were filtered out according to the rule of one count per million (cpm) in at least one sample. Library sizes were scaled using TMM normalization and log-transformed into counts per million or CPM (EdgeR package version 3.24.3). Data was corrected for the experimental batch effect using removeBatchEffect function (limma). Statistical quality controls were performed through pairwise sample correlations, clustering and sample PCA using batch corrected normalized data.
Differential expression was computed with limma-trend approach by fitting all samples into one linear model. The experimental batch factor was added to the model. Two-sided moderated t-test was used for each pairwise comparison (peptide-treated vs H2O-treated) per time point. The adjusted p-value is computed by the Benjamini-Hochberg method, controlling for false discovery rate. To determine genes significantly regulated by flg22 , the adjusted p-value was below 0.05 (P<0.05).
Assembly: A.thaliana TAIR10 genome
Supplementary files format and content: tab-delimited text files of processed raw counts for each Sample, 1st column is ATG codes, 2nd column is counts

organism: Arabidopsis thaliana

source_name: 5-day-old Seedling roots

growth_protocol: fls2 and pCASP1::FLS2-GFP fls2 seeds were grown vertically on a sterile mesh on solid  ½ MS plates for 5 days before treatment.

extract_protocol:
Total RNA was extracted with a TRIzol-adapted ReliaPrep RNA extraction kit (Promega).
Libraries were prepared by Lausanne Genome Technology Facility following the same protocol of Fujita et al 2020. RNA quality control was performed on a Fragment Analyzer (Advanced Analytical Technologies). 1000 ng of total RNA was used to prepare RNA-seq libraries with the Illumina TruSeq Stranded mRNA reagents (Illumina) on a Sciclone liquid handling robot (PerkinElmer) using a PerkinElmer-developed automated script.

treatment_protocol: The meshes containing seedlings were transferred onto fresh ½ MS solid medium containing 1 μM peptides and mock plates (mock H2O and peptide treatments always transferred in parallel). After 30-, 120- and 480-mins incubation on plates, whole roots from 2 square plates (50 ml) were cut and collected for each sample, then immediately frozen in liquid nitrogen. Three biological replicates for each sample were conducted on three different days.

value: 5-day-old Seedling roots

tag: time


title: Patient_15_Baseline_PBMC_TIL_CITEseq

value: Tumor

value: CITEseq


title: UNC18-1


title: fls2, flg22 treatment, TP 480m, Biorep3


title: MOLM-13 shDDX6 H3K4me1 rep2

city: Badalona

first: Laureano

last: Tomás-Daza

state: Barcelona

address: Ctra de Can Ruti, Camí de les Escoles s/n

country: Spain

institute: Josep Carreras Leukaemia Research Institute

description:
MOLM13_shDDX6_H3K4me1_merge_corrected_IgG_peaks.broadPeak
1206

data_processing:
*library strategy: CUT&RUN
Raw reads were processed using ENCODE standards with slight modifications
Reads were trimmed using Trim Galore! (0.6.6).
Aligment done using botwie2 (2.3.2) with --very-sensitive and --dovetail.
Filtering done following ENCODE recomendations.
Peak calling done using macs2 (2.2.7.1) with default parameters.
Assembly: GRCh38.p13
Supplementary files format and content: Narrow or Broad peak outputs of macs2 witht significant peaks called using the IgG as control. Bigwig files with the coverage of the different replicates in 10bp bins.
Library strategy: CUT&RUN

growth_protocol: MOLM-13 cells were maintained in RPMI 1640 supplemented with 20% fetal bovine serum (FBS), L-glutamine, and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Fesh cells were bound to activated concanavalin A-conjugated paramagnetic beads and incubated overnight with the desired antibody. The next day they were incubated with pAG-MNase to cleave the chromatin. Proteins were removed and chromatin was precipitated with phenol-chloroform.
Library construction was performed using the Kapa HyperPrep kit and Illumina’s TruSeq adapter system. The amplified library was size-selected to remove leftovers of primers.

treatment_protocol: DDX6 knockdown was induced by transduction of cells with shRNA-expressing lentivirus.

value: AML

value: DDX6 knockdown

value: shRNA

tag: antibody

value: H3K4me1 (Diagenode #C15410194)


title: MOLM-13 shDDX6 H3K27ac rep2

description:
MOLM13_shDDX6_H3K27ac_merge_corrected_IgG_peaks.narrowPeak
1205

value: H3K27ac (Diagenode #C15410196)


title: Patient_14_Week4_PBMC_TIL_CITEseq

value: Live CD45+ immune cells


title: MOLM-13 shDDX6 IgG rep2

value: IgG (Diagenode #C15410206)


title: Mouse, L881+LC, LC-3

value: Heart

value: Lmna shRNA+Lamin C (Batch LC)


title: Patient_14_Week4_PBMC_TIL_TCR

value: TCR sequencing

value: female


title: MOLM-13 shDDX6 IgG rep1


title: CASP, flg22 treatment, TP 480m, Biorep3

value: pCASP1::FLS2-GFP fls2


title: Mouse, L881+LC, LC-2

value: WT


title: MOLM-13 shCTRL H3K4me1 rep2

description:
MOLM13_shCTRL_H3K4me1_merge_corrected_IgG_peaks.broadPeak
1200


title: CASP, flg22 treatment, TP 120m, Biorep3


title: Mouse, L881, LC-1

value: Lmna shRNA (Batch LC)


title: MOLM-13 shCTRL H3K27ac rep2

description:
MOLM13_shCTRL_H3K27ac_merge_corrected_IgG_peaks.narrowPeak
1199


title: Mouse, L881+LC, LC-1


title: fls2, flg22 treatment, TP 120m, Biorep3

value: 5-day-old Seedling roots


title: Patient_14_Baseline_PBMC_TIL_TCR

value: Tumor

value: Baseline

value: IV


title: MOLM-13 shDDX6 H3K4me1 rep1

description:
MOLM13_shDDX6_H3K4me1_merge_corrected_IgG_peaks.broadPeak
1203

value: AML

value: DDX6 knockdown


title: CASP, H2O treatment, TP 480m, Biorep3


title: Mouse, L881, LC-2


title: Patient_14_Baseline_PBMC_TIL_GEX

value: Gene expression


title: MOLM-13 shDDX6 H3K27ac rep1

description:
MOLM13_shDDX6_H3K27ac_merge_corrected_IgG_peaks.narrowPeak
1202

value: shRNA

value: H3K27ac (Diagenode #C15410196)


title: MOLM-13 shCTRL IgG rep2

value: IgG (Diagenode #C15410206)


title: Mouse, L881, LC-3

value: Heart


title: Patient_14_Week16_PBMC_TIL_GEX

value: Week 16

value: Live CD45+ immune cells

value: relalimab+nivolumab


title: Patient_14_Baseline_PBMC_TIL_CITEseq

value: CITEseq

value: female


title: Mouse, Control, LC-1

value: WT

value: Control (Batch LC)


title: MOLM-13 shCTRL H3K27ac rep1

description:
MOLM13_shCTRL_H3K27ac_merge_corrected_IgG_peaks.narrowPeak
1196


title: CASP, flg22 treatment, TP 30m, Biorep3

value: 5-day-old Seedling roots

value: pCASP1::FLS2-GFP fls2


title: Patient_14_Week16_PBMC_TIL_CITEseq

value: Tumor

value: IV


title: Mouse, Control, LC-2


title: CASP, H2O treatment, TP 120m, Biorep3


title: fls2, H2O treatment, TP 120m, Biorep3


title: Patient_13_Week4_PBMC_TIL_TCR

value: Week 4

value: TCR sequencing

value: relatlimab


title: Org-D35-WT-1_rep2

city: Memphis

first: Wenjie

last: Qi

state: TN

address: 262 Danny Thomas Place

institute: St.Jude Children's Research Hospital

description: Day 35 WT 1 rep2

data_processing:
CUT&RUN libraries were sequenced on NovaSeq6000 sequencer and generated 50 bp paired-end reads
The reads were aligned to mouse mm10 genome reference and fruit fly dm6 genome reference by BWA (version 0.7.170.7.12, default parameter). Duplicated reads were marked by the bamsormadup from the biobambam tool (version 2.0.87) available at https://www.sanger.ac.uk/tool/biobambam/. Uniquely mapped reads were kept by samtools (parameter “-q 1 -F 1804,” version 1.14). Fragments < 2000 bp were kept for peak calling and bigwig files were generated for visualization.
SICER (PMID: 24743992) and macs2 (PMID: 18798982)   were bothwas used for peak calling, to identify both the narrow and broad peak correctly. With SICER, we assigned peaks that were at the top 1 percentile as the high-confidence peaks and the top 5 percentile as the low-confidence peaks. Two sets of peaks were generated: Strong peaks called with parameter ‘FDR < 0.05’ by at least one method (macs2 or SICER) and weak peaks called with parameter ‘FDR < 0.5’ by at least one method (macs2 or SICER). Peaks were considered reproducible if they were supported by a strong peak from all replicates or at least one strong peak and a weak peak in the other replicates.
Assembly: mm10
Supplementary files format and content: tsv, bed

source_name: organoid

growth_protocol: embryos at an indicated embryonic day were dissected out from the uterus and visceral yolk sac. A part of the tail or limbs was collected for genotyping. Brains were dissected from embryos under the dissection microscope in cold 1x PBS. Then, 300 μL Dulbecco’s Modified Eagle’s Medium (DMEM) (ATCC 30-2002) and 150 μL of 10 mg/mL collagenase Type II (Worthington LS004176) were added to each brain and incubated for 5-10 min at 37 °C. After centrifugation at 1000 xg for 3 min, the tissue was incubated with 500 μL 0.25% Trypsin-EDTA (ThermoFisher 25200056) for 5 min at 37 °C. Trypsinization was quenched with 500 μL DMEM supplemented with 10% fetal bovine serum (FBS) and pelleted by centrifugation at 1000 xg for 3 min. Alternatively, cells were dissociated from the brain using the papain dissociation system (Worthington LK003153). Cells were then resuspended in 500 μL of NPC culture media (NeuroCult™ Proliferation Media; STEMCELL Technologies 05702) supplemented with 30 ng/mL human recombinant epidermal growth factor (rhEGF) (STEMCELL Technologies 78006) and filtered through a 40 μm filter (Fisherbrand™ 22-363-547) to obtain single cells. To collect NPCs, the dissociated brain cells were cultured in ultra-low attachment 6-well plates (Corning® Costar® CLS3471) in the NPC culture media at 37 °C. NPCs formed neurospheres in suspension. For passaging, neurospheres were incubated with Accutase™ (STEMCELL Technologies 07920) for 5 min at 37 °C and then dissociated by pipetting. After adding an equal volume of the NPC culture media, dissociated cells were centrifuged at 500 xg for 5 min. Cells were then grown in the NPC culture media either in suspension in the ultra-low attachment 6-well plates or on matrigel (Corning™ 354230) coated plates. The medium was changed every 2 to 3 days. For collecting uncultured NPCs, brain cells were sorted by fluorescence-activated cell sorting (FACS) using Sox2-eGFP or NeuroFluor™ CDr3 (STEMCELL Technologies 01800)

extract_protocol:
. DNA was released from the beads by incubating them for 30 min at 37 °C and collected by centrifugation at 16,000 x g for 5 min at 4 °C. DNA was then isolated by using a phenol/chloroform extraction method
We followed CUT&RUN described in Skene and Beniof (PMID:28079019), with minor variations.
CUT&RUN

treatment_protocol: Snip1-tm1a (Infrafrontier/EMMA 04224) were first crossed with Actin-FLPe to generate the Snip1-flox line. To genetically label NPCs, Snip1-flox; Nestin-Cre mice were crossed with Sox2-eGFP transgenic mice. Embryos were harvested at embryonic days as indicated in the figures or text

value: cortical


title: fls2, flg22 treatment, TP 30m, Biorep3


title: MOLM-13 shCTRL H3K4me1 rep1

description:
MOLM13_shCTRL_H3K4me1_merge_corrected_IgG_peaks.broadPeak
1197

value: AML

value: shRNA

value: H3K4me1 (Diagenode #C15410194)


title: MOLM-13 shCTRL IgG rep1

value: IgG (Diagenode #C15410206)


title: Mouse, Control, LC-3

value: Heart


title: USP5-MKO_LPS-3h-3

city: Suzhou

first: zigang

last: qiao

address: Chongwen Road

department: Suzhou Institute of Systems Medicine

institute: Chinese Academy of MedicalSciences & Peking Union Medical College

data_processing:
Reads were treated using fastp software with parameter '-n 10 -q 5 -u 50' to discard reads which are short or in poor quality
The treated reads then mapped to mm10 reference genome using CLC Genomic Workbench 12 to get expression of genes
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: PM

extract_protocol:
The cell samples were lysed in TRIzol and extract total RNA for RNA-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PM

value: peritoneal macrophages

value: Usp5 myeloid knockout mice

value: LPS


title: Patient_13_Baseline_PBMC_TIL_TCR

value: Baseline

value: Live CD45+ immune cells

value: female


title: Patient_13_Week4_TIL_PBMC_GEX

value: Tumor

value: Gene expression

value: IV


title: USP5-MKO_LPS-0h-3


title: Patient_13_Baseline_PBMC_TIL_GEX


title: Org-D35-53BP1-S25D-14-3_rep1

description: Day 35 53BP1 S25D rep1


title: CASP, flg22 treatment, TP 480m, Biorep2

value: 5-day-old Seedling roots

value: pCASP1::FLS2-GFP fls2


title: USP5-MKO_LPS-0h-2


title: Org-D35-53BP1-S25A-79-3_rep1

description: Day 35 53BP1 S25A rep1

value: cortical


title: USP5-MKO_LPS-3h-2


title: USP5-MKO_LPS-0h-1


title: Patient_13_Week4_PBMC_TIL_CITEseq

value: Week 4

value: CITEseq

value: relatlimab


title: fls2, H2O treatment, TP 30m, Biorep3


title: CASP, H2O treatment, TP 30m, Biorep3


title: USP5-MKO_LPS-3h-1


title: Org-D35-53BP1-S25D-17_rep1

description: Day 35 53BP1 S25D-17 rep1


title: WT_LPS-3h-3

value: wild type


title: fls2, flg22 treatment, TP 480m, Biorep2


title: CASP, H2O treatment, TP 480m, Biorep2


title: WT_LPS-3h-2

value: PM


title: Patient_12_Baseline_TIL_GEX

value: male


title: CASP, flg22 treatment, TP 120m, Biorep2


title: WT_LPS-3h-1

value: peritoneal macrophages


title: Org-D35-53BP1-S25D-14-19_rep1

description: Day 35 53BP1 S25D rep1


title: Patient_12_Baseline_PBMC_TCR

value: Blood

value: TCR sequencing


title: Patient_12_Week16_PBMC_GEX

value: Week 16

value: Live CD45+ immune cells

value: relalimab+nivolumab


title: WT_LPS-0h-3

value: LPS


title: fls2, H2O treatment, TP 480m, Biorep2


title: Org-D35-53BP1-S25D-14-15_rep2

description: Day 35 53BP1 S25D rep2


title: Patient_12_Baseline_PBMC_GEX

value: Baseline

value: Gene expression

value: IV


title: fls2, H2O treatment, TP 120m, Biorep2

value: 5-day-old Seedling roots


title: CASP, H2O treatment, TP 120m, Biorep2

value: pCASP1::FLS2-GFP fls2


title: Patient_12_Baseline_TIL_TCR

value: Tumor


title: WT_LPS-0h-1


title: fls2, flg22 treatment, TP 120m, Biorep2


title: Org-D35-53BP1-S25D-14-15_rep1

description: Day 35 53BP1 S25D rep1

value: cortical


title: fls2, flg22 treatment, TP 30m, Biorep2


title: Patient_13_Baseline_PBMC_TIL_CITEseq

value: CITEseq

value: female


title: CASP, flg22 treatment, TP 30m, Biorep2


title: Org-D35-53BP1-S25A-34-4_rep2

description: Day 35 53BP1 S25A rep2


title: Org-D37-ATM-KO3_rep2

description: Day 37 ATM KO rep2

value: ATM KO


title: Patient_11_Week16_PBMC_GEX

value: male


title: fls2, H2O treatment, TP 30m, Biorep2


title: Org-D37-WT_rep2

description: Day37 WT Rep2

value: WT


title: CASP, H2O treatment, TP 30m, Biorep2


title: WT_LPS-0h-2

value: PM

value: peritoneal macrophages

value: wild type


title: Org-D37-WT_rep1

description: Day37 WT Rep1


title: Org-D35-WT-2_rep2

description: Day 35 WT 2 rep2


title: HK2 cells, Control, 24 h, rep3

city: Wuhan

first: Ben

last: Tang

address: JieFang Avenue

department: Department of Nephrology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
The image data obtained by the high-throughput sequencer is converted into sequence data (reads) by CASAVA base recognition, and the file is in fastq format. remove reads containing N, and remove low-quality reads. All subsequent analyses are based on high-quality analysis of clean data.
FeatureCounts (v2.0.1) is used to calculate the number of reads mapped to each gene. Then calculate each gene’s FPKM according to the gene’s length, and calculate the number of reads mapped to that gene. DESeq2 software (1.16.1) was used to perform differential expression analysis between two comparison groups.
GO enrichment analysis of differentially expressed genes was performed usingclusterProfiler (4.2.0) R software, and GO terms with corrected P values less than 0.05 were considered as significantly enriched GO terms for differentially expressed genes.
We used clusterProfiler R software to analyze the statistical enrichment of differentially expressed genes in KEGG pathways
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: HK2 cells were maintained in DMEM-F12 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen)
The mRNA purified by Oligo(dT)-attached magnetic beads was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis and purified using AMPure XP Beads. The cDNA library was constructed through repair, PCR amplification, and purification. Qubit 2.0 and Agilent 2100 bioanalyzer were used for quantification.

treatment_protocol: HK2 cells were untreated or treated with TGF-β1 for 24 h.

value: Kidney proximal tubualr epithelial cells

value: Control


title: fls2, flg22 treatment, TP 480m, Biorep1


title: Org-D35-53BP1-S25A-34-4_rep1

description: Day 35 53BP1 S25A rep1


title: HK2 cells, Control, 24 h, rep1


title: Org-D35-53BP1-S25A-79-3_rep2

description: Day 35 53BP1 S25A rep2


title: HK2 cells, Control, 24 h, rep2


title: Org-D37-ATM-KO43_rep1

description: Day 37 ATM KO rep1


title: HK2 cells, TGF-β1, 24 h, rep3


title: KOPN41_H3K27ac_Hi-CHIP

first: Tze King

last: Tan

address: 14 Medical Drive

department: Cancer Science Institute

institute: National University of Singapore

data_processing:
Library strategy: HiChIP
Sequencing data of H3K27ac Hi-ChIP were processed with fastp to remove adapter sequence (CTGTCTCTTATACACA) and phred quality >=Q15. Then the sequenced reads were aligned, paired, and removed of duplicates using the HiC-Pro pipeline version (2.11.1) where the fastq files were aligned to hg19 genome using bowtie2 version 2.4.1.
The MboI restriction enzyme cutsite over the human genome were generated using HiC-Pro utilities python script digest_genome function by using ^GATC as the ligation site.
The aligned data were further processed using hichipper to call the interactions. Hichipper version 2.7.9 processed the valid interactions from HiC-Pro and generate the interaction bedpe file.
Hichipper processed the interactions using parameters as shown -l 100 -mi 5000 -ma 2000000 -mg 12500.
Assembly: hg19
Supplementary files format and content: *_allValidPairs
Supplementary files format and content: txt file output from HiC-Pro
Supplementary files format and content: *.intra.loop_counts.bedpe
Supplementary files format and content: bedpe file output from hichipper
Supplementary files format and content: *.anchors.bed
Supplementary files format and content: anchor used by hichipper

source_name: KOPN41 cells

growth_protocol: All B-ALL cells were cultured in RPMI-1640 medium supplemented with 10% FBS and Pen/Strep.

extract_protocol:
Library construction from the H3K27ac HiChIP-seq samples and sequencing of paired-end 100-bp-long reads by the DNBseq were performed at BGI Biotech Solutions Co. Ltd (Hong Kong, China).
Paired-end HiChIP

treatment_protocol: All B-ALL cells were cross-linked with formaldehyde, lysed with Hi-C buffer and then sonicated. Lysates were clarified from sonicated nuclei and H3K27ac-DNA complexes were isolated with antibody. Post-ChIP DNA was tagmented with Tn5 enzyme follwed by PCR amplification library synthesis

value: B-ALL

tag: chip antibody

value: H3K27ac Antibody (abcam; ab4729)


title: Org-D37-ATM-KO43_rep2

description: Day 37 ATM KO rep2


title: PDAC 3

type: RNA

city: Bunkyo-ku

first: Yuko

last: Kinowaki

state: TOKYO

address: 1-5-45 Yushima

department: Comprehensive Pathology

country: Japan

institute: Tokyo Medical and Dental University

hyb_protocol: See manufacturer's web site

scan_protocol: See manufacturer's web site

data_processing: nSolver Analysis Software 4.0.70*

source_name: Control (neoplastic)

label_protocol: See manufacturer's web site

treatment_protocol: Case 8: sunitinib, everolimus + TAE/　Case 10: sunitinib, everolimus + TAE/　Other cases: not performed

tag: gender

value: M


title: Patient_10_Week16_PBMC_GEX

value: Blood

value: Week 16

value: Live CD45+ immune cells

value: Gene expression

value: IV

value: relalimab+nivolumab


title: HK2 cells, TGF-β1, 24 h, rep2


title: HK2 cells, TGF-β1, 24 h, rep1


title: Patient_10_Baseline_PBMC_TCR

value: Baseline

value: TCR sequencing

value: female


title: Org-D37-ATM-KO14_rep1

description: Day 37 ATM KO rep1

value: cortical

value: ATM KO


title: CASP, flg22 treatment, TP 480m, Biorep1

value: 5-day-old Seedling roots

value: pCASP1::FLS2-GFP fls2


title: Org-D35-53BP1-S25A-34-3_rep2

description: Day 35 53BP1 S25A rep2


title: Normal pancreatic epithelium 2

source_name: Control (non-neoplastic)


title: fls2, H2O treatment, TP 480m, Biorep1


title: Patient_10_Baseline_PBMC_GEX


title: Org-D35-53BP1-S25D-14-3_rep2

description: Day 35 53BP1 S25D rep2


title: L-ASK_H3K27ac_Hi-CHIP

source_name: L-ASK cells

value: L-ASK


title: Org-D37-ATM-KO2_rep1

description: Day 37 ATM KO rep1


title: PDAC 2


title: CASP, H2O treatment, TP 480m, Biorep1


title: CASP, H2O treatment, TP 120m, Biorep1


title: MBMY_H3K27ac_Hi-CHIP

source_name: MBMY cells

value: B-ALL

value: MB-MY


title: KOPN68_H3K27ac_Hi-CHIP

source_name: KOPN68 cells

value: H3K27ac Antibody (abcam; ab4729)


title: fls2, flg22 treatment, TP 120m, Biorep1


title: fls2, H2O treatment, TP 120m, Biorep1


title: Org-D37-ATM-KO3_rep1

description: Day 37 ATM KO rep1


title: Normal pancreatic epithelium 1

value: M


title: PDAC 1


title: Org-D35-53BP1-S25A-34-3_rep1

description: Day 35 53BP1 S25A rep1


title: fls2, flg22 treatment, TP 30m, Biorep1


title: Case 9, NEC

value: F


title: Org-D35-WT-1_rep1

description: Day 35 WT 1 rep1

value: WT


title: NALM6_H3K27ac_Hi-CHIP

source_name: NALM6 cells


title: Org-D35-WT-2_rep1

description: Day 35 WT 2 rep1


title: L4 C. elegans, somatic tissue, mtDNA hypermethylation, replicate 3

city: Brisbane

first: Steven

last: Zuryn

state: Queensland

address: QBI Building 79, University of Queensland

department: Queensland Brain Institute

country: Australia

institute: The University of Queensland

data_processing:
To remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1).
Hisat2 (v2.0.1) was used to index reference genome sequence and align reads.
HTSeq (v0.6.1) was used to quantifygene and isoform expression levels from the pair-end filtered data.
Assembly: WBcel235
Supplementary files format and content: Tab-delimited text file, includes raw counts and FPKM values for each sample.

organism: Caenorhabditis elegans

source_name: all somatic

growth_protocol: C. elegans with a glp-4(bn2) genetic background were raised to larval stage L4 at the restrictive temperature.

extract_protocol:
Total RNA was extracted using TriZOL reagent according to the manufacturer's instructions. 1 ug of total RNA was used for library construction.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.

value: all somatic

value: eft-3p::MTSDAMT-1, glp-4(bn2)


title: CASP, flg22 treatment, TP 30m, Biorep1


title: L4 C. elegans, somatic tissue, mtDNA hypermethylation, replicate 2


title: fls2, H2O treatment, TP 30m, Biorep1


title: Org-D35-53BP1-S25D-14-19_rep2

description: Day 35 53BP1 S25D rep2


title: L4 C. elegans, somatic tissue, mtDNA hypermethylation, replicate 1


title: Org-D35-53BP1-S25A-79-1_rep2

description: Day 35 53BP1 S25A rep2


title: L4 C. elegans, somatic tissue, mtDNA hypomethylation, replicate 3

value: eft-3p::ALKB-1, glp-4(bn2)


title: Org-D35-53BP1-S25D-17_rep2

description: Day 35 53BP1 S25D rep2


title: CASP, H2O treatment, TP 30m, Biorep1


title: Ksp-cre/PRDM16flox/flox C57BL/6J mice,UIRI model, mice1

source_name: Kidney

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen),more than 800ng total RNA was used for library construction.
The library construction kit used in library construction is Illumina’s NEBNext®UltraTM RNA Library Prep Kit

treatment_protocol: pedicle of left kidney was clipped with vascular clamp, and mice were put on constant temperature metal bath at 38.5℃ for 35 minutes. At 10 days after UIRI, right kidney was removed. Mice were sacrificed after 24 hours.

value: Kidney

tag: strain

value: Kidney cell

value: Ksp-Cre/PRDM16 flox/flox

value: UIRI model,11days


title: L4 C. elegans, somatic tissue, mtDNA hypomethylation, replicate 2


title: Ksp-cre/PRDM16flox/flox C57BL/6J mice,UIRI model, mice3


title: L4 C. elegans, somatic tissue, mtDNA hypomethylation, replicate 1


title: L4 C. elegans, somatic tissue, control, replicate 3


title: Org-D37-ATM-KO14_rep2

description: Day 37 ATM KO rep2

value: cortical

value: ATM KO


title: Org-D37-ATM-KO2_rep2

description: Day 37 ATM KO rep2


title: Case 7, NEC

source_name: Tumor


title: Case 10, MiNEN


title: Case 6, NEC


title: Case 8, NEC


title: Case 11, NEC


title: Org-D35-53BP1-S25A-79-1_rep1

description: Day 35 53BP1 S25A rep1


title: Ksp-cre/PRDM16flox/flox C57BL/6J mice,UIRI model, mice2


title: PRDM16flox/flox C57BL/6J mice,UIRI model, mice3


title: LEG92, Passage 6, Paclitaxel (10 mg/kg, every week, i.p.)

status: Public on Aug 10 2024

city: zhengzhou

first: liting

last: zhou

address: 100 Science Avenue

institute: Zhengzhou University

data_processing:
Raw sequencing data were filtered using SOAPnuke (v1.5.6) to remove reads containing adapters, reads with more than 5% unknown bases, and low-quality reads, resulting in clean data. Subsequent data analysis, visualization, and mining were performed using the Dr. Tom multi-omics data mining system. Clean data were aligned to the reference genome using HISAT2 (v2.1.0), and gene fusion detection was performed using Ericscript (v0.5.5), while alternative splicing and differential splicing were analyzed using rMATS (V3.2.5). For differential gene analysis, clean data were aligned to the reference gene set using Bowtie2 (v2.3.4.3), gene expression was quantified using RSEM (v1.3.1), and expression clustering heatmaps were generated using pheatmap (v1.0.8). Differential gene detection was performed using DESeq2 (v1.4.5), DEGseq, or PoissonDis, with criteria of Q value ≤ 0.05 or FDR ≤ 0.001. To explore gene functions related to phenotypic changes, differential genes were subjected to GO and KEGG enrichment analysis using the hypergeometric test with Phyper, setting a threshold of Q value ≤ 0.05 for significant enrichment.
Assembly: mm10
Supplementary files format and content: excel

organism: Mus

source_name: PDX Tumor

extract_protocol:
Total RNA was extracted from animal tissues and cells using TRIzol reagent. For tissue samples, an appropriate amount was placed into a labeled grinding tube, 1.5 mL of TRIzol was added, and the sample was ground for 30 seconds using a tissue grinder, followed by a 5-minute incubation to ensure complete cell lysis. Alternatively, tissue samples were ground into a powder under liquid nitrogen and transferred into 1.5 mL of TRIzol in a 2 mL EP tube, followed by a 5-minute incubation. For cell samples, 1 mL of TRIzol per 1×10^6 cells was added, vortexed to mix, and incubated at room temperature for 5 minutes. The lysates were then centrifuged at 12,000 ×g for 5 minutes at 4°C. The supernatant was transferred to an EP tube containing 300 µL of chloroform/isoamyl alcohol (24:1), shaken vigorously, and centrifuged at 12,000 ×g for 8 minutes at 4°C. The aqueous phase was transferred to a new tube, mixed with isopropanol at 2/3 the volume of the supernatant, and incubated at -20°C for at least 2 hours. The mixture was centrifuged at 17,500 ×g for 25 minutes at 4°C, the supernatant discarded, and the pellet washed with 0.9 mL of 75% ethanol. After centrifuging at 17,500 ×g for 3 minutes at 4°C, the supernatant was discarded, and the pellet was air-dried for 3-5 minutes before being dissolved in 20-200 µL of DEPC-treated or RNase-free water.
The library preparation process involves several key steps. First, RNA samples are quality-checked using appropriate methods based on sample type and product requirements. Next, mRNA is isolated by denaturing the RNA to disrupt secondary structures and using oligo(dT) magnetic beads to enrich for mRNA. The isolated mRNA is then fragmented using a fragmentation reagent at a specific temperature. Following fragmentation, first-strand cDNA synthesis is performed, followed by second-strand cDNA synthesis. The double-stranded cDNA is then end-repaired, an "A" base is added to the 3' ends, and adapters are ligated to the cDNA. The cDNA library is amplified by PCR, and the resulting library is quality-checked. Finally, the PCR products are denatured to single strands, circularized, and any remaining linear DNA is digested. The single-stranded circular DNA molecules are then used to form DNA nanoballs (DNBs) through rolling circle replication. These DNBs are loaded onto a high-density DNA nanochip and sequenced using combinatorial probe-anchor synthesis (cPAS) technology.

value: PDX Tumor

value: Paclitaxel


title: LEG34, Passage 6, Paclitaxel (10 mg/kg, every week, i.p.)


title: PRDM16flox/flox C57BL/6J mice,UIRI model, mice1


title: L4 C. elegans, somatic tissue, control, replicate 1


title: ARC HTO

first: Han

state: New York

address: 1230 York Avenue

department: Molecular Genetics

institute: Rockefeller University

description: 10 X Genomics

data_processing:
The FASTQ file was analyzed with Cell Ranger version 5.0. The snRNA-seq data for ARC (WT) was preprocessed individually using the Seurat v4 (v4.0.5). Cells with more than 800 and fewer than 5,000 RNA features were selected for further analysis. Cells with greater than 1% mitochondrial genes and greater than 12,000 total RNA counts were also removed. Genes detected in fewer than 3 cells were excluded. Then we demultiplexed the cells based on their hashtag count (positive. quantile =0.8) using the built-in function in Seurat v4. Only the cells with singlet Hashtag assignment were kept for downstream analysis. The data was then log-normalized with a scale factor of 10,000. After the initial quality control, demultiplexing, and normalization steps, all the singlets were then scaled, and dimensionally reduced with PCA and UMAP. Leiden clustering (resolution =0.55) was applied to identify clusters. We used known cell-type specific gene expression to annotate the clusters.
Assembly: mm10
Supplementary files format and content: Tab-saperated values files and matrix files

source_name: Hypothalamus ARC

extract_protocol:
Male C57BL/6J mice aged 10-12 weeks were euthanized via transcardial perfusion using ice-cold HEPES-Sucrose Cutting Solution containing NaCl (110 mM), HEPES (10 mM), glucose (25 mM), sucrose (75 mM), MgCl2 (7.5 mM), and KCl (2.5 mM) at a PH of 7.4. Subsequently, brains were quickly dissected in the same solution, frozen using liquid nitrogen, and stored at -80 °C until nuclei isolation. To isolate nuclei, as previously described, the samples were thawed on ice, resuspended in HD buffer containing tricine KOH (10 mM), KCl (25 mM), MgCl2 (5 mM), sucrose (250 mM), 0.1% Triton X-100, SuperRNaseIn (0.5 U/ml), RNase Inhibitor (0.5 U/ml). Homogenization was performed using a 1-ml dounce homogenizer. The resulting homogenates were filtered using a 40 μM filter, centrifuged at 600g for 10 minutes, and resuspended in nucleus storage buffer containing sucrose (166.5 mM), MgCl2 (10 mM), Tris buffer (pH 8.0, 10 mM), SuperRNaseIn (0.05 U/ml), RNase Inhibitor (0.05 U/ml) for subsequent staining. Nucleus quality and number were assessed using an automated cell counter (Countess II, Thermo Fisher). For staining, nuclei were labeled with Hoechst 33342 (Thermo Scientific H3570; 0.5 µl per million nuclei), anti-NeuN Alexa Fluor 647-conjugated antibody (Abcam ab190565) (0.5 µl per million nuclei), and TotalSeq anti-Nuclear Pore Complex Proteins Hashtag antibody (BioLegend 682205) (0.5 mg per million nuclei) for 15 minutes at 4 °C. Following staining, samples were washed with 10 ml 2% BSA (in PBS) and centrifuged at 600g for 5 minutes. Nuclei were then resuspended in 2% BSA (in PBS) with RNase inhibitors (SuperRNaseIn 0.5 U/ml, RNase Inhibitor 0.5 U/ml) for subsequent fluorescence-activated cell sorting. The samples were gated based on Hoechst fluorescence to identify nuclei and then further sorted based on high Alexa Fluor 647 expression, designating NeuN+ nuclei as neurons. Nuclei were captured and barcoded using 10x Genomics Chromium v3 following the manufacturer’s protocol.
Libraries were prepared using 10x Genomics Chromium v3 following the manufacturer’s protocol.

value: Hypothalamus ARC

value: Neuron

value: wild type


title: Case 3, MiNEN


title: ZW2PLASMAB185A21

first: Klaas

middle: E. A.

last: Max

department: RNA Molecular Biology

data_processing:
Sequencing data were processed using an in-house RNA-sequencing data analysis platform (RSDAP), see Brown et al. (2013) Front. Genet. for details.
Read extractions and demultiplexing was done using extraction lenth of 16 – 45 nt, a minimum 3’ overlap of adapter with 0/1 mismatches of 4/5 nt, respectively, removal of low complexity sequences.
For the read mapping and the generation of the read count matrix table, read annotations used profile annoDB_jul2014c, which included reference sequences for human and virus RNAs based on miRBASE 18 with modifications and HG19.
Supplementary_files_format_and_content: Matrixtable_exRNAdata20210810_cluster_miRNA_read_counts.csv

source_name: 100,000 x g supernatant

extract_protocol:
Low speed centrifugation (2500 g x 15 minutes, room temperature) was performed, then transfer of supernatant, 2nd round of centrifugation (same parameters), then transfer of supernatant. A self-developed method and self-developed solutions were used for nucleic-acid extraction, nucleic-acid partitioning, and column purification (RNA isolation), see Max et al. (2018) PNAS for details. For exRNA carrier subfractionation, selected samples were fractionated by differential ultracentrifugation into 10,000 xg pellet, 100,000 xg pellet and corresponding supernatant fractions: 11 ml of platelet-depleted plasma was centrifuged at 10,000 × g in 12 ml tubes (Sorvall, #03699) for 30 min. The supernatant was transferred by aspiration into a fresh 15 ml tube and mixed by inversion. Two aliquots of 500 µl of this supernatant were transferred into 1.5 ml microcentrifuge tubes for later RNA isolation. The 10,000 × g fragile pellet was suspended in 2.0 ml of phosphate-buffered saline (PBS), transferred into a 2.0 ml microcentrifuge tube, and centrifuged at 10,000 × g in a microcentrifuge for 30 min. The PBS supernatant was removed by aspiration, and the residual ≤10 µl volume pellet was resuspended in 450 µl PBS. The residual 10 ml of 10,000 × g supernatant was transferred into a 12 ml tube (Sorvall, #03699) and centrifuged at 100,000 × g for 90 min. The supernatant was transferred as described above, and two 500 µl aliquots of the 100,000 × g supernatant were transferred into 1.5 ml microcentrifuge tubes. The 100,000 × g pellet was washed with 10 ml PBS and centrifuged again at 100,000 × g for 90 min. The PBS supernatant was carefully removed as described above. The pellet was resuspended in 450 µl PBS. All pellet and supernatant fractions were flash-frozen in liquid nitrogen. Automated RNA isolation was conducted as previously described {Max:2018km} with the following modifications: Samples were organized in batches of 24 samples of 450 µl full plasma or plasma subfractions. Vesicle fractions were adjusted with PBS to 450 µl. Calibrator Set1, composed of ten 21-nt 5’-phosphorylated RNA oligos was added at an absolute amount of 2 attomoles per oligonucleotide along with the denaturant to each sample.
Large cohort sample library preparations used 3’ adapters, and PCR amplification methodologie, however, P12 family and plasma subfraction samples used novel 3’ adapters and PCR primers to accommodate changes in Illumina flow cell design after HiSeq was discontinued. RNA equivalent to an input 225 µl plasma was spiked with calibrator Set2 composed of another ten 21-nt 5’-phosphorylated RNA oligos at an absolute amount of 1 attomol per oligonucleotide and entered the first step of the cDNA library preparation. In sample libraries of plasma subfraction RNA from 225 µl supernatant or 5 ml pellet was used to which 0.2 attomoles per oligonucleotide of calibrator Set2 was added. After the 3’ ligation, up to 24 samples were multiplexed, size-selected by denaturing 15%, ligated to 5’ adapter, reverse-transcribed and PCR-amplified. To enable comparisons with earlier results (28), the PAGE size-selection limits were maintained at 19 to 45 for the large (n = 496) and P12 family cohorts (n = 12 samples). After discovering that miRNAs were noticeably underrepresented in the 10K and 100K pellet fractions, the size range for all plasma subfraction libraries (4 plasma subfractions, n = 17 samples, each) was adjusted to 19 to 24 nt in favor of miRNAs. cDNA libraries were sequenced as single-lane high-output single-read 75-bp HiSeq 2000 (Large cohort, n = 496 samples) or as Nextseq-500 100-bp single-read runs (P12 family, n = 12 samples; 4 Plasma subfractions, n = 17 samples each). Sequencing data were processed using an in-house RNA-sequencing data analysis platform (RSDAP) using extraction lenth of 16 – 45 nt, a minimum 3’ overlap of adapter with 0/1 mismatches of 4/5 nt, respectively, removal of low complexity sequences. For read annotations, profile annoDB_jul2014c was used, which included reference sequences for definitions for human and virus RNA sequences based on miRBASE 18 with modifications. Calibrator sequences (labeled by set) are: >Set1_cali_01_rc TCCACGACGTCTCATGTATTTC, >Set1_cali_04_rc GGGTACCATACCGGTTGTCTTA, >Set1_cali_17_rc TCATGAGTCCGTACCTTGATTG, >Set1_cali_18_rc ATCATTTACGATTCGGAGCTGT, >Set1_cali_20_rc GATAGTTCGGGATCGCTGTAAC, >Set1_cali_24_rc TGCTACTCCGATCTTTAGCCTC, >Set1_cali_25_rc AGGGCCCTTTAGGCACTAATAG, >Set1_cali_27_rc GTAGCTGTCAGTACGTTCGTGC, >Set1_cali_43_rc TCTAGTTGCGTGATGGAGAGAA, >Set1_cali_44_rc AGCCGCATTTCGTAGTGATATT, >Set2_cali_07_rc GTCCCACTCCGTAGATCTGTTC, >Set2_cali_11_rc GATGTAACGAGTTGGAATGCAA, >Set2_cali_12_rc TAGCATATCGAGCCTGAGAACA, >Set2_cali_14_rc CATCGGTCGAACTTATGTGAAA, >Set2_cali_15_rc GAAGCACATTCGCACATCATAT, >Set2_cali_16_rc TCTTAACCCGGACCAGAAACTA, >Set2_cali_26_rc AGGTTCCGGATAAGTAAGAGCC, >Set2_cali_28_rc TAACTCCTTAAGCGAATCTCGC, >Set2_cali_31_rc AAAGTAGCATCCGAAATACGGA, >Set2_cali_35_rc TGATACGGATGTTATACGCAGC

tag: cohort

value: Plasma Subfractions

tag: anatomical location

value: Entire cardiovascular system

tag: rna source

value: fractionated cell-free biofluid RNA

tag: rna isolation kit

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: Pregnant individual

tag: individual

tag: visit

tag: pregnant

value: yes

tag: trimester

tag: date of collection

tag: age group

tag: race

value: Asian

tag: ethnicity

tag: sequencing technology

value: NextSeq 500


title: ZW2PLASMAB185A19

tag: cohort

tag: gender

value: F

tag: age

value: Hispanic


title: CASP, flg22 treatment, TP 120m, Biorep1

tag: tissue

value: 5-day-old Seedling roots

tag: genotype

value: pCASP1::FLS2-GFP fls2

tag: treatment

tag: time


title: L4 C. elegans, somatic tissue, control, replicate 2

value: all somatic


title: LEG34, Passage 6, Control

value: PDX Tumor

value: Saline


title: ZW2PLASMAB185A18

tag: anatomical location

tag: rna source

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: Normal male reference

value: no

value: M

value: White


title: ZW2PLASMAB185A20

value: Plasma Subfractions

value: Entire cardiovascular system

value: fractionated cell-free biofluid RNA

tag: individual

tag: visit

tag: pregnant

tag: trimester

tag: date of collection

tag: age group

tag: race


title: ZW2PLASMAB185A17

tag: cohort

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

value: Pregnant individual

value: yes

tag: gender

tag: age

tag: ethnicity

tag: sequencing technology


title: ZW2PLASMAB185A16

tag: anatomical location

tag: rna source

tag: rna isolation kit

value: F

value: NextSeq 500


title: ZW2PLASMAB185A15

tag: shortid

tag: batch

tag: adapter

value: Hispanic


title: ZW2PLASMAB185A22

tag: sample subgroup (condition)

tag: individual

tag: visit


title: LEG92, Passage 6, Control

tag: tissue

tag: genotype

tag: treatment


title: ZW2PLASMAB185A08

tag: cohort

tag: pregnant

tag: trimester

tag: date of collection

tag: age group

tag: race


title: ZW2PLASMAB185A09

tag: anatomical location

tag: rna source

value: Normal female reference, not pregnant

tag: gender

tag: age

tag: ethnicity

tag: sequencing technology


title: ZW2PLASMAB185A04

tag: rna isolation kit

tag: shortid

tag: batch

tag: adapter

tag: sample subgroup (condition)

value: P12 family member

tag: individual


title: Case 5, NEC


title: Case 4, MiNEN


title: Case 2, MiNEN


title: ZW2PLASMAB185A13

tag: cohort

tag: visit

tag: pregnant


title: ZW2PLASMAB184A23

source_name: 10,000 x g supernatant

tag: trimester

tag: date of collection

tag: age group


title: ZW2PLASMAB185A06

tag: anatomical location

tag: rna source

tag: race


title: ZW2PLASMAB184A22

tag: gender

tag: age

tag: ethnicity


title: ZW2PLASMAB184A19

tag: rna isolation kit

tag: shortid

tag: sequencing technology


title: ARC cDNA

description: 10 X Genomics

tag: tissue

value: Hypothalamus ARC

tag: cell type

value: Neuron

tag: genotype

value: wild type


title: ZW2PLASMAB184A10

tag: cohort

tag: batch

tag: adapter

tag: sample subgroup (condition)

tag: individual

tag: visit


title: ZW2PLASMAB185A01

tag: anatomical location

tag: rna source

tag: pregnant

value: no

tag: trimester

tag: date of collection

tag: age group


title: ZW2PLASMAB185A02

tag: rna isolation kit

tag: shortid

tag: gender

tag: age

tag: race

tag: ethnicity


title: ZW2PLASMAB184A01

tag: cohort

tag: batch

tag: sequencing technology


title: ZW2PLASMAB183A22

source_name: 100,000 x g pellet

tag: adapter

tag: sample subgroup (condition)

tag: individual


title: ZW2PLASMAB184A24

tag: anatomical location

tag: rna source

tag: visit


title: ZW2PLASMAB183A20

tag: pregnant

tag: trimester

tag: date of collection

value: Asian


title: ZW2PLASMAB184A21

tag: rna isolation kit

tag: shortid

value: Normal male reference

value: M

tag: age group

value: White


title: ZW2PLASMAB184A18

value: Plasma Subfractions

value: Entire cardiovascular system

value: fractionated cell-free biofluid RNA

tag: gender

tag: age

tag: race


title: ZW2PLASMAB184A14

tag: cohort

value: Self developed protocol, Tuschl_RNA_isolation_library_preparation_protocol.pdf; executed on epMotion 5075 liquid handling system.

tag: batch

tag: ethnicity


title: ZW2PLASMAB184A13

tag: adapter

tag: sample subgroup (condition)

tag: sequencing technology


title: ZW2PLASMAB184A12

tag: anatomical location

tag: rna source

value: Pregnant individual

tag: individual

value: yes

value: F


title: ZW2PLASMAB184A09

tag: visit

tag: pregnant

tag: trimester

value: NextSeq 500


title: ZW2PLASMAB185A07

tag: rna isolation kit

tag: shortid

tag: date of collection

value: Hispanic


title: ZW2PLASMAB184A07

tag: gender

tag: age

tag: age group


title: ZW2PLASMAB185A11

tag: cohort

tag: batch

tag: race


title: ZW2PLASMAB183A08

tag: adapter

tag: sample subgroup (condition)

value: P12 family member

tag: ethnicity


title: ZW2PLASMAB184A06

tag: anatomical location

tag: rna source

tag: sequencing technology


title: ZW2PLASMAB184A03

tag: individual

tag: visit

tag: pregnant


title: ZW2PLASMAB183A21

tag: rna isolation kit

tag: shortid

tag: trimester


title: ZW2PLASMAB183A04

tag: date of collection

tag: gender

tag: age


title: ZW2PLASMAB183A03

tag: cohort

tag: batch

value: Normal female reference, not pregnant

tag: age group


title: ZW2PLASMAB183A19

tag: adapter

tag: sample subgroup (condition)

tag: race