title: Lesion A3-1, ROI 0811-4480

description: NanoString GeoMx


title: Lesion A1-2, ROI 0385-0342

status: Public on Aug 05 2024

type: SRA

city: Groningen

first: Astrid

last: Alsema

address: Antonius Deusinglaan 1

department: Biomedical Sciences of Cells and Systems

country: Netherlands

institute: University Medical Center Groningen

description: NanoString GeoMx

library_source: transcriptomic

data_processing:
Fastq files were converted to .dcc files using the GeoMx NGS Pipeline according to the GeoMx DSP NGS Readout User Manual (MAN-10153-01) Option 1: Standard Standalone Pipeline.
DCC files can be loaded into R for data processing with the GeomxTools open software package.
Assembly: GRCh38
Supplementary files format and content: DCC files
Supplementary files format and content: One .ini file for NanoString's NGS Pipeline software, one .xlsx metadata file with sample information, one .pkc file with probe information for loading into R, and five .png image files of the five samples.
Library strategy: Spatial Transcriptomics

molecule: total RNA

organism: Homo sapiens

source_name: Brain white matter

extract_protocol:
FFPE brain samples were sectioned at 5 µm thickness. Sections were treated with Nanostring Whole Transcriptome Atlas probes according to the GeoMx® DSP Manual Slide Preparation User Manual (MAN-10150-03), and stained for IBA1. Whole transcriptome probes were collected from IBA1+ segments as according to the GeoMx® DSP Instrument User Manual (MAN-10152-03).
Libraries were made from these probes according the GeoMx® DSP NGS Readout User Manual (MAN-10153-03).
NanoString GeoMx® Digital Spatial Profiling libraries were loaded at 650 pM molarity on the Illumina NextSeq 2000 and sequenced with a P1 v3 100 bp reagent kit.

tag: disease state

value: Multiple sclerosis (MS)

tag: tissue

value: Brain white matter

tag: cell type

value: Microglia


title: Lesion A3-1, ROI 0651-4470

description: NanoString GeoMx


title: K562-DMSO-2

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

country: USA

institute: University of Miami

description: polyA RNA

data_processing:
All samples were trimmed with Trimmomatic (v0.32) to remove low-quality and short reads and aligned to the human genome hg19 using STAR aligner (v 2.7.9a).
For total RNA and polyA RNA, RSEM (v 1.3.1) was used to obtain expected gene counts against the human gene reference Gencode (v 41). Differential expression was determined using DESeq2 and R (v 4.2.0). A gene was considered detected if the TPM (Transcripts Per Million) >1 in at least two replicates of one sample and significantly changed if the adjusted p-value was < 0.05 and fold change >1.5<−1.5.
Alternative splicing bam files with the Gencode v41 annotation file were used as input for rMATS (v4.1.2). Events with |inclusion level difference| > 0.05, P < 0.05 and FDR < 0.05 were identified as significantly differentially expressed AS events
For small RNAseq reads were aligned against human elements in RepBase (v23.08) with STAR (v2.7.9a), and the unmapped output was then mapped against the human genome (hg19), allowing three mismatches and keeping all uniquely aligned reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes the Differentially expressed genes per comparison

growth_protocol: K562 cells were cultured in 10% fetal bovine serum and 1% pencillin/streptomycin at early passages (P1-10) and then treated with either vehicle (DMSO) or 200nM selinexor for 24 hours. After 24 hours, RNA was extracted. For the combination treatment RNA sequencing, cells were treated with either vehicle/DMSO, 200nM eltanexor, 1uM venetoclax, 1uM A1331852, 1uM navitoclax, or the combinations of eltanexor+venetoclax, eltanexor+A1331852, and eltanexor+navitoclax for 24 hours.

extract_protocol:
Total RNA for mRNA sequencing was extracted using QIAGEN RNeasy mini kit. To separate nuclear and cytoplasmic fractions, pellet the cells via centrifugation for 5 minutes at 1500RPM and discard the supernatant. The pellet was then resuspended into 300mL of ice cold 0.25x lysis buffer (Tris-Cl pH 8.0, NaCl, MgCl2, Nonidet P-40). The pellet was kept on ice for two minutes and rotate the tube every 45 seconds to ensure proper lysis followed by centrifugation at highest speed at 4°C for two minutes. After centrifugation, the supernatant was carefully removed and placed in a new tube as this was the cytoplasmic fraction. For the remaining nuclear fraction pellet, 500mL of ice-cold PBS was added and centrifuged at 1500RPM for 5 minutes. The QIAGEN RNeasy mini kit was then used for long RNAs and miRNeasy Tissue/Cells Advanced Micro Kit was used for small RNA extraction.
For mRNA sequencing was Poly(A)-selected and the Illumina libraries were prepared using the TruSeq stranded mRNA Library Preparation kit. For the nuclear cytoplasmic mRNAs, ribsomoal RNA depeletion method with the TruSeq stranded Total RNA library was used with 50 million paired end reads. For the nuclear cytoplasmic small RNAs, the size selection step with the Perkin Elmer Next Flex Small RNA library preparation kit on the Illumina sequencing platform with 50 million single end reads.

tag: cell line

value: chronic myeloid leukemia cells

tag: treatment

value: Vehicle/DMSO


title: K562-DMSO-1

description: polyA RNA


title: P115_9C4B_V2_Epigenetics

type: genomic

city: Boston

first: Ofer

last: Levy

state: MA

address: 300 Longwood Avenue

department: Infectious Disease

institute: Boston Children's Hospital

hyb_protocol: [not provided]

scan_protocol: [not provided]

data_processing:
Extracted DNA send to AGRF Genotyping Service
EPIC array annotation object mapping probes IDs to hg38 human reference genome (Ensembl GRCh38v98)
Quality controlled for overall sample quality based on median methylated and unmethylated signals
QC steps included checking detection P cells, raw cell distribution, sex prediction, data normalization, and checked by density and RLE plots. Relative Log Expression computed for every spot in the array as the difference between the spot intensity and the median intensity for the same feature across all the arrays. Since majority of the spots are not expected to be differentially expressed, the plot should show boxplots centered around zero and all of them having the aproximately the same dispersion. An array showing greater dispersion than the other, or being not centered at zero could have quality problems.
Probe-level QC: removed poor-performing probes, Removed unwanted SNP and non-CG methylation probes, and then extracted Final Beta and Mvals
processed data: csv; Beta = QC/QA'd Beta values, SQN normalized

label: Cy3, Cy5

molecule: genomic DNA

source_name: Blood

label_protocol: [not provided]

extract_protocol:
Cell type: Whole blood; Extraction method:  Chemagic low volume blood kit, Bead based, Chemagic DNA 400 kit H96 (Cat# CMG-1491). ; Assay:Illumina Human Methylation EPIC v2.0. ; Extracted DNA send to AGRF Genotyping Service.
1.5ug of DNA send to AGRF for bisulphite treatment and hybridization to array

tag: geographic location

value: Papua New Guinea

value: Blood

value: Whole blood

tag: Sex

value: Female

value: BCG


title: Lesion A1-1, ROI 0922-0438

description: NanoString GeoMx


title: Lesion A3-1, ROI 0720-4675

description: NanoString GeoMx


title: P115_5A8C_V1_Epigenetics

description: Assay:Illumina Human Methylation EPIC v2.0.


title: Lesion A3-1, ROI 1336-1357

description: NanoString GeoMx


title: Lesion A3-1, ROI 1231-1509

description: NanoString GeoMx


title: P113_8A1K_V2_Epigenetics

value: Male


title: LOAD60 H2O-3

city: St. Louis

first: Zhao

last: Sun

state: MO

address: 4523 Clayton Ave

department: Developmental Biology

institute: Washington University in St. Louis

data_processing:
Basecalling: Illumina's bcl2fastq
Custom python demultiplexing
Alignment: STAR version 2.5.1a
Gene counts: Subread:featureCount 1.4.6-p5
Sequencing performance assessment: RSeQC 2.6.2
Assembly: hg38
Supplementary files format and content: tsv containing ensembl ID, entrezgene ID, gene name, type, source of name, transcript count, description, and CPM for each sample per gene.

source_name: spheroids

extract_protocol:
RNA was isolated using Qiashredder columns into Qiagen Rneasy plus mini.
Samples were prepared according to library kit manufacturer’s protocol

value: spheroids

value: neurons

tag: genotype

value: LOAD


title: Lesion A3-1, ROI 1086-1119

description: NanoString GeoMx


title: Lesion A3-1, ROI 0715-2656

description: NanoString GeoMx


title: LOAD60 H2O-2


title: P121_7G6F_V2_Epigenetics


title: K562 SF3B1 K666N-DMSO-1

description: polyA RNA


title: Lesion A3-1, ROI 0714-2694

description: NanoString GeoMx


title: P110_6H0D_V2_Epigenetics

value: HBV+BCG


title: LOAD60 H2O-1


title: Lesion A3-1, ROI 0719-2845

description: NanoString GeoMx


title: Lesion A3-1, ROI 0716-2730

description: NanoString GeoMx


title: P107_8B6G_V2_Epigenetics


title: Lesion A3-1, ROI 0718-2768

description: NanoString GeoMx


title: LOAD70 H2O-3


title: Lesion A3-1, ROI 1429-2080

description: NanoString GeoMx


title: Lesion A3-1, ROI 1339-0894

description: NanoString GeoMx


title: P106_3J2K_V1_Epigenetics


title: LOAD70 H2O-2


title: P105_7D3F_V1_Epigenetics

value: Delayed


title: Lesion A3-1, ROI 0717-2806

description: NanoString GeoMx


title: LOAD70 H2O-1


title: P101_6E6K_V1_Epigenetics

value: HBV


title: Lesion A3-1, ROI 1502-2213

description: NanoString GeoMx

value: Multiple sclerosis (MS)


title: Lesion A3-1, ROI 1445-2115

description: NanoString GeoMx

value: Brain white matter


title: Lesion A3-1, ROI 1464-2148

description: NanoString GeoMx

value: Microglia


title: P095_4A2A_V2_Epigenetics


title: Lesion A3-1, ROI 1483-2179

description: NanoString GeoMx


title: Lesion A3-1, ROI 1522-2247

description: NanoString GeoMx


title: LOAD72 H2O-1


title: LOAD72 H2O-3


title: P092_7M3B_V1_Epigenetics


title: Lesion A3-1, ROI 1569-0282

description: NanoString GeoMx


title: LOAD72 H2O-2


title: Lesion A3-1, ROI 1462-0406

description: NanoString GeoMx


title: LOAD89 H2O-2


title: Lesion A3-1, ROI 1526-0331

description: NanoString GeoMx


title: P089_8K6E_V1_Epigenetics


title: Lesion A3-1, ROI 1483-0381

description: NanoString GeoMx


title: LOAD89 H2O-1


title: Lesion A3-1, ROI 1852-1009

description: NanoString GeoMx


title: Lesion A3-1, ROI 1883-0999

description: NanoString GeoMx


title: LOAD60 3TC-3


title: Lesion A3-1, ROI 1916-0987

description: NanoString GeoMx


title: LOAD60 3TC-2


title: P085_3D1A_V2_Epigenetics


title: P084_1E1C_V2_Epigenetics


title: Lesion A3-1, ROI 2012-0957

description: NanoString GeoMx


title: Lesion A3-1, ROI 1978-0965

description: NanoString GeoMx


title: Lesion A3-1, ROI 1946-0975

description: NanoString GeoMx


title: P082_6G1E_V2_Epigenetics


title: LOAD60 3TC-1


title: P082_8N0H_V1_Epigenetics


title: Lesion A3-1, ROI 1504-0355

description: NanoString GeoMx


title: Lesion A3-1, ROI 1546-0307

description: NanoString GeoMx


title: P090_6B2G_V1_Epigenetics


title: Lesion A2-1, ROI 3183-1417

description: NanoString GeoMx


title: LOAD70 3TC-3


title: Lesion A2-1, ROI 3329-1493

description: NanoString GeoMx


title: Lesion A2-1, ROI 2922-0921

description: NanoString GeoMx


title: LOAD70 3TC-2


title: Lesion A2-1, ROI 2918-1283

description: NanoString GeoMx


title: LOAD70 3TC-1


title: P080_6F1A_V1_Epigenetics


title: P072_3N0D_V2_Epigenetics


title: Lesion A2-1, ROI 2772-1503

description: NanoString GeoMx


title: Lesion A2-1, ROI 2923-0873

description: NanoString GeoMx


title: Lesion A2-1, ROI 2912-1077

description: NanoString GeoMx


title: LOAD72 3TC-3


title: Lesion A2-1, ROI 3129-1277

description: NanoString GeoMx


title: P069_7D1K_V1_Epigenetics


title: Lesion A1-1, ROI 1201-0398

description: NanoString GeoMx


title: P059_6F3K_V1_Epigenetics


title: Lesion A2-1, ROI 2820-1863

description: NanoString GeoMx


title: LOAD72 3TC-2


title: Lesion A1-1, ROI 1106-0503

description: NanoString GeoMx


title: P081_7C3E_V1_Epigenetics


title: P054_2D1D_V1_Epigenetics


title: Lesion A1-1, ROI 1167-0540

description: NanoString GeoMx


title: LOAD72 3TC-1


title: Lesion A2-1, ROI 2915-1145

description: NanoString GeoMx


title: Lesion A1-1, ROI 1270-0313

description: NanoString GeoMx


title: Lesion A2-1, ROI 2918-1211

description: NanoString GeoMx


title: P047_6B2J_V1_Epigenetics


title: Lesion A1-2, ROI 0377-1486

description: NanoString GeoMx


title: LOAD89 3TC-2


title: Lesion A2-1, ROI 2914-1016

description: NanoString GeoMx


title: LOAD89 3TC-1


title: day30 HC83-1

description:
day30hc_463-1
thin gel time course all.gene_CPM

data_processing:
Basecalling: Illumina's bcl2fastq
Custom python demultiplexing
Alignment: STAR version 2.5.1a
Gene counts: Subread:featureCount 1.4.6-p5
Sequencing performance assessment: RSeQC 2.6.2
Assembly: hg38
Supplementary files format and content: TXT containing ensembl ID, entrezgene ID, gene name, type, source of name, transcript count, description, and CPM for each sample per gene.

value: HC


title: day30 HC83-2

description:
day30hc_463-2
thin gel time course all.gene_CPM


title: Lesion A1-1, ROI 0953-0458

description: NanoString GeoMx


title: Lesion A1-1, ROI 1324-0285

description: NanoString GeoMx


title: Lesion A1-2, ROI 0298-1490

description: NanoString GeoMx


title: day20 HC83-2

description:
day20hc_463-2
thin gel time course all.gene_CPM


title: Lesion A1-2, ROI 0337-1488

description: NanoString GeoMx


title: Lesion A1-1, ROI 1353-0260

description: NanoString GeoMx


title: day20 HC83-1

description:
day20hc_463-1
thin gel time course all.gene_CPM


title: No Template Control plate D

description: NanoString GeoMx


title: day10 HC83-2

description:
day10hc_463-2
thin gel time course all.gene_CPM


title: RNA_RUNX1_KO_2, OCL

city: Frankfurt

first: Simonida

last: Zehr

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

country: Germany

institute: Goethe University, Frankfurt am Main, Germany,

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides or Q15 in a window of 5 nucleotides and keeping only filtered reads longer than 15 nucleotides42 (Trimmomatic: a flexible trimmer for Illumina sequence data).
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104 or 109) with STAR 2.7.10a43 (STAR: ultrafast universal RNA-seq aligner). Aligned reads were filtered to remove: duplicates with Picard 2.25.5, or Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2, or featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes 44 (featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.1 or version 1.36.045 (Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2). Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585.
The Ensemble annotation was enriched with UniProt data46.
Assembly: hg38
Supplementary files format and content: .bw, normalized peaks per sample

source_name: Peripheral blood

growth_protocol: Differentiation of THP-1 to osteoclast-like cells was performed as previously described in Goettsch et al.57 with following modifications. 400,000 cells were resuspened in α-Minimum Essential Medium (α-MEM) (12571-063, Gibco/Lifetechnologies, USA), 10% heat-inactivated FCS, 1% P/S, and 30 ng/mL M-CSF (300-25, PeproTech, Thermo Fisher Scientific, Germany) for 2 days. Subsequently, cells were cultured for 26 d in differentiation medium (α-MEM, 10% FCS, 1% P/S, 30 ng/mL M-CSF, and 50 ng/mL RANKL (310-01, PeproTech, Thermo Fisher Scientific, Germany). Medium was changed every 3-4 d by centrifuging the non-adherent cells and reseeding to the cells attached to the bottom of the well.

extract_protocol:
Cells were washed in 50 µl cold PBS and centrifuged at 1200 rpm for 4 min. The cell pellet was resuspened in 50 µl of cold lysis buffer (48.5 µl of resuspension buffer (10 mM Tris-HCl pH 7.5 (15567-027, Thermo Fisher Scientific), 10 mM NaCl, 3 mM MgCl2), 0.5 µl 10% NP-40, 0.5 µl 10% Tween-20 (P1379, Sigma-Aldrich), and 0.25 µl 2% Digitonin (G9441, Promega)) and incubated for 3 min on ice. Wash buffer (990 µl of resuspension buffer, 10 µl 10% Tween-20) was added to the cell lysate and centrifuged at 1000 xg at 4°C for 5 min. The cell pellet was resuspened in transposition reaction mix (25 µl TD Buffer, 16.5 µl PBS, 0.5 µl 10% Tween-20, 0.25 µl 2% Digtonin, 2.5 µl Tn5, 5 µl H2O) and incubated at 1000 rpm at 37°C for 30 min. DNA was purified by using MinElute PCR Purification Kit (Qiagen), eluated in 20 µl elution buffer, and stored at -20 °C until sequencing.
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer). 0.3-1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio).
Sequencing was performed on the NextSeq2000 instrument (Illumina) using with 1x72bp single end setup.

value: Peripheral blood

value: Human leukemia monocyte

tag: differentiated cell_type

value: osteoclast-like cell

value: gRNA against RUNX1


title: day10 HC83-1

description:
day10hc_463-1
thin gel time course all.gene_CPM


title: RNA_SMANTIS_KO_1, OCL

value: gRNA against SMANTIS


title: RNA_RUNX1_KO_1, OCL


title: RNA_SMANTIS_KO_2, OCL


title: RNA_NTC_2, OCL

value: NTC


title: Streptococcus sample at 24 hours [2075_7344_33000_534_Mouse430A+2]

type: RNA

city: Durham

first: Nicholas

middle: G

last: O'Grady

state: NC

address: 2301 Erwin Rd

department: Department of Medicine, CRU

institute: Duke University

hyb_protocol: Samples were subsequently amplified and hybridized the samples onto Affymetrix murine 430A2.0 microarrays containing 22,690 probes.

scan_protocol: Probe intensities were detected using Axon GenePix 4000B Scanner (Molecular Devices).

data_processing: Image files were generated using Affymetrix GeneChip Command Console software. Data was normalized, robust multichip averaged and converted to an eset using the Affy R package.  Differentially expressed genes were discovered with the limma R package.  Public codebase, relevant to publication, can be found here: https://gitlab.oit.duke.edu/biocat/murine-pneumonia-project

label: biotin

organism: Mus musculus

source_name: RNA from murine whole blood

label_protocol: Samples that met the following pre-determined quality checks: 260/280 ratio > 1.8, 260/230 ratio > 1.8, and RNA integrity number >7  were amplified and biotin-labeled using MessageAmp Premier RNA Amplification kit (Ambion)

growth_protocol: Mice were housed in a clean murine housing facility and fed standard chow

extract_protocol: Total RNA was isolated using the Mouse Ribopure Isolation Kit followed by globin mRNA depletion using the GLOBINclear Kit (Ambion).  .

treatment_protocol: Mice were intranasally inoculated with either 50ul S. pneumoniae culture at a dose of 8.7 x 105 CFU, 50 ul M. pneumoniae culture at a dose of 1 x 105 CFU, or 50 ul of PBS as a control for bacterial exposured. Influenza pneumonia was induced using 40 ul of PBS or 40 ul of PBS containing 80 PFU of live influenza virus administered intranasally

tag: strain

value: Female

tag: agent

value: Streptococcus

tag: timepoint in hours

tag: agent_time combined


title: Streptococcus sample at 24 hours [2075_7344_33033_535_Mouse430A+2]


title: day0 HC83-2

description:
day0hc_463-2
thin gel time course all.gene_CPM

source_name: Fibroblasts

value: Fibroblasts


title: Lesion A1-1, ROI 1404-0210

description: NanoString GeoMx


title: Streptococcus sample at 24 hours [2075_7344_33034_539_Mouse430A+2]


title: RNA_NTC_1, OCL


title: Streptococcus sample at 24 hours [2075_7344_32999_533_Mouse430A+2]


title: Lesion A1-1, ROI 1378-0234

description: NanoString GeoMx


title: day0 HC83-1

description:
day0hc_463-1
thin gel time course all.gene_CPM


title: Lesion A1-1, ROI 0987-0477

description: NanoString GeoMx


title: NTC_d21_1

data_processing:
Reads were aligned versus Ensembl human genome version hg38 (Ensembl release 104 or 109) with STAR 2.7.10a43 (STAR: ultrafast universal RNA-seq aligner). Aligned reads were filtered to remove: duplicates with Picard 2.25.5, or Picard 3.0.0 (Picard: A set of tools (in Java) for working with next generation sequencing data in the BAM format), multi-mapping, ribosomal, or mitochondrial reads.
Gene counts were established with featureCounts 2.0.2, or featureCounts 2.0.4 by aggregating reads overlapping exons on the correct strand excluding those overlapping multiple genes 44 (featureCounts: an efficient general purpose program for assigning sequence reads to genomic features).
The raw count matrix was normalized with DESeq2 version 1.30.1 or version 1.36.045 (Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2). Contrasts were created with DESeq2 based on the raw count matrix. Genes were classified as significantly differentially expressed at average count > 5, multiple testing adjusted p-value < 0.05, and -0.585 < log2FC > 0.585.
The Ensemble annotation was enriched with UniProt data46.
Assembly: hg38
Supplementary files format and content: .bw, normalized peaks per sample

source_name: iPSC

growth_protocol: The differentiation of inducible peripheral stem cells (iPSC) into monocytes was performed by following the instructions of the STEMdiff Monocyte Kit purchased from STEMCELL Technologies (#05320, STEMdiffTM Monocyte Kit, STEMCELL Technologies). Briefly, iPSC (20 aggregates / cm2) were seeded on matrigel coated six well plates. After adhesion of the cells, medium A was added and cells were incubated for 2 days (mesodermal phase). Medium was changed at the third day to medium B to generate hematopoietic progenitor cells. During the following three days, media was diluted with fresh media by removing used and adding fresh media. On day 7, monocyte differentiation was initiated by changing media to monocyte differentiation medium and incubated for 3 d. Differentiated monocytes could be harvested from the supernatant from day 14 on. Monocytes were harvested at day 15 and further differentiated macrophage like cells were harvested after 21 d.

extract_protocol:
Cells were washed in 50 µl cold PBS and centrifuged at 1200 rpm for 4 min. The cell pellet was resuspened in 50 µl of cold lysis buffer (48.5 µl of resuspension buffer (10 mM Tris-HCl pH 7.5 (15567-027, Thermo Fisher Scientific), 10 mM NaCl, 3 mM MgCl2), 0.5 µl 10% NP-40, 0.5 µl 10% Tween-20 (P1379, Sigma-Aldrich), and 0.25 µl 2% Digitonin (G9441, Promega)) and incubated for 3 min on ice.  Wash buffer (990 µl of resuspension buffer, 10 µl 10% Tween-20) was added to the cell lysate and centrifuged at 1000 xg at 4°C for 5 min. The cell pellet was resuspened in transposition reaction mix (25 µl TD Buffer, 16.5 µl PBS, 0.5 µl 10% Tween-20, 0.25 µl 2% Digtonin, 2.5 µl Tn5, 5 µl H2O) and incubated at 1000 rpm at 37°C for 30 min. DNA was purified by using MinElute PCR Purification Kit (Qiagen), eluated in 20 µl elution buffer, and stored at -20 °C until sequencing.
RNA and library preparation integrity were verified with LabChip Gx Touch 24 (Perkin Elmer). 0.3-1µg of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio).
Sequencing was performed on the NextSeq2000 instrument (Illumina) using with 1x72bp single end setup.

value: iPSC

value: iPSC-derived macrophage


title: HC36-3

description:
yg4ct-sp 5838-3
Young HC spheroids all.gene_CPM

value: spheroids

value: neurons


title: NTC_d21_2


title: NTC_d15_1

value: iPSC-derived monocyte


title: HC36-2

description:
yg4ct-sp 5838-2
Young HC spheroids all.gene_CPM


title: NTC_d15_2


title: RNA_RUNX1_KO_3, Mono


title: NTC_d0_1

value: Human induced pluripotent stem cell


title: NTC_d0_2


title: control sample at 72 hours [2075_7344_33102_678_Mouse430A+2]

value: control


title: Streptococcus sample at 24 hours [2075_7344_32997_530_Mouse430A+2]


title: control sample at 72 hours [2075_7344_33100_676_Mouse430A+2]


title: HC36-1

description:
yg4ct-sp 5838-1
Young HC spheroids all.gene_CPM

value: HC


title: RNA_RUNX1_KO_1, Mono

value: Peripheral blood


title: Streptococcus sample at 24 hours [2075_7344_32998_531_Mouse430A+2]


title: RNA_RUNX1_KO_2, Mono

value: Human leukemia monocyte


title: RNA_SMANTIS_KO_3, Mono


title: HC44-3

description:
yg3ct-sp 4060-3
Young HC spheroids all.gene_CPM


title: RNA_SMANTIS_KO_2, Mono


title: RNA_SMANTIS_KO_1, Mono


title: HC44-2

description:
yg3ct-sp 4060-2
Young HC spheroids all.gene_CPM


title: RNA_NTC_3, Mono


title: HC44-1

description:
yg3ct-sp 4060-1
Young HC spheroids all.gene_CPM


title: RNA_NTC_2, Mono


title: control sample at 72 hours [2075_7344_33101_677_Mouse430A+2]


title: RNA_NTC_1, Mono


title: HC61-3

description:
yg2ct-sp 8260-3
Young HC spheroids all.gene_CPM


title: CnR_RUNX1_KO_3

library_source: genomic

data_processing:
Paired end CUT&RUN sequencing reads were aligned to the GRCh38 primary annotation genome build using Bowtie2 (v2.4.5)38 with the parameter –very-sensitive. Mates were fixed and duplicate reads removed using samtools fixmate and samtools markdup –r, respectively (v1.1.0)39. Reads mapping to blacklisted regions of the GRCh38 genome were removed using bedtools intersect –v (v2.27.1) 50, with the blacklisted regions taken from ENCODE51. Peaks were called per replicate using MACS3 callpeak, and differential binding analysis was performed using MACS3 bdgdiff to compare read pile-up in peak regions between conditions using a log-likelihood ratio (MACS v3.0.0)41. The relative sequencing depths of each condition are also taken into account in this test. The genomic locations of differential CUT&RUN peaks were then computed using HOMER annotatePeaks.pl (v4.1.1)52, which returns the positions of peak regions relative to genes annotated in the hg38 genome. Normalized coverage tracks for visualization in a genome browser were generated from the normalized bedGraph output of MACS3, and were converted to bigWig using bedGraphToBigWig from the kentUtils collection of tools from UCSC.
Assembly: hg38
Supplementary files format and content: .bw, normalized peaks per sample
Library strategy: CUT&RUN

extract_protocol:
DNA binding sites of RUNX1 were determined by using the CUT&RUN method, originally established by Skene and Henikoff in 201749, as described in the EpiCypher CUT&RUN Protocol v2.0 and in Boos et al. 35 with modifications for cell type and antibody. Here, 500,000 NTC, SMANTIS KO, and RUNX1 KO THP-1 were used and first washed with wash buffer (20 mM HEPES pH 7.9, 150 mM NaCl, 500 nM spermidine 1X Roche Protein Inhibitor Cocktail) at RT. Cells were then resuspended in wash buffer and immobilized on magnetic beads. Therefore, cells were incubated with 10 µl BioMag®Plus Concanavalin A (ConA) beads (Polysciences, 86057-3) for 10 min at RT. Beads were washed once on a magnetic rack in 100 µl antibody buffer (wash buffer, 0.25% Digitonin, and 2 mM EDTA) and 1 µl RUNX1 antibody (ab240639, Abcam). After an over-night incubation of the beads with antibody with gentle shaking at 4°C, the beads were washed twice with 200 µl 0.25% Digitonin wash buffer followed by resuspension and incubation in Digitonin wash buffer containing 2 µl CUTANA™ pAG-MNase (15-1016, EpiCypher) on ice for 30 min. After washing the samples twice, the samples were resuspended in 100 µl Digitonin wash buffer with addition of 2 µl CalCl2 (final concentration of 100 mM) and incubated for 2 h at 4°C with gentle shaking. To stop the enzymatic reaction, samples were incubated in 33 µl stop buffer (340 mM NaCL, 20 mM EDTA, 4 mM EGTA, 0.25 % Digitonin, 100 µg/mL RNase A, 50 µg/mL Glycoblue) for 10 min at 37°C. Samples were then placed on a magnetic rack and supernatant containing the CUT&RUN-enriched DNA was collected in a fresh 1.5 mL tube. DNA purification was performed by using 5X volume of binding buffer (20 mM HEPES pH 7.9, 20 mM KCL, 1 mM CaCl2, 1 mM MnCl2). The pH was adjusted with sodium acetate before transferring the sample into a purification column (58002, ActiveMotif). Samples were then centrifuged at 11,000 xg for 30 sec. The column was washed with 750 µl wash buffer and dried by centrifugation for 2 min. The DNA was eluted in 25 µl elution buffer and concentration was measured with Qubit 3.0 Fluormeter (Life Technologies).
For library prepration, DNA fragments were cleaned up by 1xSPRI bead cleanup and used as input for SMARTer ThruPLEX DNA-seq Kit (Takara Bio) following the manufacturer protocol with exception of individual library cleanup after final PCR.
Libraries were mixed in equimolar ratios and sequenced on NextSeq2000 platform using P3 flowcell.


title: control sample at 72 hours [2075_7344_33062_673_Mouse430A+2]


title: control sample at 72 hours [2075_7344_33060_671_Mouse430A+2]


title: control sample at 72 hours [2075_7344_33099_674_Mouse430A+2]


title: CnR_RUNX1_KO_2


title: control sample at 72 hours [2075_7344_33061_672_Mouse430A+2]


title: control sample at 72 hours [2075_7344_33059_670_Mouse430A+2]


title: HC61-2

description:
yg2ct-sp 8260-2
Young HC spheroids all.gene_CPM


title: control sample at 72 hours [2075_7344_33025_669_Mouse430A+2]


title: CnR_RUNX1_KO_1


title: CnR_SMANTIS_KO_3


title: HC61-1

description:
yg2ct-sp 8260-1
Young HC spheroids all.gene_CPM


title: CnR_SMANTIS_KO_1


title: CnR_SMANTIS_KO_2


title: HC52-3

description:
yg1ct-sp 4453-3
Young HC spheroids all.gene_CPM


title: control sample at 72 hours [2075_7344_33024_668_Mouse430A+2]


title: HC52-2

description:
yg1ct-sp 4453-2
Young HC spheroids all.gene_CPM


title: CnR_NTC_2


title: CnR_NTC_1


title: ATAC_RUNX1_KO_3

data_processing:
ATAC-seq reads were aligned to the GRCh38 primary assembly genome using Bowtie2 (v2.4.5 38 with the parameter very-sensitive.
Duplicate reads were removed using samtools rmdup (v1.1.0)39, and normalized genome browser coverage tracks were produced from the aligned reads using bamCoverage40, normalized by reads per kilobase per million mapped reads (RPKM), and using an effective genome size of 2,864,785,220.
ATAC-seq peaks were called per replicate using MACS3 (v3.0.0)41 with the parameter –scale-to-small.
Bigwig files were used to visualize peaks in Integrative Genomics Viewer (IGV) (Version 1.16.2).
Assembly: hg38
Supplementary files format and content: .bw, normalized peaks per sample

extract_protocol:
50,000 THP-1 were used for the ATAC library preparation performed with the Illumina Tagment DNA Enzyme and Buffer Kit (20034198, Illumina). Cells were washed in 50 µl cold PBS and centrifuged at 1200 rpm for 4 min. The cell pellet was resuspened in 50 µl of cold lysis buffer (48.5 µl of resuspension buffer (10 mM Tris-HCl pH 7.5 (15567-027, Thermo Fisher Scientific), 10 mM NaCl, 3 mM MgCl2), 0.5 µl 10% NP-40, 0.5 µl 10% Tween-20 (P1379, Sigma-Aldrich), and 0.25 µl 2% Digitonin (G9441, Promega)) and incubated for 3 min on ice. Wash buffer (990 µl of resuspension buffer, 10 µl 10% Tween-20) was added to the cell lysate and centrifuged at 1000 xg at 4°C for 5 min. The cell pellet was resuspened in transposition reaction mix (25 µl TD Buffer, 16.5 µl PBS, 0.5 µl 10% Tween-20, 0.25 µl 2% Digtonin, 2.5 µl Tn5, 5 µl H2O) and incubated at 1000 rpm at 37°C for 30 min. DNA was purified by using MinElute PCR Purification Kit (Qiagen), eluated in 20 µl elution buffer, and stored at -20 °C until sequencing.
The amplification of the library together with indexing primers was performed as described by Buenrostro et al. 2013. Libraries were mixed in equimolar ratios and sequenced on NextSeq2000 platform using a P3 flowcell
ATAC-seq was performed based on the protocol from Buenrostro et al. 2013 and modified by Ackermann et al. 2016.


title: HC52-1

description:
yg1ct-sp 4453-1
Young HC spheroids all.gene_CPM


title: control sample at 72 hours [2075_7344_33023_666_Mouse430A+2]


title: ATAC_RUNX1_KO_1


title: control sample at 72 hours [2075_7344_33022_665_Mouse430A+2]


title: control sample at 48 hours [2075_7344_33086_526_Mouse430A+2]


title: ATAC_SMANTIS_KO_3


title: HC68-3

description:
g5hc14251_3
LOAD vs Old HC all.gene_CPM


title: ATAC_RUNX1_KO_2


title: ATAC_SMANTIS_KO_2


title: HC68-2

description:
g5hc14251_2
LOAD vs Old HC all.gene_CPM


title: ATAC_NTC_3


title: ATAC_SMANTIS_KO_1


title: HC68-1

description:
g5hc14251_1
LOAD vs Old HC all.gene_CPM


title: ATAC_NTC_2


title: CnR_NTC_3


title: ATAC_NTC_1


title: HelaS3, 0percent mitotic, 100percent interphase, H3K9ac, rep3

city: La Jolla

first: Alon

last: Goren

state: CA

address: 9375 Gilman Dr

department: Department of Medicine

institute: University of California San Diego

data_processing:
Samples were sequenced on Illumina NextSeq 550, samples were demultiplexed with Illumina bcl2fastq.
Adapters were removed with Trimmomatic, reads with Phred score <26 over a 4bp window were truncated.
Reads were aligned to a concatenated genome containing hg38 + sacCer3 + dm6, alignment files were separated by species. Duplicate reads were removed with samtools markdup.
HOMER tag directories were made for each species, where by default read counts were filtered for primary alignments with MAPQ > 10.
Bigwig files were created with HOMER makeBigWig.pl from tag directories.
Assembly: hg38
Supplementary files format and content: Read-normalized BigWig files for hg38 genome

growth_protocol: HeLa-S3 cells were grown in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 1x penicillin-streptomycin, L-glutamine, and 110mg/L sodium pyruvate. Cells were incubated at 37°C and 5% CO2.

extract_protocol:
HeLa-S3 cells were double crosslinked on plates with 2 mM DSG for 30 minutes and 1% formaldehyde for 10 minutes. Crosslinking was quenched with 1/20th volume of 2.625 M glycine and 0.5% BSA, then cells were washed 3 times with 0.5% BSA/PBS + Protease inhibitor, spinning down at 1200g for 5 minutes at 4C. Washed pellets were snap frozen then stored in -80C. Cells were lysed with LB3 lysis buffer + PIC, then chromatin was sheared on the PIXUL sonicator for 108 minutes. S2 cells were crosslinked in 1% formaldehyde for 10 minutes at room temperature, then quenched with glycine and 0.5% BSA, lysed in LB3, and sonicated on the PIXUL for 60 minutes. Yeast cultures in log phase were crosslinked with 0.86% formaldehyde for 30 minutes. The yeast cell wall was digested with Zymolase at 37°C for 60 minutes, then cells were washed 3x in PBS + PI, then resuspended in NP-S buffer + PI. Yeast were sonicated on the PIXUL for 120 minutes. All PIXUL sonication was done with settings Pulse (N) = 50, PRF (kHz) = 1.00, Burst Rate (Hz) = 20, only Process Time was varied. Sheared chromatin from each species were combined then inputs were taken before immunoprecipitation for each condition, to assess the relative ratios of chromatin.
To each IP, 10uL of Protein A beads and 4uL of H3K9ac, 1% Triton X-100 and 1x PIC were added. Samples were incubated overnight on rotator at 4C. IP Washes were performed as follows: 3x with 180uL of WBI, 3x with 180uL of WBIII, and 2x with 185uL TET, then eluted in 25uL of cold TT Buffer. Inputs were incubated with Speedbeads, in 12% PEG and 1M NaCl for 10 minutes at room temperature, then washed twice with 80% EtOH, and eluted in 25uL cold TT Buffer. From inputs and IPs, libraries were prepared with the NEB Ultra II Library Prep Kit. Barcoded adapters were from BioO NEXTflex ChIP-seq Adapters. Libraries were decrosslinked and cleaned with Speedbeads, then PCR amplified with Solexa 1GA and 1GB primers, and size selected with a final Speedbead cleanup. Library size was estimated with agarose gel, concentrations measured with Qubit HS DNA kit.

treatment_protocol: Cells were synchronized in G1/S by adding 2 mM thymidine for 16 hr, washed with PBS, released for 3 hr in fresh medium, and pro-metaphase arrested with 10uM S-trityl-L-cysteine (STC) for 12 hr then harvested. Treated cells are treated with DMSO or 150nM TSA 9 hours before harvesting.

tag: spike-in species

value: D. melanogaster, S. cerevisiae

value: human cerival cancer

tag: chip antibody

value: CST H3K9ac (C5B11)


title: LOAD70-2

description:
g5ad633_2
LOAD vs Old HC all.gene_CPM

value: LOAD


title: HelaS3, 0percent mitotic, 100percent interphase, H3K9ac, rep1


title: control sample at 48 hours [2075_7344_33085_524_Mouse430A+2]

value: Female


title: control sample at 48 hours [2075_7344_33044_523_Mouse430A+2]


title: control sample at 48 hours [2075_7344_33087_529_Mouse430A+2]


title: HelaS3, 0percent mitotic, 100percent interphase, input


title: HelaS3, 0percent mitotic, 100percent interphase, H3K9ac, rep2


title: HelaS3, 5percent mitotic, 95percent interphase, H3K9ac, rep3


title: LOAD70-1

description:
g5ad633_1
LOAD vs Old HC all.gene_CPM


title: HC83-3

description:
g4hc463_3
LOAD vs Old HC all.gene_CPM


title: control sample at 48 hours [2075_7344_33042_520_Mouse430A+2]


title: HelaS3, 5percent mitotic, 95percent interphase, input


title: HelaS3, 25percent mitotic, 75percent interphase, H3K9ac, rep3


title: LOAD70-3

description:
g5ad633_3
LOAD vs Old HC all.gene_CPM


title: HelaS3, 5percent mitotic, 95percent interphase, H3K9ac, rep2


title: HelaS3, 5percent mitotic, 95percent interphase, H3K9ac, rep1


title: LOAD87-3

description:
g4ad623_3
LOAD vs Old HC all.gene_CPM


title: control sample at 48 hours [2075_7344_33008_518_Mouse430A+2]


title: HC83-2

description:
g4hc463_2
LOAD vs Old HC all.gene_CPM


title: HelaS3, 50percent mitotic, 50percent interphase, H3K9ac, rep3


title: LOAD87-1

description:
g4ad623_1
LOAD vs Old HC all.gene_CPM


title: control sample at 48 hours [2075_7344_33043_522_Mouse430A+2]


title: HelaS3, 50percent mitotic, 50percent interphase, H3K9ac, rep2


title: control sample at 48 hours [2075_7344_33041_519_Mouse430A+2]


title: HelaS3, 25percent mitotic, 75percent interphase, H3K9ac, rep1


title: HelaS3, 25percent mitotic, 75percent interphase, input


title: HelaS3, 50percent mitotic, 50percent interphase, input


title: HelaS3, 50percent mitotic, 50percent interphase, H3K9ac, rep1


title: LOAD87-2

description:
g4ad623_2
LOAD vs Old HC all.gene_CPM


title: control sample at 48 hours [2075_7344_33005_515_Mouse430A+2]


title: HC78-3

description:
g3hc11246_3
LOAD vs Old HC all.gene_CPM


title: control sample at 24 hours [2075_7344_33078_513_Mouse430A+2]


title: control sample at 24 hours [2075_7344_33079_514_Mouse430A+2]


title: HelaS3, 75percent mitotic, 25percent interphase, H3K9ac, rep3


title: HC78-1

description:
g3hc11246_1
LOAD vs Old HC all.gene_CPM


title: HelaS3, 75percent mitotic, 25percent interphase, H3K9ac, rep2


title: HelaS3, 25percent mitotic, 75percent interphase, H3K9ac, rep2


title: HelaS3, 75percent mitotic, 25percent interphase, H3K9ac, rep1


title: HelaS3, 100percent mitotic, 0percent interphase, H3K9ac, rep2


title: HelaS3, 100percent mitotic, 0percent interphase, H3K9ac, rep3


title: control sample at 48 hours [2075_7344_33007_517_Mouse430A+2]


title: HelaS3, 75percent mitotic, 25percent interphase, input


title: control sample at 24 hours [2075_7344_33077_512_Mouse430A+2]


title: control sample at 48 hours [2075_7344_33006_516_Mouse430A+2]


title: control sample at 24 hours [2075_7344_33076_511_Mouse430A+2]


title: HelaS3, 100percent mitotic, 0percent interphase, input


title: HelaS3, 100percent mitotic, 0percent interphase, H3K9ac, rep1


title: LOAD78-2

description:
g3ad5810_2
LOAD vs Old HC all.gene_CPM


title: LOAD78-3

description:
g3ad5810_3
LOAD vs Old HC all.gene_CPM


title: HelaS3, mitotic, TSA, 2.5x yeast spike-in, input

value: 150nM TSA


title: LOAD78-1

description:
g3ad5810_1
LOAD vs Old HC all.gene_CPM


title: control sample at 24 hours [2075_7344_33031_509_Mouse430A+2]


title: HelaS3, mitotic, TSA, 2.5x yeast spike-in, H3K9ac


title: HelaS3, mitotic, TSA, 0.25x yeast spike-in, input


title: HC78-2

description:
g3hc11246_2
LOAD vs Old HC all.gene_CPM


title: control sample at 24 hours [2075_7344_33032_510_Mouse430A+2]


title: HC66-3

description:
g2hc13246_3
LOAD vs Old HC all.gene_CPM


title: HelaS3, mitotic, TSA, 0.025x yeast spike-in, H3K9ac


title: HelaS3, mitotic, TSA, 0.025x yeast spike-in, input


title: control sample at 24 hours [2075_7344_33028_505_Mouse430A+2]


title: HelaS3, mitotic, TSA, 0.25x yeast spike-in, H3K9ac


title: HelaS3, mitotic, TSA, 0.0025x yeast spike-in, input


title: HelaS3, mitotic, TSA, 0.00025x yeast spike-in, input


title: HelaS3, mitotic, DMSO, 2.5x yeast spike-in, H3K9ac

value: DMSO


title: LOAD72-3

description:
g2ad453_3
LOAD vs Old HC all.gene_CPM


title: HelaS3, mitotic, TSA, 0.0025x yeast spike-in, H3K9ac


title: HelaS3, mitotic, DMSO, 2.5x yeast spike-in, input


title: LOAD72-2

description:
g2ad453_2
LOAD vs Old HC all.gene_CPM


title: HC66-2

description:
g2hc13246_2
LOAD vs Old HC all.gene_CPM


title: HelaS3, mitotic, DMSO, 0.25x yeast spike-in, H3K9ac


title: HC89-2

description:
g1hc634_2
LOAD vs Old HC all.gene_CPM


title: HelaS3, mitotic, DMSO, 0.25x yeast spike-in, input


title: HC89-3

description:
g1hc634_3
LOAD vs Old HC all.gene_CPM


title: HelaS3, mitotic, DMSO, 0.0025x yeast spike-in, input


title: control sample at 24 hours [2075_7344_32995_503_Mouse430A+2]


title: control sample at 24 hours [2075_7344_33030_508_Mouse430A+2]


title: control sample at 24 hours [2075_7344_33029_507_Mouse430A+2]


title: control sample at 24 hours [2075_7344_32996_504_Mouse430A+2]


title: control sample at 24 hours [2075_7344_32993_501_Mouse430A+2]


title: HelaS3, mitotic, TSA, 0.00025x yeast spike-in, H3K9ac


title: control sample at 24 hours [2075_7344_32994_502_Mouse430A+2]


title: HelaS3, mitotic, DMSO, 0.025x yeast spike-in, input


title: HelaS3, mitotic, DMSO, 0.0025x yeast spike-in, H3K9ac


title: HelaS3, mitotic, DMSO, 0.00025x yeast spike-in, input


title: LOAD89-3

description:
g1ad552_3
LOAD vs Old HC all.gene_CPM


title: PMAi+GSK484_rep3

city: Huddinge

first: Peter

last: Svensson

state: Stockholm

address: Hälsovägen 9

department: Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

data_processing:
Paired fastq-files were aligned to the hg19 genome using Bowtie2, flags --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 to generate Sam-files.
Sam-files were converted to Bam-files using Samtools (view -S-b -o, and sort).
Bam-files from replicates were normalized to effective genome size and merged using Picard MergeSamFiles 2.18.2.1 in Galaxy.
Bigwig-files produced (binLength: 50) by Deeptools Bam_coverage 3.5.1.0.0 in Galaxy.
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: Cut&Tag

source_name: cell line

growth_protocol: J-lat 5A8 were cultured in cytokine-free media (RPMI 1640 medium (Hyclone, Cat# SH30096_01), 10% FBS (Life Technologies, Cat# 10270–106), 1% Glutamax (Life Technologies, Cat# 35050), 1% Penicillin-streptomycin (Life Technologies, Cat# 15140–122)).

extract_protocol:
Version 3 CUT&Tag protocol (Kaya-Okur and Henikoff, 2020) was used as described.
A 1/400 dilution of Anti-Histone H3 (citrulline R2 + R8 + R17) antibody (Abcam, Cat# ab5103) was used per sample. Thirteen cycles of PCR were used for amplifying the libraries. Reads were trimmed, then, mapped onto the GB38 human reference genome with Bowtie2.

treatment_protocol: Cells were treated for 24 h with PMA/ionomycin (or DMSO) and GSK484 (or DMSO) before harvesting.

value: cell line

value: Jurkat, 5A8

value: human lymphoblastoid cells

tag: cut&tag antibody

value: Anti-Histone H3 citrulline R2 + R8 + R17 (Abcam, Cat# ab5103)

value: HIV-1 (R7 E- GFP)

value: PMA/ionomycin + GSK484


title: H1N1 sample at 168 hours [2075_7344_33117_Influenza30g-_Mouse430A+2]

value: Male


title: PMAi_rep3

value: PMAi/ionomycin


title: DMSO_rep3


title: HC89-1

description:
g1hc634_1
LOAD vs Old HC all.gene_CPM

value: spheroids

value: neurons

value: HC


title: control sample at 24 hours [2075_7344_32992_500_Mouse430A+2]

value: control


title: LOAD89-1

description:
g1ad552_1
LOAD vs Old HC all.gene_CPM


title: H1N1 sample at 168 hours [2075_7344_33114_Influenza27g-_Mouse430A+2]


title: LOAD72-1

description:
g2ad453_1
LOAD vs Old HC all.gene_CPM


title: DMSO_rep2


title: HelaS3, mitotic, DMSO, 0.025x yeast spike-in, H3K9ac

value: D. melanogaster, S. cerevisiae

value: human cerival cancer

value: CST H3K9ac (C5B11)


title: H1N1 sample at 168 hours [2075_7344_33116_Influenza29g-_Mouse430A+2]


title: LOAD89-2

description:
g1ad552_2
LOAD vs Old HC all.gene_CPM

value: LOAD


title: PMAi+GSK484_rep2


title: H1N1 sample at 168 hours [2075_7344_33115_Influenza28g-_Mouse430A+2]


title: DMSO_rep1

value: DMSO


title: H1N1 sample at 168 hours [2075_7344_33073_Influenza23g-_Mouse430A+2]


title: human_EoE_posi_CD45p_2

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

country: Japan

institute: Chiba univercity

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation for scRNA-seq were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10, hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: esophagitis

extract_protocol:
A FACSAria III cell sorter (BD) was used for live cell sorting.
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 according to manufacturer’s protocol (10X Genomics). The generated scRNA-seq libraries were sequenced using a 128 cycle (paired-end reads) with a NovaSeq 6000 (Illumina).

value: esophagitis

tag: disease

value: EoE

value: CD45+ cell

value: Wild-type


title: human_Control_esophagitis_CD45p_2

description: 10x Genomics

value: Control


title: GSK484_rep2

value: cell line

value: Jurkat, 5A8

value: human lymphoblastoid cells

value: Anti-Histone H3 citrulline R2 + R8 + R17 (Abcam, Cat# ab5103)

value: HIV-1 (R7 E- GFP)


title: H1N1 sample at 168 hours [2075_7344_33113_Influenza26g-_Mouse430A+2]

value: Male


title: P016

city: Stockholm

first: Kristina

last: Broliden

state: Solna

address: Visionsgatan 4, J7:20

department: Dept. of Medicine Solna

data_processing:
Base calling and demultiplexing of the Bcl2 files was performed using the bcl2fastq program.
Indexing of the human reference genome (hg38/GRCh38) was done using STAR (Spliced Transcripts Alignment to a Reference).
The resulting fastq files were aligned and uniquely mapped reads were counted and mapped to annotated exons using data from UCSC (University of Santa Cruz) genome browser (http://genome.ucsc.edu/) as reference.
Read counts were normalized to counts per million (CPM) and log2 scale. Genes with an absolute read count < 5 in at least three samples were removed
Assembly: hg38/GRCh38
Supplementary files format and content: Comma seperated files with raw gene counts of all samples
Supplementary files format and content: Comma seperated files with normalized gene values of seleted (n=108) samples
Supplementary files format and content: Comma seperated file with metadata

molecule: polyA RNA

source_name: Ectocervix

extract_protocol:
The ectocervical biopsies that were stored in RNA-later were thawed and RNA was isolated and purified using AllPrep DNA/RNA Mini Kit (QIAGEN, Hilden, Germany) and the QIAcube Connect (QIAGEN). Poly-A containing mRNA transcripts were purified, fragmented and converted to cDNA. The cDNA fragments were amplified, barcoded and sequenced using NextSeq 550 (Illumina, San Diego, CA, USA). All ectocervical biopsies displayed good quality of isolated RNA and generated >10 million reads each.
We used the low sample (LS) library prep workflow from the TruSeq Stranded mRNA Reference Guide (1000000040498 v00). The samples were split into six seperate runs and sequenced with single end 75 bp reads

value: Ectocervix

tag: luminal gr

tag: tissue gr

tag: subjectid

value: female


title: PMAi+GSK484_rep1

tag: tissue

tag: cell line

tag: cell type

value: PMA/ionomycin + GSK484


title: H1N1 sample at 168 hours [2075_7344_33075_Influenza25g-_Mouse430A+2]

tag: Sex


title: PMAi_rep2

tag: genotype

tag: treatment

value: PMAi/ionomycin


title: Muscle injury replicate 3

city: Clayton

first: Mikaël

last: Martino

state: Victoria

address: 15 Innovation Walk

department: Australian Regenerative Medicine Institute

country: Australia

institute: Monash University

description:
Processed_Endo_injured_BMS_and_healthy_Spleen_data.csv
MU_Tregs_4_S7

data_processing:
Raw fastq files were analysed using the RNAsik pipeline (Tsyganov, K., et al., 2018, Journal of Open Source Software) using STAR aligner (Dobin, A., et al., 2013, Bioinformatics) with Mus musculus GRCm38.
Reads were quantified using featureCounts (Liao, Y., et al., 2014, Bioinformatics) producing the raw genes count matrix and various quality control metrics.
Raw counts (forward stranded reads) were then analysed with Degust web tool (Powell, D.R., et al., 2019, Zenodo) which performs normalisation using trimmed mean of M values (TMM) (Robinson, M.D. and Oshlack, A., 2010, Genome Biol) and differential gene expression analysis using limma/voom (Law, C.W., et al., 2014, Genome Biol)
Samples were batched corrected to account for variation between two different sequencing facilities across replicates. This was done within Degust by adding a covariate to the linear model for each sequencing batch which reduced the noise and improved the power of the test.
Assembly: GRCm38
Supplementary files format and content: csv, gene counts, rows represent genes and each column represents different information, starting from the chromosome, gene name, biotype, followed by read counts corresponding to the individual samples.

source_name: muscle

extract_protocol:
RNA was extracted using the RNeasy Plus Micro Kit (Qiagen, #74034) according to the manufacturer’s instructions
Libraries were prepared with the Tecan/Nugen Ovation Solo Library prep kit, starting with 1 ng of input total RNA

value: muscle

value: Regulatory T cells

tag: strain

value: male

tag: age

value: 10 weeks

value: volumetric muscle loss defect

tag: time

value: day 7 post-injury


title: PMAi_rep1


title: human_Control_esophagitis_CD45p_1

description: 10x Genomics

value: esophagitis

value: Control

value: CD45+ cell

value: Wild-type


title: human_Control_esophagitis_posi_CD45

description: 10x Genomics

value: CD45- cell


title: Muscle injury replicate 2

description:
Processed_Endo_injured_BMS_and_healthy_Spleen_data.csv
MU_Tregs_3_S6


title: H1N1 sample at 168 hours [2075_7344_33074_Influenza24g-_Mouse430A+2]

tag: agent

tag: timepoint in hours

tag: agent_time combined


title: P118


title: combo biol rep 3

city: New York

first: Ilya

last: Shamovsky

state: New York

address: 450 E 29th Street

department: Biochemistry and Molecular Pharmacology

institute: NYU School of Medicine

data_processing:
Adapter and low quality sequences were removed using TrimmomaticPE.
Reads were aligned to GRCm38 reference genome using hisat2.
Reads overlapping annotated genes were counted using htseq-count.
DGE analysis was performed using DESeq2.
Assembly: GRCm38
Supplementary files format and content: comma-delimited raw counts file

source_name: orthotopic tumor

growth_protocol: 4T1 were grown in DMEM with 10% FBS

extract_protocol:
TRIZOL
500ngRNA used; NEBNext® Ultra DNA Library Prep

treatment_protocol: orthotopic mammary indcution and treatment with vehicle/MBQ/PAX/combo

value: orthotopic tumor

value: Mammary gland/Mimics human breast cancer; Stage IV

value: WT

value: MBQ+PAX combo as above


title: Control_3

city: Yinchuan

first: Xuexia

last: Tong

address: No. 804 Shenglijie

country: China

institute: General Hospital of Ningxia Medical University

description: Control

data_processing:
CLC Genomics orkbench v11.0.1
Sequence reads were trimmed for adaptor sequence / low-quality sequence using CLC genomic benchwork ( parameter-quality limit : 0.05 )
Trimmed sequence reads were mapped to GRCh38 using CLC genomic benchwork ( parameters-mismath cost : 2 insertion cost : 3 deletion cost : 3 length fraction : 0.8 similarity fraction : 0.8 )
Read count extraction and normalization were performed using CLC genomic benchwork.
Assembly: GRCh38
Supplementary files format and content: tab-delimited txt file includes raw counts values for each Sample
Supplementary files format and content: tab-delimited txt files include RPKM values for each Sample

extract_protocol:
RNA was harvested using NEBNext Ultra™ RNA Library Prep Kit for Illumina.1.5 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-SEQ were prepared using SMARTER MRNA-SEQ Library Prep Kit following manufacturers protocols.

value: Human Adenocarcinoma of the lung cells


title: Control_2

description: Control


title: human_EoE_posi_CD45p_1

description: 10x Genomics

value: EoE


title: H1N1 sample at 168 hours [2075_7344_33072_Influenza22g-_Mouse430A+2]

value: Male


title: GSK484_rep1

value: cell line

value: Jurkat, 5A8

value: human lymphoblastoid cells

tag: cut&tag antibody

value: Anti-Histone H3 citrulline R2 + R8 + R17 (Abcam, Cat# ab5103)

value: HIV-1 (R7 E- GFP)


title: Control_1

description: Control


title: combo biol rep 2


title: PAX18 biol rep 3

value: 5 mg/kg paclitaxel


title: PAX18 biol rep 2


title: Bone injury replicate 1

description:
Processed_Endo_injured_BMS_and_healthy_Spleen_data.csv
BN_Tregs_1_S1

source_name: bone

value: bone

value: Regulatory T cells

value: male

value: 10 weeks

value: calvarial bone defect

value: day 7 post-injury


title: H1N1 sample at 168 hours [2075_7344_33071_Influenza21g-_Mouse430A+2]


title: Muscle injury replicate 1

description:
Processed_Endo_injured_BMS_and_healthy_Spleen_data.csv
MU_Tregs_2_S5

value: muscle

value: volumetric muscle loss defect


title: P035

value: Ectocervix

value: female


title: Drug_3

description: By exposing H1975 cells to OSI doses of 0.03 μM, 0.1 μM, 0.3 μM, 1 μM, and 3 μM, an OSI-resistant cell line (H1975/OSI) with a concentration of 3 μM was obtained after a period of seven months.

value: Human Adenocarcinoma of the lung cells


title: MBQ biol rep 3

value: orthotopic tumor

value: Mammary gland/Mimics human breast cancer; Stage IV

value: WT

value: MBQ 100 mg/kg


title: controlH1N1 sample at 168 hours [2075_7344_33111_Influenza19g-_Mouse430A+2]

value: Male


title: combo biol rep 1

value: MBQ+PAX combo as above


title: controlH1N1 sample at 168 hours [2075_7344_33110_Influenza18g-_Mouse430A+2]


title: controlH1N1 sample at 168 hours [2075_7344_33112_Influenza20g-_Mouse430A+2]


title: PAX18 biol rep 1

value: 5 mg/kg paclitaxel


title: human_EoE_posi_CD45n

description: 10x Genomics

value: esophagitis

tag: disease

value: EoE

value: CD45- cell

value: Wild-type


title: Drug_1


title: controlH1N1 sample at 168 hours [2075_7344_33070_Influenza17g-_Mouse430A+2]


title: Drug_2


title: cnt biol rep 2

value: vehicle


title: H1N1 sample at 120 hours [2075_7344_33108_Influenza14g-_Mouse430A+2]


title: controlH1N1 sample at 168 hours [2075_7344_33069_Influenza16g-_Mouse430A+2]


title: cnt biol rep 1


title: chx_6h_1

city: Nijmegen

first: Oscar

last: Garcia-Blay

state: Gelderland

address: Heyendaalseweg 135

department: Biophysical Chemistry

institute: Institute for Molecules and Materials (Radboud University)

data_processing:
Basecalling was performed with software provided by Illumina
Demultiplexing was performed with custom script according to barcodes in R1 reads
Reads were aligned to transcriptome of reference and count tables were obtained
Assembly: mm10-2020-A transcriptome
Supplementary files format and content: Gene count tables in .csv format

source_name: E14 mESCs (129/Ola background)

growth_protocol: Mouse embryonic stem cells (mESCs) were seeded with a density of 0.5E6 cells in a gelatinized 9.6cm2 well. mESC culture medium  consisted of Dulbecco's Modified Eagle Medium, supplemented with 0.1mM betamercaptoethanol, 1000 U/mL of Penicillin, 0.1 mg/mL of Streptomycin, 1mM of sodium pyruvate , 1000 U/mL of ESGRO recombinant Mouse Leukemia Inhibitory Factor and 15% of ES-qualified heat inactivated Fetal Bovine Serum (FBS)

extract_protocol:
RNA was extracted with TRIzol reagent according to the instructions provided by the manufacturer.
RNA quantity and quality was assessed with BioAnalyzer and RNA samples were delivered in dry ice to sequencing company. RNAs from different samples were barcoded with sample specific barcodes and RNAseq was performed on a pooled RNA sample.

treatment_protocol: Mouse embryonic stem cells (mESCs) were seeded with a density of 0.5E6 cells in a 9.6cm2 well. 24 hours post-seeding, cells were exposed to 250 ug/mL cycloheximide in 0.007% EtOH in the media for 3 or 6 hours, or only EtOH as a control, for 9 hours.

value: E14 mESCs (129/Ola background)


title: Tarumatic brain injury late_TS7_2

city: Chicago

first: Yan

last: Li

state: IL

address: 900 East 57th St.

department: Center for Research Informatics

institute: The University of Chicago

data_processing:
Raw sequencing QC assessement: FastQC v0.11.9
Adapter trimming: cutadapt 3.2
Alignment: bowtie wrapped in sRNAbench v 1.5
miRNA assembly: sRNAbench v 1.5
Differentially expressed miRNA analysis: DESeq2
Assembly: GENCODE human genome model: GRCh38 v34; mature and hairpin micro RNA: miRBase release 22.1
Supplementary files format and content: tab-delimited text files include sense and anti-sense raw counts values summarized by sRNAbench for each Sample.

source_name: Serum

extract_protocol:
MiRNAs were extracted from the serum samples using QIAseq miRNA Library Kit (QIAGENÒ)
The quality of the samples was ensured using Advanced Analytical Fragment Analyzer. Sample concentration was measured with Qubit Fluorometric Quantitation, Life Technologies. Library preparation was performed according to the library preparation protocol (QIAseq miRNA Library Kit (QIAGEN). Human Brain Total RNA AM7962 (ThermoFisher Scientific) was used as positive control. Sequencing run was performed using Illumina NovaSeq 6000 SP platform using single-end 75-bp reads. Raw sequencing quality was assessed using FastQC.

value: Serum

value: Tarumatic brain injury late


title: MBQ biol rep 2


title: Tarumatic brain injury late_TS8_2

value: female


title: H1N1 sample at 120 hours [2075_7344_33109_Influenza15g-_Mouse430A+2]


title: cnt biol rep 3


title: chx_6h_2


title: Tarumatic brain injury early_TS8_1

value: Tarumatic brain injury early


title: chx_3h_2


title: MBQ biol rep 1

value: orthotopic tumor


title: control_1


title: H1N1 sample at 120 hours [2075_7344_33107_Influenza13g-_Mouse430A+2]


title: H1N1 sample at 120 hours [2075_7344_33067_Influenza9g-_Mouse430A+2]


title: H1N1 sample at 120 hours [2075_7344_33106_Influenza12g-_Mouse430A+2]


title: H1N1 sample at 120 hours [2075_7344_33105_Influenza11g-_Mouse430A+2]


title: control

description: processed data files include the matrix, barcodes and features files that correspond to the cell-to-gene matrix. Barcodes identify cells while features identify genes. Raw files include all fastw files corresponding to this sample.

data_processing:
Reads were processed with cellranger-4.0.0.
Assembly: mm10-2020-A transcriptome
Supplementary files format and content: Tab-separated files (barcodes, features) and matrix files

extract_protocol:
Cells were washed with 1xPBS and dettached with 0.05% trypsin in EDTA for 2 minutes at 37C, followed by quenching with complete growth media. Proper viability of cells prior to freezing was quantified with propidium iodide/acridine orange staining in a LUNA-FL Dual Fluorescence Cell Counter. Cells were centrifuged at 200rcf for 3 minutes. The supernatant was discaded and the pellet was resuspended in 1mL freezing media (80% complete media, 10% heat-innactivated FBS, 10% DMSO), and frozen at -80C.
Cells were shipped to comercial company in dry ice for single-cell RNA barcoding (10x Genomics' Chromium) and sequencing (NextSeq 2000 instrument, Single Cell 3' v3 chemistry), according standard procedures.

treatment_protocol: Mouse embryonic stem cells (mESCs) were seeded with a density of 0.5E6 cells in a 9.6cm2 well. 24 hours post-seeding, cells were exposed to 250 ug/mL cycloheximide in 0.007% EtOH in the media for 3 or 6 hours, or only EtOH as a control, for 6 hours.


title: chx_3h_1


title: control_2


title: Tarumatic brain injury early_TS7_1


title: untreated, replicate2

first: Shannan

last: Ho Sui

address: 401 Park Drive

institute: Harvard

data_processing:
Reads were filtered and trimmed with Atropos.
High quality reads were mapped to the mus musculus genome (build mm10) using Bowtie2.
After filtering reads from mitochondrial DNA, properly paired reads with high mapping quality (MAPQ score >10, non-duplicates, qualified reads) were retained using Sambamba for further analysis. The 'alignmentSieve' function of Deeptools and 'sort' and 'index' functions of Samtools were used to isolate fragments in nucleosome free regions (NFRs). Reads were shifted by 9 bp (+4 in positive and -5 in negative strand) to account for the dimeric binding of the Tn5 transposase that results in insertion of two adaptors separated by 9 bp.
Peaks called using MACs2
Differential binding analysis was done with Diffbind
Assembly: mm10
Supplementary files format and content: bigwig all data
Supplementary files format and content: bigwig all data

extract_protocol:
MinElute PCR Purification Kit
Tagmented DNA was barcoded using the Nextera Index Kit v2 (Illumina), PCR-amplified, and cleaned using solid-phase reversible immobilization (SPRI) beads to generated purified DNA libraries

treatment_protocol: Cells were lysed, cytosolic fractions removed, nuclei treated with Tn5 transposase


title: Tarumatic brain injury late_TS6_2

value: male


title: Tarumatic brain injury late_TS5_2


title: chx_3h


title: tub_3h

data_processing:
Reads were processed with cellranger-7.1.0.
Assembly: mm10-2020-A transcriptome
Supplementary files format and content: Tab-separated files (barcodes, features) and matrix files

source_name: E14 mESCs

extract_protocol:
Cells were washed with 1xPBS and dettached with 0.05% trypsin in EDTA for 2 minutes at 37C, followed by quenching with complete growth media. Proper viability of cells prior to freezing was quantified with propidium iodide/acridine orange staining in a LUNA-FL Dual Fluorescence Cell Counter. Cells were centrifuged at 200rcf for 3 minutes. The supernatant was discaded and the pellet was resuspended in 0.5mL 0.04% BSA in PBS.
Single-cell RNA barcoding (10x Genomics' Chromium) and sequencing (NextSeq 2000 instrument, Single Cell 3' v3 chemistry) was performed from fresh cells according to standard procedures.

treatment_protocol: Mouse embryonic stem cells (mESCs) were seeded with a density of 0.5E6 cells in a 9.6cm2 well. 24 hours post-seeding, cells were exposed to 10uM tubercidin in the media for 3 or 6 hours, or equivalent volume of DMSO as a control, for 6 hours.

value: 129/Ola background

value: E14 mESCs


title: Tarumatic brain injury early_TS5_1


title: Tarumatic brain injury early_TS6_1


title: control


title: H1N1 sample at 120 hours [2075_7344_33068_Influenza10g-_Mouse430A+2]

value: Male


title: Mycoplasma sample at 72 hours [2075_7344_33103_662_Mouse430A+2]

value: Female

value: Mycoplasma


title: IFN_beta, replicate2


title: H1N1 sample at 120 hours [2075_7344_33066_Influenza8g-_Mouse430A+2]


title: Mycoplasma sample at 72 hours [2075_7344_33104_664_Mouse430A+2]


title: tub_6h


title: chx_6h


title: IFN_beta, replicate1


title: H1N1 sample at 120 hours [2075_7344_33065_Influenza6g-_Mouse430A+2]


title: AAV-Ctrl3, Control3

city: Solna

first: Yuvarani

last: Masarapu

address: SciLifeLab, Tomtebodavägen 23

institute: SciLifeLab

data_processing:
Counts matrices were generated using Spaceranger count (v1.3.1, 10x Genomics Inc.)
The generated count matrices were then processed and analyzed using the R package Seurat (v4.1.1).
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: Count matrices with feature barcode information for each sample in .h5 format
Library strategy: Visium Spatial Transcriptomics

source_name: brain

extract_protocol:
Transcriptome capture in each tissue section with spatial resolution using the 10x genomics kit Visium Spatial Gene Expression assay for Fresh Frozen tissues
10x 382 Genomics Visium Spatial Gene Expression protocol (User Guide, CG000239 Rev F)
Untargeted_Capture

value: brain

tag: section

value: striatum

tag: section thickness

value: 10 μm

tag: mouse id

tag: treatment age

value: 6 weeks

tag: sacrifice age

value: 16 weeks


title: Tarumatic brain injury late_TS4_2

tag: tissue


title: IFN_alpha, replicate1

tag: cell line


title: AAV-Ctrl2, Control2

description: Transcriptome capture in each tissue section with spatial resolution using the 10x genomics kit Visium Spatial Gene Expression assay for Fresh Frozen tissues

tag: genotype


title: untreated, replicate1


title: Tarumatic brain injury late_TS3_2

tag: Sex


title: AAV-Nurr1cKO2, KnockOut2

tag: treatment


title: Mycoplasma sample at 72 hours [2075_7344_33064_661_Mouse430A+2]

data_processing: Image files were generated using Affymetrix GeneChip Command Console software. Data was normalized, robust multichip averaged and converted to an eset using the Affy R package.  Differentially expressed genes were discovered with the limma R package.  Public codebase, relevant to publication, can be found here: https://gitlab.oit.duke.edu/biocat/murine-pneumonia-project

extract_protocol: Total RNA was isolated using the Mouse Ribopure Isolation Kit followed by globin mRNA depletion using the GLOBINclear Kit (Ambion).  .

tag: strain


title: Mycoplasma sample at 72 hours [2075_7344_33063_660_Mouse430A+2]


title: Tarumatic brain injury early_TS4_1


title: AAV-Nurr1cKO3, KnockOut3


title: Tarumatic brain injury late_TS2_2


title: IFN_alpha, replicate2


title: Tarumatic brain injury early_TS3_1


title: scRNA-seq of M2

city: Guangzhou

first: Yingchun

last: Zheng

state: Guangdong

address: Guangdong province

institute: Southern Medical University

description: 10x Genomics

data_processing:
Sample demultiplexing, barcode processing and UMI counting were performed by using the official 10x Genomics pipeline Cell Ranger v3.1.0 (https://support.10xgenomics.com).
Assembly: mRatBN7.2
Supplementary files format and content: Tab-separated values files and matrix files

organism: Rattus norvegicus

source_name: second mandibular molar

extract_protocol:
Mandible were dissected under a stereomicroscope. The tooth germs of first mandibular molars and second mandibular molars were carefully isolated respectively, and then cut into small pieces. Subsequently, the small pieces were digested in 3 mg/mL Collagenase type I (Sigma-Aldrich) and 3 mg/mL Dispase II (Sigma-Aldrich) and 20U/ml Dnase I (Solarbio) at 37 ℃ for 1h, and then filtered through a 40 μm cell strainer (BD Biosciences). After washed with cold PBS, the cells were resuspended in PBS containing 0.04% BSA.
10x Genomics Chromium platform was used to capture and barcode cells to generate single-cell Gel Beads-in-Emulsion (GEMs) by following the manufacturer’s protocol. Briefly, along with the reverse transcription master mix, cell suspensions of all samples were loaded onto the same 10x Genomics Single Cell 3′ Chip. During this step, cells were partitioned into GEMs along with gel beads coated with oligonucleotides. These oligonucleotides enable mRNA capture by 30 bp oligo-dT and provide barcodes to index cells (16 bp) as well as transcripts (12 bp unique molecular identifier; UMI). Following reverse transcription, cDNAs with both barcodes were amplified, and a library was constructed using the Single Cell 3′ Reagent Kit (v3 chemistry) for each sample. The resulting libraries were sequenced on an Illumina NovaSeq 6000 System.

value: second mandibular molar

tag: age

value: 5 days postnatal


title: AAV-Nurr1cKO1, KnockOut1


title: AAV-Ctrl1, Control1


title: Tarumatic brain injury early_TS2_1

value: Serum


title: Mycoplasma sample at 72 hours [2075_7344_33026_650_Mouse430A+2]

tag: agent


title: Mycoplasma sample at 48 hours [2075_7344_33094_649_Mouse430A+2]

tag: timepoint in hours


title: Tarumatic brain injury late_TS1_2

value: Tarumatic brain injury late


title: Photoconverted ILC2 in Pancreas. Plate 3

city: Lisbon

first: Miguel

middle: Alves

last: Rendas

address: Avenida Brasília, 1400-038 Lisbon

department: Physiology and Cancer

country: Portugal

institute: Champalimaud Foundation

data_processing:
Libraries were sequenced on an Illumina NextSeq 500 in a double-end and 75 nucleotide read-length configuration, achieving a sequence depth of 150,000 reads per cell on average.
Mapping to the mm10 genome was done using STAR/STARsolo.
Downstream analysis was performed in R, using the scran package pipeline.
Normalized counts were further corrected for batch effect using the scran built-in function.
scRNA-seq DE analysis was performed as previously described using a single cell-adapted EdgeR/QLF approach
Assembly: mm10
Supplementary files format and content: Raw counts for each sample.
Supplementary files format and content: FACS index information for each plate.

source_name: Pancreas

extract_protocol:
ILC2 were FACS sorted into 384-wells plates containing the required components for SORT-seq protocol obtained from Single cell discoveries.
Libraries were generated using a CEL-seq2-based protocol.

value: Pancreas

tag: cell type

value: Non-photoconverted (KIKR-Green) and Photoconverted (KIKR-Red)


title: Mycoplasma sample at 48 hours [2075_7344_33092_647_Mouse430A+2]

tag: agent_time combined


title: VerificationExperiment_GE_A549cells_4weeks_DEP30_rep3

city: Kanazawa

first: Alexandra

last: Lukyanchuk

state: --Not Applicable--

address: 13-1 Takara-machi

institute: Kanazawa University

description: Gene expression after exposure to 30 μg/ml of DEP for 4 weeks

hyb_protocol: The labeled cRNA was subjected to hybridization, washing, and analysis using SurePrint G3 Human GE Microarray 8x60K Ver.3.0 (Agilent Technologies, Inc.).

scan_protocol: Microarray slide was scanned using Agilent DNA microarray scanner (Agilent Technologies). The captured fluorescence signals were quantified as signal intensity using DNA microarray expression data analysis software (Agilent Technologies, Inc.) and extracted from the images using Feature Extraction software (Agilent Technologies, Inc.).

data_processing: Th raw txt files obtained were imported into the R programming environment (v.4.1.0) and processed using the limma package (v.3.48.0)

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, 30 μg/ml of DEP, 4 weeks, rep3

label_protocol: total RNA was synthesized and purified using LowInput QuickAmp Labeling Kit (Agilent Technologies) and RNeasy Mini Kit (Qiagen, Inc.). The labeling was performed using a one-color method with Cyanin 3-CTP as the labeling reagent.

growth_protocol: A549 cells and DMEM/F12 medium with 10% fetal bovine solution (10 μg/mL gentamicin) were used. Cells adhering to the bottom of the flasks were removed with 0.25% trypsin/1 mM EDTA solution (Invitrogen, Carlsbad, CA, USA), and the cells were subcultured periodically.

extract_protocol: RNA was isolated from the cells using the RNeasy Mini Kit (Qiagen, Hilden, Germany) following the manufacturer’s protocol. The concentration of extracted total RNA was measured using a gene measurement spectrophotometer (NanoVue plus; GE Healthcare).

treatment_protocol: DEP-suspended culture medium was added to 2.5 × 10^5 A549 cells seeded in T-25 tissue culture bottles. The medium was replaced every 4 days after seeding, and the cells were subcultured. 0 μg/ml and 30 μg/ml concentrations of DEP were prepared. The exposure period spanned 4 weeks

value: cancerous lung tissue

tag: gender

value: male


title: Photoconverted ILC2 in Pancreas. Plate 2


title: Photoconverted ILC2 in Pancreas. Plate 4


title: Aneurysmal subaracnoid hemorrhage late_SS8_2

tag: disease

value: Aneurysmal subaracnoid hemorrhage late


title: Tarumatic brain injury early_TS1_1

value: Tarumatic brain injury early


title: Mycoplasma sample at 48 hours [2075_7344_33053_646_Mouse430A+2]

value: Female


title: scRNA-seq of M1

description: 10x Genomics

source_name: first mandibular molar

value: first mandibular molar


title: Photoconverted ILC2 in Pancreas. Plate 1


title: Mycoplasma sample at 72 hours [2075_7344_33027_654_Mouse430A+2]

source_name: RNA from murine whole blood

value: Mycoplasma


title: Aneurysmal subaracnoid hemorrhage late_SS7_2


title: Pancreas ILC2 from fed/fasted animals (multiplexed file 4)

data_processing:
Multiplexed labelled libraries were sequenced in an Illumina NextSeq 500, using a single-end and 75 nucleotide fragment-size setup and a mean sequence depth of 10M reads per sample was attained.
Mapping to the Mus musculus genome (mm10) was performed with STAR.
Downstream DE analysis was performed in R using EdgeR.
Log2(CPM) normalized counts were used for the generation of heatmaps.
Heatmaps were plotted using the pheatmap R package.
Assembly: mm10
Supplementary files format and content: Raw counts for each sample.
Supplementary files format and content: Index file with barcodes identifying each sample for demultiplexing

source_name: Pancreas (Langerhans islets)

extract_protocol:
RNA was harvest using Trizol.
Sequencing libraries were generated using the CEL-seq2 protocol, rendering barcoded samples.

value: Pancreas (Langerhans islets)

value: Pancreas ILC2

value: Fed/Fasted


title: VerificationExperiment_GE_A549cells_4weeks_DEP30_rep1

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, 30 μg/ml of DEP, 4 weeks, rep1


title: VerificationExperiment_GE_A549cells_4weeks_control_rep1

description: Gene expression after exposure to 0 μg/ml of DEP for 4 weeks

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, control, 4 weeks, rep1


title: Pancreas ILC2 from fed/fasted animals (multiplexed file 3)


title: R25-50,scRNAseq

city: Suzhou

first: Wanshi

address: 苏州大学

institute: 苏州大学

data_processing:
For data analysis, alignment (GRCh38), filtering, barcode counting, and UMI counting were performed using the Cell Ranger count module to generate the filtered gene-cell matrix. The matrix was then loaded into R software to filter out low-quality cells or doublets (<200 or >7500 genes/cell, >10% mitochondria genes, >50,000 transcripts/cell) and genes (<3 cells/gene) using the Seurat package (v4.2.1).
Assembly: Hg38.p13
Supplementary files format and content: Cellranger processed files, including barcodes, genes, and matrix files

source_name: lung

extract_protocol:
The 10X Genomics 3 'transcriptome utilizes short read length sequencing and microfluidic technology to achieve simultaneous transcriptome expression profiling analysis of 500-10000 cells per sample. We combine gel beads containing barcode information with the mixture of cells and enzymes, and then wrap them with oil surfactant droplets located in the microfluidic "double cross" system to form GEMs (GelBeads In Emulations). GEMs flow into the reservoir and are collected. The gel beads dissolve and release Barcode sequences, reverse transcribe cDNA fragments, and label the samples. The gel beads were broken and the oil drops were broken, and the cDNA was used as the template for PCR amplification. Mix all GEMs products and construct a standard sequencing library.
Firstly, the cDNA enzyme is cleaved into fragments of about 200-300 bp, followed by the traditional second-generation sequencing library building process such as sequencing adapter P5 and sequencing primer R1. Finally, PCR amplification is performed to obtain the DNA library.

value: lung

value: human bronchial epithelial cells

value: long-term low dose-rate exposures

value: 50th passage after low dose rate exposure (0.5Gy)


title: Mycoplasma sample at 48 hours [2075_7344_33093_648_Mouse430A+2]


title: VerificationExperiment_GE_A549cells_4weeks_control_rep2

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, control, 4 weeks, rep2


title: Mycoplasma sample at 48 hours [2075_7344_33051_643_Mouse430A+2]


title: R25-30,scRNAseq

value: 30th passage after low dose rate exposure (0.5Gy)


title: Mycoplasma sample at 48 hours [2075_7344_33050_642_Mouse430A+2]


title: Aneurysmal subaracnoid hemorrhage early_SS7_1

value: Serum

value: Aneurysmal subaracnoid hemorrhage early


title: Aneurysmal subaracnoid hemorrhage late_SS6_2


title: Pancreas ILC2 from fed/fasted animals (multiplexed file 2)


title: Mycoplasma sample at 48 hours [2075_7344_33017_641_Mouse430A+2]


title: VerificationExperiment_GE_A549cells_4weeks_DEP30_rep2

source_name: Adenocarcinomic human alveolar basal epithelial cells A549, 30 μg/ml of DEP, 4 weeks, rep2

value: cancerous lung tissue


title: Pancreas ILC2 from fed/fasted animals (multiplexed file 1)


title: Aneurysmal subaracnoid hemorrhage early_SS8_1

value: male


title: Aneurysmal subaracnoid hemorrhage early_SS6_1


title: GSK484_rep3

data_processing:
Paired fastq-files were aligned to the hg19 genome using Bowtie2, flags --end-to-end --very-sensitive --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700 to generate Sam-files.
Sam-files were converted to Bam-files using Samtools (view -S-b -o, and sort).
Bam-files from replicates were normalized to effective genome size and merged using Picard MergeSamFiles 2.18.2.1 in Galaxy.
Bigwig-files produced (binLength: 50) by Deeptools Bam_coverage 3.5.1.0.0 in Galaxy.
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: Cut&Tag

source_name: cell line

extract_protocol:
Version 3 CUT&Tag protocol (Kaya-Okur and Henikoff, 2020) was used as described.
A 1/400 dilution of Anti-Histone H3 (citrulline R2 + R8 + R17) antibody (Abcam, Cat# ab5103) was used per sample. Thirteen cycles of PCR were used for amplifying the libraries. Reads were trimmed, then, mapped onto the GB38 human reference genome with Bowtie2.

value: cell line

value: Jurkat, 5A8

value: human lymphoblastoid cells

tag: cut&tag antibody

value: Anti-Histone H3 citrulline R2 + R8 + R17 (Abcam, Cat# ab5103)

value: HIV-1 (R7 E- GFP)


title: Mycoplasma sample at 48 hours [2075_7344_33052_645_Mouse430A+2]

value: Female

value: Mycoplasma


title: R25-10,scRNAseq

value: 10th passage after low dose rate exposure (0.5Gy)


title: R1-50,scRNAseq

value: lung

value: single acute exposure

value: 50th passage after one acute exposure (0.5Gy)


title: Aneurysmal subaracnoid hemorrhage late_SS5_2

value: Aneurysmal subaracnoid hemorrhage late


title: Mycoplasma sample at 48 hours [2075_7344_33016_639_Mouse430A+2]


title: sonKD

extract_protocol:
24 hours post-transfection, cells were washed with 1xPBS and dettached with 0.05% trypsin in EDTA for 2 minutes at 37C, followed by quenching with complete growth media. Proper viability of cells prior to freezing was quantified with propidium iodide/acridine orange staining in a LUNA-FL Dual Fluorescence Cell Counter. 50% of cells were utilized to validate the knock down at the protein level. The other 50% of cells were centrifuged at 200rcf for 3 minutes. The supernatant was discaded and the pellet was resuspended in 1mL freezing media (80% complete media, 10% heat-innactivated FBS, 10% DMSO), and frozen at -80C.
Cells were brought to sequencing facility in dry ice. After quick thawing at 37C, cells were transfered to 0.04% BSA in 1xPBS. Staining with 7-AAD was performed and healthy cells were sorted in 0.04% BSA in PBS. Cells were counted to ensure viability after sorting. This step was quickly followed by single-cell RNA barcoding (10x Genomics' Chromium) and sequencing (Illumina NextSeq 500 instrument, Single Cell 3' v3 chemistry), according standard procedures.

treatment_protocol: Mouse embryonic stem cells (mESCs) were seeded with a density of 1E6 cells in a 25cm2 flask. 24 hours post-seeding, transfection of Son siRNA or control siRNA was performed in a total volume of 7 mL of transfection media. Transfection media onsisted on 70% standard complete growth media in absence of antibiotics (Penicillin, Streptomycin) and 30% lipoplex solution with the siRNA. Lipoplex solution was obtained by combining 50% of 5% Lipofectamine2000  in Opti-MEM with 50% of 1mM siRNA in Opti-MEM, and incubating at room temperature for 15 minutes.

value: E14 mESCs (129/Ola background)


title: R1-30,scRNAseq

value: human bronchial epithelial cells

value: 30th passage after one acute exposure (0.5Gy)


title: HelaS3, mitotic, DMSO, 0.00025x yeast spike-in, H3K9ac

data_processing:
Samples were sequenced on Illumina NextSeq 550, samples were demultiplexed with Illumina bcl2fastq.
Adapters were removed with Trimmomatic, reads with Phred score <26 over a 4bp window were truncated.
Reads were aligned to a concatenated genome containing hg38 + sacCer3 + dm6, alignment files were separated by species. Duplicate reads were removed with samtools markdup.
HOMER tag directories were made for each species, where by default read counts were filtered for primary alignments with MAPQ > 10.
Bigwig files were created with HOMER makeBigWig.pl from tag directories.
Assembly: hg38
Supplementary files format and content: Read-normalized BigWig files for hg38 genome

extract_protocol:
HeLa-S3 cells were double crosslinked on plates with 2 mM DSG for 30 minutes and 1% formaldehyde for 10 minutes. Crosslinking was quenched with 1/20th volume of 2.625 M glycine and 0.5% BSA, then cells were washed 3 times with 0.5% BSA/PBS + Protease inhibitor, spinning down at 1200g for 5 minutes at 4C. Washed pellets were snap frozen then stored in -80C. Cells were lysed with LB3 lysis buffer + PIC, then chromatin was sheared on the PIXUL sonicator for 108 minutes. S2 cells were crosslinked in 1% formaldehyde for 10 minutes at room temperature, then quenched with glycine and 0.5% BSA, lysed in LB3, and sonicated on the PIXUL for 60 minutes. Yeast cultures in log phase were crosslinked with 0.86% formaldehyde for 30 minutes. The yeast cell wall was digested with Zymolase at 37°C for 60 minutes, then cells were washed 3x in PBS + PI, then resuspended in NP-S buffer + PI. Yeast were sonicated on the PIXUL for 120 minutes. All PIXUL sonication was done with settings Pulse (N) = 50, PRF (kHz) = 1.00, Burst Rate (Hz) = 20, only Process Time was varied. Sheared chromatin from each species were combined then inputs were taken before immunoprecipitation for each condition, to assess the relative ratios of chromatin.
To each IP, 10uL of Protein A beads and 4uL of H3K9ac, 1% Triton X-100 and 1x PIC were added. Samples were incubated overnight on rotator at 4C. IP Washes were performed as follows: 3x with 180uL of WBI, 3x with 180uL of WBIII, and 2x with 185uL TET, then eluted in 25uL of cold TT Buffer. Inputs were incubated with Speedbeads, in 12% PEG and 1M NaCl for 10 minutes at room temperature, then washed twice with 80% EtOH, and eluted in 25uL cold TT Buffer. From inputs and IPs, libraries were prepared with the NEB Ultra II Library Prep Kit. Barcoded adapters were from BioO NEXTflex ChIP-seq Adapters. Libraries were decrosslinked and cleaned with Speedbeads, then PCR amplified with Solexa 1GA and 1GB primers, and size selected with a final Speedbead cleanup. Library size was estimated with agarose gel, concentrations measured with Qubit HS DNA kit.

tag: spike-in species

value: D. melanogaster, S. cerevisiae

value: human cerival cancer

tag: chip antibody

value: CST H3K9ac (C5B11)

value: DMSO


title: Mycoplasma sample at 48 hours [2075_7344_33015_638_Mouse430A+2]


title: control


title: Aneurysmal subaracnoid hemorrhage early_SS5_1

value: Serum

value: Aneurysmal subaracnoid hemorrhage early

value: male


title: Mycoplasma sample at 48 hours [2075_7344_33014_636_Mouse430A+2]

value: Female


title: pancreas, Par3KO cerulein, JQ1, rep 3

first: Mario

last: Shields

state: Illinois

address: 303 E Superior St

department: Medicine

institute: Northwestern University

data_processing:
The paired-end 42 bp (PE42) sequencing reads  are mapped to the genome using the STAR algorithm (v. 2.5.2b) with default settings. Alignment information for each read is stored in the BAM format.
The number of fragments overlapping predefined genomic features of interest  are counted.
Assembly: mm10
Supplementary files format and content: tab-delimited file include raw counts for each sample
Supplementary files format and content: tab-delimited file include fpkm for each sample

source_name: pancreas

extract_protocol:
RNA was extracted using the RNeasy mini kit. 1 mg of RNA was used for library preparation
Library prepapred with YourSeq (FT & 3’DGE) Strand-Specific mRNA Library Prep

value: pancreas

value: cerulein, JQ1


title: Aneurysmal subaracnoid hemorrhage late_SS4_2

value: female


title: Mycoplasma sample at 24 hours [2075_7344_33084_634_Mouse430A+2]

first: Nicholas

address: 2301 Erwin Rd

value: Mycoplasma


title: Ctrl,scRNAseq

value: lung

value: control group

value: 50th passage without exposure


title: pancreas, Par3KO, cerulein, JQ1, rep 2


title: Aneurysmal subaracnoid hemorrhage late_SS3_2

value: Aneurysmal subaracnoid hemorrhage late


title: day14_dac

first: Jiaqian

last: Qi

state: Jiangsu

address: No.188 Shizi Road

institute: The First Affiliated Hospital of Soochow University

data_processing:
GeCKO v2.0
Assembly: mm10
Supplementary files format and content: Tap-separate files
Library strategy: genome-wide CRISPR/Cas9

extract_protocol:
RNA was harvested following manufacture's protocols.
genome-wide CRISPR/Cas9 Reagent Kit v2 (dual index).

value: white blood cell

value: WT

value: treated


title: Aneurysmal subaracnoid hemorrhage early_SS4_1


title: pancreas, Par3KO, cerulein, JQ1, rep 1


title: pancreas, WT, cerulein, JQ1, rep 3


title: Aneurysmal subaracnoid hemorrhage early_SS3_1


title: Mycoplasma sample at 24 hours [2075_7344_33040_632_Mouse430A+2]

last: O'Grady

institute: Duke University


title: Mycoplasma sample at 24 hours [2075_7344_33083_633_Mouse430A+2]


title: day14_dmso

value: untreated


title: pancreas, WT, cerulein, JQ1, rep 2


title: pancreas, WT, cerulein, JQ1, rep 1


title: Aneurysmal subaracnoid hemorrhage late_SS2_2


title: Mycoplasma sample at 24 hours [2075_7344_33039_631_Mouse430A+2]


title: Mycoplasma sample at 24 hours [2075_7344_33038_630_Mouse430A+2]


title: day7_dac


title: Aneurysmal subaracnoid hemorrhage late_SS1_2


title: pancreas, Par3KO cerulein, DMSO, rep 3

value: cerulein, DMSO


title: R1-10,scRNAseq

value: human bronchial epithelial cells

value: single acute exposure

value: 10th passage after one acute exposure (0.5Gy)


title: day0


title: Aneurysmal subaracnoid hemorrhage early_SS2_1

value: Serum

value: Aneurysmal subaracnoid hemorrhage early


title: Mycoplasma sample at 24 hours [2075_7344_33004_624_Mouse430A+2]

value: Female


title: Mycoplasma sample at 24 hours [2075_7344_33037_628_Mouse430A+2]


title: pancreas, Par3KO, cerulein, DMSO, rep 2

value: pancreas


title: Aneurysmal subaracnoid hemorrhage early_SS1_1

value: female


title: Ishi-Cocul+EX527 replicate 2

city: VASCO

first: Akanksha

last: Savardekar

state: GOA

address: SANCOALE

department: BIOLOGICAL SCIENCES

country: India

institute: BITS PILANI K K BIRLA GOA CAMPUS

data_processing:
The sequence data was generated using Illumina HiSeq. Data quality was checked using FastQC and MultiQC software.
The data was checked for base call quality distribution, % bases above Q20, Q30, %GC, and sequencing adapter contamination and samples were selected which passed QC threshold (Q30>90%). Raw sequence reads were processed to remove adapter sequences and low quality bases using fastp. QC processed reads were further processed to remove rRNA reads using BBDuk.
The rRNA removed reads mapped onto indexed Human reference genome (GRCh38.p7) using STAR v2 aligner.Gene level expression values were obtained as read counts using featureCounts software
Assembly: GRCh38.p7
Supplementary files format and content: The read counts were normalized (variance stabilized normalized counts) using DESeq2 and differential enrichment analysis was performed.Genes with absolute log2 fold change ≥ 1.0 and p-value ≤ 0.05 were considered significant.

source_name: Ishikawa

growth_protocol: Ishikawa endometrial cancer cells were maintained in DMEM-F12 supplemented with 10%FBS and antibiotics in CO2 incubator at 37˚C. Preadipocytes were grown to approximately 80% confluence stage, in DMEM-high glucose medium containing 10% FBS and (5 µg/ml) insulin, for 2 days. For differentiation, cells were induced with (5 µg/ml) insulin, (0.5 µM) dexamethasone, and (0.5 mM) IBMX, with media changes every 48 hours for an additional 6 days. On day 10, the differentiated adipocytes were observed for lipid droplets and mature adipocyte markers.

extract_protocol:
Cells in Trizol were vortexed for 5 minutes. Later equal volume of absolute ethanol was added and loaded onto Zymo spin column (Cat: Zymo Research Kit (R2072))The RNA quality assessment was done using RNA ScreenTape System (Catalog: 5067- 5576, Agilent) in a 4150 TapeStation System (Catalog: G2992AA, Agilent). followed by washes with RNA Pre wash and Wash buffers. The RNA was eluted in 30uls of NFW.
RNA libraries for RNA seq were prepared, 500ng of total RNA was used to enrich the mRNA using NEBNext Poly (A) mRNA magnetic isolation module (Catalog: E7490, New England Biolabs) by following the manufacturers’ protocol.The enriched mRNAs were further taken for the library preparation using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (Catalog: E7775S, New England Biolabs).

treatment_protocol: Mature Adipocytes were indirectly co-cultured with Ishikawa EC cells using a transwell culture system (pore size, 0.4 μm; Corning Incorporated, Corning, NY, USA), maintained in DMEM with 10% FBS at 37˚C. for experiments assessing cancer cell biology, mature adipocytes were grown in the upper chamber, with Ishikawa EC cells in the bottom chamber and were incubated for 3 days. Ishikawa endometrial cancer cells cultured alone(monoculture) will serve as controls.

value: Ishikawa

value: endometrioid cancer cells

value: co-culture treated with SIRT1 inibhitor


title: Ishi-Control

value: monoculture


title: Mycoplasma sample at 24 hours [2075_7344_33003_622_Mouse430A+2]

value: Mycoplasma


title: Ishi-Cocul+EX527 replicate 1


title: Ischemic stroke late_IS8_2

source_name: Serum

extract_protocol:
MiRNAs were extracted from the serum samples using QIAseq miRNA Library Kit (QIAGENÒ)
The quality of the samples was ensured using Advanced Analytical Fragment Analyzer. Sample concentration was measured with Qubit Fluorometric Quantitation, Life Technologies. Library preparation was performed according to the library preparation protocol (QIAseq miRNA Library Kit (QIAGEN). Human Brain Total RNA AM7962 (ThermoFisher Scientific) was used as positive control. Sequencing run was performed using Illumina NovaSeq 6000 SP platform using single-end 75-bp reads. Raw sequencing quality was assessed using FastQC.

value: Ischemic stroke late

value: male


title: pancreas, Par3KO, cerulein, DMSO, rep 1


title: Ischemic stroke early_IS8_1

value: Ischemic stroke early


title: day7_dmso

value: white blood cell

value: WT

value: untreated


title: pancreas, WT, cerulein, DMSO, rep 3

value: cerulein, DMSO


title: Ishi-Cocul-replicate 2

value: co-culture with adipocytes


title: pancreas, WT, cerulein, DMSO, rep 2


title: Ischemic stroke late_IS7_2

value: Serum


title: Mycoplasma sample at 24 hours [2075_7344_33001_620_Mouse430A+2]

value: Female


title: Ischemic stroke early_IS7_1


title: K562 SF3B1 K666N-selinexor-3-cytoplasmic-smallRNA

city: Miami

first: Felipe

last: Beckedorff

state: FL

address: 1501 NW 10th Avenue room 731.G , Miami, FL

institute: University of Miami

description: cytoplasmic RNA

data_processing:
All samples were trimmed with Trimmomatic (v0.32) to remove low-quality and short reads and aligned to the human genome hg19 using STAR aligner (v 2.7.9a).
For total RNA and polyA RNA, RSEM (v 1.3.1) was used to obtain expected gene counts against the human gene reference Gencode (v 41). Differential expression was determined using DESeq2 and R (v 4.2.0). A gene was considered detected if the TPM (Transcripts Per Million) >1 in at least two replicates of one sample and significantly changed if the adjusted p-value was < 0.05 and fold change >1.5<−1.5.
Alternative splicing bam files with the Gencode v41 annotation file were used as input for rMATS (v4.1.2). Events with |inclusion level difference| > 0.05, P < 0.05 and FDR < 0.05 were identified as significantly differentially expressed AS events
For small RNAseq reads were aligned against human elements in RepBase (v23.08) with STAR (v2.7.9a), and the unmapped output was then mapped against the human genome (hg19), allowing three mismatches and keeping all uniquely aligned reads.
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes the Differentially expressed genes per comparison

extract_protocol:
Total RNA for mRNA sequencing was extracted using QIAGEN RNeasy mini kit. To separate nuclear and cytoplasmic fractions, pellet the cells via centrifugation for 5 minutes at 1500RPM and discard the supernatant. The pellet was then resuspended into 300mL of ice cold 0.25x lysis buffer (Tris-Cl pH 8.0, NaCl, MgCl2, Nonidet P-40). The pellet was kept on ice for two minutes and rotate the tube every 45 seconds to ensure proper lysis followed by centrifugation at highest speed at 4°C for two minutes. After centrifugation, the supernatant was carefully removed and placed in a new tube as this was the cytoplasmic fraction. For the remaining nuclear fraction pellet, 500mL of ice-cold PBS was added and centrifuged at 1500RPM for 5 minutes. The QIAGEN RNeasy mini kit was then used for long RNAs and miRNeasy Tissue/Cells Advanced Micro Kit was used for small RNA extraction.
For mRNA sequencing was Poly(A)-selected and the Illumina libraries were prepared using the TruSeq stranded mRNA Library Preparation kit. For the nuclear cytoplasmic mRNAs, ribsomoal RNA depeletion method with the TruSeq stranded Total RNA library was used with 50 million paired end reads. For the nuclear cytoplasmic small RNAs, the size selection step with the Perkin Elmer Next Flex Small RNA library preparation kit on the Illumina sequencing platform with 50 million single end reads.

value: chronic myeloid leukemia cells

value: 200nM selinexor


title: Ishi-Cocul-replicate 1

value: Ishikawa


title: Streptococcus sample at 72 hours [2075_7344_33098_584_Mouse430A+2]

city: Durham

value: Streptococcus


title: EPSRC4XX_atac

city: Vancouver

first: Tully

middle: Michael

last: Underhill

state: British Columbia

address: 2222 Health Sciences Mall

department: Biomedical Research Centre

country: Canada

institute: University of British Columbia

description:
Single cell ATAC-seq tdTomato epithelioid sarcoma
transposase accessible

library_source: genomic single cell

data_processing:
Samples were demultiplexed using cellranger-atac 1.1.0 mkfastq with bcl2fastq.
Samples were aligned and output matrices generated using cellranger-atac 1.1.0 count for alignment and peak calling to cell clustering.
Assembly: mm10
Supplementary files format and content: peak matrices, cell barcode and peak list are included as .mtx, .tsv and .bed files, respectively

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/LSLtdTomato;Smarcb1FL/FL sarcoma cells endpoint 4

growth_protocol: Mice were bred and raised to 8 weeks of age using standard approved animal care committee methodology.

extract_protocol:
FACS purified cells were counted and inspected by hemocytometer before input to the 10X chromium nuclei preperation pipeline.
nuclear lysis protocol: nuclei were lysed for five minutes according to 10x standard protocol and subjected to the transposition reaction followed by library preparation pipeline and subsequent NGS.
Chromium Single Cell ATAC Reagent Kits User Guide (10x Genomics; CG000168 Rev B); 2 x 75PE kit to produce 2 X 50 reads

treatment_protocol: Adult animals 8 weeks of age were injected with 2.5mg tamoxifen in 100uL sunflower oil daily for 5 consecutive days and allowed a ten day washout period before experments were performed.

value: Mesenchymal Progenitors

value: Hip


title: K562 SF3B1 K666N-selinexor-2-cytoplasmic-smallRNA

description: cytoplasmic RNA


title: Ischemic stroke early_IS6_1

data_processing:
Raw sequencing QC assessement: FastQC v0.11.9
Adapter trimming: cutadapt 3.2
Alignment: bowtie wrapped in sRNAbench v 1.5
miRNA assembly: sRNAbench v 1.5
Differentially expressed miRNA analysis: DESeq2
Assembly: GENCODE human genome model: GRCh38 v34; mature and hairpin micro RNA: miRBase release 22.1
Supplementary files format and content: tab-delimited text files include sense and anti-sense raw counts values summarized by sRNAbench for each Sample.


title: EPSRC3XX_atac

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/LSLtdTomato;Smarcb1FL/FL sarcoma cells endpoint 3

value: Head/ear


title: K562 SF3B1 K666N-selinexor-1-cytoplasmic-smallRNA

description: cytoplasmic RNA


title: Streptococcus sample at 72 hours [2075_7344_33095_581_Mouse430A+2]


title: EPSRC2XX_atac

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/LSLtdTomato;Smarcb1FL/FL sarcoma cells endpoint 2

value: Head


title: Streptococcus sample at 72 hours [2075_7344_33097_583_Mouse430A+2]


title: Streptococcus sample at 72 hours [2075_7344_33096_582_Mouse430A+2]


title: K562 SF3B1 K666N-selinexor-3-nuclear-smallRNA

description: nuclear RNA


title: Ischemic stroke early_IS5_1

value: male


title: Mycoplasma sample at 24 hours [2075_7344_33002_621_Mouse430A+2]

value: Mycoplasma


title: Streptococcus sample at 72 hours [2075_7344_33058_580_Mouse430A+2]


title: pancreas, WT, cerulein, DMSO, rep 1

value: pancreas


title: Streptococcus sample at 72 hours [2075_7344_33057_579_Mouse430A+2]


title: Ischemic stroke late_IS4_2

value: Ischemic stroke late

value: female


title: wtFasciaXX_atac

description:
Single cell ATAC-seq tdTomato MPs quiescent
transposase accessible

source_name: Hic1CreERT2/CreERT2;Rosa26LSLtdTomato/+ MSC Quiescent Fascia

value: Fascia


title: K562 SF3B1 K666N-selinexor-1-nuclear-smallRNA

description: nuclear RNA


title: Ischemic stroke early_IS4_1

value: Ischemic stroke early