title: No stimulus 3

city: Solna

first: Patrik

last: Ernfors

address: Biomedicum, Solnavägen 9

department: MBB/Molneuro

country: Sweden

institute: Karolinska Institutet

description:
10x Genomics Chromium 3'
P21816_1003_no stimulus

data_processing:
Raw sequencing data were de-multiplexed, converted into fastq format, and aligned to mouse reference mm10 using the STAR aligner to generate the gene-cell matrices.
Assembly: mm10
Supplementary files format and content: .tsv.gz files containing raw expression counts and corresponding metadata in separate .tsv.gz (meta) files

source_name: Spinal cord,  dorsal horn

extract_protocol:
Mice with a Cre dependent red fluorescent protein variant tdTomato reporter (10-20 weeks old, both males and females) were sacrificed with over dosage of isoflurane. Lumbar spinal cord was dissected out immediately and kept in freshly oxygenated artificial cerebrospinal fluid solution (modified ACSF: 87 mM NaCl, 2.5 mM KCl, 1.25 mM NaH2PO4, 26 mM NaHCO3, 75 mM Sucrose, 10 mM Glucose, 0.5 mM CaCl2, 4 mM MgSO4) on ice. Gray matter from lumbar spinal dorsal horn (or only lumbar 4-6 from ipsilateral side) was dissected out and transferred to a plastic petri dish (3 cm) with 2 mL pre-warmed digestion enzyme in ACSF solution (Papain, 25 unit/mL and DNase I, 55 unit/mL, Worthington Biochemical). For spinal dorsal horn neuronal atlas construction, each experiment included 2-3 mice (BAF53b-Cre*R26Tom). For labeled active ensembles (FosdsTVA*R26Tom) or neurons from Sni mice (BAF53b-Cre*R26Tom), 4 mice were included for each suspension experiment. The following single cell suspension was performed according to our previous protocol (6) with modifications. Briefly, spinal cord tissues were cut into pieces and triturated (10 x up and down) every 10 min (4 x) using glass Pasteur pipettes with decreasing diameter (pre-coated with 0.5% BSA). Cell suspension was filtered through a 30 µm cell strainer (CellTrics, Sysmex) and washed with additional 1.5 mL ACSF and 0.5 mL PBS. Cells were spin down with centrifugation (300 g x 5 min, 4 °C) and resuspended with 2 mL ACSF. Cell suspension was carefully loaded on top of the same volume of OptiPrep density gradient medium (5.4% iodixanol in ACSF, Sigma) and centrifuge with 300 g x 10 min at 4 °C. Gradient centrifugation step was replaced with centrifugation (300 g x 5 min, 4 °C) for some samples. Cell pellet was resuspended with 4 mL ACSF. SYTOX Blue (Invitrogen, ThermoFisher Scientific) was added to stain dead cells. Then tdTomato positive and SYTOX Blue negative cells were sorted with fluorescence activated cell sorting (FACS) cell sorters (BD FACSAria Fusion / BD FACSAria III) at 4 °C. Cells were concentrated when necessary by centrifugation (300 g x 5 min, 4 °C) and resuspended with proper volume (~1000 cells/ µl) of ACSF solution.
Sorted cells were loaded onto the 10X Chromium chip G to yield single cell droplet with v3 or v3.1 kit (10X genomics). Targeted cell recovery for neuronal atlas construction or Sni samples was settled to 5000 cells, whereas the samples from captured active ensembles were aiming for 1000 cells. Reverse transcription, cDNA amplification and library construction were performed according to the user guide provided by manufacture.

value: Spinal cord,  dorsal horn

value: Neuron and Non-neuron

value: no stim., injection


title: Meningioma 171

status: Public on Jan 31 2025

type: genomic

city: Boston

first: Scott

middle: Thomas

last: Ryall

state: Massachusetts

address: 75 Francis Street

country: USA

institute: Brigham and Women's Hospital

description: Hybridized to Agilent aCGH

hyb_protocol: As per manufacturer (Agilent)

scan_protocol: Scanned on an Agilent G2565AA scanner using Feature Extraction Software

data_processing:
As per manufacturer (Agilent)
[processed data definition] Normalized log10 ratio (Cy5/Cy3) (tumor/normal), i.e., the LogRatio column of the Agilent Feature Extraction files

molecule: genomic DNA

organism: Homo sapiens

source_name: Brain Tumor  Tissue

label_protocol: As per manufacturer (Agilent)

growth_protocol: Not applicable

extract_protocol: DNA was extracted using the QIAamp DNA FFPE Tissue Kit and stored at 4˚C

treatment_protocol: Not applicable

tag: tissue

value: Brain tumor

tag: Sex

value: F

tag: age

source_name: Normal Brain Tissue

value: Normal Brain


title: No stimulus 2

type: SRA

description:
10x Genomics Chromium 3'
P20103_1009_no stimulus

library_source: transcriptomic single cell

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: genotype

tag: treatment


title: Mechanical stim. 3

description:
10x Genomics Chromium 3'
P21401_1003_mechanical

value: Mech stim., injection


title: CTRG2N3_S63

city: Genova

first: Adriana

middle: Agnese

last: Amaro

state: Italy

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale policlinico San Martino

library_source: transcriptomic

data_processing:
RNA-Seq data preprocessing: RNA-Seq data as FastQ files were processed with the nf-core/rna-seq pipeline (v: 3.12.0). Briefly raw data files (FastQ) quality was assessed with FastQC [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/], low quality bases and adapter sequences were removed with Trim Galore [https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/], in the final step data was aligned with Salmon to produce a matrix file with genes as rows and samples as columns.
Assembly: GRCm38
Supplementary files format and content: tab-delimited quant file includes raw counts and tpm for each Sample

source_name: tumor mouse cutaneous melanocytes cells

extract_protocol:
RNA was extracted from tumor cell pellets and cell lines using an RNeasy Plus mini kit (Qiagen, Hilden, Germany). RNA quality was assessed with Nanodrop and BioAnalyzer tools (Agilent, St. Clara, CA).
Universal Plus Total RNA-Seq with NuQuant kit (Tecan Genomics, Redwood City, CA) has been used for library preparation following the manufacturer’s instructions (library type: fr-secondstrand). RNA samples were quantified and quality tested by Agilent 2100 Bioanalyzer RNA assay (Agilent technologies, Santa Clara, CA) or Caliper (PerkinElmer, Waltham, MA). Final libraries were checked with both Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA) and Agilent Bioanalyzer DNA assay or Caliper (PerkinElmer, Waltham, MA). Libraries were then prepared for sequencing and sequenced on paired-end 150 bp mode on NovaSeq6000 (Illumina, San Diego, CA).

treatment_protocol: in vivo treatment with Vorinostat

value: skin tumor

tag: cell line


title: Meningioma 173

description: Hybridized to Agilent aCGH

value: M


title: Meningioma 170

description: Hybridized to Agilent aCGH


title: Mechanical stim. 2

description:
10x Genomics Chromium 3'
P20103_1004_mechanical


title: Meningioma 169

description: Hybridized to Agilent aCGH


title: Control_Islet_Progenitor_ LPD-2

city: Nashville

first: Guoqiang

last: Gu

state: TN

address: 2213 Garland Avenue, MRB4, Rm 9415

department: Cell and Developmental Biology

institute: Vanderbilt University

description:
FACS-sorted cells
7127-GG-6

data_processing:
Sequencing reads were trimmed to remove adapter sequences using Cutadapt (v2.10).
Trimmed reads were aligned to the Gencode GRCm38.p6 genome using STAR (v2.7.8a)
Gencode vM24 gene annotations were provided to STAR to improve the accuracy of mapping.
featureCounts (v2.0.2) was used to count the number of reads mapped to each gene.
For further anaylsis, the 'countToFPKM' package was used to convert the feature counts of paired-end RNA-Seq into FPKM normalised values by library size and feature effective length.
Assembly: GRCm38.p6
Supplementary files format and content: 7127_RNAseq_mouse.count copy.xlsx (Processed data, counts of identfied features after alignments)
Supplementary files format and content: 7127_RNAseq_mouse.fpkm_original copy.xlsx (Processed data, feature levels after normalization against feature size and total counts per sample)
Supplementary files format and content: rna_stats_export_7127-GG.csv (Raw statistics from Illumina)

source_name: endocrine islet progenitors

growth_protocol: Mice were housed in AAALAC-Accredited facilitty, following protocols approved by Vanderbilt IACUC.

extract_protocol:
Pancreata were manually dissected in RPMI 1066 media with 10% FBS + antibiotics. They were then Dissociated using 0.25% trypsin at 37 degree (~ 5minutes). Cells were washed 2X with RPMI+FBS media and sent for FACS sorting. Cells were spundown, dissolved in Trizol, and used in a DNA-free RNA-isolation kit (Zymo R2050) for RNA purification.
Total RNA preps will subject to standard Sample Quality Control analysis by using fluorometry Qubit or Picogreen and integrity by BioAnalyzer or TapeStation.  Only those with a RIN>7.5 were used for down-stream studies. For each sample, 50 ng of RNA were used for linrary preparation using the Illumina Ribo-Zero Plus rRNA Depletion kit. The procedure followed that specified by manufacturer, which include the depletion of rRNAs, cDNA reverse transcription, strand specific labeling/amplification. Library Quality Control analysis will be performed by using Qubit and BioAnalyzer to determine the concentration and size bp. Only those with significan DNA fragments between 150-1000 bp were sequenced. Each library that passes the final QC undergoes qPCR using the KAPA library quantification kit and QuantStudio. qPCR allows highly accurate quantification of library molecules that can seed clusters and balance target sample representation during pooling. Multiplexed samples are pooled in equimolar or user-defined ratios to achieve the multiplexing level requested by the user using Illumina MiSeq platform.

treatment_protocol: Females were fed with ND, HFD, and lPD before crossing, with females continue with specified diet.

value: endocrine islet progenitors

value: pancreatic cells

value: LPD

value: pooled male and female


title: Control_Islet_Progenitor_ LPD-1

description:
FACS-sorted cells
7127-GG-5


title: Meningioma 168

description: Hybridized to Agilent aCGH


title: Mechanical stim. 1

description:
10x Genomics Chromium 3'
P20103_1002_mechanical


title: Heat stim. 3

description:
10x Genomics Chromium 3'
P21816_1006_heat

value: Heat stim., injection


title: VORG3N5_S59

source_name: tumor mouse cutaneous melanocytes cells treated with VORINOSTAT

value: vorinostat


title: Meningioma 166

description: Hybridized to Agilent aCGH


title: VORG3N1_S58


title: Meningioma 164

description: Hybridized to Agilent aCGH


title: Meningioma 163

description: Hybridized to Agilent aCGH


title: Meningioma 175

description: Hybridized to Agilent aCGH


title: Heat stim. 2

description:
10x Genomics Chromium 3'
P19031_1001_heat


title: Meningioma 165

description: Hybridized to Agilent aCGH


title: sni 3

description:
10x Genomics Chromium 3'
P21816_1001_sni

value: sni


title: sni 4

description:
10x Genomics Chromium 3'
P21816_1002_sni


title: CTRG1N1_S62


title: Meningioma 162

description: Hybridized to Agilent aCGH


title: Meningioma 161

description: Hybridized to Agilent aCGH


title: Heat stim. 1

description:
10x Genomics Chromium 3'
P18656_1002_heat


title: sni 2

description:
10x Genomics Chromium 3'
P21401_1002_sni


title: sni 1

description:
10x Genomics Chromium 3'
P21401_1001_sni


title: Meningioma 160

description: Hybridized to Agilent aCGH


title: Meningioma 159

description: Hybridized to Agilent aCGH


title: Reference 8 (sni control 2)

description:
10x Genomics Chromium 3'
P21816_1007_ref

value: Control


title: Meningioma 158

description: Hybridized to Agilent aCGH


title: Reference 6

description:
10x Genomics Chromium 3'
P20103_1008_ref

value: Spinal cord,  dorsal horn


title: Meningioma 157

description: Hybridized to Agilent aCGH


title: Meningioma 167

description: Hybridized to Agilent aCGH


title: Meningioma 156

description: Hybridized to Agilent aCGH


title: Reference 5

description:
10x Genomics Chromium 3'
P20103_1007_ref

value: Neuron and Non-neuron


title: Reference 3

description:
10x Genomics Chromium 3'
P20103_1003_ref


title: Meningioma 155

description: Hybridized to Agilent aCGH


title: Reference 9 (sni control 3)

description:
10x Genomics Chromium 3'
P21816_1008_ref


title: Reference 7 (sni control 1)

description:
10x Genomics Chromium 3'
P21816_1004_ref


title: Meningioma 153

description: Hybridized to Agilent aCGH


title: Meningioma 154

description: Hybridized to Agilent aCGH


title: Meningioma 149

description: Hybridized to Agilent aCGH


title: ilt3_1

city: Hangzhou

first: Jinchao

last: Hou

state: Zhejiang

address: Binsheng Road

department: Anesthesiology

country: China

institute: Zhejiang University

data_processing:
RNA-seq reads were then aligned to the Ensembl release 101 primary assembly with STAR version 2.7.9a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.32. Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.23.
Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.  The ribosomal fraction, known junction saturation, and read distribution over known gene models were quantified with RSeQC version 4.04.
Read counts were used as input and normalized using built-in algorithms in DESeq2 (1.38.3). Pairwise comparisons among the 2 conditions were done on all genes. The resultingP-values were adjusted using Benjamini and Hochberg’s approach for controlling the false discovery rate. Genes with an adjustedP<0.05 were assigned as differentially expressed.
Assembly: Ensembl release 101
Supplementary files format and content: tab-separated values (tsv) file includes raw counts for each sample
Supplementary files format and content: Excel file includes gene differential expression analysis

source_name: ILT Telo Tg x 5XFAD model with anti-LILRB4 (ilt3) treatment

extract_protocol:
After 8 consecutive injections, animals were deeply anesthetized with ketamine/xylazine. Then the mice underwent transcardial perfusion with cold PBS containing 0.1% heparin. The brain was subsequently removed and divided into halves. One half of the brain was dissected and homogenized using a Dounce homogenizer in a dissociation buffer consisting of 3% BSA and 1mM EDTA. Myelin debris was removed by 30% Percoll density gradient centrifugation, followed by the labeling of microglia with CD45 APC-Cy7 and CD11b APC. The microglia were sorted by gating CD45lowCD11b+ cells. The RNA of microglia was harvested using RNeasy Plus Micro Kit.
Total RNA integrity was determined using Agilent Bioanalyzer or 4200 Tapestation. Library preparation was performed with 10ng of total RNA with a Bioanalyzer RIN score greater than 8.0. ds-cDNA was prepared using the SMARTer Ultra Low RNA kit for Illumina Sequencing (Takara-Clontech) per manufacturer's protocol. cDNA was fragmented using a Covaris E220 sonicator using peak incident power 18, duty factor 20%, cycles per burst 50 for 120 seconds. cDNA was blunt ended, had an A base added to the 3' ends, and then had Illumina sequencing adapters ligated to the ends. Ligated fragments were then amplified for 12-15 cycles using primers incorporating unique dual index tags. Fragments were sequenced on an Illumina NovaSeq-6000 using paired end reads extending 150 bases.Basecalls and demultiplexing were performed with Illumina’s bcl2fastq software with a maximum of one mismatch in the indexing read.

treatment_protocol: 4-month-old male ILT-Telo Tg 5XFAD mice were treated intraperitoneally with Fc-mutant anti-ILT3 mAb (ZM3.1, 60mg/kg) or Fc-mutant Ctrl mAb (27D6, 60mg/kg) every week for 8 weeks in total.

value: brain

value: microglia

value: ILT Telo Tg x 5XFAD


title: Reference 4

description:
10x Genomics Chromium 3'
P20103_1005_ref


title: Meningioma 150

description: Hybridized to Agilent aCGH

value: Brain tumor

value: Normal Brain


title: Reference 1

description:
10x Genomics Chromium 3'
P19031_1003_ref


title: Meningioma 148

description: Hybridized to Agilent aCGH

value: F


title: ilt3_3


title: Meningioma 147

description: Hybridized to Agilent aCGH

value: M


title: Meningioma 146

description: Hybridized to Agilent aCGH


title: ilt3_2


title: ctrl_3

source_name: ILT Telo Tg x 5XFAD model with Ctrl IgG2a (ctrl) treatment

value: Ctrl IgG2a


title: Meningioma 145

description: Hybridized to Agilent aCGH


title: ctrl_2


title: PBMC29-Feature

city: Stanford

first: Han

last: Zhu

state: CA

address: 1291 Welch Road

institute: Stanford Cardiovascular Institute

description: processed data linked to corresponding scRNA sample

library_source: other

data_processing:
Raw single-cell RNA-seq data were processed using 10x Genomics Cell Ranger (6.0.2) to demultiplex the FASTQ reads in order to align them to the human or mouse reference genomes and count the unique molecular identifier (UMI) (through the “cellranger count” function). Human reference used was GRCh38 and mouse reference was refdata-gex-mm10-2020-A, downloaded from the 10x website.
Raw T cell receptor (TCR) sequencing data were processed using 10x Genomics Cell Ranger (v4.0.3). In summary, the algorithm aligned FASTQ reads to human GRCh38 V(D)J reference genome (v4.0.0, from 10X Genomics) by using the “cellranger vdj” function, resulting in the assembly of V(D)J sequences and clonotypes (38).
Individual sample gene expression matrices were loaded into Seurat v4.0.0 R package (https://satijalab.org/seurat/) for further analysis.
To filter out poor quality data from cells with high mitochondrial gene expression likely to be dead/damaged cells (59), we removed cells with greater than >15% mitochondrial genes present (60). Additionally, we removed cells for which less than 500 genes were detected.
Assembly: h38, mouse (from 10x website - refdata-gex-mm10-2020-A.tar.gz) - https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?
Supplementary files format and content: bam tab-delimited text files
Library strategy: CITE-seq

molecule: protein

source_name: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC)

extract_protocol:
Frozen PBMCs were removed from liquid nitrogen and resuspended in warm RPMI media + 10% FBS (@ 37ºC) by adding 1 mL, 3 mL, 4 mL, 8 mL 16 mL media at 30-60 second intervals. Cells were washed and passed through a 40 um filter, centrifuged @ 300 rcf x 5 min and resuspended in PBS with 50 ul 1% BSA and Biolegend Fc Receptor Blocking Solution (Human TrueStain FcX (Cat. No. 422301) or Mouse TruStain PLUS (mouse) Fc block for 20 minutes. Afterwards, another 50 uL of antibody mastermix containing Biolegend TotalSeq-C antibodies for staining (see manuscript for full antibody list) for final manufacture-recommended concentration of 1.0 ug of antibody in 100 ul of staining buffer for every 1 million cells for a total of 10-15 minutes incubation. After incubation, cells were washed 2x by resuspending in 1.5 mL PBS + 1% RNase-free BSA (MACS BSA Stock Solution No. 130-091-376) and then 1 mL PBS + 0.04% BSA. 10 uL of cell suspension was then taken for counting and appropriate volume of PSA + 0.04% BSA was added (200-500 uL) to aim for final target concentration of 1-1.5 million cells/mL). Cells were then loaded into Chromium Next GEM Chip G (10x PN 2000177) to achieve 4000-6000 cells target cell recovery per non-multiplexed sample or 20,000-24,000 target cells per multiplexed sample if cell hashing was performed. If cell hashing was performed, the individual samples were pooled into one sample prior to running the Chromium Controller.
All steps from cDNA isolation to library preparation were completed according to 10x’s manufacturing protocols for the Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1. Isolated cDNA was amplified (14 cycles), and then cDNA was allocated for TCR enrichment, feature barcode library generation, and 5’ cDNA library generation. cDNA and library quality was evaluated using the high sensitivity DNA kit on the Agilent 2100 Bioanalyzer.

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC)

value: Immunotherapy Only (Hash1-TotalSeqC), Immunotherapy Only (Hash2-TotalSeqC), antiCXCR3 (Hash3-TotalSeqC), antiCXCR3 (Hash4-TotalSeqC), Immunotherapy Only (Hash5-TotalSeqC)

tag: library type

value: CITE-seq data


title: PBMC30-Feature

value: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC)

value: Immunotherapy Only (Hash1-TotalSeqC), Immunotherapy Only (Hash2-TotalSeqC), antiCXCR3 (Hash3-TotalSeqC), antiCXCR3 (Hash4-TotalSeqC), antiCXCR3 (Hash5-TotalSeqC)


title: Meningioma 143

description: Hybridized to Agilent aCGH


title: PBMC25-Feature

source_name: Heart (Hash4-TotalSeqC), Heart (Hash7-TotalSeqC), Heart (Hash8-TotalSeqC)

value: MRL (Hash4-TotalSeqC), MRL (Hash7-TotalSeqC), MRL (Hash8-TotalSeqC)

value: IgG Control (Hash4-TotalSeqC), IgG Control (Hash7-TotalSeqC), IgG Control (Hash8-TotalSeqC)


title: Meningioma 144

description: Hybridized to Agilent aCGH


title: PBMC24-Feature

source_name: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Heart (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Heart (Hash8-TotalSeqC)

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL (Hash7-TotalSeqC), MRL (Hash8-TotalSeqC)

value: Immunotherapy Only (Hash1-TotalSeqC), Immunotherapy Only (Hash2-TotalSeqC), antiCXCR3 (Hash3-TotalSeqC), antiCXCR3 (Hash4-TotalSeqC), antiCXCR3 (Hash5-TotalSeqC), antiCXCR3 (Hash6-TotalSeqC)


title: Meningioma 142

description: Hybridized to Agilent aCGH


title: Reference 2

description:
10x Genomics Chromium 3'
P20103_1001_ref

value: Spinal cord,  dorsal horn

value: Neuron and Non-neuron

value: Control


title: Meningioma 152

description: Hybridized to Agilent aCGH

value: Brain tumor


title: Meningioma 151

description: Hybridized to Agilent aCGH

value: Normal Brain


title: Meningioma 141

description: Hybridized to Agilent aCGH

value: F


title: Meningioma 140

description: Hybridized to Agilent aCGH


title: PBMC29-TCR

data_processing:
Raw single-cell RNA-seq data were processed using 10x Genomics Cell Ranger (6.0.2) to demultiplex the FASTQ reads in order to align them to the human or mouse reference genomes and count the unique molecular identifier (UMI) (through the “cellranger count” function). Human reference used was GRCh38 and mouse reference was refdata-gex-mm10-2020-A, downloaded from the 10x website.
Raw T cell receptor (TCR) sequencing data were processed using 10x Genomics Cell Ranger (v4.0.3). In summary, the algorithm aligned FASTQ reads to human GRCh38 V(D)J reference genome (v4.0.0, from 10X Genomics) by using the “cellranger vdj” function, resulting in the assembly of V(D)J sequences and clonotypes (38).
Individual sample gene expression matrices were loaded into Seurat v4.0.0 R package (https://satijalab.org/seurat/) for further analysis.
To filter out poor quality data from cells with high mitochondrial gene expression likely to be dead/damaged cells (59), we removed cells with greater than >15% mitochondrial genes present (60). Additionally, we removed cells for which less than 500 genes were detected.
Assembly: h38, mouse (from 10x website - refdata-gex-mm10-2020-A.tar.gz) - https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest?
Supplementary files format and content: bam tab-delimited text files

value: single-cell TCR seq


title: PBMC30-TCR


title: PBMC25-TCR

value: Heart (Hash4-TotalSeqC), Heart (Hash7-TotalSeqC), Heart (Hash8-TotalSeqC)


title: Meningioma 138

description: Hybridized to Agilent aCGH


title: Meningioma 139

description: Hybridized to Agilent aCGH


title: PBMC28-Feature

source_name: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL/Pdcd1-/- (Hash2-TotalSeqC), MRL/Pdcd1-/- (Hash3-TotalSeqC), MRL/Pdcd1-/- (Hash4-TotalSeqC)

value: Liposomal control (Hash1-TotalSeqC), Liposomal control (Hash2-TotalSeqC), Liposomal control (Hash3-TotalSeqC), Liposomal clodronate (Hash4-TotalSeqC)


title: Meningioma 135

description: Hybridized to Agilent aCGH


title: pbmc29-scRNA

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC)

value: Immunotherapy Only (Hash1-TotalSeqC), Immunotherapy Only (Hash2-TotalSeqC), antiCXCR3 (Hash3-TotalSeqC), antiCXCR3 (Hash4-TotalSeqC), Immunotherapy Only (Hash5-TotalSeqC)

value: scRNA-seq data


title: Meningioma 136

description: Hybridized to Agilent aCGH

value: M


title: Meningioma 137

description: Hybridized to Agilent aCGH


title: pbmc24-scRNA

value: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Heart (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Heart (Hash8-TotalSeqC)


title: pbmc25-scRNA

value: MRL (Hash4-TotalSeqC), MRL (Hash7-TotalSeqC), MRL (Hash8-TotalSeqC)

value: IgG Control (Hash4-TotalSeqC), IgG Control (Hash7-TotalSeqC), IgG Control (Hash8-TotalSeqC)


title: Meningioma 132

description: Hybridized to Agilent aCGH


title: PBMC28-TCR

value: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC)


title: pbmc30-scRNA

value: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC)

value: Immunotherapy Only (Hash1-TotalSeqC), Immunotherapy Only (Hash2-TotalSeqC), antiCXCR3 (Hash3-TotalSeqC), antiCXCR3 (Hash4-TotalSeqC), antiCXCR3 (Hash5-TotalSeqC)


title: Meningioma 134

description: Hybridized to Agilent aCGH

value: Brain tumor


title: Meningioma 133

description: Hybridized to Agilent aCGH

value: Normal Brain


title: ctrl_1

value: brain

value: microglia

value: ILT Telo Tg x 5XFAD

value: Ctrl IgG2a


title: PBMC27-Feature

source_name: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL/Pdcd1-/- (Hash2-TotalSeqC)

value: Liposomal control (Hash1-TotalSeqC), Liposomal control (Hash2-TotalSeqC)

value: CITE-seq data


title: Meningioma 131

description: Hybridized to Agilent aCGH

value: F


title: PBMC27-TCR

value: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC)

value: single-cell TCR seq


title: pbmc28-scRNA

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL/Pdcd1-/- (Hash2-TotalSeqC), MRL/Pdcd1-/- (Hash3-TotalSeqC), MRL/Pdcd1-/- (Hash4-TotalSeqC)

value: Liposomal control (Hash1-TotalSeqC), Liposomal control (Hash2-TotalSeqC), Liposomal control (Hash3-TotalSeqC), Liposomal clodronate (Hash4-TotalSeqC)

value: scRNA-seq data


title: Meningioma 129

description: Hybridized to Agilent aCGH


title: Meningioma 130

description: Hybridized to Agilent aCGH


title: pbmc27-scRNA


title: Meningioma 128

description: Hybridized to Agilent aCGH

value: M


title: PBMC24-TCR

value: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Heart (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Heart (Hash8-TotalSeqC)

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL (Hash7-TotalSeqC), MRL (Hash8-TotalSeqC)

value: Immunotherapy Only (Hash1-TotalSeqC), Immunotherapy Only (Hash2-TotalSeqC), antiCXCR3 (Hash3-TotalSeqC), antiCXCR3 (Hash4-TotalSeqC), antiCXCR3 (Hash5-TotalSeqC), antiCXCR3 (Hash6-TotalSeqC)


title: PBMC33-Feature

source_name: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL/Pdcd1-/- (Hash2-TotalSeqC), MRL/Pdcd1-/- (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC)

value: Liposomal control (Hash1-TotalSeqC), Liposomal clodronate (Hash2-TotalSeqC), Liposomal clodronate (Hash3-TotalSeqC), Immunotherapy Only (Hash5-TotalSeqC), antiCXCR3 (Hash6-TotalSeqC)


title: Meningioma 127

description: Hybridized to Agilent aCGH

value: Brain tumor

value: Normal Brain


title: PBMC32-Feature

source_name: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC)

value: Liposomal clodronate (Hash1-TotalSeqC), Immunotherapy Only (Hash4-TotalSeqC), antiCXCR3 (Hash5-TotalSeqC)


title: Meningioma 125

description: Hybridized to Agilent aCGH


title: Meningioma 126

description: Hybridized to Agilent aCGH


title: PBMC31-Feature

source_name: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL/Pdcd1-/- (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL/Pdcd1-/- (Hash4-TotalSeqC)

value: Liposomal clodronate (Hash1-TotalSeqC), Liposomal clodronate (Hash2-TotalSeqC), antiCXCR3 (Hash3-TotalSeqC)

value: CITE-seq data


title: PBMC22-Feature

source_name: Blood (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL/Pdcd1-/- (Hash6-TotalSeqC), MRL/Pdcd1-/- (Hash7-TotalSeqC), MRL/Pdcd1-/- (Hash8-TotalSeqC)


title: Meningioma 124

description: Hybridized to Agilent aCGH

value: F


title: Meningioma 123

description: Hybridized to Agilent aCGH


title: PBMC20-Feature

source_name: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Blood (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL/Pdcd1-/- (Hash7-TotalSeqC), MRL/Pdcd1-/- (Hash8-TotalSeqC)


title: PBMC21-Feature

source_name: Blood (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL/Pdcd1-/- (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL (Hash7-TotalSeqC), MRL (Hash8-TotalSeqC)


title: PBMC19-Feature

source_name: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL/Pdcd1-/- (Hash3-TotalSeqC), MRL/Pdcd1-/- (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL/Pdcd1-/- (Hash7-TotalSeqC), MRL/Pdcd1-/- (Hash8-TotalSeqC)


title: Meningioma 121

description: Hybridized to Agilent aCGH

source_name: Brain Tumor  Tissue

value: U

source_name: Normal Brain Tissue


title: Meningioma 120

description: Hybridized to Agilent aCGH

value: M


title: Meningioma 122

description: Hybridized to Agilent aCGH


title: PBMC18-Feature

value: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)


title: PBMC16-Feature

source_name: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL/Pdcd1-/- (Hash5-TotalSeqC), MRL/Pdcd1-/- (Hash8-TotalSeqC)


title: Meningioma 117

description: Hybridized to Agilent aCGH


title: Meningioma 118

description: Hybridized to Agilent aCGH


title: Meningioma 119

description: Hybridized to Agilent aCGH


title: PBMC32-TCR

value: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC)

value: single-cell TCR seq


title: PBMC17-Feature


title: PBMC33-TCR

value: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL/Pdcd1-/- (Hash2-TotalSeqC), MRL/Pdcd1-/- (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC)

value: Liposomal control (Hash1-TotalSeqC), Liposomal clodronate (Hash2-TotalSeqC), Liposomal clodronate (Hash3-TotalSeqC), Immunotherapy Only (Hash5-TotalSeqC), antiCXCR3 (Hash6-TotalSeqC)


title: Meningioma 115

description: Hybridized to Agilent aCGH

value: Brain tumor

value: Normal Brain


title: PBMC31-TCR

value: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL/Pdcd1-/- (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL/Pdcd1-/- (Hash4-TotalSeqC)

value: Liposomal clodronate (Hash1-TotalSeqC), Liposomal clodronate (Hash2-TotalSeqC), antiCXCR3 (Hash3-TotalSeqC)


title: PBMC22-TCR

value: Blood (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL/Pdcd1-/- (Hash6-TotalSeqC), MRL/Pdcd1-/- (Hash7-TotalSeqC), MRL/Pdcd1-/- (Hash8-TotalSeqC)


title: Meningioma 113

description: Hybridized to Agilent aCGH

value: F


title: PBMC21-TCR

value: Blood (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL/Pdcd1-/- (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL (Hash7-TotalSeqC), MRL (Hash8-TotalSeqC)


title: PBMC20-TCR

value: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Blood (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL/Pdcd1-/- (Hash7-TotalSeqC), MRL/Pdcd1-/- (Hash8-TotalSeqC)


title: Meningioma 112

description: Hybridized to Agilent aCGH


title: PBMC19-TCR

value: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL/Pdcd1-/- (Hash3-TotalSeqC), MRL/Pdcd1-/- (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL/Pdcd1-/- (Hash7-TotalSeqC), MRL/Pdcd1-/- (Hash8-TotalSeqC)


title: Meningioma 111

description: Hybridized to Agilent aCGH


title: PBMC18-TCR

value: single-cell TCR seq


title: Meningioma 110

description: Hybridized to Agilent aCGH


title: PBMC17-TCR


title: Meningioma 109

description: Hybridized to Agilent aCGH


title: Meningioma 114

description: Hybridized to Agilent aCGH

value: M


title: pbmc33-scRNA

value: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL/Pdcd1-/- (Hash2-TotalSeqC), MRL/Pdcd1-/- (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC)

value: Liposomal control (Hash1-TotalSeqC), Liposomal clodronate (Hash2-TotalSeqC), Liposomal clodronate (Hash3-TotalSeqC), Immunotherapy Only (Hash5-TotalSeqC), antiCXCR3 (Hash6-TotalSeqC)

value: scRNA-seq data


title: PBMC16-TCR

value: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL/Pdcd1-/- (Hash5-TotalSeqC), MRL/Pdcd1-/- (Hash8-TotalSeqC)


title: Meningioma 106

description: Hybridized to Agilent aCGH

value: Brain tumor

value: Normal Brain


title: Meningioma 108

description: Hybridized to Agilent aCGH

value: F


title: Meningioma 105

description: Hybridized to Agilent aCGH


title: pbmc32-scRNA

value: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC)

value: Liposomal clodronate (Hash1-TotalSeqC), Immunotherapy Only (Hash4-TotalSeqC), antiCXCR3 (Hash5-TotalSeqC)


title: pbmc31-scRNA

value: Heart (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL/Pdcd1-/- (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL/Pdcd1-/- (Hash4-TotalSeqC)

value: Liposomal clodronate (Hash1-TotalSeqC), Liposomal clodronate (Hash2-TotalSeqC), antiCXCR3 (Hash3-TotalSeqC)


title: Meningioma 107

description: Hybridized to Agilent aCGH


title: Meningioma 116

description: Hybridized to Agilent aCGH


title: pbmc22-scRNA

value: Blood (Hash1-TotalSeqC), Heart (Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL/Pdcd1-/- (Hash6-TotalSeqC), MRL/Pdcd1-/- (Hash7-TotalSeqC), MRL/Pdcd1-/- (Hash8-TotalSeqC)


title: Meningioma 102

description: Hybridized to Agilent aCGH


title: pbmc20-scRNA

value: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Blood (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL/Pdcd1-/- (Hash7-TotalSeqC), MRL/Pdcd1-/- (Hash8-TotalSeqC)


title: pbmc21-scRNA

value: Blood (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL/Pdcd1-/- (Hash1-TotalSeqC), MRL/Pdcd1-/- (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL (Hash7-TotalSeqC), MRL (Hash8-TotalSeqC)


title: Meningioma 101

description: Hybridized to Agilent aCGH

value: M


title: pbmc18-scRNA

value: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash6-TotalSeqC), Heart (Hash7-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL/Pdcd1-/- (Hash3-TotalSeqC), MRL/Pdcd1-/- (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL/Pdcd1-/- (Hash7-TotalSeqC), MRL/Pdcd1-/- (Hash8-TotalSeqC)

value: scRNA-seq data


title: Meningioma 100

description: Hybridized to Agilent aCGH

value: Brain tumor

value: Normal Brain


title: pbmc19-scRNA


title: Meningioma 103

description: Hybridized to Agilent aCGH

value: F


title: pbmc17-scRNA


title: pbmc16-scRNA

value: Heart (Hash1-TotalSeqC), Blood (Hash2-TotalSeqC), Heart (Hash3-TotalSeqC), Blood (Hash4-TotalSeqC), Heart (Hash5-TotalSeqC), Blood (Hash8-TotalSeqC)

value: MRL (Hash1-TotalSeqC), MRL (Hash2-TotalSeqC), MRL (Hash3-TotalSeqC), MRL (Hash4-TotalSeqC), MRL/Pdcd1-/- (Hash5-TotalSeqC), MRL/Pdcd1-/- (Hash8-TotalSeqC)


title: Meningioma 099

description: Hybridized to Agilent aCGH


title: Meningioma 098

description: Hybridized to Agilent aCGH


title: PBMC15-Feature

source_name: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Heart(Hash3-TotalSeqC), Heart(Hash4-TotalSeqC), Heart(Hash5-TotalSeqC), Heart(Hash5-TotalSeqC), Heart(Hash6-TotalSeqC), Heart(Hash7-TotalSeqC), Heart(Hash8-TotalSeqC)

value: MRL/Pdcd1 -/- (Hash1-TotalSeqC), MRL/Pdcd1 -/- (Hash2-TotalSeqC)

value: CITE-seq data


title: PBMC14-Feature

source_name: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Heart (Hash6-TotalSeqC), Blood (Hash7-TotalSeqC), Heart (Hash8-TotalSeqC)

value: MRL(Hash1-TotalSeqC), MRL(Hash2-TotalSeqC), MRL/Pdcd1 -/- (Hash3-TotalSeqC), MRL/Pdcd1 -/- (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL/Pdcd1 -/- (Hash7-TotalSeqC), MRL/Pdcd1 -/- (Hash8-TotalSeqC)


title: Meningioma 096

description: Hybridized to Agilent aCGH


title: Meningioma 097

description: Hybridized to Agilent aCGH


title: Meningioma 095

description: Hybridized to Agilent aCGH


title: PBMC13-Feature

source_name: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Heart (Hash6-TotalSeqC)

value: MRL(Hash1-TotalSeqC), MRL(Hash2-TotalSeqC), MRL/Pdcd1 -/- (Hash3-TotalSeqC), MRL/Pdcd1 -/- (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC)


title: Meningioma 094

description: Hybridized to Agilent aCGH


title: PBMC12-Feature

source_name: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC)

value: MRL(Hash1-TotalSeqC), MRL(Hash2-TotalSeqC), MRL/Pdcd1 -/- (Hash3-TotalSeqC), MRL/Pdcd1 -/- (Hash4-TotalSeqC)


title: Meningioma 104

description: Hybridized to Agilent aCGH


title: Meningioma 093

description: Hybridized to Agilent aCGH


title: PBMC8-TCR

source_name: Blood

value: Blood

value: MRL

value: single-cell TCR seq


title: Meningioma 092

description: Hybridized to Agilent aCGH


title: PBMC7-TCR

source_name: Heart

value: Heart


title: PBMC15-TCR

value: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Heart(Hash3-TotalSeqC), Heart(Hash4-TotalSeqC), Heart(Hash5-TotalSeqC), Heart(Hash5-TotalSeqC), Heart(Hash6-TotalSeqC), Heart(Hash7-TotalSeqC), Heart(Hash8-TotalSeqC)


title: Meningioma 090

description: Hybridized to Agilent aCGH


title: PBMC13-TCR

value: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Heart (Hash6-TotalSeqC)


title: Meningioma 089

description: Hybridized to Agilent aCGH

value: M


title: Meningioma 091

description: Hybridized to Agilent aCGH

value: Brain tumor


title: PBMC12-TCR

value: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC)


title: Meningioma 088

description: Hybridized to Agilent aCGH

value: F

value: Normal Brain


title: Meningioma 087

description: Hybridized to Agilent aCGH


title: PBMC10-TCR

value: MRL/Pdcd1 -/-


title: PBMC11-TCR


title: Meningioma 086

description: Hybridized to Agilent aCGH


title: pbmc8-scRNA

value: scRNA-seq data


title: Meningioma 085

description: Hybridized to Agilent aCGH


title: pbmc7-scRNA


title: pbmc15-scRNA

value: MRL/Pdcd1 -/- (Hash1-TotalSeqC), MRL/Pdcd1 -/- (Hash2-TotalSeqC)


title: Meningioma 084

description: Hybridized to Agilent aCGH


title: Meningioma 083

description: Hybridized to Agilent aCGH


title: Meningioma 081

description: Hybridized to Agilent aCGH


title: pbmc14-scRNA

value: Blood (Hash1-TotalSeqC), Heart(Hash2-TotalSeqC), Blood (Hash3-TotalSeqC), Heart (Hash4-TotalSeqC), Blood (Hash5-TotalSeqC), Heart (Hash6-TotalSeqC), Blood (Hash7-TotalSeqC), Heart (Hash8-TotalSeqC)

value: MRL(Hash1-TotalSeqC), MRL(Hash2-TotalSeqC), MRL/Pdcd1 -/- (Hash3-TotalSeqC), MRL/Pdcd1 -/- (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC), MRL/Pdcd1 -/- (Hash7-TotalSeqC), MRL/Pdcd1 -/- (Hash8-TotalSeqC)


title: pbmc13-scRNA

value: MRL(Hash1-TotalSeqC), MRL(Hash2-TotalSeqC), MRL/Pdcd1 -/- (Hash3-TotalSeqC), MRL/Pdcd1 -/- (Hash4-TotalSeqC), MRL (Hash5-TotalSeqC), MRL (Hash6-TotalSeqC)


title: pbmc12-scRNA

value: MRL(Hash1-TotalSeqC), MRL(Hash2-TotalSeqC), MRL/Pdcd1 -/- (Hash3-TotalSeqC), MRL/Pdcd1 -/- (Hash4-TotalSeqC)


title: pbmc11-scRNA

value: Blood


title: Meningioma 079

description: Hybridized to Agilent aCGH


title: PBMC14-TCR

value: single-cell TCR seq


title: pbmc10-scRNA

value: Heart


title: Meningioma 078

description: Hybridized to Agilent aCGH


title: WT_hom_testis_input.ChIPseq_rep2

city: Portland

first: Mariam

last: Okhovat

state: Oregon

address: 3030 S Moody Ave.

department: Medicine

institute: Oregon Health and Science University

library_source: genomic

data_processing:
Raw reads were aligned to mm10 reference genome using bowtie2, with default settings
Alignments were converted to bam and filtered to remove low quality mapped reads using samtools
macs2 was used to generate fold-enrichment tracks for each sample
Assembly: mm10
Supplementary files format and content: Processed data are bigwig files containing CTCF ChIP-seq fold-enrichment for each sample againts corresponding input

source_name: testis

extract_protocol:
50-100mg of lightly chopped testits tissue was fixed with formaldehyde before quenching with glycine and then needle homogenized. The tissue slurry was pelleted and then lysed with 100ul of Lysis Buffer per 10mg of tissue. Using the Bioruptor Pico sonicator (Diagenode), we sheared lysates and spun the sonicated lysates at max speed for 10min at 4°C to remove cell debris and then rotated them for 2hr at 4°C with 20ul ChIP-grade Protein A/G Magnetic Beads (Pierce) to preclear the lysate. From each chromatin preparation, a 1% volume aliquot was set aside as chromatin input. Pull downs were done with 10ul CTCF (3418s, Cell Signaling Technologies) with overnight rotation at 4°C. Next, we added 20ul Pierce ChIP-grade Protein A/G Magnetic Beads (Pierce) and let samples rotate for 2hrs at 4°C. We then washed the beads consecutively with TBST buffer, Lysis buffer and 1xTE pH=8. Following washes, we eluted chromatin and incubated the ChIP and input samples overnight at 65°C in presence of NaCl to reverse crosslinks and then digested them consecutively with 8ug RNAse A and 80ug Proteinase K. Lastly, we purified the samples using traditional phenol:chloroform extraction and ethanol precipitation.
ChIP-seq libraries were contructed using the NEBNext UltraII kit according to manufactor's instructions.

tag: antibody

value: input

value: testis

value: WT


title: WT_hom_testis_input.ChIPseq_rep3


title: Meningioma 076

description: Hybridized to Agilent aCGH

value: Brain tumor

value: M


title: WT_hom_testis_input.ChIPseq_rep1


title: Meningioma 075

description: Hybridized to Agilent aCGH

value: F


title: Meningioma 074

description: Hybridized to Agilent aCGH

value: Normal Brain


title: KO_hom_testis_input.ChIPseq_rep3


title: Meningioma 073

description: Hybridized to Agilent aCGH


title: KO_hom_testis_input.ChIPseq_rep2


title: Meningioma 072

description: Hybridized to Agilent aCGH


title: KO_hom_testis_input.ChIPseq_rep1


title: WT_hom_testis_CTCF.ChIPseq_rep3

value: CTCF


title: Meningioma 071

description: Hybridized to Agilent aCGH


title: WT_hom_testis_CTCF.ChIPseq_rep2


title: Meningioma 070

description: Hybridized to Agilent aCGH


title: Meningioma 069

description: Hybridized to Agilent aCGH


title: Meningioma 082

description: Hybridized to Agilent aCGH


title: WT_hom_testis_CTCF.ChIPseq_rep1


title: KO_hom_testis_CTCF.ChIPseq_rep2


title: Meningioma 067

description: Hybridized to Agilent aCGH


title: KO_hom_testis_CTCF.ChIPseq_rep3


title: Meningioma 080

description: Hybridized to Agilent aCGH


title: Meningioma 068

description: Hybridized to Agilent aCGH


title: Meningioma 066

description: Hybridized to Agilent aCGH


title: Meningioma 064

description: Hybridized to Agilent aCGH


title: Meningioma 077

description: Hybridized to Agilent aCGH


title: Embryo L49-3, microdissected heart field at stage E8.5f, left side

city: Paris

first: Sigolène

middle: M

last: Meilhac

address: 24 boulevard du Montparnasse

country: France

institute: Institut Imagine, Institut Pasteur

description: L49-3 L

data_processing:
FASTQ files were mapped to the ENSEMBL Mouse GRCm38/mm10 reference using Hisat2 and counted by featureCounts from the Subread R package
Read count normalizations and group comparisons were performed using DESeq2 statistical method: DESeq2. Due to a high number of duplicates (on average 89%), duplicates were excluded.
P50 lists used for the statistical analysis gather genes showing flag=1 for at least half of the samples.
Clustering of samples by stage and side was controlled by hierarchical clustering using the Spearman correlation similarity measure and ward linkage algorithm.
Differential gene expression analysis was performed using the Limma R package v3.40.6 (Wu and Smyth, 2012).
Assembly: GRCm38/mm10
Supplementary files format and content: DataCount_E8-5f.txt : Table obtained after FASTQ files were mapped to the ENSEMBL Mouse GRCm38/mm10 reference using Hisat2 and counted by featureCounts from the Subread R package.
Supplementary files format and content: GSE237126_results_LimmaVoom_Lf_vs_Rf.xlsx : Table containing the differential gene expression analysis using LimmaVoom. The column "Color_fig_1B" refers to Figure 1B in the publication.

molecule: polyA RNA

source_name: microdissected heart field

extract_protocol:
RNA was extracted in TRIzol-Chloroform and purified using the RNeasy micro kit (QIAGEN). RNA quality and quantity were assessed using Fragment Analyzer (Agilent Technologies). All RQNs were higher than 9.7.
The library was established using the Nugen Universal Plus mRNA-Seq kit, using 15 ng of total RNA per sample. The oriented cDNAs produced from the poly-A+ fraction were PCR amplified (15-18 cycles). An equimolar pool of the final indexed RNA-Seq libraries was sequenced on an Illumina NovaSeq6000, with paired-end reads of 130 bases and a mean sequencing depth of 37,15 million reads per sample.

treatment_protocol: Embryos were microdissected and the tissue was flash frozen in liquid nitrogen

tag: developmental stage

value: stage E8.5f

tag: side

value: left side

value: microdissected heart field

tag: strain

value: Wild-type

value: male


title: Meningioma 065

description: Hybridized to Agilent aCGH


title: Embryo L46-8, microdissected heart field at stage E8.5f, right side

description: L46-8 R

value: right side


title: Embryo L49-3, microdissected heart field at stage E8.5f, right side

description: L49-3 R


title: Embryo L46-8, microdissected heart field at stage E8.5f, left side

description: L46-8 L


title: Meningioma 061

description: Hybridized to Agilent aCGH


title: Embryo L43-5, microdissected heart field at stage E8.5f, left side

description: L43-5 L


title: Embryo L43-5, microdissected heart field at stage E8.5f, right side

description: L43-5 R


title: Meningioma 062

description: Hybridized to Agilent aCGH


title: Meningioma 060

description: Hybridized to Agilent aCGH


title: Meningioma 063

description: Hybridized to Agilent aCGH


title: Meningioma 059

description: Hybridized to Agilent aCGH


title: Meningioma 057

description: Hybridized to Agilent aCGH


title: KO_het_testis_RNAseq_rep3

data_processing:
Reads were aligned to the mm10 genome using STAR
The raw gene counts table generated and normalized to Transcript Per Million (TPM) values using custom R scripts
We used the linear regression method from MatrixEQTL and considered genes >100Kb from the center of the deletion to be in “cis” with the genotype locus (i.e. deletion). All other genes were considered is “trans
mm10
Tables containing results of the MatrixEqtl regression for genes in Cis and Trans.

extract_protocol:
total RNA from the testis (three replicates per genotypes) was extracted  using the Monarch total RNA mini prep Kit (New England Biolabs).
RNA-seq libraries were generated using the NEBNext rRNA Depletion Kit (New-England Biolabs) and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina kit (New England Biolabs), according to manufacturer's instructions.

value: B396.BOS heterozygous KO


title: Meningioma 058

description: Hybridized to Agilent aCGH


title: Embryo L29-3, microdissected heart field at stage E8.5f, left side

description: L29-3 L


title: Meningioma 056

description: Hybridized to Agilent aCGH


title: KO_het_testis_RNAseq_rep2


title: KO_het_testis_RNAseq_rep1


title: KO_hom_testis_CTCF.ChIPseq_rep1


title: Meningioma 055

description: Hybridized to Agilent aCGH


title: Meningioma 054

description: Hybridized to Agilent aCGH


title: Meningioma 053

description: Hybridized to Agilent aCGH


title: Wild-type_testis_RNAseq_rep2


title: Wild-type_testis_RNAseq_rep1


title: Wild-type_testis_RNAseq_rep3


title: Meningioma 051

description: Hybridized to Agilent aCGH


title: Meningioma 052

description: Hybridized to Agilent aCGH


title: KO_hom_testis_RNAseq_rep3

value: B396.BOS homozygous KO


title: Meningioma 050

description: Hybridized to Agilent aCGH


title: KO_hom_testis_RNAseq_rep1


title: WT_hom_testis_CaptureHiC_rep3

data_processing:
Raw capture HiC data was aligned to mm10 genome using HiCUP.
Pairtools was used to further process data and generate interaction matrices across replicates in each genotype.
mm10
Text files containing interaction frequnecy matrice

extract_protocol:
We used the Arima HiC kit to process mouse testis and heart tissues. Briefly, frozen tissue was lysed and conditioned before chromatin digestion. The digested chromatin was then filled in and biotinylated before ligation. Next, chromatin was protein-digested and reverse crosslinking overnight, followed by purification. The purified DNA was then sonicated using the bioruptor pico (Diagenode) and size selected before library preparation using the NEB DNA Ultra II, following Arima’s protocol.
The Hi-C DNA was bound to streptavidin beads before enzymatic end prep, adaptor ligation, DNA release by heat incubation, and lastly, PCR to barcode and amplify the libraries. Capture Hi-C libraries were generated by using the Agilent SureSelect Target Enrichment Kit.


title: Meningioma 048

description: Hybridized to Agilent aCGH


title: WT_hom_testis_CaptureHiC_rep2


title: Meningioma 049

description: Hybridized to Agilent aCGH


title: Embryo L29-3, microdissected heart field at stage E8.5f, right side

description: L29-3 R


title: KO_hom_testis_RNAseq_rep2


title: Meningioma 046

description: Hybridized to Agilent aCGH


title: KO_hom_testis_CaptureHiC_rep3


title: KO_hom_testis_CaptureHiC_rep2


title: Meningioma 044

description: Hybridized to Agilent aCGH


title: Meningioma 045

description: Hybridized to Agilent aCGH


title: KO_hom_testis_CaptureHiC_rep1


title: Meningioma 043

description: Hybridized to Agilent aCGH


title: Chronic EAE infiltrating, biol rep 3

city: Cambridge

first: Regan

last: Hamel

address: Cambridge Biosciences Campus, Hills Rd

department: Clinical Neurosciences

country: United Kingdom

institute: University of Cambridge

description:
10x Genomics
barcodes.tsv.gz
features.tsv.gz
matrix.mtx.gz
cell_metadata.csv

data_processing:
Fastq files were demultiplexed and aligned to the GRCm38 (mm10) reference transcriptome using the Cell Ranger 3.1.0 pipeline (10x Genomics). ScRNAseq data processing (post-Cell Ranger) was performed in R version 4.1.3. All packages are publicly available at the Comprehensive R Archive Network (https://cran.r-project.org), the Bioconductor project (http://bioconductor.org), or their respective GitHub pages. The original code is available at https://github.com/regan-hamel/ComplexI.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz - cell barcodes in a tsv format
Supplementary files format and content: matrix.mtx.gz - gene count matrix in mtx format
Supplementary files format and content: features.tsv.gz - gene names in tsv format
Supplementary files format and content: cell_metadata.csv - medata including basic QC metrics, cell type annotations, cluster identifiers, and experimental data (e.g. FACS group, date collected)

source_name: CNS

extract_protocol:
After perfusion, spinal cords were extracted from the spinal columns using a 5 mL syringe filled with ice-cold artificial CSF (aCSF). Spinal cords were mechanically dissociated in a glass Dounce tissue homogenizer with 6 mL of homogenization buffer [aCSF plus 10 mM HEPES (Sigma), 1% bovine serum albumin (BSA) (Sigma), 1 mM EDTA (Thermo Fisher Scientific), 10 mg/ml of DNAse (3000U, Roche), and 40 units/mL of RNAse inhibitor (Invitrogen)]. After tissue dissociation, the suspension was filtered through a pre-wet 40 μM strainer and the homogenizer rinsed with 2 mL of homogenization buffer. Samples were then transferred to 15 mL Falcon tubes and 2.7 ml of 90% Percoll (GE Healthcare) in 10x PBS (Thermo Fisher Scientific) was added to each sample to remove myelin and debris. The 15 mL Falcon tubes were then inverted 10 times gently and the samples were centrifuged at 800 x g for 20 minutes at 4°C with a brake speed of 0. Myelin debris visibly layered at the surface was carefully removed with a pipette. Ice-cold buffer [95% autoMACS rinsing solution (Miltenyi Biotec) and 5% MACS BSA (Miltenyi Biotec)] was added to the samples (to fill the 15 mL tubes) and samples were centrifuged at 800 x g for 5 minutes at 4°C to remove the remaining Percoll. Pellets were resuspended in ice-cold aCSF (1 mL+7 mL) and then further centrifuged at 800 x g for 5 minutes at 4°C.  Pelleted cells were resuspended in 200 mL of FACS buffer [Cell Staining Buffer (Biolegend) plus 10 mM HEPES, 1% BSA, 1 mM EDTA, 10 mg/mL of DNAse, and 40 units/mL of RNAse inhibitor] and 7-AAD live/dead stain (Thermo Fisher Scientific) added at a concentration of 1:50.    The samples were sorted using a BD FACS Aria III cell sorter set to 3-way purity with a 100  mm nozzle at 20 psi. The live cells gates were set based on the unstained WT sample, 7-AAD stained WT sample treated with DMSO (positive control for cell death), and non-TAM treated Cx3cr1YFPCreERT2: R26tdTomato samples (to control for bleed-through). Up to 18,000 cells per sample were loaded into each well and the resultant libraries were sequenced with the NovaSeq 6000 (Illumina) to depth of at least 50,000 reads per cell as calculated by Cell Ranger.
v3 10x Genomics Chromium Single Cell 3’ Solution

value: CNS

tag: disease state

value: Chronic EAE

value: CNS infiltrating myeloid cells


title: Meningioma 042

description: Hybridized to Agilent aCGH


title: Chronic EAE resident, biol rep 3

value: CNS resident myeloid cells


title: Meningioma 041

description: Hybridized to Agilent aCGH

value: Brain tumor


title: Chronic EAE resident, biol rep 2


title: Meningioma 040

description: Hybridized to Agilent aCGH


title: Meningioma 039

description: Hybridized to Agilent aCGH

value: M


title: Meningioma 038

description: Hybridized to Agilent aCGH


title: Chronic EAE infiltrating, biol rep 1


title: Meningioma 037

description: Hybridized to Agilent aCGH

value: F


title: Chronic EAE resident, biol rep 1


title: Meningioma 036

description: Hybridized to Agilent aCGH

value: Normal Brain


title: Meningioma 035

description: Hybridized to Agilent aCGH


title: Control resident, biol rep 2

value: Control


title: Peak EAE infiltrating, biol rep 2

value: Peak EAE


title: Meningioma 047

description: Hybridized to Agilent aCGH


title: WT_hom_testis_CaptureHiC_rep1

value: testis


title: Meningioma 033

description: Hybridized to Agilent aCGH


title: Meningioma 032

description: Hybridized to Agilent aCGH


title: Control resident, biol rep 1


title: Peak EAE infiltrating, biol rep 1


title: Meningioma 031

description: Hybridized to Agilent aCGH


title: Meningioma 030

description: Hybridized to Agilent aCGH


title: Meningioma 1040

description: Hybridized to OncoScanHD

hyb_protocol: DNA was restriction digested, PCR amplified, fragmented, labeled and hybridized to each array according to the manufacturer's instructions.

scan_protocol: Arrays were then washed using Affymetrix GeneChip Fluidics Station 450, and scanned using the Gene Chip Scanner 3000.

data_processing:
Data analysis was performed using Chromosome Analysis Suite software version 1.2.2
[primary data description] Fluorescent intensity values across SNP probes

label: Biotin

source_name: Meningioma Tissue

label_protocol: As per manufacturer (Affymetrix)

value: Brain


title: Meningioma 1039

description: Hybridized to OncoScanHD


title: Meningioma 028

description: Hybridized to Agilent aCGH


title: Chronic EAE infiltrating, biol rep 2


title: Meningioma 027

description: Hybridized to Agilent aCGH


title: Meningioma 1038

description: Hybridized to OncoScanHD


title: Meningioma 025

description: Hybridized to Agilent aCGH


title: Meningioma 026

description: Hybridized to Agilent aCGH


title: Meningioma 1037

description: Hybridized to OncoScanHD


title: Control resident, biol rep 3


title: Meningioma 1036

description: Hybridized to OncoScanHD


title: Peak EAE resident, biol rep 2


title: Meningioma 024

description: Hybridized to Agilent aCGH


title: Meningioma 034

description: Hybridized to Agilent aCGH


title: Meningioma 1035

description: Hybridized to OncoScanHD


title: Peak EAE resident, biol rep 1


title: Meningioma 023

description: Hybridized to Agilent aCGH


title: Meningioma 1034

description: Hybridized to OncoScanHD


title: Meningioma 1033

description: Hybridized to OncoScanHD


title: Meningioma 021

description: Hybridized to Agilent aCGH


title: Meningioma 022

description: Hybridized to Agilent aCGH


title: Meningioma 020

description: Hybridized to Agilent aCGH


title: Meningioma 1041

description: Hybridized to OncoScanHD


title: Meningioma 029

description: Hybridized to Agilent aCGH


title: Meningioma 1032

description: Hybridized to OncoScanHD


title: Meningioma 018

description: Hybridized to Agilent aCGH


title: Meningioma 019

description: Hybridized to Agilent aCGH


title: Meningioma 017

description: Hybridized to Agilent aCGH


title: Meningioma 1028

description: Hybridized to OncoScanHD


title: Meningioma 1027

description: Hybridized to OncoScanHD


title: Meningioma 016

description: Hybridized to Agilent aCGH


title: Meningioma 015

description: Hybridized to Agilent aCGH


title: Meningioma 1026

description: Hybridized to OncoScanHD


title: Meningioma 014

description: Hybridized to Agilent aCGH


title: Meningioma 013

description: Hybridized to Agilent aCGH


title: Meningioma 1024

description: Hybridized to OncoScanHD


title: Meningioma 1023

description: Hybridized to OncoScanHD


title: Meningioma 011

description: Hybridized to Agilent aCGH


title: Meningioma 1022

description: Hybridized to OncoScanHD


title: Meningioma 010

description: Hybridized to Agilent aCGH


title: Meningioma 1021

description: Hybridized to OncoScanHD


title: Meningioma 009

description: Hybridized to Agilent aCGH


title: Meningioma 1019

description: Hybridized to OncoScanHD


title: Meningioma 1020

description: Hybridized to OncoScanHD


title: Meningioma 008

description: Hybridized to Agilent aCGH


title: Meningioma 1031

description: Hybridized to OncoScanHD


title: Meningioma 1018

description: Hybridized to OncoScanHD


title: Meningioma 1030

description: Hybridized to OncoScanHD


title: Meningioma 006

description: Hybridized to Agilent aCGH


title: Meningioma 1029

description: Hybridized to OncoScanHD


title: Meningioma 005

description: Hybridized to Agilent aCGH


title: Meningioma 1017

description: Hybridized to OncoScanHD


title: Meningioma 003

description: Hybridized to Agilent aCGH


title: Meningioma 1015

description: Hybridized to OncoScanHD


title: Meningioma 1014

description: Hybridized to OncoScanHD


title: Meningioma 1025

description: Hybridized to OncoScanHD


title: Meningioma 002

description: Hybridized to Agilent aCGH


title: Meningioma 1013

description: Hybridized to OncoScanHD


title: Meningioma 012

description: Hybridized to Agilent aCGH


title: Meningioma 1011

description: Hybridized to OncoScanHD


title: Meningioma 001

description: Hybridized to Agilent aCGH


title: Meningioma 1010

description: Hybridized to OncoScanHD


title: Meningioma 1009

description: Hybridized to OncoScanHD


title: Meningioma 703

description: Hybridized to Agilent aCGH


title: Meningioma 632

description: Hybridized to Agilent aCGH


title: Meningioma 633

description: Hybridized to Agilent aCGH


title: Meningioma 007

description: Hybridized to Agilent aCGH


title: Meningioma 1008

description: Hybridized to OncoScanHD


title: Meningioma 1007

description: Hybridized to OncoScanHD


title: Meningioma 592

description: Hybridized to Agilent aCGH


title: Meningioma 624

description: Hybridized to Agilent aCGH


title: Meningioma 1006

description: Hybridized to OncoScanHD


title: Meningioma 601

description: Hybridized to Agilent aCGH


title: Meningioma 1005

description: Hybridized to OncoScanHD


title: Meningioma 1004

description: Hybridized to OncoScanHD


title: Meningioma 591

description: Hybridized to Agilent aCGH


title: Meningioma 004

description: Hybridized to Agilent aCGH


title: Meningioma 579

description: Hybridized to Agilent aCGH


title: Meningioma 557

description: Hybridized to Agilent aCGH


title: Meningioma 1003

description: Hybridized to OncoScanHD


title: Meningioma 1012

description: Hybridized to OncoScanHD


title: Meningioma 1000

description: Hybridized to OncoScanHD


title: Meningioma 1042

description: Hybridized to Agilent aCGH


title: Meningioma 537

description: Hybridized to Agilent aCGH


title: Meningioma 999

description: Hybridized to OncoScanHD


title: Meningioma 1001

description: Hybridized to OncoScanHD


title: Meningioma 519

description: Hybridized to Agilent aCGH


title: Meningioma 522

description: Hybridized to Agilent aCGH


title: Meningioma 996

description: Hybridized to OncoScanHD


title: Meningioma 512

description: Hybridized to Agilent aCGH


title: Meningioma 511

description: Hybridized to Agilent aCGH


title: Meningioma 509

description: Hybridized to Agilent aCGH


title: Meningioma 995

description: Hybridized to OncoScanHD


title: Meningioma 1016

description: Hybridized to OncoScanHD


title: Meningioma 510

description: Hybridized to Agilent aCGH


title: Meningioma 508

description: Hybridized to Agilent aCGH


title: Meningioma 506

description: Hybridized to Agilent aCGH


title: Meningioma 992

description: Hybridized to OncoScanHD


title: Meningioma 991

description: Hybridized to OncoScanHD


title: Meningioma 994

description: Hybridized to OncoScanHD


title: Meningioma 997

description: Hybridized to OncoScanHD


title: Meningioma 507

description: Hybridized to Agilent aCGH


title: Meningioma 993

description: Hybridized to OncoScanHD


title: Meningioma 990

description: Hybridized to OncoScanHD


title: Meningioma 504

description: Hybridized to Agilent aCGH


title: Meningioma 1002

description: Hybridized to OncoScanHD


title: Meningioma 523

description: Hybridized to Agilent aCGH


title: Meningioma 505

description: Hybridized to Agilent aCGH


title: Meningioma 503

description: Hybridized to Agilent aCGH


title: Meningioma 989

description: Hybridized to OncoScanHD


title: Meningioma 988

description: Hybridized to OncoScanHD


title: Meningioma 502

description: Hybridized to Agilent aCGH


title: Meningioma 987

description: Hybridized to OncoScanHD


title: Meningioma 500

description: Hybridized to Agilent aCGH


title: Meningioma 985

description: Hybridized to OncoScanHD


title: Meningioma 501

description: Hybridized to Agilent aCGH


title: Meningioma 998

description: Hybridized to OncoScanHD


title: Meningioma 986

description: Hybridized to OncoScanHD


title: Meningioma 984

description: Hybridized to OncoScanHD


title: Meningioma 498

description: Hybridized to Agilent aCGH


title: Meningioma 982

description: Hybridized to OncoScanHD


title: Meningioma 499

description: Hybridized to Agilent aCGH


title: Meningioma 983

description: Hybridized to OncoScanHD


title: Meningioma 981

description: Hybridized to OncoScanHD


title: Meningioma 496

description: Hybridized to Agilent aCGH


title: Meningioma 495

description: Hybridized to Agilent aCGH


title: Meningioma 497

description: Hybridized to Agilent aCGH


title: Meningioma 980

description: Hybridized to OncoScanHD


title: Meningioma 979

description: Hybridized to OncoScanHD


title: Meningioma 493

description: Hybridized to Agilent aCGH


title: Meningioma 494

description: Hybridized to Agilent aCGH


title: Meningioma 977

description: Hybridized to OncoScanHD


title: Meningioma 491

description: Hybridized to Agilent aCGH


title: Meningioma 978

description: Hybridized to OncoScanHD


title: Meningioma 975

description: Hybridized to OncoScanHD


title: Meningioma 492

description: Hybridized to Agilent aCGH


title: Meningioma 489

description: Hybridized to Agilent aCGH


title: Meningioma 490

description: Hybridized to Agilent aCGH


title: Meningioma 976

description: Hybridized to OncoScanHD


title: Meningioma 974

description: Hybridized to OncoScanHD


title: Meningioma 488

description: Hybridized to Agilent aCGH


title: Meningioma 973

description: Hybridized to OncoScanHD


title: Meningioma 486

description: Hybridized to Agilent aCGH


title: Meningioma 972

description: Hybridized to OncoScanHD


title: Meningioma 487

description: Hybridized to Agilent aCGH


title: Meningioma 971

description: Hybridized to OncoScanHD


title: Meningioma 485

description: Hybridized to Agilent aCGH


title: Meningioma 970

description: Hybridized to OncoScanHD


title: Meningioma 968

description: Hybridized to OncoScanHD


title: Meningioma 484

description: Hybridized to Agilent aCGH


title: Meningioma 969

description: Hybridized to OncoScanHD


title: Meningioma 483

description: Hybridized to Agilent aCGH


title: Meningioma 967

description: Hybridized to OncoScanHD


title: Meningioma 966

description: Hybridized to OncoScanHD


title: Meningioma 481

description: Hybridized to Agilent aCGH


title: Meningioma 480

description: Hybridized to Agilent aCGH


title: Meningioma 965

description: Hybridized to OncoScanHD


title: Meningioma 479

description: Hybridized to Agilent aCGH


title: Meningioma 478

description: Hybridized to Agilent aCGH


title: Meningioma 964

description: Hybridized to OncoScanHD


title: Meningioma 963

description: Hybridized to OncoScanHD


title: Meningioma 962

description: Hybridized to OncoScanHD


title: Meningioma 475

description: Hybridized to Agilent aCGH


title: Meningioma 961

description: Hybridized to OncoScanHD


title: Meningioma 477

description: Hybridized to Agilent aCGH


title: Meningioma 476

description: Hybridized to Agilent aCGH


title: Meningioma 959

description: Hybridized to OncoScanHD


title: Meningioma 960

description: Hybridized to OncoScanHD


title: Meningioma 473

description: Hybridized to Agilent aCGH


title: Meningioma 474

description: Hybridized to Agilent aCGH


title: Meningioma 472

description: Hybridized to Agilent aCGH


title: Meningioma 958

description: Hybridized to OncoScanHD


title: Meningioma 957

description: Hybridized to OncoScanHD


title: Meningioma 471

description: Hybridized to Agilent aCGH


title: Meningioma 955

description: Hybridized to OncoScanHD


title: Meningioma 956

description: Hybridized to OncoScanHD


title: Meningioma 470

description: Hybridized to Agilent aCGH


title: Meningioma 482

description: Hybridized to Agilent aCGH


title: Meningioma 954

description: Hybridized to OncoScanHD


title: Meningioma 469

description: Hybridized to Agilent aCGH


title: Meningioma 468

description: Hybridized to Agilent aCGH


title: Meningioma 953

description: Hybridized to OncoScanHD


title: Meningioma 951

description: Hybridized to OncoScanHD


title: Meningioma 950

description: Hybridized to OncoScanHD


title: Meningioma 952

description: Hybridized to OncoScanHD


title: Resistant type- #4

type: RNA

city: Hirosaki

first: Satoru

last: Monzen

state: Aomori

address: Hon-cho 66-1

country: Japan

institute: Hirosaki University

hyb_protocol: A SurePrint G3 human miRNA microarray slide (8x60 K, Ver. 16.0) was hybridised with the Cy3-labelled miRNA in a hybridisation solution prepared with a Gene Expression Hybridisation Kit (Agilent Technologies, Inc.), following the manufacturer’s instructions.

scan_protocol: Cy3 fluorescence signal images on the slide were obtained by a microarray scanner (Agilent SureScan Microarray Scanner G 2600 D; Agilent Technologies, Inc.) and processed using the Feature Extraction version 10.7 software based on the instructions from Agilent Technologies.

data_processing: The expression data were processed using GeneSpring GX14.5 software (Agilent Technologies, Inc.) to make a normalisation to percentile shift 90% of all values on the respective microarrays, followed by normalisation of the median expression level of all samples.

label_protocol: Cy3-labelled miRNA was synthesised from 100 ng total RNA of HL60 cell of wild-type or Resistant-type cell using an miRNA Complete Labelling Reagent and Hyb kit (Agilent Technologies, Inc.).

extract_protocol: The intracellular small RNAs in each sample were extracted from cultured cell using ISOGEN kit (NIPPON Gene Inc.) according to the manufacturer's instructions.

treatment_protocol: HL60 cell was exposed from higher dose rate of X-irradiation (4 times per 4 weeks, total dose is 16 Gy) and the after samples were incubated at least 7 days in the condition of RPMI1640 medium with 10%FBS.

value: radiation-resistant


title: Meningioma 949

description: Hybridized to OncoScanHD


title: Resistant type- #2


title: Resistant type- #3


title: Meningioma 947

description: Hybridized to OncoScanHD


title: Wild type- #4

value: WT


title: Wild type- #3


title: Wild type- #2


title: Resistant type- #1


title: Meningioma 946

description: Hybridized to OncoScanHD


title: tent2ko_cloneB.rep3

city: La Jolla

first: Cody

last: Ocheltree

address: 9500 Gilman Drive

institute: UCSD

description:
Library name: Sample-160
tent2ko_cloneB.rep3_7SL_counts.csv_Taildata.csv

data_processing:
FASTQ files were first subjected to 3’ adaptor, PCR duplicate removal, and gene-specific barcode and primer sequence removal using custom python scripts (https://pypi.org/project/jla-demultiplexer/).
Reads were aligned to small RNAs of interest using in-house alignment scripts.
Gene-specific 3’ end information and graphs were subsequently generated using in-house scripts.
For SLAMseq, gene-specific alignments were performed using in-house scripts which permitted T>C conversions. The number of conversions for each read was quantified and reads with two or more conversions were subsequently analyzed as nascently-labeled reads.
Assembly: human genome (version hg38)
Supplementary files format and content: comma separated variable table with RNA counts, 3' end position, and 3' post-transcriptional nucleotides

molecule: other

source_name: HEK 293T-REx

growth_protocol: All cells were maintained in Dulbecco’s Modified Eagle Medium (DMEM, Gibco) supplemented with 10% Fetal Bovine Serum (FBS, Gibco) and 1% penicillin/streptomycin (Gibco) at 37°C, 5% CO2.

extract_protocol:
RNA was isolated using TRIzol (Thermo Fisher) per manufacturer’s recommendation. RNA was subsequently treated with DNase I (1 U/µl; Zymo research) in DNase buffer (10 mM Tris-HCl pH 7.5, 2.5 mM MgCl2, 0.5 mM CaCl2) at 25˚ C for 15 minutes, followed by extraction with phenol:chloroform:isoamyl alcohol and ethanol precipitation. For RNA immunoprecipitations, cells were harvested by scraping into ice cold PBS and flash frozen in liquid nitrogen. Cells were resuspended in ice-cold isotonic lysis buffer (50 mM Tris-HCl pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.5% Triton X-100, 80 U/mL RNaseOut (Thermo Fisher), protease inhibitor tablet/10 mL (Roche)) and incubated with rotation for 20 minutes at 4°C. Cellular debris was pelleted at 13,000 g for 15 minutes at 4°C. The supernatant was briefly pre-cleared using Protein G beads (Thermo Fisher, 10004D) for 10 minutes at 4°C with rotation. Beads for immunoprecipitation were washed with bead wash buffer (PBS pH 7.4, 0.1% Tween 20) and subsequently incubated with anti-La antibody (Santa Cruz Biotechnology, sc-80656), anti-SRP54 antibody (Invitrogen, MA5-34835), rabbit IgG (Cell Signaling Technology, 2729), or mouse IgG1 (Cell Signaling Technology, 5415) antibody for 1 hour at 4°C with rotation, then washed with bead wash buffer. Sample protein was quantified with a BCA assay (Thermo Fisher). 1 mg of protein per sample was diluted 5-fold with ice-cold detergent dilution buffer (isotonic lysis buffer without Triton X-100) and incubated with antibody-bead complexes for 1 hour at 4°C with rotation. Samples were washed 5 times with ice-cold immunoprecipitation wash buffer (PBS pH 7.4, 0.1% Tween 20, 150 mM NaCl) at 4°C. RNA from input and immunoprecipitation material was extracted with TRIzol (Thermo Fisher) according to the manufacturer’s recommendation. For SLAMSeq, samples were treated with either iodoacetamide (IAA) or dimethylsulfoxide (DMSO) for 15 minutes at 50°C prior to 3' adaptor ligation. Gene-specific 3’-end sequencing libraries were prepared as described above.
RNA adapters containing barcodes and 10- to 16-nt randomers (AG10/AG11/AG15/AG16) were ligated to the 3′ ends of 2 μg of extracted RNA in a 10-μL reaction containing 1 μL of 10xT4 RNA ligase buffer (500 mM Tris-HCl, 100 mM MgCl2, 10 mM DTT at pH at 25°C), 0.2 mg/mL bovine serum albumin (BSA), 2 μM AG10 or AG11, 1 mM ATP, 10 U of T4 RNA ligase (NEB), and 40 units of RNaseOUT (Invitrogen) for 16 h at 16°C and extracted with phenol/chloroform/isoamyl alcohol. cDNA was generated using SuperScript III (SSRT III; Thermo Fisher) in a 20-μL reaction using 0.5 μM linker-specific primer AR-17. For sequencing, snRNA cDNA 3′ ends were amplified in 16–30 cycles of polymerase chain reaction (PCR) with small RNA gene-specific forward primers and AR17 primer using Q5 DNA polymerase (NEB), and then eight cycles with primers D50x and D70x. Libraries were sequenced on an Illumina MiSeq platform.

treatment_protocol: RNA interference was performed in HEK 293T Flp-In cells (FIRT, Thermo Fisher) with 40 nM small interfering (si)RNA targeting genes of interest, or luciferase as a control, using siLentFect (Bio-Rad) transfection reagent according to manufacturer’s recommendations at 72 and 24 hours before cell harvest. Transient transfection of plasmid (10 µg/15 cm plate) containing exogenous 7SL and U1 sequences was performed 18 hours prior to harvest with Lipofectamine 2000 (Thermo Fisher) according to manufacturer’s recommendations. Control or TENT2 KO 293 T-REx cell media was treated with 4-thiouridine [s4U] at a final concentration of 100 µM and incubated for 3 hours, then refreshed with 100 µM s4U-containing media and incubated for an additional 3 hours.

value: HEK 293T-REx


title: Meningioma 945

description: Hybridized to OncoScanHD


title: mTSC,ezrmut,rna,2

city: Overland Park

first: Khyati

middle: Sudhir

last: Dalal

state: KS

address: 75th street, APT 106, 6329 W

institute: Stowers Institute for Medical Research

data_processing:
To get STAR count table for RNA-seq data:  100 bp single-end sequencing reads were aligned using STAR(v.2.7.3) (Dobin et al. 2013) to the Mus Musculus genome assembly mm10  using Ensembl 102 gene models with the following parameters: outSAMtype BAM SortedByCoordinate, outSAMprimaryFlag OneBestScore ,outFilterMultimapNmax 20, outFilterMismatchNoverLmax 0.1, outFilterType BySJout ,alignSJoverhangMin 8, alignSJDBoverhangMin 1,outFilterMismatchNmax 999,alignIntronMin 20,alignIntronMax 1000000,alignMatesGapMax 1000000,limitBAMsortRAM 10000000000 ,outSAMattributes NH HI MD AS nM, quantMode TranscriptomeSAM GeneCounts.
To get TPM for RNA-seq data : Rsem-calculate-expression (v1.3.0) (Li and Dewey 2011) was used to generate an expression table with the following parameters: no-bam-output, estimate-rspd, strandedness reverse. EdgeR analysis : Pairwise differential expression analysis was performed using Bioconductor package edgeR (3.24.3 with R 3.5.2). Only protein coding genes and long non-coding RNAs (lncRNAs) were considered from the Ens_102 annotation. Only genes with counts per million expression ≥ 0 in at least 2 sample were kept for further analyses. Statistical significance was determined by fold change cutoff of 1 and false discovery rate (FDR) cutoff of 0.05 .
For Nascent RNA captured through TT-seq method : 75 bp paired-end sequencing reads were aligned using STAR(v.2.7.3) (Dobin et al. 2013) to the Mus Musculus genome assembly mm10 with the following parameters: outFilterMismatchNmax 2, outFilterMultimapScoreRange 0. SAMtools (v.1.14) (Li et al. 2009) were then used to keep alignments with mapping quality greater than 255 (-q 255), and only proper pairs (-f 2) were selected. Strand-specific BAM files for each replicate and combined were generated using the following parameters (samtools view -b -f 128 -F 16; -b -f 80; -b -f 144; -b -f 64 -F 16) and (samtools merge plus_128.bam with plus_80.bam and minus_144.bam with minus_64.bam).
Normalized TT-seq coverage was generated using bamCoverage (v.3.1.3) (Ramírez et al. 2014) parameter Reads Per Kilobase per Million mapped reads (RPKM).
Assembly: UCSC mm10
Supplementary files format and content: BigWig, CSV,TSV

source_name: cells

growth_protocol: 70% Feeder-CM plus 30% TS medium (hereafter 70cond) supplemented with FGF4, and heparin (70cond + 1.5 F4H Medium) was used to maintain TSCs in feeder-free conditions

extract_protocol:
For RNA-seq experiments : TSCs wild-type and CRISPR-mutated ezr cells were grown separately in wells of a 6-well plate and harvested at 80% confluency (~2e6 cells) using 500 μL of TRIzol reagent (Life Technologies Corp-15596026). For RNA extraction, the lysate was quickly thawed at 65°C, cooled on ice for 5 minutes, and vortexed. Then, 100 μL of chloroform was added per 0.5 mL of TRIzol lysis reagent, shaken vigorously for 15 seconds, and incubated for 3 minutes. The sample was centrifuged at 4°C and 7000 x g for 25 minutes, and the upper colorless aqueous phase was transferred to a new tube. To this, 250 μL of isopropanol was added, incubated for 10 minutes at 4°C, and centrifuged at 4°C and 12,000 x g for 10 minutes. The total RNA precipitate formed a white gel-like pellet at the bottom of the tube, which was washed with 75% ethanol, air-dried for 5-10 minutes, and resuspended in 20 μL of RNase-free water. DNase treatment was performed using the TURBO DNase kit per the manufacturer's instructions: adding 1 ul of TURBO DNase & 2 ul of DNase buffer to the dissolved RNA and incubating at 37 degrees for 30 min. To inactivate TURBO DNase, RNA samples were extracted with phenol/chloroform (Sigma-P3803). After the total RNA pellet dissolved again in 20 ul of RNase-free water. Then, incubate the sample in a water bath or heat block set at 55-60°C for 10-15 minutes.
For RNA-seq,The RNA concentration was determined using a NanoDrop spectrophotometer, and The RNA integrity was checked on a 2100 Bioanalyzer using an Agilent RNA 6000 Nano Kit. mRNA-stranded libraries were prepared using a TruSeq poly-A Stranded mRNA Library Prep Kit and sequenced on an Illumina NextSeq 2000 P2 platform with 2 x 100 bp single-end reads.
For RNA-seq: mRNA-stranded libraries were prepared using a TruSeq poly-A Stranded mRNA Library Prep Kit
For Nascent RNA-seq, we used TT-Seq method as described: https://www.protocols.io/view/transient-transcriptome-sequencing-experimental-pr-3byl42y22vo5/v1; For trophoblast stem cells: approximately 10 million cells were seeded in a 100 cm dish (~80% confluency), and 500 µM of 4sU (Sigma, T4509) was added and kept at 37 °C, 5% CO2 for 15 mins. The cells were then collected by adding 4.5 mL of TRIzol lysis reagent (Life Technologies Corp-15596026), incubated for 5 min on ice, flash-frozen, and stored at −80°C. And in the biotinylation of 4sU labeled RNA step, acid-phenol-chloroform (ThermoFisher, AM9720) was used instead of chloroform.
For Nascent RNA-seq, Nascent RNA concentration was measured using the Qubit RNA HS Kit, and RNA integrity was analyzed on Agilent Bioanalyzer RNA 6000 Pico Chip and sequenced on an Illumina NextSeq 500  with 2 x 75 bp paired-end reads.
For Nascent RNA-seq: TruSeq Stranded Total RNA Library Prep Kit with Ribo-Zero Gold Set, which degrades rRNA with the enzyme.

value: cells

value: Wild-type

value: mouse trophoblast stem cells


title: mTSC,ezrmut,rna,1


title: Meningioma 944

description: Hybridized to OncoScanHD


title: mTSC,ezrmut,rna,3


title: Wild type- #1


title: mTSC,wildtype,rna,3


title: Meningioma 943

description: Hybridized to OncoScanHD


title: tent2ko_cloneB.rep1

description:
Library name: Sample-158
tent2ko_cloneB.rep1_7SL_counts.csv_Taildata.csv


title: mTSC,wildtype,rna,2


title: mTSC,wildtype,rna,1


title: Meningioma 942

description: Hybridized to OncoScanHD


title: Isolated hepatocytes Healthy, rep 3

city: Edinburgh

first: Stuart

last: Forbes

address: 5 Little France Drive

department: Centre for Regenerative Medicine

institute: The University of Edinburgh

data_processing:
Base call data generated by Illumina NextSeq 2000
Read quality assessed using FastQC and MultiQC (v.1.3.dev0)
Adapter, poly-G and low-quality base trimming with Cutadapt (v.1.16)
Read alignment with STAR (v.2.7.1a)
Read counting with featureCounts (Rsubread Bioconductor package v.2.0.1)
Differential expression computed using DESeq2 (v.1.34.0)
Assembly: GRCm38.100
Supplementary files format and content: Tab separated matrix table with raw gene counts for all genes and samples

source_name: liver

extract_protocol:
Hepatocytes were isolated from 10 – 12 week old mice following the standard two-step collagenase perfusion technique. Briefly, mice received a terminal dose of anesthetic and underwent laparotomy. The portal vein was cannulated and then perfused with 30 mL Liver Perfusion Medium (Gibco) followed by 50 mL Liver Digest Medium (Gibco) pre-warmed to 37°C. The liver was removed and then hepatocytes were mechanically disassociated and released from the Glisson capsule, filtered through 70 um filter and purified with a density gradient centrifugation.
500ng of each total-RNA sample was used for RNA-seq library preparation, using the NEBNEXT Ultra II Directional RNA Library Prep Kit (NEB #7760) and the Poly-A mRNA magnetic isolation module (NEB #E7490) according to the manufacturer’s protocol. AMPure XP beads (Beckman Coulter #A63881) were used to purify the cDNA library. Multiple indexing adapters were ligated to the ends of the ds cDNA to prepare them for hybridisation onto a flow cell, before 10 cycles of PCR were used to selectively enrich those DNA fragments that had adapter molecules on both ends and amplify the amount of DNA in the library suitable for sequencing. Following amplification, libraries were purified using AMPure XP beads. Completed libraries were quantified by fluorometry using the Qubit dsDNA HS assay and assessed for quality and fragment size using the Agilent Bioanalyser with the DNA HS Kit (#5067-4626).

value: liver

value: Hepatocytes

value: AhCre-

value: For Cre induction, intraperitoneal injections of β-naphthoflavone (Sigma-Aldrich) in corn oil at a dose of 20 mg/kg-1 for 48 hours


title: tent2ko_cloneA.rep3

description:
Library name: Sample-157
tent2ko_cloneA.rep3_7SL_counts.csv_Taildata.csv


title: Meningioma 941

description: Hybridized to OncoScanHD


title: Meningioma 948

description: Hybridized to OncoScanHD


title: Isolated hepatocytes Healthy, rep 1


title: tent2ko_cloneA.rep2

description:
Library name: Sample-156
tent2ko_cloneA.rep2_7SL_counts.csv_Taildata.csv


title: Meningioma 940

description: Hybridized to OncoScanHD


title: Isolated hepatocytes Senescent, rep 2


title: Isolated hepatocytes Senescent, rep 3


title: Meningioma 939

description: Hybridized to OncoScanHD


title: Isolated hepatocytes Senescent, rep 1


title: tent2ko_cloneA.rep1

description:
Library name: Sample-155
tent2ko_cloneA.rep1_7SL_counts.csv_Taildata.csv


title: IP_srp54_tent2ko_U1.rep3

description:
Library name: Sample-154
IP_srp54_tent2ko_rep3_combined_Taildata.csv


title: Inp_E

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

data_processing:
Raw sequencing reads in the fastq files were mapped with Bowtie2 (v.2.4.2)on the GRCh38.p13 reference genome.
Duplicates were marked with MarkDupliactes from Picard tools (v.2.25.1), and BAM files were filtered using samtools (v.1.12) with flag -F 1804 (remove reads unmapped, mate unmapped, not primary alignment, reads failing platform, duplicates and -q 20).
Peak calling was done with MACS2 (–nomodel –extsize) (v.2.2.7.1) for narrow peaks and EPIC2 (-g hs –genome hg38 –chromsizes –fragment-size –false-discovery-rate-cutoff 0.05) (v.0.0.52) for broad peaks.
Phantompeakqualtools was used to estimate the fragment size.
Assembly: GRCh38.p13
Supplementary files format and content: bigWig

source_name: Teratoma-derived hMSC

extract_protocol:
Cells were subjected to ChIP-PCR following standard procedures. Briefly, cells were fixed with crosslink solution (HEPES 50mM pH 8.0; NaCl 100mM; EDTA 1mM; EGTA 0.5mM; 0.5% Formaldehyde) for 10 min at room temperature, and incubated with stop solution (10% Glycine in Tris-HCl 10mM pH 8.0). Cells were lysed for 20 min on ice with 10 mM Tris-HCl pH 8.0, 0.25% Triton X-100, 10 mM EDTA, 0.5 mM EGTA, 20 mM β-glycerol-phosphate, 100 mM NA-orthovanadate, 10 mM Na Butyrate and complete protease inhibitor cocktail. The supernatants were sonicated, centrifuged at 13,000 rpm for 15 min, and supernatants were incubated overnight with the FLAG antibody (Merck Life Science) or with anti-mouse IgGs (Millipore). Precipitates were captured with protein A/G-Sepharose, extensively washed, and the crosslink was reverted by incubating the samples with Proteinase K.
NEBNext Ultra DNA Library Prep from Illumina

value: Teratoma-derived hMSC

value: hMSLC

value: EWS-FLI1 infection


title: Meningioma 938

description: Hybridized to OncoScanHD

value: M


title: IP_srp54_tent2ko_U1.rep1

description:
Library name: Sample-152
IP_srp54_tent2ko_rep1_combined_Taildata.csv


title: Meningioma 936

description: Hybridized to OncoScanHD

value: F


title: Meningioma 937

description: Hybridized to OncoScanHD


title: IgG_S

value: Control infection


title: tent2ko_cloneB.rep2

description:
Library name: Sample-159
tent2ko_cloneB.rep2_7SL_counts.csv_Taildata.csv


title: FL_S


title: FL_E


title: IP_srp54_tent2ko_U1.rep2

description:
Library name: Sample-153
IP_srp54_tent2ko_rep2_combined_Taildata.csv


title: IP_srp54_tent2ko_7sl.rep3

description:
Library name: Sample-151
IP_srp54_tent2ko_rep3_combined_Taildata.csv


title: COVID_Patient_1_Plac

city: Houston

first: Rachel

middle: A

last: Keuls

email: Rachel.Keuls@bcm.edu, rkeuls@gmail.com

state: TX

address: One Baylor Plaza

department: MCB

institute: Baylor College of Medicine

description: sci-rna-seq3 run 2

data_processing:
Demultiplexing using the BBI pipeline command bbi-demux (https://github.com/bbi-lab/bbi-dmux)
Aligment and count matrix generation using the BBI pipeline command bbi-sci (https://github.com/bbi-lab/bbi-sci/)
Cells were clustered in Seurat using cells with 10PCs, >500 features per cell, 2000 variable features used to cluster cells, and samples in the control group were merged together while samples in the COVID-19 group were merged together and then the two groups were integrated together. The processed Seurat objects containing nuclei from all patients are included as follows: the file COVIDvControl_500Features_5pctmito_2000VariableFeature_Limit-Integrated-10PCs-CLEANED-clustsless5cellsremoved.rds was used for visualization and the file COVIDvControl_500Features_5pctmito_2000VariableFeature_Limit-Integrated-10PCs-CLEANED.rds was used for covid v control differential expression
Assembly: human GRCh38 build and annotation from Ensembl (release 99)
Supplementary files format and content: Filtered Feature Matrix Files
Supplementary files format and content: Monocle3 CDS and Seurat RDS file

molecule: nuclear RNA

source_name: Chorionic Villi

growth_protocol: Placentas were delivered via cesarian section

extract_protocol:
Tissue samples were manually pulverized on dry ice, transferred to pre-chilled tubes, and stored at -80°C. Nuclei isolations were performed with the ‘hypotonic lysis buffer solution B’ [Martin et al. 2023]. Up to 200 mg of tissue was added to 5 mL of ‘hypotonic lysis buffer B’ for 5 to 25 minutes on ice with periodic agitation. For samples under 50 mg, 500 uL of ‘hypotonic lysis buffer B’ was added directly to the 1.5 mL sample tubes and a RNase-free pestle was used for 6 to 12 strokes to further dissociate the tissue. Released nuclei were passed through a 70-micron cell strainer, pelleted (500xg, 5 minutes, 4°C), and resuspended in 1 mL of cold ‘0.3 M SPBSTM’ (Martin et al. 2023). Pre-chilled fixative (5 mg of DSP resuspended in 100 uL DMSO per 4 mL of methanol) was incrementally added for every 1 mL of nuclei resuspended in ‘0.3 M SPBSTM’ and fixed on ice for 5 to 10 minutes. The nuclei were rehydrated by gradually adding 10 mL of ‘0.3 M SPBSTM’ for every 5 mL of fixed nuclei suspension prior to centrifugation (500xg, 5 minutes, 4°C) and resuspended in 1 mL of ‘0.3 M SPBSTM’. Nuclei suspensions processed in the third sci-RNA-seq3 experimental batch were additionally overlaid on 7 mL of a 1.4 M sucrose buffer (1.4 M sucrose, 1X phosphate buffered saline (8 mM Na2HPO4 (pH 7.4), 2 mM KH2PO4, 2.7 mM KCl, 137 mM NaCl), 3 mM MgCl2) and centrifuged at 3,000xg, 20 minutes, 4°C to remove excess debris; the pelleted nuclei were again resuspended in 1 mL of ‘0.3 M SPBSTM’ and passed through a 20-micron cell strainer. After counting, nuclei aliquots were centrifuged (500xg, 5 minutes, 4°C), supernatant aspirated, and pelleted nuclei stored at -80°C until use.
Methods for the first two sci-RNA-seq3 experimental batches largely followed those described by Cao et al. [Cao et al. 2019] with the following modifications: samples were counted with the ImageExpress Pico System (Molecular Devices), 2 μl of oligo(dT) primers were added to each well with 80,000 nuclei for reverse transcription, and tagmentation was performed using 1/40 μl per well of i7-loaded TDE1 enzyme prepared at the BAT-Lab following published protocols [Hennig et al. 2-18]. Libraries were sequenced on an Illumina Nextseq 200 cycles P3 kit with the following cycles: read 1, 34 cycles; read 2, 100 cycles; index 1, 10 cycles; index 2, 10 cycles. Methods for the third sci-RNA-seq3 experimental batch largely followed the optimized protocol described by Martin et al. (Martin et al. 2023) with the following modifications: samples were counted with the ImageExpress Pico System (Molecular Devices), 20,000 nuclei were loaded per reverse transcription well, tagmentation with N7 adaptor-loaded Tn5 transposases (Diagenode cat. no. C01070010-20) was performed at 1/80 uL per well across PCR plates, final library clean up was 0.5X AMPure XP supernatant followed by Qiagene GeneRead Size Selection purification column. The library was sequenced on an Illumina NovaSeq S4 flow cell at the University of Washington Northwest Genomics Center core sequencing facility with the following cycles: read 1, 34 cycles; read 2, 100 cycles; index 1, 10 cycles; index 2, 10 cycles. Read alignment and gene count matrix generation was performed using the Brotman Baty Institute (BBI) pipeline for sci-RNA-seq3 (https://github.com/bbi-lab/bbi-dmux; https://github.com/bbi-lab/bbi-sci). The human GRCh38 build and annotation from Ensembl (release 99) was used as the reference genome. The 3’ UTR annotations of genes and transcripts were extended by 500 bp to avoid misclassifying genic reads as intergenic, and haplotype sequences were removed from the FASTA to avoid mapping inefficiencies due to multimapping.

treatment_protocol: Placental biopsy tissue was washed extensively to remove maternal blood and maternal uterine tissue was largely removed and rolled membranebiopsies were washed to remove maternal blood

value: Chorionic Villi


title: Isolated hepatocytes Healthy, rep 2


title: Control_Patient_4_Plac

description: sci-rna-seq3 run 2

value: Control


title: IP_srp54_tent2ko_7sl.rep2

description:
Library name: Sample-150
IP_srp54_tent2ko_rep2_combined_Taildata.csv


title: Meningioma 935

description: Hybridized to OncoScanHD

value: Brain


title: Meningioma 934

description: Hybridized to OncoScanHD


title: Control_Patient_1_Plac

description: sci-rna-seq3 run 2


title: COVID_Patient_4_Plac

description: sci-rna-seq3 run 1


title: IP_srp54_tent2ko_7sl.rep1

description:
Library name: Sample-149
IP_srp54_tent2ko_rep1_combined_Taildata.csv

value: HEK 293T-REx


title: Control_Patient_2_Plac

description: sci-rna-seq3 run 1


title: Meningioma 933

description: Hybridized to OncoScanHD


title: Inp_S


title: IP_srp54_control_U1.rep3

description:
Library name: Sample-148
IP_srp54_control_rep3_combined_Taildata.csv


title: Control_Patient_3_Plac

description: sci-rna-seq3 run 1


title: IgG_E


title: COVID_Patient_2_Plac

description: sci-rna-seq3 run 1


title: Meningioma 932

description: Hybridized to OncoScanHD