title: multiplexed CSF cells11

city: Bethesda

first: Shinji

last: Ashdia

state: MD

address: 10 Center Drive

department: NIAID

institute: NIH

description: Library name: LIB_11267

data_processing:
In single cell RNA-seq data analysis, each raw data was counted, and QC was checked by Cellranger ver.9.0 (10X Genomics). Doublet cells were excluded by using DoubletFinder ver.2.0 and protein library from CITE-seq was denoised by using dsb package.
Assembly: human reference genome (hg38)
Supplementary files format and content: Tab-separated values (TSV) file, Indicate that the file contains processed data, such as gene expression matrices, cell metadata,generated by the 10x Cell Ranger pipeline.
Library strategy: CITE-seq

molecule: cytoplasmic RNA

source_name: CSF cells

extract_protocol:
CSF was collected on ice and processed according to a written standard operating procedure by investigators blinded to diagnoses, clinical, and imaging outcomes. Aliquots were assigned alphanumeric identifiers and centrifuged for 10 minutes at 300g at 4°C within 30 minutes of collection. The pelleted CSF cells were processed for single cell RNA sequencing. Cells were labelled with 79 Totalseq B antibodies (Biolegend, USA) and washed with PBS with 1% Bovine Serum Albumin (Thermo Fisher Scientific, USA). Labeled cells were fixed by using fixed RNA feature barcode kit (10x Genomics, USA) and stored at -80 degree.
Cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) method was used to analyze transcriptome and surface protein information based on  single-cell readout. After probe hybridization, gene expression library and surface protein library were constructed by using Chromium Next GEM Single cell 3` LT Reagent kits v3.1 (Dual index) (10X Genomics, USA) following the protocol (CG000400). Single-cell fixed RNA libraries and single-cell feature barcode libraries were sequenced  on a NextSeq 2000 P3 28 cycle + 90 cycle asymmetrical run.  Demultiplexing yielded over 27 million reads per sample when allowing for 1 mismatch per index adapter.

value: CSF cells


title: multiplexed CSF cells10

status: Public on Feb 24 2025

type: SRA

country: USA

description: Library name: LIB_11265

library_source: transcriptomic

organism: Homo sapiens

tag: cell type


title: abdominal-fat_d10_rep-3

type: RNA

city: Jingzhou

first: Tinghua

last: Huang

address: Jingmi Road #266

country: China

institute: Yangtze University

description: Gene expression data from Gallus Gallus abdominal-fat 10 days

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Chicken Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: Probeset-level intensity acquisition was performed by using Expression Console 1.1 (Affymetrix, Santa Clara, CA).

label: biotin

molecule: total RNA

organism: Gallus gallus

source_name: abdominal-fat 10 days

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

tag: gender

value: female


title: abdominal-fat_d10_rep-2

value: male


title: multiplexed CSF cells9

description: Library name: LIB_11264


title: kidney biopsy [f64]

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol:
All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNAlater.
Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

tag: center (berlin, vienna)

value: VIENNA

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Felzartamab

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo

tag: tissue

value: kidney biopsy


title: DNA-methylation array data_203960260023_R01C01

type: genomic

city: Berlin

first: Philipp

last: Euskirchen

address: Charitéplatz 1

country: Germany

institute: Charité - Universitätsmedizin Berlin

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850k or 935k Beadchip, respectively, using standard Illumina protocol.

scan_protocol: Arrays were scanned on the iscan instument acording to standarad protocol.

data_processing:
IDAT files were preprocessed using R/minfi.
*processed value definition: Average beta value

label: Cy3, Cy5

molecule: genomic DNA

source_name: tumor

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA was extracted and purified from human tumor samples using Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) according to standard instructions.

value: tumor

tag: tumor type

value: Glioblastoma, IDH-wildtype

tag: age

tag: Sex

value: Male

tag: beadchip name


title: DNA-methylation array data_201465930024_R03C01

value: Ganglioglioma


title: HEK293, Iso, rep3

city: Minneapolis

first: Emily

last: Blythe

state: MN

address: 420 Washington Avenue SE

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
Library name: Iso.3
column name in processed data files: EB14

data_processing:
Raw reads were preprocessed using HTStream, version 1.3.3.
Reads were aligned to GRCh38 using STAR, version 2.7.9a.
Differential expression analyses were conducted using limma-voom (limma version 3.50.0, edgeR version 3.36.0) in R version 4.1.0.
Assembly: GRCh38
Supplementary files format and content: text file of raw reads for all samples
Supplementary files format and content: text file of normalized reads for all samples

molecule: polyA RNA

growth_protocol: HEK293 cells (ATCC CRL1573) were cultured in DMEM (Gibco 1196511) supplemented with 10% FBS (Hyclone SH30910.03 or R&D Systems S12495 via UCSF Tissue Culture Facility) and grown at 37 °C with 5% CO2.

extract_protocol:
Cell lysis and initial RNA extraction was carried out using the Qiagen RNeasy Mini kit, and then RNA was further purified using the Zymo RNA Clean & Concentrator kit.
Barcoded 3'Tag-Seq libraries were prepared using the QuantSeq FWD kit (Lexogen, Vienna, Austria) for multiplexed sequencing according to the recommendations of the manufacturer.

treatment_protocol: Cells were washed twice in DMEM before addition of control/agonist diluted in DMEM for 90 minutes.

tag: cell line

tag: cell type

value: Human embryonic kidney cell

tag: genotype

value: WT

tag: treatment

value: 100 nM Iso in 1 μM ascorbic acid, 90 min


title: HEK293, VIP, rep2

description:
Library name: VIP.2
column name in processed data files: EB12

value: 500 nM VIP, 90 min


title: kidney biopsy [f61]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Placebo

tag: group (index, fu1, fu2)

value: Index

tag: followup (baseline, week24, week52)

value: Baseline

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt


title: kidney biopsy [f63]

tag: center (berlin, vienna)

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo

tag: tissue


title: DNA-methylation array data_201876940151_R04C01

tag: tumor type

value: Diffuse hemispheric glioma, H3 G34-mutant

tag: age

tag: Sex

value: Female

tag: beadchip name


title: kidney biopsy [f59]

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat


title: abdominal-fat_d10_rep-1

tag: gender

value: male


title: DNaseI-seq_HL_SVI_6h_exp1_2023

city: Athens

first: Marios

last: Agelopoulos

state: Attica

address: 4 Soranou Ephessiou Str

department: Center of Basic Research

country: Greece

institute: Biomedical Research Foundation Academy of Athens

library_source: genomic

data_processing:
Galaxy online platform (https://usegalaxy.org/)
Quality Control steps (QC) were employed on raw sequencing reads by the FastQC application (Galaxy Version 0.72+galaxy1).
Adaptors’ contaminants and low-quality reads, were trimmed, and thus excluded from the downstream analyses, by the application of Trim Galore (Galaxy Version 0.6.7+galaxy0).
Trimmed sequencing reads were mapped to the reference human (hg19) genome by the application of the Bowtie2 software (Galaxy Version 2.4.2+galaxy0), with “very sensitive end to end” parameters.
Duplicate reads were eliminated using the RmDup tool (Galaxy Version 2.0.1) of the SAMtools package. Samples were normalized to the same sequencing depth using the Downsample SAM/BAM (Galaxy Version 2.18.2.1) tool from Picard.
Peaks were called by MACS2 callpeak algorithm (Galaxy Version 2.1.1.20160309.6) following the above outlined parameters: (a) band width=150 bp, (b) lower mfold=5, (c) upper mfold=50, and (d) q value=0.05. Reads that mapped within peaks were tallied using bedtools' MultiCovBed tool (Galaxy Version 2.30.0).
Assembly: hg19
Supplementary files format and content: bigwig files including RPKM normalized signal and BED files of total peaks

source_name: HeLa cells

growth_protocol: Human cells were cultured under optimum conditions according to the manufacturer’s instructions. HeLa cells (ATCC, CCL-2™) were grown in DMEM medium (Sigma-Aldrich), Namalwa cells (ATCC, CRL-1432™) in RPMI 1640 medium (Sigma-Aldrich).  All culture media were supplemented with 1% Pen-Strep (Gibco) and 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS) (Gibco). All cell cultures were established in laboratory incubators under optimum conditions (37°C, 5% CO2).

extract_protocol:
DNaseI-seq assays were conducted based on a published protocol (John et al. 2013) with modifications. Intact nuclei were isolated from 15-20*10^6 cells, by sequential incubation in extraction buffers. In detail, upon completion of the time course of infection, the culture medium was removed and cells were collected and washed twice with ice-cold 1x-PBS. Cell pellets were diluted in 200μl 1xBuffer A [15mM Tris pH 8.0, 15mM NaCl, 60mM KCl, 1mM EDTA, 0.5 mM spermidine] by gentle pipetting using cut tips, followed by the addition of an equal volume of 1xBuffer A enriched in NP-40, and incubation for 4 minutes on ice. For HL 1% final (v/v) NP-40 and for NM 0.05% final (v/v) NP-40 were utilized. Cells were centrifuged at 2,000 rpm for 1 min, at 4 °C followed by aspiration, and dilution in 100μl of 1xDNaseI incubation buffer (04716728001, Roche) by gentle finger flick. Nuclei were digested by the addition of 80 units of DNase I (04716728001, Roche) for 3 minutes at room temperature, followed by quenching of the reaction by the addition of an equal volume of 2x Stop-Buffer (50 mM Tris-Cl pH 8.0, 100mM NaCl, 0.1% SDS, 100mM EDTA), gentle finger flick, incubation for 10 minutes at room temperature, addition of 20 units of RNaseI and 30 minutes incubation at room temperature. Next, the digested chromatin filaments were subjected to Proteinase K treatment (100 μg enzyme, 0.50% SDS, 400 μl total digestion reaction) (Proteinase K, recombinant, PCR Grade, 3115836001, Sigma-Aldrich) overnight at 55°C, followed by phenol chloroform extraction and ethanol-based precipitation of the isolated DNA, agarose gel (2%) electrophoresis and extraction of the digested DNA fragments, ranging from 100-300 bp, by standard procedures.
Multiplexed-DNA-libraries were prepared according to a published protocol (Ford et al. 2014).

treatment_protocol: Cell cultures were grown at 85–95% confluence and subjected to mock-infection (control; 0h) or Sendai-Virus-infection (Cantell strain, Charles River lab., 2000 HA units/ml) for 3 or 6 hrs, prior to proceeding in downstream examinations. Sendai Virus was supplied directly in the culture medium at a ratio of 1/10 (v/v).

tag: cell line

value: HeLa cells

tag: cell type

value: Epithelial cells

tag: treatment

value: Sendai Virus Cantell strain, Charles River lab

tag: time

value: 6 hrs


title: kidney biopsy [f58]

tag: center (berlin, vienna)

value: VIENNA

tag: patient

tag: datebx

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo

tag: tissue

value: kidney biopsy


title: kidney biopsy [f60]

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat


title: DNA-methylation array data_205537620156_R02C01

value: tumor

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: kidney biopsy [f57]

tag: center (berlin, vienna)

tag: patient

tag: datebx

value: Felzartamab

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: HEK293, VIP control, rep2

description:
Library name: VIP.C2
column name in processed data files: EB11

tag: cell line

tag: cell type

value: Human embryonic kidney cell

tag: genotype

value: WT

tag: treatment

value: No treatment


title: HEK293, NECA, rep2

description:
Library name: NECA.2
column name in processed data files: EB10

value: 20 μM NECA in 0.05% DMSO, 90 min


title: DNA-methylation array data_203748260067_R02C01

tag: tissue

tag: tumor type

tag: age

tag: Sex

value: Male

tag: beadchip name


title: DNA-methylation array data_203084910151_R03C01


title: DNaseI-seq_HL_SVI_0h_exp1_2023

tag: time

value: 0 hrs


title: DNaseI-seq_HL_SVI_3h_exp1_2023

value: 3 hrs


title: PD-1 Neg TIM-3 Neg CD4 C7 T Cells, 4 wpi, biol rep 5

city: Worcester

first: Samuel

middle: M

last: Behar

address: 55 Lake Ave N

department: Microbiology and Physiological Systems (MaPS)

institute: UMass Chan Medical School

data_processing:
Bioinformatics analysis was done by GENEWIZ using their standard analysis workflow package. Sequence reads were trimmed using Trimmomatic v.0.36.
Trimmed reads were mapped to the GRCm38 reference genome using the STAR aligner v.2.5.2b.
Unique hit counts calculated using featureCounts from Subread package v.1.5.2.
DESeq2 was used to perform differential gene expression analysis.
Assembly: GRCm38
Supplementary files format and content: raw gene counts (CSV) created from DESeq2 (provided by GENEWIZ)

organism: Mus musculus

source_name: Lung

extract_protocol:
RNA was extracted using Qiagen RNeasy RNA Extraction Kits following manufacturer's protocol
Library construction and sequencing were done through a third party company (GENEWIZ) using their ultra-low input library preparation. Sequencing was done using an Illumina HiSeq 2x150 PE HO configuration

value: Lung

value: C7 TCR transgenic

value: CD4 T Cell

value: 4 weeks post-infection


title: HEK293, Iso, rep2

description:
Library name: Iso.2
column name in processed data files: EB8

value: 100 nM Iso in 1 μM ascorbic acid, 90 min


title: DNA-methylation array data_207385100006_R06C01

value: Diffuse hemispheric glioma, H3 G34-mutant

value: Female


title: PD-1 Pos TIM-3 Neg CD4 C7 T Cells, 4 wpi, biol rep 5


title: HEK293, Iso control, rep2

description:
Library name: Iso.C2
column name in processed data files: EB7

value: 1 μM acsorbic acid, 90 min


title: DNA-methylation array data_206036790116_R08C01

value: tumor


title: PD-1 Pos TIM-3 Neg CD4 C7 T Cells, 25 wpi, biol rep 4

value: 25 weeks post-infection


title: HEK293, VIP, rep1

description:
Library name: VIP.1
column name in processed data files: EB6

value: Human embryonic kidney cell

value: 500 nM VIP, 90 min


title: kidney biopsy [f56]

tag: center (berlin, vienna)

value: VIENNA

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Felzartamab

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

value: kidney biopsy


title: DNA-methylation array data_204339300048_R01C01

tag: tissue

tag: tumor type

value: Ewing sarcoma

tag: Sex

tag: beadchip name


title: kidney biopsy [f54]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: PD-1 Pos TIM-3 Pos CD4 C7 T Cells, 25 wpi, biol rep 4

tag: cell line

tag: cell type

tag: treatment


title: HEK293, VIP control, rep1

description:
Library name: VIP.C1
column name in processed data files: EB5

tag: genotype

value: WT

value: No treatment


title: DNA-methylation array data_202013790104_R04C01

tag: tissue

tag: tumor type

tag: age

tag: Sex

value: Male

tag: beadchip name


title: HEK293, NECA, rep1

description:
Library name: NECA.1
column name in processed data files: EB4

value: 20 μM NECA in 0.05% DMSO, 90 min


title: PD-1 Pos TIM-3 Neg CD4 C7 T Cells, 4 wpi, biol rep 4

value: Lung

value: C7 TCR transgenic

value: CD4 T Cell

value: 4 weeks post-infection


title: HEK293, NECA control, rep2

description:
Library name: NECA.C2
column name in processed data files: EB9


title: kidney biopsy [f55]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

value: Index

value: Baseline

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat


title: DNA-methylation array data_203084910125_R05C01

tag: tissue

value: tumor

tag: tumor type

value: Supratentorial ependymoma, YAP1 fusion-positive

tag: Sex

value: Female

tag: beadchip name


title: kidney biopsy [f52]

tag: center (berlin, vienna)

value: VIENNA

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: kidney biopsy [f50]

value: Placebo

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat


title: kidney biopsy [f51]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: endat

tag: ficol

tag: tissue

value: kidney biopsy


title: HEK293, NECA control, rep1

description:
Library name: NECA.C1
column name in processed data files: EB3

tag: cell line

tag: cell type

value: Human embryonic kidney cell

tag: genotype

tag: treatment


title: DNA-methylation array data_207521860054_R07C01

tag: tumor type

value: Spinal ependymoma

tag: age

tag: Sex

tag: beadchip name


title: HEK293, Iso, rep1

description:
Library name: Iso.1
column name in processed data files: EB2

value: WT

value: 100 nM Iso in 1 μM ascorbic acid, 90 min


title: kidney biopsy [f53]

tag: center (berlin, vienna)

value: Felzartamab

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: PD-1 Neg TIM-3 Neg CD4 C7 T Cells, 4 wpi, biol rep 4

tag: tissue

value: Lung

tag: cell line

tag: cell type

tag: treatment


title: DNA-methylation array data_206999330185_R06C01

tag: tumor type

tag: age

tag: Sex

value: Male

tag: beadchip name


title: PD-1 Pos TIM-3 Neg CD4 C7 T Cells, 4 wpi, biol rep 3

value: C7 TCR transgenic

value: CD4 T Cell


title: HEK293, Iso control, rep1

description:
Library name: Iso.C1
column name in processed data files: EB1

tag: genotype

value: 1 μM acsorbic acid, 90 min


title: kidney biopsy [f48]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: endat

tag: ficol


title: THP-1_rep3

city: Edinburgh

first: Douglas

last: Vernimmen

address: The University of Edinburgh, Easter Bush Campus, Midlothian

department: Roslin Institute

country: United Kingdom

institute: University of Edinburgh

data_processing:
Our RNA-Seq data was aligned to the reference human genome (GRCh38) using STAR (v 2.5.1b) [100] allowing a maximum of 20 multimappers per read. Mapping rate varied between 76 to 80% (Supplementary Table 2). The number of mapped reads were counted at the gene level using featureCounts (v. 1.6.3). Following removal of lowly expressed genes (<20 mapped reads across all samples), and genes on the Y chromosome, analysis of differential expression was carried out using the DESeq2 package in R. Overlaps and Venn diagrams of genes up- or down-regulated (fold change > 2.5 and  padj < 0.01) in a single cell line compared to all other three cell lines were carried out using Biovenn.
Assembly: GRCh38
Supplementary files format and content: Featurecounts were used to generate  tab-delimited ".list" files, which contains gene counts.

growth_protocol: All were cultured in RPMI 1640 with the same batch of endotoxin free FBS (10%) (Gibco Lot #08F7582K). All cells were tested for mycoplasma using the VenorTM GeM Mycoplasma Detection Kit.

extract_protocol:
Total RNA was extracted with Tri Reagent per the manufacturer’s instructions (AM9738 – Thermo Fisher), followed by DNase treatment (AM2238 – Thermo Fisher). RNA quality was assessed by Agilent Tapestation 2200 with all samples achieving a RIN >9.5. We used 3 µg of total RNA for RT-qPCR, or RNA-Seq.
The Illumina TruSeq Stranded mRNA kit was used for mRNA-seq library preparation, with one round of RiboZero Gold for ribo-depletion. Pooled libraries were sequenced using the Illumina HiSeq 4000 instrument at Edinburgh Genomics (http://genomics.ed.ac.uk/) generating 2 × 150 bp paired-end reads.

tag: cell line

tag: cell type

value: monocyte

tag: genotype


title: DNA-methylation array data_206178930057_R03C01

tag: tissue

value: tumor

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: PD-1 Pos TIM-3 Pos CD4 C7 T Cells, 25 wpi, biol rep 3

tag: treatment

value: 25 weeks post-infection


title: PD-1 Neg TIM-3 Neg CD4 C7 T Cells, 4 wpi, biol rep 3

value: 4 weeks post-infection


title: DNA-methylation array data_205689110071_R01C01


title: THP-1_rep2


title: PD-1 Pos TIM-3 Neg CD4 C7 T Cells, 25 wpi, biol rep 2


title: kidney biopsy [f46]

tag: center (berlin, vienna)

value: VIENNA

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

value: Index

tag: followup (baseline, week24, week52)

value: Baseline

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: bat

tag: igt

tag: mcat

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: THP-1_rep1

tag: cell line

tag: cell type

tag: genotype


title: PD-1 Pos TIM-3 Neg CD4 C7 T Cells, 4 wpi, biol rep 2

tag: tissue

tag: treatment


title: kidney biopsy [f47]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Placebo

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: endat

tag: ficol

value: kidney biopsy


title: PD-1 Pos TIM-3 Neg CD4 C7 T Cells, 25 wpi, biol rep 3

tag: cell line

tag: cell type


title: DNA-methylation array data_206486310053_R08C01

tag: tissue

tag: tumor type

value: Spinal ependymoma

tag: age

tag: Sex

value: Female

tag: beadchip name


title: DNA-methylation array data_205689140052_R01C01


title: PD-1 Pos TIM-3 Pos CD4 C7 T Cells, 25 wpi, biol rep 2

tag: treatment


title: kidney biopsy [f45]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Felzartamab

tag: group (index, fu1, fu2)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: bat

tag: igt

tag: mcat

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: kidney biopsy [f44]

tag: followup (baseline, week24, week52)

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: endat

tag: ficol

tag: tissue


title: NOMO-1_rep2

tag: cell line

tag: cell type

value: acute myeloid leukemia

tag: genotype

value: WT


title: PD-1 Neg TIM-3 Neg CD4 C7 T Cells, 4 wpi, biol rep 2

value: Lung

value: C7 TCR transgenic

tag: treatment


title: DNA-methylation array data_205689110054_R01C01

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: kidney biopsy [f43]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: bat

tag: igt

tag: mcat

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: kidney biopsy [f49]

tag: center (berlin, vienna)

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: endat

tag: ficol

tag: tissue


title: NOMO-1_rep1

tag: cell line

tag: cell type

tag: genotype


title: PD-1 Pos TIM-3 Neg CD4 C7 T Cells, 25 wpi, biol rep 1

value: CD4 T Cell

tag: treatment


title: DNA-methylation array data_205617080096_R05C01

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: PD-1 Pos TIM-3 Neg CD4 C7 T Cells, 4 wpi, biol rep 1


title: MV4-11_rep3

value: macrophage


title: DNA-methylation array data_206503150074_R04C01

value: tumor

value: Male


title: MV4-11_rep2


title: PD-1 Pos TIM-3 Pos CD4 C7 T Cells, 25 wpi, biol rep 1

value: 25 weeks post-infection


title: kidney biopsy [f40]

tag: center (berlin, vienna)

value: VIENNA

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: bat

tag: igt

tag: mcat

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: MV4-11_rep1

tag: cell line

tag: cell type

tag: genotype


title: DNA-methylation array data_207521860161_R07C01

tag: tissue

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: NOMO-1_rep3


title: DNA-methylation array data_205828600180_R04C01


title: DNA-methylation array data_206486310051_R08C01


title: kidney biopsy [f38]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: endat

tag: ficol


title: PD-1 Neg TIM-3 Neg CD4 C7 T Cells, 4 wpi, biol rep 1

tag: tissue

tag: cell line

tag: cell type

tag: treatment

value: 4 weeks post-infection


title: kidney biopsy [f39]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: nkb

tag: bat

tag: igt

tag: mcat

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: MOLM13_rep3

tag: genotype


title: DNA-methylation array data_206359150170_R04C01

tag: tissue

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: Naïve CD4 C7 T Cells, biol rep 1

tag: cell line

tag: cell type

tag: treatment

value: Naïve


title: kidney biopsy [f42]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Placebo

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: endat

tag: ficol


title: kidney biopsy [f37]

tag: center (berlin, vienna)

value: Index

value: Baseline

tag: bat

tag: igt

tag: mcat

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo

tag: tissue

value: kidney biopsy


title: kidney biopsy [f36]

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Felzartamab

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb


title: CR_INTERMEDIATE_Patient_03

city: New York

first: Vanessa

last: Cristaldi

state: NY

address: 522 First Avenue

department: Dermatology

institute: NYU Langone Health

description:
Library name: PBMC-36
10x Genomics

library_source: transcriptomic single cell

data_processing: The barcoded processing, gene counting were made using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)

source_name: blood

extract_protocol:
PBMC werw extract from blood trough Ficoll Technique
Samples were loaded into a Chromium Single Cell 3’ Chip kit v2 (PN-120236) and processed according to the Chromium Single Cell 3’ Reagent kit v2 User Guide. Libraries were constructed using the Single Cell 3’ Library and Gel Bead Kit v2 (PN-120237) and Chromium i7 Multiplex Kit (PN-120262

value: blood

tag: cell line

value: PBMC

tag: cell type

tag: treatment


title: MT82

city: Ann Arbor

first: Lana

last: Garmire

state: Michigan

address: 1600 Huron Parkway

institute: University of Michigan

data_processing:
Reads were quality-checked with FastQC. Sequencing adapters were removed with BBMap.
STAR (version 2.7.0f) alignment with GRCh38 primary assembly
Raw counts were summarized with featureCount
Assembly: GRCh38
Supplementary files format and content: csv file includes raw counts for each sample

source_name: umbilical cord blood

extract_protocol:
DNA and RNA were extracted simultaneously using the AllPrep DNA/RNA extraction kit (Qiagen)
A total of 200 ng of high-quality RNA (RIN>7) was subjected to library construction (polyA) and sequenced on HS4000 (2x100) at the Yale Center for Genome Analysis, Connecticut to obtain at least 25M paired reads per sample.

value: umbilical cord blood

value: CD34+/CD38-/Lin- Hematopoietic stem cell

tag: sample group

value: obese


title: kidney biopsy [f35]

tag: center (berlin, vienna)

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng


title: kidney biopsy [f41]

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: abmrnk

tag: abmrendo

tag: tissue


title: PD_INTERMEDIATE_Patient_01

description:
Library name: PBMC-35
10x Genomics

tag: cell line

tag: cell type

tag: treatment


title: CR_INTERMEDIATE_Patient_02

description:
Library name: PBMC-34
10x Genomics


title: MOLM13_rep1

value: acute myeloid leukemia

tag: genotype

value: WT


title: MT81

tag: sample group


title: DNA-methylation array data_205814880119_R07C01

value: tumor

tag: tumor type

value: Spinal ependymoma

tag: age

tag: Sex

value: Female

tag: beadchip name


title: CR_INTERMEDIATE_Patient_04

description:
Library name: PBMC-33
10x Genomics


title: DNA-methylation array data_205537620171_R08C01

value: Male


title: Naïve CD4 C7 T Cells, biol rep 2

value: Lung

value: C7 TCR transgenic

value: CD4 T Cell

value: Naïve


title: DNA-methylation array data_205799780079_R06C01


title: DNA-methylation array data_205567980118_R03C01


title: DNA-methylation array data_204667540014_R03C01


title: MT78


title: MT77

value: control


title: PD_INTERMEDIATE_Patient_02

description:
Library name: PBMC-27
10x Genomics


title: MOLM13_rep2


title: CR_INTERMEDIATE_Patient_01

description:
Library name: PBMC-26
10x Genomics


title: DNA-methylation array data_204958100025_R08C01


title: MT74


title: kidney biopsy [f34]

tag: center (berlin, vienna)

value: VIENNA

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Felzartamab

tag: group (index, fu1, fu2)

value: Index

tag: followup (baseline, week24, week52)

value: Baseline

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

value: kidney biopsy


title: DNA-methylation array data_203927450029_R01C01

tag: tissue

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: PD_INTERMEDIATE_Patient_04

description:
Library name: PBMC-25
10x Genomics

value: blood

tag: cell line

value: PBMC

tag: cell type

tag: treatment


title: MT80

value: umbilical cord blood

value: CD34+/CD38-/Lin- Hematopoietic stem cell

tag: sample group


title: DNA-methylation array data_205537620011_R02C01

value: tumor

value: Spinal ependymoma


title: kidney biopsy [f29]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: abmrnk

tag: abmrendo


title: kidney biopsy [f32]

tag: center (berlin, vienna)

value: Placebo

tag: bat

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: tissue


title: kidney biopsy [f31]

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb


title: kidney biopsy [f33]

tag: center (berlin, vienna)

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: abmrnk

tag: abmrendo


title: kidney biopsy [f30]

tag: patient

tag: datebx

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: tissue


title: kidney biopsy [f28]

tag: center (berlin, vienna)

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast


title: CR_POST_Patient_04

description:
Library name: PBMC-18
10x Genomics

tag: cell line

tag: cell type

tag: treatment


title: MT72

tag: sample group


title: DNA-methylation array data_205055470013_R02C01

tag: tumor type

tag: age

tag: Sex

value: Female

tag: beadchip name


title: CR_BASELINE_Patient_04

description:
Library name: PBMC-17
10x Genomics

tag: tissue


title: DNA-methylation array data_204425710144_R02C01

value: Male


title: MT71


title: DNA-methylation array data_203072530029_R06C01

value: Posterior fossa group B (PFB) ependymoma


title: MT70


title: PD_BASELINE_Patient_03

description:
Library name: PBMC-15
10x Genomics


title: DNA-methylation array data_203821710016_R05C01


title: kidney biopsy [f27]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: PD_POST_Patient_03

description:
Library name: PBMC-16
10x Genomics

tag: tissue

tag: cell line

tag: cell type

tag: treatment


title: MT67

tag: sample group

value: obese


title: DNA-methylation array data_205862290165_R02C01

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: CR_POST_Patient_03

description:
Library name: PBMC-12
10x Genomics


title: kidney biopsy [f26]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt


title: kidney biopsy [f24]

tag: center (berlin, vienna)

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo

tag: tissue


title: MT66

tag: cell type

tag: sample group

value: control


title: kidney biopsy [f25]

value: VIENNA

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt


title: CR_BASELINE_Patient_03

description:
Library name: PBMC-11
10x Genomics

tag: cell line

tag: treatment


title: DNA-methylation array data_206503150053_R02C01

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: kidney biopsy [f23]

tag: center (berlin, vienna)

tag: patient

value: Felzartamab

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo

tag: tissue


title: MT65

tag: cell type

tag: sample group


title: DNA-methylation array data_205828600030_R02C01

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: kidney biopsy [f22]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

value: Index

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat


title: DNA-methylation array data_206152230086_R08C01

tag: tissue

tag: tumor type

tag: age

tag: Sex


title: MT63

tag: cell type

tag: sample group


title: MT69


title: PD_POST_Patient_04

description:
Library name: PBMC-10
10x Genomics

tag: cell line

tag: treatment


title: MT59


title: PD_BASELINE_Patient_04

description:
Library name: PBMC-09
10x Genomics

value: Baseline


title: MT58


title: MT57


title: DNA-methylation array data_205495890138_R05C01

value: Posterior fossa group A (PFA) ependymoma

tag: beadchip name


title: CR_POST_Patient_01

description:
Library name: PBMC-08
10x Genomics

value: blood


title: DNA-methylation array data_206648960111_R02C01


title: kidney biopsy [f21]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: bat

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo

value: kidney biopsy


title: DNA-methylation array data_206648960111_R05C01

tag: tissue

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: MT56

value: umbilical cord blood

tag: cell type

tag: sample group


title: PD_POST_Patient_02

description:
Library name: PBMC-06
10x Genomics

tag: cell line

value: PBMC

tag: treatment


title: DNA-methylation array data_206036790155_R01C01

value: tumor


title: kidney biopsy [f20]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt


title: kidney biopsy [f18]

tag: center (berlin, vienna)

value: BERLIN

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo

tag: tissue


title: PD_BASELINE_Patient_02

description:
Library name: PBMC-05
10x Genomics

tag: cell line

tag: cell type

tag: treatment


title: kidney biopsy [f17]

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb


title: kidney biopsy [f19]

tag: center (berlin, vienna)

value: Placebo

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: MT55

tag: tissue

tag: cell type

value: CD34+/CD38-/Lin- Hematopoietic stem cell

tag: sample group


title: kidney biopsy [f16]

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt


title: CR_POST_Patient_02

description:
Library name: PBMC-04
10x Genomics

tag: cell line

tag: treatment


title: DNA-methylation array data_206144080032_R07C01

tag: tumor type

tag: age

tag: Sex

value: Male

tag: beadchip name


title: DNA-methylation array data_207577170112_R02C01

tag: tissue

value: Female


title: CR_BASELINE_Patient_02

description:
Library name: PBMC-03
10x Genomics

tag: cell type


title: CR_BASELINE_Patient_01

description:
Library name: PBMC-07
10x Genomics


title: MT51

tag: sample group


title: MT53

value: obese


title: DNA-methylation array data_203867050007_R05C01

value: Myxopapillary ependymoma


title: MT48

value: control


title: DNA-methylation array data_203810690129_R04C01


title: PD_POST_Patient_01

description:
Library name: PBMC-02
10x Genomics


title: kidney biopsy [f15]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: DNA-methylation array data_204964480096_R01C01

tag: tissue

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: MT47

tag: cell type

tag: sample group


title: DNA-methylation array data_207355710100_R02C01


title: PD_BASELINE_Patient_01

description:
Library name: PBMC-01
10x Genomics

tag: cell line

tag: treatment


title: Retinal organoids at day 150 of differentiation, followed by 28 days of culture in 25 mM D-glucose, Replicate 2

city: Brno

first: Tomas

last: Barta

address: Kamenice 3

department: Faculty of Medicine

country: Czech Republic

institute: Masaryk University

description:
Library name: Dglucose R2
Replicate2

data_processing:
The adapters and quality trimming of raw fastq reads was performed using Trimmomatic v0.39 with settings CROP:250 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:35.
Assembly: Ensembl GRCh38-p10 annotation using STAR v2.7.3a
Supplementary files format and content: Mapped sequencing reads were assigned to specified genomic features using featureCounts (Rsubread library). RAW reads are in RAW_counts.txt file

source_name: Retinal organoid

extract_protocol:
Retinal organoids were washed twice with PBS and dissociated in RNA Blue Reagent (Top-Bio). Samples were either stored at −80 °C or processed immediately. Organoids were homogenized using an insulin syringe, and total RNA was extracted using the Direct-zol™ RNA MicroPrep Kit (ZYMO RESEARCH, Cat. No.: R2062), following the manufacturer’s protocol.
RNA integrity was checked on the Fragment Analyzer using RNA Kit 15 nt (Agilent Technologies). 500ng of total RNA was used as input for library preparation using QuantSeq 3′ mRNA-Seq FWD with UDI 12 nt Kit (v.2) (Lexogen) in combination with UMI Second Strand Synthesis Module for QuantSeq FWD. Quality control for library quantity and size distribution was done using QuantiFluor dsDNA System (Promega) and High Sensitivity NGS Fragment Analysis Kit (Agilent Technologies). Final library pool was sequenced on NextSeq using High Output Kit v2.5 75 cycles (Illumina) in single-end mode, resulting in a minimum of 10 million reads per sample.

value: Retinal organoid

value: iPSC Neo5

tag: genotype

value: Wt

value: 25 mM D-glucose


title: MT46


title: DNA-methylation array data_206178930022_R01C01


title: kidney biopsy [f11]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat


title: Retinal organoids at day 150 of differentiation, followed by 28 days of culture in 25 mM D-glucose, Replicate 1

description:
Library name: Dglucose R1
Replicate1

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: MT50

tag: sample group


title: kidney biopsy [f13]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

value: Index

tag: followup (baseline, week24, week52)

value: Baseline

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: endat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: kidney biopsy [f12]

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: tissue

value: kidney biopsy


title: kidney biopsy [f10]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: endat


title: DNA-methylation array data_205735150126_R06C01

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: kidney biopsy [f14]

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: kidney biopsy [f9]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Felzartamab

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: igt

tag: mcat

tag: endat

tag: tissue


title: Retinal organoids at day 150 of differentiation, followed by 28 days of culture in 25 mM D-glucose, Replicate 3

description:
Library name: Dglucose R3
Replicate3

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: MT43

value: umbilical cord blood

tag: sample group


title: Retinal organoids at day 178 of differentiation in control medium (17 mM D-glucose), Replicate 2

description:
Library name: Control R2
Replicate2


title: DNA-methylation array data_205771820056_R02C01

value: tumor

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: MT41


title: MT42


title: p65-ChIP-STARR-seq_HL_SVI_6h_exp2_2023

description: The strategy of recombining the ChIPed fragments rather than randomly sonicated genomic DNA or customized oligo pools eradicated the limitations of massive-in-parallel episomal plasmid examination studies. IRF3- and p65-ChIPed-NGS-sequenced DNA fragments, described in HL ChIP-seq experiments (SVI 6h), were subjected to end-repair, A-tailing, NebNext-adaptor molecular-indexing and limited PCR amplification with STARR-recombination primers, resulting to their bidirectional tagging with 15nt compatible with the AgeI and SalI recombination sites of 1xSp1-STARR-seq vector. Recombination reactions were conducted by the InFusion HD Cloning Kit (639650, Takara Bio) and transformed into NEB 10-beta ultra-efficient bacteria (NEB 10-beta Competent E.coli, C3019H). To increase the yield of the process, multiple reactions were set up simultaneously following a maximum ratio of 1/10 (v/v) of recombination mix/competent cells, to limit toxicity, thus significantly increasing the transformation efficiency and consequently the complexity of the libraries generated. Bacteria were recovered and then grown in 1 liter LB medium enriched in ampicillin for less than 12 hours in 32 °C, prior proceeding to plasmid DNA isolation.

data_processing:
Galaxy online platform (https://usegalaxy.org/)
Quality Control steps (QC) were employed on raw sequencing reads by the FastQC application (Galaxy Version 0.73).
Adaptors’ contaminants and low-quality reads, were trimmed, and thus excluded from the downstream analyses, by the application of Trim Galore (Galaxy Version 0.6.7). Trimmed reads were aligned to the reference genome (hg19) by the application of the Bowtie2 software (Galaxy Version 2.4.2+galaxy0), with “very sensitive end to end” parameters.
Samples were normalized to the same sequencing depth using the Downsample SAM/BAM (Galaxy Version 2.18.2.1) tool from Picard.
SAMtools “view” (Galaxy Version 1.13) was used to filter reads for proper mapping quality scores (MAPQ≥10, -q=10)  and the datasets derived from the technical replicates were combined through MergeSAMFiles from Picard. Peak calling was conducted with MACS2 callpeak (v2.1.2.2) (--bw 300, --qvalue 0.01, --keep-dup all).
The sequences corresponding to specific genomic coordinates from the merged STARR-Input library replicates were utilized as the reference of the genome during peak calling. Peaks with FDR ≤ 0.01 and enrichment over input ≥ 3 in the merged ChIP-STARR-seq datasets with an average of ≥ 25 counts, were considered as statistically and biologically significant. A reference catalogue of statistically significant peaks of both naïve and virus-infected datasets was generated by merging and concatenating (bedtool “merge” -d=50). Peaks identified in chrY, unplaced contigs (chrUn, chrM) and in ENCODE hg19 blacklisted regions  were excluded from the downstream analyses.
Assembly: hg19
Supplementary files format and content: bigwig files including RPKM normalized signal and BED files of total peaks

growth_protocol: Human  cells were cultured under optimum conditions according to the manufacturer’s instructions. HeLa cells (ATCC, CCL-2™) were grown in DMEM medium (Sigma-Aldrich). The culture media were supplemented with 1% Pen-Strep (Gibco) and 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS) (Gibco). All cell cultures were established in laboratory incubators under optimum conditions (37°C, 5% CO2).

extract_protocol:
Total RNA was extracted from cells using the TRI reagent (T9424, Sigma-Aldrich) and treated with DNase I (04716728001, Roche) for 30 minutes at 37°C to remove any DNA remnants, followed by purification with the RNeasy Mini Kit (74104, Qiagen), according to manufacturer’s instructions.
cDNA was generated using SuperScript III Reverse Transcriptase (18080044, Thermo Fisher Scientific). A STARR-vector-specific primer was used to amplify cDNA derived exclusively from the reverse-transcription of STARR-transcripts instead of total cell transcripts, followed by nested-PCR-amplification using an exon-specific primer that flanks a synthetic intron of the 1xSp1-STARR-seq vector to diminish amplification/contamination of plasmid DNA. Next Generation sequencing was carried out using standard RNA-seq processes.
STARR-transcripts-Seq

treatment_protocol: Cell cultures were grown at 85–95% confluence and subjected to mock-infection (control; 0h) or Sendai-Virus-infection (Cantell strain, Charles River lab., 2000 HA units/ml) for  6 hrs, prior to proceeding in downstream examinations. Sendai Virus was supplied directly in the culture medium at a ratio of 1/10 (v/v).

value: HeLa cells

value: Epithelial cells

tag: chip antibody

value: Sendai Virus Cantell strain, Charles River lab

tag: time

value: 6 hrs


title: MT40

value: CD34+/CD38-/Lin- Hematopoietic stem cell


title: Retinal organoids at day 178 of differentiation in control medium (17 mM D-glucose), Replicate 1

description:
Library name: Control R1
Replicate1


title: kidney biopsy [f7]

tag: center (berlin, vienna)

value: BERLIN

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: DNA-methylation array data_207577170005_R08C01

tag: tissue

tag: tumor type

value: Myxopapillary ependymoma

tag: age

tag: Sex

value: Male

tag: beadchip name


title: MT45

tag: cell type

tag: sample group

value: control


title: p65-ChIP-STARR-seq_HL_SVI_0h_exp2_2023

tag: cell line

tag: chip antibody

tag: treatment

tag: time

value: 0 hrs


title: DNA-methylation array data_203068760234_R06C01


title: p65-ChIP-STARR-seq_HL_SVI_0h_exp1_2023


title: kidney biopsy [f3]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Placebo

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat


title: MT37

tag: tissue

tag: cell type

tag: sample group


title: MT39


title: p65-ChIP-STARR-seq_HL_SVI_6h_exp1_2023

tag: cell line

tag: chip antibody

tag: treatment

tag: time


title: kidney biopsy [f4]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

value: Index

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: Retinal organoids at day 178 of differentiation in control medium (17 mM D-glucose), Replicate 3

description:
Library name: Control R3
Replicate3

tag: tissue

value: Retinal organoid

tag: cell line

value: iPSC Neo5

tag: cell type

tag: genotype

value: Wt

tag: treatment


title: MT92 [methylation]

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting

data_processing:
Preprocessed, normalized, and batch removed with ChAMP (version  2.16.2) in R
*processed value definition: Average beta

label: Cy3 and Cy5

label_protocol: Standard Illumina protocol

extract_protocol: DNA and RNA were extracted simultaneously using the AllPrep DNA/RNA extraction kit (Qiagen)

value: umbilical cord blood

value: obese


title: kidney biopsy [f6]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Felzartamab

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat

value: kidney biopsy


title: kidney biopsy [f8]

tag: group (index, fu1, fu2)

tag: followup (baseline, week24, week52)

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo

tag: tissue


title: DNA-methylation array data_204234660035_R02C01

value: tumor

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: MT91 [methylation]

tag: cell type


title: DNA-methylation array data_206648960105_R07C01


title: MT94 [methylation]


title: DNA-methylation array data_204964480134_R02C01


title: kidney biopsy [f2]

tag: center (berlin, vienna)

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

tag: group (index, fu1, fu2)

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: qcmat

tag: bat

tag: igt

tag: mcat

tag: endat


title: MT38

tag: tissue

tag: sample group


title: MT33

tag: cell type


title: Input-p65-ChIP-STARR-seq_before_transfection_exp2_2023

tag: cell line

value: HeLa cells

value: Epithelial cells

tag: chip antibody

tag: treatment

value: p65 ChIPed DNA, HeLa 6h SVI

tag: time


title: DNA-methylation array data_203890880068_R01C01

tag: tumor type

value: Myxopapillary ependymoma

tag: age

tag: Sex

tag: beadchip name


title: Input-p65-ChIP-STARR-seq_post_transfection_HL_SVI_6h_exp2_2023

value: Sendai Virus Cantell strain, Charles River lab

value: 6 hrs


title: DNA-methylation array data_204229180070_R08C01

value: Female


title: DNA-methylation array data_205460720147_R02C01

value: Male


title: MT89 [methylation]

value: CD34+/CD38-/Lin- Hematopoietic stem cell

value: control


title: DNA-methylation array data_203821710014_R05C01


title: MT36


title: MT93 [methylation]


title: Input-p65-ChIP-STARR-seq_post_transfection_HL_SVI_6h_exp1_2023


title: MT31


title: IRF3-ChIP-STARR-seq_HL_SVI_6h_exp2_2023


title: MT35


title: kidney biopsy [f1]

tag: center (berlin, vienna)

value: BERLIN

tag: patient

tag: datebx

tag: felzartamab (placebo, felzartamab)

value: Placebo

tag: group (index, fu1, fu2)

value: Index

tag: followup (baseline, week24, week52)

value: Baseline

tag: felzartamab_group (index_placebo, fu1_placebo, fu2_placebo, index_felzartamab, fu1_felzartamab, fu2_felzartamab)

tag: cortexprob

tag: abmrpm

tag: nkb

tag: dsast

tag: tcmrt

tag: tcb

tag: qcat

tag: ficol

tag: abmract

tag: abmrifng

tag: abmrnk

tag: abmrendo


title: MT34

tag: tissue

value: umbilical cord blood

tag: cell type

tag: sample group


title: Input-p65-ChIP-STARR-seq_post_transfection_HL_SVI_0h_exp1_2023

tag: cell line

tag: chip antibody

tag: treatment

tag: time

value: 0 hrs


title: MT30

value: obese


title: MT32


title: DNA-methylation array data_205096370066_R03C01

value: tumor

tag: tumor type

tag: age

tag: Sex

tag: beadchip name


title: MT86 [methylation]


title: IRF3-ChIP-STARR-seq_HL_SVI_0h_exp2_2023

value: HeLa cells

value: Epithelial cells


title: DNA-methylation array data_203249020036_R01C01

value: Myxopapillary ependymoma


title: IRF3-ChIP-STARR-seq_HL_SVI_6h_exp1_2023

value: Sendai Virus Cantell strain, Charles River lab


title: MT85 [methylation]


title: IRF3-ChIP-STARR-seq_HL_SVI_0h_exp1_2023


title: MT26


title: MT27


title: Input-IRF3-ChIP-STARR-seq_post_transfection_HL_SVI_6h_exp2_2023

value: 6 hrs


title: Input-IRF3-ChIP-STARR-seq_post_transfection_HL_SVI_6h_exp1_2023


title: Input-p65-ChIP-STARR-seq_post_transfection_HL_SVI_0h_exp2_2023


title: Input-p65-ChIP-STARR-seq_before_transfection_exp1_2023

value: p65 ChIPed DNA, HeLa 6h SVI


title: MT82 [methylation]


title: MT88 [methylation]


title: Input-IRF3-ChIP-STARR-seq_post_transfection_HL_SVI_0h_exp2_2023


title: DNA-methylation array data_204229180126_R02C01

value: Male


title: DNA-methylation array data_203866300118_R06C01


title: Input-IRF3-ChIP-STARR-seq_post_transfection_HL_SVI_0h_exp1_2023


title: MT16

value: CD34+/CD38-/Lin- Hematopoietic stem cell


title: MT90 [methylation]

value: control


title: MT87 [methylation]


title: MT14


title: MT28


title: DNA-methylation array data_205291540188_R07C01

value: Female


title: DNA-methylation array data_203866300024_R03C01


title: MT83 [methylation]


title: DNA-methylation array data_204229180126_R03C01


title: MT84 [methylation]


title: DNA-methylation array data_203810690044_R07C01


title: MT25


title: DNaseI-seq_NM_SVI_6h_2023

source_name: Namalwa cells

value: Namalwa cells

value: B lymphocytes


title: MT11


title: DNA-methylation array data_205460720133_R01C01


title: MT76 [methylation]


title: MT20


title: DNaseI-seq_NM_SVI_3h_2023

value: 3 hrs


title: MT75 [methylation]

value: umbilical cord blood


title: MT18


title: MT81 [methylation]


title: DNA-methylation array data_204068280020_R05C01

value: Embryonal tumour with multilayered rosettes


title: MT80 [methylation]

value: obese


title: Input-IRF3-ChIP-STARR-seq_before_transfection_HL_SVI_exp2_2023

value: IRF3 ChIPed DNA, HeLa 6h SVI


title: DNaseI-seq_NM_SVI_0h_2023

value: 0 hrs


title: DNA-methylation array data_206036790116_R06C01

value: tumor


title: MT73 [methylation]


title: MT77 [methylation]


title: COPD EC 4 [COPD_E61_S47_L006]

first: David

last: Redmond

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
FastQC (v0.11.8) to check FASTQ quality.
Trim Galore (v0.6.4) for adapter trimming
SortMeRNA (v2.1b) to remove rRNA reads.
STAR (v2.6.1d) to align files
Subread (v1.6.4) featureCounts to quantify gene counts
Genome_build: GRCh38
Supplementary_files_format_and_content: Gene count matrix

source_name: COPD_lung endothelium

growth_protocol: Cells were grown in M199 containing 10% fetal bovine serum, glutamine, HEPES, and antibiotics

extract_protocol:
Cells were isolated by fluorescence-activated cell sorting and subjected to TRIzol treatment for RNA extraction and sequencing.
RNA-seq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.

tag: subject status

value: chronic obstructive pulmonary disease (COPD)

value: Lung

value: endothelial cells (EC)


title: MT78 [methylation]


title: DNA-methylation array data_206486310052_R06C01


title: MT72 [methylation]


title: DNA-methylation array data_206036370031_R03C01

value: Diffuse midline glioma, H3 K27-altered


title: Input-IRF3-ChIP-STARR-seq_before_transfection_HL_SVI_exp1_2023

value: HeLa cells

value: Epithelial cells


title: DNA-methylation array data_203017150025_R05C01


title: MT12

value: CD34+/CD38-/Lin- Hematopoietic stem cell

value: control


title: COPD EC 2 [COPD_A59_S45_L006]


title: MT70 [methylation]


title: Input-ChIP-seq_NM_SVI_6h_exp1_2023

data_processing:
Galaxy online platform (https://usegalaxy.org/)
Quality Control steps (QC) were employed on raw sequencing reads by the FastQC application (Galaxy Version 0.72+galaxy1).
Adaptors’ contaminants and low-quality reads, were trimmed, and thus excluded from the downstream analyses, by the application of Trim Galore (Galaxy Version 0.6.7+galaxy0). Trimmed sequencing reads were mapped to the reference human (hg19) or mouse (mm9) genome by the application of the Bowtie2 software (Galaxy Version 2.4.2+galaxy0), with “very sensitive end to end” parameters (Langmead and Salzberg, 2012). The input data were utilized as controls.
Duplicate reads were eliminated using the RmDup tool (Galaxy Version 2.0.1) of the SAMtools package (Li et al., 2009). Samples were normalized to the same sequencing depth using the Downsample SAM/BAM (Galaxy Version 2.18.2.1) tool from Picard.
Peaks were called by MACS2 callpeak algorithm (Galaxy Version 2.1.1.20160309.6) following the above outlined parameters: (a) band width=150 bp, (b) lower mfold=5, (c) upper mfold=50, and (d) q value=0.05 (Feng et al., 2012).
Peaks detected in chrY and unplaced contigs (chrUn, chrM) and in ENCODE hg19 and mm9 blacklisted regions were excluded from the downstream analyses (Amemiya HM, et al., Sci Rep. 2019). Reads that mapped within peaks were tallied using bedtools' MultiCovBed tool (Galaxy Version 2.30.0) (Quinlan and Hall, 2010).
Assembly: hg19 (Homo sapiens), mm9 (Mus musculus)
Supplementary files format and content: bigwig files including RPKM normalized signal and BED files of total peaks

growth_protocol: Human and mouse cells were cultured under optimum conditions according to the manufacturer’s instructions. HeLa cells (ATCC, CCL-2™) were grown in DMEM medium (Sigma-Aldrich), Namalwa cells (ATCC, CRL-1432™) in RPMI 1640 medium (Sigma-Aldrich), and NIH/3T3 cells (ATCC, CRL-1658™) in DMEM medium (Sigma-Aldrich).  All culture media were supplemented with 1% Pen-Strep (Gibco) and 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS) (Gibco). All cell cultures were established in laboratory incubators under optimum conditions (37°C, 5% CO2).

extract_protocol:
ChIP-seq assays on human and mouse cells were carried out based on published protocols (Agelopoulos et al 2014; Agelopoulos et al 2012; Agelopoulos and Thanos 2006) with modifications. Cells were fixed in 1% formaldehyde (F8775, Sigma-Aldrich), for 30 minutes at room temperature, followed by quenching of the reaction by 0.125M Glycine. Cell pellets were diluted in 15 ml Buffer I [10 mM Tris-Cl pH 8.0, 10 mM EDTA, 0.25% Triton X-100] and incubated for 10 minutes on ice, followed by centrifugation at 3,500 rpm for 5 minutes at 4 °C and aspiration. Pellets were diluted in 15 ml Buffer II [10 mM Tris-Cl pH 8.0, 200 mM NaCl, 1 mM EDTA] and incubated for 10 minutes on ice, followed by centrifugation at 3,500 rpm for 5 minutes at 4 °C and aspiration. Pellets were diluted in sonication Buffer [10 mM Tris-Cl pH 8.0, 1 mM EDTA] and chromatin filaments were sheared to a range of 200-2,000 bp using a Covaris S220 Sonicator , followed by two sequential steps of 2,000 rpm and 12,000 rpm centrifugation, for 8 minutes at 4 °C, to avoid trapping of chromatin by the cell debris.
Multiplexed-DNA-libraries were prepared according to a published protocol (Ford et al., 2014) with modifications. The NEBNext Multiplex Oligos for illumina (Index Primers Set 1 and 2) (E7335S and E7500S, illumina) were used to produce compatible ends to the DNA fragments.

value: Namalwa cells

value: B-lymphocytes

value: Sendai Virus Cantell strain, Charles River lab

value: 6 hrs


title: Input-ChIP-seq_NM_SVI_3h_exp1_2023

value: 3 hrs


title: MT69 [methylation]

value: umbilical cord blood


title: DNA-methylation array data_203810690095_R08C01

value: Male


title: Input-ChIP-seq_NM_SVI_0h_exp1_2023

value: 0 hrs


title: MT74 [methylation]


title: Input-ChIP-seq_NM_SVI_0h_exp2_2023


title: Input-ChIP-seq_NM_SVI_6h_exp2_2023


title: IPF EC 5 [IPF_E59_S62_L007]

source_name: IPF_lung endothelium

value: idiopathic pulmonary fibrosis (IPF)


title: DNA-methylation array data_205041760132_R01C01

value: tumor


title: DNA-methylation array data_207513910035_R02C01

value: Embryonal tumour with multilayered rosettes


title: Input-ChIP-seq_HL_SVI_6h_exp1_2023


title: COPD EC 5 [COPD_H6_S48_L006]

value: chronic obstructive pulmonary disease (COPD)

value: Lung

value: endothelial cells (EC)


title: COPD EC 6 [COPD_m47_S49_L006]


title: MT67 [methylation]

value: obese


title: Input-ChIP-seq_HL_SVI_3h_exp1_2023

value: HeLa cells

value: Epithelial cells


title: DNA-methylation array data_206486310053_R05C01

value: Diffuse midline glioma, H3 K27-altered

value: Female


title: MT66 [methylation]

value: CD34+/CD38-/Lin- Hematopoietic stem cell

value: control


title: DNA-methylation array data_206443740176_R08C01


title: Input-ChIP-seq_NM_SVI_3h_exp2_2023

value: Namalwa cells

value: B-lymphocytes

value: Sendai Virus Cantell strain, Charles River lab

value: 3 hrs


title: COPD EC 3 [COPD_E52_S46_L006]


title: DNA-methylation array data_203020900048_R08C01


title: DNA-methylation array data_205854140012_R06C01


title: COPD EC 1 [COPD_11_S43_L006]


title: IPF EC 6 [IPF_F47_S63_L007]

value: idiopathic pulmonary fibrosis (IPF)


title: DNA-methylation array data_207309920041_R01C01

value: tumor


title: IPF EC 1 [IPF_19_S58_L007]


title: DNA-methylation array data_206178930022_R06C01


title: MT62 [methylation]

value: umbilical cord blood


title: H3K4me3-ChIP-seq_NM_SVI_0h_exp1_2023

value: H3K4Me3 (Abcam #Ab8580)

value: 0 hrs


title: DNA-methylation array data_206503150048_R08C01

value: Male


title: IPF EC 4 [IPF_E53_S61_L007]

value: Lung

value: endothelial cells (EC)


title: Control EC 4 [ctrl_abbl_S50_L006]

source_name: control_lung endothelium

value: control (no disease)


title: Input-ChIP-seq_HL_SVI_0h_exp1_2023

value: HeLa cells

value: Epithelial cells


title: MT65 [methylation]

value: CD34+/CD38-/Lin- Hematopoietic stem cell


title: H3K4me3-ChIP-seq_HL_SVI_3h_exp1_2023


title: DNA-methylation array data_206152230086_R06C01

value: Diffuse midline glioma, H3 K27-altered


title: MT64 [methylation]

value: obese


title: IPF EC 2 [IPF_E47_S59_L007]


title: H3K4me3-ChIP-seq_NM_SVI_6h_exp1_2023

value: Namalwa cells

value: B-lymphocytes

value: 6 hrs


title: DNA-methylation array data_202787550049_R08C01


title: H3K4me3-ChIP-seq_NM_SVI_3h_exp1_2023

value: Sendai Virus Cantell strain, Charles River lab

value: 3 hrs


title: IPF EC 3 [IPF_E51_S60_L007]

value: idiopathic pulmonary fibrosis (IPF)


title: DNA-methylation array data_205689110043_R04C01

value: tumor

value: Female


title: Control EC 3 [ctrl_6439_S57_L007]


title: MED1-ChIP-seq_NM_SVI_6h_2023

value: Med1 (Bethyl #A300-793A)


title: H3K4me3-ChIP-seq_HL_SVI_6h_exp1_2023

value: H3K4Me3 (Abcam #Ab8580)


title: MT61 [methylation]

value: umbilical cord blood


title: Control EC 2 [ctrl_5148_S56_L007]

value: control (no disease)

value: Lung

value: endothelial cells (EC)


title: MT57 [methylation]

value: CD34+/CD38-/Lin- Hematopoietic stem cell


title: DNA-methylation array data_203153910042_R07C01

value: Diffuse midline glioma, H3 K27-altered

value: Male


title: MT60 [methylation]

value: obese


title: MT56 [methylation]


title: DNA-methylation array data_207309920037_R04C01

value: Papillary craniopharyngioma


title: MT59 [methylation]

value: control


title: MT63 [methylation]


title: Control EC 1 [ctrl_467_S55_L007]


title: MED1-ChIP-seq_NM_SVI_0h_2023

value: Namalwa cells

value: B-lymphocytes

value: Sendai Virus Cantell strain, Charles River lab

value: 0 hrs


title: DNA-methylation array data_205617080020_R01C01

value: tumor

value: Glioblastoma, IDH-wildtype


title: H3K4me3-ChIP-seq_HL_SVI_0h_exp1_2023

value: HeLa cells

value: Epithelial cells

value: H3K4Me3 (Abcam #Ab8580)


title: DNA-methylation array data_203084910151_R01C01

value: Adamantinomatous craniopharyngioma


title: DNA-methylation array data_203013220103_R07C01

value: Female


title: RNA-seq_NM_SVI_6h_exp2_2023

data_processing:
Galaxy online platform (https://usegalaxy.org/)
Quality Control (QC) steps were employed on raw sequencing reads by the FastQC application (Galaxy Version 0.72+galaxy1).
Processed sequencing reads were mapped to the reference human (hg19) genome by the HISAT2 alignment tool (Galaxy Version 2.2.1+galaxy0) under “single-end” and “unstranded” options.
RNA integrity was measured by the Transcript Integrity Number tool (Galaxy Version 2.6.4.1). The enrichment of RNA-sequencing reads within gene bodies was examined using Gene Body Coverage (ΒΑΜ) tool.
Calculation of sequencing reads that are mapped into genes was performed with the htseq-count tool (Galaxy Version 0.9.1+galaxy1), in “union” mode, with “unstranded”, “minimum alignment quality 1” and “–nonunique All" options.
Assembly: hg19
Supplementary files format and content: bigwig files including RPKM normalized signal

growth_protocol: Human cells were cultured under optimum conditions according to the manufacturer’s instructions. HeLa cells (ATCC, CCL-2™) were grown in DMEM medium (Sigma-Aldrich), and Namalwa cells (ATCC, CRL-1432™) in RPMI 1640 medium (Sigma-Aldrich).  All culture media were supplemented with 1% Pen-Strep (Gibco) and 10% (v/v) heat-inactivated Fetal Bovine Serum (FBS) (Gibco). All cell cultures were established in laboratory incubators under optimum conditions (37°C, 5% CO2).

extract_protocol:
Total RNA was extracted from cells using the TRI reagent (T9424, Sigma-Aldrich) and treated with DNase I (04716728001, Roche) for 30 minutes at 37°C to remove any DNA remnants, followed by purification with the RNeasy Mini Kit (74104, Qiagen), according to manufacturer’s instructions.
RNA quality was evaluated at the Bioanalyzer 2100 DNA Chip 7500 (Agilent Technologies). RNA sequencing libraries were generated using the TruSeq RNA Library Prep Kit v2, Set A and B (RS-122-2001 and RS-122-2002) for Illumina following the manufacturer's instructions (Mortazavi et al. 2008). Samples were subjected to beads-purification (AMPure XP system), and the quality of the isolated libraries was evaluated at the Bioanalyzer 2100 DNA Chip 7500 (Agilent Technologies).

value: 6 hrs


title: Igf2bp2-WT-3

city: wuhan

first: Ziyan

last: Jiang

address: 237 luoyu Rd

institute: wuhan university

description: Library name: Sample 6

data_processing:
Fastp (v0.21.0) was used to further filter the sequencing data and remove reads with an average quality score lower than Q20.
The reference genome was indexed using HISAT2 v2.1.0, and paired-end clean reads were aligned to the reference genome using HISAT2 v2.1.0.
StringTie (V2.1.5) was used to count the read count values aligned to each gene.
Assembly: mm39
Supplementary files format and content: gene_count_matrixt file includes raw counts for each Sample

source_name: temporomandibular joint

extract_protocol:
RNA was harvested using Trizol. 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS® mRNA Isolation Master Kit following manufacturer's protocols.

value: temporomandibular joint

tag: genotype


title: Igf2bp2-KO-2

description: Library name: Sample 2


title: MT54 [methylation]

value: umbilical cord blood

value: CD34+/CD38-/Lin- Hematopoietic stem cell


title: MT58 [methylation]


title: DNA-methylation array data_205537620156_R03C01


title: Igf2bp2-KO-1

description: Library name: Sample 1


title: Igf2bp2-WT-2

description: Library name: Sample 5


title: DNA-methylation array data_207385100013_R07C01

value: Ganglioglioma


title: MT71 [methylation]

value: control


title: MED1-ChIP-seq_NM_SVI_3h_2023

value: Namalwa cells

value: Med1 (Bethyl #A300-793A)

value: 3 hrs


title: MT53 [methylation]

value: obese


title: MT55 [methylation]


title: Igf2bp2-KO-3

description: Library name: Sample 3


title: DNA-methylation array data_206486310038_R06C01

value: tumor


title: Igf2bp2-WT-1

description: Library name: Sample 4


title: DNA-methylation array data_206687200140_R01C01

value: Glioblastoma, IDH-wildtype

value: Male


title: Mouse_dorsal_organoids_day30_VanDerMolen

city: Santa Cruz

first: Lon

last: Blauvelt

state: CA

address: 1156 High St

institute: University of California, Santa Cruz

description: Library name: batch1

data_processing:
Samples were pooled and sequenced on the AVITI PE75 Flowcell ∼900M reads at the UCDavis Technologies Core. The sequencing data was then processed using the PIPseeker pipeline (PIPseeker v3.3, Fluent BioSciences), using the mouse genome GRCm39 (GENCODE vM29 2022.04, Ensembl 106). We used the default parameters to process the FASTQ files, perform mapping, transcript counting and cell calling.  Sensitivity 5 matrices were used for downstream analysis using R package Seurat (version 5.1.0). Souporcell was used for genotype demultiplexing and doublet identification. Doublets were also identified using the R package DoubletFinder v2.0.4131.  Cells were filtered based on doublet identification, with greater than 20% mitochondrial genes, less than the 5th percentile unique genes detected, and greater than 50,000 total RNA counts. The raw gene count matrices were normalized with SCTransform function while regressing out mitochondrial genes identified the top 3,000 highly variable genes. Principal component analysis was performed and clusters were identified by the FindNeighbors function using 40 principal components (chosen based on visual inspection of the elbow plot). The function FindClusters was run with resolutions of 2, 1, and 0.5 with leiden clustering. The clusters were then embedded and visualized with Uniform Manifold Approximation and Projection (UMAP) and the resolution of 0.5 was chosen based on visual inspection of marker genes to represent the best approximal cell type. Annotation of the dataset was performed by marker gene expression from the FindMarkers function by the Wilcoxon Rank Sum test and reference to canonical marker genes from the Allen Brain Atlas Whole Cortex and Hippocampus visualized using the UCSC Cell Browser.
Assembly: GRCm39 (GENCODE vM29 2022.04, Ensembl 106)
Supplementary files format and content: RDS file

source_name: Embryonic

extract_protocol:
Murine cortical organoid library prep was carried out following the methods described in Clarke et al. Ten murine cortical organoids per cell line (3 cell lines defined above) were pooled together and dissociated using Worthington Papain Dissociation System (Worthington # LK003150) according to the manufacturer’s instructions. Briefly, 20 units of papain per ml, 1mM L-cysteine and 0.5mM EDTA were resuspended in Earle’s Balanced Salt Solution (EBSS). The enzyme solution was activated by incubating for 30 minutes at 37° C. After activation, we included 200 units of DNase I per ml. We transferred the tissue into the papain and DNase I solution and incubated for 30 minutes at 37° C. Every 10 minutes the samples were agitated by gently shaking the tube. The tissue was mechanically dissociated using flamed glass Pasteur Pipets (Fisher Scientific # 13-678-6B). The tissue was centrifuged at 300 RCF for 3 minutes. The supernatant was removed and approximately 1mL of 1X PBS containing 0.1% Bovine Serum Albumin (Millipore Sigma # A3311) was added and the cells were resuspended, then put through a 40 µm cell strainer (Corning # 431750) into a 6 well ultra low-adhesion plate (Millipore Sigma # CLS3471).
Cells were then manually counted on a hemocytometer and 3.3K cells from each of the three dissociated organoid cell lines were pooled to make a total of 10K cells. These pooled cells were then combined into a single sequencing reaction using the PiPseq T2 kit and carried out according to the manufacturer’s instructions.

value: Embryonic

value: Mix of three lines:KH2, BRUCE4 and ES-E14TG2a


title: RNA-seq_NM_SVI_3h_exp2_2023

value: B-lymphocytes

value: Sendai Virus Cantell strain, Charles River lab


title: DNA-methylation array data_205814880089_R06C01


title: RNA-seq_NM_SVI_6h_exp1_2023

value: 6 hrs


title: MT51 [methylation]


title: RNA-seq_NM_SVI_3h_exp1_2023


title: DNA-methylation array data_204316900094_R01C01


title: CT.M.rep1

city: Guangzhou

first: Ke

last: Song

state: Guangdong

address: No.1023,South Shatai Road, Baiyun District

institute: Southern Medical University

description:
Library name: Sample 3
High glucose + ML221

data_processing:
In brief, the adaptor sequence were removed using bbduk (v 38.18) and low-quality reads were trimmed by trimmomatic (v 0.39), with the length cut-off 35 bp. The clean reads were aligned to GRCm38 genome (Ensembl version) using bowtie2 (v 2.3.5.1) with the options (--very-sensitive --end-to-end). Then, low quality mapping reads were removed using samtools with the option (-q 35). MACS2 (v 2.2.6) was used to call narrow peaks with the options (-g mm -f BAMPE -B --call-summits). Bigwig files were generated using genomeCoverageBed from bedtools (v 2.29.2) (scale factor = 20 million / <each sample’s total unique reads>) and bedGraphToBigWig (v 2.8).
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

source_name: mouse primary Leydig cells

extract_protocol:
Briefly, After washing the testicular tissue three times with PBS, the tissue digested with 1 mg/mL of type IV collagenase (ThermoFisher, 17104019) at 37°C for 15 min. After the tissues settle naturally, take the supernatant for culture in D-MEM/F-12 (Gibco, C11330500BT). After 48 hours, wash away the non-adherent cells with PBS, and then conduct immunofluorescence identification for the purity of LCs.
In order to study the distribution of NR2F2 in LC cells, we used Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903-01) to capture NR2F2-binding sites. The experimental process was performed according to the manufacturer’s instructions. In brief, 1× 105 LC cells were prepared and immobilized on concanavalin A beads. Beads are incubated with a NR2F2 primary antibody (Abcam, ab211777, 1:50), followed by incubation with a secondary antibody anti-Rabbit IgG (Abcam, ab6702). Library was quantified by Equalbit dsDNA HS Assay Kit (Vazyme, EQ111-01) using Qubit™ 4 Fluorometer (Invitrogen, Q33226). Libraries were subjected to paired-end 150 bp sequencing on NovaSeq platform at Cosmos Wisdom.

value: mouse primary Leydig cells

value: High glucose + ML221


title: CT.M.rep2

description:
Library name: Sample 4
High glucose + ML221


title: MT50 [methylation]

value: umbilical cord blood

value: CD34+/CD38-/Lin- Hematopoietic stem cell


title: RNA-seq_NM_SVI_0h_exp1_2023

value: 0 hrs


title: DNA-methylation array data_205852220179_R03C01

value: Astrocytoma, IDH-mutant

value: Female


title: CT.HG.rep2

description:
Library name: Sample 2
High glucose

value: High glucose


title: MT48 [methylation]

value: control


title: RNA-seq_NM_SVI_0h_exp2_2023

value: Namalwa cells


title: CT.HG.rep1

description:
Library name: Sample 1
High glucose


title: RNA-seq_HL_SVI_6h_exp2_2023

value: HeLa cells

value: Epithelial cells


title: MT46 [methylation]


title: DNA-methylation array data_205862290165_R04C01

value: tumor

value: Male


title: RNA-seq_HL_SVI_0h_exp2_2023


title: MT44 [methylation]

value: obese


title: MT45 [methylation]


title: MT52 [methylation]


title: DNA-methylation array data_206178930085_R04C01


title: ATAC.HG.rep1

description:
Library name: Sample 3
High glucose

data_processing:
In brief, the adaptor sequence were removed using bbduk (v 38.18) and low-quality reads were trimmed by trimmomatic (v 0.39), with the length cut-off 35 bp. The clean reads were aligned to GRCm38 genome (Ensembl version) using bowtie2 (v 2.3.5.1) with the options (--very-sensitive --end-to-end). Then, low quality mapping reads were removed using samtools with the option (-q 35). MACS2 (v 2.2.6) was used to call narrow peaks with the options (-g mm -f BAMPE -B --call-summits). Bigwig files were generated using genomeCoverageBed from bedtools (v 2.29.2) (scale factor = 20 million / <each sample’s total unique reads>) and bedGraphToBigWig (v 2.8).
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
Briefly, After washing the testicular tissue three times with PBS, the tissue digested with 1 mg/mL of type IV collagenase (ThermoFisher, 17104019) at 37°C for 15 min. After the tissues settle naturally, take the supernatant for culture in D-MEM/F-12 (Gibco, C11330500BT). After 48 hours, wash away the non-adherent cells with PBS, and then conduct immunofluorescence identification for the purity of LCs.
ATAC-seq was performed using True Prep DNA Library Prep Kit V2 for Illumina (Vazyme, TD501). Cells were collected in PBS (2% BSA) and spun at 500 g at 4°C for 10 min. The pellet was resuspended in 50 μl lysis buffer and incubated at 4°C for 15 min and spun at 500 g at 4°C for 5 min. The supernatants were removed by carefully pipetting away from the pellets. For the transposition reaction, 10 μl 5×TTBL buffer, 5 μl TTE Mix V50 were combined and added to each pellet up to 50 μl. The samples were incubated at 37°C for 30 min followed by immediate purification using Beckman Beads. The PCR was set up in a 50 μl reaction volume using 24 μl of transposed DNA, 10 μl of 5×TAB, 5 μl PPM and 5 μl P5 and P7 primers in TruePrep Index Kit V2 for Illumina (Vazyme, TD202). PCR parameters were: 72°C for 5 min, 98°C for 30 s and 15 cycles of 98°C for 10 s, 60°C for 30 s and 72°C for 30 s. The libraries were purified using QIAGEN MinElute PCR purification kit (QIAGEN, Cat#28004) followed by Agencourt AMPure XP beads (Beckman Coulter, A63880). Library fragments ranging from 200 to 700 bp were enriched and the final elution volume was 30 μl. Libraries were subjected to paired-end 150 bp sequencing on NovaSeq platform at Cosmos Wisdom.


title: DNA-methylation array data_205617080094_R06C01

data_processing:
IDAT files were preprocessed using R/minfi.
*processed value definition: Average beta value

extract_protocol: Genomic DNA was extracted and purified from human tumor samples using Maxwell RSC FFPE Plus DNA Purification Kit (Promega, USA) according to standard instructions.

value: CNS neuroblastoma, FOXR2-activated


title: RNA-seq_HL_SVI_6h_exp1_2023

value: Sendai Virus Cantell strain, Charles River lab

value: 6 hrs


title: MT43 [methylation]


title: DNA-methylation array data_203810640095_R03C01


title: MT42 [methylation]


title: DNA-methylation array data_204667540014_R05C01


title: ATAC.HG.rep2

description:
Library name: Sample 4
High glucose

value: mouse primary Leydig cells


title: DNA-methylation array data_204808700010_R03C01

value: CIC-rearranged sarcoma


title: RNA-seq_HL_SVI_0h_exp1_2023


title: Male, 28 hours fasted, batch 3

city: Houston

first: Jonathan

middle: Carter

last: Bean

state: TX

address: 1100 Bates Ave

department: Pediatrics

institute: Baylor College of Medicine

description: Library name: M_Fast_B3

data_processing:
STARsolo v2.7.10a
SoupX v1.6.2
scDblFnd v1.18.0
Seurat v4.4.0
Assembly: Genome assembly GRCm39
Supplementary files format and content: Seurat object, RDS compressed

source_name: arcuate nucleus of hypothalamus

extract_protocol:
dissection followed by nuclei isolation and FAC sorting
Chromium GEM-X Single Cell 3' Kit v3

value: arcuate nucleus of hypothalamus

value: 28 hours fasted

tag: batch


title: DNA-methylation array data_206486310038_R08C01


title: Male, 28 hours fasted, batch 2

description: Library name: M_Fast_B2


title: Male, 28 hours fasted, batch 1

description: Library name: M_Fast_B1


title: human primary chondrocytes, OA3

city: Nanjing

first: Zhuang

last: Li

state: Jiangsu

address: 87 DingjiaQaio, Nanjing, P.R. China

institute: Zhongda Hospital, Southeast University

data_processing:
CLC Genomics Workbench y 11.0.1
Assembly: GRCh38
Supplementary files format and content: excel file include RPKM values for each Sample

source_name: human primary chondrocytes

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA sequencing libraries were constructed in accordance with the manufacturer's specifications using the TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA)

value: human primary chondrocytes


title: DNA-methylation array data_203808720090_R02C01

value: Female


title: MT38 [methylation]

value: umbilical cord blood

value: CD34+/CD38-/Lin- Hematopoietic stem cell


title: human primary chondrocytes, OA2


title: ATAC.NC.rep1

description:
Library name: Sample 1
Control

value: Control


title: Male, ad. Libitum fed, batch 2

description: Library name: M_Fed_B2

value: ad. lib. Fed


title: MT41 [methylation]


title: ATAC.NC.rep2

description:
Library name: Sample 2
Control


title: MT36 [methylation]

value: control


title: DNA-methylation array data_205055470013_R01C01

value: tumor

value: Chordoma


title: DNA-methylation array data_207309920041_R03C01


title: Male, ad. Libitum fed, batch 1

description: Library name: M_Fed_B1

value: Male


title: human primary chondrocytes, control1


title: MT39 [methylation]


title: DNA-methylation array data_205310760189_R01C01


title: MT37 [methylation]


title: RNA-seq_HL_SVI_3h_exp2_2023

value: HeLa cells

value: Epithelial cells

value: 3 hrs


title: DNA-methylation array data_205096370110_R02C01

value: Central neurocytoma


title: human primary chondrocytes, OA1


title: Male, ad. Libitum fed, batch 3

description: Library name: M_Fed_B3


title: bio replicate 2, VDJ [L6b]

description: 10x Genomics

data_processing:
Demultiplexing, aligning, barcode processing, gene counting, V(D)J annotation, and aggregation were done using Cell Ranger v6.0
Assembly: mm10
Supplementary files format and content: Tab-separated values, comma-separated values, and matrix files

extract_protocol:
TCR⍺ KO mice were injected intravenously (IV) with ESAT-6 specific (C7 and C24) TCR transgenic T-cells and infected with Mtb Erdman 24 hours post-IV. At 26 wpi, mice were IV injected with anti-CD45 antibody 2 minutes before euthanizing with CO2. Lungs were then perfused and removed 3 minutes after anti-CD45 injection. Lung single cell suspensions were prepared by homogenizing lungs using a GentleMACS tissue dissociator, digesting with collagenase at 37C for 30 minutes, followed by a second run of dissociation using the GentleMACS. Suspensions were then filtered through 70 µm strainers and incubated with 1 mL ACK Lysis Buffer (GIBCO) for 1 minute at room temperature (25C). The cells were resuspended in D-PBS and filtered through 40 µm filters. The resulting single cell suspensions were stained with flow antibodies to sort for total live, parenchymal T-cells (CD45 IV Negative, TCR[b] and CD3 double positive) using the BD FACS Aria.
Library construction was performed according to the manufacturer's instructions (single cell 5' v2 protocols, 10x Genomics).

value: Lung

value: T-cells

tag: strain

value: Mtb infected TCRalpha KO mice


title: DNA-methylation array data_205828600180_R05C01


title: human primary chondrocytes, control3

value: human primary chondrocytes


title: MT31 [methylation]

value: obese


title: MT35 [methylation]

value: umbilical cord blood


title: MT30 [methylation]

value: CD34+/CD38-/Lin- Hematopoietic stem cell


title: human primary chondrocytes, control2


title: RNA-seq_HL_SVI_3h_exp1_2023

value: Sendai Virus Cantell strain, Charles River lab


title: Female, ad. Libitum fed, batch 2

description: Library name: F_Fed_B2

value: arcuate nucleus of hypothalamus

value: Female

value: ad. lib. Fed


title: Female, 28 hours fasted, batch 3

description: Library name: F_Fast_B3

value: 28 hours fasted


title: DNA-methylation array data_203867050006_R02C01

value: tumor


title: MT34 [methylation]

value: control


title: MT28 [methylation]


title: DNA-methylation array data_205310760157_R03C01

value: Atypical teratoid/rhabdoid tumour

value: Male


title: bio replicate 2, VDJ [L6a]

description: 10x Genomics


title: bio replicate 2, gene expression [L6a]

description:
Illumina NextSeq 500 and NovaSeq 6000
10x Genomics


title: BRI-433

city: Dublin

first: Aaron

last: Douglas

state: Leinster

address: 152-160 Pearse Street

department: School of Biochemistry and Immunology

country: Ireland

institute: Trinity College Dublin

data_processing:
Raw BCL files were demultiplexed using Cell Ranger v.3.0.2 mkfastq to generate fastq files with default parameters.
Fastq files were aligned to the mm10 genome (v.1.2.0) and feature reads were quantified simultaneously using the Cell Ranger count for feature barcoding.
Filtered feature-barcode UMI count matrices containing quantification of gene expression were used for downstream analysis.
Assembly: mm10 genome (v.1.2.0)
Supplementary files format and content: Tab-separated barcode, feature and matrix files

source_name: Adipose γδ T cells and iNKT cells

extract_protocol:
Mice were euthanized by CO2 inhalation and adipose tissue was removed, minced with a razor and digested in 1 mg ml−1 collagenase type II (Worthington) dissolved in RPMI, in a shaking incubator for 25–30 min at 37 °C. Digested cells were filtered through a 70-μm nylon mesh and centrifuged at 300g for 5 min to pellet the stromovascular fraction (SVF). Lymph nodes were disrupted through a 70-μm filter and centrifuged for 5 minutes at 300g to pellet. Cells were washed with 1 ml PBS and incubated in ZombieAqua Cell Viability Dye (Biolegend; 1:1,000 in PBS) for 20 min at room temperature. Cells were incubated with an extracellular fluorochrome-labelled antibody cocktail and PBS57-loaded CD1d tetramer (NIH Tetramer Core Facility/Emory Vaccine Center) with Fc block (1:200; BD Biosciences) in FACS buffer (PBS + 2% FCS) for 20 minutes at room temperature. Cells were then washed with 2% FACS buffer and resuspended for cell sorting. Cell sorting was performed using a FACSAria (BD Biosciences).
Cell suspensions were loaded onto a 10x Chromium Controller to generate single-cell Gel Beads-in-emulsion (GEMS) and GEMs were processed to generate UMI-based libraries according to the 10X Genomics Chromium Single Cell 3′ protocol. Libraries were sequenced using a NextSeq 500 sequencer.

value: Epididymal white adipose tissue


title: MT33 [methylation]


title: Female, 28 hours fasted, batch 2

description: Library name: F_Fast_B2


title: MT26 [methylation]


title: DNA-methylation array data_205041750015_R02C01

value: Chordoma


title: MT32 [methylation]


title: Female, ad. Libitum fed, batch 3

description: Library name: F_Fed_B3


title: MT25 [methylation]


title: bio replicate 1, gene expression [L5b]

value: Lung

value: T-cells


title: Sample 10: mutant 33210, root, biol rep 3

city: Poznan

first: Zofia

last: Szweykowska-Kulinska

address: Umultowska 89

department: Departemnt of Gene Expression

country: Poland

institute: Adam Mickiewicz University in Poznan

data_processing:
The adapter sequence was removed from the obtained raw reads with Cutadapt
The reads shorten than 18 nt and longer that 28 nt were removed using Cutadapt
Clean fastq reads were collapsed to fasta files using fastx_collapser from FASTX_toolkit
Supplementary files format and content: fasta format, raw read counts for each molecule in the libraries

organism: Hordeum vulgare

source_name: Root

extract_protocol:
Two week-old barley plants were collected in three biological replicates. The extraction of total RNA was performed using Direct-zol RNA Mini Prep Kit (Zymo Research) according to the manufacturer’s protocol.
Libraries were constructed using the TruSeq SmallRNA Library Preparation Kit (Illumina) as described in the manual.

value: Root

tag: cultivar

value: Golden Promise

value: mutant 33210


title: DNA-methylation array data_207269880058_R02C01

source_name: tumor

value: Pleomorphic xanthoastrocytoma


title: DNA-methylation array data_205310760157_R01C01

value: Central neurocytoma


title: MT24 [methylation]

value: umbilical cord blood

value: CD34+/CD38-/Lin- Hematopoietic stem cell

value: obese


title: bio replicate 1, VDJ [L5b]

description: 10x Genomics

value: Mtb infected TCRalpha KO mice


title: DNA-methylation array data_205689110012_R05C01

value: tumor


title: bio replicate 1, VDJ [L5a]

description: 10x Genomics


title: Sample 8: wild type, root, biol rep 2

value: wild type


title: 6 wpi, replicate 1, VDJ

description: 10x Genomics

extract_protocol:
C57Bl/6 mice were injected intravenously (IV) with ESAT-6 specific (C7) TCR transgenic T-cells and infected with Mtb Erdman 24 hours post-IV. At 6 and 41 wpi, mice were IV injected with anti-CD45 antibody 2 minutes before euthanizing with CO2. Lungs were then perfused and removed 3 minutes after anti-CD45 injection. Lung single cell suspensions were prepared by homogenizing lungs using a GentleMACS tissue dissociator, digesting with collagenase at 37C for 30 minutes, followed by a second run of dissociation using the GentleMACS. Suspensions were then filtered through 70 µm strainers and incubated with 1 mL ACK Lysis Buffer (GIBCO) for 1 minute at room temperature (25C). The cells were resuspended in D-PBS and filtered through 40 µm filters. The resulting single cell suspensions were stained with flow antibodies to sort for total live, parenchymal T-cells (CD45 IV Negative, TCR[b] and CD3 double positive) using the BD FACS Aria.
Library construction was performed according to the manufacturer's instructions (single cell 5' v1 and v2 protocols, 10x Genomics).

tag: mouse strain

tag: weeks post-infection


title: MT18 [methylation]

tag: tissue

tag: cell type


title: Sample 7: wild type, shoot, biol rep 2

source_name: Shoot

value: Shoot