title: Farage cells, Morusinol-treated, 12h rep3

city: soochow

first: Hao

last: Xu

state: State...

address: No. 1, Shizi street, Suzhou

institute: Soochow University

description: Morusinol

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

source_name: lymph node

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 libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: lymph node

value: Farage

value: diffuse large B cell lymphoma

value: Morusinol-treated

value: Morusinol


title: 18mo CD45+ RAG2GFP- thymic cells - day 7 after SL-TBI biological rep1 [single cell]

status: Public on Feb 05 2025

type: SRA

city: Duarte

first: Anastasia

middle: I

last: Kousa

state: CA

address: 1500 E Duarte Rd

department: Hematology / HCT

country: USA

institute: City of Hope

description:
Chromium - Single Cell 3’ Reagent Kit (v2)
CD45pos_thymic_RAG2-CD45+cells_all+annotation.h5ad

library_source: transcriptomic single cell

data_processing:
FASTQ files were processed using the 10x Cell Ranger package (v7.01).
Assembly: GRCm38.p5 (mm10)
Supplementary files format and content: CD45pos_thymic_RAG2-CD45+cells_all+annotation.h5ad: H5AD file with raw and normalized read counts and cell annotation (after bad quality cell filtering)
Supplementary files format and content: filtered_feature_bc_matrix files (barcodes, features, matrix): contain only detected cell-associated barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: filtered_feature_bc_matrix.h5: same information as filtered_feature_bc_matrix in HDF5 format
Supplementary files format and content: raw_feature_bc_matrix files (barcodes, features, matrix): contain all detected barcodes in MEX format; each element of the matrix is the number of UMIs associated with a feature (row) and a barcode (column)
Supplementary files format and content: raw_feature_bc_matrix.h5: same information as raw_feature_bc_matrix in HDF5 format
Supplementary files format and content: molecule_info.h5: contains per-molecule information for all molecules that contain a valid barcode, valid UMI, and were assigned with high confidence to a gene or Feature Barcode; this file is a required input to run cellranger aggr

molecule: polyA RNA

organism: Mus musculus

source_name: thymus

extract_protocol:
All steps were performed at 4 C unless indicated. 10-15 thymi of 2-month-old or 18-month-old female RAG2GFP.C57BL/6 mice were injected with 3 μg of conjugated CD45 antibody and sacrificed 3 min later. The thymic tissue was excised and enzymatically digested. Briefly, thymi were mechanically dissociated into ca. 2 mm pieces. Tissue pieces were incubated with a digestion buffer (RPMI, 10% FCS, 62.5 um/mL liberase TM, 0.4 mg/ml DNase I) twice for 30 min at 37 C. Between incubation steps, supernatant containing dissociated cells was transferred to 50 mL conical tubes equipped with 100 um filter. Cells were pelleted by centrifugation at 400g for 5 min. The fraction of CD45+ peripheral i.v.-labeled cells where removed and cells where sorted for RAG2-GFP- cells after removal of  TER119 and DAPI+ cells. Cells were sorted into tubes containing RPMI supplemented with 2% BSA. FACS-purified cells were spun down at 1200 RPM for 5 min and resuspended in PBS supplemented with 0.04 % BSA for generation of single-cell suspensions. Viability of cells was confirmed to be above 80%.
The single-cell RNA-seq of FACS-sorted cell suspensions was performed on Chromium instrument (10X genomics) following the user guide manual (CG00052 Rev E) and using Single Cell 3’ Reagent Kit (v2). The viability of cells prior to loading onto the encapsulation chip was 73-98%, as confirmed with 0.2% (w/v) Trypan Blue stain. Each sample, containing approximately 8000 cells, was encapsulated in microfluidic droplets at a final dilution of 66–70 cells/µl (a multiplet rate ~3.9%). Following reverse transcription step the emulsion droplets were broken, barcoded-cDNA purified with DynaBeads and amplified by 12-cycles of PCR: 98 ̊C for 180 s, 12x (98 ̊C for 15 s, 67 ̊ C for 20 s, 72 ̊C for 60 s), and 72 ̊C for 60 s. The 50 ng of PCR-amplified barcoded-cDNA was fragmented with the reagents provided in the kit, purified with SPRI beads and resulting DNA library was ligated to the sequencing adapter followed by indexing PCR: 98 ̊C for 45 s; 12x 98 ̊C for 20 s, 54 ̊C for 30 s, 72 ̊C for 20 s), and 72 ̊C for 60 s. The final DNA library was double-size purified (0.6–0.8X) with SPRI beads and sequenced on Illumina Nova-Seq platform (R1 – 26 cycles, i7 – 8 cycles, R2 – 70 cycles or higher) at depth of 200-270 million reads per sample.

tag: tissue

value: thymus

tag: strain

tag: cell type

value: RAG2-CD45+ thymic cells

tag: genotype

tag: age

value: 18-month old

tag: treatment

value: SL-TBI

tag: time point

value: day 7


title: Gill, Standing Stone, heatwave 2, increasing, sample ID 45

city: University Park

first: Justin

last: Waraniak

state: PA

address: 421 Forestry Resources Building

department: Ecosystem Sciences and Management

institute: Penn State University

library_source: transcriptomic

data_processing:
Reads were aligned to a decoy-aware Salvelinus fontinalis transcriptome, constructed from the Salvelinus fontinalis transcriptome available from Phylofish (Pasquier et al. 2016), and the full Salvelinus fontinalis genome (NCBI RefSeq: GCF_029448725.1). Reads that aligned to the decoy-aware transcriptome were counted for each sample using the Salmon aligner tool v.1.10.0 (Patro et al. 2017).
Assembly: GCF_029448725.1 (genome)
Supplementary files format and content: quant.sf: tab-delimited text file with 5 columns: 1) Name - transcript names from the Phylofish transcriptome, 2) Length - the total length in base pairs of the transcript, 3) Effective Length - the computed effective length of the transcript based on the probability of sampling fragments and taking GC-bias into account, 4) TPM - the estimated number of transcripts per million reads, and 5) NumReads - the expected number of reads from the library that aligned to each transcript taking into account reads that mapped to multiple transcripts

organism: Salvelinus fontinalis

source_name: gill

extract_protocol:
RNA and DNA were both extracted as part of the same reactions using the Macherey-Nage Nucleospin RNA kit with RNA/DNA buffer using the manufacturer's recommendations with an additional repeat of the final RNA elution step to increase the total amount of RNA extracted.
RNA libraries were constructed using the improved TagSeq library construction procedure as described in Lohman et al. (2016)

value: gill

tag: location

value: Standing Stone Creek

tag: date

tag: Sex

value: M

tag: water temp_at_time_of_sampling_(c)


title: Gill, Standing Stone, heatwave 2, peak, sample ID 50

value: F


title: integrin-b7posi-spl-PC-5

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research

country: Japan

institute: RIKEN

data_processing:
Basecalls performed by Illumina MiSeq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes in Illumina MiSeq
Reads were aligned to the mm10 genome assembly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of clusters for each gene was counted, which provides the number of molecules detected for each gene
The number of RNA molecules for each gene and index was listed
Assembly: mm10
Supplementary files format and content: The copy number of detected RNA molecules for genes and indexes (tubes) are summarized

source_name: spleen

extract_protocol:
RNAs from cell lysate obtained by heat elevation is directly used for the next RT reaction.
Libraries were prepared by using molecular barcoding technique. First, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains 100 cells. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

value: spleen

value: plasma cells

value: B1-8germ k/w S1pr2-creERT2-Tg Ai14 k/w CD45.1


title: Farage cells, Morusinol-treated, 12h rep2

country: China

description: Morusinol

molecule: total RNA

organism: Homo sapiens

value: lymph node

tag: cell line


title: 18mo CD45+ RAG2GFP- thymic cells - day 4 after SL-TBI biological rep3 [single cell]

value: day 4


title: Gill, Standing Stone, heatwave 2, increasing, sample ID 39


title: integrin-b7posi-spl-PC-4


title: integrin-b7posi-spl-PC-3


title: 18mo CD45+ RAG2GFP- thymic cells - day 1 after SL-TBI biological rep3 [single cell]

value: day 1


title: Gill, Standing Stone, heatwave 1, recovery, sample ID 36


title: 18mo CD45+ RAG2GFP- thymic cells - day 4 after SL-TBI biological rep2 [single cell]


title: Farage cells, Morusinol-treated, 12h rep1

description: Morusinol

value: Farage

value: diffuse large B cell lymphoma

value: Morusinol-treated


title: Farage cells, Control, 12h rep3

description: control

value: WT

value: Control


title: integrin-b7posi-spl-PC-1


title: Gill, Standing Stone, heatwave 2, increasing, sample ID 37


title: 18mo CD45+ RAG2GFP- thymic cells - day 4 after SL-TBI biological rep1 [single cell]

value: thymus

value: RAG2-CD45+ thymic cells

value: 18-month old

value: SL-TBI


title: Gill, Standing Stone, heatwave 2, peak, sample ID 46

value: gill

value: Standing Stone Creek


title: Farage cells, Control, 12h rep2

description: control


title: Gill, Standing Stone, heatwave 1, recovery, sample ID 35

value: M


title: CH12F3 EVs_Day4_small RNA_exp 3

city: Zurich

first: Richard

last: Chahwan

address: Winterthurerstrasse 190

department: Institute of Experimental Immunology

country: Switzerland

institute: University of Zurich

description:
small RNA < 200bp
CH12F3 small RNA

data_processing:
Adapter sequences, primers, number of fuzzy bases (Ns), and reads with quality scores below 30 were trimmed using fastq-mcf. Clean reads were aligned to the mouse genome (GRCm38/mm10) using the TopHat 2.0 program, and the resulting alignment files were reconstructed with Cufflinks [29]. The transcriptome of each sample was assembled separately using Cufflinks 2.0 program. All transcriptomes were pooled and merged to generate a final transcriptome using Cuffmerge. After the final transcriptome was produced, Cuffdiff was used to estimate the abundance of all transcripts based on the final transcriptome to generate read counts for each sample.
Assembly: mm10
Supplementary files format and content: Excel spreadsheet file with raw counts for each sample

extract_protocol:
Cell and EV total RNA were extracted by Trizol® (Invitrogen) and purified by RNeasy® Mini Kit (Qiagen). Briefly, cell or EV pellets 700 µl Trizol®. Subsequently, 140 µl of chloroform was used for phase separation. Trizol® and chloroform mix were centrifuged at 12,000 x g for 15 mins for phase separation. 300 µl RNA-containing top clear phase were transferred to a fresh tube and 400 µl absolute ethanol was added and mixed. 700 µl of sample were transferred to RNeasy spin column. DNAse treatment was performed after first 350 µl RW1 washing step. Finally, RNA was eluted in 30 µl RNase-free water. RNA concentration was assessed using a NanoDrop 2000 spectrophotometer (Thermo Scientific, Waltham, MA, USA). The RNA yield and size distribution were analyzed using an Agilent 2200 Tapestation with high sensitivity RNA Screentape (Agilent Technologies, Foster City, CA, USA).
For small RNA library preparation, RNA aliquots were used for library preparation using NEBNext Multiplex Small RNA library preparation kit (New England Biolabs, Ipswich, MA, USA). The PCR amplified cDNA construct (from 140–160 bp) was purified using a QIAquick PCR Purification kit (Qiagen). The purified cDNA was directly sequenced using an Illumina MiSeq 2000 platform (Illumina, San Diego, CA, USA).  For long non coding RNA library preparation, libraries were constructed using Ribo-Zero Magnetic Gold Kit (Human) (Illumina, San Diego, CA, USA) and NEBNext® Ultra™ RNA Library Prep Kit for Illumina (New England Biolabs) according to the manufacturer’s instructions. Libraries were tested for quality and quantified using qPCR (Kapa Biosystems, Woburn, MA, USA). The resulting libraries were sequenced on a HiSeq 2500 instrument that generated paired-end reads of 100 nucleotides.

value: B cells

value: Class switch recombination


title: 18mo CD45+ RAG2GFP- thymic cells - day 1 after SL-TBI biological rep2 [single cell]


title: Gill, Standing Stone, heatwave 1, recovery, sample ID 34

value: F


title: SU-DHL-8 cells, Morusinol-treated, 12h rep3

description: Morusinol

value: lymph node

value: Morusinol


title: Gill, Standing Stone, heatwave 2, increasing, sample ID 43


title: CH12F3 cells_Day4_small RNA_exp 3

description:
small RNA < 200bp
CH12F3 small RNA


title: 18mo CD45+ RAG2GFP- thymic cells - day 1 after SL-TBI biological rep1 [single cell]

value: day 1


title: Farage cells, Control, 12h rep1

description: control

value: Farage

value: diffuse large B cell lymphoma


title: SU-DHL-8 cells, Morusinol-treated, 12h rep2

description: Morusinol

value: Morusinol-treated


title: CH12F3 EVs_Day1_small RNA_exp 3

description:
small RNA < 200bp
CH12F3 small RNA


title: Gill, Standing Stone, heatwave 1, post-peak, sample ID 31


title: Gill, Standing Stone, heatwave 1, post-peak, sample ID 32


title: SU-DHL-8 cells, Morusinol-treated, 12h rep1

description: Morusinol


title: 18mo CD45+ RAG2GFP- thymic cells - steady state biological rep1 [single cell]

value: untreated


title: Gill, Standing Stone, heatwave 1, post-peak, sample ID 29


title: 02mo CD45+ RAG2GFP- thymic cells - day 7 after SL-TBI biological rep2 [single cell]

value: thymus

value: 02-month old

value: day 7


title: 18mo CD45+ RAG2GFP- thymic cells - steady state biological rep2 [single cell]

value: RAG2-CD45+ thymic cells

value: 18-month old


title: SU-DHL-8 cells, Control, 12h rep3

description: control

value: WT

value: Control


title: CH12F3 EVs_Day4_small RNA_exp 2

description:
small RNA < 200bp
CH12F3 small RNA

value: B cells


title: 02mo CD45+ RAG2GFP- thymic cells - day 7 after SL-TBI biological rep1 [single cell]

value: SL-TBI


title: SU-DHL-8 cells, Control, 12h rep2

description: control


title: Gill, Standing Stone, heatwave 1, post-peak, sample ID 26

value: gill

value: Standing Stone Creek

value: M


title: CH12F3 cells_Day4_small RNA_exp 2

description:
small RNA < 200bp
CH12F3 small RNA

value: Class switch recombination


title: SU-DHL-8 cells, Control, 12h rep1

description: control

value: lymph node


title: Gill, Standing Stone, heatwave 1, peak, sample ID 23


title: CH12F3 cells_Day1_small RNA_exp 2

description:
small RNA < 200bp
CH12F3 small RNA


title: M2 macrophages, Morusinol-treated, 12h rep3

description: Morusinol

source_name: M2 macrophages

treatment_protocol: Cells of experimental group were exposed to Morusinol (6 μM) for 12 hours

value: M2 macrophages

value: macrophages

value: Morusinol

tag: time


title: 02mo CD45+ RAG2GFP- thymic cells - day 4 after SL-TBI biological rep2 [single cell]

value: thymus

value: day 4


title: Gill, Standing Stone, heatwave 1, peak, sample ID 21


title: CH12F3 EVs_Day1_small RNA_exp 2

description:
small RNA < 200bp
CH12F3 small RNA


title: Gill, Standing Stone, heatwave 1, peak, sample ID 22


title: M2 macrophages, Morusinol-treated, 12h rep2

description: Morusinol

value: Morusinol-treated


title: 02mo CD45+ RAG2GFP- thymic cells - day 4 after SL-TBI biological rep1 [single cell]

value: RAG2-CD45+ thymic cells

value: 02-month old


title: Gill, Standing Stone, heatwave 1, peak, sample ID 20

value: F


title: 02mo CD45+ RAG2GFP- thymic cells - day 1 after SL-TBI biological rep1 [single cell]

value: day 1


title: CH12F3 EVs_Day4_small RNA_exp 1

description:
small RNA < 200bp
CH12F3 small RNA

value: B cells


title: CH12F3 cells_Day1_small RNA_exp 3

description:
small RNA < 200bp
CH12F3 small RNA


title: 02mo CD45+ RAG2GFP- thymic cells - day 1 after SL-TBI biological rep2 [single cell]

value: SL-TBI


title: M2 macrophages, Morusinol-treated, 12h rep1

description: Morusinol


title: CH12F3 cells_Day4_small RNA_exp 1

description:
small RNA < 200bp
CH12F3 small RNA


title: M2 macrophages, Control, 12h rep3

description: control

value: WT

value: Control


title: Gill, Standing Stone, heatwave 1, increasing, sample ID 14

value: gill

value: Standing Stone Creek

value: M


title: CH12F3 EVs_Day1_small RNA_exp 1

description:
small RNA < 200bp
CH12F3 small RNA

value: Class switch recombination


title: 02mo CD45+ RAG2GFP- thymic cells - steady state biological rep2 [single cell]

value: untreated


title: Gill, Standing Stone, heatwave 1, increasing, sample ID 13


title: M2 macrophages, Control, 12h rep2

description: control

value: M2 macrophages

value: macrophages


title: CH12F3 cells_Day1_small RNA_exp 1

description:
small RNA < 200bp
CH12F3 small RNA


title: 02mo CD45+ RAG2GFP- thymic cells - steady state biological rep1 [single cell]

value: thymus


title: Primary B cells_Day4_small RNA_exp 3

description:
small RNA < 200bp
Primary B small RNA

source_name: Primary splenic B cells

value: Primary splenic B cells


title: 18-mo thymus - day7 [visium]

data_processing:
FASTQ files were processed using the 10x Space Ranger package (v1.3.1).
Assembly: GRCm38 (mm10)
Supplementary files format and content: .tif: visium slide image
Supplementary files format and content: filtered_feature_bc_matrix.h5: HD5F file with feature barcode matrices that contains only tissue-associated barcodes
Supplementary files format and content: filtered_feature_bc_matrix.tgz: gzipped folder file with feature barcode matrices that contains only tissue-associated barcodes
Supplementary files format and content: raw_feature_bc_matrix.h5: HD5F file with feature barcode matrices that contains both tissue-associated as well as background barcodes
Supplementary files format and content: raw_feature_bc_matrix.tgz: gzipped folder with feature barcode matrices that contains both tissue-associated as well as background barcodes
Supplementary files format and content: spatial.tgz: gzipped folder containing visium-specific outs (QC images to check image processing pipeline, downsampled input images, and files that describe spot barcode locations in the images)
Supplementary files format and content: metrics_summary.csv: metrics for quality assessment in CSV format
Supplementary files format and content: molecule_info.h5: molecule level information used in additional pipelines (spaceranger aggr, spaceranger targeted-compare)
Library strategy: Spatial Transcriptomics

extract_protocol:
Visium spatial gene expression slides were permeabilized at 37 °C for 12–18 min and polyadenylated. mRNA was captured by primers bound to the slides. RT, second-strand synthesis, cDNA amplification and library preparation proceeded using the Visium Spatial Gene Expression Slide & Reagent Kit (10X Genomics PN 1000184) according to the manufacturer’s protocol. After evaluation by real-time PCR, cDNA amplification included 11–12 cycles.
Sequencing libraries were prepared with 8 cycles of PCR. Indexed libraries were pooled equimolar and sequenced on a NovaSeq 6000 in a PE28/120 run using the NovaSeq 6000 S1 Reagent Kit (200 cycles; Illumina).

value: wild type

value: 18-month old


title: Gill, Shavers Creek, heatwave 2, recovery, sample ID 75

value: Shavers Creek

value: F


title: M2 macrophages, Control, 12h rep1

description: control


title: 02-mo thymus - day7 [visium]

value: 02-month old


title: M1 macrophages, Morusinol-treated, 12h rep3

description: Morusinol

source_name: M1 macrophages

value: M1 macrophages

value: Morusinol-treated

value: Morusinol


title: Primary B cells_Day4_small RNA_exp 2

description:
small RNA < 200bp
Primary B small RNA

value: B cells


title: Primary B cells_Day4_small RNA_exp 1

description:
small RNA < 200bp
Primary B small RNA


title: Gill, Standing Stone, heatwave 1, increasing, sample ID 11

value: gill

value: Standing Stone Creek


title: Gill, Shavers Creek, heatwave 2, recovery, sample ID 74


title: Gill, Shavers Creek, heatwave 2, recovery, sample ID 73

value: M


title: M1 macrophages, Morusinol-treated, 12h rep2

description: Morusinol


title: M1 macrophages, Morusinol-treated, 12h rep1

description: Morusinol


title: 02-mo thymus - day4 [visium]

value: untreated


title: Primary B cells_Day1_small RNA_exp 3

description:
small RNA < 200bp
Primary B small RNA

value: Class switch recombination


title: Primary B cells_Day1_small RNA_exp 2

description:
small RNA < 200bp
Primary B small RNA


title: M1 macrophages, Control, 12h rep3

description: control

value: macrophages

value: WT

value: Control


title: M1 macrophages, Control, 12h rep2

description: control


title: ChIP-Seq_mES_RPB1_Cul3KO_untreated_rep2

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

library_source: genomic

data_processing:
Raw ChIP-Seq reads with spike-in were firstly trimmed by Cutadapt software (v3.4) and then mapped to mm10 and hg19 genome by Bowtie2 software (v2.3.5.1) in end-to-end mode.
Only uniquely and concordantly mapped reads were kept for further analysis.
The bigwig files were generated using bamCoverage from Deeptools software (v3.5.1) normalized by the reads mapped to hg19 genome.
Assembly: mm10, hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: RPB7-degron, Cul3KO mES

growth_protocol: The cell were cultured in Dulbecco’s modified Eagle’s medium (DMEM) (Sigma, D5796) with 15 % fetal bovine serum (FBS) (GeminiBio, 900-108), also supplemented with 1 mM L-glutamine (Gibco, 25030081), 1× nucleosides (Millipore, ES-008-D), 1× nonessential amino acids (Gibco, 11140050), 1× penicillin/ streptomycin (Gibco, 15140122), 1 mM Sodium Pyruvate (Gibco, 11360070), 0.1 mM β-mercaptoethanol (Sigma, M3148), 3 μM CHIR99021 (Selleck, S1036) and 1 μM PD0325901 (Selleck, S1263), 1000 U/ml mouse leukemia inhibiting factor (mLIF) (Milipore, ESG1107). All the cells were cultured in 0.2 % gelatin-coated plates at 37°C and 5% CO2 under humid environment.

extract_protocol:
The 1%(wt/vol) formaldehyde crosslinked, MNase digested and Qsonica sonicated chromatin fraction were incubated with indicated antibody overnight and Protein G magnetic beads (Thermo Fisher, 10004D) for another 3 h. After sufficient washing, elution and incubation at 65 °C overnight, DNA was purified through the DNA Extraction Reagent (phenol: chloroform: isoamyl alcohol (25: 24: 1) (pH8.0), Solarbio, P1012).
DNA library was constructed by NEB DNA Library Prep Kit for Illumina (NEB, E7645S), according to the manufacturer's instructions.

treatment_protocol: For RPB7 degradation, cells were treated with 2 μg/ml Dox for 12 h, then with 500 μM auxin for 3 h.  For transcription elongation inhibition, cells were pretreated with 0.5 μM CDK9 degrader THAL-SNS-032 (dCDK9, Selleck, S8979) for 2 h. Each sample was combiend with 10 % HEK293T cells for spike-in normalization.

value: RPB7-degron, Cul3KO mES


title: 02-mo thymus - day1 [visium]

value: thymus

value: wild type


title: M1 macrophages, Control, 12h rep1

description: control


title: Primary B EVs_Day4_small RNA_exp 3

description:
small RNA < 200bp
Primary B small RNA

value: Primary splenic B cells


title: Gill, Shavers Creek, heatwave 2, post-peak, sample ID 62

value: Shavers Creek


title: ChIP-Seq_mES_RPB1_Cul3KO_untreated_rep1


title: Primary B cells_Day1_small RNA_exp 1

description:
small RNA < 200bp
Primary B small RNA


title: Gill, Shavers Creek, heatwave 2, post-peak, sample ID 63

value: F


title: Primary B EVs_Day4_small RNA_exp 2

description:
small RNA < 200bp
Primary B small RNA


title: Gill, Shavers Creek, heatwave 2, peak, sample ID 61


title: Primary B EVs_Day4_small RNA_exp 1

description:
small RNA < 200bp
Primary B small RNA


title: RH9

city: Jinan

first: Wenqing

last: Yang

address: No. 4655, University Road, University Science and Technology Park

institute: Shandong University of Traditional Chinese Medicine

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: blood

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard illumina protocols

value: blood

tag: group

value: resistant hypertension


title: RH10


title: 18-mo thymus - day4 [visium]

value: 18-month old


title: ChIP-Seq_mES_RPB1_Cul3KO_dCDK9_rep1


title: Gill, Shavers Creek, heatwave 2, peak, sample ID 60

value: gill


title: RH8


title: ChIP-Seq_mES_RPB1_Cul3KO_both_dCDK9_RPB7_degron_3h_rep2

value: dCDK9 and RPB7 degron for 3h


title: Gill, Shavers Creek, heatwave 2, peak, sample ID 58

value: M


title: Primary B EVs_Day1_small RNA_exp 3

description:
small RNA < 200bp
Primary B small RNA

value: B cells


title: Gill, Shavers Creek, heatwave 2, recovery, sample ID 72


title: RH7


title: Primary B EVs_Day1_small RNA_exp 2

description:
small RNA < 200bp
Primary B small RNA

value: Class switch recombination


title: Gill, Shavers Creek, heatwave 2, peak, sample ID 57


title: Gill, Shavers Creek, heatwave 2, post-peak, sample ID 65


title: ChIP-Seq_mES_RPB1_Cul3KO_both_dCDK9_RPB7_degron_3h_rep1


title: RH6


title: 18-mo thymus - day1 [visium]

value: untreated


title: ChIP-Seq_mES_RPB1_Cul3KO_RPB7_degron_3h_rep2

value: RPB7 degron for 3h


title: Gill, Shavers Creek, heatwave 2, increasing, sample ID 56


title: Primary B EVs_Day1_small RNA_exp 1

description:
small RNA < 200bp
Primary B small RNA


title: ChIP-Seq_mES_RPB1_Cul3KO_RPB7_degron_3h_rep1


title: Heart, adult female 4

city: Chapel Hill

first: James

middle: Isaiah

last: Emerson

state: North Carolina

address: 132 Ridge Trail

department: Biochemsitry and Biophysics

institute: University of North Carolina- Chapel Hill

description: small RNA enriched (<200 nt)

data_processing:
Libraries were run on a HiSeq2500 (Illumina) with 2×150 bp paired end reads.
The sequence reads were aligned to the mm10 reference genome using STAR via the bcbio-nextgen RNA-sequencing pipeline. Differential gene expression was determined by genewiz.
Assembly: mm10
Supplementary files format and content: Raw expression values, expression values for mature 3' and 5' miRNAs

source_name: Heart

extract_protocol:
adult (4-6 wk.)male and female mouse hearts, n=4 for each sex, were dissected in cold PBS and immediately homogenized in Trizol solution, and were kept in -20C until use. Small RNA from individual hearts was extracted using the miRVANA miRNA isolation kit (Thermo-Fisher AM1561)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Heart

value: C57Bl6/J wt

value: female


title: Gill, Shavers Creek, heatwave 2, increasing, sample ID 55


title: RH4


title: ChIP-Seq_mES_RPB1_Cul3KO_dCDK9_rep2

value: RPB7-degron, Cul3KO mES


title: Heart, adult female 3

description: small RNA enriched (<200 nt)


title: ChIP-Seq_mES_RPB1_Cul3KO_input

value: no


title: Gill, Shavers Creek, heatwave 2, increasing, sample ID 54

value: Shavers Creek


title: Heart, adult female 2

description: small RNA enriched (<200 nt)


title: ChIP-Seq_mES_Ser2_input

source_name: RPB7-degron mES

value: RPB7-degron mES


title: Heart, adult female 1

description: small RNA enriched (<200 nt)


title: Gill, Shavers Creek, heatwave 2, increasing, sample ID 52


title: RH2

value: blood


title: ChIP-Seq_mES_Ser2_untreated_rep2


title: Heart, adult male 4

description: small RNA enriched (<200 nt)

value: male


title: ChIP-Seq_mES_Ser2_untreated_rep1


title: Gill, Shavers Creek, heatwave 1, recovery, sample ID 51

value: F


title: RH1

value: resistant hypertension


title: EH10

value: hypertensive patient


title: Heart, adult male 3

description: small RNA enriched (<200 nt)


title: Gill, Shavers Creek, heatwave 1, recovery, sample ID 49

value: gill

value: M


title: ChIP-Seq_mES_Ser2_RPB7_degron_3h_rep2


title: EH9


title: Heart, adult male 2

description: small RNA enriched (<200 nt)


title: RH5


title: ChIP-Seq_mES_Ser2_RPB7_degron_3h_rep1


title: EH8


title: EH7


title: Gill, Shavers Creek, heatwave 1, recovery, sample ID 46


title: ChIP-Seq_mES_RPB1_untreated_rep2


title: RH3


title: EH6


title: ChIP-Seq_mES_RPB1_untreated_rep1


title: CH12F3 cells_Day4_long non-coding RNA_exp 3

description: CH12F3 long non-coding RNA

value: B cells

value: Class switch recombination


title: CH12F3 EVs_Day4_long non-coding RNA_exp 3

description: CH12F3 long non-coding RNA


title: Gill, Shavers Creek, heatwave 1, post-peak, sample ID 45


title: ChIP-Seq_mES_RPB1_input


title: EH5


title: Gill, Shavers Creek, heatwave 1, post-peak, sample ID 41


title: EH4


title: Gill, Shavers Creek, heatwave 1, post-peak, sample ID 40


title: ChIP-Seq_mES_RPB1_dCDK9_rep2


title: CH12F3 cells_Day1_long non-coding RNA_exp 3

description: CH12F3 long non-coding RNA


title: Gill, Shavers Creek, heatwave 1, peak, sample ID 33


title: EH3


title: Gill, Shavers Creek, heatwave 1, recovery, sample ID 48


title: ChIP-Seq_mES_RPB1_dCDK9_rep1


title: ChIP-Seq_mES_RPB1_both_dCDK9_RPB7_degron_3h_rep2

value: dCDK9 and RPB7 degron for 3h


title: Heart, adult male 1

description: small RNA enriched (<200 nt)

value: Heart


title: CH12F3 cells_Day4_long non-coding RNA_exp 2

description: CH12F3 long non-coding RNA


title: Gill, Shavers Creek, heatwave 1, peak, sample ID 28


title: Gill, Shavers Creek, heatwave 1, post-peak, sample ID 44


title: EH2


title: CH12F3 cells_Day1_long non-coding RNA_exp 2

description: CH12F3 long non-coding RNA


title: N10

value: healthy


title: CH12F3 EVs_Day1_long non-coding RNA_exp 3

description: CH12F3 long non-coding RNA


title: Gill, Shavers Creek, heatwave 1, increasing, sample ID 14


title: ChIP-Seq_mES_RPB1_both_dCDK9_RPB7_degron_3h_rep1


title: Gill, Shavers Creek, heatwave 1, peak, sample ID 27


title: ChIP-Seq_mES_RPB1_RPB7_degron_3h_rep2

value: RPB7 degron for 3h


title: Gill, Shavers Creek, heatwave 1, peak, sample ID 22


title: EH1


title: N9


title: Gill, Shavers Creek, heatwave 1, increasing, sample ID 9


title: CH12F3 EVs_Day4_long non-coding RNA_exp 1

description: CH12F3 long non-coding RNA


title: CH12F3 EVs_Day4_long non-coding RNA_exp 2

description: CH12F3 long non-coding RNA


title: N7


title: N8


title: ChAR-Seq_mES_TIGRE_K41E_F158A_RPB7_degron_3h_rep1

data_processing:
Raw ChAR-Seq reads with spike-in were firstly trimmed by Cutadapt software (v3.4) and then mapped to mm10 and dm6 genome by Bowtie2 software (v2.3.5.1) in end-to-end mode.
Only uniquely and concordantly mapped reads were kept for further analysis. rRNA reads were discarded.
Genes shorter than 1kb were firstly removed, then reads that mapped to gene body regions (+300 to TES) of each gene were counted by featureCounts software (v2.0.1).
Assembly: mm10, dm6
Supplementary files format and content: excel file include raw read counts for each Sample

molecule: nuclear RNA

source_name: RPB7-degron, TIGRE-RPB7-K41E/F158A mES

extract_protocol:
The chromatin pellets were extracted by NP-40 lysis buffer and nuclei lysis buffer successively same as ChIP-seq. After washed by PBS, the pellets were lysed by Trizol reagent to extract the chromatin-associated RNA.
Samples were delivered to Novogene for rRNA-depleted lncRNA library construction.

treatment_protocol: Briefly, cells were pretreated with Dox for 12 h, and then 500 μM Auxin for another 3 h. About 10^7 cells were used and spiked-in with 10% Drosophila S2 cells.

value: RPB7-degron, TIGRE-RPB7-K41E/F158A mES


title: Gill, Shavers Creek, heatwave 1, increasing, sample ID 7


title: ChAR-Seq_mES_TIGRE_K41E_F158A_RPB7_degron_3h_rep2


title: ChAR-Seq_mES_TIGRE_K41E_F158A_untreated_rep2

value: untreated


title: CH12F3 cells_Day1_long non-coding RNA_exp 1

description: CH12F3 long non-coding RNA


title: ChAR-Seq_mES_TIGRE_K41E_F158A_untreated_rep1


title: CH12F3 EVs_Day1_long non-coding RNA_exp 2

description: CH12F3 long non-coding RNA


title: N6


title: N5


title: Gill, East Branch Standing Stone, heatwave 2, recovery, sample ID 47

value: East Branch Standing Stone Creek


title: Gill, East Branch Standing Stone, heatwave 2, recovery, sample ID 45


title: Primary B cells_Day4_long non-coding RNA_exp 2

description: Primary B long non-coding RNA

value: Primary splenic B cells


title: ChIP-Seq_mES_RPB1_RPB7_degron_3h_rep1

value: RPB7-degron mES


title: ChAR-Seq_mES_Cul3KO_untreated_rep1

source_name: RPB7-degron, Cul5KO mES

value: RPB7-degron, Cul5KO mES


title: Gill, East Branch Standing Stone, heatwave 2, recovery, sample ID 44

value: F


title: Primary B cells_Day4_long non-coding RNA_exp 1

description: Primary B long non-coding RNA


title: Primary B cells_Day4_long non-coding RNA_exp 3

description: Primary B long non-coding RNA


title: CH12F3 cells_Day4_long non-coding RNA_exp 1

description: CH12F3 long non-coding RNA


title: N4

value: blood


title: Gill, East Branch Standing Stone, heatwave 2, recovery, sample ID 48


title: Gill, East Branch Standing Stone, heatwave 2, post-peak, sample ID 37


title: ChAR-Seq_mES_Cul3KO_RPB7_degron_3h_rep1

value: RPB7-degron, Cul3KO mES


title: Primary B cells_Day1_long non-coding RNA_exp 3

description: Primary B long non-coding RNA


title: CH12F3 EVs_Day1_long non-coding RNA_exp 1

description: CH12F3 long non-coding RNA


title: N1


title: Primary B cells_Day1_long non-coding RNA_exp 2

description: Primary B long non-coding RNA


title: N2


title: ChAR-Seq_mES_untreated_rep2

source_name: RPB10-degron mES

value: RPB10-degron mES


title: Gill, East Branch Standing Stone, heatwave 2, post-peak, sample ID 36

value: gill

value: M


title: Gill, East Branch Standing Stone, heatwave 2, post-peak, sample ID 35


title: Dendrophenol3

city: Hefei

first: Yuanli

last: Chen

address: School of Food and Biological Engineering, Hefei University of Technology, Hefei, China

institute: Hefei University of Technology

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

source_name: Aortic

growth_protocol: HASMCs cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and  50 µg/mL penicillin/streptomycin and 2 mM glutamine.

extract_protocol:
Total RNA was extracted from treated HASMCs using TRIzol reagent
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: Phosphate medium  was prepared by adding the appropriate concentration of inorganic phosphate (Na2HPO4/NaH2PO4, 1:2) to DMEM with 2% FBS, to induce the onset of calcification in HASMCs.Addition of Dendrophenol (1mm) for osteogenic differentiation

value: Aortic

value: SMC

value: HASMC

value: WT

value: Phosphate and Dendrophenol


title: Primary B cells_Day1_long non-coding RNA_exp 1

description: Primary B long non-coding RNA

value: B cells

value: Class switch recombination


title: ChAR-Seq_mES_untreated_rep1

source_name: RPB9-degron mES

value: RPB9-degron mES

value: untreated


title: Dendrophenol2

department: School of Food and Biological Engineering


title: Gill, East Branch Standing Stone, heatwave 2, peak, sample ID 32

value: East Branch Standing Stone Creek


title: ChAR-Seq_mES_Cul3KO_untreated_rep2

source_name: RPB7-degron, Cul6KO mES

value: RPB7-degron, Cul6KO mES


title: ChAR-Seq_mES_RPB7_degron_3h_rep2

source_name: RPB8-degron mES

value: RPB8-degron mES

value: RPB7 degron for 3h


title: Primary B EVs_Day4_long non-coding RNA_exp 3

description: Primary B long non-coding RNA

value: Primary splenic B cells


title: N3

value: blood

value: healthy


title: ChAR-Seq_mES_Cul3KO_RPB7_degron_3h_rep2

source_name: RPB7-degron, Cul4KO mES

value: RPB7-degron, Cul4KO mES


title: Primary B EVs_Day4_long non-coding RNA_exp 2

description: Primary B long non-coding RNA


title: Dendrophenol1

value: Aortic


title: ChAR-Seq_mES_RPB7_degron_3h_rep1

value: RPB7-degron mES


title: Calcification3

value: SMC

value: HASMC

value: Phosphate


title: Gill, East Branch Standing Stone, heatwave 2, peak, sample ID 31

source_name: gill

value: gill

value: F


title: Primary B EVs_Day4_long non-coding RNA_exp 1

description: Primary B long non-coding RNA

value: B cells

value: Class switch recombination


title: Calcification2

value: WT


title: RNA-Seq_mES_TIGRE_G64V_RPB7_degron_24h_rep2

data_processing:
Raw RNA-Seq reads with spike-in were firstly trimmed by Cutadapt software (v3.4) and then mapped to mm10 and dm6 genome by STAR software (v2.7.10a).
Reads that were not primarily mapped, RCR duplicates and rRNA reads were discarded for further analysis.
Reads that mapped to each gene were counted by featureCounts software (v2.0.1).
Assembly: mm10, dm6
Supplementary files format and content: excel file include raw read counts for each Sample

source_name: RPB7-degron, TIGRE-RPB7-G64V mES

extract_protocol:
Total RNA was extracted by trizol according to the manufacturer’s instruction.
Samples were delivered to Novogene for poly(A) RNA library construction.

treatment_protocol: Cells were treated with 2 μg/ml Dox for 12 h, then with 500 μM auxin for another 12 h. For site-specific mutations of RPB7, 500 μM auxin treatment were prolonged for another 12 h. Each sample was combiend with 10 % Drosophila S2 cells for spike-in normalization.

value: RPB7-degron, TIGRE-RPB7-G64V mES

value: RPB7 degron for 24h


title: RNA-Seq_mES_TIGRE_G64V_RPB7_degron_24h_rep1


title: Calcification1


title: Gill, East Branch Standing Stone, heatwave 2, increasing, sample ID 25

value: East Branch Standing Stone Creek

value: M


title: RNA-Seq_mES_TIGRE_G64V_untreated_rep2

value: untreated


title: Primary B EVs_Day1_long non-coding RNA_exp 2

description: Primary B long non-coding RNA

value: Primary splenic B cells


title: Gill, East Branch Standing Stone, heatwave 2, increasing, sample ID 26


title: Primary B EVs_Day1_long non-coding RNA_exp 3

description: Primary B long non-coding RNA


title: RNA-Seq_mES_TIGRE_G64V_untreated_rep1


title: Gill, East Branch Standing Stone, heatwave 2, increasing, sample ID 24


title: s2-Mor3

description: Morusinol

source_name: SU-DHL-2 cells, Morusinol-treated, 12h

growth_protocol: SU-DHL-2 cells were maintained in 1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

treatment_protocol: Cells of experimental group were exposed to Morusinol (15 μM) for 12 hours

value: lymph node

value: diffuse large B cell lymphoma

value: Morusinol-treated

value: Morusinol


title: Primary B EVs_Day1_long non-coding RNA_exp 1

description: Primary B long non-coding RNA

source_name: Primary splenic B cells


title: s2-Mor1

description: Morusinol


title: Sample_No.72

city: Nagoya

first: Kosuke

last: Yoshida

state: Aichi

address: 65 Tsuruma-cho

institute: Nagoya University

data_processing:
The CLC Genomics Workbench version 9.5.3 program (Qiagen) was used for data analysis.
Adaptor sequences were trimmed, and sequences between 15 and 35 bps were counted.
The trimmed data were mapped to the miRbase 21 database, allowing up to two mismatches.
Assembly: miRBase 21
Supplementary files format and content: a txt file includes RPM counts of each sample

source_name: serum EV

extract_protocol:
The total RNA was extracted using the miRNeasy Mini Kit (QIAGEN, Hilden, Germany).
Small RNA libraries were prepared using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs, Ipswich, MA, USA) from 6 uL RNA. Index codes were added to attribute sequences for each sample.Then, the PCR products were purified using a QIAquick PCR Purification Kit (QIAGEN) on a 6% TBE gel (120 V, 60 min). Furthermore, DNA fragments corresponding to 140–160 bp (length of small RNA plus the 3′ and 5′ adaptors) were recovered, and the cDNA concentration was measured using a Qubit dsDNA HS Assay Kit and a Qubit2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA).

treatment_protocol: Approximately 1 mL of serum was centrifuged at 10,000 ×g for 40 min at 4 °C in the Kubota Model 7000 ultracentrifuge. The pellet was washed in PBS and centrifuged again under the same conditions to suspend it and extract the large EVs. The supernatant was filtered using a 0.45-μm filter (Millex-HV 13 mm, Millipore), and ultracentrifuged at 110,000 ×g for 90 min at 4 °C using an MLS50 rotor (Beckman Coulter Inc.). The pellet was washed with PBS, ultracentrifuged under the same conditions, and resuspended in PBS to extract the sEVs.

value: serum EV

tag: disease

value: Endometriosis

tag: pregnant outcome

value: Non-Pregnant


title: s2-Mor2

description: Morusinol


title: RNA-Seq_mES_TIGRE_P61R_RPB7_degron_24h_rep2

source_name: RPB7-degron, TIGRE-RPB7-P61R mES

value: RPB7-degron, TIGRE-RPB7-P61R mES


title: Gill, East Branch Standing Stone, heatwave 1, recovery, sample ID 23

value: gill

value: F


title: Sample_No.71


title: RNA-Seq_mES_TIGRE_P61R_RPB7_degron_24h_rep1


title: Gill, East Branch Standing Stone, heatwave 2, increasing, sample ID 27


title: Sample_No.70


title: Gill, East Branch Standing Stone, heatwave 2, peak, sample ID 29


title: s2-N3

description: control

source_name: SU-DHL-2 cells, Control, 12h

value: WT

value: Control


title: RNA-Seq_mES_TIGRE_P61R_untreated_rep2


title: s2-N2

description: control


title: Gill, East Branch Standing Stone, heatwave 1, post-peak, sample ID 18


title: Sample_No.68


title: s2-N1

description: control


title: RNA-Seq_mES_TIGRE_K41E_F158A_RPB7_degron_24h_rep2

value: RPB7-degron, TIGRE-RPB7-K41E/F158A mES

value: RPB7 degron for 24h


title: A21412 iPSC-derived motor neurons, MN Day45

city: Bunkyo-ku

first: Selena

last: Setsu

state: Tokyo

department: Institute for Quantitative Bioscience

institute: University of Tokyo

description: SMART-seq

data_processing:
Quality Control of the sequences was performed by fastp (version 0.23.2).
Read counts were calculated by salmon (version 1.7.0), and the read count data outputs by salmon were processed by tximport (version 1.22.0).
The processed data were subjected to Transcripts Per Million (TPM) normalization among groups.
Assembly: GRCh38.p13

extract_protocol:
RNA was harvested using Rneasy Micro Kit (Qiagen). 0.2 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Nextera XT DNA Library Prep Kit following manufacturer's protocols.

value: iPSC-derived motor neurons

value: TARDBP Q343A

value: MN Day45


title: Sample_No.67


title: Gill, East Branch Standing Stone, heatwave 1, post-peak, sample ID 17

value: East Branch Standing Stone Creek


title: RNA-Seq_mES_TIGRE_P61R_untreated_rep1

value: untreated


title: RNA-Seq_mES_TIGRE_K41E_F158A_RPB7_degron_24h_rep1


title: Gill, East Branch Standing Stone, heatwave 1, post-peak, sample ID 16

value: M


title: Gill, East Branch Standing Stone, heatwave 1, recovery, sample ID 19


title: FUS-008-01-E6  iPSC-derived motor neurons, MN Day45

description: SMART-seq

value: FUS P525L homo


title: Sample_No.65

value: serum EV


title: RNA-Seq_mES_TIGRE_K41E_F158A_untreated_rep2


title: A3411 iPSC-derived motor neurons, MN Day45

description: SMART-seq

value: TARDBP M337V hetero


title: Gill, East Branch Standing Stone, heatwave 1, peak, sample ID 9


title: Sample_No.66

value: Endometriosis

value: Non-Pregnant


title: RNA-Seq_mES_Cul3KO_RPB7_degron_12h_rep2

source_name: RPB7-degron, Cul3KO mES

value: RPB7-degron, Cul3KO mES

value: RPB7 degron for 12h


title: WD39 iPSC-derived motor neurons, MN Day45

description: SMART-seq

value: WT


title: Sample_No.64


title: Gill, East Branch Standing Stone, heatwave 1, peak, sample ID 8

value: gill


title: 1210B2 iPSC-derived motor neurons, MN Day45

description: SMART-seq


title: RNA-Seq_mES_Cul3KO_RPB7_degron_12h_rep1


title: Gill, East Branch Standing Stone, heatwave 1, peak, sample ID 7


title: Sample_No.63


title: RNA-Seq_mES_TIGRE_K41E_F158A_untreated_rep1

value: RPB7-degron, TIGRE-RPB7-K41E/F158A mES


title: RNA-Seq_mES_Cul3KO_untreated_rep2


title: Gill, East Branch Standing Stone, heatwave 1, increasing, sample ID 6

value: F


title: 201B7 iPSC-derived motor neurons, MN Day45

description: SMART-seq

value: iPSC-derived motor neurons


title: Sample_No.62

value: Normal


title: Gill, East Branch Standing Stone, heatwave 1, increasing, sample ID 5


title: RNA-Seq_mES_Cul3KO_untreated_rep1


title: FUS-008-01-E6  iPSC-derived motor neurons, MN Day14

description: SMART-seq

value: MN Day14


title: 414C2 iPSC-derived motor neurons, MN Day14

description: SMART-seq


title: RNA-Seq_mES_untreated_rep2

source_name: RPB7-degron mES

value: RPB7-degron mES


title: Gill, East Branch Standing Stone, heatwave 1, post-peak, sample ID 14

value: East Branch Standing Stone Creek


title: Gill, East Branch Standing Stone, heatwave 1, peak, sample ID 13


title: Gill, East Branch Standing Stone, heatwave 1, increasing, sample ID 4

value: M


title: RNA-Seq_mES_untreated_rep1

value: untreated


title: SM4-4-5 iPSC-derived motor neurons, MN Day14

description: SMART-seq

value: TARDBP N345K hetero


title: Sample_No.58

value: serum EV


title: Sample_No.69

value: Endometriosis


title: Gill, Big Poe, heatwave 2, recovery, sample ID 75

value: Big Poe Creek


title: Sample_No.59

value: Non-Pregnant


title: RNA-Seq_mES_RPB7_degron_12h_rep2

value: RPB7 degron for 12h


title: A3411 iPSC-derived motor neurons, MN Day14

description: SMART-seq

value: TARDBP M337V hetero


title: WD39 iPSC-derived motor neurons, MN Day14

description: SMART-seq

value: WT


title: Gill, Big Poe, heatwave 2, recovery, sample ID 76

value: gill


title: Sample_No.57


title: RNA-Seq_mES_RPB7_degron_12h_rep1


title: Gill, Big Poe, heatwave 2, recovery, sample ID 73

value: F


title: Sample_No.56


title: Sample_No.60


title: Sample_No.61


title: 201B7 iPSC-derived motor neurons, MN Day14

description: SMART-seq

value: iPSC-derived motor neurons


title: Purified microglia-Gpr34 deficient rep2

first: XiqQiong

last: Wang

state: Anhui

address: School of Life Sciences, No. 443 Huangshan Road

institute: University Of Science And Technology Of China

data_processing:
FastQC (version 0.11.2) was used for evaluating the quality of sequenced data.
Raw data (raw reads) of FASTQ format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing following reads: (1) reads with adapter; (2) reads with more than 3 N; (3) reads with more than 20% nucleotides with Qphred<=5; At the same time, Q20, Q30 and GC content of the clean data were calculated. Then, map the clean reads to the silva database to remove the rRNA. All the downstream analyses were based on the clean data without rRNA.
RNA-seq reads were aligned to the reference genome using HISAT2, And uniquely mapped reads were used for further analysis.
Then we use featurecounts to calculate Raw Counts, FPKM and TPM of genes
Assembly: GRCm38
Supplementary files format and content: Matrix table with raw gene counts,FPKM and TPM for every gene and every sample

source_name: Purified microglia

extract_protocol:
The RNA of all cells was harvested using Trizol reagent.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Purified microglia

value: Gpr34 deficient


title: Sample_No.55

value: Normal


title: Ovarian-endometrial-cyst_Endometriosis_5

source_name: Ovarian endometrial cyst

treatment_protocol: Total RNA was extracted using a gentleMACS Dissociator (Miltenyi Biotec, Bergisch Gladbach, Germany), and the tissues were shredded and crushed with QIAzol (QIAGEN) in a gentleMACS M tube (Miltenyi Biotec).

value: Ovarian endometrial cyst


title: 1210B2 iPSC-derived motor neurons, MN Day14

description: SMART-seq

value: MN Day14


title: Gill, Big Poe, heatwave 2, post-peak, sample ID 64


title: Sample_No.54


title: Purified microglia-5xFAD rep1


title: Purified microglia-5xFAD rep2


title: Ovarian-endometrial-cyst_Endometriosis_3


title: Sample_No.53


title: Sample_No.52


title: Ovarian-endometrial-cyst_Endometriosis_4


title: E. coli K-12 MG1655, RpoH, ChIP-mini, 200ul, replicate 2

city: Ulsan

first: Donghyuk

last: Kim

address: 50 UNIST-gil, Eonyang-eup, Ulju-gun

department: Department of Chemical Engineering

country: South Korea

institute: UNIST

description: Library name: ChIP-mini_RpoH_rep2 (200ul)

library_source: other

data_processing:
Sequenced reads of E.coli K-12 MG1655 samples were mapped onto NC_000913.3 reference genome sequence using bowtie v1.0.0 with parameters -p 8 -S. Sequenced reads of S. Typhimurium 14028s samples were mapped onto NC_016856.1 and NC_016855.1 reference genome sequence using bowtie v1.0.0 with parameters -p 8 -S
RpoD and RpoH binding sites were identified using DEOCSU(DEep-learning Optimized ChIP-exo peak calling SUite).
Assembly: NC_000913.3, NC_016856.1, NC_016855.1
Supplementary files format and content: Binding sites and their intensities of ChIP-exo and ChIP-mini datasets were included.

molecule: other

organism: Escherichia coli K-12

source_name: bacterial cell

growth_protocol: E. coli K-12 MG1655 WT and rpoH-8myc tagged cells were grown to mid-log phase aerobically at 37°C in M9 minimal media supplemented with 0.2% glucose. S. Typhimurium 14028s WT or hns-8myc tagged strains were aerobically cultured at 37°C overnight with agitation in LB media. Mouse macrophage-like cells (J774A.1, RAW 264.7) and human epithelial cells (HeLa, INT407) were infected with S. Typhimurium 14028s hns-8myc tagged strains (MOI of 1:10) in DMEM for 30 minutes. Following infection, extracellular bacteria were isolated and utilized for ChIP-mini (Extracellular Chip-mini). Subsequently, the remaining extracellular bacteria were removed by washing process and gentamycin treatment. At 6 hours post-infection (hpi), the S. Typhimurium-infected host cells  were co-crosslinked using formaldehyde. Additionally, at 2, 4, 9 and 21 hpi, the S. Typhimurium-infected J774A.1 cells were co-crosslinked using formaldehyde. Crosslinked intracellular bacteria were used for ChIP-mini method (Intracellular Chip-mini)

extract_protocol:
Chromatin Immunoprecipitation (ChIP) and, for immunomagnetic separation ChIP-mini, an antibody-magnetic bead complex, comprising an anti-Salmonella antibody (ab35156, Abcam) and Dynabeads M-280 Sheep Anti-Rabbit IgG magnetic beads (Invitrogen), was used to isolate intracellular S. Typhimurium from co-crosslinked host intracellular S. Typhimurium samples.
KAPA HiFi HotStart ReadyMix

tag: chip antibody

value: Anti-c-myc

value: bacterial cell


title: Gill, Big Poe, heatwave 2, post-peak, sample ID 59

tag: tissue

value: M


title: Ovarian-endometrial-cyst_Endometriosis_2

value: Endometriosis


title: E. coli K-12 MG1655, RpoH, ChIP-mini, 200ul, replicate 1

description: Library name: ChIP-mini_RpoH_rep1 (200ul)

tag: strain


title: Gill, Big Poe, heatwave 2, peak, sample ID 58

value: Big Poe Creek


title: Sample_No.50

value: serum EV

value: Non-Pregnant


title: Purified microglia-Gpr34 deficient rep1

tag: cell type


title: Sample_No.49


title: E. coli K-12 MG1655, RpoH, ChIP-exo, 50ml, replicate 1

description: Library name: ChIP-exo_RpoH_rep1 (50ml)

tag: genotype


title: Gill, Big Poe, heatwave 2, peak, sample ID 55


title: E. coli K-12 MG1655, RpoH, ChIP-exo, 50ml, replicate 2

description: Library name: ChIP-exo_RpoH_rep2 (50ml)


title: Endometrium_Endometriosis_4

source_name: Endometrium

value: Endometrium


title: Gill, Big Poe, heatwave 2, post-peak, sample ID 63


title: Gill, Big Poe, heatwave 2, peak, sample ID 54


title: Sample_No.47


title: Sample_No.48


title: Endometrium_Endometriosis_3


title: Gill, Big Poe, heatwave 2, post-peak, sample ID 61


title: Gill, Big Poe, heatwave 2, increasing, sample ID 53


title: Sample_No.46


title: Endometrium_Endometriosis_2


title: E. coli K-12 MG1655, RpoD, ChIP-mini, 10ul, replicate 2

description:
ChIP-mini_RpoD_rep2 (10ul)
Total_binding sites of RpoD.xlsx

data_processing:
Sequenced reads of E.coli K-12 MG1655 samples were mapped onto NC_000913.3 reference genome sequence using bowtie v1.0.0 with parameters -p 8 -S. Sequenced reads of S. Typhimurium 14028s samples were mapped onto NC_016856.1 and NC_016855.1 reference genome sequence using bowtie v1.0.0 with parameters -p 8 -S
Binding intensity of H-NS and RpoD was calculated by Signal to Noise ratio (S/N)
Assembly: NC_000913.3, NC_016856.1, NC_016855.1
Supplementary files format and content: Binding sites and their intensities of S. Typhimurium 14028s H-NS and RpoD under macrophage in vitro and in vivo conditions were included.

value: Anti-RpoD

value: WT


title: Gill, Big Poe, heatwave 2, increasing, sample ID 51

value: gill

value: F


title: Sample_No.51


title: Gill, Big Poe, heatwave 2, peak, sample ID 57


title: Ovarian-endometrial-cyst_Endometriosis_1


title: E. coli K-12 MG1655, RpoD, ChIP-mini, 5ul, replicate 1

description:
ChIP-mini_RpoD_rep1 (5ul)
Total_binding sites of RpoD.xlsx


title: Endometrium_Endometriosis_1


title: Endometrium_Endometriosis_5


title: E. coli K-12 MG1655, RpoD, ChIP-mini, 10ul, replicate 1

description:
ChIP-mini_RpoD_rep1 (10ul)
Total_binding sites of RpoD.xlsx


title: Sample_No.45


title: Sample_No.44


title: Endometrium_Control_5


title: E. coli K-12 MG1655, RpoD, ChIP-mini, 25ul, replicate 2

description:
ChIP-mini_RpoD_rep2 (25ul)
Total_binding sites of RpoD.xlsx


title: E. coli K-12 MG1655, RpoD, ChIP-mini, 25ul, replicate 1

description:
ChIP-mini_RpoD_rep1 (25ul)
Total_binding sites of RpoD.xlsx


title: Gill, Big Poe, heatwave 2, recovery, sample ID 70


title: Gill, Big Poe, heatwave 2, increasing, sample ID 49


title: Gill, Big Poe, heatwave 1, recovery, sample ID 48


title: Endometrium_Control_3


title: Endometrium_Control_4


title: Gill, Big Poe, heatwave 1, recovery, sample ID 46


title: Sample_No.43


title: Sample_No.42


title: Endometrium_Control_2


title: Gill, Big Poe, heatwave 1, recovery, sample ID 44


title: Macrophage extracellular S. Typhimurium 14028s, RpoD, ChIP-mini, replicate 2

description:
Invitro_ChIP-mini_RpoD_rep2 (macrophage extracellular)
Total_binding sites of H-NS and RpoD.xlsx

organism: Salmonella enterica subsp. enterica serovar Typhimurium

value: macrophage extracellular


title: Sample_No.39

value: Pregnant


title: Endometrium_Control_1

value: Normal


title: E. coli K-12 MG1655, RpoD, ChIP-mini, 200ul, replicate 1

description:
ChIP-mini_RpoD_rep1 (200ul)
Total_binding sites of RpoD.xlsx


title: E. coli K-12 MG1655, RpoD, ChIP-mini, 1.6ml, replicate 2

description:
ChIP-mini_RpoD_rep2 (1.6ml)
Total_binding sites of RpoD.xlsx


title: Sample_No.38


title: E. coli K-12 MG1655, RpoD, ChIP-mini, 1.6ml, replicate 1

description:
ChIP-mini_RpoD_rep1 (1.6ml)
Total_binding sites of RpoD.xlsx


title: E. coli K-12 MG1655, RpoD, ChIP-mini, 6.25ml, replicate 2

description:
ChIP-mini_RpoD_rep2 (6.25ml)
Total_binding sites of RpoD.xlsx


title: Gill, Big Poe, heatwave 1, post-peak, sample ID 40


title: Gill, Big Poe, heatwave 1, recovery, sample ID 42


title: Gill, Big Poe, heatwave 2, increasing, sample ID 50


title: E. coli K-12 MG1655, RpoD, ChIP-mini, 200ul, replicate 2

description:
ChIP-mini_RpoD_rep2 (200ul)
Total_binding sites of RpoD.xlsx


title: Sample_No.40


title: Macrophage extracellular S. Typhimurium 14028s, RpoD, ChIP-mini, replicate 1

description:
Invitro_ChIP-mini_RpoD_rep1 (macrophage extracellular)
Total_binding sites of H-NS and RpoD.xlsx


title: Gill, Big Poe, heatwave 1, post-peak, sample ID 41


title: Sample_No.37


title: Macrophage extracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 1

description:
Invitro_ChIP-mini_H-NS_rep1 (macrophage extracellular)
Total_binding sites of H-NS and RpoD.xlsx


title: Sample_No.36


title: Macrophage extracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 2

description:
Invitro_ChIP-mini_H-NS_rep2 (macrophage extracellular)
Total_binding sites of H-NS and RpoD.xlsx


title: Gill, Big Poe, heatwave 1, post-peak, sample ID 39


title: Gill, Big Poe, heatwave 1, post-peak, sample ID 38


title: E. coli K-12 MG1655, RpoD, ChIP-mini, 6.25ml, replicate 1

description:
ChIP-mini_RpoD_rep1 (6.25ml)
Total_binding sites of RpoD.xlsx


title: Sample_No.35


title: E. coli K-12 MG1655, RpoD, ChIP-exo, 50ml, replicate 2

description:
ChIP-exo_RpoD_rep2 (50ml)
Total_binding sites of RpoD.xlsx


title: Gill, Big Poe, heatwave 1, peak, sample ID 32


title: Macrophage intracellular S. Typhimurium 14028s, RpoD, ChIP-mini, replicate 2

description:
Invivo_ChIP-mini_RpoD_rep2 (macrophage intracellular)
Total_binding sites of H-NS and RpoD.xlsx

value: macrophage intracellular


title: Macrophage intracellular S. Typhimurium 14028s, RpoD, ChIP-mini, replicate 1

description:
Invivo_ChIP-mini_RpoD_rep1 (macrophage intracellular)
Total_binding sites of H-NS and RpoD.xlsx


title: E. coli K-12 MG1655, RpoD, ChIP-exo, 50ml, replicate 1

description:
ChIP-exo_RpoD_rep1 (50ml)
Total_binding sites of RpoD.xlsx


title: Sample_No.34


title: M.tuberculosis H37RV Extracellular Vesicles RNA

city: Zaragoza

first: Joaquin

last: Sanz

state: Zaragoza

address: Mariano Esquillor

department: Institute for Biocomputation & Physics of Complex Systems BIFI

country: Spain

institute: University of Zaragoza

description: Library name: EV_RNA_Mtb

data_processing:
Adapter trimming and low-quality reads removal were performed using Trim Galore version 0.6.4_dev
reads were mapped against the M. tuberculosis H37RV strain reference genome from Mycobrowser (Release 4, 2021-03-23) using kallisto (single-end run mode)
Assembly: Mycobrowser Release 4, 2021-03-23
Supplementary files format and content: Estimated counts per locus tag, txt file

organism: Mycobacterium tuberculosis

extract_protocol:
RNA was isolated from Mtb H37Rv Extracellular Membrane vesicles following and acid phenol-chlorophorm isoamyl alcohol method
Sequencing libraries were prepared using a TruSeq small RNA library (Illumina Inc., San Diego, CA, United Stated) selecting RNA sizes from 20-300 nt.

tag: cell compartment

value: Extracellular vesicles


title: Macrophage intracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 2

description:
Invivo_ChIP-mini_H-NS_rep2 (macrophage intracellular)
Total_binding sites of H-NS and RpoD.xlsx

value: Anti-c-myc

tag: treatment


title: Gill, Big Poe, heatwave 1, peak, sample ID 28


title: Sample_No.32


title: 20 day post-SIV Sample 3

city: Philadelphia

first: Benjamin

middle: C.

last: Reiner

address: 125 S 31st St

institute: University of Pennsylvania

description: 10x Genomics 3' gene expression v3.1

data_processing:
Samples were demultixpled, aligned, and counted using CellRanger v3.1.0.
Assembly: Mmul10
Supplementary files format and content: Tab separated value files and matrix files

organism: Macaca mulatta

source_name: brain

extract_protocol:
Fresh frozen tissue samples were homogenized in (Nuclease-free water with 10 mM Tris-HCL, 10 mM NaCl, 3 mM MgCl2, 0.5% NP-40), diluted, rested on ice, and further diluted with wash buffer (1X PBS with 2% BSA, 1:1000 RNase inhibitor, 0.25% Glycerol).
Libraries were constructed using the manufacturer protocol for the 10x Genomics dual index 3' gene expression assay v3.1

value: brain

tag: brain region

value: frontal cortex

value: uninfected


title: Gill, Big Poe, heatwave 1, peak, sample ID 27

data_processing:
Reads were aligned to a decoy-aware Salvelinus fontinalis transcriptome, constructed from the Salvelinus fontinalis transcriptome available from Phylofish (Pasquier et al. 2016), and the full Salvelinus fontinalis genome (NCBI RefSeq: GCF_029448725.1). Reads that aligned to the decoy-aware transcriptome were counted for each sample using the Salmon aligner tool v.1.10.0 (Patro et al. 2017).
Assembly: GCF_029448725.1 (genome)
Supplementary files format and content: quant.sf: tab-delimited text file with 5 columns: 1) Name - transcript names from the Phylofish transcriptome, 2) Length - the total length in base pairs of the transcript, 3) Effective Length - the computed effective length of the transcript based on the probability of sampling fragments and taking GC-bias into account, 4) TPM - the estimated number of transcripts per million reads, and 5) NumReads - the expected number of reads from the library that aligned to each transcript taking into account reads that mapped to multiple transcripts

tag: location

value: Big Poe Creek


title: Macrophage intracellular S. Typhimurium 14028s, H-NS, ChIP-mini, replicate 1

description:
Invivo_ChIP-mini_H-NS_rep1 (macrophage intracellular)
Total_binding sites of H-NS and RpoD.xlsx

value: bacterial cell


title: 20 day post-SIV Sample 1

description: 10x Genomics 3' gene expression v3.1


title: CRISPR_R4

city: Heidelberg

first: Katrin

last: Domsch

address: INF 230

department: COS - Developmental Biology

country: Germany

institute: Heidelberg University

description: not_used_for Analysis

data_processing:
Raw data were quality checked with FastQC
trimmed using Trimmomatic 0.36
mapped against dm6 with STAR
reads were counted by QoRTs
differential expression analyses were performed with standard conditions for DESeq2
Assembly: dm6
Supplementary files format and content: tab-delimited text file with raw counts

organism: Drosophila melanogaster

source_name: wing disc

growth_protocol: samples where crossed and the offspring were maintained by 29 °C until they were wandering larve stage (about 5 days after egg lay)

extract_protocol:
Total RNA was extracted with the Monarch from NEB (T2010S)
The library was prepared by using the ThruPLEX DNA-Seq Kit (Rubicon) for illumina sequencing.

treatment_protocol: wing disc were disected in PBS and and added to DNA/RNA protection Reagent (Part of the Monarch® RNA Miniprep Kit)

value: wing disc

value: whole wing disc

value: CRISPR


title: Sample_No.31

value: serum EV


title: Sample_No.30


title: wt_R4

description: not_used_for Analysis

value: wt


title: 10 day post-SIV Sample 3

description: 10x Genomics 3' gene expression v3.1


title: Sample_No.29


title: Gill, Big Poe, heatwave 1, increasing, sample ID 24

extract_protocol:
RNA and DNA were both extracted as part of the same reactions using the Macherey-Nage Nucleospin RNA kit with RNA/DNA buffer using the manufacturer's recommendations with an additional repeat of the final RNA elution step to increase the total amount of RNA extracted.
RNA libraries were constructed using the improved TagSeq library construction procedure as described in Lohman et al. (2016)

value: gill

tag: date

value: M


title: CRISPR_R3

description: not_used_for Analysis


title: 10 day post-SIV Sample 2

description: 10x Genomics 3' gene expression v3.1


title: Sample_No.33

value: Pregnant


title: wt_R3


title: 10 day post-SIV Sample 1

description: 10x Genomics 3' gene expression v3.1


title: Gill, Big Poe, heatwave 1, peak, sample ID 31

tag: Sex

value: F


title: Sample_No.28

value: Normal


title: Sample_No.27


title: CRISPR_R2


title: Sample_No.41

value: Endometriosis


title: human adipocytes SGBS cells,Treated VD/TNFα

type: RNA

city: Marseille

first: Lourdes

last: Mounien

address: 27 Boulevard Jean Moulin

country: France

institute: Aix Marseille University

description:
SAMPLE 4
EV containing miRNA

data_processing:
The normalization and all the data analysis were performed using a calculation table provided by Qiagen
For the normalization it uses the average of 14 housekeeping genes determined according to the stability of their expression across all conditions : hsa-let-7d-5p,hsa-miR-101-3p,hsa-miR-125a-5p,hsa-miR-125b-5p,hsa-miR-15a-5p,hsa-miR-16-5p,hsa-miR-17-5p,hsa-miR-21-5p,hsa-miR-23a-3p,hsa-miR-23b-3p,hsa-miR-29a-3p,hsa-miR-29c-3p,hsa-miR-93-5p,SNORD44 (hsa)
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The calculation table provided by Qiagen automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Matrix non-normalized worksheet reports average Ct_Target for each conditions (n=3).
Matrix normalized worksheet reports normalized signal (against housekeeping genes).
Fold Change worksheet reports test/control (i.e., mature DC/immature DC) ratios.

label: SYBR Green

source_name: pre-adipocyte

label_protocol: Screening of miRNAs contained in EVs was performed using miRCURY LNA miRNA Focus PCR Inflammation Panels (Qiagen)

growth_protocol: Simpson-Golabi-Behmel syndrome (SGBS) preadipocytes were grown in DMEM/F12 medium with 10% FCS, penicillin/streptomycin, 3.3 mM biotin and 1.7 mM pantothenate. Cells were differentiated with serum-free maintenance medium containing biotin/pantothenate, 0.1 mg/mL human transferrin, 20 nM insulin, 100 nM hydroxycortisol, 0.2 nM T3 hormone supplemented with 25 nM dexamethasone, 0.25 mM isobutylmethylxanthine (IBMX) and 2µM rosiglitazone during 4 days. Mature adipocytes were obtained at day 14.

extract_protocol: EV containing miRNA were isolated using miRCURY Exosome Cell/Urine/CSF kit (Qiagen) ; miRNAs were extracted using miRNeasy Serum/Plasma kit (Qiagen) ;

treatment_protocol: Mature adipocyte (day 14) were incubated with 100nM 1,25(OH)2D for 24h followed by either 24h treatment with 10ng/mL TNFα.

tag: condition

value: SGBS

value: Mature adipocyte

tag: activation agent

value: VD pretreated and TNFα treated

value: 16 days


title: Control Sample 3

description: 10x Genomics 3' gene expression v3.1

value: brain

value: frontal cortex

value: uninfected


title: 20 day post-SIV Sample 2

description: 10x Genomics 3' gene expression v3.1


title: wt_R2

value: wing disc

value: whole wing disc


title: Sample_No.26

value: serum EV


title: Sample_No.25


title: Gill, Big Poe, heatwave 1, increasing, sample ID 23

value: Big Poe Creek

tag: water temp_at_time_of_sampling_(c)


title: CRISPR_R1

tag: group

value: CRISPR


title: wt_R1

description: not_used_for Analysis

value: wt


title: Control Sample 1

description: 10x Genomics 3' gene expression v3.1


title: human adipocytes SGBS cells,Treated TNFα

description:
SAMPLE 2
EV containing miRNA

value: TNFα treated

tag: time


title: human adipocytes SGBS cells, Control

description:
SAMPLE 1
EV containing miRNA

value: Control


title: Vole 4947

status: Public on Feb 04 2025

city: Boulder

first: Zoe

last: Donaldson

state: CO

address: 1945 Colorado Ave

department: MCDB

institute: University of Colorado Boulder

description:
39_NAc_4947_F
10X Genomics

data_processing:
Demultiplexing, barcode processing and alignment was performed using CellRanger software v3.1.0.
Assembly: MicOch1.0
Supplementary files format and content: Tab-separated values and filtered feature barcode matrices.

organism: Microtus ochrogaster

source_name: Brain (nucleus accumbens)

extract_protocol:
Brain punches were placed on wet ice until barely thawed. 0.5 mL Complete Buffer HB (250mM sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, 0.042% BSA, 0.06 U/ul RNAsin, 0.15mM spermine, 0.5mM spermidine, 1mM DTT, coOmplete EDTA-free protease inhibitor cocktail tablet) was then added to each tube with brain punches and then Complete Buffer HB and punches were transferred to 2 mL dounce homogenizer. Samples were dounced with a tight pestle 20 times. 16 uL 5% IGEPAL CA-630 in Buffer HB (250mM sucrose, 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH) was added to the dounce homogenizer and the samples were dounced 10 more times. The samples were then filtered through a Flowmi 40 um strainer into a 2 mL LoBind Eppendorf tube. The volume of flowthrough was measured and an equal volume of Working Solution (50% iodixanol (OptiPrep), 25mM KCl, 5mM MgCl2, 20mM Tricine-KOH, 0.042% BSA, 0.064 U/ul RNAsin) was added to the homogenate and mixed by gentle pipetting using a wide-bore P1000 pipette tip. First, 50% iodixanol was made by diluting 60% iodixanol (OptiPrep) in Working Solution. Then, 30% and 40% iodixanol solutions were made by diluting the 50% iodixanol/Working Solution in Complete Buffer HB. In 0.8 uL ultracentrifuge tubes, 160 uL 30% iodixanol was carefully layered on top of 80 uL 40% iodixanol and the interface was labeled with pen. The maximum amount of filtered samples were carefully layered on top of the iodixanol gradient using a 23G angled needle attached to a 1 mL insulin syringe. The samples were centrifuged at 10,000g for 30 min in a swinging bucket ultracentrifuge at 4C with the acceleration set to slow and the brake set to slow. When the spin was finished, the majority of the layer above the interface was carefully removed using a 23G angled needle attached to a 1 mL insulin syringe. Approximately 70 uL of nuclei were collected at the 30%-40% iodixanol interface using a 14G blunt end needle attached to a 1 mL insulin syringe and put in a LoBind eppendorf tube. To check the concentration of nuclei, 10 uL trypan blue was added to 10 uL nuclei and nuclei were examined using a brightfield microscope at 10X magnification. Samples were diluted to 320-2020 nuclei/uL in Complete Buffer HB before loading onto 10X Genomics Chromium controller.
Library was constructed according to the manufacturer's instructions (10X Genomics 5' HT Kit v2).

value: Brain (nucleus accumbens)

value: Female

tag: pairing type

value: Mate


title: Vole 4908

description:
37_NAc_4908_M
10X Genomics

value: Male

value: Peer


title: Vole 4970

description:
38_NAc_4970_M
10X Genomics


title: Vole 923

description:
40_NAc_923_M
10X Genomics


title: Vole 5124

description:
36_NAc_5124_M
10X Genomics


title: Gill, Big Poe, heatwave 1, increasing, sample ID 22

source_name: gill

value: gill

value: M


title: Vole 4920

description:
34_NAc_4920_F
10X Genomics


title: Vole 4976

description:
35_NAc_4976_M
10X Genomics


title: Vole 5227

description:
31_NAc_5227_F
10X Genomics


title: Vole 4963

description:
30_NAc_4963_F
10X Genomics


title: Vole 5023

description:
29_NAc_5023_F
10X Genomics


title: Vole 4896

description:
27_NAc_4896_F
10X Genomics


title: Vole 4894

description:
28_NAc_4894_M
10X Genomics


title: Vole 4898

description:
33_NAc_4898_F
10X Genomics


title: Control Sample 2

description: 10x Genomics 3' gene expression v3.1

value: brain

value: frontal cortex


title: Vole 5209

description:
25_NAc_5209_M
10X Genomics


title: Vole 4974

description:
26_NAc_4974_M
10X Genomics


title: Vole 4917

description:
23_NAc_4917_M
10X Genomics


title: Vole 4932

description:
24_NAc_4932_M
10X Genomics


title: Vole 5121

description:
22_NAc_5121_M
10X Genomics


title: Vole 5225

description:
21_NAc_5225_F
10X Genomics


title: Vole 4960

description:
19_NAc_4960_F
10X Genomics


title: Vole 4901

description:
18_NAc_4901_F
10X Genomics


title: Vole 4928

description:
20_NAc_4928_M
10X Genomics


title: human adipocytes SGBS cells,Treated VD

description:
SAMPLE 3
EV containing miRNA

value: SGBS

value: Mature adipocyte

value: VD treated

value: 16 days


title: Vole 4958

description:
17_NAc_4958_F
10X Genomics


title: Vole 4916

description:
16_NAc_4916_M
10X Genomics


title: Vole 5228

description:
12_NAc_5228_F
10X Genomics


title: Vole 5021

description:
13_NAc_5021_F
10X Genomics


title: Vole 4931

description:
10_NAc_4931_M
10X Genomics


title: Vole 4907

description:
11_NAc_4907_F
10X Genomics


title: Vole 5122

description:
32_NAc_5122_M
10X Genomics


title: Vole 4968

description:
9_NAc_4968_F
10X Genomics


title: Vole 4909

description:
8_NAc_4909_M
10X Genomics


title: Vole 4921

description:
7_NAc_4921_F
10X Genomics


title: Vole 4910

description:
6_NAc_4910_M
10X Genomics


title: Vole 4975

description:
2_NAc_4975_M
10X Genomics


title: Vole 4918

description:
3_NAc_4918_F
10X Genomics


title: AMO1 shIRF4, Dox 24h, RNAPII-pS2 ChIP, Rep 2

city: South San Francisco

first: Ioanna

last: Oikonomidi

state: California

address: 1 DNA Way

department: Research Biology

institute: Genentech Inc

description:
Library name: LIB6228707
A24_RNAPII_2

data_processing:
ChIP-seq results were analyzed using the ENCODE ChIP-seq pipeline (v2.2.1). ChIP-seq reads were aligned to the human reference genome (hg38) using Bowtie2 (v2.3.4.3). Aligned reads were then filtered for quality and duplicates using samtools (v1.9) and Picard (Broad Institute - v2.20.7). The SPP peak caller was used to call ChIP-seq peaks, and input was used to assess the background of the experiments. Peak sets were filtered using a list of genomic regions that contain anomalous, unstructured, or experiment independent high signal. ChIP-seq bam and bed files were then used to call differential peaks in the genome by using DiffBind (v3.12.0). The rest of the analyses were conducted using a combination of `DiffBind`, `edgeR`, HOMER, and deepTools2. Briefly, DiffBind was employed for differential binding analysis. Read counts were normalized using depth normalization. The `edgeR` method was applied for statistical analysis, using a false discovery rate (FDR) threshold of <0.05 to identify differentially bound regions. HOMER was then used to perform motif enrichment analysis on these BED files, with motif lengths ranging from 6 to 16 bp, using the hg38 genome as a reference. Coverage plots were generated using deepTools to visualize ChIP-seq signal across the identified genomic regions. Bigwig files for IRF4 and RNAPIIpS2 were processed, and coverage matrices were computed with `computeMatrix`.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak

source_name: Plasmacytoma

growth_protocol: Cells grown in biological duplicate in T-75 flasks in RPMI 10% FBS

extract_protocol:
AMO-1 cells (10 x 10^6/condition) were double crosslinked by 50mM DSG (disuccinimidyl glutarate, #C1104 - ProteoChem) for 30-minutes followed by 10-minutes of 1% formaldehyde. Formaldehyde was quenched by the addition of glycine. Nuclei were isolated with ChIP lysis buffer (1% Triton x-100, 0.1% SDS, 150 mM NaCl, 1mM EDTA, and 20 mM Tris, pH 8.0). Nuclei were sheared with Covaris sonicator using the following setup: Fill level – 10, Duty Cycle – 15, PIP – 350, Cycles/Burst – 200, Time – 8-minutes). Sheared chromatin was immunoprecipitated overnight with the following antibodies: RNAPII-pS2 (Abcam – ab5095), IRF4 (Cell Signaling – 4964S). Antibody chromatin complexes were pulled down with Protein A magnetic beads and washed once in IP wash buffer I. (1% Triton, 0.1% SDS, 150 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), twice in IP wash buffer II. (1% Triton, 0.1% SDS, 500 mM NaCl, 1 mM EDTA, 20 mM Tris, pH 8.0, and 0.1% NaDOC), once in IP wash buffer III. (0.25 M LiCl, 0.5% NP-40, 1mM EDTA, 20 mM Tris, pH 8.0, 0.5% NaDOC) and once in TE buffer (10 mM EDTA and 200 mM Tris, pH 8.0). DNA was eluted from the beads by vigorous shaking for 20-minutes in elution buffer (100mM NaHCO3, 1% SDS). DNA was de-crosslinked overnight at 65C and purified with MinElute PCR purification kit (Qiagen).
DNA was quantified by Qubit and 10 ng DNA was used for sequencing library construction with the Ovation Ultralow Library System V2 (Tecan) using 14 PCR cycles according to the manufacturer’s recommendations.  Libraries were sequenced with Illumina Nextseq, using paired-end 50bp read configuration.

treatment_protocol: 0.2 ug/ml Doxycycline (Dox) for the indicated times vs Mock treatment

value: Plasmacytoma

tag: cell line

value: Tumor plasma cell

value: AMO-1 shIRF4 Cl. 1

tag: chip antibody

value: RNAPII-pS2 (ab5095, Abcam)

value: Doxycycline 24 h


title: Vole 4967

description:
4_NAc_4967_M
10X Genomics

tag: tissue

value: Brain (nucleus accumbens)


title: Vole 4905

description:
1_NAc_4905_F
10X Genomics

value: Female

value: Mate


title: Vole 4893

description:
5_NAc_4893_M
10X Genomics

value: Male

value: Peer


title: AMO1 shIRF4, Dox 24h, RNAPII-pS2 ChIP, Rep 1

description:
Library name: LIB6228706
A24_RNAPII_1

tag: cell type


title: AMO1 shIRF4, Dox 0h, RNAPII-pS2 ChIP, Rep 2

description:
Library name: LIB6228703
A0_RNAPII_2

tag: genotype

value: Mock


title: AMO1 shIRF4, Dox 24h, IRF4 ChIP, Rep 2

description:
Library name: LIB6228701
A24_IRF4_2


title: AMO1 shIRF4, Dox 0h, RNAPII-pS2 ChIP, Rep 1

description:
Library name: LIB6228702
A0_RNAPII_1


title: AMO1 shIRF4, Dox 0h, IRF4 ChIP, Rep 2

description:
Library name: LIB6228697
A0_IRF4_2


title: PXB Cells, PCSK9-EE, 3

city: Boston

first: Frederic

last: Tremblay

state: MA

address: 201 Brookline Ave, Suite 1101

institute: Chroma Medicine

data_processing:
Sequencing reads were aligned to the human reference genome (GRCh38) and gene and transcript counts and normalized counts (transcripts per million, tpm) were calculated using the nf-core RNA-seq pipeline.
Differential gene expression was detected using DESeq2, with a threshold of two-fold change (log2 fold change = 1) and an adjusted p-value < 1e-5.
TPM and volcano plots were visualized using the python matplotlib and seaborn libraries.
Assembly: GRCh38
Supplementary files format and content: genes.results tables containing the following columns: gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

source_name: Liver

growth_protocol: Primary human hepatocytes isolated from mice with a chimeric humanized liver (PXB cells®) were obtained from Phoenix Bio. Pre-plated cells were kept in hepatocyte growth medium.

extract_protocol:
Total RNA was extracted from primary liver cells using simultaneous RNA and DNA extraction from cultured cells without splitting lysate protocol and reagents (Beckman Coulter).
Total RNA-Seq libraries were constructed using the Illumina stranded Total RNA prep ligation with Ribo-Zero plus kit.

treatment_protocol: LNP formulations were mixed with recombinant human ApoE3 (R&D Systems) and added onto cells at the desired concentration. The next day, Matrigel Basement Membrane Matrix (Corning) was overlayed on hepatocytes to a final concentration of 0.25 mg/ml.

value: Liver

value: PXB Cells

value: Primary Human Hepatocyte


title: Vole 4940

description:
15_NAc_4940_F
10X Genomics


title: Vole 5204

description:
14_NAc_5204_M
10X Genomics


title: PXB Cells, PCSK9-EE, 2


title: PXB Cells, Effector only, 3

value: Effector Only


title: PXB Cells, Effector only, 2


title: PXB Cells, PCSK9-EE, 1


title: PXB Cells, Effector only, 1


title: PXB Cells, No treatment, 3

value: No Treatment


title: NPC_N832K_fs81_Rep3

first: Phillip

last: Wulfridge

state: Pennsylvania

address: 3601 Spruce St

institute: The Wistar Institute

data_processing:
RNA-Seq reads were aligned with STAR.
RNA expected counts were generated with RSEM.
Assembly: hg38
Supplementary files format and content: TXT file (RSEM gene counts)

source_name: patient derived hiPSC

growth_protocol: Human iPSCs were cultured on Geltrex (ThermoFisher, A14133020) coated plates in StemMACS iPS Brew-XF medium (Miltenyi Biotec, 130-104-368).

extract_protocol:
Total RNA was collected using Trizol (Invitrogen) and digested with Turbo Dnase (Ambion). rRNA was selectively depleted using FastSelect (Qiagen).
rRNA-depleted RNA was converted to cDNA using the Ultra II Directional RNA kit for Illumina (NEB #E7760).
DNA samples were end-repaired using End-Repair Mix (Enzymatics), A-tailed using Klenow exonuclease minus (Enzymatics), purified with MinElute columns (Qiagen), and ligated to Illumina adapters (NEB E7600) with T4 DNA ligase (Enzymatics).  Size selection for fragments >150 bp was performed with AMPure XP (Beckman Coulter).  Libraries were PCR amplified with dual index barcode primers for Illumina sequencing (NEB E7600) using Q5 DNA polymerase (NEB M0491) and purified with MinElute.

value: patient derived hiPSC

value: NPC


title: NPC_N832K_fs81_Rep2


title: NPC_Y719_Rep2


title: NPC_K274N_fs31_Rep3


title: NPC_K274N_fs31_Rep2


title: PXB Cells, No treatment, 1


title: NPC_N832K_fs81_Rep1


title: NPC_WT_Rep1

value: Wildtype

value: WT


title: NPC_K274N_fs31_Rep1


title: AMO1 shIRF4, Dox 0h, IRF4 ChIP, Rep 1

description:
Library name: LIB6228696
A0_IRF4_1

value: Plasmacytoma

value: Tumor plasma cell

value: AMO-1 shIRF4 Cl. 1


title: PXB Cells, No treatment, 2


title: NPC_WT_Rep3


title: AMO1 shIRF4, Dox 24h, IRF4 ChIP, Rep 1

description:
Library name: LIB6228700
A24_IRF4_1

value: Doxycycline 24 h


title: over weight type 2 diabetes 6

city: Ciudad de México

first: Ricardo

last: Orozco-Solis

state: TLALPAN

address: Periférico Sur 4809, Arenal Tepepan

country: Mexico

institute: Instituto Nacional de Medicina Genomica

description: Subcutaneous adipose tissue over weight type 2 diabetes 6

hyb_protocol: 150 ng of RNA was used for transcriptome analysis using the Clariom D Human microarray (Applied Biosystems) on a GeneChip 3000 scanner

scan_protocol: A GeneChip 3000 scanner (Afimetrix), was utilized. Raw data was normalized, and gene expression values were obtained using the Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fisher Scientific).

data_processing: Transcriptome Analysis Console (TAC) 4.0 software (Thermo Fisher Scientific) to generate probe level summarization files (*.CHP). (Methods used:Gene + Exon - SST-RMA, Pos vs Neg AUC Threshold: 0.7; Genome Version: hg38 (Homo sapiens); Annotation: Clariom_D_Human.r1.na36.hg38.a1.transcript.csv; Annotation: Clariom_D_Human.r1.na36.hg38.a1.transcript.csv).

label: TdT

label_protocol: The fragmented single-stranded DNA is labeled with recombinant terminal deoxynucleotidyl transferase (TdT) and the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin

extract_protocol: Subcutaneous adipose tissue (SAT) biopsies were obtained by specialized surgeons in a sterile operating room. Local anesthesia was injected 3 cm below the umbilical area, and a small incision was made to collect the SAT biopsy and immediately frozen in liquid nitrogen and then stored at -80°C for further processing. Subcutaneous adipose tissue biopsy RNA was isolated using the TRIzol method. A small sample was cut and incubated in 200 µL of TRIzol at room temperature for 5 minutes. The tissue was homogenized using an insulin syringe, and 40 µL of chloroform was added. The mixture was gently agitated manually and incubated at room temperature for 3 minutes. The samples were centrifuged at 12,000 × g at 4°C for 15 minutes. The upper aqueous phase was carefully transferred into a fresh tube. 100 µL of isopropanol and 0.5 µL of glycogen were added, and the mixture was incubated at room temperature for 10 minutes. The samples were centrifuged at 12,000 × g at 4°C for 10 minutes. Isopropanol was removed carefully. 200 µL of cold 70% ethanol was added, and the mixture was centrifuged at 17,000 × g at 4°C for 5 minutes. This step was repeated twice. Once the pellet was completely dried, it was resuspended in 15 µL of sterile distilled water. RNA was quantified using the Nanodrop 2000 (ThermoFisher Scientific™).

value: Subcutaneus adipose tissue


title: over weight type 2 diabetes 8

description: Subcutaneous adipose tissue over weight type 2 diabetes 8


title: over weight type 2 diabetes 3

description: Subcutaneous adipose tissue over weight type 2 diabetes 3


title: over weight type 2 diabetes 5

description: Subcutaneous adipose tissue over weight type 2 diabetes 5


title: over weight type 2 diabetes 2

description: Subcutaneous adipose tissue over weight type 2 diabetes 2


title: over weight type 2 diabetes 1

description: Subcutaneous adipose tissue over weight type 2 diabetes 1


title: over weight pre-type 2 diabetes 3

description: Subcutaneous adipose tissue over weight pre-type 2 diabetes 3


title: over weight pre-type 2 diabetes 4

description: Subcutaneous adipose tissue over weight pre-type 2 diabetes 4


title: over weight pre-type 2 diabetes 6

description: Subcutaneous adipose tissue over weight pre-type 2 diabetes 6


title: over weight type 2 diabetes 4

description: Subcutaneous adipose tissue over weight type 2 diabetes 4


title: NPC_Y719_Rep3


title: over weight pre-type 2 diabetes 5

description: Subcutaneous adipose tissue over weight pre-type 2 diabetes 5


title: over weight pre-type 2 diabetes 2

description: Subcutaneous adipose tissue over weight pre-type 2 diabetes 2


title: over weight pre-type 2 diabetes 1

description: Subcutaneous adipose tissue over weight pre-type 2 diabetes 1


title: over weight 8

description: Subcutaneous adipose tissue over weight 8


title: NPC_WT_Rep2


title: E. coli K-12 MG1655, RpoD, ChIP-mini, 5ul, replicate 2

description:
ChIP-mini_RpoD_rep2 (5ul)
Total_binding sites of RpoD.xlsx

tag: strain

value: Anti-RpoD

value: bacterial cell


title: over weight 7

description: Subcutaneous adipose tissue over weight 7


title: NPC_Y719_Rep1


title: over weight 4

description: Subcutaneous adipose tissue over weight 4


title: over weight 6

description: Subcutaneous adipose tissue over weight 6


title: over weight 1

description: Subcutaneous adipose tissue over weight 1


title: over weight type 2 diabetes 7

description: Subcutaneous adipose tissue over weight type 2 diabetes 7


title: normal weight 6

description: Subcutaneous adipose tissue normal weight 6


title: normal weight 5

description: Subcutaneous adipose tissue normal weight 5


title: over weight 5

description: Subcutaneous adipose tissue over weight 5


title: over weight pre-type 2 diabetes 7

description: Subcutaneous adipose tissue over weight pre-type 2 diabetes 7


title: normal weight 3

description: Subcutaneous adipose tissue normal weight 3


title: normal weight 1

description: Subcutaneous adipose tissue normal weight 1


title: normal weight 2

description: Subcutaneous adipose tissue normal weight 2


title: Homo sapiens, human pluripotent stem cells, control blank, Day14

city: Guangzhou

first: Haibo

last: Peng

address: Jinwan Road 368

institute: Zunyi Medical University

description:
Library name: WT-H9-Day14
Column name gene_count.txt: WT-D14

data_processing:
In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.0.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.0.1)
In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data
Assembly: hg19
Supplementary files format and content: Tab separated table count values of genes for each sample

source_name: human pluripotent stem cells

growth_protocol: MSCs were washed with DPBS twice and treated with TrypLE at 37℃ for 5 min. Seeded 100,000 cells/well in a 12-well plate and cultured with MSC medium overnight. Washed with DPBS twice and added 1 ml/well osteogenesis (Thermo, A1007201) and chondrogenesis (Thermo, A1007101) kits. Refresh the kit medium twice every week. The cells were fixed with 4% PFA, and osteogenesis was promoted by Alizarin Red S staining and chondrogenesis was promoted by Alcian blue staining before 14 days after differentiation. The staining was observed under a microscope (Axio observer, Germany).

extract_protocol:
Total RNA was extracted using the EasyPure® RNA Kit, quality was assessed using the 5300 Bioanalyzer (Agilent) and quantified with the ND-2000 (NanoDrop Technologies).
The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: human pluripotent stem cells

tag: treatment

value: control blank, Day14


title: Homo sapiens, human pluripotent stem cells, control blank, Day7

description:
Library name: WT-H9-Day7
Column name gene_count.txt: WT-D7

value: control blank, Day7


title: Homo sapiens, human pluripotent stem cells, B2M knockout, Day3

description:
Library name: B2MKO-H9-Day3
Column name gene_count.txt: B2MKO-D3

value: B2M knockout, Day3


title: Homo sapiens, human pluripotent stem cells, B2M knockout, Day1

description:
Library name: B2MKO-H9-Day1
Column name gene_count.txt: B2MKO-D1

value: B2M knockout, Day1


title: Homo sapiens, human pluripotent stem cells, B2M knockout, Day7

description:
Library name: B2MKO-H9-Day7
Column name gene_count.txt: B2MKO-D7

value: B2M knockout, Day7


title: Homo sapiens, human pluripotent stem cells, control blank, Day3

description:
Library name: WT-H9-Day3
Column name gene_count.txt: WT-D3

value: control blank, Day3


title: Homo sapiens, human pluripotent stem cells, B2M knockout, Day0

description:
Library name: KO-Day0
Column name gene_count.txt: KO-Day0

value: B2M knockout, Day0


title: Homo sapiens, human pluripotent stem cells, control blank, Day1

description:
Library name: WT-H9-Day1
Column name gene_count.txt: WT-D1

value: control blank, Day1


title: Homo sapiens, human pluripotent stem cells, control blank, Day0

description:
Library name: WT-Day0
Column name gene_count.txt: WT-D0

value: control blank, Day0


title: normal weight 7

description: Subcutaneous adipose tissue normal weight 7


title: Spleen resident tumor cells of ANKL3-PDX mouse, #3

city: Saga

first: Ryo

last: Yanagiya

state: Saga

address: 5-1-1 Nabeshima

department: Department of Internal Medicine

institute: Saga University

description:
Library name: Spleen-tropic ANKL3_3
gene_count_matrix_ankl3.csv

data_processing:
Gene_count_matrix files: sequenced reads were trimmed with fastp v0.19.8, mapped to GRCh38 with Hisat2 v2.2.1, and counted with StringTie v2.1.4. Liver_niche data of ANKL1-PDX: sequenced reads were mapped to hg38 or mm10 with bowtie v1.1.1 and CASTIN, then counted with CASTIN.
Assembly: hg38 or mm10
Supplementary files format and content: tab- or comma-delimited text files including raw counts and normalized counts for every genes.

source_name: spleen

extract_protocol:
Livers were removed from healthy mice or PDX mice, and RNA was harvested using Sepasol-RNA I Super G (nacalai tesque, Cat#09379-55).
RNA library was constructed with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs, Cat#E7760L) following the manufacturer's protocol.

value: spleen

value: lymphocyte

tag: cell purification

value: Leukemic cells were purified by human CD45 expression using flow cytometer.


title: over weight 3

description: Subcutaneous adipose tissue over weight 3


title: NK cells derived from PBMC of healthy donor, #3

description:
Library name: Normal NK cell_3
gene_count_matrix_normalNK.csv

source_name: peripheral blood

value: peripheral blood

value: CD3-CD56+ lymhocytes were purified from peripheral blood mononuclear cells of a healthy volunteer


title: over weight 2

description: Subcutaneous adipose tissue over weight 2

value: Subcutaneus adipose tissue


title: Spleen resident tumor cells of ANKL3-PDX mouse, #2

description:
Library name: Spleen-tropic ANKL3_2
gene_count_matrix_ankl3.csv


title: NK cells derived from PBMC of healthy donor, #2

description:
Library name: Normal NK cell_2
gene_count_matrix_normalNK.csv


title: Liver resident tumor cells of ANKL3-PDX mouse, #3

description:
Library name: Liver-tropic ANKL3_3
gene_count_matrix_ankl3.csv

source_name: liver

value: liver


title: NK cells derived from PBMC of healthy donor, #1

description:
Library name: Normal NK cell_1
gene_count_matrix_normalNK.csv


title: normal weight 4

description: Subcutaneous adipose tissue normal weight 4


title: Liver resident tumor cells of ANKL3-PDX mouse, #1

description:
Library name: Liver-tropic ANKL3_1
gene_count_matrix_ankl3.csv


title: hiPSC_N832K_fs81_Rep1

value: patient derived hiPSC

value: hiPSC


title: Spleen resident tumor cells of ANKL3-PDX mouse, #1

description:
Library name: Spleen-tropic ANKL3_1
gene_count_matrix_ankl3.csv


title: hiPSC_S763P_fs9_Rep3


title: Homo sapiens, human pluripotent stem cells, B2M knockout, Day14

description:
Library name: B2MKO-H9-Day14
Column name gene_count.txt: B2MKO-D14

value: human pluripotent stem cells

value: B2M knockout, Day14


title: Liver resident tumor cells of ANKL3-PDX mouse, #2

description:
Library name: Liver-tropic ANKL3_2
gene_count_matrix_ankl3.csv


title: hiPSC_N832K_fs81_Rep2


title: hiPSC_N832K_fs81_Rep3


title: hiPSC_S763P_fs9_Rep2


title: hiPSC_Y719_Rep3


title: hiPSC_K274N_fs31_Rep2


title: hiPSC_Y719_Rep2


title: hiPSC_K274N_fs31_Rep1


title: hiPSC_K274N_fs31_Rep3


title: hiPSC_WT_Rep3

value: Wildtype

value: WT


title: hiPSC_Y719_Rep1