title: CK666 72h -LIF2i rep3

city: San Francisco

first: Diane

last: Barber

address: 513 Parnassus Ave HSW618

department: Department of Cell & Tissue Biology

institute: University of California San Francisco

data_processing:
Quality assessment and basic processing of the reads was performed using the FastQC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc).
Sequencing adapters were trimmed from the 3′ ends of the reads using cutadapt (v.1.8.1; https://pypi.python.org/pypi/cutadapt/1.8.1).
We quantified transcript abundance with Kallisto (Bray et al., 2016) and built index with reference to the GRCh38 reference transcriptome.
Expression analysis was performed using Sleuth (Pimentel et al., 2017) to assess differentially expressed genes between +LIF2i, control -LIF2i, and CK666 -LIF2i. Differentially expressed genes were identified using the Wald test with a cut-off of qval <0.05.
Genome_build: mm10
Supplementary_files_format_and_content: A plaintext file (.tsv) of the abundance estimates for each target ID including estimated counts, TPM, and effective length.

source_name: E14 mESC

growth_protocol: E14 mESCs, provided by A. Smith (University of Cambridge), were maintained in tissue culture dishes coated with 0.2% gelatin (G1393; Sigma) at 37°C and 5% CO2 in DMEM (10569; Gibco) supplemented with 15% FBS (FB-11, Omega Scientific, Inc.), glutamine (2 mM), non-essential amino acids (0.1 mM), penicillin-streptomycin (100 U/mL Penicillium and 100 µg/mL Streptomycin), and 2-mercaptoethanol (55 µM). Cells received fresh medium every 24 h and were passaged every three days after dissociating with 0.25% Trypsin-EDTA (25200-056; Gibco). For self-renewal, cells were maintained in medium containing LIF (ESGRO Cat#ESG1106; EMD Millipore) and inhibitors for MEK (1 µM; PD0325901, Cat#S1036; Selleck Chemicals) and glycogen synthase kinase-3β (1 µM; CHIR99021, Cat#S2924; Selleck Chemicals), collectively termed LIF2i. Mycoplasma contamination was tested 2x/year using media obtained from cells maintained for 48h in the absence of penicillin-streptomycin by using a PCR Mycoplasma Detection Kit (abm Cat#G238). Cell lines were authenticated commercially by IDEXX BioAnalytics (USA).

extract_protocol:
RNA was extracted with the RNeasy Mini kit (Qiagen, 74104) according to the manufacturer’s instructions and sample concentrations were determined by NanoDrop. RNA degradation and contamination were monitored on 1% agarose gels, RNA purity was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA), and RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. To select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system. The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the library preparations were sequenced on an Illumina platform and paired-end reads were generated with >20 million reads per sample. The above protocol, with the exception of RNA extraction, was performed externally by Novogene Co. Ltd (USA).

treatment_protocol: For Control +LIF2i samples, cells were maintained in medium containing LIF (ESGRO Cat#ESG1106; EMD Millipore) and inhibitors for MEK (1 µM; PD0325901, Cat#S1036; Selleck Chemicals) and glycogen synthase kinase-3β (1 µM; CHIR99021, Cat#S2924; Selleck Chemicals) for the duration of the experiment. To induce spontaneous differentiation, cells were washed in PBS and then incubated in medium without LIF2i for 72h with medium replacements every 24h. CK666 (80 µM final; 182515; EMD Millipore) was added at 1:000 from stock solutions prepared in DMSO upon removal of LIF2i and included in medium replacements every 24h.

value: CK666 -LIF2i

tag: timepoint


title: Control 72h -LIF2i rep3

status: Public on Apr 01 2022

type: SRA

state: CA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: treatment

value: Untreated -LIF2i

tag: cell line


title: s1_A7: 43905 T4 V3

city: Boston

first: Haiqing

last: Bai

state: MA

address: 5th floor, Center for Life Science, 3 Blackfan Circle

institute: Wyss Institute

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Homo sapiens GRCh38 reference genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2 followed by differential expression analysis using DESeq2.
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Homo sapiens

source_name: Human airway epithelial cells

growth_protocol: Primary human lung bronchial-airway epithelial basal cells (Lonza, cat. no. CC2540; obtained from healthy donors 655308, 623950, 672447, and 626776) were expanded in 75-cm2 tissue-culture flasks using airway epithelial cell growth medium (Promocell) to 60-70% confluency. Primary diseased human lung bronchial-airway epithelial basal cells (Lonza, cat. no. 00195275; obtained from donors 18TL343179, 18TL103224, 436083, 440551, 430905) were expanded in 75-cm2 tissue-culture flasks using airway epithelial cell growth medium (Promocell) to 60-70% confluency. Primary human pulmonary microvascular endothelial cells (Cell Biologics) were expanded in 75-cm2 tissue-culture flasks using human endothelial cell growth medium (Cell Biologics) to 70-80% confluency. To create human airway transwells, 6.5mm transwells with 0.4μm pores (Sigma-Aldrich) were coated with collagen type IV from human placenta (0.5mg ml-1 in water; Sigma-Aldrich) at room temperature overnight. The solution was aspirated from the transwell, which was then used for seeding cells. Lung bronchial-airway epithelial basal cells (1.0 X 105 cells ml-1) were first seeded in the apical chamber of transwell in airway epithelial growth medium (Promocell) and incubated at 37 ˚C with 5% CO2 until 100% confluent. The adherent cells were maintained using airway epithelial growth medium (Promocell). Once confluent, the apical medium was removed and the basal chamber received PneumaCult-ALI medium (StemCell) to establish ALI. The airway epithelial cells were cultured for 3-4 additional weeks at 37oC with 5% CO2, and the apical surface of the epithelium was washed with PBS once a week to remove mucus and cellular debris. Prior to infection experiment, human pulmonary microvascular endothelial cells (1.5 X 106 cells ml-1) were seeded on the basal side of the membrane and incubated for 2 hours at 37˚C with 5% CO2. The transwells were then returned to ALI using PneumaCult-ALI media (StemCell) supplemented with 0.1% VEGF, 0.01% EGF, and 1mM CaCl2.

extract_protocol:
total RNA were prepared using Qiagen Rneasy mini plus kit
RNA libraries were prepared for sequencing using standard Illumina Illumina NovaSeq 6000 with 150-bp pair-ended reads

treatment_protocol: Prior to infection, human airway transwells were equilibrated for 24 hours in reduced hydrocortisone (10nmol/L) differentiation media (StemCell). The airway epithelial cells were infected with influenza virus (MOI=0.1) in 50ul PBS for 1.5 hours at 37 ˚C with 5% CO2. After the incubation period, the apical solution was aspirated and the transwells were returned to 37oC with 5% CO2. The apical surface of the epithelium was washed with PBS 4 hours and 18 hours post-infection and collected for analysis. The basal supernatant was collected 4 hours and 18 hours post-infection and analyzed for cytokines and chemokines.

tag: donor

tag: time point

value: 4 hr

tag: condition

value: COPD

tag: infection

value: influenza A virus

tag: cell type

value: Human airway epithelial cells


title: s2_A6: 18TL 103224 T4 V2


title: CD_1_12_BSseq

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

library_source: genomic

data_processing:
Adapters and low quality bases (-q 20) were trimmed with Trim Galore (v0.6.2). Reads were also trimmed by 9 bp from the 5' ends to remove pull-down biases (--clip_r1 9).
Alignment was performed in single-end, non-directional mode followed by deduplication (deduplicate_bismark) and methylation calling (bismark_methylation_extractor) using Bismark (v0.22.1)
Genome_build: GRCm38
Supplementary_files_format_and_content: Bismark coverage report; tab-delimited text files include methylated and unmethylated calls

molecule: genomic DNA

source_name: MII oocyte_control diet

extract_protocol:
The lysate containing genomic DNA was purified on AMPureXP beads
Libraries were prepared according to the scBS-seq protocol

value: MII oocyte

tag: diet

value: control diet


title: Control +LIF2i rep3

value: Untreated +LIF2i


title: s1_A5: 43905 T4 V1


title: CD_1_11_BSseq


title: hfd_5_7_RNAseq

data_processing:
Adapters and low quality bases (-q 20) were trimmed using Trim Galore (v0.6.2_dev), reads were aligned using HISAT2 (v2.1.0) with penalties --sp 1000,1000.
Primary alignments were assigened to features of the mouse oocyte transcriptome (Veselovska et al., 2015) using Seqmonk with the options 'Generate Raw Counts' and 'merge transcript isoforms'
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text file includes counts for each Sample

molecule: polyA RNA

source_name: MII oocyte_high fat diet

extract_protocol:
Cell lysis was performed and Poly-A RNA was captured using oligo-dT conjugated to magnetic beads.
Libraries were prepared and analysed according to the G&T-seq and Smart-seq2 protocol.

value: high fat diet


title: CK666 72h -LIF2i rep1


title: Control 72h -LIF2i rep2


title: Control +LIF2i rep2


title: CD_1_10_BSseq


title: s1_A4: 43905 T4 C4

value: control


title: hfd_5_6_RNAseq


title: CK666 72h -LIF2i rep2


title: Control 72h -LIF2i rep1


title: s2_A5: 18TL 103224 T4 V1


title: normal mouse brain, C2

city: Tel Aviv

first: Guy

last: Shapira

address: Chaim Levanon 30

country: Israel

institute: Tel Aviv University

data_processing:
fastp 0.20.1 used for trimming and filtering
STAR 2.7.2a used for alignment to the GRCm38 assembly
DESeq2 1.30.1 used for normalization of count data
Genome_build: GRCm38
Supplementary_files_format_and_content: Tab-delimited text files including raw counts for each sample
Supplementary_files_format_and_content: Supplementary tab-delimited text files including normalized counts for all samples, compressed using gzip

source_name: normal mouse brain

growth_protocol: Mouse glioblastomas were induced by lentiviral vector expressing PDGFB and shRNA against p53. Tumor tissues were isolated from mice reached clinical endpoints. Normal brain tissue was trimmed away from GFP+ tumor tissue using a dissecting microscope.

extract_protocol:
RNA was isolated using the Rneasy kit according to manufacturer's protocol with the addition of Dnase (Qiagen).
cDNA libraries were prepared using the TruSeq RNA Sample Prep kit (Illumina).

tag: tissue

value: brain

tag: strain

value: GFAP-Cre transgenic

tag: lentiviral vector


title: CD_1_14_BSseq


title: s2_A3: 18TL 103224 T4 C3


title: Control +LIF2i rep1


title: hfd_5_3_RNAseq


title: mouse glioblastoma, PN5

source_name: mouse glioblastoma

value: glioblastoma


title: hfd_5_2_RNAseq


title: s2_A4: 18TL 103224 T4 C4


title: hfd_5_1_RNAseq


title: mouse glioblastoma, PN4


title: s1_A3: 43905 T4 C3


title: hfd_4_5_RNAseq


title: s1_A2: 43905 T4 C2


title: hfd_4_8_RNAseq


title: normal mouse brain, C5


title: HepG2-CXCR2-1D1 rep2

city: Memphis

first: Liqin

last: Zhu

state: TN

address: 262 Danny Thomas Pl

department: Department of Pharmacy and Pharmaceutical Sciences

institute: St. Jude Children’s Research Hospital

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19  using STAR v2.6.1c with default parameters
Raw reads count from HT-Seq were provided for each sample
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file includes raw reads counts for each Sample ...

extract_protocol:
RNA was harvested using Trizol reagent. TruSeq stranded mRNA library prep kit (Illumina) was used for whole-transcriptome library preparation, and paired-end sequencing was performed using the Illumina NovaSeq 6000 platform with a 101-bp.
RNA libraries were prepared for sequencing using standard Illumina protocols and sequenced by NovaSeq 6000

tag: genotype

value: CXCR2 KO

value: Normoxia


title: hfd_4_4_RNAseq


title: s2_A2: 18TL 103224 T4 C2


title: Digoxin 1

city: Xi'an

first: Zhengtao

last: Xiao

state: Shaanxi

address: No.76,Western Yanta Road

department: Department of Biochemistry and Molecular Biology

country: China

institute: Xi’an Jiaotong University

data_processing:
The single cell sequencing data were processed into the gene expression tables using the pipelines from Cell Ranger v3.0.2 (https://support.10xgenomics.com/).
Quality control and filtering steps were performed to remove the low-quality cells (with fewer than 1800 genes detected) and uninformative genes (detected in fewer than 10 cells) for the downstream analyses.
The gene expression data were log-normalized and scaled using Seurat v3.0.2 (http://satijalab.org/seurat/) R package.
Genome_build: mm10
Supplementary_files_format_and_content: csv file with log-normalized read counts per gene; csv file with cell annotations

source_name: sarcoma

extract_protocol:
The tumor was dissected from the hind limb and dissociated by shaking for 45 minutes at 37°C in collagenase Type IV (Gibco), dispase (Gibco), and trypsin (Gibco). Cell suspension was then strained through a 40 µm filter, washed in PBS, and plated for culture.
After tumor dissociation, the cells were filtered through a 40 µM strainer. Red blood cells were lysed using ACK Lysing Buffer (Lonza) and washed with flow buffer made of HBSS (cat 13175-095, Gibco), 5 mM EDTA (E7899, Sigma-Aldrich), and 2.5% FBS (Gibco). Cells were washed twice more in 0.04% bovine serum albumin (BSA) in PBS, then resuspended at 1000 cells per  µL. Cell suspensions were loaded on the 10x Genomics Chromium Controller Single-Cell Instrument (10x Genomics) using the Chromium Single Cell 3’ Reagent V3 Kit.

treatment_protocol: Mice were administered an intraperitoneal (i.p.) injection of either vehicle (PBS) or 2 mg/kg digoxin (prepared in DMSO and then diluted in PBS) with a volume not exceeding 250 µL. Injections were administrered every 24 hours and collected tumors after the fourth dose.

tag: background strain

value: hind limb

tag: disease state

value: sarcoma

tag: replicate

value: Rep 1


title: mouse glioblastoma, PN6


title: hfd_4_9_RNAseq


title: Digoxin 2

value: Rep 2


title: HepG2-CXCR2-1B5 rep2


title: hfd_4_6_RNAseq


title: hfd_4_2_RNAseq


title: mouse glioblastoma, PN3


title: HepG2-CXCR2-1D1 rep1


title: hfd_4_7_RNAseq


title: HepG2-CXCR2-1B5 rep1


title: s1_A1: 43905 T4 C1

value: 4 hr

value: COPD


title: HepG2-1B5-H rep2

value: Hypoxia


title: HepG2 rep2

value: wild type


title: hfd_4_16_RNAseq

value: MII oocyte


title: Vehicle 1


title: hfd_4_1_RNAseq


title: HepG2-1B5-H rep1


title: KI_12m_5

city: Saarbrücken

first: Julia

middle: Maria

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

country: Germany

institute: Saarland University

data_processing:
Paired-end fastq files were aligned with STAR (v2.4.5b) allowing gapped alignments to account for splicing, otherwise default parameters.
Read counts for all genes were determined using Rsubread (v2.0.0).
Genome_build: Ensembl v91 M.musculus
Supplementary_files_format_and_content: CVS file with raw read counts per gene identified by Ensembl gene ID

source_name: Cerebellum

extract_protocol:
total RNA form cerebellar samples was extracted using AllPrep DNA/RNA/miRNA Universal Kit (Qiagen, Cat No.: 80224)
total RNA was subjected to polyA enrichment and cDNA libraries were constructed using the resulting mRNA and the TruSeq Stranded mRNA (Illumina, Cat No.: 20020595)

treatment_protocol: Cerebella were incubated in RNAlater (Qiagen, Cat No.: 76104) before storage at -80°C

value: Cerebellum

tag: age

value: 12 months

value: 304 CAG repeats in both ataxin-3 alleles (knock-in)


title: KI_12m_4


title: KI_12m_3


title: Vehicle 2


title: HB214-CXCR2-KO-1C4 rep2


title: hfd_4_14_RNAseq

value: high fat diet


title: KI_12m_2


title: hfd_4_11_RNAseq


title: hfd_4_12_RNAseq


title: HB214-CXCR2-KO-1F7 rep1


title: hfd_3_6_RNAseq


title: HB214-CXCR2-KO-1C4 rep1


title: WT_12m_3

value: wild-type ataxin-2 in both alleles


title: hfd_3_8_RNAseq


title: WT_12m_5


title: WT_12m_4


title: HepG2 rep1


title: hfd_3_7_RNAseq


title: hfd_3_5_RNAseq


title: HB214 rep2


title: HB214 rep1


title: WT_12m_2


title: hfd_4_15_RNAseq


title: Sample 7 pre treatment

city: Hamilton

first: Mark

middle: A

last: Tarnopolsky

state: Ontario

address: 1200 Main St. West

department: Pediatrics and Medicine

country: Canada

institute: McMaster University Medical Center

data_processing:
Sequencing was performed on an Illumina NovaSeq 6000 instrument
FASTQ generation was performed by Illumina's BaseSpace Sequence Hub
Alignment of FASTQ files was performed against the GRCh37 reference by HISAT2 (v2.1.0)
Gene read count abundance determined by HTSeq (v2.0)
Differential expression analysis was performed by DESeq2
Pathway analysis was performed using iDEP (v0.93) using the Go Biological Process gene ontology reference
Differential alternative splicing events and their significance were determined by rMATS (v4.1.1)
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files with Ensembl gene ID, gene symbol, and read counts.
Supplementary_files_format_and_content: tab-delimited text files of skipped exon alternative splicing rMATs results

source_name: skeletal muscle biopsy from the vastus lateralis

extract_protocol:
RNA was extracted from ~5 – 10 mg of muscles using QIAGEN miRNeasy Mini Kit (Qiagen, 217004). Next generation sequencing (NGS) libraries were created using the TruSeq Stranded Total RNA library (Illumina) kit
Next generation sequencing (NGS) libraries were created using the TruSeq Stranded Total RNA library (Illumina) kit

value: Myotonic dystrophy type 1 (DM1)

value: untreated


title: WT_12m_1


title: Sample 9 pre treatment


title: HB214-CXCR2-KO-1F7 rep2

value: CXCR2 KO

value: Normoxia


title: hfd_3_4_RNAseq


title: hfd_3_2_RNAseq


title: Sample 8 pre treatment


title: KI_2m_3

value: 2 months


title: KI_2m_5


title: KI_2m_4


title: KI_2m_2


title: hfd_1_8_RNAseq


title: hfd_1_7_RNAseq


title: KI_12m_1


title: WT_2m_4


title: hfd_1_4_RNAseq


title: hfd_1_9_RNAseq


title: hfd_1_3_RNAseq


title: hfd_3_1_RNAseq


title: WT_2m_3


title: Sample 6 pre treatment


title: Sample 3 pre treatment


title: Sample 5 pre treatment


title: KI_2m_1


title: Sample 4 pre treatment


title: hfd_3_3_RNAseq


title: WT_2m_2


title: Sample 13 pre treatment


title: Sample 12 pre treatment


title: hfd_1_13_RNAseq


title: hfd_1_15_RNAseq


title: hfd_1_14_RNAseq


title: Sample 8 post treatment

value: 12-weeks of cycle ergometry


title: Sample 9 post treatment


title: Sample 1 pre treatment


title: WT_2m_1


title: hfd_1_12_RNAseq


title: Sample 7 post treatment


title: Sample 2 pre treatment


title: hfd_1_10_RNAseq


title: Sample 6 post treatment


title: Sample 5 post treatment


title: Sample 4 post treatment


title: CD_3_7_RNAseq

value: control diet


title: CD_3_8_RNAseq


title: Sample 3 post treatment


title: CD_3_6_RNAseq


title: hfd_1_11_RNAseq


title: Sample 13 post treatment


title: CD_3_5_RNAseq


title: Orange 2

type: RNA

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from APC 50% for 48 h

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array (HG-219). GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) for the top DEGs.
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).

label: biotin

source_name: cell treated with Orange cells (BT-OC)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: HFDPCs were purchaced from Cell application and were maintained in Papilla cell culture meduim

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.

treatment_protocol: After the initial 24 hour seeding  in 6-well-collagen-coated plates.  The medium was changed with 0 (Control) and 1:2000 Orange cells (BT-OC) for 48 h.

tag: tag

value: hair follicle dermal papilla cells


title: Orange 3


title: Green 2

source_name: cell treated with Green cells (BT-GC)

treatment_protocol: After the initial 24 hour seeding  in 6-well-collagen-coated plates.  The medium was changed with 0 (Control) and 1:2000 Green cells (BT-GC) for 48 h.


title: CD_3_4_RNAseq


title: CD_3_3_RNAseq


title: Sample 1 post treatment

tag: treatment


title: CD_3_2_RNAseq


title: Green 3


title: Green 1


title: Control matched for sample 7

value: healthy


title: Control matched for sample 8


title: WT_2m_5


title: Control cell treated with meduim 3

description: Gene expression data from meduim treated for 48 h

source_name: cell treated with meduim


title: Control cell treated with meduim 2


title: Sample 2 post treatment


title: CD_2_9_RNAseq


title: Sample 12 post treatment


title: Early failure case EF10

city: Lisboa

first: Ivan

last: Dlouhy

address: Rua Prof Lima Basto

department: Hematology

country: Portugal

institute: IPO Lisboa

description: Gene expression data from DLBCL EF cases

hyb_protocol: RNA samples were processed to Affymetrix GeneChip HT HG-U219 arrays.

scan_protocol: Scanning was processed in the Gene Titan instrument.

data_processing:
Determination of the signal value for each probe set of the array were obtained with GeneChip® Command Console® Software (AGCC) (Affymetrix).
Raw data were normalized using the Robust Multichip Analysis (RMA) algorithm implemented in the Expression Console Software v1.1 (Affymetrix).

source_name: Early failure case

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

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

treatment_protocol: Diffuse large B-cell lymphoma (DLBCL) patient samples from frozen lymph node biopsies.

value: Frozen lymph node biopsy

value: Diffuse large B-cell lymphoma (DLBCL)

tag: response to r-chop

value: Early failure


title: CD_2_8_RNAseq

value: MII oocyte


title: Early failure case EF9


title: CD_2_7_RNAseq


title: Control matched for sample 6


title: CD_3_1_RNAseq


title: Control cell treated with meduim 1


title: Control matched for sample 3


title: Early failure case EF7


title: Control matched for sample 4


title: Control matched for sample 2


title: CD_2_6_RNAseq


title: CD_2_5_RNAseq


title: Early failure case EF8


title: Control matched for sample 13


title: CD_2_3_RNAseq


title: CD_2_2_RNAseq


title: Early failure case EF6


title: Early failure case EF3


title: Early failure case EF5


title: Early failure case EF4


title: Control matched for sample 1


title: CD_2_1_RNAseq


title: CD_2_4_RNAseq


title: ROI2_11

city: Jinan

first: Dongping

last: Lyu

address: No. 44, Wenhuaxi Road

institute: Shandong University

description:
MIPCC_DSP_20210402C_02 | 011 | Segment 2
Patient_HS_011

data_processing:
The raw reads (raw sequencing FASTQ files) are selected for a DSP pipeline run.
The raw reads are processed for high quality (if more than 50% base's Phred Q <=19), the adapters (for SE, if the adapter contamination length is greater than 5bp; for PE, if one read has adapter contamination, then both reads are removed) are removed, and the paired-end reads are merged.
The reads are aligned to the DSP readout tag sequence identifier barcodes, then PCR duplicates are removed by matching on the Unique Molecular Index (UMI).
Genome_build: GRCh38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every Regions of Interest (ROIs).
Supplementary_files_format_and_content: Initial_Dataset.csv is the initial gene count matrix, without normalization or other transformation.
Supplementary_files_format_and_content: Normalized_Data.csv is the count matrix after normalization.

source_name: Control

extract_protocol:
To prepare slides for DSP, 4-μm slides from the TMA blocks were deparaffinized and boiled in pressure cooker (Bio SB, Santa Barbara, USA) in Tris-EDTA buffer to expose RNA targets. The slides were digested using GeoMx DSP RNA Slide Prep Kit for FFPE (NanoString, Seattle, USA) to remove RNA-binding proteins and fixed in 16% formaldehyde for 5 min at room temperature. An overnight incubation with GeoMx Panel & Seqcode kit (NanoString) containing probes for 18,676 endogenous targets was then performed in autostainer. Prepared slides were incubated with EpCAM for epithelial cell and 5-HT for EC cell , as well as Syto13 (NanoString) for nuclear identification. After 1 hour incubation at room temperature, slides were washed and stained with fluorescent secondary antibodies at 37℃ for 30 min.
After the GeoMx DSP system has completed collection, each GeoMx DSP aspirate in the collection plate contains photocleaved DNA oligos comprised of an RNA analyte identifier, a unique molecular identifier (UMI) barcode, and primer binding sites. When PCR is performed on the aspirates, Illumina adapter sequences and unique dual sample indices are added. Following a pooling purification and quality control process, the final library is ready for sequencing on an Illumina NGS platform using a dualindex workflow.

tag: diagnosis

value: Healthy

tag: location

value: Large Intestine

value: Epithelium


title: ROI2_10

description:
MIPCC_DSP_20210402C_02 | 010 | Segment 2
Patient_HS_010


title: Early failure case EF1


title: ROI2_9

description:
MIPCC_DSP_20210402C_02 | 009 | Segment 1
Patient_HS_009

value: EC cell


title: CD_2_15_RNAseq


title: ROI2_7

description:
MIPCC_DSP_20210402C_02 | 007 | Segment 1
Patient_HS_007


title: Case in remission RC28

description: Gene expression data from DLBCL cases in remission

source_name: Case in remission

value: remission


title: CD_2_11_RNAseq


title: CD_2_14_RNAseq


title: Case in remission RC29


title: Case in remission RC27


title: Early failure case EF2


title: Case in remission RC26


title: Case in remission RC24


title: CD_2_10_RNAseq


title: CD_2_13_RNAseq


title: ROI2_8

description:
MIPCC_DSP_20210402C_02 | 008 | Segment 1
Patient_HS_008


title: CD_1_8_RNAseq


title: ROI2_2

description:
MIPCC_DSP_20210402C_02 | 002 | Segment 1
Patient_HS_002


title: CD_1_7_RNAseq


title: ROI2_5

description:
MIPCC_DSP_20210402C_02 | 005 | Segment 1
Patient_HS_005


title: ROI2_3

description:
MIPCC_DSP_20210402C_02 | 003 | Segment 1
Patient_HS_003


title: CD_1_9_RNAseq


title: CD_1_5_RNAseq


title: ROI2_4

description:
MIPCC_DSP_20210402C_02 | 004 | Segment 2
Patient_HS_004

value: Terminal Ileum


title: ROI2_6

description:
MIPCC_DSP_20210402C_02 | 006 | Segment 1
Patient_HS_006


title: CD_1_6_RNAseq


title: Case in remission RC22


title: Control matched for sample 9

value: untreated


title: Case in remission RC21


title: ROI1_12

description:
MIPCC_DSP_20210402C_01 | 012 | Segment 1
Patient_UC_012

source_name: Ulcerative Colitis

value: Ulcerative colitis


title: Case in remission RC25


title: ROI2_1

description:
MIPCC_DSP_20210402C_02 | 001 | Segment 1
Patient_HS_001


title: CD_1_24_RNAseq


title: Orange 1


title: Case in remission RC20


title: CD_1_2_RNAseq


title: Case in remission RC18


title: CD_1_23_RNAseq


title: Case in remission RC19


title: ROI1_11

description:
MIPCC_DSP_20210402C_01 | 011 | Segment 2
Patient_UC_011


title: ROI1_10

description:
MIPCC_DSP_20210402C_01 | 010 | Segment 2
Patient_UC_010


title: ROI1_7

description:
MIPCC_DSP_20210402C_01 | 007 | Segment 1
Patient_UC_007


title: Case in remission RC16


title: CD_1_22_RNAseq


title: CD_1_20_RNAseq


title: CD_1_21_RNAseq


title: ROI1_9

description:
MIPCC_DSP_20210402C_01 | 009 | Segment 1
Patient_UC_009


title: Case in remission RC14


title: ROI1_6

description:
MIPCC_DSP_20210402C_01 | 006 | Segment 1
Patient_UC_006


title: CD_1_3_RNAseq


title: CD_1_19_RNAseq


title: Case in remission RC17


title: Case in remission RC15


title: ROI1_5

description:
MIPCC_DSP_20210402C_01 | 005 | Segment 1
Patient_UC_005


title: Case in remission RC13


title: CD_1_16_RNAseq


title: ROI1_3

description:
MIPCC_DSP_20210402C_01 | 003 | Segment 2
Patient_UC_003


title: CD_1_14_RNAseq


title: Case in remission RC23


title: Case in remission RC12


title: Case in remission RC10


title: ROI1_8

description:
MIPCC_DSP_20210402C_01 | 008 | Segment 1
Patient_UC_008


title: ROI1_4

description:
MIPCC_DSP_20210402C_01 | 004 | Segment 1
Patient_UC_004


title: CD_1_15_RNAseq


title: Case in remission RC11

description: Gene expression data from DLBCL cases in remission


title: ROI1_2

description:
MIPCC_DSP_20210402C_01 | 002 | Segment 1
Patient_UC_002


title: Case in remission RC8


title: CD_1_13_RNAseq


title: CD_1_12_RNAseq


title: Case in remission RC9


title: ROI1_1

description:
MIPCC_DSP_20210402C_01 | 001 | Segment 1
Patient_UC_001


title: ovarian granulosa cells from younger women YWYQ IP

city: Wuhan

first: Chang

last: Liu

state: Hubei

address: Jiefang Avenue

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

description:
ovarian granulosa cells from younger women
YWYQ
This sample was collected from a women aged 25-30 and experienced controlled ovarian stimulation.
Y_peak
OVSY.All.fpkm.anno
OVSY.log2FC1.Pvalue0.05.fpkm.anno

data_processing:
Trimming was performed for known Illumina TruSeq adapter sequences, poor reads, and ribosomal RNA reads.
Then, clean reads were aligned to the human reference genome with the use of Hisat2 software (v2.0.4).
Methylated sites on RNAs were identified by MACS software. Differentially methylated sites with a |fold change| cutoff of >2 and a false discovery rate cutoff of <0.05 were identified by diffReps.
The peaks identified by MACS and diffReps overlapping with exons of mRNA were determined and selected for further analysis.
Genome_build: hg19

source_name: ovarian granulosa cells

extract_protocol:
Total RNA of granulosa cells were extracted using RNA-easy Isolation Reagent according to the manufacturer's instructions.
The quality of the raw reads was determined by FastQC. Trimming was performed for known Illumina TruSeq adapter sequences, poor reads, and ribosomal RNA reads. Then, clean reads were aligned to the human reference genome with the use of Hisat2 software (v2.0.4).
immunoprecipitation

tag: sample type

value: IP

value: primary ovarian granulosa cells

value: no treatment


title: ovarian granulosa cells from younger women YWYQ input

value: input


title: mm_DC_IFNb_6h_RNA-seq_rep3

city: Debrecen

first: Lajos

last: Széles

address: Egyetem tér 1.

country: Hungary

institute: University of Debrecen

description:
IFNB-stimulated dendritic cell (6h)
mRNA_expression_table_all_genes_all_samples.txt

data_processing:
alignment with HISAT2 version 2.1.0 using default parameters
bam generation with Picard tools v2.8.1 using SortSam with default parameters
bam files and StrandNGS program were used to generate  table (tsv) of expression values
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph (continuous-valued data in track format), bed (position of peaks)
Supplementary_files_format_and_content: table (tsv) of expression values

source_name: dendritic cells from the spleen

growth_protocol: CD8-positive dendritic cells were cultured in IMDM-glutamax medium supplemented with 10% FCS, 1% penicillin + streptomycin and 0,1% β-mercaptoethanol

extract_protocol:
Cells were double cross-linked with DSG (40 min) and  formaldehyde (10 min). Nuclei were isolated using lysis buffer containing 150 mM NaCl, 1 nM EDTA pH 8, 20 mM Tris-HCl pH 8, 1% Triton x-100, 1% SDS with EDTA-free protease inhibitor (Roche). Chromtain was sheared with sonication and immunoprecipitated overnight using antibodies against IRF3 (D83B9, Cell Signaling), IRF5 (ab21689, Abcam), IRF9 (AF5629, R&D Systems). Chromatin-antibody complexes were washed and eluted after pull-down by superparamagnetic beads (ThermoFisher Scientific). Eluted complexes were decrosslinked overnight and purified by NucleoSpin Gel and PCR Clean-up Kit (Macherey-Nagel). ChIP-DNA was quantified by Qubit fluorometer. In case of unstimulated cells for ATAC-seq after lysis, nuclei were subjected to tagmentation.
Indexed cDNA libraries were prepared from 1-10 ng ChIP-DNA using TruSeq ChIP Library Preparation Kit (Illumina) or Ovation Ultralow System V2 (Tecan Genomics) according to manufacturer’s instructions. Nextera DNA Library Prep Kit was used for library generation according to manufacturer's protocol (Illumina) for ATAC-seq. RNA-Seq libraries were prepared from total RNA using Ultra II RNA Sample Prep kit (New England BioLabs) according to the manufacturer’s protocol. Libraries were sequenced on NextSeq 500 or HiSeq 2500.

treatment_protocol: Cells were left unstimulated or stimulated with 5 μg/ml poly(I:C) HMW or 1 mM class B CpG oligonucleotide 1826 (CpG)  or 10U IFN-beta for 90 min.

value: CD8-positive dendritic cell line

tag: stimulation

value: 6h min; 10U IFN-beta

tag: chip antibody


title: CD_1_11_RNAseq

tag: cell type

tag: diet

value: control diet


title: ovarian granulosa cells from younger women YWJL IP

description:
ovarian granulosa cells from younger women
YWJL
This sample was collected from a women aged 25-30 and experienced controlled ovarian stimulation.
Y_peak
OVSY.All.fpkm.anno
OVSY.log2FC1.Pvalue0.05.fpkm.anno


title: CD_1_10_RNAseq


title: ovarian granulosa cells from younger women YWJL input


title: mm_DC_IFNb_6h_RNA-seq_rep2


title: Control matched for sample 12

value: healthy


title: Case in remission RC7

tag: tissue

value: Frozen lymph node biopsy

value: Diffuse large B-cell lymphoma (DLBCL)


title: Case in remission RC5


title: Case in remission RC3


title: mm_DC_IFNb_6h_RNA-seq_rep1


title: Case in remission RC4


title: PC-3_shHOXB13_H3K27Ac

city: Atlanta

first: Jindan

last: Yu

state: GA

address: E330, 1760 Haygood Dr NE

department: Urology

institute: Emory University

description:
PC-3_shHOXB13_H3K27Ac
m960

data_processing:
Reads were aligned to the hg19 reference human genome using bowtie2
Peak-calling by HOMER v4.2
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph file and peak txt file

source_name: prostate tumor

growth_protocol: LNCaP and PC3 cells were maintained in RPMI supplemented with 10% FBS and 1% penicillin and streptomycin

extract_protocol: Chromatin in nuclear fraction were sheared to 200-500bp using an Covaris M220 Focused-ultrasonicator, Lysates were clarified from sonicated nuclei and protein-DNA complexes were immunoprecipitated using the indicated antibody. DNA was then reverse crosslinked from protein and purified.  ChIP-seq libraries were prepared from 3-5ng ChIPped DNA by using NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645S), according to the manufacturer’s instructions. Postamplification libraries were size selected at 250–450 bp in length using Agencourt AMPure XP beads from Beckman Coulter and were quantified using the Library Quantification Kit from Illiumina (Kapa Biosystems, KK4603). Libraries were pooled to a final concentration of 10nM and sequenced single-end using the Illumina HiSeq 4000.

treatment_protocol: LNCaP cells were infected with control shRNA (pGIPZ), shRNA targeting HOXB13 (shHOXB13), shHOXB13 with concomitant infection by HOXB13-WT or G84E lentiviruses for 7 days.

tag: cell line

tag: antibody


title: Case in remission RC1


title: LNCaP_pGIPZ_ATAC-seq

description:
LNCaP_pGIPZ_ATAC-seq
m426

extract_protocol: The Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq ) assay in LNCaP was performed as previously reported (Corces et al., 2016). 50,000 cells were washed in PBS, pelleted by centrifugation and lysed and tagmented in 1x TD buffer, 2.5 μl Tn5 (Illumina), 0.01% Digitonin (Promega, G9441), 0.3x PBS in a 50 μl reaction volume. Samples were incubated at 37°C for 30 min at 300 rpm. Tagmented DNA was purified using the DNA Clean & Concentrator™-5 kit (ZYMO Research). Libraries were amplified as described previously (Buenrostro et al., 2013). 50bp paired-end reads were sequenced on a Illumina HiSeq 4000.

value: LNCaP

value: pGIPZ


title: ovarian granulosa cells from older women OZJM IP

description:
ovarian granulosa cells from older women
OZJM
This sample was collected from a women over 40 years of age and experienced controlled ovarian stimulation.
O_peak
OVSY.All.fpkm.anno
OVSY.log2FC1.Pvalue0.05.fpkm.anno

tag: genotype


title: ovarian granulosa cells from younger women YQTT input

description:
ovarian granulosa cells from younger women
YQTT
This sample was collected from a women aged 25-30 and experienced controlled ovarian stimulation.
Y_peak
OVSY.All.fpkm.anno
OVSY.log2FC1.Pvalue0.05.fpkm.anno


title: Case in remission RC6

tag: disease state


title: ovarian granulosa cells from younger women YQTT IP


title: Case in remission RC2


title: mm_DC_CpG_6h_RNA-seq_rep2

description:
CpG-stimulated dendritic cell (6h)
mRNA_expression_table_all_genes_all_samples.txt

value: 6h; 1 mM class B CpG oligonucleotide (1826)


title: mm_DC_CpG_6h_RNA-seq_rep3


title: LNCaP_shHOXB13_AR

description:
LNCaP_shHOXB13_AR
m443

value: AR, Santa Cruz, SC-816X, C2515


title: ovarian granulosa cells from older women OZJM input


title: ovarian granulosa cells from older women OZH IP

description:
ovarian granulosa cells from older women
OZH
This sample was collected from a women over 40 years of age and experienced controlled ovarian stimulation.
O_peak
OVSY.All.fpkm.anno
OVSY.log2FC1.Pvalue0.05.fpkm.anno


title: PC-3_pGIPZ_H3K27Ac

description:
PC-3_pGIPZ_H3K27Ac
m959


title: mm_DC_CpG_6h_RNA-seq_rep1


title: ovarian granulosa cells from older women OZH input


title: LNCaP_shHOXB13_ATAC-seq

description:
LNCaP_shHOXB13_ATAC-seq
m463


title: mm_DC_PIC_6h_RNA-seq_rep3

description:
pIC-stimulated dendritic cell (6h)
mRNA_expression_table_all_genes_all_samples.txt

value: 6h; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: ovarian granulosa cells from older women OYDX IP

description:
ovarian granulosa cells from older women
OYDX
This sample was collected from a women over 40 years of age and experienced controlled ovarian stimulation.
O_peak
OVSY.All.fpkm.anno
OVSY.log2FC1.Pvalue0.05.fpkm.anno


title: LNCaP_pGIPZ_AR

description:
LNCaP_pGIPZ_AR
m442


title: mm_DC_PIC_6h_RNA-seq_rep2


title: ovarian granulosa cells from older women OYDX input


title: LNCaP_shHOXB13+WT_HOXB13

description:
LNCaP_shHOXB13+WT_HOXB13
m856


title: mm_DC_IFNb_90min_RNA-seq_rep3

description:
IFNB-stimulated dendritic cell (90 min)
mRNA_expression_table_all_genes_all_samples.txt

value: 90 min; 10U IFN-beta


title: mm_DC_PIC_6h_RNA-seq_rep1


title: mm_DC_IFNb_90min_RNA-seq_rep2


title: MR_042_Mf_10_D99

city: Madison

first: Bryan

last: Zabel

state: wi

address: 3329 Agriculture Dr

department: GEM

institute: International Flavors & Fragrances Inc

description:
stimulated immune cells
MR_042_Mf_10_D99_GAACTGTAT-GCCGTTACA_L001

data_processing:
Library strategy: TempO-seq
The pooled libraries were sent to Roy J. Carver Biotechnology Center at the University of Illinois at Urbana-Champaign for TempO-Seq sequencing using the Illumina NovaSeq platform (1x50nt). The target read-depth per sample was 5 million reads with the minimum reads per sample at 1 million.
The reads were quality filtered, trimmed and demultiplexed and aligned to the BioSpyder Human Whole Transcriptome v2.0 annotated reference using Salmon (v1.1.0). Two samples did not pass the 5 million read minimum, which were both from pIC+R848 treated DC and were not included in the analysis.
Differential expression analysis was conducted using DESeq2 (v1.26.1) in R (v 3.6.2). Mf and DC were analyzed separately as initial analysis determined the cell types to have distinct expression profiles. Genes were considered differentially expressed if the adjusted p-value < 0.1 and the absolute value of the log2 fold change > 1. Principal component analysis (PCA) was performed to determine overall relatedness of the samples under the various experimental conditions using ggplot2 (v 3.3.3)
Genome_build: Biospyder Human Whole Transcriptome 2.0
Supplementary_files_format_and_content: Raw count table created from SALMON alingment to biospyder probe sequences

source_name: human derived macrophage

growth_protocol: Probiotic strains were grown to logarithmic growth phase, collected by centrifugation, washed once with PBS and suspended to cell culture medium. The optical density (OD)600 was adjusted to correspond to bacteria:host cell ratio of 10:1. The bacteria in the consortia were applied on cells in equal proportions 2+2+2+2+2.          Monocytes were purified from freshly collected leukocyte-rich buffy coats obtained from healthy blood donors through the Finnish Red Cross Blood Service (permission no 46/2016, renewed annually). The use of human blood was approved by the Ethics Committee of the Hospital District of Helsinki and Uusimaa, Finland (216/13/03/00/2016). Human peripheral blood mononuclear cells were isolated by density gradient centrifugation followed by purification of monocytes with CD14+ magnetic beads. To obtain macrophages purified monocytes were plated on 24 well plates 3 x 105 cells/well and cultured for 7 days in Macrophage-SFM (Gibco, Life Technologies, Grand Island, NY, USA) with recombinant human GM-CSF (Miltenyi Biotech) 1000 IU/ml and 1% Antibiotic-Antimycotic. To differentiate monocytes into immature dendritic cells, monocytes were plated on 12 well plates 5 x 105 cells/well (Falcon, Corning, NY, USA) and cultured for 7 d in RPMI-1640 (Sigma) supplemented with 1% Antibiotic-Antimycotic, 10% fetal bovine serum (FBS), IL-4 (400 IU/ml) and GM-CSF (1000 IU/ml).

extract_protocol:
Monocyte-derived macrophages and dendritic cells were lysed upon collection with MagMAX™ Lysis/Binding Solution (Invitrogen, Thermo Fisher Scientific) and frozen in -80°C. RNA was extracted with KingFisher Flex automated extraction instrument (Thermo Scientific, Thermo Fisher Scientific Inc. Waltham, MA, USA) using MagMAX™-96 Total RNA Isolation Kit (Invitrogen, Thermo Fisher Scientific) following manufacturer’s instructions. The RNA quality and quantity were analyzed with Agilent 4200 TapeStation System (Agilent, Santa Clara, CA, USA).
Targeted RNA-seq library preparation was conducted with Tempo-Seq (BioSpyder) detector oligonucleotides designed to target all human genes (~23,000). Library preparation was conducted in 96 sample batches according to BioSpyder kit user manual.

treatment_protocol: Cells from four blood donors were stimulated with consortia alone (bacteria:cell ratio of 10:1) or in combination with TLR ligand blend, Poly I:C (pIC), 30μg/ml + R848, 10μM (both from Sigma-Aldrich, St. Louis, MO, USA) for 24 h (Mf) or 48 h (DC). PBMCs without stimulation were used as a control, dimethyl sulfoxide (DMSO), a carrier for the TLR-ligands, were used as a control for pI:C+R848 containing treatments.

tag: condition

value: DMSO

value: human derived macrophage

tag: time point

value: 24 hours


title: LNCaP_shHOXB13+G84E_H3K27ac

description:
LNCaP_shHOXB13+G84E_H3K27ac
m807


title: LNCaP_shHOXB13_HOXB13

description:
LNCaP_shHOXB13_HOXB13
m855


title: mm_DC_CpG_90min_RNA-seq_rep3

description:
CpG-stimulated dendritic cell (90 min)
mRNA_expression_table_all_genes_all_samples.txt

value: 90 min; 1 mM class B CpG oligonucleotide (1826)


title: MR_042_Mf_10_D98

description:
stimulated immune cells
MR_042_Mf_10_D98_GAACTGTAT-ATACGCAGC_L001


title: MR_042_Mf_10_D100

description:
stimulated immune cells
MR_042_Mf_10_D100_GAACTGTAT-GCACCTATT_L001


title: mm_DC_IFNb_90min_RNA-seq_rep1


title: MR_042_Mf_5_D100

description:
stimulated immune cells
MR_042_Mf_5_D100_GAACTGTAT-GGTCTAGCT_L001


title: MR_042_Mf_10_D97

description:
stimulated immune cells
MR_042_Mf_10_D97_GAACTGTAT-TCTAACCAT_L001


title: LNCaP_shHOXB13+G84E_HOXB13

description:
LNCaP_shHOXB13+G84E_HOXB13
m857


title: mm_DC_CpG_90min_RNA-seq_rep1


title: MR_042_Mf_5_D99

description:
stimulated immune cells
MR_042_Mf_5_D99_GAACTGTAT-CGTAACTTA_L001


title: LNCaP_pGIPZ_H3K27ac

description:
LNCaP_pGIPZ_H3K27ac
m804


title: mm_DC_CpG_90min_RNA-seq_rep2


title: mm_DC_PIC_90min_RNA-seq_rep2

description:
pIC-stimulated dendritic cell (90 min)
mRNA_expression_table_all_genes_all_samples.txt

value: 90 min; 5 mg/ml of high molecular weight Polyinosinic-polycytidylic acid (pIC)


title: LNCaP_shHOXB13_HDAC3

description:
LNCaP_shHOXB13_HDAC3
m683


title: LNCaP_shHOXB13_H3K27ac

description:
LNCaP_shHOXB13_H3K27ac
m805


title: MR_042_Mf_5_D98

description:
stimulated immune cells
MR_042_Mf_5_D98_GAACTGTAT-ATACCGGCA_L001


title: mm_DC_PIC_90min_RNA-seq_rep3

value: CD8-positive dendritic cell line


title: LNCaP_pGIPZ_HDAC3

description:
LNCaP_pGIPZ_HDAC3
m682


title: mm_DC_PIC_90min_RNA-seq_rep1


title: LNCaP_pGIPZ_HOXB13

description:
LNCaP_pGIPZ_HOXB13
m854


title: MR_042_Mf_5_D97

description:
stimulated immune cells
MR_042_Mf_5_D97_GAACTGTAT-GATTGTGTT_L001


title: LNCaP_shHOXB13+WT_H3K27ac

description:
LNCaP_shHOXB13+WT_H3K27ac
m806


title: MR_042_Mf_4_D100

description:
stimulated immune cells
MR_042_Mf_4_D100_AAGACTCTT-GCACCTATT_L001


title: PC3_pGIPZ_HOXB13

description:
PC3_pGIPZ_HOXB13
m681

value: HOXB13, Santa Cruz, sc-66923, F0710


title: mm_DC_UT_RNA-seq_rep3

description:
unstimulated CD8-positive dendritic cells
mRNA_expression_table_all_genes_all_samples.txt


title: MR_042_Mf_4_D98

description:
stimulated immune cells
MR_042_Mf_4_D98_AAGACTCTT-ATACGCAGC_L001


title: MR_042_Mf_4_D97

description:
stimulated immune cells
MR_042_Mf_4_D97_AAGACTCTT-TCTAACCAT_L001


title: LNCaP_pGIPZ_HDAC1

description:
LNCaP_pGIPZ_HDAC1
m496


title: MR_042_Mf_4_D99

description:
stimulated immune cells
MR_042_Mf_4_D99_AAGACTCTT-GCCGTTACA_L001


title: mm_DC_PIC_ChIP-seq_IRF3_rep2

description:
pIC-stimulated dendritic cell (90 min)
GSM3569290

data_processing:
read trimming with Trimmomatic using SE and -phread33 parameters, TruSeq3-SE.fa:2:30:10 adapter and LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36 values
alignment with bwa v0.7.17 using default parameters
bam generation with Picard tools v2.8.1 using SortSam, AddOrreplaceReadGroups, CollectAlignmentSummaryMetrics, CollectInsertSizeMetrics, MarkDuplicates with default parameters
tag directory generation with homer v4.9.1 makeTagDirectory using -checkGC and -single parameter
peak calling with MACS2 using -B, -q 0.001, --call-summits parameters
mm10 ENCODE blacklist were subtracted from the peak list
in case of ATAC-seq: calculating FPKM values from the previously created BAM and BED files
Genome_build: mm10
Supplementary_files_format_and_content: bedGraph (continuous-valued data in track format), bed (position of peaks)
Supplementary_files_format_and_content: table (tsv) of expression values

value: IRF3 (D83B9, Cell Signaling)


title: MR_042_Mf_2_D98

description:
stimulated immune cells
MR_042_Mf_2_D98_TCCTCAGCC-ATACCGGCA_L001


title: mm_DC_UT_RNA-seq_rep2


title: MR_042_Mf_1_D99

description:
stimulated immune cells
MR_042_Mf_1_D99_TCCTCAGCC-GCCGTTACA_L001

value: ctrl


title: MR_042_Mf_2_D100

description:
stimulated immune cells
MR_042_Mf_2_D100_TCCTCAGCC-GGTCTAGCT_L001


title: mm_DC_UT_RNA-seq_rep1


title: mm_DC_PIC_ChIP-seq_IRF3_rep1

description:
pIC-stimulated dendritic cell (90 min)
GSM3569289


title: mm_DC_CpG_ChIP-seq_IRF5_rep2

description:
CpG-stimulated dendritic cell (90 min)
GSM3569292

value: IRF5 (ab21689, Abcam)


title: THP-1-M2-mCherry mono

city: Düsseldorf

first: Daniel

last: Nettersheim

state: NRW

address: Moorenstr. 5

department: Dep. of Urology

institute: Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University

data_processing:
The bcl2fastq tool was used to convert the bcl files to fastq files as well for adapter trimming and demultiplexing. Data analyses on fastq files were conducted with CLC Genomics Workbench (version 20.0.4, QIAGEN, Venlo. NL). The reads of all probes were adapter (Illumina TruSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides max. 2).
Genome_build: Mapping was done against the Homo sapiens (hg38) (May 25, 2017) genome sequence.
Supplementary_files_format_and_content: Statistical differential expression tests were determined using the ‘Differential Expression in Two Groups’ tool (version 1.02). The resulting p-values were corrected for multiple testing by false discovery rate- (FDR) and Bonferroni-correction. A p-value of ≤0.05 was considered significant.

source_name: M2 macrophage

growth_protocol: 2102EP and JAR cells were cultivated in DMEM medium (10% FCS, 1% Penicillin / Streptomycin 10,000 U, 1% L-glutamine 200 mM); TCam-2, GCT72, JURKAT and THP-1-M2 were cultivated in RMPI medium  (10% FCS, 1% Penicillin / Streptomycin 10,000 U, 1% L-glutamine 200 mM); HVHF2 cells were  cultivated in DMEM medium (10% FCS, 1% Penicillin / Streptomycin 10,000 U, 1% L-glutamine 200 mM, 1% MEM non-essential amino acids 100x). HUVEC cells were cultivated in 'Endothelial Cell Growth Medium 2 (ready-to-use)' medium from PromoCell including the manufacturers provided supplements. All cell lines have been cultivated at 37°C and 7.5% CO2.

extract_protocol:
RNA was isolated using the RNAeasy Mini Kit (Qiagen, Hilden, Germany) according to the manual
RNA samples used for transcriptome analyses were quantified (Qubit RNA HS Assay, Thermo Fisher Scientific, Meerbusch, Germany) and quality was measured by capillary electrophoresis using the Fragment Analyzer and the ‘Total RNA Standard Sensitivity Assay’ (Agilent Technologies Inc., Santa Clara, USA). The library preparation was performed according to the manufacturer’s protocol (‘VAHTS Stranded mRNA-Seq Library Prep Kit’). 300 ng total RNA were used for mRNA capturing, fragmentation, synthesis of cDNA, adapter ligation, and library amplification. Bead purified libraries were normalized.

treatment_protocol: 3D culture for 72 h

tag: culture method

value: 3D monoculture

value: M2 macrophage


title: MR_042_Mf_1_D98

description:
stimulated immune cells
MR_042_Mf_1_D98_TCCTCAGCC-ATACGCAGC_L001


title: MR_042_Mf_1_D100

description:
stimulated immune cells
MR_042_Mf_1_D100_TCCTCAGCC-GCACCTATT_L001


title: mm_DC_IFNb_ChIP-seq_Pol-II_rep2

description: IFNB-stimulated dendritic cell (90 min)

value: RNAPII-pS5 (ab5131, Abcam)


title: mm_DC_IFNb_ChIP-seq_Pol-II_rep1

description: IFNB-stimulated dendritic cell (90 min)


title: THP-1-M2-mCherry co-cultured with JAR-GFP

value: 3D co-culture with JAR-GFP


title: THP-1-M2-mCherry co-cultured with TCam-2-GFP

value: 3D co-culture with TCam-2-GFP


title: control cells, biological rep3

city: xi'an

first: zhengyang

last: lu

state: shannxi

address: xi'an shannxi

institute: the first affiliated hospital of xi'an jiaotong university

description: Gene expression data from knockdown of EIF3C in TE-1 cells

hyb_protocol: Following fragmentation, cRNA were hybridized for 16 hr at 45 ℃on GeneChip human Gene. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G3000.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: control TE-1cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ug total RNA

growth_protocol: TE-1 cells were cultured in RPMI-1640 supplemented with 10% foetal bovine serum at 37 ℃ in a humidified atmosphere containing 5% CO2.

treatment_protocol: EIF3C expression was stably knocked-down in TE-1 cells. RNA from this clone and parental (control) cells were purified for microarray analysis.

value: Human esophageal squamous cell carcinoma cell line

tag: genotype/variation

value: control


title: MR_042_Mf_1_D97

description:
stimulated immune cells
MR_042_Mf_1_D97_TCCTCAGCC-TCTAACCAT_L001


title: MR_042_DC_26_D100

description:
stimulated immune cells
MR_042_DC_26_D100_TGCATGACA-GCACCTATT_L001

source_name: human derived dentritic cell

value: DMSO

value: human derived dentritic cell

value: 48 hours


title: MR_042_DC_26_D99

description:
stimulated immune cells
MR_042_DC_26_D99_TGCATGACA-GCCGTTACA_L001


title: mm_DC_CpG_ChIP-seq_IRF5_rep1

description:
CpG-stimulated dendritic cell (90 min)
GSM3569291

value: 90 min; 1 mM class B CpG oligonucleotide (1826)


title: EIF3C knockdown cells, biological rep2

description: Gene expression data from TE-1 cells knockdown of EIF3C

source_name: EIF3C knockdown TE-1 cells

value: EIF3C knockdown


title: EIF3C knockdown cells, biological rep3


title: EIF3C knockdown cells, biological rep1


title: control cells, biological rep1


title: mm_DC_UT_ChIP-seq_Pol-II_rep2

description: unstimulated CD8-positive dendritic cells

value: CD8-positive dendritic cell line


title: TCam-2-GFP mono

source_name: germ cell tumor, seminoma

value: germ cell tumor, seminoma


title: TCam-2-GFP co-cultured with JURKAT-mCherry

value: 3D co-culture with JURKAT-mCherry


title: TCam-2-GFP co-cultured with THP-1-M2-mCherry

value: 3D co-culture with THP-1-M2-mCherry


title: THP-1-M2-mCherry co-cultured with 2102EP-GFP

value: 3D co-culture with 2102EP-GFP


title: MR_042_DC_21_D100

description:
stimulated immune cells
MR_042_DC_21_D100_ATTCGCTCT-GGTCTAGCT_L001


title: mm_DC_IFNb_ChIP-seq_GCN5_rep1

description: IFNB-stimulated dendritic cell (90 min)

value: 90 min; 10U IFN-beta

value: purified anti-GCN5 rabbit poly-clonal antibody pAb 2676


title: MR_042_DC_26_D98

description:
stimulated immune cells
MR_042_DC_26_D98_TGCATGACA-ATACGCAGC_L001


title: mm_DC_UT_ChIP-seq_GCN5_rep2


title: mm_DC_UT_ChIP-seq_Pol-II_rep1

value: RNAPII-pS5 (ab5131, Abcam)


title: THP-1-M2-mCherry co-cultured with GCT72-GFP

value: 3D co-culture with GCT72-GFP

value: M2 macrophage


title: MR_042_DC_21_D97

description:
stimulated immune cells
MR_042_DC_21_D97_ATTCGCTCT-GATTGTGTT_L001


title: MR_042_DC_20_D100

description:
stimulated immune cells
MR_042_DC_20_D100_ATTCGCTCT-GCACCTATT_L001


title: mm_DC_UT_ChIP-seq_GCN5_rep1


title: MR_042_DC_26_D97

description:
stimulated immune cells
MR_042_DC_26_D97_TGCATGACA-TCTAACCAT_L001


title: control cells, biological rep2

value: Human esophageal squamous cell carcinoma cell line


title: MR_042_DC_20_D99

description:
stimulated immune cells
MR_042_DC_20_D99_ATTCGCTCT-GCCGTTACA_L001


title: MR_042_DC_21_D99

description:
stimulated immune cells
MR_042_DC_21_D99_ATTCGCTCT-CGTAACTTA_L001


title: mm_DC_IFNb_ChIP-seq_STAT2_rep2

description: IFNB-stimulated dendritic cell (90 min)

value: STAT2 (07-140, Merck Millipore)


title: mm_DC_IFNb_ChIP-seq_STAT1_rep2

description: IFNB-stimulated dendritic cell (90 min)

value: STAT1 (sc-346, Santa Cruz Biotechnology),


title: JURKAT-mCherry mono

source_name: T lymphoblast

value: 3D monoculture

value: T lymphoblast


title: MR_042_DC_20_D97

description:
stimulated immune cells
MR_042_DC_20_D97_ATTCGCTCT-TCTAACCAT_L001

value: human derived dentritic cell

value: 48 hours


title: MR_042_DC_20_D98

description:
stimulated immune cells
MR_042_DC_20_D98_ATTCGCTCT-ATACGCAGC_L001


title: mm_DC_UT_ChIP-seq_STAT2_rep2

value: CD8-positive dendritic cell line


title: JURKAT-mCherry co-cultured with JAR-GFP

value: 3D co-culture with JAR-GFP


title: MR_042_DC_18_D100

description:
stimulated immune cells
MR_042_DC_18_D100_ACTCATGTA-GGTCTAGCT_L001


title: TCam-2-GFP co-cultured with HUVEC-mCherry

value: 3D co-culture with HUVEC-mCherry

value: germ cell tumor, seminoma


title: TCam-2-GFP co-cultured with HVHF2-deepred

value: 3D co-culture with HVHF2-deepred


title: mm_DC_IFNb_ChIP-seq_STAT1_rep1

description: IFNB-stimulated dendritic cell (90 min)

value: 90 min; 10U IFN-beta


title: JURKAT-mCherry co-cultured with GCT72-GFP


title: JURKAT-mCherry co-cultured with TCam-2-GFP

value: 3D co-culture with TCam-2-GFP


title: JAR-GFP co-cultured with JURKAT-mCherry

source_name: non-seminoma germ cell tumor, choriocarcinoma

value: 3D co-culture with JURKAT-mCherry


title: JAR-GFP co-cultured with HVHF2-deepred

value: non-seminoma germ cell tumor, choriocarcinoma


title: JURKAT-mCherry co-cultured with 2102EP-GFP

value: 3D co-culture with 2102EP-GFP


title: MR_042_DC_17_D99

description:
stimulated immune cells
MR_042_DC_17_D99_ACTCATGTA-GCCGTTACA_L001

value: ctrl


title: MR_042_DC_18_D99

description:
stimulated immune cells
MR_042_DC_18_D99_ACTCATGTA-CGTAACTTA_L001


title: JAR-GFP mono


title: MR_042_DC_18_D97

description:
stimulated immune cells
MR_042_DC_18_D97_ACTCATGTA-GATTGTGTT_L001


title: mm_DC_UT_ChIP-seq_STAT1_rep1


title: mm_DC_IFNb_ChIP-seq_IRF9_rep1

description:
IFNB-stimulated dendritic cell (90 min)
GSM3569293

value: IRF9 (AF5629, R&D Systems)


title: HVHF2-deepred mono

source_name: fibroblast

value: fibroblast


title: MR_042_DC_18_D98

description:
stimulated immune cells
MR_042_DC_18_D98_ACTCATGTA-ATACCGGCA_L001


title: MR_042_DC_17_D100

description:
stimulated immune cells
MR_042_DC_17_D100_ACTCATGTA-GCACCTATT_L001


title: JAR-GFP co-cultured with THP-1-M2-mCherry

value: 3D co-culture with THP-1-M2-mCherry


title: mm_DC_UT_ChIP-seq_IRF9_rep2

description: unstimulated CD8-positive dendritic cells


title: 11_Mfn2

first: Yae-Huei

last: Liou

address: 665 Huntington Ave.

department: MET

institute: Harvard School of Public health

data_processing:
Trimming of Illumina adapters (CLC Genomics Workbench v.10 )
Quality control for individual samples (CLC Genomics Workbench v.10 )
Mapping against the reference genome (CLC Genomics Workbench v.10 )
Calculation of expression values using unique matches (CLC Genomics Workbench v.10)
Normalisation by scaling 10.000.000 reads per sample per transcript (TPM),
Genome_build: Genome_build: mouse mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: Primary hepatocyte

growth_protocol: All sample are 48hr post-infected primary hepatocyte.

extract_protocol:
RNA was harvest by spin column.
RNA libraries were prepared for sequencing using Illumina’s TruSeq Stranded mRNA Library Preparation Kit based on the Kit’s manual. 2 ug total RNA was used as input.

treatment_protocol: Ad-LacZ, Ad-Mfn2 infected

tag: strain

value: wild type

tag: treatment

value: Ad-Mfn2 infected


title: mm_DC_IFNb_ChIP-seq_IRF9_rep2

description:
IFNB-stimulated dendritic cell (90 min)
GSM3569294


title: 12_Mfn2


title: 10_Mfn2


title: HVHF2-deepred co-cultured with TCam-2-GFP


title: MR_042_DC_17_D97

description:
stimulated immune cells
MR_042_DC_17_D97_ACTCATGTA-TCTAACCAT_L001

value: human derived dentritic cell

value: 48 hours


title: mm_DC_UT_ChIP-seq_IRF9_rep1

value: CD8-positive dendritic cell line


title: D1 scRNA-seq

city: Tianjin

first: xuan

last: zhou

address: West huanhu road

institute: Tianjin Medical University Cancer Institute and Hospital

data_processing:
The raw scRNA-seq data were processed using CellRanger 3.0.2 (10x Genomics).
Subsequent data analysis, including standardization, cell subpopulation, difference of gene expression, and marker gene screening, were achieved using Seurat software.
Genome_build: GRCh38
Supplementary_files_format_and_content: matrix.mtx, matrix file exported by cellranger
Supplementary_files_format_and_content: genes.tsv, features file exported by cellranger
Supplementary_files_format_and_content: barcodes.tsv, barcode file exported by cellranger

source_name: tongue

extract_protocol:
Fresh HNSCC tissues were dissociated with Gentle MACS Dissociator (Miltenyi Biotec) according to the manufacturer’s instructions. Next, single cells were counted using an automated cell counter and adjusted to a concentration of 1000 cells/μL, and we retained single-cell transcriptomes for 13,903 cells after initial quality controls. Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs).
The cells were lysed, and RNA was reverse-transcribed into cDNA. Libraries were generated from the cDNA with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1.
the cDNA libraries were sequenced using the Nova 6000 Sequencing System (Illumina).

treatment_protocol: two HNSCC patients before and after cetuximab treatment

value: head and neck squamous cell carcinoma (HNSCC)

tag: Sex

value: male

value: tumor cell

tag: age

value: 43, 47 (multiplexed)

value: cetuximab treatment


title: HVHF2-deepred co-cultured with JAR-GFP

value: 3D co-culture with JAR-GFP


title: C1 scRNA-seq

value: untreated


title: CV rep3

city: PORTLAND

first: JUNGSUN

last: KIM

state: OR

address: KCRB 5001.51, 2720 SW Moody Ave

institute: Oregon Health & Science University

description:
backbone control vector
H6_GFP_3

data_processing:
Original image data file from high-throughput sequencing is transformed to sequenced reads by CASAVA base recognition (Base Calling)
Reads with adaptor contamination, with more than 10 percent of uncertain nucleotides, and reads with more than 50 percent of low quality nucleotides (Base Quality less than 5) were removed.
Clean reads were mapped to reference genome (hg38) using Spliced Transcripts Alignment to Reference (STAR) software.
Supplementary_files_format_and_content: Matrix table with DESeq2-normalized counts:  gene counts for every gene and every sample

source_name: Human Pancreatic Duct Epithelial

growth_protocol: H6c7 cells were cultured in Keratinocyte SFM media supplemented with EGF and bovine pituitary extract (Invitrogen Cat#:17005042).

extract_protocol:
RNA was prepared from frozen cells using the QIAGEN RNeasy kit. RNA quality was tested using the Bioanalyzer 2100 (Agilent) and concentration was determined using the Life Technologies Qubit.
RNA libraries were prepared for sequencing with NEBNext Ultra II non-directional RNA Library Prep kit.

treatment_protocol: H6c7 cells were transduced with either control GFP lentiviral vector with 575 infection units (IU) per cell or HBP1 overexpression lentiviral vectors (3.25 IU/cell, low expression and 32.5 IU/cell, high expression). After addition of lentiviral vector cells were incubated with virus for 24 hours. At 72 hours after transduction cells were collected and frozen at -80 C.

value: Transduced with GFP lentiviral  vector


title: 4_LacZ

city: Boston

value: Ad-Lacz infected


title: 3_LacZ


title: CV rep2

description:
backbone control vector
H6_GFP_2


title: HVHF2-deepred co-cultured with GCT72-GFP

value: 3D co-culture with GCT72-GFP


title: HVHF2-deepred co-cultured with 2102EP-GFP

value: 3D co-culture with 2102EP-GFP

value: fibroblast


title: 9_Mfn2

value: wild type


title: JAR-GFP co-cultured with HUVEC-mCherry

value: 3D co-culture with HUVEC-mCherry

value: non-seminoma germ cell tumor, choriocarcinoma


title: HUVEC-mCherry mono

source_name: endothelial cells

value: 3D monoculture

value: endothelial cells


title: MR_042_DC_17_D98

description:
stimulated immune cells
MR_042_DC_17_D98_ACTCATGTA-ATACGCAGC_L001

value: ctrl

value: human derived dentritic cell

value: 48 hours


title: 1_LacZ


title: HUVEC-mCherry co-cultured with TCam-2-GFP

value: 3D co-culture with TCam-2-GFP


title: 2_LacZ


title: HBP1-OE high rep3

description:
high HBP1 overexpressing
H6H102_3

value: Transduced with HBP1 lentiviral  vector


title: HUVEC-mCherry co-cultured with JAR-GFP

value: 3D co-culture with JAR-GFP


title: HBP1-OE high rep2

description:
high HBP1 overexpressing
H6H102_2


title: P17 YY1cKO; KM7

city: Richmond

first: Tomasz

last: Kordula

state: VA

address: 1101 E Marshall ST

department: Biochemistry and Molecular Biology

institute: Virginia Commonwealth University

data_processing:
cellranger count
cellranger aggr
Downstream processing with Seurat
Genome_build: mm10
Supplementary_files_format_and_content: filtered_feature_bc_matrix in MEX format from CellRanger. These files were loaded to Seurat for downstream analysis.

source_name: P17 cerebellum

growth_protocol: Cerebellum were isolated from mice at P10 or P17, and meninges were removed in cold ACSF (120 mM NaCl, 3 mM KCl, 2 mM MgCl, 0.2 mM CaCl, 26.2 mM NaHCO3, 11.1 mM glucose, 5 mM HEPE, 3 mM AP5, and 3 mM CNQX) bubbled with 95% oxygen.

extract_protocol:
A targeted cell recovery of 5000 single cells per sample, which was loaded onto the Chromium Controller (10x Genomics).
The libraries were made with the Chromium Single Cell 3’ Library and Gel Bead Kit (10x Genomics), following the manufacturers protocol. Unique Chromium i7 Sample Indexes (10xGenomics) were added to each sample, following the manufacturers protocol. Prior to sequencing, all four samples were combined.
scRNA-seq

treatment_protocol: The tissue was cut 15 times and dissociated with the Worthington Papain Dissociation kit (# LK003153). The manufactures protocol was followed. Briefly, the tissue was dissociated in the papain DNase solution for 30 minutes at 37°C with 5% CO2, gently swirling every 5 minutes. The cells were filtered through a 70 µm filter (BD Falcon) to ensure a single cell suspension. The cells were resuspended in cold PBS with 0.5% BSA, and the cell viability and concentration were determined using the TC20 Automated Cell Counter (Biorad). The cells were diluted to a final concentration of 1x106 cells/ml.

value: Cerebellum

value: YY1flox/flox; GFAP-CRE+/-


title: HBP1-OE high rep1

description:
high HBP1 overexpressing
H6H102_1


title: CV rep1

description:
backbone control vector
H6_GFP_1

value: Transduced with GFP lentiviral  vector


title: HBP1-OE low rep2

description:
low HBP1 overexpressing
H6H103_2


title: P17 YY1cKO; KM6


title: GCT72-GFP co-cultured with JURKAT-mCherry

source_name: non-seminoma germ cell tumor, yolk sac tumor

value: 3D co-culture with JURKAT-mCherry


title: GCT72-GFP co-cultured with HVHF2-deepred

value: 3D co-culture with HVHF2-deepred

value: non-seminoma germ cell tumor, yolk sac tumor


title: parental rep3

description:
control
H6_p_3

value: Not transduced


title: P10 YY1cKO; KM04

source_name: P10 cerebellum


title: HUVEC-mCherry co-cultured with GCT72-GFP

value: 3D co-culture with GCT72-GFP


title: P10 YY1cKO; KM02


title: HBP1-OE low rep3

description:
low HBP1 overexpressing
H6H103_3


title: GCT72-GFP co-cultured with HUVEC-mCherry

value: 3D co-culture with HUVEC-mCherry


title: P10 WT; KM03

value: YY1flox/flox; GFAP-CRE-/-


title: P17 WT; KM8


title: GCT72-GFP mono

value: 3D monoculture


title: P17 WT; KM5


title: mm_DC_IFNb_ChIP-seq_GCN5_rep2

description: IFNB-stimulated dendritic cell (90 min)

source_name: dendritic cells from the spleen

value: CD8-positive dendritic cell line

tag: stimulation

value: 90 min; 10U IFN-beta

value: purified anti-GCN5 rabbit poly-clonal antibody pAb 2676


title: 2102EP-GFP co-cultured with JURKAT-mCherry

source_name: non-seminoma germ cell tumor, embryonal carcinoma


title: AD2_SOX9neg

city: New York

first: Shane

middle: A.

last: Liddelow

state: NY

address: 435 E. 30th Street

department: Neuroscience Institute

institute: NYU Langone Medical Center

data_processing:
Basecalling was completed using Illumina NovaSeq 6000 RTA v3.4.4 software.
BCL base call files were converted to FASTQ files using bcl2fastq Conversion software (v2.20).
Using Cell Ranger software suite (v4.0.0) (10X Genomics), FASTQ files were aligned to a premRNA-modified GRCh38 human reference genome (modification steps provided by 10x Genomics), and gene-barcode count matrices were generated for all demultiplexed samples.
Genome_build: premRNA-modified GRCh38
Supplementary_files_format_and_content: We provided both raw sequencing FASTQ files as well as filtered_feature_bc_matrix files (e.g., barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz)--the latter which may be directly imported into R/Seurat for analysis.

source_name: Prefrontal cortex

extract_protocol:
Processing of tissue was completed on ice or at 4°C for the entirety of the protocol. In brief, ~100 mg of postmortem frozen human prefrontal cortex per donor was homogenized in 2 mL homogenization buffer (10 mM Tris pH 8, 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 0.1% Triton X100, 1% RNasin Plus, 1X Protease inhibitor, and 0.1 mM DTT in DNase- and RNase-free water) using a Wheaton Dounce tissue grinder (10 strokes with loose pestle, followed by 10 strokes with the tight pestle). Then, the homogenized tissue was filtered through 30 mm pre-separation filters to remove major debris. Samples were then centrifuged at 900 xg for 10 minutes at 4°C. Nuclei were then immunolabeled for SOX9. SOX9-positive or SOX9-negative nuclei were collected using a MoFlo XDP sorter with a 100 mm nozzle at 4°C. Collected nuclei were processed using the Single Cell 3’ Gene Expression kit v3 (10x Chromium) according to manufacturer’s instructions, and libraries were sequenced an Illumina NovaSeq 6000.
Sequencing libraries were prepared using the Single Cell 3’ Gene Expression kit v3 (10x Chromium) according to manufacturer’s instructions.

value: Prefrontal cortex

value: Alzheimer's disease

value: Male


title: AD2_SOX9pos


title: 2102EP-GFP mono

value: non-seminoma germ cell tumor, embryonal carcinoma


title: 2102EP-GFP co-cultured with THP-1-M2-mCherry

value: 3D co-culture with THP-1-M2-mCherry


title: 2102EP-GFP co-cultured with HVHF2-deepred


title: DMR179

city: Lausanne

first: Anna

last: Anchimiuk

state: Vaud

address: UNIL-Sorge District

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

description: sporulation_1kb_ChIPseq_DMR178_179_181.txt

data_processing:
End trimming using trimmomatic Version 0.39
Reads were mapped using bowtie2 (--very sensitive-local mode)
Downstream data analysis was conducted using SeqMonk (Babraham Institute), with a bin size of 1 kb. Data was visualized using R.
Genome_build: NC_000964.3
Supplementary_files_format_and_content: txt format for read count in 1 kb bins

organism: Bacillus subtilis

source_name: anti-ScpB ChIP-seq of ATP-Soj mutant Bs cells conducted 3 h after re-suspension in sporulation salts

growth_protocol: For the single time point ChIP-seq, 10 ml overnight cultures of strains DMR178, DMR179 and DMR181 grown in CH media were diluted to OD600 = 0.1 in 50 ml fresh CH. For the time-course ChIP-seq, 10 ml overnight cultures of strains DMR312, DMR314 and DMR363 grown in CH media were diluted to OD600 = 0.1 in 100 ml fresh CH. Each strain was then grown at 30°C or 37°C until the OD600 reached 0.8. Cultures were then pelleted and resuspended into an equal volume of A+B sporulation salts, which marked t0 of sporulation. All subsequent time points for sporulation (in min or h) are measured similarly (e.g. t90 min marks 90 minutes after re-suspension in sporulation salts). For the time-course ChIP-seq,upon re-suspension in A+B sporulation salts, each sample was split into 2x 50 ml samples, with expression of the ectopic copy of soj being induced in one of each pair by the addition of 0.5 % (final) xylose.

extract_protocol:
To purify the DNA, 500 μl phenol:chloroform:isoamyl alcohol mix (Sigma) was added to the IP and WCE tubes, mixed vigorously and centrifuged for 10 min at 13,000 rpm (at room temperature). 450 μl of aqueous phase was collected and precipitated with 1 ml 100 % ethanol in the presence of 45 μl NaOAc (Sigma) and 1.2 μl of Glycoblue (Invitrogen) for 20 min at −20°C. DNA pellets were collected by centrifugation and resuspended in 100 μl EB (Qiagen) by vigorous shaking for 10 min at 55°C. Final purification was performed using a PCR purification kit (Qiagen), eluting the DNA in 50 μl EB. Prior to deep sequencing, the success of the IP was verified with qPCR.
For deep sequencing, the DNA libraries were prepared by the Genomic Facility at CIG, UNIL, Lausanne. Briefly, the DNA was fragmented by sonication (Covaris S2) until the DNA was sheared to 220-250 bp. The Ovation Ultralow Library Systems V2 kit (NuGEN) including 15 cycles of PCR amplification was used to prepare the DNA libraries. 12-15 million sequence reads per sample were obtained on a HiSeq4000 (Illumina) with 150 bp read length.

treatment_protocol: At respective time points the samples were crosslinked with formaldehyde (1 % final) for 30 min at room temperature with shaking every 10 mins. Each sample pellet was washed twice in PBS, prior to rapid freezing and storage at −80°C until further processing. Each sample pellet was resuspended in 2 ml cold PBS and adjusted to 4 OD600 units (4 ml at OD600=1). Adjusted sample pellets were resuspended in TSEMS buffer (50 mM Tris pH 7.4, 50 mM NaCl, 10 mM EDTA pH 8.0, 0.5 M sucrose and PIC (Sigma)) supplemented with 10 mg/ml lysozyme from chicken egg white (Sigma) and incubated for 30 min at 37°C with vigorous shaking. Resulting protoplasts were collected by centrifugation, washed twice with TSEMS, resuspended in 1 ml TSEMS and split into 3 aliquots. Pelleted samples were rapidly frozen in liquid nitrogen for storage at −80°C until further processing. For immunoprecipitation (IP), the sample pellets were resuspended in 2 ml buffer L (50 mM HEPES-KOH pH 7.5, 140 mM NaCl, 1 mM EDTA pH 8.0, 1 % (v/v) Triton X-100, 0.1 % (w/v) Na-deoxycholate, 0.1 mg/ml RNaseA and PIC (Sigma)) and transferred to 50 ml round bottom tubes. Sonication was performed using a Bandelin Sonoplus with an MS72 tip (90 % pulse and 35 % power output) for 3 rounds of 20 sec. Lysates were transferred to 2 ml tubes and, after centrifugation for 10 min at 21,000 g at 4°C, 800 μl of the supernatant was collected for IP and 200 μl was kept as whole-cell extract (WCE) at −20°C.    Prior to IP, the anti-scpB antibody serum (Gruber Lab) was incubated with Protein G coupled Dynabeads (Invitrogen) in a 1:1 ratio for 2.5-3.5 hrs at 4°C with rotation. The antibody-bead mixture was then washed and resuspended in buffer L, prior to adding 50 μl to each IP sample, which were incubated for 2.5-3 hrs at 4°C with rotation. Next, the samples were washed with the following buffers: buffer L, buffer L5 (buffer L containing 500 mM NaCl), buffer W (10 mM Tris-HCl pH 8.0, 250 mM LiCl, 0.5 % (v/v) NP-40, 0.5 % (w/v) Na-deoxycholate, 1 mM EDTA pH 8.0), and buffer TE (10 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0). Finally, for crosslink reversal, the IP samples were resuspended in 520 μl buffer TES (50 mM Tris-HCl pH 8.0, 10 mM EDTA pH 8.0, 1 % (w/v) SDS) and transferred to 1.5 ml screw-cap tubes. WCE samples were thawed and 300 μl of TES and 20 μl of 10 % SDS were added. Both tubes were incubated overnight at 65°C with vigorous shaking.

tag: chip antibody

value: anti-ScpB


title: P10 WT; KM01

value: Cerebellum


title: SHED-exos_rep3

city: BeiJing

first: Zhihao

last: Du

address: No.22, Zhongguancun South Avenue, Haidian District

institute: Peking University School and Hospital of Stomatology

description: SHED-exos_replicate3 miRNAs expresion profile

hyb_protocol: According to the Agilent miRNA Microarray Protocol (Agilent Technologies).

scan_protocol: After hybridization and washes, slides were scanned immediately in Agilent Microarray Scanner with Surescan High Resolution Technology (Agilent Technologies, Santa Clara, CA).

data_processing: Feature Extraction v10.10 (Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and Bioconductor software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: SHED-exos_ replicate3

label_protocol: The miRNAs were labeled using the Agilent miRNA labeling reagent. Total RNA (200 ng) was dephosphorylated and ligated with pCp-Cy3, the labeled RNA was purified and hybridized to miRNA arrays.

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's

value: exosomes obtained from the supernatant of stem cells derived from human exfoliated deciduous teeth


title: parental rep2

description:
control
H6_p_2


title: HBP1-OE low rep1

description:
low HBP1 overexpressing
H6H103_1

value: Transduced with HBP1 lentiviral  vector


title: SHED-exos_rep2

description: SHED-exos_replicate2 miRNAs expresion profile

source_name: SHED-exos_ replicate2


title: NS2_SOXpos

value: Non-symptomatic


title: J82_NSP_RNAseq_rep3

city: Alhambra

first: Yi-Tsung

last: Lu

address: 516 SAN PASQUAL DR

institute: University of Southern California

data_processing:
Illumina Casava1.8 was used for basecalling.
After adaptor trimming, we used STAR for alignment to hg19 using gencode v19.
Counts for each gene from the gencode19 were assigned using the Subread package’s featureCounts program with BAM files as inputs
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: J82 bladder cancer cell

growth_protocol: J82 is cultured in DMEM, 10% FBS

extract_protocol:
Trizol was used for RNA extraction.
Libraries were constructed using the KAPA mRNA HyperPrep Kit (Roche, Basel, Switzerland) using the NEXTflex DNA Barcodes (Bioo Scientific, Austin, TX).
RNA-seq, single-ended 50bp reads

treatment_protocol: We used FACS to isolated side-population and non-side population from J82 cells.

value: J82 bladder cancer cell line

tag: population

value: non-side population


title: J82_NSP_RNAseq_rep2


title: MR_042_DC_21_D98

description:
stimulated immune cells
MR_042_DC_21_D98_ATTCGCTCT-ATACCGGCA_L001

source_name: human derived dentritic cell

tag: cell type

value: human derived dentritic cell

value: 48 hours


title: Donor17

extract_protocol:
Processing of tissue was completed on ice or at 4°C for the entirety of the protocol. In brief, ~100 mg of postmortem frozen human prefrontal cortex per donor was homogenized in 2 mL homogenization buffer (10 mM Tris pH 8, 250 mM sucrose, 25 mM KCl, 5 mM MgCl2, 0.1% Triton X100, 1% RNasin Plus, 1X Protease inhibitor, and 0.1 mM DTT in DNase- and RNase-free water) using a Wheaton Dounce tissue grinder (10 strokes with loose pestle, followed by 10 strokes with the tight pestle). Then, the homogenized tissue was filtered through 30 mm pre-separation filters to remove major debris. Samples were then centrifuged at 900 xg for 10 minutes at 4°C. Nuclei were then immunolabeled for LIM/Homeobox protein (LHX2) and NeuN, and LHX2-positive/NeuN-negative nuclei were collected using a MoFlo XDP sorter with a 100 mm nozzle at 4°C. Collected nuclei were processed using the Single Cell 3’ Gene Expression kit v3 (10x Chromium) according to manufacturer’s instructions, and libraries were sequenced an Illumina NovaSeq 6000.
Sequencing libraries were prepared using the Single Cell 3’ Gene Expression kit v3 (10x Chromium) according to manufacturer’s instructions.

tag: tissue

value: Female


title: HepG2_RNA_KO_ADRminus_rep1

city: Guangzhou

first: Jian-Hua

last: Yang

address: No. 135, Xingang Xi Road

department: School of Life Sciences

institute: Sun Yat-sen University

data_processing:
RNA-seq data reads were aligned to UCSC hg38 reference genome using HISAT2 with default parameters
DESeq2 package was used to detect the differential expressed genes (p<0.05 and |FC|>2)
Assembly: hg38

growth_protocol: HepG2_KO-TP53 cells were cultured in MEM medium (GIBCO) supplemented with 10% foetal bovine serum plus antibiotics.Cells were maintained in a 5% CO2 atmosphere at 37℃.

extract_protocol:
For RNA-seq profiling, the total RNA was purified from HepG2_KO-TP53 cells with two independent samples, respectively. The total RNA was isolated from cells using the RNA isolation reagent TRIzol (Invitrogen).
RNA libraries were prepared for sequencing using standard Illumina protocols
Paired-end and strand-specific RNA-seq libraries were prepared according to Illumina’s instructions and sequenced on HiSeq X Ten (ANOROAD) with a sequence length of 150 bp.

treatment_protocol: without ADR treatment

value: TP53 protein knockout

tag: cell line


title: DMR181

source_name: anti-ScpB ChIP-seq of Apo-Soj mutant Bs cells conducted 3 h after re-suspension in sporulation salts


title: 2102EP-GFP co-cultured with HUVEC-mCherry

value: 3D co-culture with HUVEC-mCherry


title: parental rep1

description:
control
H6_p_1

value: Not transduced


title: Donor15

value: Prefrontal cortex

value: Alzheimer's disease


title: GCT72-GFP co-cultured with THP-1-M2-mCherry

value: non-seminoma germ cell tumor, yolk sac tumor


title: J82_SP_RNAseq_rep3

value: side-population


title: AD1_SOX9pos

value: Male


title: J82_SP_RNAseq_rep2


title: Donor13


title: HUVEC-mCherry co-cultured with 2102EP-GFP

value: 3D co-culture with 2102EP-GFP

value: endothelial cells


title: DMR178

source_name: anti-ScpB ChIP-seq of wt Bs cells conducted 3 h after re-suspension in sporulation salts

value: anti-ScpB


title: HepG2_RNA_KO_ADRminus_rep2


title: NS1_SOXpos

value: Non-symptomatic


title: J82_SP_RNAseq_rep1

value: J82 bladder cancer cell line


title: Donor16


title: NS3_SOXneg


title: NS3_SOXpos


title: Acly C3

first: Tatsuya

last: Kobayashi

address: 50 Blossom Street, Thier 1101

department: Endocrine Unit

institute: Massachusetts General Hospital

description: Acly C3

data_processing:
Low quality reads were filtered with adaptors and reads with unknown bases with software SOAPnuke v1.5.2 with parameters -l 15 -q 0.2 -n 0.05 -A 0.25. Mapped clean reads to mm9 reference using HISAT2 V. 2.0.4 with the parameters, --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000.
Genome_build: mm9
Supplementary_files_format_and_content: FPKM and read count

source_name: primary rib chondrocytes RNA from E18.5 mouse

growth_protocol: Primary rib chondrocytes were isolated by O/N digestion with 0.02%  collagenase II.  After removing collagenase by spinning, cells were resuspended in 10% FCS-containing DMEM and cultured for an additional day.

extract_protocol:
Cells were lysed in Trizol.  RNA was extracted by BGI, and quality was checked before sequencing
Libraries were made BGI's platform.
BGI-seq library construction method: mRNA molecules were purified from total RNA using oligo(dT) attached magnetic beads. mRNA molecules were fragmented into small pieces using fragmentation reagent. First and Second Strand cDNA synthesis. Prepare the end repair & add "A", adaptor ligation and PCR.

treatment_protocol: KO (knockout) and C (Control) were isolated from littermates

value: rib chondrocytes

value: C57BL/6-dominant mixed

tag: developmental stage

value: Acly


title: J82_NSP_RNAseq_rep1

value: non-side population


title: J82_NSP_RNAseq_rep4


title: SHED-exos_rep1

description: SHED-exos_replicate1 miRNAs expresion profile

source_name: SHED-exos_ replicate1

value: exosomes obtained from the supernatant of stem cells derived from human exfoliated deciduous teeth


title: Acly C2

description: Acly C2

tag: genotype


title: sgZNF730-MER57E3-95-2

first: Zhang

last: Tianzhe

address: Donghu Road 116, District Wuchang

department: Medical Research Institute

institute: Wuhan University

data_processing:
Bustard used for basecalling
Sequenced reads were trimmed for adaptor sequence by cutadapt ,then mapped to hg38 whole genome using HISAT2 version 2.1.0
Use the bam file and Gencode.v29.gtf (protein_coding_gene) as input of featurecounts to generate Raw_counts
Genome_build: hg38
Supplementary_files_format_and_content: TPM expression

source_name: embryonic stem cell

extract_protocol:
Total RNA of human ESCs and EPSCs were prepared in duplicate with the HiPure Total RNA Mini Kit (Magen) according to the manufacturer’s instruction.
RNA libraries were prepared by NEB Next Ultra Directional RNA Library Prep Kit for Illumina.

value: embryonic stem cell


title: sgControl-MER57E3-2


title: hESC_sgLTR5_HS-1


title: hESC_sgControl-2


title: Donor12

tag: disease state


title: sgControl-MER57E3-1


title: sgZNF730-MER57E3-95-1


title: Donor8


title: J82_SP_RNAseq_rep4


title: sgZNF730-MER57E3-53-1


title: Acly KO2

description: Acly KO2

value: Acly KO


title: iPS263 exosomes

city: Gifu City

first: Ken-ichi

last: Tezuka

state: Gifu

address: 1-1 Yanagido

department: Gifu University Graduate School of Medicine

description: exosomes purified from iPS263

hyb_protocol: hybridized to an Agilent Microarray Sure Print G3 Human miRNA 8 × 60 K miRBase 16.0 array with the miRNA Complete Labeling and Hyb Kit (Agilent Technologies, Tokyo, Japan).

scan_protocol: After hybridization for 20 h, the slides were washed with the Gene Expression Wash Buffer Kit and scanned by an Agilent Scanner.

data_processing: The images were processed and analyzed with Agilent Feature Extraction Software. The raw data were normalized by quantile normalization and then analyzed in GeneSpring GX software 12.5 (Agilent Technologies).

source_name: 263 induced pluripotent stem cells derived from exosomes

label_protocol: After dephosphorylation and denaturation, 100 ng of total RNA was labeled with cyanine 3-pCp.

growth_protocol: Using a protocol approved by the Institutional Review Board of Gifu University, we collected normal human third molars at the Gifu University Medical Hospital after having obtained informed consent from each patient. (Takeda et al. 2008). We isolated DPCs from more than 300 patients, mostly from young patients with maturing wisdom teeth. Three HHH-DPCs lines (DP74, 16-year-old-female; DP94,16-year-old-female; and DP263, 15-year-old-male) were picked up. Briefly, the pulp tissues were minced into small clumps and digested with 1 mg/mL collagenase type I (Sigma-Aldrich, St. Louis, MO, USA) for 1 hour at 37°C. We also established iPSC lines from DP74 and DP94 using episomal or lenti virus vector, respectively (Tamaoki et al. 2010; Okita et al. 2011). In this report, following the guidelines for the generation of human iPSCs approved by the Institutional Review Board of Gifu University, we used DP263 for generating iPSCs within 10 passages. Using a Sendai viral vector kit (ID Pharma, Tokyo, Japan), we generated iPSCs as reported previously (Takeda-Kawaguchi et al. 2014 ). Briefly, we first introduced Sendai viruses carrying OCT3/4, SOX2, KLF4, and c-MYC into HHH-DPCs according to the manufacturer's instruction. HHH-DPCs were seeded at 5.0×105cells/well in a 6 well plate and cultured in MSCGM medium. From the day after infection, the culture media were changed daily up to day 7. Then, the cells were dissociated using 0.05% trypsin-EDTA (Life Technologies, Tokyo, Japan), and HHH-DPCs (5.0×104 cells/6 cm dish) were seeded onto mitomycin C-treated SNL feeder layers (SNL cell line obtained from Sanger Institute, Cambridge, UK) in Primate ES cell medium (ReproCell, Tokyo, Japan) supplemented with 4 ng/ml basic fibroblast growth factor (bFGF, Wako, Osaka, Japan), and cultured for a further 14 days until colonies were ready to be picked up. Afterwards, HHH-iPSCs (iPS74, iPS94, iPS263) were cultured on mitomycin C-treated SNL feeder layers in Primate ES cell medium supplemented with 4 ng/mL bFGF at 37℃ in a humidified atmosphere containing 5% CO2.

extract_protocol: Exosomes prepared from DP74, DP94, and DP263 and iPSCs derived from these cells were subjected for miRNA isolation using miRCURY™ RNA Isolation Kit- Cells&Plant content（EXIQON, Woburn, USA) Agilent miRNA labeling system was used for RNA expression analyses.

treatment_protocol: HHH-DPCs were cultured in MSCGM medium. When they became 70 to 80% confluent, they were washed three times with PBS and medium was replaced by serum free-DMEM (SIGMA-ALDRICH, Tokyo, Japan) and cultured for 24 hours. Then, the medium was collected and filtrated 0.45μm and 0.22μm syringe filters (Minisart, Goettingen, FRG), before ultracentrifugation at 90,000 rpm for 3h at 4℃. The pellet was resuspended in PBS and stored at 80℃.  HHH-iPSCs cultured on SNL feeder cells were first replated to 6cm culture dish coated by laminin 5-1-1 (BioLamina, SUNDBYBERG, SWEDEN), replated onto another 6cm dish, and then half of the medium was replaced by fresh medium and the medium was collected after 24 hours. Exosomes were collected with the same manner with HHH-DPCs.

tag: gender

value: male


title: Donor6

value: Prefrontal cortex

value: Female


title: hESC_sgLTR5_HS-2


title: iPS74 exosomes

institute: Gifu University Graduate School of Medicine

description: exosomes purified from iPS74

source_name: 74 induced pluripotent stem cells derived from exosomes

value: female


title: Acly KO3

description: Acly KO3


title: sgZNF730-MER57E3-53-2


title: Donor11

value: Alzheimer's disease

value: Male


title: Donor10


title: DP263 exosomes

description: exosomes purified from DP263

source_name: 263 dental pulp derived from exosomes

value: dental pulp derived from exosomes


title: Donor9


title: iPS94 exosomes

description: exosomes purified from iPS94

source_name: 94 induced pluripotent stem cells derived from exosomes


title: Acly C1

description: Acly C1


title: Donor5


title: DP74 exosomes

description: exosomes purified from DP74

source_name: 74 dental pulp derived from exosomes


title: LDH C3

description: LDH C3

source_name: primary rib chondrocytes RNA from P5 mouse

value: LDH


title: Overexpression MazF6 Rep3

city: Bangalore

first: Munmun

last: Bhasin

state: Karnataka

address: CV Raman Rd

department: Molecular Biophysics Unit

country: India

institute: Indian Institute of Science

data_processing:
Data was subjected to quality control check by FastQC_v0.11.8
Reads were mapped to H37Rv genome by TopHat v2.1.1
Abundance calculations (FPKM) by Cufflink
Differential expression analysis by Cuffdiff
Visuaization of results by R
Genome_build: ASM19595v2 (H37Rv)
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for MazF6 overexpression study.

organism: Mycobacterium tuberculosis

source_name: Microbe

growth_protocol: For overexpression studies, early log phase cultures were induced were anhydrotetracycline addition for 24 hrs. For deletion strains, total RNA was isolated from mid log phase culture grown in 7H11 media.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy minikit.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Donor7

source_name: Prefrontal cortex


title: DP94 exosomes

description: exosomes purified from DP94

source_name: 94 dental pulp derived from exosomes


title: ffEPSC_sgLTR5_HS-2

city: Wuhan


title: LDH C2

description: LDH C2


title: Overexpression MazF6 Rep2


title: Acly KO1

description: Acly KO1


title: Donor3

value: Non-symptomatic


title: LDH C1

description: LDH C1


title: ffEPSC_sgLTR5_HS-1


title: hESC_sgControl-1


title: Donor4


title: Overexpression MazF6 Rep1


title: Control Rep3 (Overexpression Study)

value: pTetR-Int Vector only


title: ffEPSC_sgControl-1


title: Donor2


title: DamOnly - 15-somite embryo (KIN3845_KIN4223_index06)

city: Utrecht

first: Jop

last: Kind

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description: Raw data files include both DamID and CEL-seq reads

data_processing:
Library strategy: scDam&T-seq
Libraries are demultiplexed based on the sample-specific and readout-specific barcode present in R1, using custom pipelines (available at: https://github.com/KindLab/scDamAndTools).
DamID alignment: DamID reads are aligned using bowtie2 (v. 2.3.3.1) with the following parameters: “--seed 42 --very-sensitive -N 1”.
DamID filtering: Alignments with a MAPQ < 10 are removed.
DamID procesing: Using our own custom pipeline (see KindLab GitHub), aligned reads are matched to known GATC positions in the genome to get the number of observations per (strand-specific) GATC position.
DamID processing: GATC-position counts are deduplicated using UMI information to allow a maximum of 4 unique UMIs per GATC position.
DamID processing: Unique GATC counts are summarized in genomic intervals at the desired resolution.
CELseq alignment: CELseq reads are aligned using GRCm38 (v. 89) transcript models and tophat2 (v. 2.1.1) with the following paramters: : “--segment-length 22 --read-mismatches 4 --read-edit-dist 4 --min-anchor 6 --min-intron-length 25 --max-intron-length 25000 --no-novel-juncs --no-novel-indels --no-coverage-search --b2-very-sensitive --b2-N 1 --b2-gbar 200”.
CELseq filtering: Alignments with a MAPQ < 10 are removed.
CELseq processing: Using our own custom pipeline (see KindLab GitHub), we assign alignments to genes using a method similar to htseq-count with mode "intersection_strict".
CELseq processing: Transcript counts are deduplicated using UMI information, allowing an unlimited number of UMI-unique counts per gene.
Genome_build: mm10
Supplementary_files_format_and_content: celseq count table: count table containing UMI-unique transcript counts per gene for all single-cell samples; damid count table: count table containing UMI-unique GATC counts per 10-kb interval for all single-cell samples; sample annotation: table containing detailed sample information for all single-cell samples; sample barcodes: sample-specific and readout-specific barcodes that can be used to demultiplex the raw data. Barcodes follow a 3-NNN-3-NNN format, where "N" positions indicate the barcode-specific sequence, and the "3" indicates positions of a 3nt UMI sequence.

organism: Danio rerio

source_name: 15-somite zebrafish embryo

growth_protocol: Adult zebrafish (Danio Rerio) were maintained and embryos raised and staged as previously described (PMID: 31510859).

extract_protocol:
At 15-somite stage, embryos were transferred to 2ml Eppendorf tubes and digested with 0.1% Collagenase type II from Cl. Histolyticum (Gibco) in Hanks Balanced Salt Solution without Mg2+/Ca2+ (Thermofisher) for 20-30 mins at 32oC with constant shaking. Once embryos were noticeably digested, cell solution was spun at 2000g 5mins at room temperature and the supernatant was removed. Cell pellet was resuspended with TrypLE Express (Thermofisher) and digested for 10mins at 32oC with constant shaking. Cell solution was inactivated with 10% Fetal Bovine Serum (Thermofisher) in Hanks Balanced Salt Solution without Mg2+/Ca2+ and filtered through a 70um cell strainer (Greiner BIo-One). Cells were pelleted at 2000g 5min room temperature and washed twice with 10% Fetal Bovine Serum (Thermofisher) in Hanks Balanced Salt Solution without Mg2+/Ca2+. Hoescht at a final concentration of 16.8ug/ml was added to the cell solution and incubated for 30mins at 28oC in the dark. Solution was then filtered through a 40um cell strainer (Greiner BIo-One), Propidium iodide was added at a final concentration of 5ul/ml and immediately sorted on a FACS Influx (BD) gating for alive cells in the G2M phase into 384well plates containing primer solution.
The scDam&T protocol and library preparation was performed as previously described in detail (PMID: 32350457).

treatment_protocol: Tübingen longfin (WT) pairs were set up and the following morning, approximately 1nL of 1ng/ul Dam-Mphosph8 mRNA or 0.5ng/ul Dam-GFP mRNA was injected into the yolk at the 1 cell stage. Embryos were slowed down overnight at 23oC and the following morning all embryos were manually dechorionated.

value: 15-somite embryo

tag: dam-fusion protein

value: untethered Dam

tag: molecule subtype

value: genomic DNA; mRNA


title: LDH KO2

description: LDH KO2

value: rib chondrocytes

value: C57BL/6-dominant mixed

value: LDH KO


title: Control Rep2 (Overexpression Study)


title: Donor1_replicate2


title: LDH KO1

description: LDH KO1


title: ffEPSC_sgControl-2

value: embryonic stem cell