title: 2_DONOR 42

city: Farmington

first: Mohammed

last: Toufiq

state: Connecticut

address: 10 Discovery Drive, Farmington, CT 06032

department: Research Department

institute: The Jackson Laboratory for Genomic Medicine

data_processing:
Fluidigm Real Time PCR software (Fluidigm Corporation) was used to merge the technical runs and threshold cycle (Ct) values were processed using Partek Genomic Suite (version 7.18; Partek, USA). Genes with Ct values beyond the detectable range were set as missing values for downstream analysis. Raw data were assessed for inter- and intra- sample variation and our internal control samples were validated. Samples not passing our QC criteria were excluded. Each gene was then normalized to a validated house-keeping gene pool (DOCK2, EEF1A1, FAM105B, FTL, MYL6, MYL12B, RPS10, and RPS25) and reported as dCt and transformed to -dCt for principal component (PCA) and hierarchical clustering analyses. Fold-changes and statistical tests were calculated from the comparison of normalized gene expression of phase II vs. I (i.e. post- vs. pre-vitamin D supplementation). Unless otherwise stated, data analyses were performed in R. Missing values were estimated using missMDA (75) prior to PCA. Euclidean distances and the complete linkage method were used for the hierarchical clustering analysis. Differentially expressed genes (DEGs) between phase II and I were determined using a paired non-parametric two sample Wilcoxon test (aka Wilcoxon Signed Rank test) with the following criteria to denote significance: FC >2 and adjusted p-value <= 0.01.
Matrix_non-normalized.txt file contains non-normalized data, i.e., raw Ct values, along with the PsuedoRefGene (i.e., Geometric Mean of eight housekeeping genes).
Fold_Changes.txt reports test/control (i.e., Phase II / I (post/pre vitamin D supplementation)) ratios.

label: not provided

source_name: Whole Blood, Responders, Phase II

label_protocol: RNA quantity and purity were checked by NanoDrop (Thermo Fisher Scientific, UES) and quality was determined on the Fragment Analyzer System (Agilent, USA). Reverse transcription was performed on the isolated RNA using Fluidigm cDNA synthesis kit (Fluidigm Corporation, USA). Gene expression was performed by parallel quantitative PCR using Fluidigm BioMark HD platform (Fluidigm Corporation). The PCR reaction conditions were as follows: denaturation at 95°C for 10 minutes followed by 30 cycles at 95°C for 15 sec and 60°C for 1 min according to the protocol for gene expression. Three dynamic arrays were ran for each sample and each dynamic array included 88 genes of interest and the eight housekeeping genes.

growth_protocol: na/

extract_protocol: Total RNA from whole blood was extracted using the QIAsymphony PAXgene Blood RNA Kit (Qiagen, Germany), following the manufacturer’s recommendations.

tag: donor

value: Vitamin D deficiency

tag: gender

value: Female

value: Whole Blood

value: Vitamin D3

tag: phase

tag: response status

value: Responders


title: 2_DONOR 66

status: Public on May 19 2021

type: RNA

country: USA

molecule: total RNA

organism: Homo sapiens

tag: diagnosis

tag: tissue

tag: treatment


title: VM Veh 3

type: SRA

city: New York

first: Jordan

last: Marrocco

state: NY

address: 1230 York Ave

institute: The Rockefeller University

description:
21_S9
processed data file: limmaVoom-male-BDNF.VEH.vs.BDNF.CORT.csv

library_source: transcriptomic

data_processing:
Illumina NextSeq 500
Quality control was performed on the reads obtained from the core and reads with a score of less than 15 were discarded.
The reads were then aligned to the GRCm genome using the STAR aligner with Ensembl annotation and quantified to the gene-level using featureCounts.
The read counts were analyzed using the R/Bioconductor framework (www.R-project.org).
Differentially expressed gene (DEG) expression analysis was conducted using the Limma-Voom package.
Genome_build: mm10
Supplementary_files_format_and_content: limmaVoom files contain logFC between VEH vs CORT animals and WT vs BDNF animals

organism: Mus musculus

extract_protocol:
After rapid decapitation, brains were immediately dissected to separate the ventral hippocampus, which was rapidly flash frozen and stored at -80 °C. RNA was extracted from the ventral hippocampal tissue using Qiagen Lipid Tissue Mini Kit.
A total of  at least 200ng of RNA per replicate was prepared for sequencing by The Rockefeller University Genomics Core Facility using the Tru-Seq Stranded RNA-Seq library preparation kit (Illumina, USA). Three biological replicates were used per experimental group, comprising of RNA pooled from 2 animals each. cDNA libraries were sequenced on an Illumina NextSeq 500 in a single lane to obtain 75-bp single-end reads at an approximate sequencing depth of 35-40 million reads per sample.

treatment_protocol: At two months of age mice were randomly assigned to either vehicle- (1% ethanol) or CORT- (25mg/l, 1% ethanol) treated groups for 6 weeks of treatment.

tag: strain background

tag: Sex

value: Male

tag: genotype

value: BDNF Val66Met

value: Vehicle

value: Ventral Hippocampus


title: PFC1-A3-c58

city: London

first: Florian

last: Klimm

address: Exhibition Rd, South Kensington

country: United Kingdom

institute: Imperial College London

data_processing:
Alignment with STAR
Filtering for genes expressed in at least three cells
Filtering for cell with at least 200 genes
Genome_build: Mus_musculus.GRCm38.98
Supplementary_files_format_and_content: h5ad

source_name: germ cell

extract_protocol:
The illumina Nextera XT DNA preparation kit was used to prepare the library directly from the lysate of single cell.
The RNA library was prepared using the standard illumina protocol

treatment_protocol: Single cells were sorted in 96 well plates containing 4ul of lysis buffer and frozen on dry ice.

tag: cell type

value: germ cell

tag: developmental stage

tag: oxygen condition

value: Norm

tag: cell

value: positive


title: PFC1-A3-c57


title: PFC1-A3-c69

value: Hypo

value: negative


title: 2_DONOR 63


title: VM Veh 2

description:
20_S8
processed data file: limmaVoom-male-BDNF.VEH.vs.BDNF.CORT.csv


title: PFC1-A3-c56


title: 2_DONOR 80


title: Control_1_RNAseq

city: Suzhou

first: Lei

last: Wei

state: Jiangsu

address: Suzhou Municipal Hospital Affiliated to Nanjing Medical University, Suzhou, Jiangsu

country: China

description: mRNA

data_processing:
RNA-seq analysis: After running fastQC (0.11.8) for quality control, Cutadapt (2.1.0) was used for trimming adapters and low-quality sequence from the raw fastq files. The cleaned fastq files were then mapped to rn4 rat genome refence by STAR (2.7.0) with suggested setting. Differential expression analysis was then performed by DEseq2 (1.29.0).
smallRNA-seq analysis: Small RNA-seq data was analyzed by using sRNAnalyzer pipeline. Adapter sequences was provided as input to the pipeline for removing adapter contamination. The cleaned reads were then mapped to rat miRNA database to generate count matrix, which was further analyzed by DEseq2 to identify differentially expressed miRNA.
Bisulfite-seq analysis: TrimGalore (0.6.4) was used for sequencing data quality control, adapter removing and trimming low-quality sequence. The cleaned data was then mapped to the rn4 rat genome reference by using Bismark (0.22.0). The generated CpG methylation ratios were then used as input for metilene to call differentially methylated regions (DMRs).
Genome_build: rn4
Supplementary_files_format_and_content: rawcount file of each sample for RNA-seq and smallRNA-seq data in txt file
Supplementary_files_format_and_content: mean methylation of DMR of each sample for target Bisulfite-seq in bed file

organism: Rattus norvegicus

source_name: dorsal root ganglion

extract_protocol:
DRG tissues from 10 randomly selected pairs of CFA-treated and untreated rats were extracted.
NEBNext Ultra RNA with Poly-A selection
NEBNext Multiplex Small RNA Library Prep Kit for Illumina

treatment_protocol: The SD rats were maintained in a standardized feeding environment under a 12-hour light-dark cycle at an ambient temperature of 24 ± 1°C. The CFA-induced chronic inflammatory pain model was established through unilateral subcutaneous injections of 0.1 mL CFA into the sterile foot skin, as described in our previous research

value: no treatment


title: PFC1-A3-c55


title: PFC1-A3-c54


title: 2_DONOR 39


title: PFC1-A3-c63


title: VM Veh 1

description:
19_S7
processed data file: limmaVoom-male-BDNF.VEH.vs.BDNF.CORT.csv


title: PFC1-A3-c53


title: PFC1-A3-c52


title: VV CORT 3

description:
18_S6
processed data file: limmaVoom-male-WT.VEH.vs.WT.CORT.csv

source_name: Wild Type_CORT_Ventral Hippocampus

value: Wild Type

value: CORT


title: PFC1-A3-c50


title: PFC1-A3-c51


title: VV CORT 2

description:
17_S5
processed data file: limmaVoom-male-WT.VEH.vs.WT.CORT.csv


title: PFC1-A3-c48


title: VV CORT 1

description:
16_S4
processed data file: limmaVoom-male-WT.VEH.vs.WT.CORT.csv


title: PFC1-A3-c47


title: PFC1-A3-c46


title: PFC1-A3-c45


title: 2_DONOR 28

value: Vitamin D deficiency


title: VV Veh 2

description:
14_S2
processed data file: limmaVoom-male-WT.VEH.vs.WT.CORT.csv

source_name: Wild Type_Vehicle_Ventral Hippocampus


title: PFC1-A3-c43


title: 2_DONOR 10

value: Female


title: VV Veh 3

description:
15_S3
processed data file: limmaVoom-male-WT.VEH.vs.WT.CORT.csv


title: VV Veh 1

description:
13_S1
processed data file: limmaVoom-male-WT.VEH.vs.WT.CORT.csv


title: PFC1-A3-c42


title: PFC1-A3-c44


title: 2_DONOR 100

value: Whole Blood


title: 2_DONOR 76

value: Vitamin D3


title: PFC1-A3-c41


title: 2_DONOR 46

value: Responders


title: 2_DONOR 59


title: PFC1-A3-c40


title: PFC1-A3-c39


title: 2_DONOR 01


title: MibrT3 Treg co-cultured 3

city: Pittsburgh

first: Xiaoming

last: Hu

state: PA

address: 200 lothrop street

department: Neurology

institute: University of Pittsburgh

data_processing:
STAR (https://github.com/alexdobin/STAR) to align the trimmed reads to mouse reference genome sequences (GRCm38.95) and to annotate the reads.
We applied HTSeq (version: 0.11.2) to quantify the gene expression by number of read counts.
The abundance of mapped reads is expressed as Fragment Per Kilobase of transcript per Million mapped reads (FPKM) format.
We used R software (version: 3.6.0) with several packages for the bioinformatics analysis.
Genome_build: GRCm38.95

source_name: Primary microglia

extract_protocol:
Frozen cell pellet samples were disrupted in Trizol®. Chloroform was added to the reaction and mixed vigorously. Following phase separation by centrifuging for 15 minutes at 12,000g, the aqueous phase was removed to a clean microcentrifuge tube. RNA was precipitated by isopropanol and pelleted by centrifugation for 10 minutes at 12,000g. The SMART-Seq HT Kit was used to generate cDNA from total RNA
The sequencing library was constructed by following the Illumina Nextera XT Sample Preparation Guide. One nanogram of input cDNA was tagmented (tagged and fragmented) and amplified using the Illumina Nextrera XT kit. Sequence libraries of each sample were finally equimolarly pooled and sequenced on an Illumina Nextseq 500 system, using a paired-end 75-bp strategy.

tag: strain

value: Treg co-cultured


title: PFC1-A3-c49


title: MibrT2 Treg co-cultured 2


title: 2_DONOR 37


title: 2_DONOR 98


title: PFC1-A3-c37


title: PFC1-A3-c36


title: PFC1-A3-c35


title: MibrT1 Treg co-cultured 1


title: 2_DONOR 67


title: PFC1-A3-c34


title: PFC1-A3-c33


title: PFC1-A3-c32


title: 2_DONOR 44


title: 2_DONOR 35


title: Mi3 Control 2

value: Control


title: Mi2 Control 1


title: PFC1-A3-c30


title: PFC1-A3-c31


title: 2_DONOR 16


title: sham blood 2

source_name: Treg

extract_protocol:
500-1000 cells were sorted to a plate with lysis buffer. cDNA was generated from cell lysis using the SMART-Seq Ultralow Input RNA Kit (Qiagen).
The sequencing library was constructed by following the Illumina Nextera XT Sample Preparation Guide. One nanogram of input cDNA was tagmented (tagged and fragmented) and amplified using the Illumina Nextrera XT kit. Sequence libraries of each sample were finally equimolarly pooled and sequenced on an Illumina Nextseq 500 system, using a paired-end 75-bp strategy.

tag: allelic composition

tag: age

value: 9-week old

tag: genetic background

value: blood

value: Sham


title: PFC1-A3-c38

value: germ cell

value: Norm


title: 2_DONOR 08

tag: donor

tag: gender


title: PFC1-A3-c27

value: positive


title: PFC1-A3-c28


title: PFC1-A3-c26


title: PFC1-A3-c25


title: sham blood 1


title: PFC1-A3-c24


title: 2_DONOR 97

tag: phase

tag: response status


title: 2_DONOR 84

tag: diagnosis

tag: tissue


title: Mi4 Control 3

tag: treatment


title: PFC1-A3-c23


title: PFC1-A3-c22


title: tMCAO blood 1

value: transient (60 min)middle cerebral artery occlusion (tMCAO)


title: PFC1-A3-c21


title: 2_DONOR 74


title: PFC1-A3-c29


title: tMCAO brain 2

value: brain


title: PFC1-A3-c19


title: 2_DONOR 43


title: tMCAO brain 1


title: PFC1-A3-c18


title: 2_DONOR 23


title: PFC1-A3-c16

value: negative


title: PFC1-A4-c7


title: 2_DONOR 15


title: PFC1-A3-c14


title: PFC1-A3-c13


title: tMCAO blood 2


title: PFC1-A3-c12


title: 2_DONOR 07


title: PFC1-A3-c11


title: 2_DONOR 96


title: FACS sorted WT monocytes from the CNS of mice with EAE replicate 1

city: PHILADELPHIA

first: Adam

last: Ertel

address: 233 S 10TH ST

department: Cancer Biology

institute: Thomas Jefferson University

data_processing:
Bases were trimmed from R2 reads per the library kit recommendations (Takara SMARTer Stranded Total RNA-Seq kit v2 Pico input)
Paired-end reads were aligned quantified against GRCm38/GENCODE.M18 reference annotations using RSEM-STAR (RSEM v1.2.31, STAR 2.6.0c) in strand-specific mode with parameters --strand-specific --forward-prob 0
Genome_build: GRCm38
Supplementary_files_format_and_content: .genes.results files from RSEM-STAR include columns with Ensembl gene_id, transcript_id(s), length, effective_length, expected_count, TPM, FPKM

source_name: monocytes from the CNS of mice

growth_protocol: Recipient GFP+ mice were lethally irradiated with 2 x 550 Rad with a 12 h interval between  irradiations. Mice received 5 x 10^6 BM cells from WT (CD45.1) and Ifnar1-/- (CD45.2) mice in a 1:1ratio (total 1 x 10^7 cells). Chimeric mice were used for EAE induction 6-7 weeks after BM cell transfer.

extract_protocol:
At disease peak, WT (CD45.1) and Ifnar1-/- (CD45.2) monocytes (GFP-CD45+CD11b+Ly6ChiLy6G-) were FACS sorted from the CNS of mice, and RNA was extracted.
Takara SMARTer Stranded Total RNA-Seq kit v2 Pico input

treatment_protocol: Mice with EAE were treated with IFN-b (30000 IU) daily

value: WT


title: PFC1-A3-c10


title: FACS sorted WT monocytes from the CNS of mice with EAE replicate 3


title: FACS sorted WT monocytes from the CNS of mice with EAE replicate 2


title: 2_DONOR 82

value: Vitamin D deficiency


title: PFC1-A3-c17


title: PFC1-A3-c9


title: PFC1-A3-c8


title: FACS sorted Ifnar1-/- monocytes from the CNS of mice with EAE replicate 2


title: PFC1-A3-c7


title: PFC1-A3-c20


title: PFC1-A3-c6


title: 2_DONOR 65

value: Female


title: 2_DONOR 73

value: Whole Blood


title: PFC1-A3-c4


title: FACS sorted Ifnar1-/- monocytes from the CNS of mice with EAE replicate 1


title: PFC1-A4-c4


title: lung endothelium treated with tumor extracellular vesicles (TEVs) plus reserpine replicate 2

city: Philadelphia

first: daniel

last: beiting

address: 380 S. University Ave

department: Pathobiology

institute: University of Pennsylvania

data_processing:
Raw reads from fastq files were mapped to the mouse reference transcriptome (Ensembl; ; Mus musculus version 79, GRCh38 Release 102) using Kallisto, version 0.45.0
All subsequent analyses were carried out using the statistical computing environment, R version 4.0.0 in RStudio version 1.1.453 and Bioconductor version 3.11.1
Transcript-level counts and abundance data were imported into R and summarized to gene level using the TxImport package
Data was normalized using the TMM method in EdgeR
Normalized data was variance stabilized using the VOOM function in limma
Differentially expressed genes (FC>2 and FDR<.01) were identified on filtered-normalized, not batch-corrected gene expression matrix by linear modeling and Bayesian statistics using the Limma package
Genome_build: Ensembl; Mus musculus version 79, GRCh38 Release 102
Supplementary_files_format_and_content: Tab-delimited text raw data includes raw gene counts summarized by tximport package
Supplementary_files_format_and_content: Tab-delimited text filtered normalized data includes gene expression for each sample after normalization with EdgeR package (TMM method)

molecule: polyA RNA

source_name: lung

growth_protocol: Before treatment, endothelial cells were isolated from 3 weeks age mice and cultrured in advanced DMEM media contained 15% FBS,1%Glutamine,1%penicillin-streptomycin,0.1mg/ml endothelial cell growth factor and 0.5 mg/ml heparin sodium

extract_protocol:
Cells were collected and RNA were extracted by using Trizol reagent.
Sequencing libraries were prepared with the TruSeq mRNA and sequenced on an Illumina NextSeq 500 to produce 75 bp single-end reads
RNA quality and quantity were assessed Tapestation 2100 and Qubit 3, respectively.

tag: host sex

value: female

tag: host strain

tag: treatment group

value: TEV and reserpine


title: 2_DONOR 33

value: Vitamin D3

value: Responders


title: PFC1-A3-c3

tag: cell type

tag: developmental stage


title: lung endothelium treated with tumor extracellular vesicles (TEVs) plus reserpine replicate 1


title: FACS sorted Ifnar1-/- monocytes from the CNS of mice with EAE replicate 3


title: PFC1-A3-c1

tag: oxygen condition

tag: cell


title: 2_DONOR 14


title: PFC1-A2-c96

value: Hypo


title: lung endothelium treated with tumor extracellular vesicles (TEVs) replicate 2

value: TEV


title: PFC1-A2-c94


title: PFC1-A2-c95


title: lung endothelium treated with tumor extracellular vesicles (TEVs) replicate 1


title: PFC1-A2-c93


title: PFC1-A3-c5


title: lung endothelium treated with vehicle alone replicate 2

value: control


title: PFC1-A2-c92

value: germ cell


title: PFC1-A2-c91


title: 2_DONOR 95


title: lung endothelium treated with vehicle alone replicate 1


title: PFC1-A2-c90


title: 2_DONOR 81


title: PFC1-A2-c88


title: PFC1-A2-c89


title: Induced TLR2 Knockout - Heart 3

city: Cleveland

first: Michael

last: McCoy

state: OH

address: 9500 Euclid Ave

department: Neuroscience

institute: Cleveland Clinic Foundation

description: Experimental

data_processing:
A quality check with an Agilent 2100 Bioanalyzer
~20 million reads per sample; 2x75bp single end
Quality of the data was assessed using FastQC (v0.11.7) quality control analysis tool
Data were aligned to the mm10 mouse reference genome using Bowtie 2 (v2.3.4.1) alignment tool
Sequence reads were assigned to genomic features using featureCounts program (v1.6.3)
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM and TPM values for each sample

source_name: Cardiac Lysate

extract_protocol:
Hearts were removed and flash frozen in liquid nitrogen. RNA was isolated according to mmanufacturer's protocol from Qiagen's RNA Sequencing kit.
Truseq Stranded mRNA LT (Illumina) - rRNA Depletion (RiboZero), Synthesize first strand cDNA, Synthesize second strand cDNA, Adenylate 3' ends, Adapter ligation, Enrich DNA Fragments

treatment_protocol: Tamoxifen-fed for 5 days from p1 to p6

tag: strain

tag: agent

value: tamoxifen

tag: genotype

value: Cdh5-Cre Ert2 TLR2 lox/lox


title: 2_DONOR 54

tag: donor


title: PFC1-A2-c87

value: positive


title: PFC1-A3-c2

value: Norm


title: PFC1-A2-c86


title: Induced TLR2 Knockout - Heart 2

description: Experimental


title: 2_DONOR 13

tag: gender


title: PFC1-A2-c85


title: 2_DONOR 06

tag: phase


title: 2_DONOR 21

tag: response status


title: PFC1-A2-c83


title: PFC1-A2-c82


title: Induced TLR2 Knockout - Heart 1

description: Experimental


title: Flox TLR2 - Heart 3

description: Control

value: TLR2 lox/lox


title: 2_DONOR 05

tag: diagnosis


title: PFC1-A2-c81


title: PFC1-A2-c80

value: negative


title: Flox TLR2 - Heart 2

description: Control


title: 2_DONOR 94

value: Vitamin D deficiency

tag: tissue


title: 2_DONOR 71

value: Female

tag: treatment


title: Flox TLR2 - Heart 1

description: Control


title: PFC1-A2-c79


title: PFC1-A2-c78


title: 2_DONOR 61

value: Whole Blood


title: PFC1-A2-c75


title: PFC1-A2-c84


title: PFC1-A2-c73


title: PFC1-A2-c72


title: PFC1-A2-c76


title: 2_DONOR 31


title: PFC1-A2-c77


title: PFC1-A2-c71


title: 2_DONOR 20


title: 2_DONOR 53


title: dMQ1 T1-1 BSPCR [P1_T1_1]

city: Los Angeles

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

library_source: genomic

data_processing:
For BS-PCR samples, reads were pre-processed by a custom script to keep only reads flanked by correct primer sequence and to truncate the primer sequences from each read. Pre-processed reads were mapped to TAIR10 using Bismark and processed into per-position methylation data.
For BS-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using Bismark, and PCR duplicates were removed using a custom Bismark script. A bismark function was used to process alignments into per-position methylation data.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR, and only uniquely mapped reads were kept. Presumed PCR duplicates were removed using MarkDuplicates from the Picard tools suite. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 1 --normalizeUsing CPM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq and BSPCR, processed files are BED-like files containing per-position DNA methylation data over the primer-amplified regions (one file each for cytosines in the CG, CHG and CHH context). These files are in BED-like format and have 6 fields: chromosome, position of cytosine (0-based index), position+1, number of unmethylated reads, number of methylated reads, and percent methylated reads. For RNA-seq, count files are text files listing gene IDs and the number of overlapping reads (by htseq-count) in the first and second column, respectively. Coverage tracks are bigWig files and contain per-position sequencing coverage data for each RNA-seq library.

molecule: genomic DNA

organism: Arabidopsis thaliana

source_name: dMQ1 T1-1 BSPCR

growth_protocol: Plants were grown under long-day conditions (16h light/8h dark) at 23°C in controlled growth chambers.

extract_protocol:
CTAB-based method was used to extract DNA
Qiagen EpiTect bisulfite kit was used to treat DNA per manufacturer’s instruction. Libraries were made from purified PCR products amplified by using previously described primers (Gallego-Bartolomé et al. 2019) using an Ovation Ultralow V2 kit (NuGEN).

tag: ecotype background

tag: genetic background

value: fwa

tag: transgene present

value: yes (dMQ1)

tag: generation

value: rosette stage

value: rosette leaf


title: PFC1-A2-c70

tag: cell type

tag: developmental stage

value: Hypo


title: MQ1v T1-7 BSPCR [P1_T1_7]

source_name: MQ1v T1-7 BSPCR

value: yes (MQ1v)


title: PFC1-A2-c68

tag: oxygen condition

tag: cell


title: PFC1-A2-c69


title: hippocampal_CA1-sh-3

city: Shanghai

first: Weiwei

last: Xian

address: Dongan Road 131

institute: Fudan University

data_processing:
Illumina Casava1.7 software used for basecalling.
The Skewer software was used to dynamically remove the adapter sequence fragments and low-quality fragments from the 3'end of the sequencing data, and the FastQC software was used to perform quality control analysis on the preprocessed data and count the base ratios of Q20 and Q30.
For all samples, StringTie software was used to count the original sequence counts of known genes, and the expression of known genes was calculated using FPKM-Fragments Per Kilobase of transcript per Million fragments mapped.The DESeq2 software was used to screen the differentially expressed genes between different sample groups, and the differential expression range of |log2FC| >= 1 and Pvalue <= 0.05 was used to screen the differentially expressed genes between the two groups.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Neural progenitor cells

growth_protocol: Primary hippocampal neurons were prepared from E14.5 wild-type embryonic brain，plated at a density of 2-5 × 104 cells / well on coverslips coated with poly-L-lysine (Sigma, P9155) in advance in 24-well plate, and cultured on a neurobasal medium supplemented with 2% B27 supplement, 1% GlutaMAX-1.

extract_protocol:
RNA was harvested using Trizol reagen,dissolved it in a suitable volume of RNase-free water, and determined the RNA concentration with a spectrophotometer.
RNA libraries were prepared for the paired-end sequencing mode of the Illumina Hiseq sequencing platform to perform high-throughput sequencing on multiple samples

treatment_protocol: cultured neurons at days in vitro (DIV) 3 were infected with either AAV2-scramble-GFP or AAV2-shBrpf1-GFP，while AAV2-scramble-GFP and AAV2-shBrpf1-GFP were injected into left and right hippocampal CA1 of four-week-old mice

tag: strain

tag: development stage

value: 8 weeks after birth

value: Nerve tissue


title: 2_DONOR 12

tag: donor

value: Vitamin D3

value: Responders


title: 2_DONOR 93

tag: gender


title: PFC1-A2-c66

value: germ cell


title: PFC1-A2-c67


title: PFC1-A2-c65


title: PFC1-A2-c74


title: hippocampal_CA1-sh-1


title: MQ1v T1-3 BSPCR [P1_T1_3]

source_name: MQ1v T1-3 BSPCR


title: PFC1-A2-c64

value: positive


title: 2_DONOR 79

tag: phase


title: hippocampal_CA1-sc-3


title: PFC1-A2-c63


title: 2_DONOR 70

tag: response status


title: PFC1-A2-c62


title: hippocampal_CA1-sc-2


title: PFC1-A2-c61


title: PFC1-A2-c60


title: PFC1-A2-c59


title: hippocampal_CA1-sc-1


title: hippocampal_CA1-sh-2


title: PFC1-A2-c58


title: PFC1-A2-c57


title: PFC1-A2-c56


title: hippocampal_neurons-sh-3

value: embryonic day 18-19


title: 2_DONOR 60

tag: diagnosis


title: 2_DONOR 52

tag: tissue


title: hippocampal_neurons-sh-2

tag: treatment


title: 2_DONOR 38


title: PFC1-A2-c55


title: 2_DONOR 29


title: PFC1-A2-c54


title: hippocampal_neurons-sh-1


title: 2_DONOR 03


title: PFC1-A2-c53


title: hippocampal_neurons-sc-3


title: PFC1-A2-c50


title: PFC1-A2-c52


title: 2_DONOR 92


title: hippocampal_neurons-sc-2


title: 2_DONOR 78


title: PFC1-A2-c49


title: PFC1-A2-c48

value: negative


title: hippocampal_neurons-sc-1


title: PFC1-A2-c47


title: PFC1-A2-c46


title: PFC1-A2-c45


title: PFC1-A2-c44


title: PFC1-A2-c43


title: 2_DONOR 18

value: Vitamin D deficiency


title: 2_DONOR 02

value: Female


title: PFC1-A2-c42


title: PFC1-A2-c41


title: PFC1-A2-c40


title: PFC1-A2-c51


title: 2_DONOR 99

value: Whole Blood


title: 2_DONOR 91


title: PFC1-A2-c38


title: PFC1-A2-c37


title: PFC1-A2-c39


title: PFC1-A2-c36


title: SF1_VMH_B2

city: Ann Arbor

first: Martin

middle: G

last: Myers Jr

state: MI

address: 1000 Wall St

institute: University of Michigan

data_processing:
read filtering for phred score of 20 with fastx_toolkit 0.0.14
read alignment with STAR 2.7.3a
Genome_build: GRCm38 v92
Supplementary_files_format_and_content: CSV file of counts from STAR

source_name: Ventromedial hypothalamus

growth_protocol: Chow with ad libitum food

extract_protocol:
Mice were euthanized, the VMH was dissected, and ribosomes were isolated using an anti-GFP-coated bead
Illumina TruSeq LT

value: Ventromedial hypothalamus

tag: fraction

value: Bead


title: SF1_VMH_S3

value: Supernatant


title: SF1_VMH_S2


title: SF1_VMH_S1


title: 2_DONOR 68


title: 2_DONOR 58


title: SF1_VMH_B1


title: 2_DONOR 47


title: Sample_J

data_processing:
alignment, mapping, and demultiplexing with cellranger
Genome_build: GRCm38
Supplementary_files_format_and_content: sparse matrix of counts with associated barcodes and features

extract_protocol:
Mice were euthanized, the VMH was dissected, nuclei were isolated, and submitted to 10x library preparating and sequencing
10x 3’ Gene Expression


title: 2_DONOR 36


title: PFC1-A2-c33


title: PFC1-A2-c32


title: Sample_I


title: 2_DONOR 25


title: PFC1-A2-c30


title: SF1_VMH_B3


title: PFC1-A2-c29


title: PFC1-A2-c28


title: 2_DONOR 09


title: 2_DONOR 17


title: PFC1-A2-c27


title: Sample_G


title: PFC1-A2-c35


title: PFC1-A2-c26


title: Sample_F


title: PFC1-A2-c25


title: Sample_E


title: 2_DONOR 90

source_name: Whole Blood, Non-Responders, Phase II


title: PFC1-A2-c24


title: PFC1-A2-c34


title: PFC1-A3-c15

value: Norm


title: PFC1-A2-c21

value: Hypo


title: Sample_D


title: PFC1-A2-c31


title: 2_DONOR 57


title: Sample_H


title: 2_DONOR 75


title: Sample_C


title: PFC1-A2-c20


title: PFC1-A2-c19


title: PFC1-A2-c18


title: Sample_B


title: 2_DONOR 24


title: PFC1-A2-c16


title: Vglut-LepRb_VMH_S1


title: PFC1-A2-c23


title: 2_DONOR 34


title: PFC1-A2-c15


title: 2_DONOR 55


title: Vglut-LepRb_VMH_B1


title: VglutLepR_VMN_S


title: PFC1-A2-c22


title: PFC1-A2-c11


title: 2_DONOR 72


title: PFC1-A2-c13


title: 2_DONOR 22


title: PFC1-A2-c12


title: PFC1-A2-c10


title: VglutLepR_VMN_B


title: PFC1-A2-c17


title: PFC1-A2-c9


title: PFC1-A2-c8


title: PFC1-A2-c7


title: PFC1-A2-c6


title: PFC1-A2-c5


title: VMHCRLepLepR

data_processing:
read filtering for phred score of 20 with fastx_toolkit 0.0.14
read alignment with STAR 2.7.3a
Genome_build: GRCm38 v100
Supplementary_files_format_and_content: CSV file of counts from STAR

treatment_protocol: PBS or Leptin intraperitoneal injection

value: Leptin


title: VMHCRLepNon


title: 2_DONOR 40


title: 2_DONOR 04


title: PFC1-A2-c4


title: 2_DONOR 19


title: 2_DONOR 11


title: VMHCRPBSNon

value: PBS


title: VMHCRPBSLepR


title: PFC1-A2-c2


title: PFC1-A1-c96


title: 2_DONOR 69


title: PFC1-A1-c95


title: PFC1-A1-c93


title: PFC1-A1-c92


title: 14d after tMCAO 2

description: Sorted CD45 positive cells

data_processing:
Single cell RNA-seq raw data were processed by Cell Ranger version 3.0.1 (10X Genomics) and aligned to the GRCm38 (mm10) mouse reference genome
Seurat V2.3.4 was used for the downstream analysis, including tSNE, heatmap, and violin plots
We used R software (version: 3.6.0) with several packages for the bioinformatics analysis.
Genome_build: GRCm38.95

source_name: Brain CD45+ immune cell

extract_protocol:
Ischemic hemispheres were perfused with ice-cold saline and freshly harvested at 5 or 14 days after tMCAO. Single cell suspensions were prepared for flow cytometry. Single cells were incubated with anti-CD45-PE-Cy5 antibody for 30 minutes on ice at 4 ℃ in the dark. The CD45high cells were sorted by FACSAriaTM (BD Bioscience).
Single live cells were separated into Gel bead in emulsion (GEM)s formed by oil micro-droplets by the Chromium instrument (10X Genomics) using Single Cell 3' v2 reagents. Each GEM contains a gel bead and a cell. A greater than 1000-fold excess of partitions compared to cells assures that most GEMs were only one cell/GEM. The reaction mixture/emulsion with captured and barcoded mRNAs were removed from the Chromium instrument followed by reverse transcription. The cDNA samples were fragmented and amplified per 10X protocol. The libraries were then purified, quantified, and sequenced on an Illumina HiSeq.

tag: model

value: tMCAO

tag: days after tmcao


title: 14d after tMCAO 1

description: Sorted CD45 positive cells


title: PFC1-A1-c91


title: 5d after tMCAO 2

description: Sorted CD45 positive cells


title: DONOR 80

source_name: Whole Blood, Responders, Phase I


title: PFC1-A1-c90

source_name: germ cell


title: DONOR 63


title: 5d after tMCAO 1

description: Sorted CD45 positive cells


title: PFC1-A1-c88


title: PFC1-A1-c89


title: cDC1s, o_WT3

city: Madrid

first: Manuel

middle: J

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using Casava v1.8.2.
Illumina and SMARTer adapter contaminations were removed from reads using Cutadapt v1.3.
Preprocessed reads were mapped and quantified on the transcriptome using RSEM v1.2.3.
Genome_build: GRCm38 assembly, Ensembl genebuild 91
Supplementary_files_format_and_content: Matrix_table.xls file contains ENSEMBL gene Ids and TMM-Normalized counts per million for each sample.

growth_protocol: Experiments were conducted using dendritic cells purified from B16F10 tumors implanted in WT or DNGR-1-deficient (Clec9agfp/gfp) mice. One day later, were inoculated with B16F10 tumors. At day 13 of tumor development, tumors were collected and single cell suspensions were obtained. A prepurification of CD11c+ cells was performed using Miltenyi's mouse CD11c MicroBeads UltraPure, and cDC1s were FACS-sorted as CD45+MHCII+Ly6C-F4/80-CD24+CD11b-CD103+.

extract_protocol:
RNA was isolated using RNeasy Micro Kit RNA Isolation Kit (QIAGEN)
cDNA libraries were generated using SMARTer RNA-Seq system (ClonTech).
RNA-seq libraries were generated using the Nextera XT DNA library preparation kit (Illumina). Libraries were sequenced (single-end mode and length of 61 bp) on the Illumina HiSeq 2500 system.

treatment_protocol: Mice were hydrodynamically injected with a Flt3L-encoding plasmid (FL) or an empty plasmid (control) one day before injection of B16F10 tumor cells.

value: Tumor-infiltrating CD103+ dendritic cells

tag: genotype

value: WT

value: Empty vector


title: PFC1-A2-c1

tag: cell type

value: germ cell


title: cDC1s, o_WT2


title: PFC1-A1-c87

tag: developmental stage

value: positive


title: PFC1-A1-c84

tag: oxygen condition


title: DONOR 59

value: Responders


title: DONOR 100

value: Vitamin D deficiency


title: PFC1-A1-c94

tag: cell


title: PFC1-A1-c85


title: DONOR 76

value: Female


title: PFC1-A1-c83


title: PFC1-A1-c82


title: cDC1s, o_KO3


title: PFC1-A1-c81


title: cDC1s, o_WT1


title: PFC1-A1-c80

value: negative


title: PFC1-A1-c79


title: DONOR 46

value: Whole Blood


title: PFC1-A1-c78


title: PFC1-A2-c3


title: cDC1s, o_KO1


title: PFC1-A1-c86


title: PFC1-A1-c77


title: PFC1-A1-c76


title: DONOR 39


title: DONOR 37


title: cDC1s, mFLex_WT3

value: FL


title: PFC1-A1-c75


title: PFC1-A1-c74


title: cDC1s, mFLex_WT2


title: PFC1-A1-c73


title: DONOR 66


title: PFC1-A1-c72


title: PFC1-A1-c71


title: cDC1s, mFLex_WT1


title: DONOR 28


title: cDC1s, o_KO2


title: DONOR 01


title: PFC1-A1-c70


title: cDC1s, mFLex_KO3


title: cDC1s, mFLex_KO2


title: DONOR 92


title: DONOR 82


title: PFC1-A1-c66


title: cDC1s, mFLex_KO1


title: PFC1-A2-c14


title: DONOR 10


title: DONOR 73


title: PFC1-A1-c64


title: PFC1-A1-c63


title: DONOR 65


title: PFC1-A1-c61


title: DONOR 44


title: PFC1-A1-c59


title: PFC1-A1-c69


title: PFC1-A1-c58


title: PFC1-A1-c60


title: PFC1-A1-c68


title: PFC1-A1-c67


title: DONOR 35


title: DONOR 16


title: PFC1-A1-c56


title: DONOR 08


title: PFC1-A1-c55


title: PFC1-A1-c53


title: PFC1-A1-c54


title: DONOR 91


title: DONOR 99


title: DONOR 42


title: PFC1-A1-c51


title: PFC1-A1-c62


title: PFC1-A1-c50


title: PFC1-A1-c52


title: PFC1-A1-c57


title: PFC1-A1-c49


title: PFC1-A1-c46


title: PFC1-A1-c47


title: MDSC mobilized_8

city: Rome

first: Andrea

last: Pelosi

state: RM

address: Viale di San Paolo, 15

department: Laboratories

country: Italy

institute: Ospedale Pediatrico Bambino Gesù

description: gene expression data from purified MDSC (mobilized donor)

hyb_protocol: Biotynilated RNA was  hybridized to a HT HG-U133+ PM 16-Array Plate (Thermo Fisher Scientific). The hybridization, wash and staining procedures were done in according to the manufacturer’s protocol (Thermo Fisher Scientific).

scan_protocol: The scanning procedure was done in a GeneTitan™ Instrument (Thermo Fisher Scientific).

data_processing: The .cel file output were used as input in Partek Genomics Suite software (Partek®) for generation of quantile normalized data with RMA alghoritm.

label: biotin

source_name: MDSC purified from peripheral blood of G-CSF mobilized donor

label_protocol: Biotynilated cRNA was preparated by GeneChip 3' IVT Plus Reagent Kit

extract_protocol: Total RNA extraction, including on-column Dnase I digestion, was performed with miRNeasy mini kit, following manufacturer's instructions.

treatment_protocol: Mononuclear cells from apheresis (mobilized healthy donors) or from buffy coat (non-mobilized healthy donors) were obtained after density gradient centrifugation, followed by MDSC purification with CD66b microbeads kit as manufacturer instructions. Purified cells were washed in PBS before cell lysis for RNA extraction.

tag: donor type

value: healthy, G-CSF mobilized

value: peripheral blood

value: myeloid-derived suppressor cells (MDSC)


title: PFC1-A1-c48

value: Norm


title: MDSC mobilized_6


title: MDSC mobilized_7


title: PFC1-A1-c45


title: DONOR 54


title: MDSC mobilized_5


title: DONOR 81


title: PFC1-A1-c44


title: PFC1-A1-c43


title: MDSC mobilized_4


title: PFC1-A1-c42


title: DONOR 23


title: DONOR 43


title: MDSC mobilized_3


title: PFC1-A1-c41


title: MDSC mobilized_1


title: MDSC mobilized_2


title: MDSC control_5

description: gene expression data from purified MDSC (non-mobilized donor)

source_name: MDSC purified from peripheral blood of healthy donor

value: healthy, non-mobilized


title: PFC1-A1-c40


title: PFC1-A1-c39


title: MDSC control_3


title: MDSC control_2


title: PFC1-A1-c38


title: PFC1-A1-c37


title: DONOR 07


title: PFC1-A1-c36


title: DONOR 98


title: DONOR 71


title: PFC1-A1-c35


title: PFC1-A1-c34


title: MDSC control_1


title: PFC1-A1-c33


title: PFC1-A1-c32


title: DONOR 15


title: PFC1-A1-c30


title: DONOR 61


title: PFC1-A1-c31


title: MDSC control_4


title: Old-irradiated-rep6

first: Constantinos

last: Broustas

address: 630 168th Street

department: Center for Radiological Research

institute: Columbia University

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 µl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k v.2 array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 12.0.2 (Agilent) using default parameters (protocol GE1_1200_Jun14 and Grid: 026655_D_F_20140728) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was purified following the PAXgene RNA kit recommendations with on-column DNase I treatment

treatment_protocol: Blood was collected by cardiac puncture at the time of euthanasia 24 h post-irradiation. Each sample  was added to a 15 ml centrifuge tube that contained of PAXgene Blood RNA stabilization and lysis solution and mixed thoroughly

value: male

tag: strain


title: PFC1-A1-c29


title: PFC1-A1-c28


title: Old-irradiated-rep5


title: DONOR 33

data_processing:
Fluidigm Real Time PCR software (Fluidigm Corporation) was used to merge the technical runs and threshold cycle (Ct) values were processed using Partek Genomic Suite (version 7.18; Partek, USA). Genes with Ct values beyond the detectable range were set as missing values for downstream analysis. Raw data were assessed for inter- and intra- sample variation and our internal control samples were validated. Samples not passing our QC criteria were excluded. Each gene was then normalized to a validated house-keeping gene pool (DOCK2, EEF1A1, FAM105B, FTL, MYL6, MYL12B, RPS10, and RPS25) and reported as dCt and transformed to -dCt for principal component (PCA) and hierarchical clustering analyses. Fold-changes and statistical tests were calculated from the comparison of normalized gene expression of phase II vs. I (i.e. post- vs. pre-vitamin D supplementation). Unless otherwise stated, data analyses were performed in R. Missing values were estimated using missMDA (75) prior to PCA. Euclidean distances and the complete linkage method were used for the hierarchical clustering analysis. Differentially expressed genes (DEGs) between phase II and I were determined using a paired non-parametric two sample Wilcoxon test (aka Wilcoxon Signed Rank test) with the following criteria to denote significance: FC >2 and adjusted p-value <= 0.01.
Matrix_non-normalized.txt file contains non-normalized data, i.e., raw Ct values, along with the PsuedoRefGene (i.e., Geometric Mean of eight housekeeping genes).
Fold_Changes.txt reports test/control (i.e., Phase II / I (post/pre vitamin D supplementation)) ratios.

extract_protocol: Total RNA from whole blood was extracted using the QIAsymphony PAXgene Blood RNA Kit (Qiagen, Germany), following the manufacturer’s recommendations.

tag: donor


title: Old-irradiated-rep4

tag: gender


title: DONOR 14

tag: phase


title: Old-irradiated-rep3


title: PFC1-A1-c27


title: PFC1-A1-c26


title: PFC1-A1-c25


title: DONOR 06

tag: response status


title: Old-irradiated-rep2


title: PFC1-A1-c24


title: PFC1-A1-c23


title: DONOR 97

tag: diagnosis


title: PFC1-A1-c22


title: DONOR 79

tag: tissue


title: DONOR 53

tag: treatment


title: PFC1-A1-c18


title: Old-irradiated-rep1


title: Old-Unirradiated-rep6


title: DONOR 70


title: DONOR 60


title: Old-Unirradiated-rep5


title: PFC1-A1-c17


title: PFC1-A1-c16


title: PFC1-A1-c15


title: DONOR 52


title: PFC1-A1-c13


title: DONOR 21


title: Old-Unirradiated-rep3


title: PFC1-A1-c11


title: Old-Unirradiated-rep2


title: DONOR 13


title: Young-Irradiated-rep6


title: PFC1-A1-c10


title: PpPep2_48h_rep3

city: Girona

first: Maria

middle: Pla

last: de Solà-Morales

state: Catalonia

address: Campus Montilivi (EPS-1)

department: Institute for Agricultural and Food Technology

institute: Universitat de Girona

data_processing:
RNA-Seq reads were mapped to the Prunus persica NCBIv2 reference genome using the STAR v2.5.3a software with ENCODE parameters from long RNA.
Gene quantification was performed with RSEM version 1.3.0 with default parameters using the Prunus persica NCBIv2.38 annotation version.
Differential expression analysis was performed with  R package DESeq2 version 1.20.0 with default parameters.
The annotation of P. persica genes based on their corresponding orthologues in Arabidopsis thaliana was performed using the Genome Database for Rosaceae.
Genome_build: Prunus persica NCBIv2.38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Prunus persica

source_name: leaf

growth_protocol: Prunus persica var. Big Top (peach) juvenile plants were produced using in vitro technology and grown in individual small pots by a professional grower (Agromillora Iberia S.A., Barcelona, Spain). Prior to experiments they were acclimatized for two weeks in a glasshouse (21ºC, 16/8 h light/dark photoperiod).

extract_protocol:
RNA was extracted from a 200 mg aliquot of ground leaf sample using a two-step TRIzol-based procedure (Invitrogen Life Technologies, Carlsbad, CA, USA) followed by DNAse I (Ambion, Grand Island, NY, USA) digestion of remaining DNA. For Illumina sequencing, RNA was further purified using RNeasy MinElute Cleanup Kit (Qiagen, Sollentuna, Sweden) according to the manufacturer’s instructions. Total RNA from Prunus persica was quantified by Qubit® RNA BR Assay kit (Thermo Fisher Scientific) and the RNA integrity was estimated by using RNA 6000 Nano Bioanalyzer 2100 Assay (Agilent).
The RNA-Seq libraries were prepared with KAPA Stranded mRNA-Seq Illumina® Platforms Kit (Roche) following the manufacturer´s recommendations. Briefly, 500 ng of total RNA was used for the poly-A fraction enrichment with oligo-dT magnetic beads, following the mRNA fragmentation. The strand specificity was achieved during the second strand synthesis performed in the presence of dUTP instead of dTTP. The blunt-ended double stranded cDNA was 3´adenylated and Illumina platform compatible adaptors with unique dual indexes and unique molecular identifiers (Integrated DNA Technologies) were ligated. The ligation product was enriched with 15 PCR cycles and the final library was validated on an Agilent 2100 Bioanalyzer with the DNA 7500 assay. The libraries were sequenced on HiSeq 2500 (Illumina) with a read length of 2x76bp+8bp+8bp using TruSeq SBS Kit v4 (Illumina). Image analysis, base calling and quality scoring of the run were processed using the manufacturer’s software Real Time Analysis (RTA 1.18.66.3).

treatment_protocol: For treatment with Peps, the five youngest fully expanded leaves of each plant were selected and labelled; and the corresponding Pep (optimus doses for each peptide: PpPep1 100 nM, PpPep2 1000 nM) was sprayed onto both abaxial and adaxial leaf surfaces. Plants were incubated under standard conditions in the glasshouse. Treated leaves were detached 1, 24 and 48 h after peptide treatment, the central vein was cut out and the leaf blades were immediately frozen in liquid nitrogen for subsequent RNA extraction.

tag: time point


title: PFC1-A1-c9

data_processing:
Alignment with STAR
Filtering for genes expressed in at least three cells
Filtering for cell with at least 200 genes
Genome_build: Mus_musculus.GRCm38.98
Supplementary_files_format_and_content: h5ad

extract_protocol:
The illumina Nextera XT DNA preparation kit was used to prepare the library directly from the lysate of single cell.
The RNA library was prepared using the standard illumina protocol


title: PpPep2_48h_rep2


title: PFC1-A1-c8


title: Young-Irradiated-rep5


title: DONOR 96


title: Young-Irradiated-rep4


title: PpPep2_48h_rep1


title: Old-Unirradiated-rep1


title: Old-Unirradiated-rep4


title: PpPep2_24h_rep3


title: PFC1-A1-c20


title: PFC1-A1-c19


title: PFC1-A1-c12


title: PFC1-A1-c21


title: Young-Irradiated-rep3


title: PFC1-A1-c7


title: DONOR 05


title: PFC1-A1-c6


title: Young-Irradiated-rep2


title: DONOR 20


title: PpPep2_24h_rep2


title: PpPep2_24h_rep1


title: Young-Irradiated-rep1


title: DONOR 12


title: Young-Unirradiated-rep6


title: PFC1-A1-c5


title: PFC1-A1-c4


title: PpPep2_1h_rep3


title: DONOR 31


title: Young-Unirradiated-rep5


title: PpPep2_1h_rep2


title: DONOR 68


title: DONOR 95


title: PFC1-A1-c65


title: PFC1-A1-c2


title: PpPep2_1h_rep1


title: PFC1-A1-c3


title: DONOR 58


title: Young-Unirradiated-rep4


title: PFC1-A1-c1


title: Young-Unirradiated-rep3


title: DONOR 38


title: PpPep1_48h_rep2


title: PGN+RVT-3

city: Nanjing

first: Ziyu

address: Pujian Road 160, Shanghai

department: Genetic Skin Disease Center

institute: Institute of Dermatology, Chinese Academy of Medical Sciences and Peking Union Medical College

description: inflammation.txt

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 Homo sapiens whole genome using hisat v2.1.0 with default parameter
The expression level of each transcript was calculated according to the (TPM) method. RSEM v1.3.1 was used to quantify gene abundances
Differential gene expression analysis was done using R package DESeq2 v1.24.0
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each Sample

source_name: human sebaceous gland

extract_protocol: RNA libraries were prepared for sequencing using standard Illumina protocols

value: human sebocytes

tag: cell line

value: SZ95 sebocytes

value: PGN+RVT


title: HPC_5

city: Seoul

first: Hee Doo

last: Hee Doo

address: Banpo-Dong Seocho-Gu

country: South Korea

institute: The Catholic Univ. of Korea

description: Sample 74

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using star method.
Transcript per million (TPM) were calculated. In short, all small RNAs were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.

source_name: liver tissue

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

tag: disease state

value: HPC


title: HPC_6

description: Sample 75


title: PGN+RVT-2

description: inflammation.txt


title: DONOR 03

first: Mohammed

address: 10 Discovery Drive, Farmington, CT 06032


title: Young-Unirradiated-rep2


title: DONOR 94


title: DONOR 47


title: HPC_4

description: Sample 73


title: PGN+RVT-1

description: inflammation.txt


title: HPC_3

description: Sample 72


title: PpPep1_24h_rep2


title: PGN-3

description: inflammation.txt

value: PGN


title: PpPep1_48h_rep3


title: HPC_2

description: Sample 71


title: PpPep1_24h_rep1


title: DONOR 67

value: Responders


title: PGN-2

description: inflammation.txt


title: DONOR 18

value: Vitamin D deficiency


title: DONOR 02

value: Female


title: PGN-1

description: inflammation.txt


title: PpPep1_1h_rep3


title: HPC_1

description: Sample 70


title: PpPep1_48h_rep1


title: PpPep1_1h_rep2


title: TG3_20

description: Sample 69


title: LA+RVT-3

description: lipid.txt

value: LA+RVT


title: PpPep1_1h_rep1


title: Young-Unirradiated-rep1


title: TG3_19

description: Sample 68


title: PpPep1_24h_rep3


title: LA+RVT-2

description: lipid.txt


title: t0_rep3

value: mock


title: TG3_17

description: Sample 67


title: DONOR 93

value: Whole Blood


title: LA+RVT-1

description: lipid.txt


title: DONOR 84


title: t0_rep2


title: TG3_16

description: Sample 66


title: LA-3

description: lipid.txt

value: LA


title: DONOR 74


title: TG3_15

description: Sample 65


title: LA-2

description: lipid.txt


title: TG3_14

description: Sample 64


title: DONOR 36


title: LA-1

description: lipid.txt


title: DONOR 17


title: DONOR 25


title: TG3_13

description: Sample 63


title: NH200 EN1 siRNA + TGF

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

country: Germany

institute: Hanover Medical School

data_processing:
Paired-end clean reads were mapped to thereference genome (hg19) using HISAT2 software
HTSeq was used to count the read numbers mapped of each gene, including known and novel genes
Genome_build: hg19
Supplementary_files_format_and_content: csv table containing raw counts

source_name: Dermal fibroblasts

growth_protocol: The fibroblasts were cultured in DMEM-F12 with 10% FBS, 1% penicillin-streptomycin, 2 mM l-glutamine and 2.5 μg ml−1 amphotericin B until reaching 90% confluence. For the experiment, fibroblasts of passage 6 were used. One T75 flask of approximately 1*106 cells was used for each transfection.

extract_protocol:
Total RNA was extracted from adherent cells using the Nucleo Spin RNA isolation kit (Macherey-Nagel).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The cells were treated with siRNA targeting EN1 or control, non-targeting siRNA by nucleofection. One day later, the cells were serum-starved, and after further 24 hours the cells were stimulated with 10 ng/ml of TGFβ and incubated for further 24 hours.

value: Human dermal fibroblasts

value: TGFBeta

tag: phenotype

value: knockdown of EN1


title: TG3_12

description: Sample 62


title: watercore_2

city: 扬州

first: 东贺

last: 刘

address: wenhuilu

department: Yuanzhi College

institute: yzau

data_processing:
Illumina Novaseq 6000 platform used for basecalling.
Clean reads were obtained by removing adapters, high contents of unknown bases reads and low quality reads
Gene expression levels were estimated according to Fragments Per Kilobase of transcript sequence per Millions (FPKM)
The clean reads were mapped to the reference genome of Chinese white pear deposited in the NCBI database (ftp://ftp.ncbi.nlm.nih.gov/genomes/genbank/plant/Pyrus_x_bretschneideri/) using Hisat2
Genome_build: Pyrus x bretschneideri (assembly Pbr_v1.0)
Supplementary_files_format_and_content: Excel files include genes read count and FPKM values for each sample (.txt)

organism: Pyrus pyrifolia

source_name: Qiurong

growth_protocol: Five-year-old  ‘Qiurong’ pears growing in an orchard in Yizheng, Jiangsu, China.

extract_protocol:
Total RNA was extracted by the ethyl ammonium bromide (CTAB) method using skin tissues collected from fruits
RNA-Seq library was generated with NEB Next® UltraTM RNA Library Prep Kit for Illumina (NEB, USA) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: After picking the pulp, find out the water heart disease pulp and normal pulp

tag: cultivar

value: Qiurong

value: pear fruit harvest 120D with watercore

tag: organ

value: fruit skin tissue


title: watercore_1


title: DONOR 09

city: Farmington

last: Toufiq

institute: The Jackson Laboratory for Genomic Medicine


title: t0_rep1


title: healthy_3

value: pear fruit harvest 120D health


title: DONOR 55

source_name: Whole Blood, Non-Responders, Phase I


title: NH198 EN1 siRNA + TGF

tag: cell type


title: healthy_2


title: DONOR 29


title: DONOR 24


title: NH200 nT siRNA + TGF

value: unchanged


title: healthy_1


title: NH140 EN1 siRNA + TGF


title: watercore_3


title: TG3_9

description: Sample 59


title: DONOR 72


title: NH140 nT siRNA + TGF


title: TG3_10

description: Sample 60


title: DONOR 34


title: TG3_8

description: Sample 58


title: TG3_7

description: Sample 57


title: DONOR 78


title: ox-LDL-4

city: 长沙

first: Mengqing

last: jiang

address: tongzipo road 138

department: cardiology

institute: The Third Xiangya Hospital of Central South University

data_processing:
Data quality was assessed with FastQC,
reads were aligned to a mouse genome (mm9) with HiSat2 2.0.5,
sorted with SamTools 1.4
assembled with StringTie (1.3.3.13 R package);
Genome_build: mm9
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Peritoneal Macrophages

growth_protocol: Peritoneal macrophages collected from peritoneal cavity were resuspended in RPMI medium 1640 supplemented with 10% fetal bovine serum and 1% antibiotics-Antimycotic contains 10,000 units/mL of penicillin, 10,000µg/mL of streptomycin, and 25µg/mL of Fungizone™

extract_protocol:
Total RNA was isolated from ox-LDL-treated peritoneal macrophages using TRIzol. Then, RNA degradation and contamination were examined with 1% agarose gels,We checked RNA purity by using a NanoPhotometer spectrophotometer (IMPLEN, Munich, Germany), and RNA concentration was measured using the Qubit RNA Assay Kit with a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, CA, USA). RNA sequencing was performed with a standard protocol using a BGISEQ-500 platform (BGI, Guangdong, China).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 16 hours of ox-LDL stimulation

tag: genotype

tag: age

value: 8 weeks

value: primed with LPS (100ng/ml) followed by 16 hours of ox-LDL(100ug/ml) stimulation


title: ox-LDL-5


title: ox-LDL-3


title: RNAseq of CD34_BCL11B_2

city: Memphis

first: Chunxu

last: Qu

state: TN

address: 262 Danny Thomas Pl

department: Pathology

institute: St Jude Children's Research Institute

description: RNAseq of CD34_BCL11B_2

data_processing:
Raw reads were first trimmed using Trim-Galore v0.60 , mapped to the human genome assembly (GRCh38) using STAR v2.7 and then the gene level values were quantified using RSEM v1.31 based on GENCODE v31 annotation.
To identify differentially expressed genes, only confidently annotated protein coding transcripts were considered, and low count genes were removed from analysis using a counts per million (CPM) cutoff of 10 reads. Normalization factors were generated using the TMM method. Counts were normalized using voom. Voom normalized counts were analyzed using the lmFit and eBayes functions of the limma software package. Genes with an absolute fold change of 2.0 or greater and and FDR <0.05 were considered differentially expressed.
Genome_build: hg38
Supplementary_files_format_and_content: CD34_EV_BCL11B_TPM.txt  (tab-delimited text file with TPM counts for each gene across the 6 samples)

source_name: cord blood CD34+

growth_protocol: Cells were grown in StemSpanSFEMII supplemented with recombinant human IL6, TPO, SCF and FLT3L

extract_protocol:
RNA was harvested using the Qiagen AllPrep Kit and RNA was quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599).
RNAseq: paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

tag: cell surface marker

value: cord blood

value: neonatal

value: wild type

value: CD34+ progenitors isolated from human umbilical cord blood

tag: transduction


title: TG3_6

description: Sample 56


title: RNAseq of CD34_BCL11B_3

description: RNAseq of CD34_BCL11B_3


title: TG3_5

description: Sample 55


title: DONOR 90

tag: donor

value: Vitamin D deficiency

tag: gender

value: Female


title: DONOR 22

value: Whole Blood

tag: phase

tag: response status

value: Responders


title: TG3_11

description: Sample 61


title: RNAseq of CD34_BCL11B_1

description: RNAseq of CD34_BCL11B_1

tag: tissue


title: ox-LDL-1

tag: treatment


title: NH198 nT siRNA + TGF

value: Human dermal fibroblasts

value: TGFBeta


title: DONOR 40

tag: diagnosis


title: TG3_4

description: Sample 54


title: RNAseq of CD34_EV_3

description: RNAseq of CD34_EV_3

value: empty vector


title: TG3_3

description: Sample 53


title: DONOR 69


title: DONOR 04


title: control 5

value: untreated


title: control 4


title: TG3_2

description: Sample 52


title: DONOR 19


title: RNAseq of CD34_EV_1

description: RNAseq of CD34_EV_1


title: DONOR 11


title: ox-LDL-2


title: TG3_1

description: Sample 51


title: TG2_25

description: Sample 50


title: control 2


title: TG2_24

description: Sample 49


title: control 1


title: T4 MQ1 wtransgene rep3 RNA-seq [F57_T4_122_8_183_73]

data_processing:
For BS-PCR samples, reads were pre-processed by a custom script to keep only reads flanked by correct primer sequence and to truncate the primer sequences from each read. Pre-processed reads were mapped to TAIR10 using Bismark and processed into per-position methylation data.
For BS-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using Bismark, and PCR duplicates were removed using a custom Bismark script. A bismark function was used to process alignments into per-position methylation data.
For RNA-seq samples, reads were filtered and trimmed using trim_galore to remove adapters, aligned to TAIR10 using STAR, and only uniquely mapped reads were kept. Presumed PCR duplicates were removed using MarkDuplicates from the Picard tools suite. Reads over genes were counted using htseq-count using default parameters. Sequencing depth tracks (bigWig) were obtained using bamCoverage (deepTools, options --binSize 1 --normalizeUsing CPM).
Genome_build: TAIR10
Supplementary_files_format_and_content: For BS-seq and BSPCR, processed files are BED-like files containing per-position DNA methylation data over the primer-amplified regions (one file each for cytosines in the CG, CHG and CHH context). These files are in BED-like format and have 6 fields: chromosome, position of cytosine (0-based index), position+1, number of unmethylated reads, number of methylated reads, and percent methylated reads. For RNA-seq, count files are text files listing gene IDs and the number of overlapping reads (by htseq-count) in the first and second column, respectively. Coverage tracks are bigWig files and contain per-position sequencing coverage data for each RNA-seq library.

source_name: T4 MQ1 wtransgene RNA-seq

extract_protocol:
Total RNA extraction was performed by using Direct-zol RNA Miniprep kit (Zymo) and using in column DNase digestion.
1 microgram of RNA was used to prepare libraries by using Illumina TruSeq Stranded Total RNA with Ribo-Zero Plant as per manufacturers protocol.

tag: ecotype background

tag: genetic background

value: fwa

tag: transgene present

value: yes (MQ1v)

tag: generation

tag: developmental stage

value: rosette stage

value: rosette leaf


title: TG2_23

description: Sample 48

tag: disease state


title: DONOR 75


title: SJALL067671 cells - BCL11B

data_processing:
ChIP-seq reads were quality trimmed using Trim_Galore v0.4.4 with the cutadapt program and FastQC was used to filter reads with quality scores >20 for downstream analysis. Reads were mapped to the hg38 reference genome using BWA v0.7.12 and duplicates were marked using biobambam2 v2.0.87.
ChIP-seq peaks were called using MACS2 v2.1.1 with a minimum false discovery rate (FDR) cutoff of 0.01 using default parameters for both H3K27ac and BCL11B with input DNA used as the control.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using deepTools v3.4.0 with RPMK used for normalization and a bin size of 10.
Supplementary_files_format_and_content: significant peaks were called using MACS2 with FDR < 0.01 (bed format)

source_name: primary TALL

extract_protocol:
Thawed cryopreserved leukemia cells were washed once in PBS and resuspended in PBS at a concentration of 1 million cells/ml. 37% formaldehyde was added to a final concentration of 1% and cells were crosslinked for 10 minutes at room temperature. Crosslinking was quenched with the addition of glycine at a final concentration of 0.1M and incubated at room temperature for 5 minutes. Cells were spun at 4˚C, washed once more with ice-cold PBS and flash frozen in aliquots of 4 million cells. For each immunoprecipitation, one aliquot of 4 million crosslinked cells was used. Cells were sheared in Covaris microTUBEs (Covaris 520045) at the equivalent of 2 million cells per tube using a Covaris E220 instrument with the following settings: peak power = 140 watts, duty factor = 5, cycles/burst = 200, time = 9 minutes, temperature = 4˚C. The following antibodies were used: 1 ug of H3K27ac (Active Motif am91193) or a cocktail of 4 antibodies for BCL11B, 0.5 ug each (Cell Signaling Technologies 12120, Abcam ab18465, Bethyl Laboratories A300-383A and A300-385A).
Immunoprecipitated DNA was prepared for Illumina sequencing using the Kapa Hyper Prep Kit (Kapa KR0961) and 11 (H3K27ac) or 19 (BCL11B) PCR cycles.  Libraries were sequenced in paired-end mode to an average depth of 387 million reads.

treatment_protocol: no treatment

tag: cell type

value: primary T cell

tag: chip antibody

value: BCL11B (Cell Signaling Technologies 12120 lot# 1, Abcam ab18465 lot# GR3272266-10, Bethyl Laboratories A300-383A lot# 2 and A300-385A lot# 2)

tag: cell line


title: T4 MQ1 wtransgene rep2 RNA-seq [F57_T4_122_8_183_70]


title: RNAseq of CD34_EV_2

description: RNAseq of CD34_EV_2

tag: cell surface marker

value: cord blood

tag: age

value: neonatal

tag: genotype

tag: transduction


title: SJALL068666 cells - input


title: TG2_22

description: Sample 47


title: SJALL067672 cells - BCL11B


title: Mic_Tom_96h_2

city: 昆明市

first: zhengxiang

last: feng

address: 云南大学呈贡校区

institute: 云南大学

data_processing:
raw reads were processed using Trimmomatic.The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat2,The software parameters are the default parameters.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: Micro-Tom
Supplementary_files_format_and_content: Files include filtered data, reads mapped in proper pairs, read counting and FPKM.

organism: Solanum lycopersicum

source_name: Leaves

extract_protocol:
The four-week seedlings were treated with 42 °C high temperature at 0h, 24h, 48h and 96h. Leaves were collected and frozen in liquid nitrogen immediately for total RNA extraction. Total RNA was extracted from collected tomato fruit samples using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). The resulting total RNA samples were checked for RNA concentration and purity using a Nanodrop2000 instrument (Thermo Fisher Scientific, Waltham, MA, USA) and followed by electrophoresis in agarose gels. The cDNA library was constructed by Illumina TruseqTM RNA sample prep Kit. After analysis of RIN values using an Agilent 2100 Bioanalyzer Lab-on-Chip system (Agilent, Santa Clara, CA, USA), the pair-end sequencing was performed on Illumina platform.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: strain

value: Micro-Tom

value: four-week seedlings

tag: stress

value: heat

tag: time

value: Leaves


title: SJALL067671 cells - input


title: Mic_Tom_96h_1

tag: tissue


title: control 3

value: 8 weeks

tag: treatment


title: T4 MQ1 notransgene rep3 RNA-seq [F57_T4_122_8_183_89]

source_name: T4 MQ1 notransgene RNA-seq

tag: ecotype background

tag: genetic background

value: no (MQ1v null segregant)


title: TG2_21

description: Sample 46


title: TG2_20

description: Sample 45


title: Mic_Tom_48h_3


title: T4 MQ1 wtransgene rep1 RNA-seq [F57_T4_122_8_183_67]

tag: transgene present

tag: generation


title: SJALL067672 cells - input


title: sc RNAseq of SJTALL006_D

description: sc RNAseq of SJTALL006_D

data_processing:
bcl2fastq/2.20.0.422 software used for basecalling.
Sequenced reads were mapped using 10X Cellranger (v5.0.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: *barcodes.tsv.gz: cell barcodes
Supplementary_files_format_and_content: *features.tsv.gz: gene list
Supplementary_files_format_and_content: *matrix.mtx.gz: gene expression  in each cell

source_name: bone marrow

extract_protocol:
Frozen mononuclear cells from diagnosis bone marrow samples from patients were thawed and enriched for live cells using the Dead Cell Removal Kit (Miltenyi Biotec, # 130-090-101) according to the manufacturer’s instructions.
10X Genomics Single Cell RNA version 3.1

tag: diagnosis

value: TALL

tag: Sex

value: male


title: Mic_Tom_48h_2


title: Mic_Tom_96h_3


title: T4 MQ1 notransgene rep1 RNA-seq [F57_T4_122_8_183_68]

tag: developmental stage


title: T4 MQ1 notransgene rep2 RNA-seq [F57_T4_122_8_183_78]


title: DONOR 57

tag: donor

value: Vitamin D deficiency

tag: gender

value: Female

value: Whole Blood

tag: phase

tag: response status


title: Mic_Tom_48h_1

tag: age


title: TG2_18

description: Sample 43

tag: disease state


title: sc RNAseq of SJMPAL068275_D1

description: sc RNAseq of SJMPAL068275_D1

value: MPAL


title: T4 dMQ1 wtransgene rep3 RNA-seq [F58_T4_126_21_226_9]

source_name: T4 dMQ1 wtransgene RNA-seq

value: fwa

value: yes (dMQ1)

value: rosette stage

value: rosette leaf


title: sc RNAseq of SJAML068287_D1

description: sc RNAseq of SJAML068287_D1

value: AML

value: unknown


title: ATAC and RNAseq of SJMPAL011913_GEX

description: RNAseq of SJMPAL011913

data_processing:
bcl2fastq/2.20.0.422 software used for basecalling.
Sequenced reads were mapped using 10X Cellranger-arc (v1.0.1)
Genome_build: GRCh38
Supplementary_files_format_and_content: *filtered_feature_bc_matrix.h5: gene expression and fragment counts
Supplementary_files_format_and_content: *atac_fragments.tsv.gz: fragment location

extract_protocol:
Frozen mononuclear cells from diagnosis bone marrow samples from patients were thawed and enriched for live cells using the Dead Cell Removal Kit (Miltenyi Biotec, # 130-090-101) according to the manufacturer’s instructions.
10X Single Cell ATAC + Gene Expression

value: bone marrow


title: Mic_Tom_24h_3

tag: strain

value: Micro-Tom

value: four-week seedlings

tag: stress

value: heat


title: Mic_Tom_24h_2

tag: time

tag: tissue

value: Leaves


title: TG2_16

description: Sample 41


title: T4 dMQ1 wtransgene rep2 RNA-seq [F58_T4_126_21_226_5]

tag: ecotype background


title: TG2_17

description: Sample 42


title: PFC1-A1-c14

city: London

first: Florian

last: Klimm

address: Exhibition Rd, South Kensington

institute: Imperial College London

source_name: germ cell

tag: cell type

value: germ cell

tag: oxygen condition

value: Norm

tag: cell

value: negative


title: SJALL068666 cells - BCL11B

value: primary T cell

tag: chip antibody

value: BCL11B (Cell Signaling Technologies 12120 lot# 1, Abcam ab18465 lot# GR3272266-10, Bethyl Laboratories A300-383A lot# 2 and A300-385A lot# 2)

tag: cell line


title: T4 dMQ1 wtransgene rep1 RNA-seq [F58_T4_126_21_226_1]

tag: genetic background

tag: transgene present

tag: generation

tag: developmental stage


title: TG2_15

description: Sample 40


title: ATAC and RNAseq of SJTALL005006_D_GEX

description: RNAseq of SJTALL005006_D

tag: diagnosis

value: TALL

tag: Sex

value: male


title: Mic_Tom_24h_1

tag: age


title: T4 dMQ1 notransgene rep3 RNA-seq [F58_T4_126_21_226_14]

source_name: T4 dMQ1 notransgene RNA-seq

value: fwa

value: no (dMQ1 null segregant)


title: TG2_19

description: Sample 44

tag: disease state


title: Mic_Tom_0h_3

tag: strain

tag: stress

value: control


title: ATAC and RNAseq of SJTALL005006_D_ATAC

description: ATAC of SJTALL005006_D

tag: tissue


title: T4 dMQ1 notransgene rep2 RNA-seq [F58_T4_126_21_226_10]

tag: ecotype background

value: rosette stage

value: rosette leaf


title: Mic_Tom_0h_2

tag: time


title: TG2_13

description: Sample 38


title: TG2_12

description: Sample 37


title: fwa rep3 RNA-seq [FWA_216]

source_name: fwa RNA-seq

value: no transgene


title: T4 dMQ1 notransgene rep1 RNA-seq [F58_T4_126_21_226_7]


title: Sample_794-AA-3

data_processing:
alignment, mapping, and demultiplexing with cellranger
Genome_build: Mmul_10
Supplementary_files_format_and_content: sparse matrix of counts with associated barcodes and features

organism: Macaca mulatta

source_name: Ventromedial and dorsomedial hypothalamus

extract_protocol:
Whole Rhesus macaque brains were obtained from the Tissue Distribution Program at ONPRC. Brains were centered within a chilled brain matrix (ASI Instruments, catalog # MBM-2000C) and 2mm sliceswere obtained from rostral to caudal. Slices containing the hypothalamus were placed in saline and the PVH, ARC, VMH and DMH were punched out and samples were placed in pre-chilled tubes on dry-ice. Samples were stored at -80C until shipment on dry ice. Nuclei were isolated from frozen macaque tissue and subjected to 10x snRNA-seq.
10x 3’ Gene Expression

value: female


title: MOLM14 FGF2 plus Gilt R1

city: Portland

first: Sunil

middle: Kumar

last: Joshi

state: OR

address: 3181 SW Sam Jackson Park Rd. Mail Code: KR-HEM

department: Knight Cancer Institute

institute: Oregon Health & Science University

description: MOLM14_Parental_plus_48_hr_GILT_100nM_plus_FGF2_10ng_mL

data_processing:
kallisto quant --bias --rf-stranded --plaintext --bootstrap-samples=50 -t 4 -i Homo_sapiens.GRCh37.75.cdna.all.fa.idx ${INPUT_FQ}
Bioconductor R: tximport(countsFromAbundance = "lengthScaledTPM", txOut = F, type="kallisto")
Genome_build: NCBI GRCh37
Supplementary_files_format_and_content: Kallsto counts from estimated abundance

source_name: MOLM14 Parental cells after 48hr Gilteritinib Treatment and FGF2 treatment

growth_protocol: Early and late gilteritinib resistant MOLM14 cells were grown in RPMI-1640 supplemented with 20% serum  pen/strep  fungizone. Early cell lines were also supplemented with 10 ng/mL  or FGF2 or FL.

extract_protocol:
RNA was extracted using Qiagen miRNAeasy kit
RNA was run on a Bioanalyzer to assess quality. Libraries were prepared from total RNA using the TruSeq Stranded mRNA Kit (Illumina). Briefly, poly(A)+ was extracted using oligo-dT-coated beads, then fragmented by treatment with divalent cations and heat. Double stranded cDNA was then generated using random hexamer primers. Second strand synthesis was done with dUTP replacing dTTP to generate strand-specificity. The cDNAs were ligated to sequencing adapters and amplified using limited rounds of polymerase chain reaction. The libraries were quantified using real time PCR on an ABI StepOnePlus Real Time PCR Workstation (Thermo) using a Kapa Library Quantification kit (Roche).  Libraries were sequenced on a NovaSeq 6000 (Ilumina). Fastq files were assembled using Bcl2Fastq (Ilumina).

treatment_protocol: 100 nM of Gilteritinib for 48 hrs

value: MOLM14 Parental cells

tag: treatment

value: 48hrs 100nM Gilteritinib and FGF2 10 ng/mL


title: Mic_Tom_0h_1

value: Micro-Tom

value: four-week seedlings

value: Leaves


title: MOLM14 Parental plus Gilt R1

source_name: MOLM14 Parental cells after 48hr Gilteritinib Treatment

value: 48hrs 100nM Gilteritinib


title: MOLM14 FL plus Gilt R1

description: MOLM14_Parental_plus_48_hr_GILT_100nM_plus_FL_10ng_mL

source_name: MOLM14 Parental cells after 48hr Gilteritinib Treatment and FL treatment

value: 48hrs 100nM Gilteritinib and FL 10 ng/mL


title: Sample_794-AA-2

value: Ventromedial and dorsomedial hypothalamus


title: fwa rep2 RNA-seq [FWA_215]

first: Colette

address: 610 Charles E Young Dr East, Room 4045

institute: University of California - Los Angeles


title: TG2_10

description: Sample 35

source_name: liver tissue


title: MOLM14 Parental R3

source_name: MOLM14 Parental cells


title: fwa rep1 RNA-seq [FWA_214]


title: TG2_9

description: Sample 34


title: MOLM14 Parental R2


title: ATAC and RNAseq of SJMPAL011913_ATAC

description: ATAC of SJMPAL011913

value: bone marrow

value: MPAL


title: Col rep3 RNA-seq [Col_219]

source_name: Col RNA-seq

value: wild-type


title: MOLM14 Parental R1


title: TG2_14

description: Sample 39


title: TG2_8

description: Sample 33


title: death 8_N16P1

city: Hangzhou

first: Shanshan

last: Ms

state: Zhejiang

address: No.79 Qingchun Road

institute: The First Affiliated Hospital, College of Medicine, Zhejiang University

description: SAMPLE 16

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan

data_processing: The scanned images were analyzed with Feature Extraction Software 9.1 (Agilent) using default parameters (protocol GE1-v1_91 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: peripheral blood mononuclear cells

growth_protocol: PBMCs were obtained when patients were admitted to our hospital and  isolated using the Ficoll-Histopaque technique.

extract_protocol: Total RNA was extracted from PBMCs using Trizol and quantified by using NanoDrop ND-2000 spectrophotometer.

treatment_protocol: Total RNA of PBMCs was extracted using TRIzol reagent.

value: whole blood

tag: disease

value: hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF)

tag: gender

value: male

tag: survival state of 28-day

value: dead


title: TG2_7

description: Sample 32


title: FL Early MOLM14 plus Gilt R4

description: MOLM14_FL_EarlyFlask_9_plus_48_hr_GILT_100nM

source_name: FL Early Gilteritinib Resistant MOLM14 cells after 48hr Gilteritinib Treatment

tag: cell line


title: Col rep1 RNA-seq [Col_217]

city: Los Angeles

last: Picard

tag: genetic background

tag: transgene present

value: no transgene

value: rosette stage

value: rosette leaf


title: death 7_115P1

description: SAMPLE 15

value: female


title: death 6_99P1

description: SAMPLE 14


title: TG2_6

description: Sample 31


title: TG2_11

description: Sample 36


title: fwa (Fig2) BSseq [P2_fwa]

source_name: fwa  BSseq

extract_protocol:
CTAB-based method was used to extract DNA
75 to 150 ng of DNA was treated with Qiagen EpiTect bisulfite kit as per manufacturers instruction for bisulfite treatment.  WGBS libraries were made using the Ovation Ultralow Methyl-seq kit (NuGEN).

value: fwa

tag: developmental stage


title: TG2_5

description: Sample 30


title: FL Early MOLM14 plus Gilt R3

description: MOLM14_FL_EarlyFlask_12_plus_48_hr_GILT_100nM

value: FL Early Gilteritinib Resistant MOLM14 cells after 48hr Gilteritinib Treatment


title: FL Early MOLM14 plus Gilt R1

description: MOLM14_FL_EarlyFlask_10_plus_48_hr_GILT_100nM


title: TG2_3

description: Sample 28


title: TG2_4

description: Sample 29


title: MQ1v T4-3-b-1-a(+TG) BSseq [P2_T4_3_b_1_a]

source_name: MQ1v T4-3-b-1-a BSseq

value: yes (MQ1v)

tag: generation


title: TG2_2

description: Sample 27


title: Col rep2 RNA-seq [Col_218]


title: dMQ1 T4-1-a-1-a(+TG) BSseq [P2_T4_1_a_1_a]

source_name: dMQ1 T4-1-a-1-a BSseq

value: yes (dMQ1)


title: Col (Fig2) BSseq [P2_Col]

source_name: Col  BSseq


title: FL Early MOLM14 plus Gilt R2

description: MOLM14_FL_EarlyFlask_11_plus_48_hr_GILT_100nM

value: 48hrs 100nM Gilteritinib


title: FGF2 Early MOLM14 plus Gilt R4

description: MOLM14_FGF2_EarlyFlask_8_plus_48_hr_GILT_100nM

source_name: FGF2 Early Gilteritinib Resistant MOLM14 cells after 48hr Gilteritinib Treatment


title: TG1_10

description: Sample 25


title: survival 8_100P1

description: SAMPLE 8

value: survivial


title: death 4_D-P-5

description: SAMPLE 12


title: dMQ1 T2-1-a BSseq [P1_T2_1_a]

source_name: dMQ1 T2-1-a BSseq


title: death 3_D-P-4

description: SAMPLE 11


title: death 1_D-P-2

description: SAMPLE 9


title: MQ1v T4-3-b-1-b(-TG) BSseq [P2_T4_3_b_1_b]

source_name: MQ1v T4-3-b-1-b BSseq

value: no (MQ1v null segregant)


title: FGF2 Early MOLM14 plus Gilt R1

description: MOLM14_FGF2_EarlyFlask_5_plus_48_hr_GILT_100nM

value: FGF2 Early Gilteritinib Resistant MOLM14 cells after 48hr Gilteritinib Treatment


title: MQ1v T2-7-b BSseq [P1_T2_7_b]

source_name: MQ1v T2-7-b BSseq


title: FGF2 Early MOLM14 plus Gilt R2

description: MOLM14_FGF2_EarlyFlask_6_plus_48_hr_GILT_100nM


title: TG1_9

description: Sample 24


title: death 2_D-P-3

description: SAMPLE 10


title: death 5_B141

description: SAMPLE 13


title: TG1_8

description: Sample 23


title: survival 7_98P1

description: SAMPLE 7


title: MQ1v T2-7-a BSseq [P1_T2_7_a]

source_name: MQ1v T2-7-a BSseq


title: MQ1v T2-3-b BSseq [P1_T2_3_b]

source_name: MQ1v T2-3-b BSseq


title: FGF2 Early MOLM14 plus Gilt R3

description: MOLM14_FGF2_EarlyFlask_7_plus_48_hr_GILT_100nM


title: TG1_7

description: Sample 22


title: survival 6_97P1

description: SAMPLE 6


title: TG2_1

description: Sample 26


title: survival 5_93P1

description: SAMPLE 5


title: TG1_6

description: Sample 21


title: Col (Fig1) BSseq [P1_Col]

value: wild-type


title: survival 4_S-P-5

description: SAMPLE 4

value: whole blood


title: TG1_5

description: Sample 20


title: UT-SCC-118 negative control siRNA

city: Turku

first: Liisa

last: Nissinen

address: Medisiina D, 5th floor; Kiinamyllynkatu 10

department: Dermatology

country: Finland

institute: University of Turku

description: mRNA sequencing data from cSCC

data_processing:
The samples were sequenced with the HiSeq3000 instrument using single-end sequencing chemistry and 50 bp read length.
The reads obtained from the instrument were base called using the instrument manufacturer’s Bcl2fastq2 version 1.8.4 base calling software and aligned against the human reference genome (hg38) using Star version 2.5.0c assembly.
The reads were then associated with known genes and the number of reads associated with each gene was counted using subreads package (v. 1.5.0).
The counts were normalized using the TMM normalization method of the edgeR R/Bioconductor package (R version 3.2, Bioconductor version 3.2).
Genome_build: human hg38
Supplementary_files_format_and_content: For statistical testing the data were further transformed using the voom approach in the limma package. For the visualizations and result files the TMM normalized counts are represented as RPKM values (Reads Per Kilobase of exon per Million reads mapped).

source_name: Cutaneous squamous cell carcinoma 118

growth_protocol: cSCC cells were cultured and incubated at 37C.

extract_protocol:
Total RNAs were extracted according to the manufacturer's instruction and eluted in sterile water (miRNAeasy Mini Kit, Qiagen GmbH, Hilden, Germany).
mRNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: cSCC cell lysates were harvested 72 hours after siRNA-treatment and serum-starved 24 hours before harvesting.

value: Cutaneous squamous cell carcinoma

tag: origin

value: Derived from cSCC tumors

tag: cell type

value: Primary cSCC cells

value: Negative control siRNA


title: UT-SCC-118_CFI siRNA

description: mRNA sequencing data from cSCC

value: CFI siRNA


title: TG1_2

description: Sample 17

tag: disease state


title: TG1_4

description: Sample 19


title: UT-SCC-59A_CFI siRNA

description: mRNA sequencing data from cSCC

source_name: Cutaneous squamous cell carcinoma 59A

value: Metastatic cSCC cells


title: TG1_1

description: Sample 16

source_name: liver tissue


title: survival 2_S-P-3

description: SAMPLE 2

value: hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF)

value: male

tag: age


title: survival 1_S-P-1

description: SAMPLE 1


title: TG1_3

description: Sample 18


title: N015

description: Sample 15

value: Normal


title: SJTALL005006 cells - input DNA

data_processing:
Basecalls performed using CASAVA version 2.20.0
ChIP-seq reads were aligned to the hg38 genome assembly using BWA 0.7.17
ChIP-seq reads were quality trimmed using Trim_Galore v0.4.4 with the cutadapt program and FastQC was used to filter reads with quality scores >20 for downstream analysis. Reads were mapped to the hg38 reference genome using BWA v0.7.12 and duplicates were marked using biobambam2 v2.0.87.
ChIP-seq peaks were called using MACS2 v2.1.1 with a minimum false discovery rate (FDR) cutoff of 0.01 using default parameters for both H3K27ac and BCL11B with input DNA used as the control.
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files were generated using deepTools v3.4.0 with RPMK used for normalization and a bin size of 10.
Supplementary_files_format_and_content: peak files: narrowPeak from MACS2

source_name: primary TALL

growth_protocol: The DND-41 cell line was grown in RPMI 1640 supplemented with 10% fetal bovine serum and 50 U/ml penicillin, 50 ug/ml streptomycin and 2 mM L-glutamine.

extract_protocol:
Freshly harvested DND-41 or thawed cryopreserved cells from sample SJTALL005006 were washed once in PBS and resuspended in PBS at a concentration of 1 million cells/ml. 37% formaldehyde was added to a final concentration of 1% and cells were crosslinked for 10 minutes at room temperature. Crosslinking was quenched with the addition of glycine at a final concentration of 0.1M and incubated at room temperature for 5 minutes. Cells were spun at 4˚C, washed once more with ice-cold PBS and flash frozen in aliquots of 4 million cells. For each immunoprecipitation, one aliquot of 4 million crosslinked cells was used. Cells were sheared in Covaris microTUBEs (Covaris 520045) at the equivalent of 2 million cells per tube using a Covaris E220 instrument with the following settings: peak power = 140 watts, duty factor = 5, cycles/burst = 200, time = 9 minutes, temperature = 4˚C. The following antibodies were used: 1 ug of H3K27ac (Active Motif am91194) or a cocktail of 4 antibodies for BCL11B, 0.5 ug each (Cell Signaling Technologies 12120, Abcam ab18465, Bethyl Laboratories A300-383A and A300-385A).
Immunoprecipitated DNA was prepared for Illumina sequencing using the Kapa Hyper Prep Kit (Kapa KR0961) and 11 (H3K27ac) or 19 (BCL11B) PCR cycles.  Libraries were sequenced to an average depth of 387 million reads.

treatment_protocol: No treatment

value: primary T cell

tag: chip antibody


title: UT-SCC-7_CFI siRNA

description: mRNA sequencing data from cSCC

source_name: Cutaneous squamous cell carcinoma 7

tag: tissue


title: UT-SCC-59A negative control siRNA

description: mRNA sequencing data from cSCC


title: survival 3_S-P-4

description: SAMPLE 3

source_name: peripheral blood mononuclear cells


title: EHBD-KRAS-adherent-from 6weeks primary tumor

city: Shinjuku-ku

first: Akiyoshi

last: Kasuga

state: Tokyo

address: 35, Shinanomachi

country: Japan

institute: Keio University

description: Gene expression data from secondary EHBD tumor initiating cells from 6 weeks primary tumor under adherent culture

hyb_protocol: The Agilent array were hybridized and washed using the manufacturer's protocol.

scan_protocol: Agilent arrays were scanned using the Agilent Technologies Scanner G2505C.

data_processing: The raw data for each spot were normalized by subtraction of the mean background signal intensity determined from the intensities of all blank spots with 95% confidence intervals.

source_name: EHBD, KRAS, secondary tumor initiating cells from 6 weeks primary tumor under adherent culture

label_protocol: Cy3 labeled cRNA were prepared according to the standard Agilent protocol.

extract_protocol: RNA was extracted using an RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.

value: secondary EHBD, from 6 weeks primary tumor

tag: culture

value: adherent culture


title: N014

description: Sample 14

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


title: MQ1v T2-3-a BSseq [P1_T2_3_a]

source_name: MQ1v T2-3-a BSseq

tag: ecotype background

value: fwa

value: yes (MQ1v)

value: rosette stage

value: rosette leaf


title: GB-KRAS-adherent-from 3weeks primary tumor

description: Gene expression data from secondary GB tumor initiating cells from 3 weeks primary tumor under adherent culture

source_name: GB, KRAS, secondary tumor initiating cells from 3 weeks primary tumor under adherent culture

value: secondary GB, from 3 weeks primary tumor


title: UT-SCC-7 negative control siRNA

description: mRNA sequencing data from cSCC

value: Cutaneous squamous cell carcinoma

tag: treatment


title: N013

description: Sample 13


title: SJTALL005006 cells - BCL11B, rep1

value: BCL11B (Cell Signaling Technologies 12120, Abcam ab18465, Bethyl Laboratories A300-383A and A300-385A)


title: SJTALL005006 cells - BCL11B, rep2


title: IHBD-KRAS-adherent-from 3weeks primary tumor

description: Gene expression data from secondary IHBD tumor initiating cells from 3 weeks primary tumor under adherent culture

source_name: IHBD, KRAS, secondary tumor initiating cells from 3 weeks primary tumor under adherent culture

value: secondary IHBD, from 3 weeks primary tumor


title: SJTALL005006 cells - H3K27ac

value: H3K27ac (Active Motif am91194)


title: YAP_H727_Dox3_S39_L005_R1_001

city: Kingston

first: Neil

last: Renwick

state: ON

address: 88 Stuart Street

country: Canada

institute: Queen's University

data_processing:
Raw sequence reads were assessed for quality using FastQC (v.0.11.8)
Low-quality reads removed using Trimmomatic (v.0.36)
Reads were annotated against the human reference transcriptome GRCh38 (release 97) using an established alignment and quantification tool (Kallisto v.0.46.0)
Genome_build: hg38
Supplementary_files_format_and_content: expression spreadsheet files

source_name: Lung carcinoid cells (H727)

growth_protocol: H727 cells were grown in ATCC-formulated RPMI-1640 (Invitrogen) supplemented with 10% fetal bovine serum (FBS). Cells were maintained at 37°C in a humidified 5% CO2 incubator.

extract_protocol:
Total RNA was isolated from miR-375-depleted, YAP overexpression, and control cells using TRIzol Reagent (Invitrogen) according to manufacturer’s instructions.
RNA-seq libraries were prepared using the NEBNext Ultra RNA Library Prep Kit (NEB, E7530) and the NEBNext rRNA depletion kit (NEB, E6310) according to the manufacturer’s instructions; RNA fragmentation was performed for 10 min.

treatment_protocol: Stable miR-375-depleted H727 or doxycycline (Dox)-inducible YAP overexpression H727 (H727-YAP-S127A) cells were established by infection with lentivirus and subsequent antibiotic selection. Briefly, H727 cells were grown to 30-50% confluence in 6-well plates prior to replacement of the complete growth medium (ATCC-formulated RPMI-1640 containing 10% FBS) with virus solution containing 8 mg/ml Polybrene (Sigma Aldrich). Following an incubation period of 12 h at 37°C, virus-containing medium was refreshed and cells further cultured for 24 h. Stable miR-375-depleted H727 or H727-YAP-S127A cells were respectively selected with 2 mg/ml puromycin or 800 mg/ml hygromycin over a period of 8-9 days. Once established, stable cells were used for molecular characterization or in functional assays below; H727-YAP-S127A cells were treated with 1 µg/ml doxycycline hyclate (Bioshop Canada) for 48 h prior to use.

tag: experiment

value: YAP OE


title: YAP_H727_Dox2_S37_L005_R1_001


title: N011

description: Sample 11

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using star method.
Transcript per million (TPM) were calculated. In short, all small RNAs were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.


title: DND41 cells - input DNA


title: YAP_H727_Dox1_S35_L005_R1_001


title: EHBD-KRAS-3D-from 6weeks primary tumor

description: Gene expression data from secondary EHBD tumor initiating cells from 6 weeks primary tumor under organoid cultures

source_name: EHBD, KRAS, secondary tumor initiating cells from 6 weeks primary tumor under 3D culture

value: organoid culture


title: N010

description: Sample 10


title: DND41 cells - BCL11B


title: YAP_H727_3_S33_L005_R1_001

value: YAP Ctrl


title: GB-KRAS-3D-from 6weeks primary tumor

description: Gene expression data from secondary GB tumor initiating cells from 6 weeks primary tumor under organoid culture

source_name: GB, KRAS, secondary tumor initiating cells from 6 weeks primary tumor under 3D culture

value: secondary GB, from 6 weeks primary tumor


title: IHBD-KRAS-adherent-from 6weeks primary tumor

description: Gene expression data from secondary IHBD tumor initiating cells from 6 weeks primary tumor under adherent culture

source_name: IHBD, KRAS, secondary tumor initiating cells from 6 weeks primary tumor under adherent culture

value: secondary IHBD, from 6 weeks primary tumor


title: YAP_H727_2_S30_L005_R1_001


title: N007

description: Sample 7

value: Normal


title: N009

description: Sample 9


title: N008

description: Sample 8


title: IHBD-KRAS-clone1

description: Gene expression data from primary IHBD clone1 cells.

source_name: IHBD, transduction of KRAS, single cell clone 1

value: IHBD, KRAS, clone 1


title: DND41 cells - H3K27ac


title: A549 cells, shY2-2_IP

city: guangzhou

first: Yin

last: Li

state: State...

address: No.601,Huangpu avenue,tianhe area, guangzhou

institute: The First Affiliated Hospital of Jinan University

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter.
We used HISAT2 to map reads to the genome of Homo sapiens (Version: GRCh38) with default parameters.
Mapped reads of IP and input libraries were provided for R package exomePeak, which identifies m6A peaks with bed or bam format that can be adapted for visualization on the UCSC genome browser or IGV software (http://www.igv.org/). HOMER were used for de novo motif finding. Called peaks were annotated by intersection with gene architecture using ChIPseeker.
Then StringTie was used to perform expression level for all mRNAs from input libraries by calculating FPKM (FPKM=[total_exon_fragments/mapped_reads(millions)× exon_length (kB)]).
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample and the m6A peaks for IP and Input

growth_protocol: The human LUAD cell lines A549 were cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel. Poly (A) RNA is purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification.
The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4C with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). Then the IP RNA was reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: Transcriptome-wide m6A-Seq and RNA-Seq assays were then performed on A549 cells after YTHDF2 knockdown or on the vector control

value: lung adenocarcinoma

tag: genotype

value: YTHDF2 knockdown

tag: ip antibody

value: m6A-specific antibody (No. 202003, Synaptic Systems)


title: A549 cells, shY2-2_input

tag: cell line


title: YAP_H727_1_S27_L005_R1_001


title: sgRNA_miR375_H727_3_S24_L005_R1_001

value: miR-375 KO


title: N006

description: Sample 6


title: GB-KRAS

description: Gene expression data from primaty GB tumor initiating cells

source_name: GB, transduction of KRAS

value: GB, KRAS


title: A549 cells, shNC_IP

value: control


title: sgRNA_miR375_H727_2_S21_L005_R1_001


title: A549 cells, shNC_input


title: sgRNA_miR375_H727_1_S12_L004_R1_001


title: EHBD-KRAS

description: Gene expression data from primaty EHBD tumor initiating cells

source_name: EHBD, transduction of KRAS

value: EHBD, KRAS


title: N004

description: Sample 4


title: Empty_Ctrl_H727_3_S9_L004_R1_001

value: miR-375 Ctrl


title: N003

description: Sample 3


title: N002

description: Sample 2