title: Mouse_JF1xC57BL/6_Epiblast_rep1 [JxC_EB1]

description:
WGBS (Illumina's TruSeq DNA Methylation Kit)
mouse_epiblast_maternal_rep1-3_x1.bw
mouse_epiblast_maternal_rep1-3_x5.bw
mouse_epiblast_paternal_rep1-3_x1.bw
mouse_epiblast_paternal_rep1-3_x5.bw

source_name: epiblast

value: epiblast


title: P42_CM_p300_bioChIP-seq_rep1

status: Public on Jan 19 2023

type: SRA

city: Boston

first: Pingzhu

last: Zhou

state: MA

address: 320 Longwood Ave

department: Cardiology

country: USA

institute: Boston Children's Hospital

library_source: genomic

data_processing:
For ChIP-seq data, reads mapped to mm10 reference genome using Bowtie.
Sam converted to BAM using Samtools
For ChIP-seq data, Peak calling was done by MACS2.
Genome_build: mm10
Supplementary_files_format_and_content: bigwig file of chip-seq signal

molecule: genomic DNA

organism: Mus musculus

source_name: Heart

extract_protocol:
E12.5 to P42 heart ventricles were harvested, homogenized, and crosslinked in 1% formaldehyde in PBS for 10 minutes at room temperature and subsequently quenched with 125 mM glycine for 5 min.
Chromatin was fragmented using a microtip sonicator (Qsonica, S-3000) at 30% amplitude for 8 minutes. Biotinylated P300 and bound chromatin was pulled down by incubation with streptavidin beads (ThermoFisher Scientific, 11206D). Bead-bound chromatin was resuspended in SDS elution buffer (50 mM Tris–HCl pH 8,10 mM EDTA, 1% SDS) and incubated overnight at 65 °C to reverse crosslinking. After RNAse A and Proteinase K treatment, ChIP DNA was purified using Qiagen MinElute columns.
Libraries were constructed using the KAPA HyperPrep ChIP-seq library preparation kit (Roche, cat# 07962347001).

tag: strain

tag: tissue

value: ventricle cardiomyocytes

tag: developmental stage


title: C104

type: RNA

city: Sao Paulo

first: Carlos

middle: Alberto

last: Moreira-Filho

state: SP

address: Av. Dr. Eneas Carvalho de Aguiar 647

department: Departments of Pediatrics

country: Brazil

institute: Faculdade de Medicina da Universidade de Sao Paulo

description: Gene expression from human leukocytes

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 and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4845A) for 17 hours at 65°C in a rotating Agilent hybridization oven.

scan_protocol: Slides were scanned immediately after washing on the Agilent Bundle using one color scan setting for 4x44k array slides.

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.3 (Agilent) and considering spots present none or only one flag (i.e. low intensity, saturation, controls, etc.). The selected transcripts were used for analysis using the R software and considering none NA.

molecule: total RNA

organism: Homo sapiens

source_name: leukocytes, whole blood

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 ug RNA using the One-Color Microarray-Based Gene Expression Analysis - Quick Amp Labeling (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (Qiagen). RNA concentration and purity was determined by reading the absorbance at 260 and 280 nm on a spectrophotometer (NanoVue, GE Health Care, USA).

extract_protocol: A total of 0.5 - 1.5 mL of whole blood were used for white blood cells (WBC) RNA extraction using the QIAamp RNA Blood Mini kit (Qiagen).

treatment_protocol: Whole blood samples were collected during hospitalization (average of 14 days after symptoms) or from volunteers (average of 9 days after symptoms). Whole blood was collected in an EDTA-containing tube as storage in maximum 6 hours for RNA extraction and plasma separation.

tag: gender

value: Male

tag: age (yr)

tag: group

value: Severe

tag: comorbidity

value: Obesity


title: late gastrula replicate 2

city: Providence

first: Nathalie

last: Oulhen

state: RI

address: 185 meeting street

institute: Brown university

description: LG

library_source: transcriptomic

data_processing:
Aggregate technical replicates of early blastula (EB), mesenchyme blastula (MB), early gastrula (EG), and late gastrula (LG) using cellanger aggr.
To compare transcriptional profiles between Lv and Sp, 993 genes from the Lv dataset and 1218 genes from the Sp dataset (Foster et al, 2020) were selected with adjusted p value < 1.00E-200. In addition, about 1000 genes that may play important roles during development were added manually. Next, the homologous genes between Lv and Sp were identified by checking the reciprocal best hits of BLASTP analysis. Genes without reciprocal best hit were not used for the downstream analysis because the genes are likely to be species-specific and not suitable for inter-species comparison. Finally, 886 genes were identified as the homologous genes between Lv and Sp. The homologous gene information was extracted from Lv annotation file (Li et al, 2020) and Sp annotation file (S. purpuratus v4.2) and then the gene names were unified with exactly the same conventional gene names in both annotation files. Sequenced reads from Lv and Sp embryos were mapped to corresponding genome sequence and then counted based on the newly made annotation files containing 886 homologous genes. The resulting datasets were combined between species and then normalized by scaling gene expression in each cell by total gene expression. The batch effects between species were corrected by Ligar with the following settings: k = 20, lambda = 5.  UMAP analysis was performed with the following parameters: dims = 1:20, resolution = 0.5. These interspecies comparisons were performed using EB, MB, EG and LG embryos separately.
Assembly: Li et al, (2020)

organism: Lytechinus variegatus

source_name: late gastrula

extract_protocol: Single cell encapsulation was performed using the Chromium Single Cell Chip B kit on the 10x Genomics Chromium Controller. Single cell cDNA and libraries were prepared using the Chromium Single Cell 3’ Reagent kit v3 Chemistry. Libraries were sequenced by Genewiz on the Illumina Hiseq (2x150 bp paired-end runs). Single cell unique molecular identifier (UMI) counting was performed using Cell Ranger Single Cell Software Suite 3.0.2 from 10X Genomics. Duplicate blastula and gastrula stage libraries were aggregated using the cellranger aggr function. Cellranger gene expression matrices were further analyzed using the R package Seurat v 3.1.4. A seurat object was created by simply combining the individual datasets and then normalized by scaling gene expression in each cell by total gene expression. The top 2000 highly variable genes were then used for downstream analysis. The batch effects between samples were corrected by Harmony with default setting. UMAP analysis was performed with the following parameters: dims = 1:20, resolution = 1.

tag: development stage

value: late gastrula


title: P28_CM_p300_bioChIP-seq_rep1


title: KO2--LPS1

city: Shanghai

first: Juan

last: Liu

state: Shanghai

address: 800 Xiangyin Road

country: China

institute: Institute of Immunology, Second Military Medical University

description: Bone marrow cells from Extl1-dificient  mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with  LPS for 12 h and then subjected to RNA seq.

data_processing:
cDNA library construction and sequencing were performed by Shanghai Biotechnology Corporation using Illumina HiSeq platform.
High-quality reads were aligned to the mouse reference genome GRCm38.p4 (mm10).
The expression levels for each of the genes were normalized to fragments per kilobase of exon model per million mapped reads (FPKM).
Genome_build: GRCm38.p4 (mm10)
Supplementary_files_format_and_content: FPKM, counts

source_name: mouse BMDC_KO_LPS

extract_protocol:
BMDC were stimulated with or without  LPS for 12 h and  collected for RNA extraction, total RNA was extracted with TRIzol reagent.
cDNA library construction and sequencing were performed by Shanghai Biotechnology Corporation using Illumina HiSeq platform.

treatment_protocol: Bone marrow cells from Extl1-dificient  and wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with or without  LPS for 12 h and then subjected to RNA seq.

tag: strain background

tag: genotype

tag: cell type

value: bone-marrow derived DC (BMDC)

tag: treatment

value: LPS for 12 h


title: late gastrula replicate 1

description: LG


title: KO1--LPS2


title: P14_CM_p300_bioChIP-seq_rep2


title: cKO-rep3

city: Shenzhen

first: Mengru

last: Zhuang

state: Guangdong

address: 1088 Xueyuan Avenue, Nanshan District

institute: Southern University of Science and Technology

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house  perl scripts. In this step, clean data (clean reads) were obtained by removing reads  containing adapter, reads containing ploy-N and low quality reads from raw data. At  the same time, Q20, Q30 and GC content the clean data were calculated. All the  downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 v2.0.5  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Genome_build: GRCm38

source_name: Hippocampus dentate gyrus

extract_protocol:
Total RNA was extracted from DG deficient in YTHDF2 and the negative control DG by Trizol.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Hippocampus dentate gyrus granule cell

value: Hippocampus dentate gyrus

tag: age

value: post natal day 40


title: early gastrula replicate 2

description: EG

source_name: early gastrula

value: early gastrula


title: P14_CM_p300_bioChIP-seq_rep1


title: KO1--LPS1

description: Bone marrow cells from Extl1-dificient mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with  LPS for 12 h and then subjected to RNA seq.


title: cKO-rep2


title: P7_CM_p300_bioChIP-seq_rep1


title: KO2-Ctrl

description: Bone marrow cells from Extl1-dificient  mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated without  LPS for 12 h and then subjected to RNA seq.

source_name: mouse BMDC_KO_Ctrl


title: KO1-Ctrl

description: Bone marrow cells from Extl1-dificient mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated without  LPS for 12 h and then subjected to RNA seq.


title: P7_CM_p300_bioChIP-seq_rep2


title: mesenchyme blastula replicate 2

description: MB

source_name: mesenchyme blastula

value: mesenchyme blastula


title: mesenchyme blastula replicate 1

description: MB


title: WT2--LPS2

description: Bone marrow cells from wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with LPS for 12 h and then subjected to RNA seq.

source_name: mouse BMDC_WT_LPS

value: wild type


title: P0_CM_p300_bioChIP-seq_rep1


title: early blastula replicate 2

description: EB

source_name: early blastula

value: early blastula


title: WT2--LPS1

description: Bone marrow cells from wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated with  LPS for 12 h and then subjected to RNA seq.


title: 8 hpf

source_name: 8 hpf

value: 8 hpf


title: WT1--LPS2


title: E16.5_CM_p300_bioChIP-seq_rep2


title: early blastula replicate 1

description: EB


title: 6 hpf

source_name: 6 hpf

value: 6 hpf


title: WT1-LPS1


title: early gastrula replicate 1

description: EG


title: E16.5_CM_p300_bioChIP-seq_rep1


title: WT2-Ctrl

description: Bone marrow cells from wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated without  LPS for 12 h and then subjected to RNA seq.

source_name: mouse BMDC_WT_Ctrl


title: E12.5_CM_p300_bioChIP-seq_rep1


title: KMUP77_16S rRNA

status: Public on Jan 18 2023

city: Hsinchu

first: Jinn-Moon

last: Yang

address: 75 Po-Ai Street

country: Taiwan

institute: National Chiao Tung University

description: Recruited patient 129

data_processing:
Library strategy: 16S rRNA DNA-seq
The de-multiplexed sequencing reads were trimmed by using QIIME2.0 (v2019.10), qualify-filtered by DADA2 pipeline and then merged the reads into Amplicon sequence variants (ASVs) for downstream analysis. Taxonomy identification was mapped based on the SILVA 16S rRNA gene reference database (version 132).
Supplementary files format and content: 16S_rRNA_abundance.txt: Abundance value of bacteria in genus level for each sample.

organism: human feces metagenome

source_name: Feces

extract_protocol:
Total genome DNA was extracted using the QIAmp fast DNA Stool Mini Kit (Qiagen, Germany) according to the manufacturer's recommended protocol and DNA was quantified using NanoDrop 2000 (Thermo Fisher Scientific, USA).
DNA libraries were produced by PCR amplicons targeting the V3 and V4 regions of the 16S rRNA gene by using 341F and 805R primers, and sequenced by using the Illumina MiSeq (Illumina, USA).

treatment_protocol: The fecal samples were obtained from patients for microbiota analysis and stored in collection tubes with DNA stabilizer. These samples were frozen at -80°C until analysis.

value: Human fecal tissue

tag: diagnosis

value: DM-LTBI

tag: Sex

value: Female

tag: bmi


title: KMUP99_16S rRNA

description: Recruited patient 130


title: 4 hpf

source_name: 4 hpf

value: 4 hpf


title: KMUP473_16S rRNA

description: Recruited patient 126


title: KMUP69_16S rRNA

description: Recruited patient 127


title: P0_CM_p300_bioChIP-seq_rep2

value: ventricle cardiomyocytes


title: KMUP457_16S rRNA

description: Recruited patient 124

value: Male


title: KMUP465_16S rRNA

description: Recruited patient 125


title: KMUP272_16S rRNA

description: Recruited patient 120


title: KMUP406_16S rRNA

description: Recruited patient 121


title: E12.5_CM_p300_bioChIP-seq_rep2


title: KMUP453_16S rRNA

description: Recruited patient 123


title: KMUP410_16S rRNA

description: Recruited patient 122


title: KMUP261_16S rRNA

description: Recruited patient 118


title: KMUP258_16S rRNA

description: Recruited patient 117


title: KMUP257_16S rRNA

description: Recruited patient 116


title: KMUP250_16S rRNA

description: Recruited patient 115


title: KMUP238_16S rRNA

description: Recruited patient 112


title: KMUP236_16S rRNA

description: Recruited patient 111


title: KMUP221_16S rRNA

description: Recruited patient 110


title: KMUP242_16S rRNA

description: Recruited patient 113


title: KMUP243_16S rRNA

description: Recruited patient 114


title: KMUP71_16S rRNA

description: Recruited patient 128


title: WT1-Ctrl

description: Bone marrow cells from wild-type mice were cultured with GM-CSF and IL-4 for 6 days to generate bone-marrow derived DC (BMDC). BMDC were stimulated  without  LPS for 12 h and then subjected to RNA seq.

value: bone-marrow derived DC (BMDC)


title: KMUP208_16S rRNA

description: Recruited patient 107


title: 2 hpf

source_name: 2 hpf

value: 2 hpf


title: KMUP209_16S rRNA

description: Recruited patient 108


title: KMUP198_16S rRNA

description: Recruited patient 106


title: KMUP216_16S rRNA

description: Recruited patient 109


title: KMUP188_16S rRNA

description: Recruited patient 104


title: KMUP186_16S rRNA

description: Recruited patient 103


title: KMUP192_16S rRNA

description: Recruited patient 105


title: KMUP183_16S rRNA

description: Recruited patient 101


title: KMUP182_16S rRNA

description: Recruited patient 100


title: KMUP179_16S rRNA

description: Recruited patient 99


title: KMUP266_16S rRNA

description: Recruited patient 119


title: KMUP185_16S rRNA

description: Recruited patient 102


title: KMUP171_16S rRNA

description: Recruited patient 98


title: KMUP153_16S rRNA

description: Recruited patient 95


title: KMUP156_16S rRNA

description: Recruited patient 96


title: KMUP147_16S rRNA

description: Recruited patient 93


title: KMUP150_16S rRNA

description: Recruited patient 94


title: KMUP114_16S rRNA

description: Recruited patient 92


title: KMUP108_16S rRNA

description: Recruited patient 91


title: KMUP107_16S rRNA

description: Recruited patient 90


title: KMUP76_16S rRNA

description: Recruited patient 84

value: DM-nonLTBI


title: KMUP98_16S rRNA

description: Recruited patient 87


title: KMUP97_16S rRNA

description: Recruited patient 86


title: KMUP103_16S rRNA

description: Recruited patient 88


title: KMUP79_16S rRNA

description: Recruited patient 85


title: KMUP70_16S rRNA

description: Recruited patient 82


title: KMUP72_16S rRNA

description: Recruited patient 83


title: KMUP477_16S rRNA

description: Recruited patient 81


title: KMUP469_16S rRNA

description: Recruited patient 80


title: KMUP467_16S rRNA

description: Recruited patient 78


title: KMUP464_16S rRNA

description: Recruited patient 77


title: KMUP462_16S rRNA

description: Recruited patient 75


title: KMUP468_16S rRNA

description: Recruited patient 79


title: KMUP459_16S rRNA

description: Recruited patient 74


title: KMUP463_16S rRNA

description: Recruited patient 76


title: KMUP158_16S rRNA

description: Recruited patient 97


title: KMUP452_16S rRNA

description: Recruited patient 70


title: KMUP273_16S rRNA

description: Recruited patient 69


title: KMUP458_16S rRNA

description: Recruited patient 73


title: KMUP270_16S rRNA

description: Recruited patient 68


title: KMUP269_16S rRNA

description: Recruited patient 67


title: KMUP456_16S rRNA

description: Recruited patient 72


title: KMUP259_16S rRNA

description: Recruited patient 66


title: KMUP455_16S rRNA

description: Recruited patient 71


title: KMUP251_16S rRNA

description: Recruited patient 62


title: KMUP255_16S rRNA

description: Recruited patient 65


title: KMUP252_16S rRNA

description: Recruited patient 63


title: KMUP253_16S rRNA

description: Recruited patient 64


title: KMUP247_16S rRNA

description: Recruited patient 59


title: KMUP248_16S rRNA

description: Recruited patient 60


title: KMUP249_16S rRNA

description: Recruited patient 61


title: KMUP104_16S rRNA

description: Recruited patient 89


title: KMUP244_16S rRNA

description: Recruited patient 57


title: KMUP231_16S rRNA

description: Recruited patient 56


title: KMUP230_16S rRNA

description: Recruited patient 55


title: KMUP229_16S rRNA

description: Recruited patient 54


title: KMUP226_16S rRNA

description: Recruited patient 53


title: KMUP225_16S rRNA

description: Recruited patient 52


title: KMUP214_16S rRNA

description: Recruited patient 50


title: KMUP219_16S rRNA

description: Recruited patient 51


title: KMUP211_16S rRNA

description: Recruited patient 48


title: KMUP204_16S rRNA

description: Recruited patient 45


title: KMUP205_16S rRNA

description: Recruited patient 46


title: KMUP203_16S rRNA

description: Recruited patient 44


title: KMUP202_16S rRNA

description: Recruited patient 43


title: KMUP200_16S rRNA

description: Recruited patient 42


title: KMUP194_16S rRNA

description: Recruited patient 39


title: KMUP187_16S rRNA

description: Recruited patient 36


title: KMUP245_16S rRNA

description: Recruited patient 58


title: KMUP184_16S rRNA

description: Recruited patient 35


title: KMUP181_16S rRNA

description: Recruited patient 34


title: KMUP178_16S rRNA

description: Recruited patient 33


title: KMUP174_16S rRNA

description: Recruited patient 31


title: KMUP175_16S rRNA

description: Recruited patient 32


title: KMUP213_16S rRNA

description: Recruited patient 49


title: KMUP170_16S rRNA

description: Recruited patient 30


title: KMUP167_16S rRNA

description: Recruited patient 29


title: KMUP163_16S rRNA

description: Recruited patient 27


title: KMUP160_16S rRNA

description: Recruited patient 26


title: KMUP210_16S rRNA

description: Recruited patient 47


title: KMUP148_16S rRNA

description: Recruited patient 21


title: KMUP157_16S rRNA

description: Recruited patient 25


title: KMUP146_16S rRNA

description: Recruited patient 20


title: KMUP149_16S rRNA

description: Recruited patient 22


title: KMUP155_16S rRNA

description: Recruited patient 24


title: KMUP152_16S rRNA

description: Recruited patient 23


title: KMUP197_16S rRNA

description: Recruited patient 40


title: KMUP193_16S rRNA

description: Recruited patient 38


title: KMUP142_16S rRNA

description: Recruited patient 17


title: KMUP199_16S rRNA

description: Recruited patient 41


title: KMUP189_16S rRNA

description: Recruited patient 37


title: KMUP140_16S rRNA

description: Recruited patient 16


title: KMUP125_16S rRNA

description: Recruited patient 15


title: KMUP144_16S rRNA

description: Recruited patient 18


title: KMUP119_16S rRNA

description: Recruited patient 11


title: KMUP124_16S rRNA

description: Recruited patient 14


title: KMUP165_16S rRNA

description: Recruited patient 28


title: KMUP123_16S rRNA

description: Recruited patient 13


title: KMUP118_16S rRNA

description: Recruited patient 10


title: KMUP112_16S rRNA

description: Recruited patient 7


title: KMUP116_16S rRNA

description: Recruited patient 9


title: KMUP115_16S rRNA

description: Recruited patient 8


title: KMUP121_16S rRNA

description: Recruited patient 12


title: KMUP109_16S rRNA

description: Recruited patient 5


title: KMUP105_16S rRNA

description: Recruited patient 4


title: KMUP111_16S rRNA

description: Recruited patient 6


title: KMUP102_16S rRNA

description: Recruited patient 3


title: KMUP100_16S rRNA

description: Recruited patient 1


title: KMUP101_16S rRNA

description: Recruited patient 2


title: KMUP145_16S rRNA

description: Recruited patient 19


title: Donor 1 and donor 2 GPC2.CD28H.BBz, Pre

city: Bethesda

first: Yingying

last: Cao

address: 9000 Rockville pike

institute: National Institutes of Health

library_source: transcriptomic single cell

data_processing:
Raw scRNA-seq fastq files from sequencing were processed using CellRanger (v.6.1.2, 10X Genomics) software suite with corresponding human GRCh38 reference. Cell barcodes were determined based on the distribution of UMI counts, and filtered gene-barcode matrix was generated by CellRanger (v.6.1.2).
Assembly: GRCh38
Supplementary files format and content: H5 file of filtered gene-barcode matrix

source_name: T cells

extract_protocol:
CAR T cells are manufactured and injected into tumor-bearing mice. The tumors are dissected on day 8 post injection and analyzed. The input cells are also analyzed.
We followed the 10x Genomics instructions for library generation.

tag: individual

value: Donor 1 and donor 2

value: T cells

tag: cell line

value: WT

value: CAR T

tag: construct

tag: time

value: Pre


title: Donor 1 and donor 2 UT, Pre

tag: tissue

value: Untreated

value: UT


title: Donor 1 and donor 2 GPC2.CD8H.BBz, Pre


title: Donor 1 and donor 2 GPC2.CD8H.28BBz, Pre


title: STm-delta-aroA 16 h biol rep 2 [S16h2]

city: Birmingham

first: David

last: Bending

address: IBR

department: Institute of Immunology and Immunotherapy

country: United Kingdom

institute: University of Birmingham

data_processing:
Basecalls by Illumina software on NextSeq500
Zipped FASTQC files were generated using illumina BaseSpace, and then uploaded to the Lexogen Bluebee software platform. Briefly, Bbduk was used for trimming, before alignment using STAR v2.5.2a to the mm10 mouse genome before samtools index to create .bam files. Gene read counting was generated using HTSeq-count to generate raw read count files for each sample
Raw count matrix files were read into DESeq2 in R and rows with read counts <10 removed from the analysis. Raw counts were then normalised using the regularised Log2 (rLog) function to generate normalised expression data for each sample.
Assembly: mm10
Supplementary files format and content: csv file includes regularised Log2 normalised expression values for each sample.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Spleen

extract_protocol:
Live CD4+ T cells were sorted on a FACS Aria cell sorter and collected into eppendorfs. Cells were lysed in 100uL extraction buffer using PicoPure RNA extraction kit according to manufacturer's instructions. An on column DNase digest was performed.
Libraries were constructed using Lexogen Quantseq 3' mRNA Forward kits according to the manufacturer's instructions using a starting amount of 5ng of RNA and UMIs
3' mRNA-seq FWD UMI

value: Spleen

value: CD4+ T cell

value: Nr4a3-Tocky Great Smart-17A

value: STm-delta-aroA 16 h

value: anti-CD3 and anti-CD28


title: STm-delta-aroA 16 h biol rep 3 [S16h3]


title: non-treated 16 h biol rep 3 [C16h3]

value: non-treated 16 h


title: non-treated 16 h biol rep 2 [C16h2]


title: STm-delta-aroA 16 h biol rep 1 [S16h1]


title: STm-delta-aroA 4 h biol rep 3 [S4h3]

value: STm-delta-aroA 4 h


title: non-treated 16 h biol rep 1 [C16h1]


title: Pan troglodytes PBL, LPS

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (10x Genomics).
Assembly: Homo sapiens: GRCh38.p13 (RefSeq accession: GCF_000001405.39); Pan troglodytes: Clint_PTRv2 (RefSeq accession: GCF_002880755.1); Macaca mulatta: Mmul_10 (RefSeq accession: GCF_003339765.1); Rousettus aegyptiacus: mRouAeg1.p (RefSeq accession: GCF_014176215.1)
Supplementary files format and content: HDF5 format including count matrices

molecule: polyA RNA

organism: Pan troglodytes

source_name: peripheral blood

growth_protocol: One million PBMCs were maintained in 500 μl RPMI 1640 (Sigma-Aldrich, Cat# R8758-500ML).

extract_protocol:
One day post infection, infected/stimulated PBMCs were centrifuged and resuspended with PBS.
Library construction was performed following the manufacter’s instructions (Next GEM Single Cell 3' Reagent Kits v3.1, 10x Genomics). Briefly, PBMCs were washed with PBS, then resuspended in the master mix.  Cells, gel-beads and oils were loaded into the Next GEM chip G to generate GEMs using Chromium controller. Reverse transcription were performed in each GEM and barcoded cDNA were produced. After cDNA amplification, enzymatic fragmentation end repair, A-tailing, adaptor ligation and index PCR were processed. QC for constructed libraries were conducted by Agilent Bioanalyzer.

treatment_protocol: One million PBMCs were infected with HSV-1 or SeV at a multiplicity of infection 0.1. LPS (Sigma-Aldrich, Cat# L5024-10MG) was added at 200 ng/ml final concentration. One day post infection, infected/stimulated PBMCs were used for scRNA-seq.

value: peripheral blood

value: PBMC

value: LPS


title: Pan troglodytes PBL, mock

description: 10x Genomics

value: Mock


title: Pan troglodytes PBL, HSV-1

description: 10x Genomics


title: Pan troglodytes PBL, SeV

description: 10x Genomics

value: SeV


title: STm-delta-aroA 4 h biol rep 2 [S4h2]


title: non-treated 4 h biol rep 3 [C4h3]

value: non-treated 4 h


title: 10129

city: Biella

first: Paola

last: Ostano

address: via Malta 3

country: Italy

institute: Fondazione Edo ed Elvo Tempia

hyb_protocol: Hybridization was carried out on 8x60K oligonucleotides arrays miRbase V21 (Agilent Technologies Italia S.p.A., Cernusco sul Naviglio, Milan, Italy).

scan_protocol: After hybridization, washing and scanning, by Agilent G2505C scanner.

data_processing: Images were analyzed using Feature Extraction software v10.7. Raw data were processed by means of the limma R library, applying background correction (normexp) and quantile normalization, and averaging miRNA levels when they are represented with the same probe on the array.

source_name: CRC patient who did not experience a cardiovascular event

label_protocol: For miRNA profiling, 4 µl of totRNA of each sample were used and individually processed with the miRNA Complete Labeling and Hybridization kit (Agilent Technologies S.p.A., Cernusco sul Naviglio, Milan, Italy).

extract_protocol: Total circulating RNA was extracted from 200 µl of plasma using the Mirneasy serum/plasma advanced kit (Qiagen, Hilden, Germany) following the manufacturer’s instructions. To improve RNA extraction, MS2 carrier (Merck Life Science S.r.l., Milan, italy) was added to each sample before lysis step. RNA elution was performed in 30 µl of nuclease-free water.

tag: disease state

value: CRC

value: plasma


title: non-treated 4 h biol rep 2 [C4h2]


title: Treg ITA 2  ATAC

city: Sapporo

first: Kuniyuki

last: Aso

address: Kita 14, Nishi 5, Kita-ku

institute: Hokkaido university

description: 8 group4

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis.
Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files.
Peaks were identified using the MACS 2.1.0 algorithm at a cutoff of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false peaks were removed.
Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations.
Assembly: mm10
Supplementary files format and content: The excel table contains detailed information on sample comparison, peak metrics, peak locations and gene annotations.

source_name: spleen

growth_protocol: Naive CD4+ T cells isolated from C57BL/6J spleen by magnetic cell sorting with the naïve CD4+ T Cell Isolation kit (Miltenyi Biotec). Approximately 0.3 million naive CD4+ T cells were plated into 48-well-plate pre-coated with goat anti-hamster IgG (MP Biomedicals). Cells were stimulated for 2-3 days with anti-CD3 and anti-CD28 antibodies (CD3: 0.25 μg/mL, CD28: 0.5 μg/mL). For each T cell differentiation, subset-specific cytokines and antibodies were further supplemented. For Th17 differentiation, cells were cultured with anti-IL-4 (2 μg/mL), anti-IFNγ (2 μg/mL), IL-6 (30 ng/mL), and TGF-β (0.3 ng/mL). For Treg differentiation, cells were cultured with anti-IL-4 (2 μg/mL), anti- IFNγ (2 μg/mL), IL-2 (20 ng/mL), and TGF-β (1 ng/mL).

extract_protocol:
Cell pellets from T cells in the presence or absecnce ITA on day2  were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen).
For ATAC sequencing, tagmented DNA was amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter).  Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), according to the manufacture’s protocol.

treatment_protocol: All cells were cultured in RPMI 1640 medium containing 10% FBS, 0.1% 2-mercaptoethanol, and penicillin-streptomycin at 37°C under 5% CO2. Itaconate (ITA; Sigma-Aldrich) were prepared as 750 mM stock solutions in phosphate buffered saline (PBS) and diluted directly into culture media.

value: spleen

value: T cells

value: wild type

value: treated with ITA for 2 days


title: 10107


title: 10127


title: non-treated 4 h biol rep 1 [C4h1]

value: Spleen

value: CD4+ T cell

value: Nr4a3-Tocky Great Smart-17A


title: Treg Ctrl 2  ATAC

description: 6 group3

value: untreated


title: Treg ITA 1  ATAC

description: 7 group4


title: 10123


title: 10120


title: 10124


title: 10126


title: 10128

source_name: CRC patient who experienced a cardiovascular event


title: 10104


title: 1077


title: Treg Ctrl 1  ATAC

description: 5 group3


title: Th17 ITA2  ATAC

description: 4 group2


title: STm-delta-aroA 4 h biol rep 1 [S4h1]

value: STm-delta-aroA 4 h

value: anti-CD3 and anti-CD28


title: PAB7_5

first: Debao

last: Li

address: No. 1678 Dongfang Road, Tangqiao Street

institute: Shanghai Children's Medical Center

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.
GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to annotation for the Variablesite).
Assembly: GCA_000001895.4
Supplementary files format and content: FPKM

organism: Rattus

source_name: Upper lobe of the right lung tissue

growth_protocol: The suckling rats were breastfed by the mother rats and were housed in groups of 8-10 per cage, fed under the same conditions with free access to food and water, maintained in the 12h: 12h day: night cycle.

extract_protocol:
Lung tissue from the upper lobe of the right  lung was rapidly removed from executed rat and flash frozen in -80℃ refrigerator , RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: Newborn rats were anesthetized by brief hypothermia on crushed ice for approximately 3 minutes and then transferred to an ice bed to maintain anesthesia during the surgery. The operation was performed under the stereomicroscope in the supine position, including sternum clipping, thoracic cavity opening, pericardium incising, pulmonary artery quantitative constriction, thoracic cavity closing, etc. The constriction procedure which was only performed in the PAB group. After the surgery was completed, the rats were removed from the ice bed and placed on a heat plate of 37℃ to warm and wake up. The pups were not put back to their moms until they were absolutely conscious (around 3h after surgery).

value: Upper lobe of the right lung tissue

tag: strain

value: SD

tag: developmental stage

value: Postnatal day 7

value: Wild type

value: pulmonary artery banding surgery at the age of 10 day

tag: protocol


title: PAB7_2

value: pulmonary artery banding surgery at the age of 7 day


title: Th17 Ctrl 2  ATAC

description: 2 group1


title: Th17 ITA1  ATAC

description: 3 group2


title: PAB7_1

value: pulmonary artery banding surgery at the age of 6 day


title: PAB7_3

value: pulmonary artery banding surgery at the age of 8 day


title: Th17 Ctrl 1  ATAC

description: 1 group1

value: spleen

value: T cells


title: 1084

value: CRC

value: plasma


title: 10111


title: 10103


title: Sham7_4

value: pulmonary artery banding surgery at the age of 4 day

value: Sham


title: H1299_ctl

city: Dalian

first: Wang

address: 9 Lvshun South Rd West Section, Lüshunkou District, Dalian, Liaoning, China

department: Institute of Cancer Stem Cell

institute: Dalian Medical University

description: sample :RBM5 knockdown ctrl

data_processing:
Raw data(raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data(clean reads) were obtained by removing reads containing adapter, reads on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Genome_build: human NCBI genome build 38
Supplementary_files_format_and_content: The gene expressiong matrix from RNA-seq

source_name: lung cancer cells

growth_protocol: H1299 cells were cultured in 1640 medium and A549 cells were cultured in F12K  medium containing 10% FBS and growed in the 5% carbon dioxide environment.

extract_protocol:
RNA samples were extracted using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: We generated RBM4 knockdown sample in A549 and H1299 lung cancer cells

value: human lung cancer cells

tag: treated with

value: control


title: Sham7_3

tag: genotype

value: pulmonary artery banding surgery at the age of 3 day


title: 1069


title: Sham7_1

value: Upper lobe of the right lung tissue

value: pulmonary artery banding surgery at the age of 1 day


title: 1092


title: H1299_shRBM4

description: sample :RBM5 knockdown

tag: cell type

value: RBM5 knocked down


title: 10125


title: A549_shRBM4

description: sample :RBM4 knockdown

value: RBM4 knocked down


title: Sham7_5

value: SD

value: Postnatal day 7

value: Wild type

tag: treatment

value: pulmonary artery banding surgery at the age of 5 day


title: 10106

tag: age


title: AmmoniaExos_miRNA_biol rep 1 [NH3_Exos_1_S7]

city: Newark

first: Jessica

last: Belliveau

state: DE

department: Dept. of Chemical and Biomolecular Engineering

institute: University of Delaware

description:
counts-20221123 reformat.xlsx
expression-table-export-20221123.xlsx

data_processing:
Quality of sequencing data was assessed using FastQC (ver. 0.10.1; Babraham Bioinformatics).  All reads were mapped to the Cricetulus griseus genome PICR assembly (RefSeq GCF_003668045.1, Annotation version 103) to determine the overall biotype (e.g. mRNA, miRNA, etc.) composition of reads using CLC Genomics Map Reads to Reference tool with default settings (ver 20.0.2). For samples from standard cultures, candidate smRNA sequences were identified from raw sequence data using cutadapt (ver. 2.8) with parameters “-u -4 -a A{10}” as recommended by PerkinElmer NextFlex Combo-Seq kit.  All reads shorter than 50 bp and containing the poly-A adapter were utilized for miRNA analysis.  Reads passing filter were analyzed using the CLC Genomics Server (ver. 20.0.2; Qiagen Bioinformatics).  Samples were processed in batch using CLC Quantify miRNA with “strand specific=yes” and allowing up to 2 mismatches.  For miRNA, miRbase (ver. 22.1) was used as a reference database with species in this priority order: C. griseus, Mus musculus, Rattus norvegicus, and Homo sapiens and results were grouped on mature miRNA exact matches.  Differential expression analysis utilized TMM normalization and the CLC Differential Expression Analysis based on negative binomial Generalized Linear Model (GLM) using the Wald test for determining statistical significance and FDR correction.
Assembly: For miRNA, miRbase (ver. 22.1) was used as a reference database with species in this priority order: C. griseus (CriGri_1.0), Mus musculus (GRCm38), Rattus norvegicus (Rnor_6.0), and Homo sapiens (GRCh38) and results were grouped on mature miRNA exact matches.
Supplementary files format and content: counts-20221123 reformat.xlsx contains the total counts and counts per million (CPM) of each microRNA for all samples
Supplementary files format and content: expression-table-export-20221123.xlsx contains differential analysis comparisons between standard and stressed samples

organism: Cricetulus griseus

growth_protocol: CHO cells were cultured in HyClone™ ActiPro™ Media supplemented with 6 mM L-glutamine at 200 RPM, 37°C, and 5% CO2.  Ammonium chloride (NH4Cl) dissolved in PBS (pH 7.4), was added to ammonia stressed cultures at the start of culture for a starting concentration of 9 mM NH4Cl. Cultures were seeded at a density of 0.4 x 106 cells/mL in a total volume of 15 mL.  Cultures were harvested on day 3 for samples (cells, MPs, exosomes).

extract_protocol:
Followed protocol of TruSeq Small RNA Sample Prep Kit (Illumina)
Following isolation of cells, MPs, and exosomes, total RNA was isolated with the miRNeasy micro kit (Qiagen). RNA concentration was determined using the Qubit RNA High Sensitivity (HS) kit and size distribution of total RNA was determined by fragment analysis (AATI Fragment Analyzer, Agilent). The 9 standard culture sample libraries were pooled together.  The 18 osmolarity and ammonia stressed sample libraries were pooled together.

value: Chinese Hamster Ovary (CHO) cells

value: Added 9 mM Ammonium Chloride at start of culture


title: AmmoniaExos_miRNA_biol rep 2 [NH3_Exos_2_S8]


title: 10119

value: CRC


title: AmmoniaExos_miRNA_biol rep 3 [NH3_Exos_3_S9]


title: 10116

value: plasma


title: 10118


title: 100% resistant (monoculture)

city: Houston

first: Jeffrey

last: Chang

address: 6431 Fannin St

institute: University of Texas

data_processing:
Sequence reads were processed with CellRanger v3.0.2 using reference genome (GRChg37).
A gene-barcode matrix was generated for each sample containing counts of unique molecular identifiers (UMIs) for each gene in each barcode (cell).
The pipelines were created and executed using BETSY.
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include read counts for each cell

source_name: CAMA-1 cell line

growth_protocol: For CAMA-1 spheroid experiments, 2000 cells were plated in different proportions (100% CAMA-1 sensitive, 50% CAMA-1 sensitive—50% CAMA-1 resistant, 100% CAMA-1 resistant) in 96-well round-bottom ultra-low attachment spheroid microplate (Corning, Cat. No.: 4520). 24 h later, spheroids were washed and fresh medium including treatment drugs was applied.

extract_protocol:
After 11 days, speroids were harvested, washed and cell suspensions were viably frozen for further processing. Once thawed, cells were centrifuged at 300 x g washed twice with in 37°C pre-warmed 1x PBS, pH 7.4 (Gibco, Cat #10010) + 0.04% Nuclease-Free Bovine Serum Albumin (BSA, EMD Millipore, Cat # 12661525mL).  Cells were resuspended to a target concentration of 1,000 cell/µL, concentrations were confirmed using trypan blue staining and counted on a hemocytometer.
scRNA-Seq was performed on resuspended cells using the 10X Genomics Chromium Single Cell 3’ GEM, Library, & Gel Bead Kit v3 (10X Genomics, Cat # 1000075) according to manufacturer instructions at a target of 10,000 cells per sample.  Each sample was barcoded with a unique i7 Index during library preparation using the Chromium i7 Multiplex Kit (10X Genomics, Cat# 120262) to allow sample multiplexing during sequencing.

treatment_protocol: Spheroids of different composition (100% sensitive, 50% sensitive – 50% resistant, 100% resistant) were initiated from Venus-labeled CAMA-1 and mCherry-labeled CAMA-1_ribociclib_resistant cells and were subjected to 1 uM ribociclib treatment.  Media change was performed at every 4th and 7th day of the week.

value: breast cancer cell line

value: DMSO + 1 uM ribociclib


title: AmmoniaCells_miRNA_biol rep 3 [NH3_Cells_3_S3]


title: 50% sensitive and 50% resistant (coculture)


title: AmmoniaCells_miRNA_biol rep 2 [NH3_Cells_2_S2]


title: AmmoniaMPs_miRNA_biol rep 1 [NH3_MPs_1_S4]


title: AmmoniaMPs_miRNA_biol rep 3 [NH3_MPs_3_S6]


title: Sham7_2

value: pulmonary artery banding surgery at the age of 2 day

value: Sham


title: OsmoticExos_miRNA_biol rep 3 [NaCl_Exos_3_S18]

growth_protocol: CHO cells were cultured in HyClone™ ActiPro™ Media supplemented with 6 mM L-glutamine at 200 RPM, 37°C, and 5% CO2.  Sodium chloride (NaCl) dissolved in PBS (pH 7.4), was added to osmotic stressed cultures at the start of culture, corresponding to an additional 120 mOsm/L, for a starting concentration of 60 mM NaCl. Cultures were seeded at a density of 0.4 x 106 cells/mL in a total volume of 15 mL.  Cultures were harvested on day 3 for samples (cells, MPs, exosomes).

value: Additional 120 mOsm/L as 60 mM NaCl at start of culture


title: 10108


title: 100% sensitive (monoculture)


title: A549_ctl

description: sample :RBM4 knockdown ctrl

value: human lung cancer cells

value: control


title: 1063


title: AmmoniaCells_miRNA_biol rep 1 [NH3_Cells_1_S1]


title: OsmoticExos_miRNA_biol rep 1 [NaCl_Exos_1_S16]


title: OsmoticExos_miRNA_biol rep 2 [NaCl_Exos_2_S17]


title: OsmoticMPs_miRNA_biol rep 3 [NaCl_MPs_3_S15]


title: AmmoniaMPs_miRNA_biol rep 2 [NH3_MPs_2_S5]


title: 1061


title: 1052


title: OsmoticMPs_miRNA_biol rep 1 [NaCl_MPs_1_S13]


title: Pol2ser5_Abcam_DPY30mAID_8h

city: Beijing

first: Hua

last: Wang

address: 38 Xueyuan Rd

institute: Peking University

description: DPY30-mAID degron

data_processing:
Illumina bcl2fastq2 Conversion Software v2.20 used for basecalling.
FASTQ reads were mapped to the GRCm38 (mm10) genome using Bowtie2 (v2.4.1) using the standard settings.
DeepTools (v3.3.0) was used to generate occupancy heat maps, and the resulting normalized occupancy matrix was used as input for custom R scripts to generate average profile plots and to calculate processivity indices.
Genome_build: mm10
Supplementary_files_format_and_content: All other processed data is made available as supplementary files to the manuscript

source_name: mESCs

growth_protocol: E14 ESCs (129/Ola background) were maintained on 0.2% gelatin-coated plates in Glasgow Minimum Essential Medium (GMEM, Sigma-Aldrich, G5154) containing 15% fetal bovine serum (Gibco, 26140079), supplemented with 1× Pen-Strep (Thermofisher Scientific, 15140122), 2 mM Glutamax (Thermofisher Scientific, 35050061), 50 µM β-mercaptoethanol (Thermofisher Scientific, 21985023), 0.1 mM nonessential amino acids (Thermofisher Scientific, 11140050), 1 mM sodium pyruvate (Thermofisher Scientific, 11360070), and Leukemia Inhibitory Factor (LIF, 1000U/mL, Millipore).

extract_protocol:
ES cells were cross-linked by the addition of 1% formaldehyde (Sigma-Aldrich, 252549-1L) in the dish for 10 minutes at RT before quenching with 0.125 M glycine. The fixed cells were washed with PBS and resuspended in SDS buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.0, 5 mM EDTA, 0.5% SDS, 1x protease inhibitor cocktail from Roche). The resulting nuclei were spin down, resuspended in the immunoprecipitation buffer at 1 mL per 16 million cells (SDS buffer and Triton Dilution buffer (100 mM NaCl, 100 mM Tris-HCl pH 8.0, 5 mM EDTA, 5% Triton X-100) mixed in 2:1 ratio with the addition of 1x protease inhibitor cocktail from Roche) and processed on a Bioruptor Plus Sonicator (Diagenode) to achieve an average fragment length of 200-300 bps.
Libraries were constructed using NEBNext Ultra II DNA Library prep kit (NEB, E7645L).

treatment_protocol: Auxin or dTAG-13 was added at the indicated time point.

value: mESCs

value: DPY30-mAID degron

tag: antibody


title: OsmoticMPs_miRNA_biol rep 2 [NaCl_MPs_2_S14]


title: OsmoticCells_miRNA_biol rep 2 [NaCl_Cells_2_S11]


title: Pol2ser5_Abcam_DPY30mAID_0h

description: DPY30-mAID degron


title: Thp1-macro-ATAC

city: Wuhan

first: Ping

last: Hong

state: Hubei

address: No.1,Shizishan Street

department: college of informatics

institute: Huazhong Agricultural University

data_processing:
Trimmomatic (version: 0.33) was used to filter out the low quality bases and adapter sequences.
Trimmed reads were aligned to the human genome assembly (hg19) with the Burrows-Wheeler Aligner-MEM (version: 0.7.17-r1188)
For each sample, SAMtools (version: 1.7) was used to sort the mapped reads by position.
After marking the duplication reads by Picard toolkit (version: 1.119), uniquely mapped reads and non-redundant sequences were kept for further analysis.
F-Seq (version: 3) was used to call ATAC-Seq peaks, and the top 100,000 accessible regionsfor all samples were kept.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated using deepTools (version: 2.5.0.1).

source_name: Peripheral blood

growth_protocol: THP-1 cells (ATCC, TIB-202) were grown in RPMI-1640 containing 10 % FBS

extract_protocol: 100,000 cells were centrifugation at 800 g for 5 min and then washed once using 500 µl of cold 1× PBS and centrifugation at 800 g for another 5 min. Cells were lysed using cold lysis buffer (10 mM Tris-HCl (pH 8.0 at 25 °C), 10 mM NaCl, 0.3% Igepal CA-630). After lysis, nuclei were spun at 800g in 4 °C for 10 min. The pellet was resuspended in the transposase reaction mix (10 µl 5× TTBL buffer (Vazyme, TD501-02), 5 µl TTE Mix V50 buffer (Vazyme, TD501-02) and 35 µl ddH2O water). Tagmentation was carried out for 10 min at 55 °C. Immediately following transposition, The DNA was purified using a Qiagen MinElute PCR Purification Kit (Qiagen, 28004) and eluted with 10 μl elution buffer. The ATAC-Seq library was amplified by the primers in TruePrepTM Index Kit V2 for Illumina® (Vazyme, TD202).

treatment_protocol: To differentiate the monocytes to macrophages, cells were treated with PMA (phorbol 12-myristate 13-acetate) (final concentration = 40 ng/µl) for 48 h at 37 °C in a 5% CO2 atmosphere, and then washed with pre-warmed PBS and incubated with fresh culture medium for another 24 h. For M.tb infection experiment, H37Ra were pelleted (4,000 rpm, RT, 10 min), washed twice with RPMI-1640, resuspended in 1 ml THP-1 culture medium, and dispersed using BD insulin syringes (BD, 328421). Monocyte derived macrophages (Thp1-macro) were infected with H37Ra at MOI (multiplicity of infection) 20. Four hour later the infected cells were washed twice with pre-warmed PBS and incubated with fresh culture medium for another 8 h.

value: THP-1 cells after differentiation


title: Thp1-M.tb-ATAC

value: THP-1 cells after differentiation and activated by M.tb H37Ra


title: OsmoticCells_miRNA_biol rep 3 [NaCl_Cells_3_S12]


title: Thp1-mono-ATAC

value: THP-1 cells before differentiation


title: Thp1-M.tb-rep2-RNAseq

data_processing:
Trimmomatic (version: 0.33) was used to filter out the low quality bases and adapter sequences. Clean reads longer than 36 bp at both ends were kept for further processing.
TopHat (version: v2.1.1) with bowtie2 (version: 2.3.5.1) was used to align the paired end RNA-Seq reads to human reference genome (hg19).
HTSeq (version: 0.11.2) was used to count the mapped reads on the transcripts corresponding to each gene.
DESeq2 was used for normalization and differential expression analysis.
Genome_build: hg19
Supplementary_files_format_and_content: The number of reads correspond each genes counted by HTSeq for each sample.

extract_protocol: RNA was extracted using the RNAiso Plus (Takara, 9109) according to manufacturer’s protocol. Sequencing libraries were prepared using the VAHTS Stranded mRNA-Seq Library Prep Kit (Vazyme, NR602-02) according to manufacturer's protocol.


title: Pol2_Santa_DPY30mAID_8h

description: DPY30-mAID degron


title: OsmoticCells_miRNA_biol rep 1 [NaCl_Cells_1_S10]


title: StandardExos_miRNA_biol rep 2 [Base_Exos_2_S5]

growth_protocol: CHO cells were cultured in HyClone™ ActiPro™ Media supplemented with 6 mM L-glutamine at 200 RPM, 37°C, and 5% CO2.  Cultures were seeded at a density of 0.4 x 106 cells/mL in a total volume of 15 mL.  Cultures were harvested on day 3 for samples (cells, MPs, exosomes).

extract_protocol:
Followed protocol of NextFlex Combo-Seq mRNA/miRNA kit (PerkinElmer)
Following isolation of cells, MPs, and exosomes, total RNA was isolated with the miRNeasy micro kit (Qiagen). RNA concentration was determined using the Qubit RNA High Sensitivity (HS) kit and size distribution of total RNA was determined by fragment analysis (AATI Fragment Analyzer, Agilent). The 9 standard culture sample libraries were pooled together.  The 18 osmolarity and ammonia stressed sample libraries were pooled together.


title: StandardExos_miRNA_biol rep 3 [Base_Exos_3_S6]


title: Pol2_Santa_DPY30mAID_2h

description: DPY30-mAID degron


title: StandardExos_miRNA_biol rep 1 [Base_Exos_1_S4]


title: Thp1-M.tb-rep1-RNAseq


title: StandardMPs_miRNA_biol rep 3 [Base_MPs_3_S3]


title: Thp1-macro-rep2-RNAseq


title: StandardMPs_miRNA_biol rep 2 [Base_MPs_2_S2]


title: Pol2_Santa_DPY30mAID_24h

description: DPY30-mAID degron


title: StandardCells_miRNA_biol rep 3 [Base_Cells_3_S9]


title: NELFA_DPY30mAID_8h

description: DPY30-mAID degron

value: NELFA


title: Thp1-macro-rep1-RNAseq


title: StandardMPs_miRNA_biol rep 1 [Base_MPs_1_S1]

value: Chinese Hamster Ovary (CHO) cells


title: Pol2_Santa_DPY30mAID_0h

description: DPY30-mAID degron


title: Thp1-mono-rep2-RNAseq


title: Thp1-mono-rep1-RNAseq


title: StandardCells_miRNA_biol rep 1 [Base_Cells_1_S7]


title: Thp1-M.tb-H3K9me3-ChIP

data_processing:
FastQC (version: v0.11.8) was used to assess the quality of raw reads.
Trimmomatic (version: 0.33) was used to filter out the low quality bases and adapter sequences.
Burrows-Wheeler Aligner-MEM (version: 0.7.17-r1188) was applied to map the reads to the human genome assembly (hg19).
Mapped reads were sorted by position and duplications were discarded by SAMtools (version: 1.3.1).
Peaks were called by MACS2 (version: 2.1.1.20160309). For broad peaks, the parameterswere-B --broad -q 0.05. For narrow peaks, the parameter was -B.
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated using deepTools (version: 2.5.0.1).

extract_protocol: 4×106 cells and 3 μg antibody were used per immunoprecipitation. Antibody of H3K4me1 (Abcam, ab8895), H3K4me3 (Abcam, ab8580), H3K9me3 (Abcam, ab8898), H3K27ac (Abcam, ab4729), and H3K27me3 (Millipore, 07-449) were used in this study. The ChIP DNA was obtained using SimpleChIP® Enzymatic Chromatin IP Kit (CST, #9003). After immunoprecipitation, ChIP-seq library was constructed using NEBNext® Ultra™ DNA Library Prep Kit (NEB, E7370S).

tag: chip antibody

value: H3K9me3 (Abcam, ab8898)


title: H3K4me3_DPY30mAID_2h

description: DPY30-mAID degron


title: Thp1-M.tb-H3K4me1-ChIP

value: H3K4me1 (Abcam, ab8895)


title: H3K4me3_DPY30mAID_24h

description: DPY30-mAID degron


title: H3K4me3_DPY30mAID_0h

description: DPY30-mAID degron


title: StandardCells_miRNA_biol rep 2 [Base_Cells_2_S8]


title: HEK293 ROR1- conventional selection rep 1

city: Jupiter

first: Henry

last: Wilson

state: FL

address: 130 Scripps Way

institute: The Scripps Research Institute

description: plasmid DNA

library_source: other

data_processing:
HCDR3 DNA reads without proper adapters were removed using R.
DNA sequences were aligned to correct antibody reading frame and translated.
Rabbit HCDR3 sequences were extracted using a REGEX recognizing rabbit HCDR3 junctional sequences.
Read counts were compiled and count matrices generated across multiple sequenced libraries.
Differential expression analysis was carried out using DESeq2.
Supplementary files format and content: HCDR3 amino acid counts per sample
Supplementary files format and content: Processed output for DE comparisons after DESeq2 analysis

molecule: other

organism: Oryctolagus cuniculus

source_name: In vitro IgG repertoire

growth_protocol: Phage Fab-antibody repertoires were propagated in ER2738 bacterial cells using VCSM13 helper phage. The following cell lines were all cultured at 37ºC in 5% CO2 in complete medium consisting of RPMI-1640 medium containing 10% (v/v) FBS (BioFluid) and 1x PS: NCI-H929 (H929), U266. HEK293-ROR1-TetOn cells cells were cultured identically, but with DMEM as the base medium, and with or without 100 ng/mL doxycycline to induce ROR1 cell surface expression. Fresh healthy donor PBMCs were bought from AllCells and cryopreserved prior to use with 50% FBS, 10% DMSO in RPMI-1640 medium.

extract_protocol:
0.5 mL of the bacterial panning output glycerol stocks was subjected to purified phagemid preparation using the QIAprep Spin Miniprep Kit (Qiagen).
Rabbit VH domains were amplified via a two-step PCR procedure in which Illumina P5 and P7 adapters were added.
Libraries were sequenced on a MiSeq sequencer (Illumina) using MiSeq Reagent Kit v3 (150-cycle) in a single end configuration with reads originating from the P5 primer binding site.

treatment_protocol: Phage libraries and human cells were incubated in 3% (w/v) Bovine Serum Albumin (BSA), 0.025% (w/v) NaN3, and 1 mM EDTA in PBS. After incubation and 3x PBS washing, phage were eluted using low pH. Output phage were processed with or without the FBC method,, and were then rescued and reamplified in ER2738 bacterial cells, followed by glycerol stock preparation.

value: In vitro IgG repertoire

value: Selection against HEK293-ROR1-TetOn no dox conventional panning


title: HEK293 ROR1- conventional selection rep 3

description: plasmid DNA


title: HEK293 ROR1+ FBC selection rep 2

description: plasmid DNA

value: Selection against HEK293-ROR1-TetOn + dox with FBC


title: HEK293 ROR1- FBC selection rep 3

description: plasmid DNA

value: Selection against HEK293-ROR1-TetOn no dox with FBC


title: HEK293 ROR1+ conventional selection rep 3

description: plasmid DNA

value: Selection against HEK293-ROR1-TetOn + dox conventional panning


title: HEK293 ROR1+ conventional selection rep 1

description: plasmid DNA


title: HEK293 ROR1+ conventional selection rep 2

description: plasmid DNA


title: HEK293 ROR1- conventional selection rep 2

description: plasmid DNA


title: HEK293 ROR1+ FBC selection rep 3

description: plasmid DNA


title: HEK293 ROR1- FBC selection rep 1

description: plasmid DNA


title: Thp1-M.tb-H3K27me3-ChIP

value: H3K27me3 (Millipore, 07-449)


title: Thp1-M.tb-H3K27ac-ChIP

value: H3K27ac (Abcam, ab4729)


title: HEK293 ROR1+ FBC selection rep 1

description: plasmid DNA


title: H3K4me2_DPY30mAID_48h

description: DPY30-mAID degron


title: H3K4me2_DPY30mAID_8h

description: DPY30-mAID degron


title: NELFA_DPY30mAID_0h

description: DPY30-mAID degron


title: HEK293 ROR1- FBC selection rep 2

description: plasmid DNA


title: PBMCs FBC selection rep 2

description: plasmid DNA

value: Selected against PBMCs with FBC method


title: Thp1-M.tb-Input-ChIP


title: H3K4me3_DPY30mAID_8h

description: DPY30-mAID degron

value: mESCs


title: H3K4me2_DPY30mAID_2h

description: DPY30-mAID degron

value: DPY30-mAID degron


title: PBMCs FBC selection rep 1

description: plasmid DNA


title: U266 FBC selection rep 3

description: plasmid DNA

value: Selected against U266 cell line with FBC method


title: H3K4me2_DPY30mAID_24h

description: DPY30-mAID degron


title: Thp1-macro-Input-ChIP

value: THP-1 cells after differentiation


title: Thp1-M.tb-H3K4me3-ChIP

value: THP-1 cells after differentiation and activated by M.tb H37Ra

value: H3K4me3 (Abcam, ab8580)


title: U266 FBC selection rep 2

description: plasmid DNA


title: PBMCs FBC selection rep 3

description: plasmid DNA


title: U266 FBC selection rep 1

description: plasmid DNA


title: H929 FBC selection rep 3

description: plasmid DNA

value: Selected against H929 cell line with FBC method


title: H3K4me2_DPY30mAID_0h

description: DPY30-mAID degron


title: H929 FBC selection rep 1

description: plasmid DNA


title: H929 FBC selection rep 2

description: plasmid DNA


title: Thp1-macro-H3K9me3-ChIP

value: H3K9me3 (Abcam, ab8898)


title: Thp1-macro-H3K4me3-ChIP


title: H3K4me1_DPY30mAID_48h

description: DPY30-mAID degron


title: H3K4me1_DPY30mAID_24h

description: DPY30-mAID degron


title: Thp1-macro-H3K27ac-ChIP


title: H3K4me1_DPY30mAID_0h

description: DPY30-mAID degron


title: Thp1-mono-Input-ChIP

value: THP-1 cells before differentiation


title: H3K4me1_DPY30mAID_2h

description: DPY30-mAID degron


title: Thp1-mono-H3K27me3-ChIP


title: DPY30_DPY30mAID_8h

description: DPY30-mAID degron


title: colorectal cancer tissue_rep2

city: Harbin

first: boyang

last: fan

address: 246 Xuefu Road, Nangang District

department: Department of Colorectal Cancer Surgery

institute: The Second Affiliated Hospital of Harbin Medical University

description: circRNA expression data from colorectal cancer tissue

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays (8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Data was extracted using Agilent Feature Extraction software.A series of data processing including quantile normalization were performed using the R software package. The circRNAs that at least 5 out of 10 samples have flags in P or M (defined by GeneSpring software) were retained for further differential analyses. Differentially expressed circRNAs with statistical significance between the two groups were identified through Volcano Plot filtering.

source_name: colorectal cancer tissue

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA. The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.).

growth_protocol: Colorectal cancer tissue and paired adjacent normal tissue

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

treatment_protocol: Tissues from colorectal cancer surgury and promptly frozen in liquid nitrogen.

tag: gender

value: male

tag: tumor stage


title: Thp1-mono-H3K4me1-ChIP

value: H3K4me1 (Abcam, ab8895)


title: colorectal cancer tissue_rep1


title: colorectal cancer tissue_rep4

value: female


title: Thp1-macro-H3K27me3-ChIP


title: Thp1-macro-H3K4me1-ChIP


title: H3K4me1_DPY30mAID_8h

description: DPY30-mAID degron


title: colorectal cancer tissue_rep3


title: paired adjacent normal tissue_rep5

description: circRNA expression data from normal tissue

source_name: paired adjacent normal tissue


title: DPY30_DPY30mAID_2h

description: DPY30-mAID degron


title: Rousettus aegyptiacus PBL, SeV

description: 10x Genomics

organism: Rousettus aegyptiacus

value: peripheral blood

value: PBMC

value: SeV


title: paired adjacent normal tissue_rep4


title: paired adjacent normal tissue_rep3


title: Rousettus aegyptiacus PBL, mock

description: 10x Genomics

value: Mock


title: Rousettus aegyptiacus PBL, LPS

description: 10x Genomics

value: LPS


title: colorectal cancer tissue_rep5


title: Rousettus aegyptiacus PBL, HSV-1

description: 10x Genomics


title: Thp1-mono-H3K4me3-ChIP


title: DPY30_DPY30mAID_24h

description: DPY30-mAID degron

value: mESCs


title: paired adjacent normal tissue_rep1


title: Thp1-mono-H3K27ac-ChIP

value: H3K27ac (Abcam, ab4729)


title: DPY30_DPY30mAID_0h

description: DPY30-mAID degron

value: DPY30-mAID degron


title: RBBP5_RBBP5FKBP_DSG_8h

description: RBBP5-FKBP degron

value: RBBP5-FKBP degron


title: UB cells,Mutant,E16.5,CUTTAG,biol rep 2 [K4me3_cko_5]

first: Ziyi

last: Zhao

address: 320 Yueyang Road

institute: Shanghai jiaotong university school of medicine

data_processing:
libraries were sequenced on Illumina® platform, raw reads were filtered and mapped to the mouse genome (GRCm39) using bowtie2 (v2.2.9). Peak calling was accomplished using SEACR (v1.3), and peaks were annotated using ChIPseeker (v 1.12.1).
Assembly: GRCm39
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: ureteric bud,FACS-sorted,E16.5

extract_protocol:
E16.5 embryonic kidneys were dissected and cut into small pieces, trypsinized for 30 min at 37℃, and trypsinization was terminated by adding DMEM/F12 supplemented with 10% FBS. After centrifugation, cells were resuspended in DMEM/F12 supplemented with 2% FBS and filtered 2 times through 70µm cell-strainer cap (Biosharp, BS-70-XBS). The single cell suspension was transferred into a polypropylene tube (Falcon, 352063) and kept on ice until FACS. The GFP+ cells were isolated into DMEM/F12 supplemented with 10% FBS using Sony MA900 Cell Sorter.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
CUT&Tag-seq, For library preparation, the NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit was purchased from Novoprotein, and libraries were generated according to the manufacturer’s instructions.

value: ureteric bud,FACS-sorted,E16.5

value: intermediate mesoderm epithelial cells

value: Hoxb7Cre-GFP+,Ash2l F/F

value: H3K4me3 (Invitrogen,MA5-11199)


title: UB cells,Mutant,E16.5,CUTTAG,biol rep 1 [K4me3_cko_4]


title: Thp1-M.tb-DLOHiC

data_processing:
Library strategy: Hi-C
ChIA-PET Tool was modified and used for linker filtering.
Two end of interacted fragments were seperated by the command awk.
Two end of interacted fragments were separately mapped to hg19 by bwa v0.7.12-r1039 with the parameter -n 0, and then unique mapping reads were kept.
Samtools v1.2 was used to transfer the sam format to bed format.
Two end bed format files were combined to bedpe file by a perl script.
Redundancies and same fragment interactions were discard by perl scripts.
The bedpe format file sorted by the command sort.
The sorted file transferred to matrix by a python script.
The interactions were convered to .hic files by Juicer tools and loops were called with default paremeters.
Genome_build: hg19
Supplementary_files_format_and_content: Loop list for  each Sample

extract_protocol: In situ DLO Hi-C library construction strategies refer to previously published articles: “Lin, D. et al. Digestion-ligation-only Hi-C is an efficient and cost-effective method for chromosome conformation capture. Nature genetics 50, 754 (2018).”

value: THP-1 cells after differentiation and activated by M.tb H37Ra


title: UB cells,cKO,E16.5,biol rep 2 [B_2]

data_processing:
The clean reads were mapped to the mouse genome (GRCm39) using HISAT2 . FPKM of each gene was calculated using Cufflinks , and the read counts of each gene were obtained by HTSeq_x0002_count. Differential expression analysis was performed using the DESeq (2012) R package. P value < 0.05 and foldchange > 1.5 or foldchange < 0.67 was set as the threshold for significantly differential expression. Hierarchical cluster analysis of differentially expressed genes (DEGs) was performed to demonstrate the expression pattern of genes in different groups and samples. GO enrichment and KEGG pathway enrichment analysis of DEGs were performed respectively using R based on the hypergeometric distribution.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using mirVana miRNA Isolation Kit (Ambion).
RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: no treatment


title: UB cells,cKO,E16.5,biol rep 3 [B_3]


title: Thp1-macro-DLOHiC

value: THP-1 cells after differentiation


title: paired adjacent normal tissue_rep2

value: male


title: Thp1-mono-H3K9me3-ChIP

value: THP-1 cells before differentiation

value: H3K9me3 (Abcam, ab8898)


title: RBBP5_RBBP5FKBP_DSG_24h

description: RBBP5-FKBP degron


title: Thp1-mono-DLOHiC


title: RBBP5_RBBP5FKBP_DSG_0h

description: RBBP5-FKBP degron


title: UB cells,Control,E16.5,biol rep 2 [A_2]

value: Hoxb7Cre-GFP+,Ash2l F/+


title: UB cells,cKO,E16.5,biol rep 1 [B_1]


title: Macaca mulatta PBL, LPS

description: 10x Genomics

organism: Macaca mulatta

extract_protocol:
One day post infection, infected/stimulated PBMCs were centrifuged and resuspended with PBS.
Library construction was performed following the manufacter’s instructions (Next GEM Single Cell 3' Reagent Kits v3.1, 10x Genomics). Briefly, PBMCs were washed with PBS, then resuspended in the master mix.  Cells, gel-beads and oils were loaded into the Next GEM chip G to generate GEMs using Chromium controller. Reverse transcription were performed in each GEM and barcoded cDNA were produced. After cDNA amplification, enzymatic fragmentation end repair, A-tailing, adaptor ligation and index PCR were processed. QC for constructed libraries were conducted by Agilent Bioanalyzer.

value: peripheral blood

value: PBMC


title: Donor 2 GPC2.CD8H.28BBz, day7

data_processing:
Raw scRNA-seq fastq files from sequencing were processed using CellRanger (v.6.1.2, 10X Genomics) software suite with corresponding human GRCh38 reference. Cell barcodes were determined based on the distribution of UMI counts, and filtered gene-barcode matrix was generated by CellRanger (v.6.1.2).
Assembly: GRCh38
Supplementary files format and content: H5 file of filtered gene-barcode matrix

organism:
Homo sapiens
Mus musculus

source_name: T cells/tumor

extract_protocol:
CAR T cells are manufactured and injected into tumor-bearing mice. The tumors are dissected on day 8 post injection and analyzed. The input cells are also analyzed.
We followed the 10x Genomics instructions for library generation.

tag: individual

value: Donor 2

value: T cells/tumor

tag: cell line

value: WT/MYCN-amplified

value: CAR T


title: UB cells,Control,E16.5,CUTTAG,biol rep 1 [K4me3_Ctrl_2]

value: ureteric bud,FACS-sorted,E16.5


title: UB cells,Control,E16.5,CUTTAG,biol rep 2 [K4me3_ctrl_4]

value: intermediate mesoderm epithelial cells


title: UB cells,Control,E16.5,biol rep 3 [A_3]


title: UB cells,Control,E16.5,biol rep 1 [A_1]


title: Pol2ser2_Motif_DPY30mAID_8h

description: DPY30-mAID degron

value: mESCs

value: DPY30-mAID degron

tag: time


title: Donor 2 GPC2.CD8H.BBz, day7

tag: tissue

tag: construct


title: Donor 2 GPC2.CD28H.BBz, day7


title: Macaca mulatta PBL, SeV

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (10x Genomics).
Assembly: Homo sapiens: GRCh38.p13 (RefSeq accession: GCF_000001405.39); Pan troglodytes: Clint_PTRv2 (RefSeq accession: GCF_002880755.1); Macaca mulatta: Mmul_10 (RefSeq accession: GCF_003339765.1); Rousettus aegyptiacus: mRouAeg1.p (RefSeq accession: GCF_014176215.1)
Supplementary files format and content: HDF5 format including count matrices

value: SeV


title: Pol2ser2_Motif_DPY30mAID_0h

description: DPY30-mAID degron

tag: strain


title: Macaca mulatta PBL, mock

description: 10x Genomics

value: Mock


title: RBBP5_RBBP5FKBP_DSG_2h

description: RBBP5-FKBP degron

value: RBBP5-FKBP degron


title: Pol2_NTD_CST_RBBP5FKBP_8h

description: RBBP5-FKBP degron


title: Donor 2 UT, day7

value: Untreated

value: UT


title: Pol2_NTD_CST_RBBP5FKBP_2h

description: RBBP5-FKBP degron


title: Donor 1 GPC2.CD8H.28BBz, day7

value: Donor 1


title: Macaca mulatta PBL, HSV-1

description: 10x Genomics


title: Donor 1 GPC2.CD28H.BBz, day7


title: saliva from 23383380_REP1

type: genomic

first: Paul

last: Meltzer

address: 9100 Rockville Pike

institute: NCI/NIH

description: saliva from 23383380_REP1

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing:
Illumina protocol
For the data set, both the beta values as well as the intensity values were generated by using methylumi R package against the raw idat data files, and no normalization method is applied for the beta values.
Average Beta and Unmethylated and methylated signal intensities files are linked to the Series record.

label: Cy5 and Cy3

label_protocol: Illumina protocol

extract_protocol:
Illumina protocol
Bisulfite conversion

treatment_protocol: Saliva collection

value: saliva

tag: kindred

tag: mother or child

value: MOM

value: FEMALE

tag: study

value: Taicang-main


title: Pol2_NTD_CST_RBBP5FKBP_24h

description: RBBP5-FKBP degron

tag: genotype


title: saliva from 23367980_REP1

description: saliva from 23367980_REP1

value: Taicang-substudy


title: F0TCDD [TCDD_P_E2]

city: Columbia

first: Narendra

middle: P

last: Singh

state: South Carolina

address: 6439 Garners Ferry Road,

department: Pathology, Microbiology, and Immunology

institute: University of South Carolina

description:
Total RNA including microRNAs
Total RNAs/Thymic cells

hyb_protocol: Afymetrix GeneChip miRNA Arrays kits and their protocol for hybridization, labeling and blocking was used

scan_protocol: strandard Affymetrix protocol

data_processing:
Command Console was used to scan the samples
Expression Console software was used for data summarization, normalization, and quality control

label: Biotin

organism: Mus

source_name: Pregnanat (GD14) mice exposed to TCDD

label_protocol: FlashTag Biotin HSR RNA labeling Kit from Affymetrix was used.

extract_protocol: Rneasy Mini Kit (Cat No#74104 from Qiagen was used to isolate total RNAs including microRNAs

treatment_protocol: 14GD pregnant mice were exposed to TCDD (10 µg/kg bw)

tag: Sex

value: female

value: Thymus

value: exposed to TCDD (10 µg/kg bw)


title: F1VEH [Veh_F1_E1]

source_name: Pregnanat (GD14) mice exposed to vehicle


title: F1TCDD [TCDD_F1_E2]

tag: treatment


title: F0VEH [Veh_P_E2]


title: Donor 1 GPC2.CD8H.BBz, day7

value: T cells/tumor

tag: cell type

value: WT/MYCN-amplified

value: CAR T


title: Pol2_NTD_CST_RBBP5FKBP_0h

description: RBBP5-FKBP degron

value: mESCs

tag: antibody


title: saliva from 23356311_REP1

description: saliva from 23356311_REP1

value: KID

value: MALE


title: saliva from 23382891_REP1

description: saliva from 23382891_REP1


title: saliva from 23354630_REP1

description: saliva from 23354630_REP1


title: Donor 1 UT, day7

value: Untreated


title: saliva from 23360001_REP1

description: saliva from 23360001_REP1


title: saliva from 23205001_REP1

description: saliva from 23205001_REP1


title: Sorted NK cells from Ugandan child in 2015

city: Stanford

first: Prasanna

last: Jagannathan

state: CA

address: 240 Pasteur Drive Room 3456

department: Department of Medicine

institute: Stanford Universit

description:
Primary patient cells
75bp kit, 36 base pair reads, ~20-30 million reads/sample
NK_All.peaks.500bp.bed

data_processing:
We aligned ATAC-seq reads using Bowtie 2 v.2.4.5. The Bowtie 2 index was constructed with the default parameters for the hg19 reference genome. For peak calling, we used ChrAccR, an R package for comprehensive analysis of chromatin accessibility data (https://greenleaflab.github.io/ChrAccR/). The package implements methods for data quality control and the identification and characterization of differentially accessible regions.
Assembly: hg19

source_name: Blood

extract_protocol:
50 μl of TN5 transposase mixture was added to the cells and incubated at 37oC for 30 min
Transposed DNA was then purified and eluted, and transposed fragments amplified, purified, and sequenced using paired-end, dual-index library sequencing

value: Blood

value: NK cells

value: WT


title: saliva from 23210951_REP1

description: saliva from 23210951_REP1

value: saliva


title: Pol2_CTD_DPY30mAID_Kdm5dKO_Auxin_8h

description: Kdm5a and Kdm5b double knock out

value: DPY30-mAID degron_Kdm5dKO


title: saliva from 23193660_REP1

description: saliva from 23193660_REP1

value: MOM

value: FEMALE

value: Taicang-main


title: Pol2_CTD_DPY30mAID_Kdm5dKO_Auxin_2h

description: Kdm5a and Kdm5b double knock out


title: Pol2_CTD_DPY30mAID_Kdm5dKO_Auxin_0h

description: Kdm5a and Kdm5b double knock out


title: saliva from 23189951_REP1

description: saliva from 23189951_REP1


title: Pol2NTD_DPY30mAID_IAA2h_RA_8h

description: DPY30-mAID degron

value: DPY30-mAID degron


title: I12

city: Boston

first: Hiroaki

last: Wakimoto

address: 185 Cambridge Street, CPZN-3800

department: Neurosurgery

institute: Massachusetts General Hospital

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N, and low quality reads.
Paied-end clean reads were aligned to the reference genome using Spliced Transcripts Alignment to a Reference (STAR)
The mapped reads were assembled by StringTie (v1.3.3b) to quantitate full-length transcripts representing multiple splice variants for each gene locus.
Assembly: hg38, mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

source_name: IOMM-Lee tumor, G47delta-KillerRed injected and laser irradiated

growth_protocol: Tumor cells were implanted subcutanously in athymic mice

extract_protocol:
RNA was extracted using Trizol (Invitrogen). 1 ug of total RNA was used for the construction of sequencing libraries.
Double-stranded cDNA was generated using the Superscript III First-Strand Synthesis System (Invitrogen, Carlsbad, CA). The cDNA products were used to construct libraries with the Nextera XT DNA Sample Preparation Kit (Illumina, Inc., San Diego, CA).

treatment_protocol: Tumors were treated with PBS, laser, G47delta-KillerRed, or G47delta-KillerRed and laser

value: IOMM-Lee tumor

value: IOMM-Lee

value: Malignant meningioma cells

value: G47delta-KillerRed and laser


title: Sorted NK cells from Ugandan child in 2013


title: F2VEH [Veh_F2_E2]

value: female

value: Thymus


title: F2TCDD [TCDD_F2_E2]

value: exposed to TCDD (10 µg/kg bw)


title: saliva from 23188071_REP1

description: saliva from 23188071_REP1

value: KID

value: MALE


title: Pol2NTD_DPY30mAID_IAA2h_RA_0h

description: DPY30-mAID degron

value: mESCs


title: saliva from 23189951_REP2

description: saliva from 23189951_REP2


title: saliva from 23187890_REP1

description: saliva from 23187890_REP1

value: Taicang-substudy


title: I11

value: WT


title: Pol2NTD_DPY30mAID_DMSO2h_RA_8h

description: DPY30-mAID degron


title: saliva from 23184690_REP1

description: saliva from 23184690_REP1

value: saliva


title: saliva from 23172971_REP1

description: saliva from 23172971_REP1


title: saliva from 23167591_REP1

description: saliva from 23167591_REP1


title: I8

source_name: IOMM-Lee tumor, G47delta-KillerRed injected


title: saliva from 23173461_REP1

description: saliva from 23173461_REP1


title: saliva from 23164211_REP1

description: saliva from 23164211_REP1


title: HEXIM1_DSG_RBBP5FKBP_8h

description: RBBP5-FKBP degron

value: RBBP5-FKBP degron


title: I7


title: I9


title: saliva from 23154980_REP1

description: saliva from 23154980_REP1

value: MOM

value: FEMALE


title: saliva from 19229981_REP1

description: saliva from 19229981_REP1

value: Taicang-main


title: Pol2NTD_DPY30mAID_DMSO2h_RA_0h

description: DPY30-mAID degron

value: DPY30-mAID degron


title: saliva from 23152381_REP1

description: saliva from 23152381_REP1


title: saliva from 19218131_REP1

description: saliva from 19218131_REP1


title: I6

source_name: IOMM-Lee tumor, laser irradiated

value: IOMM-Lee tumor

value: IOMM-Lee

value: Laser


title: saliva from 19192461_REP2

description: saliva from 19192461_REP2


title: HEXIM1_DSG_DPY30mAID_8h

description: DPY30-mAID degron


title: saliva from 19192461_REP1

description: saliva from 19192461_REP1


title: saliva from 19175860_REP1

description: saliva from 19175860_REP1


title: I5

value: Malignant meningioma cells


title: HEXIM1_DSG_DPY30mAID_0h

description: DPY30-mAID degron


title: H3K4me3_RBBP5FKBP_8h

description: RBBP5-FKBP degron


title: saliva from 19175551_REP2

description: saliva from 19175551_REP2


title: I4


title: I10

value: G47delta-KillerRed and laser


title: I3

source_name: IOMM-Lee tumor, PBS injected

value: PBS


title: saliva from 19148821_REP1

description: saliva from 19148821_REP1

value: KID


title: H3K4me3_RBBP5FKBP_2h

description: RBBP5-FKBP degron


title: H3K4me3_RBBP5FKBP_24h

description: RBBP5-FKBP degron


title: saliva from 19172621_REP1

description: saliva from 19172621_REP1

value: MALE


title: HEXIM1_DSG_RBBP5FKBP_0h

description: RBBP5-FKBP degron

value: mESCs


title: saliva from 19162651_REP1

description: saliva from 19162651_REP1

value: Taicang-substudy


title: H3K4me3_RBBP5FKBP_0h

description: RBBP5-FKBP degron


title: I2

value: WT


title: H3K4me3_DPY30mAID_Kdm5dKO_Auxin_8h

description: Kdm5a and Kdm5b double knock out

value: DPY30-mAID degron_Kdm5dKO


title: saliva from 23389190

description: saliva from 23389190

value: saliva


title: saliva from 23390790

description: saliva from 23390790

value: MOM


title: saliva from 23389191

description: saliva from 23389191


title: H3K4me3_DPY30mAID_Kdm5dKO_Auxin_4h

description: Kdm5a and Kdm5b double knock out


title: saliva from 23389641

description: saliva from 23389641


title: U12

source_name: U87 tumor, G47delta-KillerRed injected and laser irradiated

value: U87 tumor

value: Glioblastoma cells


title: I1


title: saliva from 23386701

description: saliva from 23386701

value: Taicang-main


title: saliva from 23383451

description: saliva from 23383451

value: FEMALE


title: U11


title: saliva from 19175551_REP1

description: saliva from 19175551_REP1


title: H3K4me3_DPY30mAID_Kdm5dKO_Auxin_48h

description: Kdm5a and Kdm5b double knock out


title: saliva from 23383450

description: saliva from 23383450


title: saliva from 23383381

description: saliva from 23383381


title: saliva from 23386700

description: saliva from 23386700


title: U9

source_name: U87 tumor, G47delta-KillerRed injected


title: H3K4me3_DPY30mAID_Kdm5dKO_Auxin_2h

description: Kdm5a and Kdm5b double knock out


title: saliva from 23383380

description: saliva from 23383380


title: saliva from 23382891

description: saliva from 23382891


title: saliva from 23390791

description: saliva from 23390791


title: U8


title: saliva from 23378020

description: saliva from 23378020


title: saliva from 23376891

description: saliva from 23376891


title: saliva from 23376881

description: saliva from 23376881


title: H3K4me3_DPY30mAID_Kdm5dKO_Auxin_0h

description: Kdm5a and Kdm5b double knock out


title: H3K4me3_DPY30mAID_Kdm5dKO_Auxin_0.5h

description: Kdm5a and Kdm5b double knock out


title: saliva from 23374601

description: saliva from 23374601


title: saliva from 23371391

description: saliva from 23371391


title: saliva from 23374600

description: saliva from 23374600


title: U10


title: H3K4me3_DPY30mAID_IAA2h_RA8h

description: DPY30-mAID degron

value: DPY30-mAID degron


title: U4

source_name: U87 tumor, laser irradiated

value: Laser


title: U5


title: H3K4me3_DPY30mAID_IAA2h_RA0h

description: DPY30-mAID degron

source_name: mESCs


title: saliva from 23362901

description: saliva from 23362901


title: saliva from 23360001

description: saliva from 23360001


title: U3

source_name: U87 tumor, PBS injected


title: saliva from 23358461

description: saliva from 23358461


title: H3K4me3_DPY30mAID_Kdm5dKO_Auxin_24h

description: Kdm5a and Kdm5b double knock out


title: H3K4me3_DPY30mAID_DMSO2h_RA8h

description: DPY30-mAID degron


title: H3K4me3_DPY30mAID_Kdm5dKO_Auxin_1h

description: Kdm5a and Kdm5b double knock out


title: saliva from 23367980

description: saliva from 23367980


title: saliva from 23356551

description: saliva from 23356551


title: saliva from 23376890

description: saliva from 23376890


title: U7


title: H3K4me3_DPY30mAID_DMSO2h_RA0h

description: DPY30-mAID degron


title: saliva from 23356311

description: saliva from 23356311


title: saliva from 23378021

description: saliva from 23378021


title: saliva from 23356310

description: saliva from 23356310


title: U1


title: U2


title: saliva from 23355411

description: saliva from 23355411


title: H3K4me2_RBBP5FKBP_48h

description: RBBP5-FKBP degron

value: RBBP5-FKBP degron


title: saliva from 23355410

description: saliva from 23355410


title: saliva from 23354631

description: saliva from 23354631


title: PBMC, benzo(a)pyrene, biological replicate 2

city: RENNES

first: Lydie

last: SPARFEL

address: 2 avenue du Pr Léon Bernard

department: IRSET U1085

country: France

institute: Inserm

description: Expression data from benzo(a)pyrene

data_processing:
Fastq files were aligned using the QIAGEN pipeline (QIAseq® miRNA Primary Quantification). The number of differentially expressed miRNAs between the two conditions was determined with the DESeq2 (DESeq2_1.26.0). The standard DESeq2 normalization method (DESeq2’s median of ratios with the DESeq function) was used, with a pre-filter of reads and genes (reads uniquely mapped on the genome, or up to 10 different loci with a count adjustment, and genes with at least 10 reads in at least 3 different samples). Following the package recommendations, the Wald test was used with the contrast function and the Benjamini-Hochberg False Discovery Rate (FDR) control procedure to identify differentially expressed genes.
R scripts and parameters are available on GitHub (https://github.com/BSGenomique/genomic-rnaseq-pipeline/releases/tag/v1.0420).
Assembly: GRCh38
Supplementary files format and content: raw.count, TSV file
Supplementary files format and content: DEseq2_NormalizedMatrix.tsv, TSV file

source_name: primary culture from blood donors

growth_protocol: PBMCs were isolated from blood donor buffy coats (written consent for the use of blood samples for the research protocol obtained according to the regulation for blood transfusion of the French blood organization Etablissement Français du Sang, Rennes (France)) by Ficoll (Eurobio, Les Ulis, France) gradient centrifugation

extract_protocol:
Isolation of small RNA from PBMCs was perfomed using the NucleoSpin RNAs kit (Macherey-Nagel, Düren, Germany).
To construct the libraries, 12 independent PBMC cultures each grown in untreated (DMSO) and 2 µM B[a]P-treated conditions for 48 h, were combined in 3 equal pools (with 4 separate blood donors per pool) for each condition.
Pools were used to isolate 5-15 ng of the small RNA fraction and processed using Qiaseq miRNA library prep kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.

treatment_protocol: PBMCs were cultivated at 37°C with 5% CO2 in RPMI medium (Eurobio) supplemented with 20 IU/mL penicillin, 20 μg/mL streptomycin, and 10% decomplemented fetal calf serum (Lonza, Bale, Swiss) and exposed to PAHs, stocked in DMSO. The final concentration of DMSO in the culture medium was always < 0.2% v/v and control cultures received the same dose of DMSO as treated cultures.

value: PBMC

value: benzo(a)pyrene (BAP)

value: RNA

value: library preparation and small RNA sequencing


title: PBMC, benzo(a)pyrene, biological replicate 3

description: Expression data from benzo(a)pyrene


title: U6


title: saliva from 23352471

description: saliva from 23352471

value: KID


title: saliva from 23354630

description: saliva from 23354630


title: saliva from 23354271

description: saliva from 23354271


title: H3K4me2_RBBP5FKBP_2h

description: RBBP5-FKBP degron

extract_protocol:
ES cells were cross-linked by the addition of 1% formaldehyde (Sigma-Aldrich, 252549-1L) in the dish for 10 minutes at RT before quenching with 0.125 M glycine. The fixed cells were washed with PBS and resuspended in SDS buffer (100 mM NaCl, 50 mM Tris-HCl pH 8.0, 5 mM EDTA, 0.5% SDS, 1x protease inhibitor cocktail from Roche). The resulting nuclei were spin down, resuspended in the immunoprecipitation buffer at 1 mL per 16 million cells (SDS buffer and Triton Dilution buffer (100 mM NaCl, 100 mM Tris-HCl pH 8.0, 5 mM EDTA, 5% Triton X-100) mixed in 2:1 ratio with the addition of 1x protease inhibitor cocktail from Roche) and processed on a Bioruptor Plus Sonicator (Diagenode) to achieve an average fragment length of 200-300 bps.
Libraries were constructed using NEBNext Ultra II DNA Library prep kit (NEB, E7645L).

value: mESCs


title: saliva from 23367981

description: saliva from 23367981

value: Taicang-substudy


title: PBMC, benzo(a)pyrene, biological replicate 1

description: Expression data from benzo(a)pyrene


title: saliva from 23353831

description: saliva from 23353831


title: PBMC, CTR (dimethylsulfoxide), biological replicate 3

description: Expression data from CTR

value: DMSO


title: saliva from 23351501

description: saliva from 23351501

value: saliva


title: saliva from 23351191

description: saliva from 23351191


title: saliva from 23351500

description: saliva from 23351500

value: MOM


title: saliva from 23351180

description: saliva from 23351180


title: H3K4me2_RBBP5FKBP_0h

description: RBBP5-FKBP degron


title: H3K4me1_RBBP5FKBP_48h

description: RBBP5-FKBP degron


title: H3K4me2_RBBP5FKBP_8h

description: RBBP5-FKBP degron


title: PBMC, CTR (dimethylsulfoxide), biological replicate 2

description: Expression data from CTR


title: saliva from 23351181

description: saliva from 23351181


title: saliva from 23351811

description: saliva from 23351811


title: H3K4me1_RBBP5FKBP_8h

description: RBBP5-FKBP degron


title: saliva from 23351011

description: saliva from 23351011

value: MALE


title: PBMC, CTR (dimethylsulfoxide), biological replicate 1

description: Expression data from CTR


title: H3K4me1_RBBP5FKBP_24h

description: RBBP5-FKBP degron


title: H3K4me1_RBBP5FKBP_2h

description: RBBP5-FKBP degron


title: saliva from 23351010

description: saliva from 23351010


title: saliva from 23210951

description: saliva from 23210951


title: H3K4me2_RBBP5FKBP_24h

description: RBBP5-FKBP degron


title: saliva from 23351810

description: saliva from 23351810


title: DNase Hi-C on RUES2 differentiated to mesoderm with DNaseI - 4DNEXY9AKMVH

last: DCIC

address: 10 Shattuck St

institute: 4D Nucleome - Data Coordination and Integration Center

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEXY9AKMVH
pcr_cycles: 10
submitted_by: Kris Alavattam
ligation_time: 960
biotin_removed: No
digestion_time: 7
tagging_method: Biotin dTTP
experiment_type: DNase Hi-C
ligation_volume: 1.1
digestion_enzyme: DNaseI
library_prep_kit: Kapa HiFi ReadyStart Master Mix (Roche, KK2602) with barcode-containing primers
contributing_labs: William Noble, UW
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 2% Formaldehyde
fragmentation_method: none
ligation_temperature: 16
digestion_temperature: 20
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXY9AKMVH/

data_processing:
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/f3ee50e5-f93e-4953-8bf6-7a30d5784901/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIZWQK64O.bam, 4DNFIE5O49O7.bam, 4DNFI7G84DQ4.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline

source_name: biosource_summary: RUES2 differentiated to mesoderm

extract_protocol:
description: The Official 4DN Standard in situ DNase Hi-C Protocol adapted from Ramani et al. PMID: 27685100 and approved by SC 01-16-2018
download: https://data.4dnucleome.org/protocols/1f97bb2b-180f-4a6d-b4ea-4e96c90eecdc/@@download/attachment/4DN_DNase_Hi-C_protocol_20180108.pdf

treatment_protocol:
description: Protocol for passaging hPSCs and differentiating them to endothelial cells
download: https://data.4dnucleome.org/protocols/5390905f-7a27-4c82-816f-5a848c1ae21d/@@download/attachment/Alavattam-Mitzelfelt_endothelial-cells_protocol_passaging-differentiation.pdf

value: mesoderm

value: female

value: in vitro differentiated cells

tag: url

value: embryonic


title: RNA-seq on RUES2 differentiated to mesoderm - 4DNEXV26Q4OX

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEXV26Q4OX
strandedness: reverse
submitted_by: Kris Alavattam
experiment_type: RNA-seq
contributing_labs: William Noble, UW
biosample_quantity: 1.0 ug
url: https://data.4dnucleome.org/experiments-seq/4DNEXV26Q4OX/

data_processing:
https://data.4dnucleome.org/resources/data-analysis/rnaseq-processing-pipeline
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/91657637-f3c9-4450-8e9f-224db82ee022/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFISYE1XHW.fastq.gz, 4DNFI9A14OCZ.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (plus)
file_format: bw
file name: 4DNFIDDH6QWG.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/91657637-f3c9-4450-8e9f-224db82ee022/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFISYE1XHW.fastq.gz, 4DNFI9A14OCZ.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: read counts (minus)
file_format: bw
file name: 4DNFI4147I9D.bw
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/91657637-f3c9-4450-8e9f-224db82ee022/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFISYE1XHW.fastq.gz, 4DNFI9A14OCZ.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: gene expression
file_format: tsv
file name: 4DNFIEDF987X.tsv
***************
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/91657637-f3c9-4450-8e9f-224db82ee022/
genome_assembly: GRCh38
derived_from: 4DNFI3FCGSW2.starIndex.tgz, 4DNFIZJB62D1.chrom.sizes, 4DNFISYE1XHW.fastq.gz, 4DNFI9A14OCZ.fastq.gz, 4DNFIHBJI984.tsv, 4DNFIB4HV398.rsemindex.tgz
description: Output file from RNA seq pipeline
file_type: isoform expression
file_format: tsv
file name: 4DNFIRPNBUOG.tsv

extract_protocol:
description: Protocol for Illumina TruSeq Stranded Total RNA Human/Mouse/Rat
download: https://data.4dnucleome.org/protocols/bd3a9473-196d-4191-8e89-c49e05618907/@@download/attachment/truseq-stranded-total-rna-sample-prep-guide-15031048-e.pdf


title: DNase Hi-C on RUES2 differentiated to endothelial cell with DNaseI - 4DNEXT2XYQBB

description:
lab: Chuck Murry, UW
award: 1U54DK107979-01
4DN accession: 4DNEXT2XYQBB
pcr_cycles: 10
submitted_by: Kris Alavattam
ligation_time: 960
biotin_removed: No
digestion_time: 7
tagging_method: Biotin dTTP
experiment_type: DNase Hi-C
ligation_volume: 1.1
digestion_enzyme: DNaseI
library_prep_kit: Kapa HiFi ReadyStart Master Mix (Roche, KK2602) with barcode-containing primers
contributing_labs: William Noble, UW
crosslinking_time: 10
biosample_quantity: 2000000 cells
crosslinking_method: 2% Formaldehyde
fragmentation_method: none
ligation_temperature: 16
digestion_temperature: 20
crosslinking_temperature: 20
fragment_size_selection_method: SPRI beads
url: https://data.4dnucleome.org/experiments-hi-c/4DNEXT2XYQBB/

data_processing:
workflow_run: https://data.4dnucleome.org/workflow-runs-awsem/a650ba03-2b76-49b9-96d3-59f711789e4a/
genome_assembly: GRCh38
derived_from: 4DNFI823LSII.chrom.sizes, 4DNFIO8BXCCJ.bam, 4DNFIH9MANEF.bam, 4DNFIHY26UI3.bam
description: This is an output file of the Hi-C processing pipeline
file_type: contact list-replicate
file_format: pairs
https://data.4dnucleome.org/resources/data-analysis/hi_c-processing-pipeline

source_name: biosource_summary: RUES2 differentiated to endothelial cell

value: endothelial cell


title: saliva from 23210190

description: saliva from 23210190

tag: gender

value: FEMALE

value: Taicang-main


title: saliva from 23210191

description: saliva from 23210191


title: saliva from 23208161

description: saliva from 23208161