title: cDC1s, KO3_PBS

city: Houston

first: LI

last: SHEN

address: 1400 Pressler Street

institute: MD Anderson Cancer Center

data_processing:
Basecalls performed by Illumina CASAVA 1.8.2
RNA-seq reads were aligned to GRCm38/mm10 genome using tophat v2.1.1
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: pool.genes.results_expected_count.tsv: RNA-seq reads count were calculated using RSEM v1.2.31.
Supplementary_files_format_and_content: TTC_JI_2022_STab1.xlsx: Differentially expressed genes.

source_name: Type I conventional dendritic cells (cDC1s)

growth_protocol: Mouse bone marrow cultured in the presence of GM-CSF and FLT3L for 17 days followed by FACS-purification for cDC1s.

extract_protocol:
RNA was extracted using the Qiagen RNeasy Mini Kit following manufacturer's instruction
Libraries were prepared using the Illumina TruSeq RNA Library Prep kit following the manufacturer's instruction.

treatment_protocol: Facs-purified STAT3fl/fl CD11c-Cre- and STAT3fl/fl CD11c-Cre+ cDC1s were treated with PBS, IL-10 (10 ng/mL), poly I:C (20 ug/mL), or IL-10 + poly I:C for 6 hours. n = 3 per genotype and treatment condition

value: STAT3fl/fl CD11c-Cre+

value: PBS


title: cDC1s, KO3_IL10

status: Public on Jul 26 2022

type: SRA

state: TX

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

value: Type I conventional dendritic cells (cDC1s)

tag: genotype

tag: treatment


title: RC_036_2w_IFX_R_RNA

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

country: Germany

institute: Institute of Clinical Molecular Biology

data_processing:
Fastq files were mapped and aligned using nf-core ((https://github.com/nf-core/rnaseq)) rnaseq pipeline.
Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore (version 0.4.4), which is a wrapper tool for Cutadapt and FastQC. Reads that were shorter than 35 bp after trimming were discarded.
The filtered reads were mapped to the human genome (GRCh38, gencode version 25) using STAR aligner (version 2.5.2b).
featureCounts (version 1.5.2) was used to estimate the expression counts of the genes.
Genome_build: (GRCh38, gencode version 25)
Supplementary_files_format_and_content: tab-delimited text files include feature counts

organism: Homo sapiens

source_name: Peripheral Whole-Blood

extract_protocol:
Patient peripheral blood was collected in 2.5mL tubes PAXgene Blood RNA Tubes, RNA was automated isolated in QIAGEN’s QIAcube using the PAXgene Blood miRNA Kit from QIAGEN PreAnalytiX.
RNA Sequencing libraries were prepared from Paxgene™ Blood RNA Tubes (Qiagen) according to the Illumina TruSeq® messenger RNA (mRNA) sequencing protocol (TruSeq® RNA Seq Library Prep Kit v2)
Paired-end sequencing (2x75bp) was performed on Illumina HiSeq 4000

tag: patient

tag: cohort

value: Replication

value: Infliximab

tag: remission at week 14

value: Remission

tag: time point

tag: diagnosis

value: CD


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Spring-Rep4 F5X_S29

city: Seattle

first: Mark

last: Jankowski

state: WA

address: 1200 6th Ave

institute: USEPA

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Spring-Rep4
Organism Source: Carolina Biological Supply, 2014

data_processing:
Raw sequences were evaluated via FastQC (Andrews, 2010) to determine the baseline quality of the sequencing results. To improve these overall statistics, reads were trimmed to remove Illumina‐specific adapter sequences and low‐quality sequences or sequence tails using the Trimmomatic software (Bolger et al., 2014). FastQC was run again to verify that only high‐quality sequences were retained.
High‐quality sequences were then mapped to D. magna reference transcripts using Kallisto (Bray et al., 2016), a kmer‐based mapper. Kallisto produces a matrix of read counts with transcripts along one axis and samples along the other. To produce a data set for direct differential expression analysis, each cell of this matrix was rounded to the nearest integer value to be compatible with the DESeq. 2 algorithm (Love et al., 2014; an R Package available through Bioconductor). To produce a data set to identify minimal gene signatures separating conditions, each read count was divided by the total reads counted for that sample, producing a fractional matrix. All genes that showed no variance in any one data set were removed from analysis for all data sets to ensure cross‐data set comparability. Initial comparisons indicated a modest batch effect between the wetland and storm‐water samples. A linear model was therefore used to identify and remove batch variance that may have been a result of employing two different genetic backgrounds for each study.
Assembly: RNA-seq reads from this study were aligned to a transcriptome created from the RNA sequencing of 12 Daphnia magna colonies under different stress conditions. Orsini, L., D. Gilbert, R. Podicheti, M. Jansen, J. B. Brown, O. S. Solari, K. I. Spanier, J. K. Colbourne, D. B. Rusch, and E. Decaestecker. 2016. Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors. Scientific Data 3:1-16.
Supplementary files format and content: Kallisto.counts is a matrix of raw counts. Kallisto produces a matrix of read counts with transcripts along one axis and samples along the other. Matrix of read counts with transcripts along one axis and samples along the other.
Supplementary files format and content: Kallisto.tpm is a matrix processed as described herein. Kallisto produces a matrix of read counts with transcripts along one axis and samples along the other. Matrix of read counts with transcripts along one axis and samples along the other. Each cell of this matrix was rounded to the nearest integer value to be compatible with the DESeq2 algorighim. Each read count was then divided by the total reads counted for that sample, producing a fractional matrix. All genes that showed no variance in any one dataset were removed from analysis for all datasets to ensure cross-dataset comparability.

organism: Daphnia magna

source_name: D.magna whole body

growth_protocol: Live D. magna (purchased from Carolina Biological Supply) were placed into aerated St. Cloud State University well water and maintained as an experimental culture under a 16:8‐h light:dark photoperiod. All test water conditions were within Organisation for Economic Co‐operation and Development (OECD) Test No. 211 (OECD, 2012) guidelines.

extract_protocol:
Total RNA extration via PureLink RNA Mini Kit (catalog no. 12183018 A; Thermo Fisher Scientific)
Strand‐specific messenger RNA libraries were created for each total RNA sample of pooled daphnia (n = 5 individual neonates per replicate sample; five groups per treatment).

treatment_protocol: At the end of the 96‐h exposure period, to obtain sufficient RNA quantity for sequencing, the 30 treated (less 0%–7% mortality) neonates were randomly divided into five groups of five individuals, then stored in 100 µl of RNAlater (catalog no. R0901; Sigma‐Aldrich) at −80 °C until RNA extraction. RNA was extracted by sonication (30 s)

tag: tissue

value: D.magna whole body


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep4 F4Z_S130

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: RC_140_6w_IFX_R_RNA


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep2 F4Y_S82

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: cDC1s, KO3_BOTH

value: IL-10 + Poly I:C


title: cDC1s, WT3_IL10

value: STAT3fl/fl CD11c-Cre-


title: cDC1s, WT3_BOTH


title: RC_022_baseline_IFX_R_RNA

value: baseline


title: cDC1s, KO3_PIC

value: Poly I:C


title: MPNST_S462_P_3

city: Shanghai

first: Zhichao

last: Wang

address: 639 Zhizaoju Road, Shanghai 200011, P.R. China

department: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

country: China

institute: Department of Plastic and Reconstructive Surgery

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters.
Reads Oer Kilobase of exon per Megabase of libarary size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms
Genome_build: mm8
Supplementary_files_format_and_content: tab-delimitied text files include RPKM values for each Sample.

source_name: MPNST cell lines

growth_protocol: All cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Gibco), supplemented with 10% fetal bovine serum (FBS, Gibco), glutamine and 1 x penicillin/streptomycin (Gibco) at 37℃ in a ddH2O humidified atmosphere with 5% CO2.

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

treatment_protocol: To generate MEKi-resistant cell lines, the parental NF1-MPNST cell line S462 was induced by conventional continuous exposure to trametinib, TAK-733 and selumetinib in a dose-stepwise increment for five months (with a change in medium three times per week).

value: Malignant peripheral nerve sheath tumors (MPNSTs)

value: control 3


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Spring-Rep3 F4X_S28

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Spring-Rep3
Organism Source: Carolina Biological Supply, 2014


title: cDC1s, WT2_BOTH


title: cDC1s, WT3_PBS


title: cDC1s, WT2_PIC


title: cDC1s, WT2_IL10


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep1 F3Y_S81

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Early Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: RC_111_baseline_IFX_NR_RNA

value: Non-remission

value: UC


title: cDC1s, WT2_PBS


title: cDC1s, KO2_PIC


title: RC_154_baseline_IFX_R_RNA


title: RC_070_2w_IFX_R_RNA


title: RC_060_baseline_IFX_NR_RNA


title: cDC1s, KO2_IL10


title: cDC1s, WT3_PIC


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Spring-Rep2 F3X_S27

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Spring-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep2 F2Z_S128

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: cDC1s, WT1_BOTH


title: cDC1s, WT1_IL10


title: RC_010_baseline_IFX_NR_RNA


title: cDC1s, KO1_PIC


title: RC_070_6w_IFX_R_RNA


title: cDC1s, KO1_IL10


title: RC_031_2w_ADA_NR_RNA

value: Adalimumab


title: RC_116_baseline_IFX_R_RNA


title: D.magna whole body, Woodland Wetland-119 ng/L pyriproxyfen-Summer-Rep4 8_S50

description:
D.magna whole body, Woodland Wetland-119 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: cDC1s, KO1_PBS

value: STAT3fl/fl CD11c-Cre+


title: cDC1s, WT1_PIC


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep3 F3Z_S129

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Spring-Rep1 F2X_S26

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Spring-Rep1
Organism Source: Carolina Biological Supply, 2014


title: cDC1s, WT1_PBS

value: PBS


title: D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep1 F1Z_S127

description:
D.magna whole body, BMP-37ST-Inflow-0 ng/L pyriproxyfen-Late Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Woodland Wetland-119 ng/L pyriproxyfen-Summer-Rep2 56_S53

description:
D.magna whole body, Woodland Wetland-119 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Woodland Wetland-119 ng/L pyriproxyfen-Summer-Rep1 52_S55

description:
D.magna whole body, Woodland Wetland-119 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: RC_142_6w_IFX_R_RNA


title: D.magna whole body, Woodland Wetland-119 ng/L pyriproxyfen-Summer-Rep5 99_S59

description:
D.magna whole body, Woodland Wetland-119 ng/L pyriproxyfen-Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: cDC1s, KO2_BOTH

value: Type I conventional dendritic cells (cDC1s)


title: cDC1s, KO2_PBS


title: RC_054_2w_IFX_NR_RNA

value: Replication


title: RC_012_6w_IFX_R_RNA

value: Infliximab


title: RC_004_6w_IFX_NR_RNA


title: cDC1s, KO1_BOTH


title: D.magna whole body, Woodland Wetland-119 ng/L pyriproxyfen-Summer-Rep3 81_S57

description:
D.magna whole body, Woodland Wetland-119 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: RC_042_baseline_IFX_NR_RNA


title: D.magna whole body, Woodland Wetland-0 ng/L pyriproxyfen-Summer-Rep5 80_S56

description:
D.magna whole body, Woodland Wetland-0 ng/L pyriproxyfen-Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: RC_144_baseline_IFX_R_RNA

value: Remission


title: RC_116_2w_IFX_R_RNA

value: CD


title: RC_055_baseline_IFX_R_RNA


title: RC_054_6w_IFX_NR_RNA


title: RC_116_6w_IFX_R_RNA


title: D.magna whole body, Woodland Wetland-0 ng/L pyriproxyfen-Summer-Rep2 48_S52

description:
D.magna whole body, Woodland Wetland-0 ng/L pyriproxyfen-Summer-Rep2
Organism Source: Carolina Biological Supply, 2014

value: D.magna whole body


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep5 L7Z_S161

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Woodland Wetland-0 ng/L pyriproxyfen-Summer-Rep3 4_S49

description:
D.magna whole body, Woodland Wetland-0 ng/L pyriproxyfen-Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Woodland Wetland-0 ng/L pyriproxyfen-Summer-Rep1 33_S51

description:
D.magna whole body, Woodland Wetland-0 ng/L pyriproxyfen-Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, Woodland Wetland-0 ng/L pyriproxyfen-Summer-Rep4 53_S54

description:
D.magna whole body, Woodland Wetland-0 ng/L pyriproxyfen-Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: RC_010_6w_IFX_NR_RNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep4 L4Z_S160

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep3 L3Z_S159

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: RC_022_2w_IFX_R_RNA


title: RC_063_baseline_IFX_NR_RNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep2 L2Z_S158

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep1 L1Z_S157

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: RC_144_6w_IFX_R_RNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Early Summer-Rep5 J7Y_S57

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Early Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: 33_14w_VDZ_NR_RNA

value: Discovery - Vedolizumab

value: Vedolizumab


title: RC_162_baseline_IFX_NR_DNA

type: genomic

hyb_protocol: Illumina protocol

scan_protocol: The Infinium© MethylationEPIC BeadChip was used to measure the DNA methylation levels. The EPIC arrays were processed according to Illumina recommendations.

data_processing:
DNA methylation data was analysed using the Bioconductor package RnBeads (version 1.12.1) with human reference genome version hg19.
The signal intensity values were normalized using the dasen method.

label: cy3, cy5

molecule: genomic DNA

source_name: Peripheral Whole Blood

label_protocol: Illumina protocol

extract_protocol: Blood (2.7 mL) was taken from each patient into an Ethylenediaminetetraacetic acid (EDTA) monovette (Sarstedt) to decelerate blood coagulation. The monovette was centrifuged for 15 min at 3000 rpm and the buffy coat was frozen in micronic tubes at -80°C. DNA was extracted using the QIAamp DNA Blood Mini Kit (Qiagen) according to manufacturer’s protocol with a QIACube (Qiagen).

tag: timepoint

value: baseline


title: RC_161_6w_IFX_NR_DNA


title: RC_161_2w_IFX_NR_DNA


title: RC_070_baseline_IFX_R_DNA


title: RC_161_baseline_IFX_NR_DNA


title: RC_162_2w_IFX_NR_DNA


title: RC_142_2w_IFX_R_DNA


title: RC_111_baseline_IFX_NR_DNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Spring-Rep6 J7X_S51

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Spring-Rep6
Organism Source: Carolina Biological Supply, 2014

value: SCSU Control-0 ng/L pyriproxyfen-Spring


title: RC_154_baseline_IFX_R_DNA


title: RC_140_2w_IFX_R_DNA


title: 32_4h_VDZ_NR_RNA


title: RC_063_6w_IFX_NR_DNA


title: RC_142_6w_IFX_R_DNA


title: RC_140_baseline_IFX_R_DNA


title: 33_6w_VDZ_NR_RNA


title: RC_063_2w_IFX_NR_DNA


title: RC_144_baseline_IFX_R_DNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Early Summer-Rep4 J6Y_S63

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Early Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: RC_111_6w_IFX_NR_DNA


title: RC_111_2w_IFX_NR_DNA


title: RC_162_6w_IFX_NR_DNA


title: RC_142_baseline_IFX_R_DNA


title: 33_2w_VDZ_NR_RNA


title: RC_116_baseline_IFX_R_DNA


title: RC_070_2w_IFX_R_DNA


title: RC_063_baseline_IFX_NR_DNA


title: 31_14w_VDZ_R_RNA


title: RC_060_baseline_IFX_NR_DNA


title: 32_baseline_VDZ_NR_RNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Spring-Rep4 J5X_S49

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Spring-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Spring-Rep5 J6X_S50

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Spring-Rep5
Organism Source: Carolina Biological Supply, 2014


title: RC_070_6w_IFX_R_DNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep5 J5Z_S151


title: 31_6w_VDZ_R_RNA


title: 33_4h_VDZ_NR_RNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep4 J4Z_S150


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Early Summer-Rep3 J4Y_S74

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Early Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: RC_055_6w_IFX_R_DNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep3 J3Z_S149


title: 31_2w_VDZ_R_RNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Spring-Rep3 J4X_S48

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Spring-Rep3
Organism Source: Carolina Biological Supply, 2014


title: 33_baseline_VDZ_NR_RNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep2 J2Z_S148


title: 31_baseline_VDZ_R_RNA


title: RC_042_baseline_IFX_NR_DNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Early Summer-Rep2 J3Y_S80

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Early Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: 30_14w_VDZ_R_RNA


title: RC_036_baseline_IFX_R_DNA


title: RC_055_baseline_IFX_R_DNA


title: RC_054_baseline_IFX_NR_DNA


title: 33_24h_VDZ_NR_RNA


title: 30_6w_VDZ_R_RNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Late Summer-Rep1 J1Z_S147


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Spring-Rep2 J2X_S47

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Spring-Rep2
Organism Source: Carolina Biological Supply, 2014


title: RC_031_2w_ADA_NR_DNA


title: RC_036_2w_IFX_R_DNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Early Summer-Rep1 J1Y_S91

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Early Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: RC_031_6w_ADA_NR_DNA


title: 30_baseline_VDZ_R_RNA


title: 30_2w_VDZ_R_RNA


title: RC_036_6w_IFX_R_DNA


title: RC_016_2w_IFX_NR_DNA


title: RC_010_baseline_IFX_NR_DNA


title: RC_004_baseline_IFX_NR_DNA


title: RC_016_baseline_IFX_NR_DNA


title: RC_004_2w_IFX_NR_DNA


title: D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Spring-Rep1 J1X_S46

description:
D.magna whole body, SCSU Control-0 ng/L pyriproxyfen-Spring-Rep1
Organism Source: Carolina Biological Supply, 2014


title: RC_004_6w_IFX_NR_DNA


title: RC_007_2w_IFX_NR_DNA


title: RC_012_baseline_IFX_R_DNA


title: RC_007_baseline_IFX_NR_DNA


title: 41_4h_VDZ_NR_RNA


title: 44_2w_IFX_NR_DNA

value: Discovery-Infliximab


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep4 K4Z_S155

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: 32_24h_VDZ_NR_RNA


title: 44_6w_IFX_NR_DNA


title: 42_6w_IFX_R_DNA


title: 42_baseline_IFX_R_DNA


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep5 K5Z_S156

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: RC_031_baseline_ADA_NR_DNA


title: 44_baseline_IFX_NR_DNA


title: 43_6w_IFX_R_DNA


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep3 K3Z_S154

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: 25_24h_VDZ_R_RNA


title: 20_2w_VDZ_R_RNA


title: 37_6w_VDZ_NR_RNA


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep2 K2Z_S153

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep1 K1Z_S152

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: 41_baseline_VDZ_NR_RNA


title: 43_baseline_IFX_R_DNA


title: 42_2w_IFX_R_DNA


title: 26_14w_VDZ_NR_RNA


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Early Summer-Rep5 I7Y_S101

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Early Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: 40_6w_IFX_R_DNA


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep5 I7Z_S146


title: 25_4h_VDZ_R_RNA


title: 43_2w_IFX_R_DNA


title: 40_2w_IFX_R_DNA


title: 39_baseline_IFX_NR_DNA


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Spring-Rep5 I7X_S45

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Spring-Rep5
Organism Source: Carolina Biological Supply, 2014

value: PIPE-SAP-0 ng/L pyriproxyfen-Spring


title: 37_2w_VDZ_NR_RNA

value: Non-remission


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep4 I6Z_S145


title: 26_6w_VDZ_NR_RNA


title: 39_6w_IFX_NR_DNA

value: UC


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Early Summer-Rep4 I6Y_S100

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Early Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: 39_2w_IFX_NR_DNA


title: 40_baseline_IFX_R_DNA


title: 25_baseline_VDZ_R_RNA


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Early Summer-Rep3 I5Y_S99

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Early Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: 20_baseline_VDZ_R_RNA


title: 38_baseline_IFX_NR_DNA


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Spring-Rep4 I5X_S44

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Spring-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep3 I4Z_S144


title: 26_2w_VDZ_NR_RNA


title: 37_baseline_VDZ_NR_RNA


title: H2B8 ChIP-seq input rep 2 (50% PEG drought)

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

country: United Kingdom

institute: John Innes Centre

library_source: genomic

data_processing:
ChIP-seq: Reads were mapped to TAIR10 using Bowtie2-2.3.4.1, retaining mononucleosomal fragments with using parameters -I 130 -X 200. Mapped reads were sorted and indexed using SAMtools-1.9.
ChIP-seq: Bigwig files were generated by normalising IP bam files to respective inputs with the bamCompare tool from deepTools-3.1.1. Bigwig files of enrichment were generated at single base resolution (w1) and at 50 bp intervals (w50).
ChIP-seq: To generate peaks, H2B.8 enrichment was calculated over 50 bp windows and those with > 0.5 log2(IP/input) were retained. Windows within 501 bp were merged using BEDtools-2.28.0. Regions were filtered by size, with those < 201 bp removed from analysis. H2B.8 enrichment was then calculated over the new regions, those with < 0.5 log2(IP/input) were discarded. The remaining regions were defined as H2B.8 peaks.
ChIP-seq: Overlaps with genes and TEs were determined using BEDtools-2.28.0; 50% of the feature was required to be overlapped by a peak to be defined as an overlap.
RNA-seq: Adapters were trimmed using TrimGalore-0.4.2.
RNA-seq: For differential expression analysis, reads were mapped to TAIR10 with TopHat-2.0.10. Kallisto-0.43.0 was used to obtain TPM (Transcripts Per Million) values. Pairwise statistical analysis was undertaken with Sleuth-0.30.0 in R-3.6.0. Differentially expressed genes and TEs were identified by log2 fold change of ≥ 2 and q < 0.05.
Hi-C: For Hi-C data assay, clean reads were mapped to TAIR10 genome using the HiC-Pro (version 2.11.1) pipeline. The bam files (bwt2merged.bam) generated by HiC-Pro containing mapping information were used as input files for Fan-C (version 0.9.8). The module ‘fanc auto’ was applied to generate 500 kb, 100 kb, 50 kb, 10 kb, 1kb contact matrix (hic files).
Assembly: TAIR10
Supplementary files format and content: ChIP-seq: Bigwig files generated with bamCompare in deepTools-3.1.1. Scores at w1 or w50 resolution represent log2(IP/input).
Supplementary files format and content: ChIP-seq: BED file of H2B.8 peaks in sperm and seedling.
Supplementary files format and content: ChIP-seq: BED file of H2B.8 peaks in sperm and seedling.
Supplementary files format and content: ChIP-seq: BED file of genes or TEs marked by H2B.8 in sperm and seedling.
Supplementary files format and content: RNA-seq: Matrix (.txt) file of WT and h2b.8 sperm cell replicate TPM values, fold change and q values for genes or TEs.
Supplementary files format and content: RNA-seq: Matrix (.txt) file of WT and p35S::H2B.8-eGFP seedling replicate TPM values, fold change and q values for genes or TEs.
Supplementary files format and content: RNA-seq: Matrix (.txt) file of drought treated and respective control WT and p35S::H2B.8-eGFP seedling replicate TPM values, fold change and q values for genes.
Supplementary files format and content: Hi-C: matrix and regions files of different resolution generated by Fan-C contain genomic contact and corresponding index information, respectively.

organism: Arabidopsis thaliana

source_name: p35S::H2B.8-eGFP seedling

growth_protocol: Plants were grown under long day (16 hr light; 8 hr dark) conditions at 22 °C.

extract_protocol:
Ten-day-old seedlings of a p35S::H2B.8-eGFP line were ground with a pestle and mortar in liquid N2 and homogenized in nuclei isolation buffer (0.25 M sucrose, 15 mM PIPES pH 6.8, 5 mM MgCl2, 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 0.9% Triton X-100, 1 mM PMSF, 1x proteinase inhibitor Cocktail). Nuclei were separated from debris by filtering through two layers of miracloth. Chromatin was fragmented by micrococcal nuclease (MNase, New England Biolabs) digestion. For IP samples, fragmented chromatin was immunoprecipitated with GFP-Trap beads. For input, no immunoprecipitation was undertaken. Protein and RNA was removed by digestion with Proteinase K and RNase A, respectively. Phenol-chloroform extraction was used to obtain DNA.
Libraries were prepared using the Ovation Ultralow System V2 (Nugen, 0344) and sequenced on the NextSeq 500 (Illumina) with 76 bp single end reads at the John Innes Centre, Norwich, UK.

tag: ecotype

value: ten-day-old seedlings

tag: chip antibody


title: H2B8 ChIP-seq input rep 2 (PBS control)


title: 19_14w_VDZ_NR_RNA


title: H2B8 ChIP-seq input rep 1 (50% PEG drought)


title: 29_baseline_IFX_NR_DNA


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep2 I3Z_S143


title: H2B8 ChIP-seq input rep 1 (PBS control)


title: 28_baseline_IFX_NR_DNA


title: 24_baseline_IFX_NR_DNA


title: 19_6w_VDZ_NR_RNA


title: H2B8 anti-GFP ChIP-seq rep 2 (50% PEG drought)

value: GFP-Trap beads


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Early Summer-Rep2 I4Y_S98

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Early Summer-Rep2
Organism Source: Carolina Biological Supply, 2014


title: H2B8 anti-GFP ChIP-seq rep 2 (PBS control)


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Early Summer-Rep1 I3Y_S97

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Early Summer-Rep1
Organism Source: Carolina Biological Supply, 2014


title: 15_baseline_IFX_R_DNA


title: 29_6w_IFX_NR_DNA


title: 28_6w_IFX_NR_DNA


title: 46_14w_VDZ_R_RNA


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Spring-Rep3 I3X_S43

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Spring-Rep3
Organism Source: Carolina Biological Supply, 2014


title: 24_6w_IFX_NR_DNA


title: 14_baseline_IFX_R_DNA


title: H2B8 anti-GFP ChIP-seq rep 1 (50% PEG drought)


title: 24_2w_IFX_NR_DNA


title: 13_baseline_IFX_R_DNA


title: 28_2w_IFX_NR_DNA


title: 14_6w_IFX_R_DNA


title: 23_6w_IFX_NR_DNA


title: 13_6w_IFX_R_DNA


title: H2B8 seedling  50% PEG drought stress RNA-seq replicate 2

description: H2B8_drought_experiment_gene_expression_master.txt

extract_protocol:
The Plant RNeasy mini kit (QIAGEN) was used to extract RNA from 10-day-old seedlings.
Libraries were prepared with the Nugen Universal RNA-Seq library preparation kit (0364) and sequenced on the NextSeq 500 (Illumina) with 76 bp single end reads at the John Innes Centre, Norwich, UK.


title: 26_24h_VDZ_NR_RNA


title: 23_baseline_IFX_NR_DNA


title: 38_6w_IFX_NR_DNA


title: 29_2w_IFX_NR_DNA


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Late Summer-Rep1 I2Z_S142


title: 38_2w_IFX_NR_DNA


title: H2B8 seedling 50% PEG drought stress RNA-seq  replicate 1


title: H2B8 seedling  PBS control RNA-seq replicate 2


title: 15_2w_IFX_R_DNA


title: 19_2w_VDZ_NR_RNA


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Spring-Rep2 I2X_S42

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Spring-Rep2
Organism Source: Carolina Biological Supply, 2014


title: H2B8 anti-GFP ChIP-seq rep 1 (PBS control)


title: D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Spring-Rep1 I1X_S41

description:
D.magna whole body, PIPE-SAP-0 ng/L pyriproxyfen-Spring-Rep1
Organism Source: Carolina Biological Supply, 2014


title: WT seedling  50% PEG drought stress RNA-seq replicate 2

source_name: WT seedling

value: WT


title: 26_4h_VDZ_NR_RNA


title: WT seedling 50% PEG drought stress RNA-seq  replicate 1


title: 13_2w_IFX_R_DNA


title: 22_14w_VDZ_R_RNA


title: WT seedling  PBS control RNA-seq replicate 2


title: 14_2w_IFX_R_DNA


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Early Summer-Rep5 G7Y_S90

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Early Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Early Summer-Rep4 G6Y_S89

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Early Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: 23_2w_IFX_NR_DNA


title: H2B.2-GFP anti-GFP ChIP rep2

source_name: p35S::H2B.2-eGFP seedling

extract_protocol:
Ten-day-old seedlings of a p35S::H2B.2-eGFP line were ground with a pestle and mortar in liquid N2 and homogenized in nuclei isolation buffer (0.25 M sucrose, 15 mM PIPES pH 6.8, 5 mM MgCl2, 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 0.9% Triton X-100, 1 mM PMSF, 1x proteinase inhibitor Cocktail). Nuclei were separated from debris by filtering through two layers of miracloth. Chromatin was fragmented by micrococcal nuclease (MNase, New England Biolabs) digestion. For IP samples, fragmented chromatin was immunoprecipitated with H3K9me2 containing beads. For input, no immunoprecipitation was undertaken. Protein and RNA was removed by digestion with Proteinase K and RNase A, respectively. Phenol-chloroform extraction was used to obtain DNA.
Libraries were prepared using the Ovation Ultralow System V2 (Nugen, 0344) and sequenced on the NextSeq 500 (Illumina) with 76 bp single end reads at the John Innes Centre, Norwich, UK.


title: 19_baseline_VDZ_NR_RNA


title: 12_6w_IFX_R_DNA


title: 15_6w_IFX_R_DNA


title: H2B.2-GFP input rep1


title: 46_2w_VDZ_R_RNA


title: H2B.2-GFP anti-GFP ChIP rep1


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Early Summer-Rep3 G5Y_S88

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Early Summer-Rep3
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Late Summer-Rep5 G5Z_S136

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Late Summer-Rep5
Organism Source: Carolina Biological Supply, 2014


title: H2B8-eGFP anti H3K9me2 ChIP-seq rep2

extract_protocol:
Ten-day-old seedlings of a p35S::H2B.8-eGFP line were ground with a pestle and mortar in liquid N2 and homogenized in nuclei isolation buffer (0.25 M sucrose, 15 mM PIPES pH 6.8, 5 mM MgCl2, 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 0.9% Triton X-100, 1 mM PMSF, 1x proteinase inhibitor Cocktail). Nuclei were separated from debris by filtering through two layers of miracloth. Chromatin was fragmented by micrococcal nuclease (MNase, New England Biolabs) digestion. For IP samples, fragmented chromatin was immunoprecipitated with H3K9me2 containing beads. For input, no immunoprecipitation was undertaken. Protein and RNA was removed by digestion with Proteinase K and RNase A, respectively. Phenol-chloroform extraction was used to obtain DNA.
Libraries were prepared using the Ovation Ultralow System V2 (Nugen, 0344) and sequenced on the NextSeq 500 (Illumina) with 76 bp single end reads at the John Innes Centre, Norwich, UK.

value: H3K9me2 antibody


title: 22_6w_VDZ_R_RNA


title: H2B8-eGFP anti H3K9me2 ChIP-seq rep1


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Spring-Rep5 G5X_S35

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Spring-Rep5
Organism Source: Carolina Biological Supply, 2014


title: 46_baseline_VDZ_R_RNA


title: H2B.2-GFP input rep2


title: H2B8-deltaIDR-eGFP-line 5 input

extract_protocol:
Ten-day-old seedlings of a p35S::H2B.8-deltaIDR-eGFP line were ground with a pestle and mortar in liquid N2 and homogenized in nuclei isolation buffer (0.25 M sucrose, 15 mM PIPES pH 6.8, 5 mM MgCl2, 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 0.9% Triton X-100, 1 mM PMSF, 1x proteinase inhibitor Cocktail). Nuclei were separated from debris by filtering through two layers of miracloth. Chromatin was fragmented by micrococcal nuclease (MNase, New England Biolabs) digestion. For IP samples, fragmented chromatin was immunoprecipitated with GFP-Trap beads. For input, no immunoprecipitation was undertaken. Protein and RNA was removed by digestion with Proteinase K and RNase A, respectively. Phenol-chloroform extraction was used to obtain DNA.
Libraries were prepared using the Ovation Ultralow System V2 (Nugen, 0344) and sequenced on the NextSeq 500 (Illumina) with 76 bp single end reads at the John Innes Centre, Norwich, UK.


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Late Summer-Rep4 G4Z_S135

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Late Summer-Rep4
Organism Source: Carolina Biological Supply, 2014


title: D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Spring-Rep4 G4X_S34

description:
D.magna whole body, PIPE-Crystal-Lake-0 ng/L pyriproxyfen-Spring-Rep4
Organism Source: Carolina Biological Supply, 2014


title: 25_14w_VDZ_R_RNA


title: H2B8-deltaIDR-eGFP-line 5 antiGFP ChIP-seq


title: Citrus unshiu-normal-shoots [Bisulfite-Seq]

city: Taizhou

first: Bei

last: Huang

state: Zhejiang

address: Daqiao street No.157

institute: Zhejiang citrus research institute

description: Bisulfite DNA

data_processing:
BS-Seq--reads were first processed with SOAPnuke (version 2.0.5), the clean reads were mapped to the sweet orange genome ,  and the duplicated reads were removed using Bismark (version 0.20.1).
The depth and coverage on of chromosomes were calculated with samtools (version 1.4) and bedtools (version 2.26.0)
The methylation detection along the whole genome were was conducted by using Bismark, which calculates the proportion of methylated reads at every genome site.
The differentially methylated regions (DMRs) between different groups were detected with metilene (version 0.2–7).
The pathway enrichment analysis of DMRs annotated genes were was conducted with KOBAS (version 2.1.1).
Assembly: Citrus sinensis v1.0
Supplementary files format and content: tab-delimited text files include DMR in different methylated site for each Sample

organism: Citrus unshiu

source_name: shoots; mature stems

growth_protocol: All the plants were grown in the rain-proof plastic tunnel of Zhejiang citrus institute (Zhejiang, China), and 20 healthy trees were selected for water deficit treatment and control, respectively. 1–1.5 m growing in an 80-cm plastic root-limiter containing a potting mix of goat manure and clay (7:3) . The trees in the greenhouse were exposed to natural variations in photoperiod throughout the experiment for 5 months (from October to flower bud appearance) from 2020 to 2021

extract_protocol:
Total DNA was extracted from shoots using the Hi-DNAsecure Plant Kit (Tiangen Biotech Co., Ltd. Beijing, Cat. No. DP350) following the instructor’s manual.
The conversion of unmethylated cytosines to thymidines of 1 µg fragmented DNA was carried out using the EZ DNA Methylation-Gold™ Kit (Zymo Research, Cat. No. D5005) following the instructor’s manual. The Sequencing libraries were prepared using the Accel-NGS® Methyl-Seq DNA Library kit (Swift BiosciencesTM, Cat. No. 30024), and PCR products corresponding to 300–500 bp were enriched, and quantified, and then finally sequenced on NovaSeq 6000 (Illumina).

treatment_protocol: At the beginning of the water deficit treatment, trees were fully watered, and soil moisture was measured at 9:00 am every day using the soil moisture meter (Zhejiang TOP Cloud-Agri Technology Co., Ltd, Zhejiang, China), followed by the evaporation of soil water naturally until reaching the set level (around 15%). The LD treatment lasted 75 days.

value: normal water

value: shoots; mature stems


title: 12_2w_IFX_R_DNA

label_protocol:
Illumina protocol
Illumina protocol

value: Infliximab

value: Remission


title: 26_baseline_VDZ_NR_RNA

value: CD


title: 22_2w_VDZ_R_RNA

value: Discovery - Vedolizumab


title: H2B8-deltaIDR-eGFP-line 2 antiGFP ChIP-seq


title: H2B8_seedling_RNAseq_rep3

description:
Seedling_genes_RNAseq_TPM_foldchange_Pval_matrix.txt
Seedling_TEs_RNAseq_TPM_foldchange_Pval_matrix.txt

data_processing:
RNA-seq: Adapters were trimmed using TrimGalore-0.4.2.
RNA-seq: For differential expression analysis, reads were mapped to TAIR10 with TopHat-2.0.10. Kallisto-0.43.0 was used to obtain TPM (Transcripts Per Million) values. Pairwise statistical analysis was undertaken with Sleuth-0.30.0 in R-3.6.0. Differentially expressed genes and TEs were identified by fold change of ≥ 2 and p < 0.05.
RNA-seq: For comparisons of expression between cell types, reads were mapped using HISAT2-2.1.0. Cufflinks-2.2.1 and Ballgown-2.16.0 in R-3.6.0 were used to generate FPKM (Fragments Per Kilobase of transcript per Million mapped reads) values.
Genome_build: TAIR10
Supplementary_files_format_and_content: RNA-seq: Matrix (.txt) file of WT and h2b.8 sperm cell replicate TPM values, fold change and P values for genes or TEs.
Supplementary_files_format_and_content: RNA-seq: Matrix (.txt) file of WT and 35Sp::H2B.8-eGFP seedling replicate TPM values, fold change and P values for genes or TEs.

source_name: 35Sp::H2B.8-eGFP seedling

extract_protocol:
The Plant RNeasy mini kit (QIAGEN) was used to extract RNA from 10-day-old seedlings. RNA was converted to cDNA by RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific).
Libraries were prepared with the Nugen Universal RNA-Seq library preparation kit (0364) and sequenced on the NextSeq 500 (Illumina) with 2 × 38 bp paired end reads at the John Innes Centre, Norwich, UK.


title: 25_6w_VDZ_R_RNA

value: Vedolizumab


title: 12_baseline_IFX_R_DNA

value: baseline


title: Citrus unshiu, control [CK RNA-seq]

data_processing:
The raw sequencing data was initially first filtered by Trimmomatic (version 0.36), low-quality reads were discarded, and the reads contaminated with adaptor sequences were trimmed
Clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the the same cluster.
Reads in the the same cluster were compared to each other by pairwise alignment, followed by extraction into a new sub-cluster of and then reads with sequence identity over 95% were extracted to a new sub-cluster.
Al the sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters.
Assembly: Citrus sinensis v1.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using TRIzol Reagent (Invitrogen, cat. NO 15596026. 2 µg of total RNAs wasere used for to strandedstandardize the RNA sequencing library.
RNA libraries for RNA-seq were prepared using KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) according to following the manufacturer’s instruction.

tag: time

value: Day 75


title: H2B8_seedling_RNAseq_rep2


title: Citrus unshiu-light drought 75 d-shoots [Bisulfite-Seq]

description: Bisulfite DNA

value: light drought


title: Citrus unshiu, light drought treated 75 d  [LD RNA-seq]


title: 22_baseline_VDZ_R_RNA


title: 25_2w_VDZ_R_RNA


title: WT_seedling_RNAseq_rep3


title: H2B8_seedling_RNAseq_rep1


title: 20_14w_VDZ_R_RNA


title: 20_6w_VDZ_R_RNA


title: Horse Y, control

city: Raleigh

first: Lauren

middle: V

last: Schnabel

state: North Carolina

address: 1060 William Moore Dr

institute: North Carolina State University

data_processing:
Sequence reads were trimmed to remove possible adaptor sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the EquCab 3.0 reference genome available on ENSEMBL using the STAR aligner v2.5.2b.
Unique gene hit counts were calculated using featureCounts from the Subread package v1.5.2.
Read count extraction and normalization were performed using DESeq2.
Assembly: EquCab 3.0
Supplementary files format and content: tab-deliniated text file containing normalized gene expression data

organism: Equus caballus

source_name: mesenchymal stem cells

growth_protocol: Primary equine bone marrow-derived mesenchymal cells were maintained in low glucose DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted using the Rneasy Mini Kit (Qiagen). 1.0 ug of total RNA was used for the construction of sequencing libraries.
PolyA selection

treatment_protocol: MSCs were seeded at 0.35x10^6 cells per 100 mm plate and grown for 72 hours in standard MSC media or media containing 2 ng/ml recombinant human IL-1b OR 2 ng/ml recombinant human IL-6

tag: Sex

value: Female

tag: source

value: bone marrow

value: mesenchymal stem cells

value: Control


title: Horse Y, IL-6 licensed


title: Horse Y, IL-1b licensed


title: Horse W, IL-6 licensed

value: Male


title: WT_seedling_RNAseq_rep2

value: WT

value: ten-day-old seedlings


title: WT_seedling_RNAseq_rep1


title: Horse W, IL-1b licensed


title: 5_2w_VDZ_R_RNA

value: UC


title: Horse S, IL-6 licensed


title: h2b8_sperm_cell_RNAseq_rep1

description:
Sperm_cell_genes_RNAseq_TPM_foldchange_Pval_matrix.txt
Sperm_cell_TEs_RNAseq_TPM_foldchange_Pval_matrix.txt

source_name: h2b.8 sperm cells

extract_protocol:
Sperm cells were isolated from pollen by FACS. RNA was extracted with Direct-zol RNA Microprep (ZYMO RESEARCH) and converted to cDNA by RevertAid First Strand cDNA Synthesis Kit (Thermo Fisher Scientific).
Libraries were prepared with the Nugen Universal RNA-Seq library preparation kit (0364) and sequenced on the NextSeq 500 (Illumina) with 76 bp single end reads at the John Innes Centre, Norwich, UK.

value: sperm cells


title: WT_sperm_cell_RNAseq_rep2

source_name: WT sperm cells


title: Horse S, IL-1b licensed


title: WT_sperm_cell_RNAseq_rep1


title: Horse S, control


title: 8_14w_VDZ_NR_RNA

value: Non-remission


title: H2B8 seedling PBS control RNA-seq replicate 1


title: 5_4h_VDZ_R_RNA

value: Remission


title: 8_6w_VDZ_NR_RNA


title: Horse L, IL-6 licensed


title: 5_baseline_VDZ_R_RNA


title: H2B8_seedling_IP_rep2

description:
H2B8_seedling_peaks.bed
Genes_with_H2B8_seedling_peak.bed
TEs_with_H2B8_seedling_peak.bed

data_processing:
ChIP-seq: Reads were mapped to TAIR10 using Bowtie2-2.3.4.1, retaining mononucleosomal fragments with using parameters -I 130 -X 200. Mapped reads were sorted and indexed using SAMtools-1.9.
ChIP-seq: Bigwig files were generated by normalising IP bam files to respective inputs with the bamCompare tool from deepTools-3.1.1. Bigwig files of enrichment were generated at single base resolution (w1) and at 50 bp intervals (w50).
ChIP-seq: To generate peaks, H2B.8 enrichment was calculated over 50 bp windows and those with > 0.5 log2(IP/input) were retained. Windows within 501 bp were merged using BEDtools-2.28.0. Regions were filtered by size, with those < 201 bp removed from analysis. H2B.8 enrichment was then calculated over the new regions, those with < 0.5 log2(IP/input) were discarded. The remaining regions were defined as H2B.8 peaks.
ChIP-seq: Overlaps with genes and TEs were determined using BEDtools-2.28.0; 50% of the feature was required to be overlapped by a peak to be defined as an overlap.
Genome_build: TAIR10
Supplementary_files_format_and_content: ChIP-seq: Bigwig files generated with bamCompare in deepTools-3.1.1. Scores at w1 or w50 resolution represent log2(IP/input).
Supplementary_files_format_and_content: ChIP-seq: BED file of H2B.8 peaks in sperm and seedling.
Supplementary_files_format_and_content: ChIP-seq: BED file of genes or TEs marked by H2B.8 in sperm and seedling.

extract_protocol:
Ten-day-old seedlings of a 35Sp::H2B.8-eGFP line were ground with a pestle and mortar in liquid N2 and homogenized in nuclei isolation buffer (0.25 M sucrose, 15 mM PIPES pH 6.8, 5 mM MgCl2, 60 mM KCl, 15 mM NaCl, 1 mM CaCl2, 0.9% Triton X-100, 1 mM PMSF, 1x proteinase inhibitor Cocktail). Nuclei were separated from debris by filtering through two layers of miracloth. Chromatin was fragmented by micrococcal nuclease (MNase, New England Biolabs) digestion. For IP samples, fragmented chromatin was immunoprecipitated with GFP-Trap beads. For input, no immunoprecipitation was undertaken. Protein and RNA was removed by digestion with Proteinase K and RNase A, respectively. Phenol-chloroform extraction was used to obtain DNA.
Libraries were prepared using the Ovation Ultralow System V2 (Nugen, 0344) and sequenced on the NextSeq 500 (Illumina) with 2 × 38 bp paired end reads at the John Innes Centre, Norwich, UK.

value: GFP-Trap beads


title: Horse L, IL-1b licensed


title: Horse L, control


title: 4_14w_VDZ_R_RNA

value: Discovery - Vedolizumab


title: H2B8_sperm_input_rep2

description:
H2B8_sperm_peaks.bed
Genes_with_H2B8_sperm_peak.bed
TEs_with_H2B8_sperm_peak.bed

source_name: H2B.8p::H2B.8-eGFP pollen

extract_protocol:
Pollen was collected in Galbraith buffer (45 mM MgCl2, 30 mM Sodium Citrate, 20 mM MOPS, 1% Triton-100, pH 7.0) from open flowers of a H2B.8p::H2B.8-eGFP line. Nuclei were released from pollen by vortexing and subsequent debris was removed by filtration. Chromatin was fragmented by micrococcal nuclease (MNase, New England Biolabs) digestion. For IP samples, fragmented chromatin was immunoprecipitated with GFP-Trap beads. For input, no immunoprecipitation was undertaken. Protein and RNA was removed by digestion with Proteinase K and RNase A, respectively. Phenol-chloroform extraction was used to obtain DNA.
Libraries were prepared using the Ovation Ultralow System V2 (Nugen, 0344) and sequenced on the NextSeq 500 (Illumina) with 2 × 38 bp paired end reads at the John Innes Centre, Norwich, UK.

value: whole pollen


title: H2B8_seedling_IP_rep1


title: Horse F, IL-6 licensed


title: H2B8_seedling_input_rep1


title: 8_2w_VDZ_NR_RNA

value: Vedolizumab


title: h2b8_sperm_cell_RNAseq_rep2


title: 41_24h_VDZ_NR_RNA

value: CD


title: 5_24h_VDZ_R_RNA


title: Horse F, IL-1b licensed


title: Horse W, control


title: 8_baseline_VDZ_NR_RNA

value: baseline


title: H2B8_sperm_IP_rep2


title: 4_6w_VDZ_R_RNA


title: H2B8_seedling_input_rep2


title: H2B8_sperm_input_rep1


title: 7_14w_VDZ_R_RNA


title: Horse A, IL-6 licensed


title: Horse A, IL-1b licensed


title: 4_2w_VDZ_R_RNA


title: T1_21_TFI

city: Munich

first: Maryam

last: Kazerani

address: Feodor-Lynen-Strasse 25

institute: LMU Gene Center

data_processing:
Sequencing reads were aligned to release 101 of Ensembl GRCh38 prior to counting reads per gene with Star (version 2.7.6a) using default parameters. Values for expression (in transcripts per million, TPM) were calculated with RSEM (1.3.3) using default parameters.
Genome_build: GRCh38
Supplementary_files_format_and_content: *rsem.genes.results were generated with RSEM

source_name: healthy donor T cells

extract_protocol:
Total RNA was extracted with Trizol and RNA clean and concentrator kit (Zymo research), including the on-column DNAse step.
NEBNext Ultra II Directional RNA Library Prep Kit for Illumina

treatment_protocol: T cells from 3 different heathy donors in coculture with a lymphoma cell line (OCI-Ly1), T cells were stimulated with the CD19xCD3 Bispecific T-cell engager, either continuously (Cont) or intermittently (Treatment-free interval=TFI from day 7-14), T cells were FACS sorted at day 0, 7, 14, 21.

tag: donor id

value: T cells

value: treatment-free interval (TFI) during CD19xCD3 stimulation from day 7-14, restimulation with CD19xCD3 from day 14-21

value: day 21

tag: facs sorting marker


title: 7_6w_VDZ_R_RNA

extract_protocol:
Patient peripheral blood was collected in 2.5mL tubes PAXgene Blood RNA Tubes, RNA was automated isolated in QIAGEN’s QIAcube using the PAXgene Blood miRNA Kit from QIAGEN PreAnalytiX.
RNA Sequencing libraries were prepared from Paxgene™ Blood RNA Tubes (Qiagen) according to the Illumina TruSeq® messenger RNA (mRNA) sequencing protocol (TruSeq® RNA Seq Library Prep Kit v2)
Paired-end sequencing (2x75bp) was performed on Illumina HiSeq 4000


title: T2_21_TFI

tag: cell type


title: 4_baseline_VDZ_R_RNA


title: 3_14w_VDZ_NR_RNA


title: Horse F, control

value: Female

value: bone marrow

value: mesenchymal stem cells

value: Control


title: 7_2w_VDZ_R_RNA


title: 3_6w_VDZ_NR_RNA


title: 7_baseline_VDZ_R_RNA


title: H2B8_sperm_IP_rep1

tag: genotype


title: Horse A, control

value: Male

tag: treatment


title: T1_21_Cont

value: continuous stimulation with CD19xCD3 Bispecific T-cell engager


title: T3_21_TFI


title: T2_21_Cont


title: 3_2w_VDZ_NR_RNA

tag: patient

value: Non-remission


title: MSC, Sh-CLOCK, rep2

city: Shenzhen

first: Peitao

last: Xu

address: No.3025, Shennan Middle Street

institute: The Eighth Affiliated Hospital of Sun Yat-sen University

data_processing:
The sequencing data were filtered with SOAPnuke (v1.5.2)11 by (1) removing reads containing sequencing adaptors; (2) removing reads whose low-quality base ratio (base quality less than or equal to 5) was more than 20%; and (3) removing reads whose unknown base ('N' base) ratio was more than 5%
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5)13 was used to align the clean reads to the reference coding gene set, and then the expression level of the gene was calculated by RSEM (v1.2.12)
Differential expression analysis was performed using DESeq2 (v1.4.5)15 with a Q value ≤ 0.05
Assembly: Grch38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow

growth_protocol: MSCs were seeded in 12-well plates at a density of 5×104/well and cultured with DMEM (1000 mg/L glucose) with 10% FBS

extract_protocol:
Total RNA was extracted from MSCs using TRIzol (Invitrogen), and 1 μg of isolated RNA was the construction of sequencing libraries.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was  generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end  repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on  the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the  final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300  copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Lentiviruses were used to diminish BMAL1 or CLOCK in MSCs, and culture medium was changed to osteogenic medium (OM) to induce osteogenic differentiation, consisting of DMEM (glucose 1000 mg/L) with 10% FBS, 100 IU/mL penicillin, 100 IU/mL streptomycin, 0.1 μM dexamethasone, 10 mM β-glycerol phosphate, and 50 μM ascorbic acid (Sigma-Aldrich). The OM was changed every 3 days thereafter for 7 days

value: Bone marrow

value: Mesenchymal stem cells

value: Sh-CLOCK


title: MSC, Sh-NC, rep3

value: Sh-NC


title: T2_14_TFI

value: treatment-free interval (TFI) during CD19xCD3 stimulation from day 7-14

value: day 14


title: MSC, Sh-CLOCK, rep3


title: MSC, Sh-NC, rep2


title: 5_14w_VDZ_R_RNA

tag: cohort

value: Discovery - Vedolizumab

value: Vedolizumab

value: Remission

value: UC


title: MSC, Sh-BMAL1, rep3


title: MSC, Sh-BMAL1, rep2


title: MSC, Sh-NC, 1, rep1


title: T1_14_TFI

value: T cells


title: 5_6w_VDZ_R_RNA

tag: remission at week 14


title: T3_21_Cont

value: day 21


title: WT seedling PBS control RNA-seq replicate 1

value: WT

value: ten-day-old seedlings


title: 3_baseline_VDZ_NR_RNA

tag: time point

value: baseline

value: CD


title: T3_14_Cont

value: continuous stimulation with CD19xCD3 Bispecific T-cell engager


title: MSC, Sh-BMAL1, rep1

value: Bone marrow


title: T3_14_TFI


title: 14_2w_IFX_R_RNA

value: Discovery - Infliximab

value: Infliximab

tag: diagnosis


title: T2_14_Cont


title: KO_E115_3 [scRNAseq]

city: San Francisco

first: Sanjeev

last: Ranade

state: CA

address: 1650 Owens St

institute: Gladstone Institutes

description:
Single cell transcriptomes (10X Genomics)
barcodes_WTplusTbx1.tsv.gz,features_WTplusTbx1.tsv.gz,matrix_WTplusTbx1.mtx.gz

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with intronic reads kept with the Cellranger Suite (v5) from 10X genomics
Additional filtering, quality control and doublet removal was done using Seurat v3 (scripts at https://github.com/sanjeevRJMU1)
Assembly: mm10
Supplementary files format and content: Cellranger aggr tab-delimited cell barcode information
Supplementary files format and content: Cellranger aggr tab-delimited feature information
Supplementary files format and content: Cellranger aggr sparse expression matrix

source_name: Embryonic mouse heart outflow tract only and cardiopharyngeal region at E11.5

growth_protocol: Similar to deSoysa et al., Nature 2019, timed matings were set up between WT C57Bl6/J male and female mice or Tbx1 Het x Het male and female mice in the evening. Morning of plug detection was considered E0.5 and embryos were harvested at indicated stage.

extract_protocol:
Similar to deSoysa et al., Nature 2019, single cell suspensions containing between 5k - 10k cells were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell NEXTGEM v3.1 Library & Gel Bead Kit

treatment_protocol: Similar to deSoysa et al., Nature 2019, embryos were dissected in PBS and 1% FBS on ice. Regions of interest were microdissected and dissociated in 200ul TryplE for 5-15 minutes at 37C followed by brief trituration and incubation as needed. TryplE was quenched with 600ul PBS/1% FBS, cells were strained with a FACS tube strainer to dissociate clumps and centrifuged at 150 rcf for 3 minutes and resuspended in 50-100 ul of PBS/1% FBS. Cells were then counted and loaded onto 10X Chromium instrument according to manufacturer's directions.

value: Tbx1 KO Littermate

tag: strain

tag: specific heart region

value: Cardiogenic and cardiopharyngeal region

value: Non-cardiac mesoderm, ectoderm and endoderm


title: 29_72h_IFX_NR_RNA

value: Non-remission


title: WT_E105_2

description: Single cell transposase accessible chromatin fragmented nuclei (10X Genomics)

data_processing:
Illumina Casava v1.8 was used for base-calling.
Reads were demultiplexed, aligned, read normalized and quantified with the Cellranger-atac Suite (v1.2) from 10X genomics
Additional filtering, quality control and doublet removal was done using ArchR v1.1 (scripts at https://github.com/sanjeevRJMU1)
Assembly: mm10
Supplementary files format and content: aligned fragments.tsv.gz file, individual fragments used as input for peak calling ArchR

source_name: Embryonic mouse heart and cardiopharyngeal region at E10.5

extract_protocol:
Single nuclei suspensions containing between 10k nuclei post transposition with Tn5 were loaded into the Chromium controller (10X genomics) microfluidic chip for single cell droplet library preparation.
Libraries were prepared according to the manufacturer’s instructions (10X Genomics) using the Chromium Single Cell NEXTGEM v1.1 scATAC-seq reagents

treatment_protocol: Similar to deSoysa et al., Nature 2019, embryos were dissected in PBS and 1% FBS on ice. Regions of interest were microdissected and dissociated in 200ul TryplE for 5-15 minutes at 37C followed by brief trituration and incubation as needed. TryplE was quenched with 600ul PBS/1% FBS, cells were strained with a FACS tube strainer to dissociate clumps and centrifuged at 150 rcf for 3 minutes and resuspended in 50-100 ul of PBS/1% FBS. Nuclei were then isolated according to manufacturer's protocols (https://support.10xgenomics.com/single-cell-gene-expression/sample-prep/doc/demonstrated-protocol-isolation-of-nuclei-for-single-cell-rna-sequencing-and-tissues-for-single-cell-rna-sequencing). Nuclei were then counted and processed according to 10x v1.1 NEXTGEM scATAC-seq protocols.

value: WT C57Bl6/J

tag: additional cell lineages present in dataset


title: WT_E95_2

source_name: Embryonic mouse heart and cardiopharyngeal region at E9.5


title: T1_14_Cont

tag: timepoint

value: day 14


title: WT_E95_3


title: KO_E115_2 [scRNAseq]


title: T3_7_Cont

value: day 7


title: KO_E115_1 [scRNAseq]


title: KO_E105_1 [scRNAseq]


title: 38_baseline_IFX_NR_RNA

source_name: Peripheral Whole-Blood


title: H3K27me3_dKO_2

city: Boston

first: Dong Feng

last: Chen

state: Massachusetts

address: 20 Staniford St

institute: Schepens Eye Research Institute

data_processing:
ChIP-seq: Alignments were carried out with Bowtie2, Samtools and macs2 were used for data processing.
Genome_build: mm10

source_name: retinal ganglion cells

extract_protocol:
ChIP-seq:  P1 retinal ganglion cells were collected as described in extract protocol for RNA-seq and chromatin immunoprecipitation was performed with EZ- CHIP kit from Millipore according to manufacturer's protocol.
For ChIP-seq: Library preparation was done with Rubicon Genomics Thruplex DNAseq.

tag: strain/genotype

value: Math5Cre;G9a+/fEzh2-/- (dKO)

tag: tissue

value: retina

tag: chip antibody

value: H3K27me3 (07-449, Merck Millipore)


title: WT_E95_1


title: T1_7_Cont

tag: donor id

value: T cells


title: T3_0_Cont

value: day 0

tag: facs sorting marker


title: MSC, Sh-CLOCK, rep1

tag: cell type

value: Mesenchymal stem cells

value: Sh-CLOCK


title: KO_E105_2 [scRNAseq]

tag: genotype


title: 29_4h_IFX_NR_RNA

tag: treatment

value: UC


title: input dKO_1

value: none (input)


title: 44_14w_IFX_NR_RNA

tag: patient

value: Discovery - Infliximab

value: Infliximab


title: KO_E925_1 [scRNAseq]

value: Tbx1 KO Littermate

value: Cardiogenic and cardiopharyngeal region


title: 44_6w_IFX_NR_RNA

tag: cohort

value: Non-remission


title: T1_0_Cont

value: continuous stimulation with CD19xCD3 Bispecific T-cell engager


title: T2_0_Cont


title: WT_E115_2 [scRNAseq]

description:
Single cell transcriptomes (10X Genomics)
barcodes_WT.tsv.gz,features_WT.tsv.gz,matrix_WT.mtx.gz,barcodes_WTplusTbx1.tsv.gz,features_WTplusTbx1.tsv.gz,matrix_WTplusTbx1.mtx.gz

value: Tbx1 WT Littermate

value: Non-cardiac mesoderm, ectoderm and endoderm


title: 44_baseline_IFX_NR_RNA

tag: remission at week 14

value: baseline


title: H3K27me3_WT_1

value: WT

value: retina


title: H3K27me3_dKO_1

value: Math5Cre;G9a+/fEzh2-/- (dKO)

value: H3K27me3 (07-449, Merck Millipore)


title: 40_14w_IFX_R_RNA

value: Remission

tag: time point

value: CD


title: 29_24h_IFX_NR_RNA

tag: diagnosis

value: UC


title: 40_2w_IFX_R_RNA


title: 14_24h_IFX_R_RNA


title: input dKO_2

value: none (input)


title: WT_E115_1 [scRNAseq]

tag: strain


title: input WT_2


title: T2_7_Cont

value: T cells

value: day 7


title: H2B8-deltaIDR-eGFP-line 2 input

tag: ecotype

value: ten-day-old seedlings


title: WT_E105_4 [scRNAseq]

tag: specific heart region

value: Cardiogenic and cardiopharyngeal region


title: input WT_1


title: Input sKO_2

value: Math5Cre;Ezh2-/- (single knockout)


title: B3: High phosphorus treated endothelial cells- exosome-Rep-3

type: RNA

city: Changsha

first: Su-Kang

last: Shan

address: 139 Middle Renmin Road

institute: Central South University

description: Mice ECs were purchased from CHI Scientific, Inc. (1-3029) with STR certification.

hyb_protocol: The Hy3TM-labeled samples were hybridized on the miRCURYTM LNA Array (v.19.0) (Exiqon) according to array manual

scan_protocol: The slides were scanned using the Axon GenePix 4000B microarray scanner (Axon Instruments, Foster City, CA).

data_processing: Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and data extraction. Replicated miRNAs were averaged and miRNAs that intensities>=30 in all samples were chosen for calculating normalization factor. Expressed data were normalized using the Median normalization. After normalization, significant differentially expressed miRNAs between two groups were identified through Fold change and P-value. Differentially expressed miRNAs between two samples were filtered through Fold change. Finally, hierarchical clustering was performed to show distinguishable miRNA expression profiling among samples.

source_name: HPi Exo,replicate 3

label_protocol: The miRCURYTM Array Power labeling kit (Cat #208032-A,Exiqon, Vedbaek, Denmark) was used according to the manufacturer’s guideline for miRNA labelling.

growth_protocol: ECs were cultured in F-12k medium (Hyclone, Logan, USA) supplemented with 12% FBS (Gibco, Invitrogen, New York, USA), penicillin (100 U/mL) and streptomycin (100 μg/mL), 0.05 mg/mL endothelial cell growth supplement (ECGS) and 0.1 mg/mL heparin (Sciencell, San Diego, USA).

extract_protocol: RNA was extracted using the TRIzol method and purified using the RNasey Mini Kit (QIAGEN). Purified RNA concentration was measured using NanoDrop ND-1000, and RNA integrity was detected by electrophoresis

treatment_protocol: Upon reaching 50% to 70% confluency, ECs were treated with normal concentration phosphate (0.9 mM of inorganic phosphate) or high concentration phosphate (3.5 mM of inorganic phosphate) for 48 h.Then exosomes were isolated from ECs culture supernatants by the differential centrifugation method.

tag: parent cell

value: endothelial cell


title: KO_E925_2 [scRNAseq]

value: Tbx1 KO Littermate


title: H3K27me3_WT_2

tag: strain/genotype


title: B2: High phosphorus treated endothelial cells-exosome-Rep 2

source_name: HPi Exo,replicate 2


title: 23_72h_IFX_NR_RNA

value: Discovery - Infliximab

value: Infliximab

value: Non-remission


title: WT_E105_3 [scRNAseq]

value: Tbx1 WT Littermate

value: Non-cardiac mesoderm, ectoderm and endoderm


title: Input sKO_1

tag: tissue

value: retina


title: WT_E105_2 [scRNAseq]

description:
Single cell transcriptomes (10X Genomics)
barcodes_WT.tsv.gz,features_WT.tsv.gz,matrix_WT.mtx.gz

value: WT


title: WT_E105_1 [scRNAseq]


title: 43_14w_IFX_R_RNA

value: Remission


title: H3K27me3_sKO_2

tag: chip antibody

value: H3K27me3 (07-449, Merck Millipore)


title: 14_4h_IFX_R_RNA

value: CD


title: A2: Normal phosphorus treated endothelial cells-exosome-Rep2

source_name: NPi Exo,replicate 2


title: B1: High phosphorus treated endothelial cells-exosome-Rep1

source_name: HPi Exo,replicate 1


title: A3: Normal phosphorus treated endothelial cells- exosome-Rep3

source_name: NPi Exo,replicate 3


title: WT_E95_3 [scRNAseq]


title: 40_baseline_IFX_R_RNA

value: baseline


title: H3K27me3_sKO_1


title: WT_E95_2 [scRNAseq]


title: A1: Normal phosphorus treated endothelial cells-exosome-Rep1

source_name: NPi Exo,replicate 1


title: WT_E95_4 [scRNAseq]


title: 23_24h_IFX_NR_RNA

value: UC


title: WT_E95_1 [scRNAseq]


title: SC248

city: Ann Arbor

first: Lam

last: Tsoi

state: MI

address: Medical Sciences 1 Bldg. 1301 E. Catherine

institute: University of Michigan

library_source: transcriptomic single cell

data_processing:
data processing including quality control, read alignment and gene quantification were conducted using the 10X Cell Ranger software
Seurat was then used for normalization, data integration, and clustering analysis
Assembly: GRCh38
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Skin

extract_protocol:
A skin biopsy (3 mm) of the involved forearm skin was performed on each participant, at baseline and at week 12.
Biopsies were stored in RNAlater® and fresh skin tissue was transferred to University of Pittsburgh on the same day. Further details are included in the Supplementary files.

tag: condition

value: Systemic sclerosis (SSc)

value: Skin

value: TOFA

tag: individual

tag: time


title: 43_6w_IFX_R_RNA

data_processing:
Fastq files were mapped and aligned using nf-core ((https://github.com/nf-core/rnaseq)) rnaseq pipeline.
Adapters and low-quality bases from the RNA-seq reads were removed using Trim Galore (version 0.4.4), which is a wrapper tool for Cutadapt and FastQC. Reads that were shorter than 35 bp after trimming were discarded.
The filtered reads were mapped to the human genome (GRCh38, gencode version 25) using STAR aligner (version 2.5.2b).
featureCounts (version 1.5.2) was used to estimate the expression counts of the genes.
Genome_build: (GRCh38, gencode version 25)
Supplementary_files_format_and_content: tab-delimited text files include feature counts


title: E82_Grain_R1

city: Córdoba

first: Francisco

last: Barro Losada

state: Córdoba

address: Alameda Del Obispo

country: Spain

institute: Institute of Sustainable Agriculture

data_processing:
The adaptor sequences of raw reads were trimmed and the reads were filter by Trimmomatic-0.36 (params: ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 AVGQUAL:20 LEADING:3 TRAILING:3 MINLEN:36). The reads were pseudoaligned to the RefSeq v1.1 transcriptome with kallisto v0.44.0 with default parameters (--pseudobam included).
Differential Gene Expression (DGE) analysis was performed with edgeR v.3.22.5 in R v.3.6.3. We established that differentially expressed (DE) genes had a False Discovery Rate (FDR) < 0.05. Two pair-wise comparisons were performed: BW208 grain tissue vs E82 grain tissue, and BW208 leaf tissue vs E82 leaf tissue. The genes with a sum of Counts Per Million (CPM) in all samples higher than 1 were considered in the DGE analysis.
Assembly: RefSeq v1.1 wheat transcriptome IWGSC
Supplementary files format and content: csv files include TPM values for each Sample
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Triticum aestivum

source_name: Grain

extract_protocol:
Grains and leaves were milled and frozen with liquid nitrogen, and RNA was harvested using Trizol reagent with the Direct-zol RNA Kits (zymoresearch.com). rRNA was removed using the Ribo-Zero kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: replicate

tag: genotype

value: E82 line


title: 13_72h_IFX_R_RNA

tag: patient

tag: treatment


title: WT_E825_1 [scRNAseq]

source_name: Embryonic mouse heart and cardiopharyngeal region at E8.5

value: Cardiogenic and cardiopharyngeal region

tag: cell type


title: E82_Grain_R3


title: SC238

value: PBO


title: SC254


title: WT_E825_2 [scRNAseq]


title: BW208_Grain_R3

value: wild type


title: 39_14w_IFX_NR_RNA

tag: cohort

value: Discovery - Infliximab

value: Infliximab

tag: remission at week 14

value: Non-remission

tag: time point


title: SC239


title: BW208_Grain_R2


title: BW208_Grain_R1


title: 23_4h_IFX_NR_RNA

tag: diagnosis


title: 43_2w_IFX_R_RNA


title: E82_Grain_R2


title: SC245


title: SC235


title: WT_E775_1 [scRNAseq]

source_name: Embryonic mouse heart and cardiopharyngeal region at E7.75

tag: strain

tag: specific heart region

value: Non-cardiac mesoderm, ectoderm and endoderm


title: 39_2w_IFX_NR_RNA


title: SC177


title: WT_E775_5 [scRNAseq]

value: WT


title: E82_Leaf_R2

source_name: Leaf


title: 12_72h_IFX_R_RNA

value: Remission


title: SC183


title: E82_Leaf_R3


title: KO_E115_1

value: Tbx1 WT Littermate (C57Bl6/J background)

tag: additional cell lineages present in dataset


title: 13_24h_IFX_R_RNA

value: CD


title: WT_E775_4 [scRNAseq]


title: SC214

tag: tissue


title: WT_E775_3 [scRNAseq]


title: LN229, metformin 6

city: Taipei

first: YAO FENG

last: LI

address: No.161, Sec. 6, Minquan E. Rd., Neihu Dist., Taipei City 11490, Taiwan

department: Pathology

country: Taiwan

institute: National Defense Medical Center

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

growth_protocol: LN229 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using total RNA using TRIzol reagent (Invitrogen) and assessed its quality at 260/280 nm and 260/230 nm.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: LN229 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics supplemented 100mM metformin with  in humidified atmosphere with 5% CO2 at 37C

tag: cell line

value: glioblastoma

value: IDH wildtype

value: Metformin


title: SC225

tag: condition

value: Systemic sclerosis (SSc)

value: Skin


title: SC236

value: TOFA

tag: individual


title: KO_E115_3

value: Cardiogenic and cardiopharyngeal region


title: BW208_Leaf_R3


title: KO_E105_2

value: Tbx1 KO Littermate (C57Bl6/J background)


title: WT_E775_2 [scRNAseq]


title: SC190

value: PBO

tag: time


title: KO_E115_2


title: E82_Leaf_R1

tag: replicate

value: E82 line


title: 13_4h_IFX_R_RNA

value: Discovery - Infliximab

value: Infliximab


title: 43_baseline_IFX_R_RNA

value: baseline

value: UC


title: SC178


title: 12_24h_IFX_R_RNA

value: Remission


title: 38_14w_IFX_NR_RNA

value: Non-remission


title: LN229, metformin 4

tag: genotype


title: KO_E925_2

value: Non-cardiac mesoderm, ectoderm and endoderm


title: LN229, metformin 3

value: glioblastoma


title: KO_E925_1


title: 12_4h_IFX_R_RNA

tag: patient


title: KO_E825_2


title: SC176

tag: treatment


title: 39_6w_IFX_NR_RNA


title: SC229

value: TOFA-Bsl


title: SC172


title: 13_baseline_IFX_R_RNA

value: CD


title: WT_E115_2


title: BW208_Leaf_R1

value: wild type


title: LN229, metformin 5

tag: cell type

value: IDH wildtype

value: Metformin


title: LN229, control 6

value: no treat


title: KO_E105_1

value: Tbx1 KO Littermate (C57Bl6/J background)

value: Cardiogenic and cardiopharyngeal region


title: 39_baseline_IFX_NR_RNA

tag: cohort


title: SC230

value: Systemic sclerosis (SSc)

value: Skin

value: PBO

value: PBO-Bsl


title: 23_2w_IFX_NR_RNA

value: Discovery - Infliximab

value: Infliximab

tag: remission at week 14

value: UC


title: WT_E115_1

value: Tbx1 WT Littermate (C57Bl6/J background)

value: Non-cardiac mesoderm, ectoderm and endoderm


title: LN229, control 4

value: glioblastoma


title: SC224

value: TOFA

value: TOFA-Bsl


title: SC237


title: BW208_Leaf_R2

value: wild type


title: LN229, metformin 2

value: IDH wildtype

value: Metformin


title: SC240


title: LN229, metformin 1


title: 38_2w_IFX_NR_RNA

value: Non-remission

tag: time point

value: CD


title: SC247

value: Systemic sclerosis (SSc)


title: 38_6w_IFX_NR_RNA

tag: diagnosis


title: LN229, control 5

value: no treat


title: SC226

value: Skin


title: 12_14w_IFX_R_RNA

value: Remission


title: WT_E105_3

value: Cardiogenic and cardiopharyngeal region

tag: strain


title: WT_E105_1

value: WT C57Bl6/J

tag: specific heart region


title: KO_E825_1

value: Tbx1 KO Littermate (C57Bl6/J background)

tag: additional cell lineages present in dataset


title: 23_baseline_IFX_NR_RNA

value: Discovery - Infliximab

value: Infliximab

value: baseline

value: UC


title: 12_6w_IFX_R_RNA


title: WT_E95_4

value: Tbx1 WT Littermate (C57Bl6/J background)

value: Non-cardiac mesoderm, ectoderm and endoderm


title: 28_2w_IFX_NR_RNA


title: WT_E95_5


title: 28_baseline_IFX_NR_RNA


title: SC164

tag: tissue

value: TOFA

value: TOFA-Bsl


title: LN229, control 1

tag: cell line

value: glioblastoma

value: IDH wildtype


title: 15_6w_IFX_R_RNA


title: 15_14w_IFX_R_RNA


title: LN229, control 2


title: WT_E105_4


title: SC184

tag: condition

value: Systemic sclerosis (SSc)

value: PBO

value: PBO-Bsl


title: WT_E825_5


title: SC202

value: Skin

tag: individual


title: PA1 cells, sisox2, rep2

city: Birmingham

first: Ryan

last: Miller

state: AL

address: 1824 Sixth Ave S

institute: UAB

data_processing:
Basecall to fastq file generation (bcl2fastq2/2.20.0-foss-2016b-Python-2.7.12)
Fragments aligned to the human genome using Star (STAR/2.7.3a-GCC-6.4.0-2.28)
Aligned fragments counted using Salmon (Salmon/0.14.1-foss-2018b)
DESeq2 analysis performed (variables for modeling: replicate, genotype, treatment) to obtain differential gene expression data, raw counts, and normalized counts (DESeq2_1.28.1)
Data was filtered to exclude genes where there were less than 3 samples with normalized read counts less than or equal to 5
Genome_build: GENCODE v32 (GRCh38.p13)
Supplementary_files_format_and_content: raw_counts.csv file is a matrix of raw read counts (every gene for every sample) obtained from R package DESeq2

source_name: ovarian teratocarcinoma

extract_protocol:
RNA from cultured cells was extracted using Trizol
Library prep was performed using a KAPA mRNA HyperPrep Kit (KK8581) and prepared for sequencing using standard Illumina protocol (final loading concentration 1.65pM)

value: Human ovarian teratocarcinoma

value: wildtype


title: PA1 cells, sicontrol, rep3

value: control siRNA


title: SC169

tag: time


title: WT_E825_4

value: Cardiogenic and cardiopharyngeal region


title: WT_E825_3

value: WT C57Bl6/J


title: LN229, control 3

value: no treat


title: SC212


title: PA1 cells, sisox2, rep1


title: PA1 cells, sisox2, rep3


title: SC160


title: 15_2w_IFX_R_RNA

value: Discovery - Infliximab

value: Infliximab

value: Remission

value: UC


title: WT_E825_2

value: Non-cardiac mesoderm, ectoderm and endoderm


title: 12_2w_IFX_R_RNA


title: PA1 cells, sicontrol, rep1


title: SC163

value: TOFA

value: TOFA-Bsl


title: WT_E825_1


title: SC159

value: Systemic sclerosis (SSc)


title: 14_14w_IFX_R_RNA

value: CD


title: Col_24h_30WL_2

city: Rishon LeZion,

first: Yogev

last: Burko

address: 68 HaMaccabim Rd.,

department: Plant Biology

country: Israel

institute: Volcani Institute

data_processing:
base calling was done by RTA 1.17.20 (Illumina, CA)
demultiplexing was done by CASAVA 1.8.2 (Illumina, CA)
Sequenced reads were trimmed for adaptor sequence, then aligned to TAIR10 whole genome build STAR (v2.5.4) (Dobin, Davis et al. 2013) with default parameter except --alignIntronMax 2000 and --outFilterMismatchNmax 2.
Mapped reads were counted by HTSeq (v0.6.0) with default parameters except "-m intersection-strict -s reverse" (Anders, Pyl et al. 2015) and differential expression was determined using edgeR (v3.16.5) (Robinson, McCarthy et al. 2010, Chen, Lun et al. 2016). Only genes with CPM (counts-per-million) values greater than 1 in at least two samples were kept for differential expression analysis. A design matrix was set up where each treatment (light conditions) at each time point is one group, and a generalized linear model was fitted to the read counts with this design matrix. For differential gene expression, contrasts were set up between 21WL and each of the light condition (21FR, 30WL or 30FR) at each time point.
Genome_build: TAIR10
Supplementary_files_format_and_content: HTSeqcounts_All_Samples: tab-delimited text files include counts for each gene in each sample based on HtseqCount
Supplementary_files_format_and_content: CPM_All_Samples: tab-delimited text files include normalized counts per million reads mapped  (cpm) generated using edgeR
Supplementary_files_format_and_content: LOG2_Fold_Change_relative_to_21WL: xlsx file include Log2 Fold Change between each of the conditions and 21WL at the same time point with FDR.

molecule: polyA RNA

source_name: Whole seedlings

growth_protocol: Seedlings were grown vertically on 0.5X LS plates

extract_protocol:
The seedlings (~ 25 seedllings) were collected directly in the described condition and snap-frozen in liquid nitrogen.
Libraries were prepared according to Illumina's instructions accompanying TruSeq Stranded mRNA Library Prep Kit. Briefly, total RNA (0.5µg) from each sample was used to isolate poly(A) mRNA. Steps involved in library preparation were mRNA fragmentation, first strand cDNA synthesis followed by second strand cDNA synthesis and adaptor ligation, cDNA fragments isolation and amplification.

treatment_protocol: Seedlings grown in constant LED white light (~70µE) at 21°C (21WL) for three days and moved to 21FR, 30WL, 30FR or left at 21WL for one, three, six, or 24 hours

value: Whole seedlings

value: 30C white light

tag: ecotype

value: Columbia


title: Col_24h_30FR_1

value: 30C white light + Far-red

tag: genotype


title: 24_14w_IFX_NR_RNA

tag: patient

value: Non-remission


title: WT_E775_1

value: Cardiogenic and cardiopharyngeal region


title: WT_E775_2

value: WT C57Bl6/J


title: 15_baseline_IFX_R_RNA

tag: treatment

value: baseline


title: Col_24h_30FR_2


title: Col_24h_21FR_1

value: 21C white light + Far-red


title: PA1 cells, sicontrol, rep2

tag: cell type

value: Human ovarian teratocarcinoma

value: wildtype

value: control siRNA


title: NC_rep1

city: Philadelphia

first: Yemin

last: Lan

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
Sequenced reads were mapped to reference genome either in unique or multiple mapping mode.
The alignments in the unique mapping mode were used to evaluate expression of protein coding genes and individual repeats. For this, we used STAR for alignment with the default parameters. The annotation of genes and individual repeats were acquired from UCSC RefSeq annotation and RepeatMasker, separately. Number of reads mapping to genes and repeats were determined by using FeatureCount. Differential gene and repeat expression was determined by using edgeR, with a FDR cutoff of 5%.
The alignments in the multiple mapping mode were used to evaluate repeat families. Before alignment, adapters were trimmed and reads mapping to ribosomal RNA (GenBank identifiers: 18S NR_003278.3, 28S NR_003279.1, 5S D14832.1, 5.8S K01367.1) by up to three mismatches were discarded. We used Bowtie for alignment, keeping reads that map up to 10,000 sites. Each mapping read was assigned a score of 1/N, where N is the number of sites in the genome the read mapped to. Expression values for each repeat family was calculated by adding the scores contained within the repeat body, divided by the total million reads mapped and average length of repeats (kb) within the family. Differential expression for each repeat family was determined by simple t-test and FDR correction.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include raw read counts for each sample (mRNA and repeat family separately).

growth_protocol: SSCs from postnatal day 5-8 DBA2 testes were cultured in vitro.

extract_protocol:
RNA extraction by TRIzol Reagent (Cat# 15596026) from Thermo Fisher Scientific
RNA-seq libraries were made by using TruSeq Stranded mRNA Library Preparation Kit Set A(Cat# RS-122-2101) from Illumina

treatment_protocol: SSCs were cultured in the prescence of 2 uM EPZ5676 or 0.2% ethanol (control) for 2 weeks.

tag: strain background

tag: age

value: postnatal day 5-8

tag: isolation

value: Cultured

value: spermatogonial stem cells (SSCs)

value: ethanol-treated


title: NC_rep3


title: Col_24h_21FR_2


title: Hep-3B cells, shControl, Day11

city: Guangzhou

first: Yuanping

last: Zhang

state: None Selected

address: 651 Dongfeng Road East

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

growth_protocol: Hep-3B epithelial cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol:
Hep-3B cells were transfected with shControl or shRNA ,after 7, 9 and 11 days, total RNA of these cells were collected for analysis.
shRNA lentiviruses were produced in 293T cells according to the procedure of Lenti-Pac™ Lentiviral Packaging Systems from GeneCopoeia (LT003) using Lipofectamine 3000 (Invitrogen L3000008) as a transfection reagent. Lentiviruses were harvested 72 h after transfection. Hep-3B cells with lentivirus transduction were cultured in 2 μg/mL of puromycin (MP 0219453925) for one weeks for selection. After selection, cells at 7, 9 and 11 days were collected for further analysis.

value: epithelial cells

value: WT

value: transfected with shControl plasmid

value: Day 11


title: 24_6w_IFX_NR_RNA

city: Kiel

first: Neha

last: Mishra

address: Rosalind-Franklin-Str. 12

institute: Institute of Clinical Molecular Biology

tag: cohort

value: Discovery - Infliximab

value: Infliximab

tag: remission at week 14

tag: time point

tag: diagnosis

value: UC


title: Col_24h_30WL_1

tag: tissue

value: Whole seedlings

value: 30C white light

value: Columbia


title: Hep-3B cells, shNXN, Day9

tag: cell line

value: NXN knockdown

value: transfected with shRNA

value: Day 9


title: Hep-3B cells, shNXN, Day7

value: Day 7


title: Hep-3B cells, shNXN, Day11


title: NC_rep2

value: postnatal day 5-8

value: Cultured


title: EPZ_rep3

value: spermatogonial stem cells (SSCs)


title: 12_baseline_IFX_R_RNA

value: Remission

value: baseline


title: 14_baseline_IFX_R_RNA

value: CD


title: Hep-3B cells, shControl, Day7

value: epithelial cells

value: WT

value: transfected with shControl plasmid


title: 24_2w_IFX_NR_RNA

value: Discovery - Infliximab

value: Infliximab

value: Non-remission

value: UC


title: Col_24h_21WL_2

value: Whole seedlings

tag: condition

value: 21C white light

value: Columbia


title: EPZ_rep2


title: 14_6w_IFX_R_RNA


title: W8_CO_3

city: St Lucia

first: Mohammed

middle: R

last: Shaker

state: QLD

address: Building 75,Cnr College Rd & Cooper Rd,, Brisbane

department: AIBN

country: Australia

institute: The University of Queensland

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.
At the same time, Q20, Q30 and GC content of the clean data were calculated.
ll the downstream analyses were based on the clean data with high quality
Assembly: Paired-end clean reads were mapped to the reference genome using HISAT2 software
Supplementary files format and content: Prcessed data contain up, down and unchanged expression of genes in two groups.

source_name: Organoid

growth_protocol: iPSCs-derived brain organoids were routinely generated using neuroectodermal cells derived from iPSCs before embedding these organoids with matrigel. Organoids were maintained in termianl differentiation media (see method in mansucript), media were changed every other day throughout the in vitro culture.

extract_protocol:
RNA were extract using the Applied Biosystem, Cat. #A25742. RNA integrity and quantitation were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
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. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptorligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Organoid

value: WTC-iPSCs


title: Hep-3B cells, shControl, Day9

value: Day 9


title: W8_CO_2


title: 13_14w_IFX_R_RNA


title: Col_24h_21WL_1


title: Col_6h_30FR_2

value: 30C white light + Far-red


title: EPZ_rep1

value: postnatal day 5-8

value: Cultured

value: spermatogonial stem cells (SSCs)


title: W8_CO_1


title: 13_6w_IFX_R_RNA

value: Remission

value: CD


title: iN, APP V717I, HuD KO, HuD tv1, biol rep3

city: Nijmegen

first: Geert

last: Poelmans

country: Netherlands

institute: Radboud UMC

description: 2x150 bp

data_processing:
Trimmomatic was used for trimming the beginning and ending bases from each read and identifying and trimming adapter sequences from the reads
For quantifying gene level transcript abundances, we (pseudo)aligned the trimmed reads to a human reference genome (GRCh38) using Kallisto
Detection of differentially expressed genes (DEGs) was performed with Limma-voom using the count data (transcripts per million) obtained from Kallisto
P-values were corrected for multiple testing using the false discovery rate (FDR) method
Assembly: GRCh38
Supplementary files format and content: tsv text files include TPM values for each Sample
Supplementary files format and content: xslx file includes differential gene expression data for all comparisons made

source_name: iPSC 153 fAD

growth_protocol: iPSCs were plated at 95K/cm2 in mTeSR1 media one-day prior to viral transduction. Ultrahigh titer lentiviruses were obtained from Alstem for plasmids FUdeltaGW-rtTA (Addgene #19780), pTet-O-Ngn2-puro (Addgene #52047), and DRH-307 (Addgene #112670), and were transduced at MOIs 5, 2, and 2, respectively. On day in vitro (DIV) 1, differentiation was induced by Doxycycline (2µg/ml). On DIV 2, puromycin (5 µg/ml) was added to select for cells expressing Ngn2. On DIV 4, iNs were plated on Poly-L-Ornithine laminin-coated plates and cultured in Neurobasal medium containing Glutamax, dextrose, NEAA, B27, Doxycycline, puromycin, BDNF, CNTF, and GDNF. Culturing media was conditioned starting at DIV 18, and media, protein, and RNA samples were harvested at DIV 21

extract_protocol:
RNA was harvested using PureLink RNA mini kits (ThermoFisher). 2 ug of total RNA was used for the construction of sequencing libraries.
Library preparation, Illumina, RNA with PolyA selection (executed by Genewiz)

treatment_protocol:
ELAVL4 KO was generated with CRISPR-Cas9 in iPSCs preceeding neuronal differentiation
ELAVL4 OE and rescue experiments were perfomed using lentivirus containing cDNA for ELAVL4 splice variant 1 (Origene #RC218612) or splice variant 2 (Genscript #OHu28682D)

value: iPSC 153 fAD

value: iPSC-derived neurons

tag: app genotype

tag: hud genotype

value: KO

tag: lentivirus

value: HuD tv1


title: W8_CP_3


title: Col_6h_30WL_1

value: 30C white light

tag: ecotype

tag: genotype


title: Col_6h_30FR_1

value: Whole seedlings


title: iN, APP V717I, HuD KO, HuD tv1, biol rep2

description: 2x150 bp


title: Col_6h_30WL_2


title: W8_CP_2


title: 23_14w_IFX_NR_RNA

source_name: Peripheral Whole-Blood

tag: patient

value: Discovery - Infliximab

tag: treatment

value: Infliximab

value: Non-remission

value: UC


title: Col_6h_21FR_2

value: 21C white light + Far-red

value: Columbia


title: 13_2w_IFX_R_RNA


title: W8_CP_1

value: Organoid

value: WTC-iPSCs


title: W4_CP_3


title: 23_6w_IFX_NR_RNA


title: W4_CP_2


title: iN, APP V717I, HuD KO, HuD tv2, biol rep2

description: 2x150 bp

tag: cell type

value: HuD tv2


title: iN, APP V717I, HuD KO, HuD tv2, biol rep3

description: 2x150 bp


title: 29_14w_IFX_NR_RNA


title: iN, APP V717I, HuD KO, HuD tv2, biol rep1

description: 2x150 bp


title: Col_6h_21WL_2

value: 21C white light


title: W4_CP_1


title: iN, APP V717I, HuD KO, empty vector, biol rep3

description: 2x150 bp

value: Empty vector


title: 24_baseline_IFX_NR_RNA

value: baseline


title: Col_6h_21WL_1


title: 29_2w_IFX_NR_RNA


title: iN, APP V717I, HuD KO, empty vector, biol rep2

description: 2x150 bp

value: iPSC 153 fAD

value: iPSC-derived neurons


title: iN, APP V717I, HuD KO, HuD tv1, biol rep1

description: 2x150 bp

value: KO

value: HuD tv1


title: Col_3h_30FR_2

value: Whole seedlings

value: 30C white light + Far-red


title: iN, APP V717I, HuD KO, empty vector, biol rep1

description: 2x150 bp


title: Col_3h_30FR_1


title: iN, APP V717I, HuD KO, media, biol rep3

description: 2x150 bp

value: No


title: sicircIPO7 rep3

first: Yingqin

last: Li

state: Guangdong

address: Room 927, Building 2, No. 651 Road Dong Feng East

institute: Sun Yat-sen University Cancer Center

data_processing:
Paired-end sequence files (fastq) were mapped to the reference genome (hg38) using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5). The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM). Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Genome_build: hg38

growth_protocol: S18 cells were maintained in DMEM supplemented with 10% fetal bovine serum.

extract_protocol:
TRIzol reagent was used to extract total RNA from S18 cell line.
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Paired-end libraries were synthesized by using the TruSeq™ RNA Sample Preparation Kit (Illumina, USA) following TruSeq™ RNA Sample Preparation Guide. Briefly, the poly-A containing mRNA molecules were purified using poly-T oligo-attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under 94℃ for 8 min. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. Purified libraries were quantified by Qubit® 2.0 Fluorometer (Life Technologies, USA) and validated by Agilent 2100 bioanalyzer (Agilent Technologies, USA) to confirm the insert size and calculate the mole concentration. Cluster was generated by cBot with the library diluted to 10 pM and then were sequenced on the Illumina NovaSeq 6000 (Illumina, USA).

treatment_protocol: S18 cells were treated with circIPO7 siRNA or control siRNA using Lipofectamine 3000 reagent. The cells were harvested after transfection at 48h for assays.

value: nasopharyngeal carcinoma cell


title: sicircIPO7 rep2


title: sicircIPO7 rep1


title: 28_14w_IFX_NR_RNA

value: Discovery - Infliximab

value: Infliximab

value: Non-remission

value: UC


title: Col_3h_30WL_1

value: 30C white light

value: Columbia


title: Col_3h_30WL_2


title: iN, APP V717I, HuD KO, media, biol rep2

description: 2x150 bp


title: siSCR rep3


title: 28_6w_IFX_NR_RNA


title: 29_6w_IFX_NR_RNA


title: Col_6h_21FR_1

value: 21C white light + Far-red


title: Col_3h_21FR_2


title: siSCR rep2


title: iN, APP V717I, HuD wt, HuD tv1, biol rep3

description: 2x150 bp

value: WT


title: iN, APP V717I, HuD wt, HuD tv1, biol rep2

description: 2x150 bp


title: K28BM, KDPKCa

city: Singapore

first: Phyllis

last: Chong

address: 14 Medical Drive #12-01

country: Singapore

institute: Cancer Science Institute of Singapore

data_processing:
Trimming of adapter from
the sequencing fragments (raw data) was performed with Trip Galore
(version 0.3.7) with default settings. The trimmed data were mapped to
the human reference genome GRCh37 using STAR aligner
Basecalling and data filtering based on the BGI method.
Bowtie2 to map clean reads to reference gene and use HISAT to reference hg19 genome.
FPKM method is used in calculated expression level
Assembly: hg19
Supplementary files format and content: FPKM file

source_name: multiple myeloma

extract_protocol:
Total RNA was extracted with miRNeasy Mini Kit (Qiagen)
sequenicng library was generated with 100ng total RNA using TruSeq RNA sample preparation kit v2 (Illumina)

value: Bone marrow

value: plasma cell

value: PKCalpha knockdown


title: iN, APP V717I, HuD wt, HuD tv1, biol rep1

description: 2x150 bp

value: iPSC 153 fAD

value: iPSC-derived neurons