title: mouse ovary_Aged+CEFFE1(Aged+CF32)

city: Shanghai

first: Mengyu

last: Liu

state: Shanghai

address: 197 Ruijin 2nd Road

department: Department of Obstetrics and Gynecology

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

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 whole genome（version:GRCm38.p4）using TopHat（version:2.0.9).
Cufflinks v2.1.1 was used to count the read numbers mapped to each gene
To identify most differentially expressed genes, we ranked genes according to their size and sequencing coverage normalized FPKM (fragments per kilo base of exon per million). The log2 fold changes of gene FPKM between two genotypes were tested statistically to determine whether an individual gene expression was altered significantly or not.
Assembly: GRCm38.p4
Supplementary files format and content: tab-delimited text files include FPKM values for each sample.

source_name: mouse ovary

extract_protocol:
Total RNA was extracted using miRNeasy Mini Kit (Qiagen, USA) following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNeasy micro kit (Cat#74004, QIAGEN, GmBH, Germany) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Ovaries from different groups were collected in DMEM/F12 medium 48 h after the mice were intraperitoneally injected with 10 IU of PMSG, and then stored at -80 ℃ for further RNA-seq

tag: strain background

value: genetic background of C57BL/6J

value: Ovary

tag: age

value: 11 months

value: 200 μL CEFFE (protein concentration:3 μg/μL)


title: 11491_Fb2

status: Public on May 27 2022

type: SRA

city: Marseille

first: Frederique

last: Magdinier

address: 27 Bvd Jean Moulin, Aix-Marseille Université. Faculté de Médecine. Campus La Timone

country: France

institute: Aix-Marseille Université - Marseille Medical Genetics

library_source: transcriptomic

data_processing:
We assessed fastq sequence data quality using FastQC v0.11.5 (Andrews, 2010) and trimmed the reads to remove adapter sequences and low quality bases using Trimmomatic v0.36
Paired end reads were aligned using STAR v2.5.3a  to the GRCh38 human genome release
BAMS index were generated using Sambamba v0.6.6
DEGs and abundance measurements were identified using StringTie v1.3.1c and R package DESeq2 v1.30.1 (median of ratio)
Genome_build: GRCh38 human genome
Supplementary_files_format_and_content: tab-delimited text files (.xlsx) include TPM values for each Sample and DEGs

molecule: total RNA

organism: Homo sapiens

source_name: Fibroblasts

growth_protocol: Fibroblasts were cultivated in DMEM + 10% FBS + 1% penicilline/streptomycine. hiPSCs were grown in mTESR1.

extract_protocol:
Total RNA was extracted using the RNAeasy kit (Qiagen) following manufacturer’s instructions. Quality, quantitation and sizing of total RNA was evaluated using the RNA 6000 Pico assay.  (Agilent Technologies Ref. 5067-1513) on an Agilent 2100 Bioanalyzer system.
RNA-Seq libraries were generated from 600 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and TruSeq RNA Single Indexes kits A and B (Illumina, San Diego, CA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 2 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using AMPure XP beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

tag: disease


title: mouse ovary_Aged+CEFFE1(Aged+CF34)

country: China

organism: Mus musculus

tag: tissue

tag: treatment


title: mouse ovary_Aged3(Aged34)


title: mouse ovary_Aged2(Aged33)


title: mouse ovary_Control4(Con34)

value: 8 weeks


title: mouse ovary_Aged1(Aged31)


title: mouse ovary_Aged+CEFFE1(Aged+CF30)


title: mouse ovary_Control3(Con33)


title: mouse ovary_Control2(Con32)


title: mouse ovary_Control1(Con31)


title: WT CD4+ T cells cultured under Treg conditions for 2 days #3

city: Derio

first: Ana

middle: Maria

last: Aransay

state: BIZKAIA

address: Parque tecnologico de Bizkaia, Building 801-A

department: Genome Analysis Platform

country: Spain

institute: CIC bioGUNE

data_processing:
STAR program  against Mus musculus genome (GRCm38) was used for mapping the reads followed by the quantification of genes with the RSEM  program using GENCODE m15 reference annotation. After to eliminate genes with at least a expected value greater than ten, we used TMM method and limma-voom transformation [4]  to normalize the non-biological variability. Differential expression between different groups was assessed using moderated t-statistics .
Genome_build: GRCm38
Supplementary_files_format_and_content: A matrix is generated as a plain text file (*.tsv), in which each column is a sample, each row is a gene (ensembl_ID), and in each cell indicates the number of raw counts obtained by STAR per sample and gene.

source_name: Wild type T regulatory (Treg)

growth_protocol: naïve T cells were freshly isolated (not cultured)

extract_protocol:
The CD4+ T cells were washed with PBS and pelleted. Then the cells were resuspended in RLT buffer from the RNeasy Mini kit (Qiagen) and from there we followed the protocol of the kit.
Sequencing libraries were prepared following the protocol "TruSeqStrandedmRNASamplePreparationGuide(Part#15031047Rev.E)" with the "TruSeq stranded mRNAseq library preparation kit” (Illumina Inc., Cat.#RS-122-2101orRS-122-2102 (SetAorB,respectively))
mRNA stranded library sequencing

treatment_protocol: Treg cells were cultured for 48h with anti-CD3/CD28 antibodies in the presence of TGF-beta (recombinant human) and IL-2 (recombinant mouse).

tag: genotype

value: WT

value: stimulated under Treg conditions (2 days)

tag: cell type

value: CD4+ T cells


title: WT CD4+ T cells cultured under Treg conditions for 2 days #4


title: naïve CD4+ T cells from spleen of WT mice #3

source_name: Wild type T naïve (Tn)

value: naïve cell (control)


title: naïve CD4+ T cells from spleen of WT mice #4


title: AG08C5_IPS_2

source_name: hIPSCs

value: CT


title: naïve CD4+ T cells from spleen of WT mice #2


title: WT CD4+ T cells cultured under Treg conditions for 2 days #2


title: naïve CD4+ T cells from spleen of WT mice #1


title: WT CD4+ T cells cultured under Treg conditions for 2 days #1


title: Aim2 KO CD4+ T cells cultured under Treg conditions for 2 days #1

source_name: Aim2-/- T regulatory (Treg)

value: KO


title: Aim2 KO CD4+ T cells cultured under Treg conditions for 2 days #3


title: naïve CD4+ T cells from spleen of Aim2 KO mice #3

source_name: Aim2-/- T naïve (Tn)


title: naïve CD4+ T cells from spleen of Aim2 KO mice #4


title: naïve CD4+ T cells from spleen of Aim2 KO mice #2


title: naïve CD4+ T cells from spleen of Aim2 KO mice #1


title: KO-S4: STZ-treated KO 4

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011).
Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1).
Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Mus musculus.GRCm38.92 genome using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.92 gene annotation.
Genome_build: Mus musculus.GRCm38.92
Supplementary_files_format_and_content: raw gene counts for every gene in every sample

source_name: Whole kidney

growth_protocol: Animals were maintained ad libitum on the standard laboratory chow diet (KLIBA NAFAG diet 3800). Inactivation of the Bmal1 gene was induced by 2-week treatment with DOX (2 mg/ml in drinking water) of 8-week old Bmal1 lox/lox /Pax8-rtTA/LC1 mice (cKOt mice). Their littermate controls (Bmal1lox/lox mice) received the same DOX treatment.

extract_protocol:
Tissue acollection was performed from mice sacrificed at ZT9 (ZT – Zeitgeber time units; ZT0 is the time of light on and ZT12 is the time of light off). RNA from whole kidneys was isolated with the standard method of Chomczynski and Sacchi (Anal Biochem, 162: 156-159, 1987).
RNA-seq libraries were prepared using 500 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA)

treatment_protocol: One week after the end of DOX treatment, Type I diabetes was induced by intraperitoneal injections of streptozotocin (STZ, 50 mg/kg BW, daily for 5 days). Vehicle-treated mice received vehicle injections of PBS. All experiments were performed 8 weeks after the last STZ or vehicle injection.

value: Streptozotocin-treated

value: Renal tubule BMAL1 KO

value: Whole kidney


title: KO-S9: STZ-treated KO 9


title: KO-S6: STZ-treated KO 6


title: KO-S2: STZ-treated KO 2


title: KO-S7: STZ-treated KO 7


title: KO-S8: STZ-treated KO 8


title: KO-S3: STZ-treated KO 3


title: KO-P9: PBS-treated KO 9

value: Vehicle


title: KO-P8: PBS-treated KO 8


title: KO-S5: STZ-treated KO 5


title: KO-S1: STZ-treated KO 1


title: KO-P6: PBS-treated KO 6


title: Aim2 KO CD4+ T cells cultured under Treg conditions for 2 days #4


title: KO-P3: PBS-treated KO 3


title: KO-P7: PBS-treated KO 7


title: KO-P2: PBS-treated KO 2


title: KO-P5: PBS-treated KO 5


title: Ctrl-S8: STZ-treated Control 8

value: Control


title: Aim2 KO CD4+ T cells cultured under Treg conditions for 2 days #2


title: KO-P4: PBS-treated KO 4


title: Ctrl-S9: STZ-treated Control 9


title: Ctrl-S7: STZ-treated Control 7


title: KO-P1: PBS-treated KO 1


title: Ctrl-S6: STZ-treated Control 6


title: Ctrl-S5: STZ-treated Control 5


title: Ctrl-S4: STZ-treated Control 4


title: Ctrl-S3: STZ-treated Control 3


title: Ctrl-S2: STZ-treated Control 2


title: Ctrl-S1: STZ-treated Control 1


title: Ctrl-P9: PBS-treated Control 9


title: Ctrl-P5: PBS-treated Control 5


title: Ctrl-P7: PBS-treated Control 7


title: Ctrl-P8: PBS-treated Control 8


title: Ctrl-P6: PBS-treated Control 6


title: Rat_ileum_scRNA

city: Beijing

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

department: School of life science

institute: Tsinghua University

data_processing:
Raw reads were aligned to the Rnor_6.0 rat genome, and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers
Raw aligned features were loaded and processed using the Seurat package (v4.0.2)
Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: UMI counts

organism: Rattus norvegicus

source_name: Rat intestine

extract_protocol:
Ileum crypts were isolated and digested with collagenⅠ and Tryple, alive cells were sorted by flow cytometry. Single cell suspensions were captured using the 10X Genomics Chromium Single cell 3’ Solution according to the manufacturers protocol. Briefly, a single-cell suspension was mixed with RT-PCR master mix and loaded together with Single Cell 3’ Gel beads and partitioning Oil into a Single Cell 3’ Chip. About 5,000 cells were loaded into each reaction. RNA transcripts from single cell were uniquely barcoded and reverse-transcribed.
ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000.

value: intestine

value: wild type


title: Ctrl-P2: PBS-treated Control 2


title: Ctrl-P3: PBS-treated Control 3


title: Ctrl-P4: PBS-treated Control 4


title: Ctrl-P1: PBS-treated Control 1


title: 1310_H3K27ac

city: Berkeley

first: Axel

last: Visel

state: CA

address: 1 Cyclotron Road

country: USA

institute: Lawrence Berkeley National Laboratory

description: Chromatin IP against H3K27ac

library_source: genomic

data_processing:
Reads were aligned/processed using the standard ENCODE-DCC ChIP-seq pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline)
Assembly: hg38
Supplementary files format and content: *replicated.broadPeak, peaks called by MACS2 with a q-value <= 0.05

molecule: genomic DNA

source_name: adult left ventricle, H3K27ac ChIP

extract_protocol:
Chromatin immunoprecipitation were performed as previously described (PMID: 19212405) with some modifications. Briefly, frozen left ventricle tissue was pulverized with a mortar and pestle, resuspeneded in PBS, and cross-linked with 1% formaldehyde at room temperature for 10 min. Chromatin was sonicated to obtain fragments with an average size ranging between 100-600 bp.  Chromatin was inclubated for 2h at 4 C with 5 µg of antibody. Protein A and G Dynabeads (Invitrogen) were then added to this chromatin/antibody mixture for 30 minutes at 4 C. Immuno-complexes were sequentially washed. The protein/DNA complexes were eluted in an SDS buffer (1% SDS, 50 mM Tris pH 8.0, 10 mM EDTA) at 37 C for one hour. Samples were treated  with Proteinase K at 37 C and reverse-crosslinked overnight. Finally, the DNA was purified on Zymo ChIP clean and concentrate columns (Zymo Research) and the quality was assessed on the Agilent bioanalyzer.
The ChIP-seq libraries were prepared using the Illumina TruSeq library preparation kit followed by sequencing on an Illumina HiSeq 2500 or 4000.

value: left ventricle

tag: developmental stage

value: adult

tag: chip antibody

value: anti-H3K27ac (Active motif, 39133)


title: 1205_H3K27ac

description: Chromatin IP against H3K27ac


title: 1173_H3K27ac

description: Chromatin IP against H3K27ac


title: 1211_H3K27ac

description: Chromatin IP against H3K27ac


title: M8

city: Guangzhou

first: Yijun

last: Zhu

state: Guangdong

address: Zhongshan Er Lu

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

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2) by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The clean reads were mapped to the reference genome using HISAT2 (v2.0.4).
Ericscript (v0.5.5) and rMATS (V3.2.5) were used to fusion genes and differential splicing genes (DSGs), respectively. Bowtie2 (v2.2.5) was applied to align the clean reads to Ensembl reference genome GRCm38 and read counts were calculated by RSEM (v1.2.12).
The differential expression profile between vehicle and PAGly group was analyzed using DeSeq2.
Supplementary files format and content: csv files include read counts for each Sample

source_name: xtran sodium sulfate (DSS)-induced colitis mice

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2 mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25μL~100μL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
RNA libraries for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Kit following manufacturer's protocols.

value: Colon

tag: strain

value: i.p. injection of saline


title: 1167_H3K27ac

description: Chromatin IP against H3K27ac


title: M9


title: Ctrl_7

type: RNA

city: Oxford

first: Andrea

last: Magri

address: Old Road Campus, Roosevelt Dr, Headington

country: United Kingdom

institute: University of Oxford

description:
R17_33
255 genes on nCounter® Inflammation Panel

hyb_protocol: 40 ng of each samples were incubated with Probe Set at 65 degree for 16 hours

scan_protocol: Samples were loaded into cartridges and loaded into an nCounter fluorescence detector (Nanostring)

data_processing: Raw Counts were thresholded using Max negative control counts. Adjusted for geometric mean of positive controls and scaled for geometric mean of 6 housekeeper genes. Negative control threshold subtracted at the end to uniform reads between samples.

source_name: Liver Biopsy

label_protocol: 1 ug of total RNA was digested with Turbo DNAse (Life technologies) and 500 ng were reverse-transcribed using oligo-dT primers and SuperScript III  ((Invitrogen)

extract_protocol: Human liver biopsies were extracted with Trizol (Life Technologies) from aqueous phase and RNA integrity and concentration assessed by Tape Station (Agilent)

tag: hbv infection

value: No

tag: easl group

value: Liver


title: M4

value: i.p. injection of 100 mg/kg PAGly


title: 1155_H3K27ac

description: Chromatin IP against H3K27ac


title: Ctrl_8

description:
R18_34
255 genes on nCounter® Inflammation Panel


title: M7


title: M5


title: Ctrl_6

description:
R16_32
255 genes on nCounter® Inflammation Panel


title: M2


title: 1137_H3K27ac

description: Chromatin IP against H3K27ac


title: M1


title: Ctrl_4

description:
R13_30
255 genes on nCounter® Inflammation Panel


title: Ctrl_5

description:
R15_31
255 genes on nCounter® Inflammation Panel


title: 1224_H3K27ac

description: Chromatin IP against H3K27ac


title: 1310_input

description: input chromatin

source_name: adult left ventricle, input ChIP


title: pDCKO2

first: Zhimin

last: He

address: No. 1 Qinghuayuan Street

department: School of Medicine

data_processing:
Basecalling using Real-Time Analysis software (RTA 2.7.7)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 or GCF_000001635.26_GCRm38.p6 whole genome using bowtie2
Fragments per kilobase of transcript per million fragments mapped (FPKM) were calculated using RSEM (Li,B et al. BMC Bioinfomatics, 2011).
Genome_build: mm10 for LMPP and CDP, GCF_000001635.26_GCRm38.p6 for pDCs
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...

extract_protocol:
LPMMs and CDPs were lyzed in specialized lysis buffer for RNA extraction of small numbers of cells, pDCs were lyzed in Trizol.
RNA libraries were prepared for sequencing using standard Illumina protocols or BGI protocols

treatment_protocol: Hdac3fl/fl mice or Hdac3fl/fl CreERT2 mice were i.p. injected with tomaxifen for 5 days and waited for 7 days before LMPPs and CD115-CDPs and bone marrow pDCs were sorted using FACS

tag: stain

value: bone marrow pDCs


title: 1224_input

description: input chromatin


title: pDCWT2

value: control


title: Ctrl_3

description:
R11_29
255 genes on nCounter® Inflammation Panel


title: Ctrl_2

description:
R10_28
255 genes on nCounter® Inflammation Panel


title: M3


title: 1211_input

description: input chromatin


title: pDCWT1


title: 1205_input

description: input chromatin


title: Ctrl_1

description:
R9_27
255 genes on nCounter® Inflammation Panel


title: 1173_input

description: input chromatin


title: WGS data of Organogenesis-derived-susceptible-line rep3

city: Los Angeles

first: Zhenhui

last: Zhong

address: 610 Charles E Young Dr East

department: Department of Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Whole genome bisulfite sequencing data of cassava Organogenesis-derived-susceptible-line rep3

data_processing:
For WGBS, WGBS reads were mapped to TME7 phase0 genome with BSMAP (v2.90) allowing 1 mismatch and 1 best hit (-v 1 -w 1) (Xi, Y., 2009;  Ben N. Mansfeld, 2021). Duplicated reads were removed with SAMtools (v1.3.1). Reads with three or more consecutive methylated CHH sites were considered as unconverted reads and removed in the following analysis. Conversion rate was estimated by calculating methylation level of the chloroplast genome. DNA methylation level at each cytosine was calculated by number of methylated C vs. total C and T account. Methylation levels of each chromosome were determined by calculating CG, CHG, and CHH level of 100 kb bins. Methylation track files were visualized with Integrative Genomics Viewer (IGV, v3.0) (James T. Robinson,2011).
Genome_build: TME204
Supplementary_files_format_and_content: bigWig

organism: Manihot esculenta

source_name: Organogenesis-derived-susceptible-line

growth_protocol: Cassava plants of the TME7 and TME204 ecotype were used in this study. All plants were grown under green house condition. Leaf tissues were collected from 7-8 week plants

extract_protocol:
Leaf tissues from 7-8 week old plant were used for DNA extraction.
Genomic DNA from samples were end-repaired and ligated with TruSeq LT DNA single adapters (Illumina) using Kapa DNA HyperPrep kit (Roche). Adapter-ligated DNA was converted with EpiTect Bisulfite Kit (Qiagen). Converted DNA was PCR-amplified by MyTaq polymerase (Bioline) for 12 cycles. Library quality and size were determined by D1000 ScreenTape (Agilent) and libraries were subsequently purified by AMPure XP beads (Beckman Coulter). Library concentrations were measured with Qubit dsDNA Broad-Range Assay kit (ThermoFisher). Libraries were sequenced on NovaSeq 6000 sequencer (Illumina).
WGBS

value: leaf tissue

value: 7-8 weeks

tag: ecotype

tag: line

value: Organogenesis-derived-susceptible-line


title: WGS data of Organogenesis-derived-susceptible-line rep2

description: Whole genome bisulfite sequencing data of cassava Organogenesis-derived-susceptible-line rep2


title: WGS data of Organogenesis-derived-susceptible-line rep1

description: Whole genome bisulfite sequencing data of cassava Organogenesis-derived-susceptible-line rep1


title: WGS data of Organogenesis-derived-resistant-line rep3

description: Whole genome bisulfite sequencing data of cassava Organogenesis-derived-resistant-line rep3

source_name: Organogenesis-derived-resistant-line

value: Organogenesis-derived-resistant-line


title: CHB_25

description:
1710_25
255 genes on nCounter® Inflammation Panel

value: Yes

value: Infection


title: 1167_input

description: input chromatin


title: WGS data of Organogenesis-derived-resistant-line rep1

description: Whole genome bisulfite sequencing data of cassava Organogenesis-derived-resistant-line rep1


title: WGS data of OES-derived-line rep2

description: Whole genome bisulfite sequencing data of cassava OES-derived-line rep2

source_name: OES-derived-line

value: OES-derived-line


title: WGS data of OES-derived-line rep3

description: Whole genome bisulfite sequencing data of cassava OES-derived-line rep3


title: pDCKO1


title: 1155_input

description: input chromatin

value: left ventricle


title: CHB_23

description:
1677_23
255 genes on nCounter® Inflammation Panel

value: Hepatitis


title: CHB_22

description:
1673_22
255 genes on nCounter® Inflammation Panel


title: WGS data of OES-derived-line rep1

description: Whole genome bisulfite sequencing data of cassava OES-derived-line rep1


title: WGS data of FEC-derived-line

description: Whole genome bisulfite sequencing data of cassava FEC-derived-line

source_name: FEC-derived-line

value: FEC-derived-line


title: CHB_21

description:
1669_21
255 genes on nCounter® Inflammation Panel


title: WGS data of Organogenesis-derived-resistant-line rep2

description: Whole genome bisulfite sequencing data of cassava Organogenesis-derived-resistant-line rep2


title: Input DNA BAMS rep2 [neural crest stem cells]

data_processing:
Image analysis and base calling were performed using RTA 2.7.3 and bcl2fastq 2.17.1.14.
Sequence reads were mapped to reference genome hg38 using Bowtie 1.0.0 with the following parameters -m 1 --strata --best -y -S -l 40 -p 2.
Peak calling was performed using MACS2(v2.2.6) with –broad parameter for (H3K4me3 and H3K27me3), --nomodel –extsize 200 for replicates with lower quality, -q 0.05
Genome_build: hg38
Supplementary_files_format_and_content: Wig files were generated using with an in-house script from IGBMC (Variable step, span=25, reads were elongated to 200b).

source_name: neural crest stem cells

growth_protocol: The hIPSc were differentiated into functional neural crest stem cells according to the protocol described in Mica et al. (PMID: 23583175)

extract_protocol:
Between 10-20 millions cells  were cross-linked with 1% formaldehyde in fixation solution directly in culture dishes and incubated for 5 minutes at RT and then 40 minutes at 4°C. Cross linking reaction was stopped by addition of 0.125M Glycine. For ChIP-seq, we used the iDeal ChIP-seq kit for Transcription Factors and iDeal ChIP-seq kit for Histones (Diagenode). Chromatin extraction, immunoprecipitations and DNA purifications is performed as recommended by the manufacturer
ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7  cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

value: BAMS (bosma arhinia microphthalmia syndrome)


title: WGS data of TME7 wild type rep2

description: Whole genome bisulfite sequencing data of cassava TME7 wild type rep2

source_name: TME7 wild type

value: TME7 wild type


title: CHB_26

description:
1724_26
255 genes on nCounter® Inflammation Panel


title: WGS data of TME7 wild type rep1

description: Whole genome bisulfite sequencing data of cassava TME7 wild type rep1


title: Input DNA BAMS rep1 [neural crest stem cells]


title: CHB_20

description:
1663_20
255 genes on nCounter® Inflammation Panel


title: CTCF BAMS rep2 [neural crest stem cells]


title: Narta TriTag-BFP (HSPB8) 48hpf rep2 [HSPB82M2]

city: Hang Zhou

first: Tao

last: cheng

state: Zhe Jiang

address: 886 Yuhangtang Road

department: Institute of genetics

institute: Zhejiang University

data_processing:
The sequencing reads were aligned to the human GRCh38 genome using STAR, and reads mapped to multiple genomic location were removed. Gene expression counts of each sample were calculated by featureCounts. Differential expression analysis was performed by DESeq2 package.
Assembly: GRCh38
Supplementary files format and content: comma-delimited csv files included read counts  of each sample and each gene

source_name: HeLa cells

growth_protocol: HeLa cells  were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM) with high glucose (Gibco) in the presence of 10% FBS (Hyclone) and 1% penicillin/streptomycin (Gibco).

extract_protocol:
Total RNAs was extracted using TRIzol following the manufacturer’s instruction
RNA libraries were prepared for sequencing using bgiseq500 protocols

treatment_protocol: BFPTriTag-LMNA and HSPB8-BFPTriTag cell lines were seeded into 6-well plates, respectively. The next day, 4 μg stdMCP-PH-T2A-GFP or stdPCP-PH-T2A-GFP was transfected into cells.

tag: cell line

value: HeLa

value: Narta TriTag-BFP (HSPB8)

tag: time point

value: 48 hpf


title: Narta TriTag-BFP (LMNA) 48hpf rep2 [LMNA2M2]

value: Narta TriTag-BFP (LMNA)


title: control TriTag-BFP (LMNA) 48hpf rep2 [LMNA1P2]

value: control TriTag-BFP (LMNA)


title: 1137_input

description: input chromatin

value: adult


title: CTCF BAMS rep1 [neural crest stem cells]


title: Narta TriTag-BFP (LMNA) 48hpf rep1 [LMNA2M]


title: CHB_19

description:
1661_19
255 genes on nCounter® Inflammation Panel

value: Liver


title: H3K27me3 BAMS rep2 [neural crest stem cells]

value: Diagenode C15410195


title: CHB_18

description:
1654_18
255 genes on nCounter® Inflammation Panel


title: WGS data of TME204 wild type

description: Whole genome bisulfite sequencing data of cassava TME204 wild type

source_name: TME204 wild type

value: leaf tissue

value: 7-8 weeks

value: TME204 wild type


title: H3K4me3 BAMS rep2 [neural crest stem cells]


title: Narta TriTag-BFP (HSPB8) 48hpf rep1 [HSPB2M]


title: H3K27me3 BAMS rep1 [neural crest stem cells]


title: CHB_17

description:
1643_17
255 genes on nCounter® Inflammation Panel

value: Yes

value: Infection


title: WGS data of TME7 wild type rep3

description: Whole genome bisulfite sequencing data of cassava TME7 wild type rep3


title: CHB_16

description:
1629_16
255 genes on nCounter® Inflammation Panel

value: Hepatitis


title: CHB_15

description:
1627_15
255 genes on nCounter® Inflammation Panel


title: control TriTag-BFP (HSPB8) 48hpf rep2 [HSPB81P2]

value: control TriTag-BFP (HSPB8)


title: Input DNA FSHD2 rep2 [neural crest stem cells]


title: control TriTag-BFP (HSPB8) 48hpf rep1 [HSPB1P]


title: SKBR3-dCas9-VP64-MPH-AC-sgRNA_Dox_Rep2

first: Han

last: Yang

state: Beijing

address: 38 xueyuan road

institute: Peking University Health Science Center

data_processing:
RNA-Seq reads were filtered using SOPAnuke v1.5.2 to remove reads with adaptors.
The trimmed reads were aligned to the human reference genome (hg19) using HISAT v2.0.4.and aligned to reference gene using Bowtie2 v2.2.5.
The matched reads were calculated and then normalized using RSEM software.
Differential gene expression was analyzed using DESeq2.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

source_name: SKRB3 cells

growth_protocol: SKBR3 cells were maintained in DMEM, supplemented with 10% FBS at 37°C, 5 % CO2. SKBR3-dCas9-VP64-MPH-AC-sgRNA were maintained in DMEM, supplemented with 10% FBS, 10 μg/mL of blasticidin and 200 μg/mL of hygromycin and 0.5 μg/mL puromycin at 37°C, 5 % CO2.

extract_protocol:
Total RNA was extracted using TRIzol.
Library construction was performed by BGI Genomics following standard Ilumina protocol

treatment_protocol: SKBR3-dCas9-VP64-MPH-AC-sgRNA cells were treated with or without 50 ng/μL Dox for 3 days.

value: Breast cancer cells

value: 50ng/mL Dox

tag: transduction


title: Input DNA FSHD2 rep1 [neural crest stem cells]


title: CHB_13

description:
1615_13
255 genes on nCounter® Inflammation Panel


title: CHB_14

description:
1618_14
255 genes on nCounter® Inflammation Panel


title: control TriTag-BFP (LMNA) 48hpf rep1 [LMNA1P]

value: HeLa


title: SKBR3-dCas9-VP64-MPH-AC-sgRNA_Dox_Rep3


title: CTCF FSHD2 rep2 [neural crest stem cells]


title: SKBR3-dCas9-VP64-MPH-AC-sgRNA_Dox_Rep1


title: CHB_12

description:
1613_12
255 genes on nCounter® Inflammation Panel


title: SKBR3-dCas9-VP64-MPH-AC-sgRNA_NoDox_Rep2

value: untreated


title: CHB_10

description:
1604_10
255 genes on nCounter® Inflammation Panel


title: CHB_11

description:
1608_11
255 genes on nCounter® Inflammation Panel


title: CDPK2


title: SKBR3-dCas9-VP64-MPH-AC-sgRNA_NoDox_Rep1


title: CDPK1


title: H3K4me3 FSHD2 rep1 [neural crest stem cells]


title: CDPC2

value: control


title: CHB_9

description:
1603_09
255 genes on nCounter® Inflammation Panel


title: H3K4me3 FSHD2 rep2 [neural crest stem cells]


title: Input DNA CT rep2 [neural crest stem cells]

value: Control


title: CHB_7

description:
590_07
255 genes on nCounter® Inflammation Panel


title: CHB_8

description:
591_08
255 genes on nCounter® Inflammation Panel


title: SKBR3-dCas9-VP64-MPH-AC-sgRNA_NoDox_Rep3


title: CDPC1


title: H3K27me3 FSHD2 rep2 [neural crest stem cells]


title: CHB_6

description:
586_06
255 genes on nCounter® Inflammation Panel


title: Input DNA CT rep1 [neural crest stem cells]


title: H3K27me3 FSHD2 rep1 [neural crest stem cells]


title: LMPP_K1

value: LMPPs


title: CTCF CT rep2 [neural crest stem cells]


title: CTCF CT rep1 [neural crest stem cells]


title: CHB_5

description:
584_05
255 genes on nCounter® Inflammation Panel


title: H3K27me3 CT rep2 [neural crest stem cells]


title: LMPP_C2


title: Subject 4 with normal HbF

city: Nanning

first: Ketong

last: Lai

address: Shuangyong Road

department: Department of Pediatrics

institute: the First Affiliated Hospital of Guangxi Medical University

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human circRNA Arrays V2(8x15K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

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

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering.

source_name: peripheral blood

label_protocol: The enriched circRNAs were amplified and transcribed into Cy3-labeled cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar)

growth_protocol: 10 mL peripheral blood anticoagulated by ethylene diamine tetraacetic acid EDTA was collected from every subject and stored at 4 ℃.

extract_protocol: RNA was extracted using TRIzol and RNAiso Plus (Takara, Japan), according to the manufacturer's instructions

treatment_protocol: Each sample was depleted of CD45+ cells to remove leukocytes and then enriched for CD71+ erythroid cells by Miltenyi magnetic microbeads (Miltenyi Biotec), and placed on ice in the Trizol solution(invitrogen)

value: peripheral blood

value: circulating CD71+ erythroid progenitors

tag: Sex

value: male

tag: age

tag: phenotype

value: healthy control


title: LMPP_C1


title: CHB_4

description:
582_04
255 genes on nCounter® Inflammation Panel

tag: tissue

value: Liver


title: CHB_3

description:
581_03
255 genes on nCounter® Inflammation Panel


title: CHB_2

description:
576_02
255 genes on nCounter® Inflammation Panel


title: Subject 5 with normal HbF

value: female


title: Subject 3 with high HbF

value: β-thalassemia carriers with high HbF


title: LMPP_K2

tag: genotype


title: H3K27me3 CT rep1 [neural crest stem cells]

tag: disease

value: Diagenode C15410195


title: Subject 2 with high HbF

tag: cell type


title: H3K4me3 CT rep1 [neural crest stem cells]

tag: chip antibody


title: C_QG_3 mRNA

city: Harbin

first: Shiwen

last: Xu

address: NO.600 Changjiang Street, Xiangfang District, HarBin, China

department: College of Veterinary Medicine

institute: Northeast Agricultural University

description: all.counts.exp.txt

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: Gallus_gallus-5.0 / miRBase 21.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

organism: Gallus gallus

source_name: trachea

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Anhydrous hydrogen sulfide was metered continuously into chambers H (the hydrogen sulfide group) to maintain 24-h levels of 3.5≤H2S≤4.5 mg/kg from week 0 to 3, and 19.5≤H2S≤20.5 mg/kg, from week 4 to 6. No H2S was added to chamber C (the control group).

value: trachea

tag: stress

value: normal tissue


title: C_QG_3 miRNA

description:
All.miRNA.mature.Counts.exp.txt
small RNA

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: a) 30% base quality <13 b) read length < 17bp c) adaptor sequence.
Utilizing the BWA software, we mapped the clean data to miRBase 21.0 Gallus gallus miRNA database and   Gallus_gallus-5.0 genome.
count counting
Genome_build: Gallus_gallus-5.0 / miRBase 21.0
Supplementary_files_format_and_content: TXT file contain counts for each sample

extract_protocol:
Total RNA was extracted from cell or animal tissue by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Bioanalyzer 2200 (Aligent) and kept at -80℃.The RNA with RIN >8.0 is right for miRNA purification. miRNA was purified by miRNeasy Mini Kit (Qiagen) and the purification result was validated by Gel electrophoresis.
RNA libraries were prepared for sequencing using standard Illumina protocols


title: 170712_T_XY_E16

city: Geneve

first: Chloe

last: MAYERE

address: Michel Servet, 1

institute: UNIGE

description:
all_samples_raw_counts.mtx
all_samples_lognorm_counts.mtx

data_processing:
Demultiplexing, alignment, barcode filtering and UMI counting were performed with the Cell Ranger v2.1 pipeline (10x Genomics). Data was aligned on a personalized Gencode reference genome (GRCM38) including GFP.
For cell-associated barcode selection, we computed the knee point and the inflection point of the ranked barcodes distribution plot. The local minimum between these points on the density curve (density base R function, bw=500, n=4096) of the UMI number per barcode was detected using the quantmod package. This local minimum was used as a threshold for cell-associated barcode selections. When no local minimum could be detected between the two points, the nearest local minimum was used.
UMI counts per gene per cell were divided by the total UMI detected in the cell with exclusion of very highly expressed genes (accounting to more than 5% of total counts in cell), multiplied by a scale factor of 10,000 and log transformed.
Genome_build: Genecode grcm38
Supplementary_files_format_and_content: mtx, raw counts values
Supplementary_files_format_and_content: tsv, barcodes identifiers
Supplementary_files_format_and_content: tsv, genes official symbol
Supplementary_files_format_and_content: csv, metadata

source_name: Testis

growth_protocol: The day when a vaginal plug was designated as embryonic day E0.5. Embryos were collected at E10.5 (8±2 caudal somites), E11.5 (19±4 ts), E12.5, E13.5, and E16.5 from time-mated pregnant female CD-1 outbred mice (Charles River) and heterozygous Tg(Nr5a1-GFP) transgenic male mice .

extract_protocol:
he presence of the Nr5a1-GFP transgene was assessed under UV light and genetic sexing was performed by PCR, as described previously . Urogenital ridges (E10.5, E11.5) from both sexes, and testes or ovaries, were isolated at each time point and enzymatically dissociated as described previously . Approximately 5000 single cells were loaded on a 10x Chromium instrument
cRNA-seq libraries were prepared using the 10X Genomics Chromium Controller and Chromium Single Cell 3′ Library & Gel Bead Kit V2, as per the manufacturer’s instructions. The prepared libraries were sequenced on an Illumina HiSeq4000 using paired-end 26 + 98 + 8 bp as the sequencing mode. Libraries were sequenced at a targeted depth of 100 000 to 150 000 total reads per cell. Sequencing was performed at the Health 2030 Genome Center, Geneva.

tag: Stage

tag: strain

tag: transgene

tag: genetic sex

value: XY

tag: assay type

value: Gene expression


title: CHB_1

description:
571_01
255 genes on nCounter® Inflammation Panel

tag: hbv infection

value: Yes

tag: easl group

value: Infection


title: Subject 6 with normal HbF


title: C_QG_2 miRNA


title: C_QG_1 miRNA


title: prEpiSCs_ATAC_seq_3

first: Manqi

address: No. 135, Xingang Xi Road

institute: Sun Yat-Sen University

data_processing:
The analyses of raw ATAC-seq data were performed in following steps. Adapter sequence and low-quality reads were first trimmed and filtered by TrimGalore(release 0.6.6) with default parameter. After that, qualified reads were aligned to reference genome GRCh38 by Bowtie2 (release 2.4.5) with parameters "-t -q -N 1 -L 25 -p 12 --no-mixed --no-discordant". To remove biological and optical duplicates, we ultilized package Sambamba (release 0.8.2). For downstream analysis, package deepTools (release 3.5.1) was used to generate bigwig files and quantify RPKM value on specific genomic regions.
Assembly: hg38
Supplementary files format and content: wig files were generated using deeptools; Scores represent RPKM values.

source_name: Embryonic stem cells

growth_protocol: The prEpiSCs are cultured in the GIX medium which contains DMEM/F12 (Thermo Fisher Scientific, catalog. no. 21331020), Neurobasal medium (Thermo Fisher Scientific, catalog. no. 21103049), 2 mM L-glutamine (Thermo Fisher Scientific, catalog. no. 25030081), non-essential amino acids (Thermo Fisher Scientific, catalog. no. 11140050), 1% N2 supplement (Thermo Fisher Scientific, catalog. no. 17502048), 2% B27 supplement (Thermo Fisher Scientific, catalog. no. 12587010, minus vitamin A), 100 mg/ml Vitamin C (Sigma, catalog no. A4403), 50 ng/ml Bovine Albumin Fraction V (Thermo Scientific, cat. no. 15260-037), 20 ng/ml IL6 (PeproTech, catalog. no. AF-200-06), 20 ng/ml sIL-6R (PeproTech, catalog. no. 200-06R),5 ng/ml BMP4 (PeproTech, catalog. no. 120-05ET), 0.1 mM 2-mercaptoethanol (Thermo Fisher Scientific, catalog. no. 21985023), 0.2 μM GSK112022 (Selleckchem, catalog. no. S2673), 2.5 μM XAV939 (Tocris, catalog. no. 3748), 1 μM Go6983 (Tocris, 2285) and Primocin (InvivoGen, catalog. no. ant-pm-2).To get ci8CLCs, Human prEpiSCs were cultured with the GIX medium plus the chemical cocktail (0.05 μM DZNep, 0.25 μM CBL0137, 0.5 μM AG14361, 1 μM GSK872, and 0.25 μM Ac-EVCD).The medium was changed every other day. The cells were treated with Accutase to dissociate into single cells, and then passaged onto new Matrigel- or feeder-coated plates every 3 - 4 days.

extract_protocol:
A total of 50,000 cells were resuspended in 50 µl lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) NP-40). The nuclei were collected by centrifuged for 10 minutes at 500g at 4°C  and then mixed with the transposition reaction mix (10 µl TTBL, 5 µl TTE Mix V50 and nuclease-free H2O up to 50 µl in total) of TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, catalog. no. TD501) for 10 minutes at 55 °C.
DNA Samples were then PCR amplified. PCR products were mixed with 1.2 volume of DNA clean beads to clean up. Library integrity was checked by the Agilent bioanalyzer. The libraries were sequenced on an Illumina Hiseq X10 platform and 150 bp paired-end reads were generated.

treatment_protocol: prEpiSCs are culturered in the GIX medium containing a chemical cocktail (0.05-0.1 μM GSK112022, 2.5 μM XAV939, 1 μM Go6983) without any other treatment.

value: Embryonic stem cells

tag: treatment


title: prEpiSCs_ATAC_seq_1


title: prEpiSCs_ATAC_seq_2


title: 170316_T_XY_E16


title: H_QG_3 mRNA

description: all.counts.exp.txt

value: hydrogen sulfide exposed tissue


title: H_QG_3 miRNA


title: H_QG_1 miRNA


title: prEpiSCs_Input

data_processing:
The analyses of raw ChIP-seq data were performed in following steps. Adapter sequence and low-quality reads were first trimmed and filtered by TrimGalore(release 0.6.6) with default parameter. After that, qualified reads were aligned to reference genome GRCh38 by Bowtie2 (release 2.4.5) with parameters "-t -q -N 1 -L 25 -p 12". To remove biological and optical duplicates, we ultilized package Sambamba (release 0.8.2). For downstream analysis, package deepTools (release 3.5.1) was used to generate bigwig files and quantify RPKM value on specific genomic regions.
Assembly: hg38
Supplementary files format and content: wig files were generated using deeptools; Scores represent RPKM values.

extract_protocol:
5×10^6 prEpiSCs were fixed in fresh 1% formalin/prEpiSC medium (v/v) for 10 min followed by quenching with glycine (125 mM)  for 5 minutes at room temperature. Fixed cells were washed twice in ice-cold PBS, re-suspended in Lysis buffer 1 (50 mM HEPES-KOH, pH 7.5, 140 mM NaCl, 1 mM EDTA, 10% glycerol, 0.5%NP-40, 0.25% Triton X-100 and protease inhibitors) and incubated on ice for 10 minutes. Cells were then pelleted by centrifugation and resuspended in Lysis buffer 2 (10 mM Tris-HCl, pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA and protease inhibitors) with incubation on ice for 10 minutes. Cells were then pelleted and resuspended in 0.25ml of freshly prepared Lysis buffer 3 (10 mM Tris-HCl, pH 8.0,100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% Na-deoxycholate, 0.5%N-lauroylsarcosine and protease inhibitors) and sonicated to about 100 - 500 bp fragments using a Bioruptor (Diagenode). Anti-H3K4me3 antibody was  incubated with preblocked protein A magnetic beads (Invitrogen) at 4°C with gentle agitation on a rotator for 4 hours. Antibody-bead complexes were added into the sonicated chromatin solution and rotated for overnight at 4°C. Chromatin-bead immunoprecipitates were collected by the magnetic device and washed sequentially with high-salt wash buffer (20 mMTris·HCl, pH 8.0, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, and 1% Triton X-100), then with LiCl wash buffer (10 mM Tris·HCl, pH 8.0, 250 mM LiCl, 1 mM EDTA, and 1% Nonidet P-40), and then with Tris-EDTA (TE)-NaCl buffer (1 mM EDTA, 10 mM Tris·HCl, pH 8.0, and 50 mM NaCl). Immunoprecipitated DNA was eluted by incubating the beads with 100 µl elution buffer (50 mM Tris·HCl, pH 8.0, 10 mM EDTA, and 1% SDS), shaking at a setting of 1300 rpm for one hour at room temperature. For reverse crosslinking, sample was treated with proteinase K and incubated at 65°C for 4 hours. The DNA was purified using phenol-chloroform extraction, and suspended in 40 µl TE buffer.
ChIP-seq library was constructed with the Accel-NGS 2S Plus DNA Library kit (Swift Biosciences, catalog. no. 21096) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Hiseq platform and 100 bp single-end reads were generated.


title: prEpiSCs_H3K4me3

value: H3K4me3 (Millipore 07-473)


title: H_QG_2 miRNA


title: CHB_24

description:
1685_24
255 genes on nCounter® Inflammation Panel


title: 180222_O_XX_E13

source_name: Ovary

value: XX


title: Subject 1 with high HbF

value: peripheral blood

value: circulating CD71+ erythroid progenitors

tag: Sex


title: 170712_O_XX_E16


title: 170802_T_XY_E13


title: RNAseq_SW480_HUNK_KO2

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

data_processing:
Raw reads were filtered to remove the adaptors and low-quality bases using trim_galore 0.6.6.
The filtered reads were mapped to the hg38 genome using STAR.
The counted and normalized expression of lncRNA and protein-coding transcripts were estimated using all mapped reads by featureCounts.
Differentially expressed merged transcripts were quantified using EdgeR.
Assembly: hg38
Supplementary files format and content: xls files include RPKM values for each Sample.

source_name: SW408 total RNA

growth_protocol: Colonial cultures were maintained in the DMEM medium

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Knocked out HUNK

value: Knocked out HUNK


title: RNAseq_SW480_HUNK_KO3


title: RNAseq_SW480_HUNK_KO1


title: muscle12

city: Sao Carlos

first: Simone

middle: C M

last: Niciura

state: Sao Paulo

address: Rodovia Washington Luiz, Km 234

country: Brazil

institute: Embrapa

data_processing:
Sequencing read quality control was performed using FastQC version 0.10.1(https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
adaptors were removed by Trim Galore! version 0.4.1. (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/)
Bismark version 0.23.0 was used to align the reads to the Bos taurus reference genome UCD1.2/bosTau9 and to identify methylated cytosines.
Using methylKit version 1.8.1 in R version 3.5.1, all cytosines were filtered for minimum coverage of 10 reads and maximum percentile of 99.9%. The methylKit function that normalize the coverage was applied using default settings.
Genome_build: ARS-UCD1.2
Supplementary_files_format_and_content: Matrix with coverage for each CpG

organism: Bos indicus

source_name: Longissimus thoracis skeletal muscle

growth_protocol: Longissimus thoracis skeletal muscle samples were collected at slaughter, stored in liquid nitrogen, and kept in a freezer at -80 °C until processing.

extract_protocol:
DNA extraction was carried out using the DNeasy® Blood & Tissue kit (Qiagen Inc., Germantown, MD, USA), according to the manufacturer's protocol. DNA concentration was measured using Qubit dsDNA High Sensitivity Assay (Thermo Fisher Scientific Waltham, MS, EUA) and the quality measured by Fragment Analyzer™ and the DNF-487 Standard Sensitivity or the DNF-488 High Sensitivity genomic DNA Analysis Kit (Advanced Analytical).
Each sample library was prepared from 100 ng of genomic DNA using the Premium RRBS kit (Diagenode), according to the manufacturer's protocol. Bisulfite conversion efficiency independent of CpG context was assessed by adding methylated and unmethylated spike-in controls (0.1% concentration). Briefly, the protocol consists in the digestion of DNA by MspI enzyme followed by the fragment end repair, and addition of adaptors. Next, samples were quantified by qPCR and the Ct values were used to pool samples by similarity. Bisulfite conversions were performed using the Premium RRBS kit (Diagenode) followed by library enrichment by PCR, based on the manufacturer’s protocol. Adequate fragment size distributions were confirmed by Bioanalyzer High Sensitivity DNA chips (Agilent). Libraries were sequenced on Illumina HiSeq 3000 using single-end 50 bp reads.

treatment_protocol: Steaks were used to measure the shear force (SF) using a TA XT2i (Stable Micro Systems Ltd., Surrey, United Kingdom) texture analyzer coupled to a Warner-Bratzler blade, at 1.016 mm thickness (58). Samples were kept in a 2°C chamber for aging and measurements of SF were obtained at 7 days after slaughter.

tag: group

value: Lower Shear force value

tag: tenderness

value: higher tenderness

value: Longissimus thoracis skeletal muscle


title: 170726_T_XY_E13


title: 170313_O_XX_E16


title: 170816_T_XY_E12


title: RNAseq_SW480_WT3

value: WT


title: 180410_O_XX_E13


title: muscle10

tag: tissue


title: RNAseq_SW480_WT2


title: 170816_O_XX_E12


title: 170724_T_XY_E12


title: muscle08


title: muscle11


title: Refed_8h_rep_4 [RUN-048-12]

city: Tsukuba

first: takehito

last: sugasawa

state: Select State

address: Ibaraki

country: Japan

institute: University of tsukuba

data_processing:
RNA-seq reads were aligned to the GRCz11 genome assembly using CLC genomics workbench 20.0.4 with the default settings.
A statistical differential expression test was used "Differential Expression for RNA-Seq tool" in the CLC software.
Assembly: GRCz11 genome assembly
Supplementary files format and content: Excel file of statistic test and expression data.

organism: Danio rerio

source_name: Zebrafish muscle between anus and caudal tail fin

growth_protocol: Standard protocol.

extract_protocol:
RNA were extracted from the muscle between the anus and caudal tail fin, using RNAiso Blood (Cat#9112; Takara Bio)
Library was constructed using NEBNext Ultra II RNA Library Prep Kit for Illumina, and NEBNext Poly(A) mRNA Magnetic Isolation Module (Cat# E7770 and E7490; New England Biolabs).

treatment_protocol: The following 3 experimental conditions were set for zebrafish: 24-hour fasting group (Fast), 3-hour refeeding group (Refed_3h), and 8-hour refeeding group (Refed_8h).

value: Not applicable

value: Muscle

tag: age

value: 2-3 month

tag: genotype

value: Wild type

value: refeeding (after 8 hours)


title: RNAseq_SW480_WT1

tag: cell type


title: muscle07


title: 170724_O_XX_E12

value: Gene expression


title: Refed_8h_rep_3 [RUN-048-11]


title: muscle09


title: 170823_AGP_XY_E11

source_name: Adreno Gonadal Primordium

value: XY


title: Aedes aegypti SCK3

city: Rome

first: Bruno

last: Arca

address: P.le Aldo Moro 5

department: Public Health and Infectious Diseases

country: Italy

institute: Sapienza University

data_processing:
Raw reads were quality control checked by FastQC then trimmed by cutadapt 1.9.1 to remove adapters and discard reads shorter than 14 nucleotides.
Processed reads were mapped to the Ae. aegypti AaegL5 genome assembly using Bowtie 1.3.0 (-n 0 -l 18 -e 80). Reads not mapping to AaegL5 where aligned (-n 0 -l 18 -e 80 --norc) to the chikungunya virus RNA genome and antigenome (strain 06-21, Reunion isolate, Virus Pathogen Resource AM258992). Reads aligned to AaegL5 were subtracted of ribosomal RNAs then mapped (-n 0 -l 18 -a --best --strata -e 80 --norc) to a list composed of 327 miRNA precursors (known + predicted by the miRDeep* software) and other noncoding RNAs from Ae. aegypti. Reads aligning to this list of hairpins and ncRNAs were used for correlation analysis, mapping to mature miRNAs and differential expression analysis; unaligned reads were sequentially mapped, using the same parameters as above, to collections of Ae. aegypti lncRNAs, transcripts (AaegL5.2) and repeats retrieved from VectorBase.
Read counts for each Ae. aegypti small RNA were computed from SAM files using a Python custom script. Reads with multiple highest score mappings were discarded. Expression values were calculated as count per million (CPM) and used for sample clustering. Reads mapping to precursor miRNAs were assigned to mature miRNAs based on their mapping position; overhangs of maximum 3 nucleotides for each side of the mature form were tolerated. Differential expression analysis of mature miRNAs with 1 CPM in at least three samples was performed using glmFIT and glmLRT functions provided by the edgeR software package. Log2 Fold change (FC) and false discovery rates (FDR) were calculated to provide statistical validation.
Genome_build: AaegL5
Supplementary_files_format_and_content: Excel file including, for each sample, the CPM values of the 208 expressed miRNAs.

organism: Aedes aegypti

source_name: chikungunya-infected saliva

growth_protocol: Aedes aegypti mosquitoes were reared under standard insectary conditions (28°C, 70% humidity, 14:10 hours light:dark photoperiod).

extract_protocol:
Saliva was collected in microcapillary tubes and small RNAs extracted by the miRNeasy Serum/Plasma kit (Qiagen 217184) . Salivary glands were dissected in PBS and small RNAs  extracted by the miRNeasy Micro kit (Qiagen 217084).
Libraries were prepared at the EMBL Genomic Core facility using the NEXTflex small RNA-seq kit v3 (Perkin Elmer).

treatment_protocol: 10 days-old adult females were infected with the chikungunya virus strain 06-21(Reunion Island, AM258992).

value: laboratory strain PAEA

tag: origin

value: originally collected at Paea (Tahiti)

value: saliva from adult females


title: Refed_8h_rep_2 [RUN-048-10]


title: 170823_AGP_XX_E11

value: XX


title: Aedes aegypti SCK2


title: 170814_AGP_XY_E11


title: Refed_3h_rep_4 [RUN-048-08]

value: refeeding (after 3 hours)


title: Aedes aegypti SCK1


title: muscle05

value: Higher Shear force value

value: lower tenderness


title: muscle04


title: Refed_8h_rep_1 [RUN-048-09]


title: muscle03


title: Refed_3h_rep_3 [RUN-048-07]


title: oxidative bisulfite treated genomic DNA from single cell clone M2

type: genomic

city: Lebanon

first: Min Kyung

last: Lee

state: NH

address: 1 Medical Center Dr

institute: Geisel School of Medicine at Dartmouth

description: Isolated single cell clone

hyb_protocol: oxidative-bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina iScan scanner setting

data_processing:
Data were loaded and processed using minfi Bioconductor R package. preprocessfunnorm normalized using minfi R package, 5hmC estimated beta values using OxyBS R package.
Unmethylated and methylated signal intensities

label: Cy5, Cy3

source_name: single cell clone M2

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted using Qiagen DNeasy Kit according to standard instructions

tag: gender

value: Female

value: oxidative bisulfite treated


title: Aedes aegypti S3

source_name: uninfected saliva


title: 170830_AGP_XY_E10

tag: Stage


title: muscle02

value: Longissimus thoracis skeletal muscle


title: Aedes aegypti S2

tag: strain


title: Refed_3h_rep_2 [RUN-048-06]

value: Not applicable


title: Refed_3h_rep_1 [RUN-048-05]

value: Muscle


title: 170830_AGP_XX_E10

tag: transgene


title: Aedes aegypti S1


title: muscle01


title: Aedes aegypti GCK3

source_name: chikungunya-infected salivary glands

value: salivary glands from adult females


title: bisulfite treated genomic DNA from single cell clone P

description: Isolated single cell clone

source_name: Parental cell line (SUM149-PT)

value: bisulfite treated


title: bisulfite treated genomic DNA from single cell clone M1

description: Isolated single cell clone

source_name: single cell clone M1


title: Aedes aegypti GCK2


title: 170814_AGP_XX_E11

tag: genetic sex


title: 170828_AGP_XY_E10

tag: assay type


title: bisulfite treated genomic DNA from single cell clone M2

description: Isolated single cell clone


title: muscle06


title: AgedA

city: Carson

first: Karin

middle: E.

last: Kram

state: California

address: 1000 E. Victoria St.

department: Biology

institute: California State University Dominguez Hills

data_processing:
Alighned using TopHat2
SAMTools to generate BAM files
Read counts calculated by HTSeq
Genome_build: E. coli K12 MG1655 from UCSC
Supplementary_files_format_and_content: Comma separated text files for each sample include count files for each gene

organism: Escherichia coli

source_name: LB culture

growth_protocol: Cells inoculated 1:1000 dilution into LB Lenox broth from overnight growth

extract_protocol:
Culture sacrificed, RNAprotect and RNeasy extraction kit used (Qiagen)
Illumina Ribo-zero and RNA library kit

treatment_protocol: Incubated for 4 hours

value: PFM2 (MG1655 derivative)

tag: time incubated

value: 4 hours

tag: growth medium

value: LB Lenox


title: bisulfite treated genomic DNA from single cell clone EM3

description: Isolated single cell clone

source_name: single cell clone EM3

tag: treatment


title: Fast_rep_2 [RUN-048-02]

value: 2-3 month

value: Wild type

value: fasting (for 24 hours)


title: Left Ventricle_Replicate (E10 dataset) 3

city: ATLANTA

first: Dong

last: Li

state: GEORGIA

address: 2015 UPPERGATE DR

department: Pediatrics

institute: Emory University

data_processing:
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Indexes of the reference genome was built using STAR and paired-end clean reads were aligned to the reference genome using STAR (v2.5).
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels
Differential expression analysis between two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (2_1.6.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate(FDR). Genes with an adjusted P-value <0.05 found by DESeq2 were assigned as differentially expressed.
GO and KEGG enrichment were implemented by the ClusterProfiler. Gene fusion and difference of alternative splicing event were detected by Star-fusion and rMATS software
Supplementary files format and content: tab delimited text file containing raw or normalized read counts for each sample (in columns) and each annotated transcript (in rows).

molecule: polyA RNA

source_name: Cardiomyocytes

extract_protocol:
IMR90 iPSCs were induced for cardiac differentiation using a growth factor-guided protocol. Cardiac spheres were generated from cells at differentiation day 5 and subjected to maturation factors or DMSO treatment from day 14 to day 21. RNA samples from cells at differentiation day 21 or LV samples were prepared using Bio-Rad RNA extraction kit and 1 µg of total RNA/sample was used for the construction of sequencing libraries using Illumina TruSeq RNA Sample Prep Kit.
Libraries were generated using the Illumina standard TruSeq protocol and next-generation sequencing was done through an Illumina HiSeq 2500, 75bp paired end sequencing.

value: pediatric heart samples

tag: developmental stage

value: tissue samples of left ventricle

tag: condition

value: tissue

value: No treatment


title: Left Ventricle_Replicate (E10 dataset) 2


title: Fast_rep_3 [RUN-048-03]


title: Macaque_ileum_scRNA

first: Ye-guang

last: Chen

address: Tsinghua Road, Medical Building

institute: Tsinghua University

data_processing:
Raw reads were aligned to the Mmul_10 macaque genome, and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers
Raw aligned features were loaded and processed using the Seurat package (v4.0.2)
Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes
Genome_build: Mmul_10
Supplementary_files_format_and_content: UMI counts

organism: Macaca mulatta

source_name: Macaque intestine

extract_protocol:
Ileum crypts were isolated and digested with collagenⅠ and Tryple, alive cells were sorted by flow cytometry. Single cell suspensions were captured using the 10X Genomics Chromium Single cell 3’ Solution according to the manufacturers protocol. Briefly, a single-cell suspension was mixed with RT-PCR master mix and loaded together with Single Cell 3’ Gel beads and partitioning Oil into a Single Cell 3’ Chip. About 5,000 cells were loaded into each reaction. RNA transcripts from single cell were uniquely barcoded and reverse-transcribed.
ScRNA-seq libraries were generated using the Chromium Single Cell 3’ Reagent Ki V3 (10X Genomics). The libraries were sequenced as paired-end with Illumina Novaseq 6000.

value: intestine

value: wild type


title: Fast_rep_4 [RUN-048-04]


title: Left Ventricle_Replicate (E10 dataset) 1


title: Aedes aegypti G3

source_name: uninfected salivary glands

value: laboratory strain PAEA

value: originally collected at Paea (Tahiti)


title: oxidative bisulfite treated genomic DNA from single cell clone EM3

description: Isolated single cell clone

value: Female

value: oxidative bisulfite treated


title: oxidative bisulfite treated genomic DNA from single cell clone P

description: Isolated single cell clone


title: oxidative bisulfite treated genomic DNA from single cell clone M1

description: Isolated single cell clone


title: Aedes aegypti GCK1

value: salivary glands from adult females


title: E10_Replicate 3

value: IMR90 iPSC derived cardiomyocytes

value: Day 21 differentiated cells

value: 3D cardiac spherese

value: maturation culture+E10


title: UnagedB

value: PFM2 (MG1655 derivative)

value: 4 hours

value: LB Lenox


title: E10_Replicate 2


title: E10_Replicate 1


title: Aedes aegypti G2


title: Aedes aegypti G1


title: oxidative bisulfite treated genomic DNA from single cell clone EM2

description: Isolated single cell clone

source_name: single cell clone EM2


title: DMSO_Replicate (E10 control) 3

value: 3D cardiac spheres

value: maturation culture+DMSO


title: DMSO_Replicate (E10 control) 2


title: Fast_rep_1 [RUN-048-01]

value: Not applicable

value: Muscle

value: 2-3 month

value: Wild type

value: fasting (for 24 hours)


title: Pig_ileum_scRNA

data_processing:
Raw reads were aligned to the Sscrofa11.1 pig genome, and Cell Ranger (v3.1.0) was used to estimate unique molecular identifiers
Raw aligned features were loaded and processed using the Seurat package (v4.0.2)
Low-quality cells were filtered if they expressed no more than 200 genes or with more than 20% of mitochondrial genes
Genome_build: Sscrofa11.1
Supplementary_files_format_and_content: UMI counts

organism: Sus scrofa

source_name: Pig intestine

value: wild type


title: DMSO_Replicate (E10 control) 1


title: AgedB


title: Muscle cell, control, rep1

city: SHANGHAI

first: sun

last: jingyu

address: SIPINGLU

institute: Tongji university

data_processing:
Remove reads with Adaptor
Remove reads containing N(N indicates that base information cannot be determined) of more than 5%
Removal of low quality Reads (more than 20% of the total read with a mass value of Q≤10
The original sequencing amount, effective sequencing amount, Q20, Q30 and GC contents were counted and comprehensively evaluated
Removal of low quality Reads (more than 20% of the total read with a mass value of Q≤10
Assembly: PE150
Supplementary files format and content: Excel,expression profiles

source_name: Skeletal muscle tissue

growth_protocol: High-glucose DMEM with 10% FBS (#10270-106, Thermo Fisher Scientific, Waltham, Massachusetts, USA) supplemented with L-glutamine (2 mmol/L) was used to culture C2C12 mouse skeletal muscle cells. C2C12 cells were cultured in 96-well plates at a density of 6000 cells/well, grown at 37 °C overnight, treated with different concentrations of PA (0, 50, 100, 150, 200, and 300 μM) for 24 h, added with 10 μL CCK8 solution (#40203ES60, Yeasen, Shanghai, China), and incubated for 4 h at 37 °C.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) according to manufacturer's instructions. The NanoDrop ND-1000 was used to determine the amount and purity of RNA in each sample (NanoDrop, Wilmington, DE, USA). The Agilent 2100 with RIN number > 7.0 was used to assess RNA integrity.Total RNA was isolated using TRIzol (Invitrogen, Carlsbad, CA, USA) reagent. The RNA was fully released after 5 min at room temperature and added with 100 μl chloroform. Centrifuge at 12000 r for 15 min, take about 160 μl of the upper aqueous phase, add an equal amount of isopropanol, and mix them thoroughly. The RNA precipitate was washed twice with 75% ethanol and dissolved in 20 μl RNase-free water, and the RNA concentration was measured by NanoDrop. The 260/280 ratio was used to determine the RNA quality. The cDNA was obtained by taking 1 μg total RNA and reverse transcription in accordance with the instructions of cDNA synthesis kit (#KR106-02, TIANGEN, Beijing, China). The reaction system of real-time fluorescence PCR was as follows: 1 μl cDNA template, 5 μl 2×FastStart Universal SYBR GreenMaster (#FP205-02, TIANGEN, Beijing, China), 0.5 μl each of forward and reverse primers, and 4 μl RNAse-free water. The PCR reaction procedure was as follows: predenaturation at 95 °C for 10 min; product amplification cycle reaction at 95 °C for 10 s; and heating at 60 °C for 10 s and 72 °C for 10 s for 40 cycles. The total RNA quantity of the samples was calibrated using GAPDH as an internal reference, and the RNA expression level of the target gene was calculated using the 2−ΔΔCt method.
After the total RNA was qualified, eukaryotic mRNA was enriched by magnetic beads connected with Oligo(dT). The extracted mRNA was fragmented into short fragments by Fragmentation Buffer at Random. A cDNA strand was synthesized with Random hexamers using fragment mRNA as template. Then buffer solution, dNTPs, RNaseH and DNA Polymerase I were added to synthesize the two-stranded cDNA. AMPureXP Beads were purified double chain products. The STICKY end of DNA was repaired to flat end using T4 DNA polymerase and Klenow DNA polymerase activity. Base A was added to the 3'end and joints were added. Finally, PCR amplification was performed to obtain the final sequencing library.

treatment_protocol: Low cytometry analysis of the cell cycle was conducted by treating C2C12 cells with 200 μM PA after siCD36 interference. Then, cells were harvested and washed thrice in PBS. Single-cell suspension was prepared by digesting cells with trypsin, centrifugation for 3–5 min at 1000 g, and precipitating the cells. Wash the cells with pre-chilled PBS and centrifuge again. For cell fixation, resuspend the pellets with 1 ml of pre-chilled 70% ethanol at 4 °C for 2 h. An appropriate amount of propidium iodide (PI) staining solution was prepared in accordance with the cell cycle assay kit (#C1052, Beyotime Biotechnology, Shanghai, China). Cells were resuspended with 500 μL PI staining solution per tube, incubated for 30 min at 37 °C, protected from light, and subjected to BD flow cytometry (FACSVerse, BD Biosciences, New York, USA) at the excitation wavelength of 488 nm for red fluorescence and light scattering at the same time. The cell cycle percentage was analysed using the FlowJo V10 software (V10.0.7).

value: myoblast

value: Skeletal muscle tissue


title: Muscle cell, control, rep3


title: Muscle cell, control, rep2


title: Muscle cell, CD36 KD, rep3


title: Mutant pls4, 2

city: Nanchang

first: shaochun

last: Liu

address: Jiaoqiao town

institute: Jiangxi Agricultural University

data_processing:
Tophat2
Low-quality reads were removed to get clean reads, the alignment software Tophat2 (2.1.1) was used to align the clean reads to the reference genome of rice, and unique alignments were extracted for subsequent analysis.
Assembly: Oryza sativa Japonica IRGSP-1.0
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Oryza sativa Japonica Group

source_name: leaf

extract_protocol:
Total RNA was isolated according to the protocol of Trizol Reagent kit and purification (Invitrogen)
RNA-seq library was performed by TruSeq RNA Sample Preparation Kit v2.

value: leaf

tag: cell line

value: MESOPHYLL cell

value: knockdown


title: Wild type 2

tag: tissue

value: WT

value: Non knockdown


title: Mutant pls4, 1


title: Wild type 3


title: Wild type 1


title: Achilles tendon-derived cells, vehicle treatment, replicate 1 [C1]

city: WEST LAFAYETTE

first: Chad

middle: C

last: Carroll

state: IN

address: 800 W Stadium Ave

institute: Purdue University

data_processing:
RNAseq raw data set quality and analysis was completed using Basepair software (New York, NY) pipelines. Reads were first aligned to the transcriptome derived from rn6 genome assembly using STAR with default parameters. Next, read counts for each transcript were measured using featureCounts, and differentially expressed genes were determined using DESeq2 using a paired analysis (20, 21). An adjusted p-value cut-off of 0.05 (corrected for multiple hypotheses testing) was used. Finally, GSEA was performed on normalized gene expression counts, using gene permutations for calculating p-value. A log2 fold change cut-off of 1.5 was enforced.
Assembly: rn6
Supplementary files format and content: .fg.gz

source_name: Achilles tendon

extract_protocol:
Tendon-derived fibroblasts utilized in this study were from a previous investigation (Patel et al. 2019 Sci Reports). Briefly, Achilles tendons were rinsed with sterile PBS, minced, placed in DMEM containing 0.2% type I collagenase, and incubated in a 37°C shaking water bath for four hours. After digestion, the cell suspension was filtered through a 100μm mesh filter, pelleted by centrifugation, and resuspended in 5.5mM glucose DMEM containing 10% FBS, 1% sodium pyruvate (Sigma, St. Louis, MO), and 1% penicillin/streptomycin (Thermo Scientific, Waltham, MA). Samples were then plated in 100mm collagen-coated dishes. After reaching confluency, tendon fibroblasts were split and seeded (100,000 cells) in 100mm collagen-coated culture plates.
Libraries from 500ng of input total RNA were constructed as directed by the Nugen Universal Plus mRNA-Seq + UDI kit (PN#9144-96), but the RNA fragmentation time was decreased from 8 minutes to 4 minutes. Final library products were subjected to a 0.7 Ampure:1 Sample ratio purification to reduce lower molecular weight amplicons. The resulting libraries were assessed with an Agilent DNA High Sensitivity Chip for yield and quality and sequenced by Novogene (Sacramento, CA).
Ten libraries were pooled and evenly distributed across a single HiSeq lane to generate ~40,000,000 2X150bp reads on the HiSeq 4000 platform (Illumina, San Diego, CA).

treatment_protocol: Each donor animal’s tendon fibroblasts were treated separately with 200μg/ml of bovine serum albumin (BSA)-Control or AGE-BSA for 48 hours for downstream paired DESeq2 analysis. Tendon fibroblasts treated at passages 2-4 were used for RNA isolation and RNA-sequencing

tag: Sex

value: Female

value: Achilles tendon

value: tendon fibroblast

value: non-glycated bovine serum albumin


title: Achilles tendon-derived cells, AGE treatment, replicate 1 [D2]

value: glycolaldehyde-derived advanced glycation end-product (200ug/ml) for 48 hours


title: Achilles tendon-derived cells, vehicle treatment, replicate 1 [E1]


title: Achilles tendon-derived cells, AGE treatment, replicate 1 [C2]


title: Achilles tendon-derived cells, AGE treatment, replicate 1 [E2]


title: Achilles tendon-derived cells, AGE treatment, replicate 1 [B2]


title: Achilles tendon-derived cells, vehicle treatment, replicate 1 [D1]


title: Muscle cell, CD36 KD, rep1


title: Muscle cell, CD36 KD, rep2


title: Sox2 F1 ns rep2

city: Illkirch

first: Tom

last: Sexton

address: 1 rue Laurent Fries

institute: IGBMC (Institute of Genetics and Molecular and Cellular Biology)

description: 4C-seq with Sox2 bait

data_processing:
Library strategy: 4C-seq
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq
Individual 4C-seq experiments were demultiplexed according to bait primer sequence using sabre, with two mismatches permitted (-m 2)
Reads were aligned using Bowtie (v1.0.0) with the settings -a -m 1 --best --strata
Mapped reads were filtered and mapped to DpnII restriction fragments with the 4See utilities described in Ben Zouari et al. 4See: a flexible browser to explore 4C data. Front. Genet. 10: 1372.
Assembly: mm10
Supplementary files format and content: Cis files, containing a header and two columns (restriction fragment midpoint coordinate, counts), the input format for 4See (Ben Zouari et al. 4See: a flexible browser to explore 4C data. Front. Genet. 10: 1372.)

organism: Mus musculus musculus x Mus musculus castaneus

source_name: Embryonic stem cells

growth_protocol: Mouse F1 ESCs (M. musculus129 × M. castaneus, female cells obtained from Barbara Panning) and derivatives were cultured on 0.1% gelatin-coated plates in ES medium (DMEM containing 15% FBS, 0.1 mM MEM nonessential amino-acids, 1 mM sodium pyruvate, 2 mM GlutaMAX, 0.1 mM 2-mercaptoethanol, 1000 U/mL LIF, 3 µM CHIR99021 [GSK3β inhibitor; Biovision], and 1 µM PD0325901 [MEK inhibitor; Invitrogen]), which maintains ESCs in a pluripotent state in the absence of a feeder layer.

extract_protocol: Cells were fixed with 2% paraformaldehyde in 10% FBS in PBS for 10 min at 23°C. The fixation was quenched with cold glycine at a final concentration of 125 mM, then cells were washed with PBS and permeabilized on ice for 1 h with 10 mM Tris-HCl, pH 8, 100 mM NaCl, 0.1% NP-40, and protease inhibitors. Nuclei were resuspended in DpnII restriction buffer at 10 million nuclei/mL concentration, and 5 million nuclei aliquots were further permeabilized by treatment for 1 h with 0.4% SDS at 37°C, then incubating for a further 1 h with 3.33% Triton X-100 at 37°C. Nuclei were digested overnight with 1500 U DpnII at 37°C, then washed twice by centrifuging and resuspending in T4 DNA ligase buffer. In situ ligation was performed in 400 μL T4 DNA ligase buffer with 20,000 U T4 DNA ligase overnight at 23°C. DNA was purified by reverse cross-linking with an overnight incubation at 65°C with proteinase K, followed by RNase A digestion, phenol/chloroform extraction, and isopropanol precipitation. The DNA was digested with 5 U/μg Csp6I at 37°C overnight, then re-purified by phenol/chloroform extraction and isopropanol precipitation. The DNA was then circularized by ligation with 200 U/μg T4 DNA ligase under dilute conditions (3 ng/μL DNA), and purified by phenol/chloroform extraction and isopropanol precipitation. For allele-specific 4C from the SCR-proximal bait, samples of the DNA were digested with BveI or Alw26I, cutting specifically at the region between the DpnII site and the 4C reading primer annealing site on the 129 or castaneus allele, respectively. For 129-specific 4C from the SCR bait, the material was digested with AvaIII, cutting specifically at the region between the Csp6I site and the 4C non-reading primer annealing site on the castaneus allele. There were no SNPs allowing castaneus-specific 4C from this bait. No digestion was required for allele-specific 4C from the human insertion sequence, since this was only present on the 129 allele. 100 ng aliquots of treated DNA were then used as template for PCR with bait-specific primers containing Illumina adapter termini. PCR reactions were pooled, primers removed by washing with 1.8× AMPure XP beads, then quantified on a Bioanalyzer (Agilent) before sequencing with a HiSeq 4000 (Illumina).

tag: hybrid generation

tag: genotype

tag: restriction enzyme

value: DpnII - Csp6I


title: Sox2 F1 ns rep1

description: 4C-seq with Sox2 bait


title: Sox2 ΔSCR/ΔSCR ns rep1

description: 4C-seq with Sox2 bait

value: {delta}SCR/{delta}SCR


title: UnagedA

value: PFM2 (MG1655 derivative)

value: 4 hours

value: LB Lenox


title: Achilles tendon-derived cells, vehicle treatment, replicate 1 [B1]

tag: cell type


title: 170828_AGP_XX_E10

source_name: Adreno Gonadal Primordium

tag: Stage

value: XX

value: Gene expression


title: Achilles tendon-derived cells, AGE treatment, replicate 1 [A2]


title: oxidative bisulfite treated genomic DNA from single cell clone E

description: Isolated single cell clone

source_name: single cell clone E

tag: gender

value: oxidative bisulfite treated


title: Achilles tendon-derived cells, vehicle treatment, replicate 1 [A1]


title: No insulin/No rMmp12 [5]

city: Corvallis

first: Andrey

last: Morgun

state: OR

address: Pharmacy Building, 1601 SW Jefferson Way

department: Pharmaceutical Sciences

institute: Oregon State University

data_processing:
Sequences were processed to remove the adapter, polyA and low-quality bases by BBTools (https://jgi.doe.gov/data-and-tools/bbtools/) using bbduk parameters of k=13, ktrim=r, forcetrimleft=12, useshortkmers=t, mink=5, qtrim=r, trimq=15, minlength=20.
Reads were aligned to mouse genome and transcriptome (ENSEMBL NCBIM37) using Tophat (v2.1.1) 70 with default parameters.
Number of reads per million for mouse genes were counted using HTSeq (v 0.6.0) 71
Assembly: ENSEMBL NCBIM37
Supplementary files format and content: CSV files includes relativized counts per million values for each Sample.

growth_protocol: 3T3-L1 cells were grown in DMEM (high glucose) media supplemented with 10% fetal bovine serum (FBS) in a 5% CO2 incubator at 37 °C.

extract_protocol:
RNA was extracted using an OMNI Bead Ruptor and 2.8 mm ceramic beads (OMNI International) followed by Qiashredder and an RNeasy kit. Total RNA was quantified using Quant-iT RNA Assay Kit (Thermo Fisher Scientific). Complementary DNA was prepared using qScript reverse transcription kit (QuantaBio).
RNA libraries were prepared with the QuantSeq 3’mRNA-Seq Library Prep Kit (Lexogen) for the Apollo 324 NGS Library Prep System and sequenced using Illumina NextSeq.

treatment_protocol: For differentiation, cells were seeded in a 96 well plate at a density of 5000 cells/well. After 24 h, the medium was shifted to differentiation medium (90% DMEM, 10% FBS, 1.0 µM Dexamethasone, 0.5 mM Methylisobutylxanthine, 1.0 µg/mL insulin). After 48 h, the medium was removed and the cells were cultured in adipocyte maintenance medium (90% DMEM, 10% FBS, 1.0 µg/mL Insulin) for another 48 h. Then the medium was changed to regular growth medium (90% DMEM, 10% FBS) and cells were treated with activated rMmp12 or vehicle for 24 h. Afterwards, the cells were incubated in glucose uptake testing medium (low glucose DMEM containing 0.2% BSA) with or without 100 nM insulin for 12 h. Cells were frozen in RLT buffer and stored in -80°C for RNA extraction.

value: adipocyte

value: No insulin/No rMmp12 [5]


title: No insulin/No rMmp12 [4]

value: WT

value: No insulin/No rMmp12 [4]


title: fl/fl Cre+ rep3

city: Mainz

first: Christoph

last: Hieber

department: Dermatology

country: Germany

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v20.0 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome.
Assembly: GRCm38
Supplementary files format and content: txt

source_name: bone marrow

growth_protocol: Bone marrow cells were cultured at a concentration of 2*10^5 cells per mL in GM-CSF containing medium. After 3 days, 500 mL fresh medium was added and at day 7, 1 mL of medium was replaced. After 10 days, BMDC were used for sequencing.

extract_protocol:
MHCII positive cells were immunomagnetically isolated (Miltenyi Biotec) and lysed (RLT PlusLysis Buffer; Qiagen, Hilden, Germany). RNA was purified with the RNeasy Plus Micro Kit as recom-mended by the manufacturer (Qiagen) and quantified using a Qubit 2.0 fluorometer (Invi-trogen). RNA quality was assessed on a Bioanalyzer 2100 using a RNA 6000 Pico chip (both from Agilent, Santa Clara, CA)
RNA quality was assessed on a Bioanalyzer 2100 using a RNA 6000 Pico chip (both from Agilent, Santa Clara, CA). 10 ng of total RNA (integrity > 8) was used to generate barcoded mRNA-seq cDNA library using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (both from NEB, Ipswich, MA) with a final amplification of 15 PCR cycles. RNA was quantified using the Qubit HS assay kit (Thermo Fisher) and the library size distribution was determined using the Bioanalyzer HS DNA assay (Agilent). Afterwards, barcoded RNA-Seq libraries were clustered using the HiSeq® Rapid SR Cluster Kit v2 (Illumina, San Diego, CA) using 8pM and 59bps were sequenced on the Illumina HiSeq2500 using HiSeq® Rapid SBS Kit v2 (59 cycles).

treatment_protocol: Three replicates of CD18fl/fl and CD18ΔCD11c BMDC were treated with 100 ng/mL LPS for 24 h.

value: bone marrow

value: bone marrow-derived dendritic cell (BMDC)

value: untreated


title: Insulin, rMmp12 [4]

value: Insulin, rMmp12 [4]


title: fl/fl Cre+ 24 h LPS rep3

value: 24 h LPS


title: fl/fl Cre- 24 h LPS rep3


title: fl/fl Cre+ 24 h LPS rep1


title: Control, Insulin, no rMmp12 [4]

value: Control, Insulin, no rMmp12 [4]


title: Control, Insulin, no rMmp12 [3]

value: Control, Insulin, no rMmp12 [3]


title: fl/fl Cre+ rep2


title: Control, Insulin, no rMmp12 [5]

value: Control, Insulin, no rMmp12 [5]


title: fl/fl Cre+ rep1


title: fl/fl Cre+ 24 h LPS rep2


title: bisulfite treated genomic DNA from single cell clone EM2

description: Isolated single cell clone

value: Female

value: bisulfite treated


title: fl/fl Cre- 24 h LPS rep2


title: fl/fl Cre- 24 h LPS rep1


title: Insulin, rMmp12 [5]

value: Insulin, rMmp12 [5]


title: fl/fl Cre- rep3


title: No insulin/No rMmp12 [3]

value: No insulin/No rMmp12 [3]


title: bisulfite treated genomic DNA from single cell clone EM1

description: Isolated single cell clone

source_name: single cell clone EM1


title: Control, Insulin, no rMmp12 [2]

value: Control, Insulin, no rMmp12 [2]


title: Control, Insulin, no rMmp12 [1]

value: adipocyte

value: Control, Insulin, no rMmp12 [1]


title: Insulin, rMmp12 [1]

value: WT

value: Insulin, rMmp12 [1]


title: oxidative bisulfite treated genomic DNA from single cell clone EM1

description: Isolated single cell clone

value: oxidative bisulfite treated


title: fl/fl Cre- rep1

value: bone marrow

value: bone marrow-derived dendritic cell (BMDC)


title: Insulin, rMmp12 [3]

value: Insulin, rMmp12 [3]


title: 298 S 9/26 S3F1 3979T Female #60

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

data_processing:
After sequencing, reads were filtered, sorted by their barcode of origin and aligned to the reference transcriptome using DROPEST pipeline (https://github.com/hms-dbmi/dropEst). Mapped reads were quantified into UMI-filtered counts per gene, and barcodes that correspond to cells were retrieved based on previously established methods
Barcodes were filtered using dropkick (Heiser et al., 2021), resulting in the processed data table.
NovaSeq:Technical read: read1 - UMI/cell barcode - the oligo barcodes are TruDrop which is positioned exactly as in (Southard-Smith et al., 2020). Biological read: read2 - 3' end
Assembly: Mouse: GRCm38.85
Supplementary files format and content: Delimited tables, with cells and genes, as columns and rows, filtered

source_name: M220, colon

growth_protocol: primary cells

extract_protocol:
Mouse colonic cell suspensions were generated according to protocol in (Chen et al., 2021). Cells were encapsulated using the inDrop platform (1CellBio), and RNA was extracted according to the protocol of Klein et al., 2015.
CEL-Seq linear amplification of using TruDrop library structure (Southard-Smith et al., 2020)

value: female

tag: time

value: 2 weeks


title: 16HBE14o cells, CSE + 20 MOI_2

city: Braunschweig

first: Andreas

last: Jeron

state: Nierdersachsen

address: Inhoffenstraße 7

department: Viral Immunology

institute: Helmholtz Center for Infection Research

hyb_protocol: Hybridization was performed acording to Clariom S microarray manufacturer recommendations

scan_protocol: Scanning was performed acording to Clariom S microarray manufacturer recommendations

data_processing:
Data were processed with Transcriptome Analysis Console 4.0 (Thermo Fischer) using SST-RMA algorithm
SST-RMA normalized log2-transformed signal intensities from Transcriptome Analysis Console 4.0
Clariom_S_Human.r1.bgp

label: biotin

source_name: 16HBE14o cell line

label_protocol: Labeling was performed acording to Clariom S microarray manufacturer recommendations

growth_protocol: Cells were cultivated in T75 flask in minimum essential medium with earle’s salt supplemented with 10 % fetal bovine serum, 200 mM L-Glutamine and  penicillin/streptomycin. Cells were incubated in a humidified incubator at 37 °C with 7.5% CO2. Upon 90% confluency, the cells were detached and harvested with Trypsin/EDTA 0.025%.

extract_protocol: Total RNA was isolated using RNeasy Mini plus Kit (Qiagen)

treatment_protocol: Cells were stimulated with either untreated medium and cigarette smoke extract (CSE) for 28h, or with CSE 24h followed by 4h medium (CSE cessation), Streptococcus pneumoniae (Sp) MOI 10 and MOI 20 for 4h, FCCP 50 µM for 4h, CSE for 24h followed by Sp MOI 10 and 20 for 4h as well as CSE for 24h followed by FCCP 50 µM.

value: bronchial epithelial cell

value: 15 % cigarette smoke extract for 24 h, then Streptococcus pneumonia infection with 20 MOI for 4 h


title: 16HBE14o cells, CSE + 20 MOI_1


title: BEAS-2B with PBS control, rep1

city: Taipei

first: Zi-yi

last: Huang

address: No. 155, Sec. 2, Linong St. Beitou Dist., Taipei City 112304, Taiwan

department: School of Life Sciences

country: Taiwan

institute: National Yang Ming Chiao Tung University

data_processing:
Trimmomatic (v.0.38) for the data clearance
HISAT2 performs clean reads and reference genome alignment. HISAT2 is an alignment tool based on HISAT and Bowtie2 that provides fast and accurate alignment results.
Used featureCounts (v1.6.3) to calculate the number of sequence mappings  and organized the gene expression in each sample.
Standardization will be done by TPM (Transcript Per Million) method
Assembly: GRCh38
Supplementary files format and content: Original read counts, TPMs

growth_protocol: BEAS-2B cells were grown in RPMI medium containing 10% FBS, supplemented with 1% NEAA, penicillin/streptomycin, and L-glucose.

extract_protocol:
Total RNA was extracted by the RNeasy Mini Kit and frozen at -80℃
The DNA library generates two sequence data (R1 and R2) files for the DNA sequence annotation and quality control through Illumina Paired-End sequencing technology. Before sequenced the raw data, Trimmomatic (v.0.38) was used to remove low-quality reads and artificially added adapter to obtain high-quality information (clean reads).
KAPA mRNA HyperPrep Kit (KAPA Biosystems, Roche, Basel,  Switzerland)

treatment_protocol: 1×10^6 cells were seeded on 10-cm petri dish and incubated overnight at 37oC. On the next day, cells were washed by PBS before treated with 66.67 or 500 µg/ml of Virofree for another 4 h.

value: epithelial cell

value: control


title: Insulin, rMmp12 [2]

value: Insulin, rMmp12 [2]


title: 292 S 9/26 S2F1 3979T Female #6

source_name: M219, colon


title: BEAS-2B with PBS control, rep2


title: bisulfite treated genomic DNA from single cell clone E

description: Isolated single cell clone

value: Female

value: bisulfite treated


title: fl/fl Cre- rep2

value: untreated


title: WT_Osci_4

source_name: IMM

growth_protocol: Wild type and Myd88ko Immortalized Mouse Macrophages (IMM) were originally generated in Katherine A. Fitzgerald lab and grown in DMEM high glucose media supplemented with 10% FBS and 20 mM HEPES.

treatment_protocol: 100,000 cells were seeded in 24 well plate in 500 ul complete medium for 24 h. All three types were seeded in the same plate. After 24 h of seeding, cells were treated with either 5% CFS or control for 24 h, then collected in RLT buffer and stored at -80°C.

value: IMM

value: Wild type Immortalized Mouse bone-marrow derived Macrophages (IMM)

value: Oscillibacter valericigenes


title: BEAS-2B with 500 ug/ml Virofree

value: Virofree (500 ug/ml Virofree)


title: 293 S 9/27 S3F1 3728T Female #60

source_name: M214, colon

value: WT


title: No insulin/No rMmp12 [1]

value: adipocyte

value: No insulin/No rMmp12 [1]


title: Myd88_KO_Osci_4


title: No insulin/No rMmp12 [2]

value: No insulin/No rMmp12 [2]


title: Myd88_KO_Osci_3


title: 285 S 9/26 S1F1 3979T Male #4

source_name: M215, colon

value: male

value: 2 weeks


title: 299 S 9/27 S1F1 3728T Female #5

source_name: M212, colon

value: female


title: 311 S 9/26 S3F2 3979T Female #60


title: 286 S 9/27 S2F1 3728T Male #5

source_name: M210, colon


title: TL_IgG4, replicate 1, scRNAseq

city: Durham

first: George

last: Fromm

state: NC

address: 21 Parmer Way, Suite 200

institute: Shattuck Labs, Inc.

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Libraries were sequenced on an Illumina NovaSeq 6000 and processed with the 10X cellranger pipeline (v 6.0.2) for demultiplexing, barcode and UMI counting and read alignments.
Assembly: hg38
Supplementary files format and content: cloupe and .h5

source_name: TIGIT-Fc(IgG4)-LIGHT fusion protein

extract_protocol:
Human PBMC cultured for 2 days in AIMV media +/- 150 nM TIGIT-Fc(IgG1)-LIGHT or TIGIT-Fc(IgG4)-LIGHT fusion proteins were harvested from suspension and also those that adhered to tissue culture plates using Corning non-enzymatic cell stripping solution. Single cells from treated healthy donor human PBMCs were isolated using the 10x Genomics Chromium handler.
Single cell libraries were generated using 10x Genomics Chromium Next GEM Single Cell 3’ v3.1: Dual Index reagents.

value: PBMC

value: TIGIT-Fc(IgG4)-LIGHT fusion protein


title: UT, replicate 1, scRNAseq

description: 10x Genomics

source_name: untreated


title: TL_IgG1, replicate 1, scRNAseq

description: 10x Genomics

source_name: TIGIT-Fc(IgG1)-LIGHT fusion protein

value: TIGIT-Fc(IgG1)-LIGHT fusion protein


title: WT_Control_4


title: WT_Osci_3


title: 16HBE14o cells, CSE + 10 MOI_1

value: bronchial epithelial cell

value: 15 % cigarette smoke extract for 24 h, then Streptococcus pneumonia infection with 10 MOI for 4 h


title: ML-DS2, combination, rep1

city: Frankfurt

first: Jan-Henning

last: Klusmann

address: Theodor-Stern-Kai 7

department: Pediatric Hematology and Oncology

institute: Goehte University Frankfurt

data_processing:
Raw reads were trimmed and filtered by Novogene Company, Ltd. using in-house scripts, then mapped to human reference genome hg38 using HISAT2.
Gene expression values (FPKM) were calculated using the featureCounts package in R.
Assembly: hg38
Supplementary files format and content: Normalized read counts (FPKM) in tab-separated format

source_name: patient sample expanded via xenotransplantation

growth_protocol: Patient samples were maintained in StemSpan supplemental with a cytokine cocktail (FLT3-L, SCF, IL-6, IL-3, TPO) for the duration of the treatment (48 hours).

extract_protocol:
Total RNA was extracted using the Zymo Quick-RNA Miniprep Kit with on-column DNase treatment (R1054).
Illumina sequencing libraries were prepared by Novogene Company, Ltd. using total cellular RNA, and sequenced on an Illumina NovaSeq platform (150 bp paired-end reads).

treatment_protocol: ML-DS patient samples were treated with DMSO (vehicle control), 350nM of the LSD1 inhibitor T-3775440, 1uM ruxolitinib, or the combination of T-3775440 and ruxolitinib for 48 hours.

value: LSD1 inhibitor + ruxolitinib

value: 48 hours


title: ML-DS2, combination, rep2

value: patient sample expanded via xenotransplantation


title: 16HBE14o cells, 20 MOI_2

value: Streptococcus pneumonia infection with 20 MOI for 4 h


title: ML-DS2, ruxolitinib, rep1

value: ruxolitinib


title: 16HBE14o cells, CSE + FCCP_2

value: 15 % cigarette smoke extract for 24 h, then  addition of 50 µM FCCP for 4 h


title: 16HBE14o cells, CSE + FCCP_1


title: 16HBE14o cells, CSE + 10 MOI_2


title: 16HBE14o cells, CSE cessation_1

value: 15 % cigarette smoke extract for 24 h, then medium replacement for 4 h


title: 16HBE14o cells, 20 MOI_1


title: Non-tumor, CD45+NK1.1- cells, with HET genotype

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description:
CD45_barcodes.tsv.gz
CD45_features.tsv.gz
CD45_matrix.mtx.gz

data_processing:
Cellranger was executed with refdata-cellranger-mm10 transcriptome. Both, cellranger count for individual samples as well as cellranger aggr for NK1.1+ and all CD45+ samples was executed
Assembly: mm10
Supplementary files format and content: standard cellranger output

source_name: normal liver

extract_protocol:
FACS sorted cells from Hepatocellular carcinoma were processed according to 10x genomics protocol
The single-cell droplets were generated with chromium single-cell controller using Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics, 1000121)

value: HET

tag: tumor

value: NT


title: 16HBE14o cells, CSE cessation_2


title: Non-tumor, CD45+NK1.1+ cells, with KO genotype

description:
CD45_barcodes.tsv.gz
CD45_features.tsv.gz
CD45_matrix.mtx.gz
CD45NK11_barcodes.tsv.gz
CD45NK11_features.tsv.gz
CD45NK11_matrix.mtx.gz

value: KO


title: Non-tumor, CD45+NK1.1- cells, with KO genotype


title: Myd88_KO_Osci_2

value: IMM

value: Wild type Immortalized Mouse bone-marrow derived Macrophages (IMM)

value: Oscillibacter valericigenes


title: 16HBE14o cells, FCCP_2

value: incubation with 50 µM FCCP for 4 h


title: 16HBE14o cells, CSE_1

value: 15 % cigarette smoke extract for 28 h


title: Tumor, CD45+NK1.1- cells, with KO genotype

source_name: hepatocellular carcinoma

value: T


title: ML-DS2, LSD1 inhibitor, rep2

value: LSD1 inhibitor


title: 16HBE14o cells, 10 MOI_1

value: bronchial epithelial cell

value: Streptococcus pneumonia infection with 10 MOI for 4 h


title: 16HBE14o cells, FCCP_1


title: WT_Control_3

value: WT


title: WT_Control_2


title: 16HBE14o cells, CSE_2


title: 16HBE14o cells, 10 MOI_2


title: Non-tumor, CD45+NK1.1+ cells, with HET genotype


title: Low Ca shRoot4-mi8

city: Greensboro

first: Muhammad

last: Numan

state: North Carolina

address: 321 McIver Street

institute: University of North Carolina Greensboro

data_processing:
Assembly
annotation
Go terms
target identification
Supplementary_files_format_and_content: excel

organism: Eragrostis tef

source_name: shoot

growth_protocol: Plants were grown in hydroponic solution with low calcium and optimum calcium

extract_protocol:
RNA was extracted and sequenced
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit.

treatment_protocol: 4 replicates  for each treatment

value: low calcium


title: ML-DS2, LSD1 inhibitor, rep1

value: patient sample expanded via xenotransplantation

value: 48 hours


title: WT_Osci_2


title: ML-DS2, ruxolitinib, rep2

value: ruxolitinib


title: Tumor, CD45+NK1.1- cells, with HET genotype

value: HET


title: Myd88_KO_Osci_1


title: WT_Osci_1


title: Low Ca shoot3-mi7


title: ML-DS2, DMSO, rep2

value: DMSO (vehicle)


title: ML-DS2, DMSO, rep1


title: Tumor, CD45+NK1.1+ cells, with KO genotype

value: KO


title: BEAS-2B with 66.67 ug/ml Virofree

value: epithelial cell

value: Virofree (66.67 ug/ml)