title: Th17-1 rep3

city: Guangzhou

first: Xiao

last: Ruipei

address: Guangzhou North Stress

institute: Southern Medical University

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Hisat2 tools soft were used to map with reference genome.
Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.
Differential expression analysis of two conditions/groups was performed using the DESeq2.
Assembly: mm10
Supplementary files format and content: TXT files include FPKM values for each Sample

source_name: splenocytes

growth_protocol: RPMI 1640, 10% fetal bovine serum，1%Penicillin-Streptomycin，1×glutamine,1×β-Mercaptoethanol，cells were cultured at 37°C at 5%CO2.

extract_protocol:
Total RNA of T cells was prepared using RNAex Pro RNA Reagent(AG,AG21102) on the tenth day.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology (Shanghai) Co., Ltd.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: T cells were souted from the spleens of C57BL/6 and cultured with the presence of anti-CD3(5ug/mL),anti-CD28(1ug/mL) for 3 days. And cells were re-stimulated with anti-CD3(0.05ug/mL),anti-CD28(0.05ug/mL) ,IL2(100U/mL) on the seventh day. Th1 for 10 ng/mL IL-12, 5 mg/mL anti-IL-4; Th17 for 1 ng/mL TGF-b, 20 ng/mL IL-6, 10 ng/mL IL-1b, 20 mg/mL anti-IFN-g, 5 mg/mL anti-IL-12 and 5 mg/ml anti-IL-4; Th17 derived Th1(Th17-1) was first grown in Th17 differentiation condition, after re-stimulated on the seventh day, Th1 differentiation condition was employed.

tag: tissue

value: splenocytes

tag: strain background

value: T cell

tag: genotype

value: WT

value: Th17-1 differentiation


title: Th17-1 rep2

status: Public on Jun 01 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: cell type

tag: treatment


title: Animal_A7N104_W8_D1

city: Palo Alto

first: Dmitri

middle: A

last: Kazmin

state: CA

address: 240 Pasteur Dr

department: Institute for Immunity, Transplantation and Infection

country: USA

institute: Stanford University

data_processing:
Reads were aligned using STAR 2.7.10a
Assembly: Mmul-10
Supplementary files format and content: Reads per transcript, tab-delimited text

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
The blood Paxgene tubes were stored until all samples were collected. The whole blood samples were then subjected to RNA extraction using the Thermo Fisher “MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes.”
Sample QC was performed with Agilent 2100 bioanalyzer to identify samples with RIN > 7. Qualified RNA from each sample was processed with non-stranded mRNAseq library prep (with globin mRNA removal). In brief, mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. Globin mRNA was depleted using globin mRNA probes. mRNA molecules were fragmented into small pieces using a fragmentation reagent, and the first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. They were then end-repaired, followed by A-tailing and adapter ligation reactions. The library was subsequently PCR enriched and purified by the Ampure XP bead size selection method. All libraries are quantified by Agilent Technologies 2100 bioanalyzer. The double-stranded PCR products were heat-denatured and circularized by the splint oligo sequence. The single-strand circle DNA (ssCir DNA) was formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were loaded into the patterned nanoarray and paired-end 150-base reads were generated by sequencing using the sequencer G400.

value: PBMC

tag: animal

tag: week

tag: day

tag: group

tag: regimen


title: sample10epicardium

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

country: Japan

institute: Kobe University Graduate School of Medicine

description: 10x Genomics

library_source: transcriptomic single cell

data_processing: Cell Ranger Single Cell Software (v 6.1.2) by 10X Genomics against the GRCh38 human reference genome with default parameter

organism: Homo sapiens

source_name: cell, permanent atrial fibrilattion

extract_protocol: cell：Each sample was washed, chopped into small pieces, and digested in enzymatic digestion buffer with 450 U/ml collagenase I (Sigma, C0130), 125 U/ml collagenase XI (Sigma, C7657), 60 U/ml DNase I (Roche, 04536282001) and 60 U/ml hyaluronidase (Sigma, H3506) at 37 °C for 30 minutes while shaking.1 The digested samples were filtered through 40-μm cell strainers (BD, 352340), washed, and centrifuged at 300g for 10 minutes.　nuclei：LA samples were cut into small pieces and frozen into liquid nitrogen within 8 hours after sample collection. Nuclei isolation was performed according to Chromium Nuclei Isolation Kit with RNase Inhibitor (PN-1000494). Frozen tissue samples are homogenized with a pestle in Lysis Buffer and passed through a column. Next, debris is removed via centrifugation in Debris Removal Buffer. The isolated nuclei are then washed and resuspended and loaded directly into compatible 10x Genomics protocol for making libraries.

value: heart

value: immune cell


title: Animal_A7N104_Baseline_D0

value: Baseline


title: wild type adult hermaphrodite on Y34F4.3 RNAi, screen group rep n/a

city: Bethesda

first: Katherine

last: McJunkin

state: MD

address: 50 South Drive, Building 50 Room 3148

institute: National Institutes of Health

data_processing:
Deep sequencing data were analyzed using the miTRATA web interface (https://wasabi.ddpsc.org/~apps/ta/) after preprocessing the data using miTRATA’s accompanying Python3-based preprocess.seq pipeline, installed on the NIH High Performance Computing Cluster in a dedicated miniconda environment. The matureC. elegansmiRNAs from miRBase Release 22.1 were used for miTRATA mapping. A custom C++ script reformatted the miTRATA output by consolidating read numbers for all reads meeting the following criteria into a tabular format: a tail:head ratio >0.12 and a tail length≤3nt. These reformatted tailing data were further analyzed in RStudio. (One non-unique miRNA pair was of sufficient abundance to be included in tailing analysis—mir-44/45-3p;mir-45-3pwas therefore culled from tabular data to avoid plotting this data twice). To calculate reads per million, reads were normalized by the number of genome-mapping reads in the library (Supplementary Table S3). The number of genome-mapping reads was determined using Bowtie to align to the C. elegans genome (WS215) with the arguments -v 3 -f -B 1 -a –best –strata. Alignments were then filtered based on the length of the reads and the number of mismatches as follows: for sequence lengths 16–17, 18–19, 20–24or >24: zero, one, twoor three mismatches were allowed, respectively. Reads passing this threshold were considered ‘genome-mapping reads’. A custom bash/R pipeline was used to calculate trimming relative to canonical miRNA length from the miTRATA output files.
Assembly: WBcel_235
Assembly: WS215
Supplementary files format and content: xlsx file containing sample metadata, normalized reads and percent tailing for microRNAs above minimum abundance threshhold

organism: Caenorhabditis elegans

source_name: whole animal

growth_protocol: N2 (wild type) and SX1137 (pash-1(mj100) I) worms were maintained at 15°C. For RNA samples, L1s were synchronized by alkaline hypochlorite lysis of gravid adults followed by hatching in M9 with 1 mM cholesterol at 15°C for 48–72 h. L1s were plated on NGM seeded with either OP50 or RNAi bacteria and maintained at 15°C until early day one of gravid adulthood (until just a few embryos were laid on the plate, ∼76 h after plating). (This time point was chosen because it achieved the best synchrony of SX1137, which tends to develop slightly asynchronously, even at permissive temperature). This time point was harvested for N2 samples, SX1137 samples in the RNAi screen, and served as 0h in time courses involving SX1137. Additional SX1137 plates were shifted to 25°C, and samples were collected at the indicated time points after upshift for time courses on OP50 or RNAi. pup-1(tm1021), pup-2(tm4344) and pup-1/-2(om129) mutations were maintained over a balancer chromosome at 15–20°C; RNA was isolated from homozygous F2 (M-Z-) 1-day adult hermaphrodites raised at 22°C.

extract_protocol:
Total RNA was isolated by Trizol extraction. Spike-ins were added at a final concentration of 0.1pg/μl (OP50 samples) or 1pg/μl (RNAi samples) in 100ng/μl total RNA.
Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.

treatment_protocol: RNAi plates were supplemented with 1μg/ml IPTG and 1μg/ml Carbenicillin (and poured no more than two weeks prior to use and stored at 4°C). The RNAi bacteria (HT115 expressing an RNAi vector) were prepared from single clones derived from the Ahringer library (Source Bioscience), the Vidal library (Source Bioscience), or custom RNAi vectors (Supplementary Table S1). All previously-reported RNAi phenotypes were observed. Furthermore, a robust RNAi response in each sample was confirmed by the presence of abundant siRNAs mapping to the targeted locus.

tag: sample

tag: strain

tag: time point

tag: RNAi

tag: replicate

tag: sample group

value: screen

tag: dev stage

value: adult

value: wild type

tag: Sex

value: hermaphrodite

value: whole animal


title: sample11 permanent atrial fibrillation

description: 10x Genomics

tag: tissue


title: Th17-1 rep1

tag: strain background

tag: genotype


title: wild type adult hermaphrodite on R07H5.11 RNAi, screen group rep n/a

description: Library preparation was performed using the NEBNext Small RNA Library Prep Set for Illumina with modifications. Size selection was performed only after reverse transcription, using 8% urea gels to purify ~65-75nt RT products. Prior to loading on the gel, each RT reaction was treated with 5000units of RNAse H (New England Biolabs) for 30 minutes at 37C.


title: Th17-17 rep3

tag: cell type

tag: treatment

value: Th17 differentiation


title: Animal_A7N070_W12_D0

tag: animal

tag: week


title: WT_NPC_Hi-C_Rep3

city: Shanghai

first: Yan

last: Jiang

address: 131 Dongan rd

department: Institutes of Brain Science

institute: Fudan University

library_source: genomic

data_processing:
Quality control was conducted by FastQC (version 0.11.9), and reads were trimmed with Trim Galore (version 0.6.7, --quality 20 --phred33 --stringency 1 --length 20 --fastqc --paired).
Restriction sites of MboI on mm10 were generated with “hiccup_digester” function of HiCUP (version 0.8.0).
High quality clean reads were aligned to mm10 with Bowtie2 program (version 2.4.1) in HiCUP (max di-tag length: 700, min di-tag length: 50).
“ValidPairs” were generated with the “mapped_2hic_fragments.py” script of HiC-Pro (version 2.11.4) in default settings.
“.hic” files were generated with “hicpro2juicebox.sh” utility of HiC-Pro and JuicerTools (version 1.22.01).
Assembly: mm10
Supplementary files format and content: HIC: binary contact matrix for visualization in Juicebox

molecule: genomic DNA

source_name: Neural progenitor cells

growth_protocol: Ganglionic eminences of fetal brains were harvested, dissociated with Accutase solution (Sigma A6964), and cultured in ultra-low attachment plates (Corning 3471) with advanced DMEM/F-12 (Gibco 12634-010) supplemented with N-2 (Gibco 17502048), B-27 (Gibco 12587010), GlutaMAX (Gibco 35050061), P/S (Sigma V900929), heparin (5 ug/ml), EGF (20 ng/ml) and FGF (20 ng/ml). Fresh medium was added every 3 days, and neurospheres were dissociated with Accutase and passed every 5 days.

extract_protocol:
3 million cells were lysed in NP40 lysis buffer (0.32 M sucrose, 5 mM CaCl2, 3 mM Mg(Ace)2, 0.1 mM EDTA, 10 mM Tris pH8, 0.1% NP40) , fixed in 1% formaldehyde (Sigma 252549) at RT for 5 minutes and quenched with 125 mM glycine at RT for 10 minutes. Nuclei were incubated in 0.5% SDS at 62 ℃ for 10 minutes, and quenched with 1.25% Triton X-100 (Sigma 93443) at 37 ℃ for 15 minutes. Chromatin was digested with 100 U of MboI restriction enzyme (NEB R0147) in 1X NEBuffer2 (NEB B7002S) at 37 ℃ overnight with rotation. Enzyme digestion was inactivated with incubation at 65 ℃ for 20 minutes, and nuclei were collected with centrifugation. Restriction fragment overhangs were filled and DNA ends were marked with biotin using End-it DNA Repair Kit (Epicentre ER0720) supplemented with 0.256 mM biotin-14-dATP (Life Technologies 19524-016), 0.4 mM dCTP, 0.4 mM dGTP and 0.4 mM dTTP (NEB N0446S). For proximity ligation, DNA fragments were ligated with 2000 U of T4 DNA ligase (NEB M0202) in 1200 μl of ligation master mix (T4 DNA ligase buffer (NEB B0202), 0.83% Triton X-100, 0.1 mg/ml bovine serum albumin (NEB B9200S)) at RT for 4 hours with slow rotation. After ligase inactivation at 65 ℃ for 5 minutes, nuclei were collected with centrifugation, and the chromatin was reverse-crosslinked in PK lysis buffer (1 M Tris pH8, 50 mM EDTA, 2% SDS, 2 M NaCl) at 65 ℃ for 4 hours, followed by RNase A (Sigma R6513) and proteinase K (Sigma P2308) digestion. DNA was further purified by phenol/chloroform (1:1) and ethanol precipitation, dissolved in buffer EB (Qiagen 19086) and sonicated to ~ 300 base pairs by Covaris E220 ultrasonicator system. For biotin pull-down, 100 μl per sample of 10 mg/ml Dynabeads MyOne Streptavidin T1 beads (Life technologies 65602) was washed with 400 μl per sample of 1 X TWB (5 mM Tris-HCl pH7.5, 0.5 mM EDTA, 1 M NaCl, 0.05% Tween-20), resuspended in 100 μl per sample of 2X binding buffer (10 mM Tris-HCl pH7.5, 1 mM EDTA, 2 M NaCl) and incubated with samples at RT for 15 minutes with rotation. The beads were separated on magnetic stand, washed three times with 1 X TWB (pre-warmed to 55 ℃) and once in 100 μl buffer EB (Qiagen 19086).
The beads were collected for DNA end repair with End-it DNA Repair Kit, A-tailing with Klenow Exo-minus (Epicentre KL06041K), adapter (Vazyme N802-01) ligation with Fast-Link kit (Epicentre LK11025) and PCR amplification with VAHTS HiFi Universal Amplification Mix for Illumina (Vazyme N618-02). Supernatant was taken as the library, which was further size-selected with SPRIselect beads (Beckman B23318) and sent for deep sequencing on Illumina NovaSeq 6000 (paired-end, 150 bp).

value: Neural progenitor cells from ganglionic eminence

tag: restriction enzyme

value: MboI

value: Wildtype

tag: age

value: Embryonic day 15.5

tag: fetus id


title: wild type adult hermaphrodite on T08B2.4 RNAi, screen group rep n/a

tag: sample

tag: strain


title: wild type adult hermaphrodite on pup-3 RNAi, screen group rep n/a

tag: time point

tag: RNAi


title: sample10endocardium

description: 10x Genomics


title: Animal_A7N070_W9_D0

tag: day

tag: group

tag: regimen


title: sample12 permanent atrial fibrillation

description: 10x Genomics

tag: tissue


title: Th17-17 rep2

value: splenocytes

tag: strain background

value: T cell


title: sample10blood

description: 10x Genomics


title: Animal_A7N070_W8_D1


title: Th17-17 rep1

tag: genotype

value: WT


title: sample9endocardium

description: 10x Genomics

tag: cell type


title: wild type adult hermaphrodite on pap-1 RNAi, screen group rep n/a

tag: replicate

tag: sample group

tag: dev stage

tag: Sex


title: Animal_A7N070_W8_D0

value: PBMC

tag: treatment

tag: animal

tag: week


title: Th1-1 rep3

value: Th1 differentiation


title: wild type adult hermaphrodite on mut-2 RNAi, screen group rep n/a

tag: sample

tag: strain


title: Th1-1 rep2


title: sample9blood

description: 10x Genomics

value: heart

value: immune cell


title: Animal_A7N070_W1_D0


title: wild type adult hermaphrodite on L4440 RNAi, screen group rep 3

tag: time point

tag: RNAi

value: screen


title: Animal_A7N070_W4_D0

tag: day

tag: group


title: Th1-1 rep1

tag: tissue


title: Animal_A7N070_Baseline_D0

value: Baseline

tag: regimen


title: Animal_A7N070_W0_D1


title: oxamate-2

city: beiijing

first: wei

last: zhao

address: Haidian Distric

institute: China Agricultural University

data_processing:
The quality assessment of raw data was performed using FastQC
Cleaned reads were aligned to the mm10 genome using Bowtie2 (v 2.2.5)
PCR duplicates were removed using samtools (v1.7) rmdup.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value<=0.01
Genome coverage bedGraph files for UCSC genome browser were generated by deeptools (v 3.0.2)
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

source_name: uterine stromal cell

extract_protocol:
samples were lysed in lysis buffer (10 mM Tris-HCl ([pH 7.4]), 10 mM NaCl, 3 mM MgCl2 and NP-40) for 10 min on ice to prepare the nuclei. Immediately after lysis, nuclei were spun at 500g for 5 min to remove the supernatant.
The ATAC-seq libraries of primary mouse uterine stromal cells were prepared using Hyperactive ATAC-Seq Library Prep Kit for Illumina (TD711, Vazyme Biotech) according to the manufacturer’s instructions

value: uterine stromal cell

value: estrogen 10nM+progesterone 1μM+oxamate 25mM


title: wild type adult hermaphrodite on L4440 RNAi, screen group rep 1

value: adult

tag: genotype

value: wild type

value: hermaphrodite

value: whole animal


title: wild type adult hermaphrodite on L4440 RNAi, screen group rep 4


title: sample8 early atrial fibrillation

description: 10x Genomics

source_name: cell, early atrial fibrillation

tag: cell type


title: sample9epicardium

description: 10x Genomics


title: sample6 early atrial fibrillation

description: 10x Genomics


title: wild type adult hermaphrodite on pup-2 RNAi, screen group rep n/a

tag: replicate


title: oxamate-1


title: sample5 permanent atrial fibrillation

description: 10x Genomics

source_name: nuclei, permanent atrial fibrilattion


title: Animal_A7N043_W12_D0


title: EP-2.

value: estrogen 10nM+progesterone 1μM


title: EP-1.


title: sample1and2 early atrial fibrillation

description: 10x Genomics

source_name: nuclei, early atrial fibrillation


title: wild type adult hermaphrodite on L4440 RNAi, screen group rep 2

tag: sample group


title: Animal_A7N043_W8_D1


title: wild type adult hermaphrodite on hpo-31 RNAi, screen group rep n/a

tag: dev stage


title: wild type adult hermaphrodite on gld-4 RNAi, screen group rep n/a

tag: Sex


title: control-2

tag: treatment

value: vehicle


title: sample7 early atrial fibrillation

description: 10x Genomics


title: wild type adult hermaphrodite on gld-2 RNAi, screen group rep n/a


title: HT29, Input

city: Shenzhen

first: Epigenomics

last: Gao

address: Dapeng district

department: Agricultural Genomics Institute at Shenzhen

institute: Chinese Academy of Agricultural Sciences

data_processing:
ChIP-seq reads were aligned to the UCSC hg38 genome using BWA with paired-end alignment.
Duplicated reads were removed by using SAMtools with mapping quality score > 15.
Peaks were called using MACS2 with the significant cut-off q-value <= 0.05
Assembly: hg38
Supplementary files format and content: norrowPeak

growth_protocol: HCT116 and HT29 cells were cultured in DMEM/F-12 supplied with 10% FBS.

extract_protocol:
Cells for each assay were crosslinked with 1% formaldehyde in PBS for 15 min in a 37 oC incubator, lysed by lysis buffer (1% SDS, 10 mM EDTA, 50 mM Tris-HCl, 1×PIC). The chromatin DNA was precipitated by 4 μg specific antibodies, eluted and reversed the crosslink. The DNA was purified with the Qiaquick PCR purification kit (Qiagen, Germany).
The Immunoprecipited and Input DNA was subujected to end repair, “A” base addition and adapter ligation,respectively. Finally, the ChIP library was constructed by PCR amplification.

tag: cell line

value: human colorectal cancer cells

tag: chip antibody


title: control-1


title: Animal_A7N043_W8_D0

tag: animal

tag: week


title: HT29, TET3, ChIP, rep2


title: OXA-2

data_processing:
The quality assessment of raw data was performed using FastQC
Cleaned reads were aligned to the mm10 genome using Bowtie2 (v 2.2.5)
PCR duplicates were removed using samtools (v1.7) rmdup.
Peaks were called using MACS v2.1.0 with the significance cut-off q-value<=0.01
Genome coverage bedGraph files for UCSC genome browser were generated by deeptools (v 3.0.2)
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

extract_protocol:
Cells were counted and collected and bound to Concanavalin A–coated beads
CUT&Tag libraries were prepared using Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) (TD901, Vazyme Biotech) according to the manufacturer’s instructions

tag: antibody


title: HT29, TET3, ChIP, rep1


title: wild type adult hermaphrodite on F43H9.3 RNAi, screen group rep n/a

tag: sample

tag: strain

tag: time point

tag: RNAi


title: Animal_A7N043_W4_D0

tag: tissue

tag: day

tag: group

tag: regimen


title: HT29, TET2, ChIP, rep2

tag: cell type


title: Animal_A7N043_W1_D0


title: wild type adult hermaphrodite on F43E2.1 RNAi, screen group rep n/a

tag: replicate

tag: sample group

tag: dev stage

tag: genotype


title: OXA-1


title: sample3and4 permanent atrial fibrillation

description: 10x Genomics

source_name: nuclei, permanent atrial fibrillation


title: HT29, TET2, ChIP, rep1

tag: cell line

tag: chip antibody


title: EP-2


title: wild type adult hermaphrodite on F43G6.5 RNAi, screen group rep n/a

tag: Sex


title: Animal_A7N043_Baseline_D0

tag: treatment

tag: animal

tag: week


title: Animal_A7N043_W0_D1


title: wild type adult hermaphrodite on K05C4.4 RNAi, screen group rep n/a

tag: sample

tag: strain

tag: time point


title: Animal_A7N043_W9_D0

tag: tissue

tag: day


title: EP-1

tag: antibody


title: wild type adult hermaphrodite on F31C3.2 RNAi, screen group rep 1

tag: RNAi


title: HT29, TET1, ChIP, rep2

tag: cell type


title: wild type adult hermaphrodite on F31C3.2 RNAi, screen group rep 2

tag: replicate

tag: sample group


title: Animal_A7N035_W12_D0

tag: group

tag: regimen


title: CON-2


title: Animal_A7N035_W9_D0


title: wild type adult hermaphrodite on exos-7 RNAi, screen group rep n/a

tag: dev stage

tag: genotype


title: CON-1


title: Animal_A7N035_W8_D1

tag: treatment


title: Aged_3

city: Hangzhou

first: Xiangjun

last: Zeng

address: Zhejiang univerisity

institute: Zhejiang univerisity

data_processing:
After quality control, paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
Reference genome and gene model annotation files were downloaded from genome website directly.  Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).  We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Assembly: mm10
Supplementary files format and content: xls files include count values for each Sample

source_name: bone marrow

extract_protocol:
RNA of cells was extracted using Trizol.
Library construction and sequencing were performed by Novogene Corporation. In short, mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads and Illumina NovaSeq 6000 was applied to generate the end reading of 150bp pairing. After quality control, paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).

value: bone marrow

value: Aged HSPC

value: c57bl/15 WT

value: unculture

tag: condition

value: Uncultured aged HSPCs.


title: HT29, GR, ChIP, rep1

tag: cell line

tag: chip antibody

value: GR


title: Aged_2

value: c57bl/14 WT


title: wild type adult hermaphrodite on exos-4.1 RNAi, screen group rep n/a

tag: sample

tag: strain

value: screen

tag: Sex


title: wild type adult hermaphrodite on disl-2 RNAi, screen group rep n/a

tag: time point

tag: tissue


title: Animal_A7N035_W8_D0

value: PBMC

tag: animal

tag: week

tag: day


title: wild type adult hermaphrodite on dis-3 RNAi, screen group rep n/a

tag: RNAi

tag: replicate

tag: sample group


title: Aged_1

tag: cell type

value: c57bl/13 WT


title: HT29, GR, ChIP, rep2


title: wild type adult hermaphrodite on dcs-1 RNAi, screen group rep n/a

tag: dev stage

value: adult

tag: genotype


title: Young_2

value: Young HSPC

value: c57bl/11 WT

tag: treatment

tag: condition

value: Uncultured young HSPCs.


title: HCT116, TET3, ChIP, rep1

tag: cell line

tag: chip antibody


title: HCT116, Input


title: Animal_A7N035_W4_D0

tag: group

tag: regimen


title: HCT116, TET3, ChIP, rep2


title: Young_3

value: c57bl/12 WT


title: wild type adult hermaphrodite on cid-1 RNAi, screen group rep 1

tag: sample

tag: strain

tag: time point

value: wild type

tag: Sex

value: hermaphrodite

value: whole animal


title: Animal_A7N035_W0_D1

tag: tissue

tag: animal

tag: week

tag: day


title: HT29, TET1, ChIP, rep1

tag: cell type

value: human colorectal cancer cells


title: Animal_A7N035_Baseline_D0

value: Baseline


title: wild type adult hermaphrodite on cid-1 RNAi, screen group rep 2

tag: RNAi

tag: replicate

tag: sample group

tag: dev stage


title: HCT116, TET2, ChIP, rep1

tag: cell line


title: Animal_A6X018_W12_D0

tag: treatment


title: Uridine_3

value: bone marrow

value: Aged HSPC

tag: genotype

value: c57bl/9 WT

value: uridine

tag: condition

value: Aged HSPCs treated with uridine.


title: cdbEx36 adult hermaphrodite, sample group 5 rep 2

tag: sample


title: Animal_A7N035_W1_D0

value: PBMC

tag: group

tag: regimen


title: HCT116, TET1, ChIP, rep2

tag: chip antibody


title: cdbEx36 adult hermaphrodite, sample group 5 rep 1

tag: strain

tag: time point

tag: Sex

tag: tissue


title: Animal_A6X018_W9_D0

tag: animal

tag: week

tag: day


title: Uridine_2

tag: cell type

value: c57bl/8 WT


title: HCT116, TET1, ChIP, rep1


title: cdbEx35 adult hermaphrodite, sample group 5 rep n/a

tag: RNAi

tag: replicate

tag: sample group

tag: dev stage

value: adult


title: Animal_A6X018_W8_D1

tag: treatment


title: HCT116, GR, ChIP, rep2

tag: cell line

value: GR


title: Vehicle_3

tag: genotype

value: c57bl/6 WT

value: vehicle

tag: condition

value: Aged HSPCs treated with vehicle.


title: Uridine_1

value: c57bl/7 WT


title: Young_1

value: Young HSPC

value: c57bl/10 WT

value: unculture

value: Uncultured young HSPCs.


title: Animal_A6X018_W8_D0

tag: group

tag: regimen


title: cdbEx33 adult hermaphrodite, sample group 5 rep 1

tag: sample

tag: strain

tag: time point

value: hermaphrodite

value: whole animal


title: HCT116, TET2, ChIP, rep2

value: human colorectal cancer cells

tag: chip antibody


title: HMC3, EphB2 + ephrin-B1 siRNA, rep 3

city: Riverside

first: Marcus

last: Kaul

state: California

address: 900 University Ave, SOM RB Room 311

department: Biomedical Sciences

institute: University of California, Riverside

data_processing:
FASTQ files were processed using the human reference genome (GRCh38), from Ensembl database (release 109). Kallisto [PMID: 27043002] was utilized as the software to generate an index facilitating transcript quantification.
Assembly: GRCh38 / hg38
Supplementary files format and content: Tab-delimited .txt file containing: target_id, lengths of transcripts (length), effective lengths (eff_length), estimated counts (est_counts), transcripts per million (tpm).

source_name: HMC3 cells, EphB2-Fc + ephrin-B1 siRNA

extract_protocol:
RNA was extracted from HMC3 (lysed in Qiagen RLT buffer + 1% Beta-mercaptoethanol) using the Rneasy Plus Mini Kit (Qiagen). RNA samples were first analyzed using the Agilent 2100 Bioanalyzer in the UCR Genomics Core. Samples with RIN > 9.0 were sent to the UCSD genomics core (IGM), for RNAseq (rRNA depletion, PE100, 25M)
RNA libraries for RNA-seq were prepared by the UCSD genomics core (IGM): Illumina Total RNA Prep (Ribodepletion).

treatment_protocol: HMC3 microglia were cultured in a 12 well plate, and treated with ephrin-B1 siRNA or negative control-siRNA with RNAiMAX transfection reagent for 48 hours. EphB2-Fc or Ctrl-Fc was then pre-clustered with goat anti-human IgG on ice for 1 hour, with mixing every 15 minutes. Cell were then treated with either pre-clustered EphB2-Fc (2ug/mL) or Ctrl-Fc (2ug/mL) for 24 hours before being supernatants were removed and the cells lysed for RNA isolation.

tag: tissue

value: Brain

value: Microglia

value: Immortalized

tag: transfection

value: ephrin-B1 siRNA


title: Animal_A6X018_W1_D0

value: PBMC

tag: animal

tag: week

tag: day


title: Vehicle_2

value: bone marrow

tag: cell type

value: Aged HSPC


title: cdbEx33 adult hermaphrodite, sample group 5 rep 2

tag: RNAi

tag: replicate

tag: sample group

tag: dev stage

value: adult

tag: Sex


title: Animal_A6X018_W4_D0

tag: treatment

tag: group


title: Vehicle_1

tag: genotype

value: c57bl/6 WT

value: vehicle

tag: condition

value: Aged HSPCs treated with vehicle.


title: HCT116, GR, ChIP, rep1

tag: cell line

value: GR


title: Animal_A6X018_W0_D1

tag: regimen


title: cdbEx32 adult hermaphrodite, sample group 5 rep n/a

tag: sample

tag: strain

tag: time point

tag: tissue


title: HMC3, EphB2 + ephrin-B1 siRNA, rep 2

tag: transfection


title: cdbEx31 adult hermaphrodite, sample group 5 rep n/a


title: HMC3, EphB2 + ephrin-B1 siRNA, rep 1

tag: cell type


title: Clu-mes_h6e894hn1w

city: shanghai

first: Minjun

last: Wang

address: xiangyin road

department: Cell biology

institute: Naval Medical University

description: Clu-mes.expression

data_processing:
Celescope was used to base-calling, alignment, filtering and generation of normalized abundance measurements.
Read 1: contains the 24bp GEXSCOPE barcode and the 12bp UMI (bases 25-36). Read 2 contains the cDNA information.
Assembly: GRCm38
Supplementary files format and content: matrix files

molecule: polyA RNA

source_name: liver

extract_protocol:
Different components were macrodissected and stored at 4 ℃ GEXSCOPETM Tissue Preservation Solution. Then, we washed samples for 3 times with Hanks Balanced Salt Solution (HBSS) and minced them into 1–2 mm-thick pieces, 2 ml GEXSCOPETM Tissue Dissociation Solution (Singleron Biotechnologies) was added to each sample and allowed for digestion at 37 ℃ for 15 minutes to dissociate the tissue into single cells. Then, we filtrate the samples using 40-μm sterile strainers, followed by centrifuging at 1,000 rpm for 5 minutes. After the centrifugation, the precipitation was resuspended in 1 ml phosphate-buffered saline (PBS; HyClone, Marlborough, United States). Subsequently, 2 ml GEXSCOPETM Red Blood Cell Lysis Buﬀer (Singleron Biotechnologies) was added into the cell suspension and incubated at 25°C for 10 minutes to remove red blood cells. After that, the mixture was centrifuged at 500 × g for 5 minutes, followed by re-suspending the precipitation with PBS.
We used GEXSCOPETM Single Cell RNA Library Kit Tissue (Singleron Biotechnologies) to barcode single cells, capture mRNA from isolated single cells, and generate cDNA libraries for scRNA-seq. Then, individual libraries were diluted to 4 ng/μl, and pooled for sequencing on a Novaseq6000 platform (Illumina, San Diego, USA) with 150 bp paired-end reads.

value: liver cells

value: liver

value: CluKO

tag: age

value: 6-8 weeks old


title: Animal_A6N134_W12_D0

tag: animal

tag: week

tag: day


title: cdbEx30 adult hermaphrodite, sample group 5 rep 2

tag: RNAi

tag: replicate

tag: sample group

tag: dev stage

tag: Sex

value: hermaphrodite

value: whole animal


title: Clu-mes_h5efrzc37u

description: Clu-mes.expression

tag: genotype


title: Clu-mes_h5fehov2z6

description: Clu-mes.expression


title: Animal_A6N134_W8_D1

tag: treatment

tag: group

tag: regimen


title: cdbEx30 adult hermaphrodite, sample group 5 rep 1

tag: sample

tag: strain

tag: time point


title: HMC3, ephrin-B1 siRNA, rep 3

source_name: HMC3 cells, Ctrl-Fc + ephrin-B1 siRNA

tag: tissue

value: Brain

tag: cell line

tag: cell type

value: Microglia

tag: transfection

value: Ctrl-Fc


title: HMC3, ephrin-B1 siRNA, rep 2

value: Immortalized

value: ephrin-B1 siRNA


title: Animal_A6N134_W9_D0

value: PBMC

tag: animal

tag: week

tag: day


title: Clu-mes_h4ulf729jp

description: Clu-mes.expression

tag: age


title: Animal_A6N134_W4_D0


title: cdbEx29 adult hermaphrodite, sample group 5 rep 1

tag: RNAi

tag: replicate

tag: sample group

tag: dev stage

value: adult


title: Clu-mes_h4ulf4ldgq

description: Clu-mes.expression

tag: genotype


title: cdbEx28 adult hermaphrodite, sample group 5 rep n/a

tag: Sex


title: Animal_A6N134_W8_D0

tag: treatment

tag: group

tag: regimen


title: HMC3, ephrin-B1 siRNA, rep 1

tag: tissue


title: HMC3, EphB2, rep 3

source_name: HMC3 cells, EphB2-Fc + neg ctrl siRNA

tag: cell line

value: neg ctrl siRNA


title: wild type adult hermaphrodite on L4440 RNAi, sample group 4 rep 4

tag: sample

tag: strain

tag: time point

value: wild type


title: HMC3, EphB2, rep 2

tag: cell type

tag: transfection


title: CCl4 4w

description: CCl4 4w.expression

value: wildtype

tag: age


title: Animal_A6N134_W1_D0

tag: animal

tag: week

tag: day


title: Animal_A6X018_Baseline_D0

value: Baseline


title: WT_NPC_Hi-C_Rep1

value: Neural progenitor cells from ganglionic eminence

tag: restriction enzyme

value: MboI

value: Wildtype

value: Embryonic day 15.5

tag: fetus id


title: CCl4 2w

description: CCl4 2w.expression

value: liver cells

value: liver

tag: genotype

value: 6-8 weeks old


title: wild type adult hermaphrodite on L4440 RNAi, sample group 4 rep 3

tag: RNAi

tag: replicate

tag: sample group

tag: dev stage

tag: Sex

value: hermaphrodite

value: whole animal


title: HMC3, Ctrl, rep 3

source_name: HMC3 cells, Ctrl-Fc + neg ctrl siRNA

tag: tissue

value: Brain

tag: cell line

value: Microglia

value: Immortalized

tag: treatment

value: Ctrl-Fc


title: Animal_A6N134_W0_D1

value: PBMC

tag: group

tag: regimen


title: wild type adult hermaphrodite on L4440 RNAi, sample group 4 rep 2

tag: sample

tag: strain

tag: time point

value: adult

value: wild type


title: CCl4 0w

description: CCl4 0w.expression

tag: cell type

value: wildtype

tag: age


title: cdbEx29 adult hermaphrodite, sample group 5 rep 2


title: HMC3, Ctrl, rep 2

tag: transfection

value: neg ctrl siRNA


title: Animal_A6N134_Baseline_D0

tag: animal

tag: week

value: Baseline

tag: day


title: wild type adult hermaphrodite on L4440 RNAi, sample group 4 rep 1

tag: RNAi

tag: replicate

tag: sample group

tag: genotype


title: Animal_A5R055_W12_D0

tag: tissue


title: TCL1, Tbx21-KO, replicate 2, scRNA-seq

city: Heidelberg

first: Isabelle

last: Seufert

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

description:
10x Genomics
TCL1_Tbx21KO_52

data_processing:
Demultiplexing, barcode processing, genome mapping, gene counting (including introns) and aggregation were conducted using the Cell Ranger software v5.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10-2020-A
Supplementary files format and content: pseudo-bulk bam, h5 single cell count matrix

molecule: nuclear RNA

source_name: Spleen

growth_protocol: Tbx21-KO (-/-) and Tbx21-WT (+/+) TCL1 cells were expanded in immunodeficient NSG animals.

extract_protocol:
Mice were euthanized by increasing concentrations of carbon dioxide (CO2). Single-cell suspensions from spleens were prepared using the GentleMacs system. Splenocytes were enriched in TCL1 cells using EasySep™ Mouse Pan-B Cell Isolation Kit for further analyses, resulting in a purity above 97% of CD5+ CD19+ cells.
Libraries were prepared according to the Chromium single-cell Multiome ATAC +Gene Expression protocol v1 (10x Genomics).

value: E{mu}-TCL1 cells

value: Spleen

value: NSG


title: Clu-mes_h4uldvwrub

description: Clu-mes.expression

value: liver cells

value: liver

value: CluKO


title: TCL1, Tbx21-KO, replicate 1, scRNA-seq

description:
10x Genomics
TCL1_Tbx21KO_49


title: wild type adult hermaphrodite on gld-2 RNAi, sample group 4 rep 4

tag: dev stage

tag: Sex

value: hermaphrodite

value: whole animal


title: HCT116 cells, negative control, cell invasion, rep1

data_processing:
raw RNA-sequencing reads were trimmed using TrimGalore (version 0.6.6; parameter- )
Trimmed sequence reads were mapped to GRCh38/hg38 using STAR (parameters- )
Read count extraction and normalization were performed using
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

growth_protocol: HCT116 and HT29 cells were maintained in DMEM/F-12 medium with 10% FBS, 1% GlutaMAX and 0.1% Mycoplasma prevention reagentat 37 °C in a 5% CO2 humidified incubator.

extract_protocol:
Total RNA was extracted by using RNA mini kit (Qiagen, Germany). 200 ng of total RNA was used for the construction of sequencing library.
RNA libraries for RNA-seq were prepared using TruePerp DNA Library Perp Kit V2 for Illumina (Vazyme, China) according to the manufacturer’s protocol

treatment_protocol: 5×104 HCT116 or HT29 cells was suspended in DMEM/F-12 with dexamethasone (0.1 μM), seeded in the upper chamber of 8.0 mm Falcon Cell Culture Inserts.

tag: cell line

value: human colorectal cancer cells

tag: treatment

value: Negative control


title: HMC3, EphB2, rep 1

value: Brain

value: Microglia

value: Immortalized


title: HCT116 cells, belinostat and GC treated, rep1

value: Dexamethasone and belinostat treated


title: wild type adult hermaphrodite on gld-2 RNAi, sample group 4 rep 3

tag: sample

tag: strain

value: adult

value: wild type


title: Animal_A5R055_W9_D0

value: PBMC

tag: group

tag: regimen


title: TCL1, Tbx21-WT, replicate 1, scRNA-seq

description:
10x Genomics
TCL1_Tbx21WT_34

tag: cell type

value: E{mu}-TCL1 cells


title: wild type adult hermaphrodite on gld-2 RNAi, sample group 4 rep 2

tag: time point


title: TCL1, Tbx21-WT, replicate 2, scRNA-seq

description:
10x Genomics
TCL1_Tbx21WT_37

value: Spleen


title: Animal_A5R055_W8_D1

tag: animal

tag: week


title: HCT116 cells, GC treated, cell inversion, rep1

value: Dexamethasone treated


title: Animal_A5R055_W8_D0

tag: day


title: Animal_A5R055_W4_D0


title: TCL1, Tbx21-KO, replicate 2, scATAC-seq

description:
10x Genomics
TCL1_Tbx21KO_291

data_processing:
Demultiplexing, barcode processing, genome mapping and aggregation were conducted using the Cell Ranger ATAC software v2.0.0 (https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac).
Assembly: mm10-2020-A
Supplementary files format and content: pseudo-bulk bam, h5 single cell peak count matrix, tab-separated fragment file, comma-separated single cell info file

source_name: Eµ-TCL1 cells

extract_protocol:
Mice were euthanized by increasing concentrations of carbon dioxide (CO2). Single-cell suspensions from spleens were prepared using the GentleMacs system. Splenocytes were enriched in TCL1 cells using EasySep™ Mouse Pan-B Cell Isolation Kit for further analyses, resulting in a purity above 97% of CD5+ CD19+ cells.
Libraries were prepared according to the Chromium single-cell ATAC v1.1 protocol (10x Genomics) using an in-house loaded Tn5.

value: NSG


title: HCT116 cells, belinostat treated, rep1

value: Belinostat treated


title: gldr-2(cdb187) I adult hermaphrodite on L4440 RNAi, sample group 4 rep 4

tag: RNAi

tag: replicate

value: gldr-2(cdb187) I


title: wild type adult hermaphrodite on gld-2 RNAi, sample group 4 rep 1

tag: sample group

tag: genotype

value: hermaphrodite


title: HCT116 cells, negative control, layer separated, cell invasion, rep1


title: Animal_A5R055_W1_D0

source_name: PBMC

tag: tissue


title: TCL1, Tbx21-WT, replicate 2, scATAC-seq

description:
10x Genomics
TCL1_Tbx21WT_268


title: HMC3, Ctrl, rep 1

tag: transfection

value: neg ctrl siRNA

value: Ctrl-Fc


title: gldr-2(cdb187) I adult hermaphrodite on L4440 RNAi, sample group 4 rep 3

tag: dev stage

tag: Sex

value: whole animal


title: HCT116 cells, belinostat and GC treated, non-invaded-layer, rep1

tag: cell line

value: human colorectal cancer cells

tag: treatment


title: TCL1, Tbx21-KO, replicate 1, scATAC-seq

description:
10x Genomics
TCL1_Tbx21KO_290

tag: strain


title: Animal_A5R055_W0_D1

tag: group

tag: regimen


title: TCL1, Tbx21-WT, replicate 1, scATAC-seq

description:
10x Genomics
TCL1_Tbx21WT_260

tag: cell type


title: gldr-2(cdb187) I adult hermaphrodite on L4440 RNAi, sample group 4 rep 2

tag: sample

tag: time point


title: HCT116 cells, belinostat and GC treated, invaded-layer, rep1


title: HO_2cell_biol rep 3

city: Jinan

first: Rongrong

last: Zhang

address: 44 Wenhuaxi Road

institute: Shandong University

data_processing:
Clusters were obtained by cBot, then, diluted to 10 pM and sequenced using Illumina NovaSeq 6000 platform (Illumina).
Each gene was expressed as fragments per kilobase of exon per million reads mapped (FPKM), calculating by Stringtie software.
Fragments of each gene segments were normalised by the trimmed mean of M values (TMM) algorithm.
Assembly: GRCm38.100
Supplementary files format and content: tab-delimited text files include FPKM values of each sample

source_name: embryo

extract_protocol:
Oocytes and embryos at four different stages (5 oocytes or embryos per sample) were collected from wild type and Nlrp14 knockout mice. Each sample had three biological replicates. Total RNA was extracted from samples with lysis buffer.
The cDNA library was prepared using SMART-Seq® HT Kit. The first strand cDNA was replicated using reverse transcriptase and templateless C nucleotides. The second strand cDNA was formed using oligonucleotide Primers. The purified cDNA was amplified by PCR to form the final cDNA library.

value: embryo

value: Nlrp14 knockout

tag: Stage


title: Animal_A5R055_Baseline_D0

tag: animal

tag: week

value: Baseline

tag: day


title: HO_2cell_biol rep 1

tag: genotype


title: gldr-2(cdb187) I adult hermaphrodite on gld-2 RNAi, sample group 4 rep 4

source_name: whole animal

tag: RNAi

tag: replicate

tag: sample group

value: adult

tag: tissue


title: Animal_A2X042_W8_D1


title: HO_2cell_biol rep 2


title: Animal_A2X042_W12_D0


title: HCT116 cells, GC treated, invaded-layer, rep1

tag: cell line


title: HCT116 cells, belinostat treated, non-invaded-layer, rep1

tag: treatment


title: gldr-2(cdb187) I adult hermaphrodite on gld-2 RNAi, sample group 4 rep 3

tag: strain

tag: dev stage

tag: Sex


title: gldr-2(cdb187) I adult hermaphrodite on gld-2 RNAi, sample group 4 rep 2


title: HCT116 cells, GC treated, non-invaded-layer, rep1

tag: cell type


title: gldr-2(cdb187) I adult hermaphrodite on gld-2 RNAi, sample group 4 rep 1

tag: sample


title: HT29 cells, negative control, rep1

value: Negative control


title: WT_2cell_biol rep 3

value: WT


title: Animal_A2X042_W8_D0

value: PBMC

tag: group

tag: regimen


title: Animal_A2X042_W9_D0

tag: animal


title: HT29 cells, GC treated, rep1


title: pash-1(mj100)I adult hermaphrodite on L4440 RNAi 24 hrs after upshift to restrictive temperature, sample group 2 rep 1

tag: time point


title: Animal_A2X042_W0_D1

tag: week

tag: day


title: pash-1(mj100)I adult hermaphrodite on L4440 RNAi 24 hrs after upshift to restrictive temperature, sample group 2 rep 2

tag: RNAi

tag: genotype


title: WT_2cell_biol rep 2

tag: Stage


title: Animal_A2X042_W1_D0

tag: tissue


title: HO_PN5_biol rep 3

source_name: zygote

value: zygote


title: HT29 cells, negative control, layer separated, rep1

tag: cell line


title: gldr-2(cdb187) I adult hermaphrodite on L4440 RNAi, sample group 4 rep 1

tag: replicate

tag: sample group


title: pash-1(mj100)I adult hermaphrodite on F31C3.2 RNAi 24 hrs after upshift to restrictive temperature, sample group 2 rep 2

tag: strain

tag: dev stage


title: HO_PN5_biol rep 2

tag: cell type


title: HT29 cells, GC treated, unmigrated-layer, rep1

tag: treatment

value: Dexamethasone treated


title: Animal_A2X042_Baseline_D0

tag: group


title: pash-1(mj100)I adult hermaphrodite on cid-1 RNAi 24 hrs after upshift to restrictive temperature, sample group 2 rep 2

tag: sample

tag: Sex


title: pash-1(mj100)I adult hermaphrodite on cid-1 RNAi 24 hrs after upshift to restrictive temperature, sample group 2 rep 1

tag: time point


title: WT_PN5_biol rep 3


title: Animal_A2X010_W12_D0

tag: animal

tag: week

tag: regimen


title: HT29 cells, GC treated, migrated-layer, rep1


title: HCT116 cells, negative control, cell migration, rep1


title: Animal_A2X010_W9_D0

tag: day


title: pash-1(mj100)I adult hermaphrodite on L4440 RNAi 0 hrs after upshift to restrictive temperature, sample group 2 rep 2

tag: RNAi

tag: genotype


title: HCT116 cells, negative control, layer separated, cell migration, rep1

tag: cell line


title: WT_2cell_biol rep 1

tag: Stage


title: Animal_A2X010_W8_D1

tag: tissue


title: WT_PN5_biol rep 1


title: Animal_A2X042_W4_D0


title: Animal_A2X010_W8_D0


title: HCT116 cells, GC treated, cell migration, rep1


title: pash-1(mj100)I adult hermaphrodite on L4440 RNAi 0 hrs after upshift to restrictive temperature, sample group 2 rep 1

tag: strain

tag: replicate

tag: sample group


title: pash-1(mj100)I adult hermaphrodite on F31C3.2 RNAi 0 hrs after upshift to restrictive temperature, sample group 2 rep 2

tag: dev stage


title: pash-1(mj100)I adult hermaphrodite on F31C3.2 RNAi 0 hrs after upshift to restrictive temperature, sample group 2 rep 1


title: HCT116 cells, GC treated, unmigrated-layer, rep1

tag: cell type

tag: treatment


title: HO_MII_biol rep 2

source_name: oocyte

value: oocyte

value: MII


title: Animal_A2X010_W1_D0

tag: group


title: HCT116 cells, GC treated, migrated-layer, rep1


title: HO_MII_biol rep 3


title: HO_PN5_biol rep 1


title: pash-1(mj100)I adult hermaphrodite on cid-1 RNAi 0 hrs after upshift to restrictive temperature, sample group 2 rep 2

tag: sample

tag: time point

tag: Sex


title: THP1-OE-FLASH

first: Zhicheng

last: Pan

address: 79 Qingchun Road

department: Department of Cardiology

institute: The First Affiliated Hospital, Zhejiang University School of medicine

library_source: other

data_processing:
Trimmomatic (v0.39) was utilized to remove contaminating adaptor sequences and low-quality reads from the raw sequencing data. Subsequently, HISAT2 (v2.2.1) was employed to align the clean data to the reference genome. Peak calling was performed using Piranha (v1.2.1).
Assembly: hg38
Supplementary files format and content: tab-delimited text file include raw counts for each sample
Library strategy: FLASH-Seq

molecule: other

growth_protocol: THP-1 cells were cultured in an RPMI 1640 medium containing 10% fetal bovine serum (FBS) and treated with phorbol-12-myristate-13-acetate (PMA) (100 ng/mL; Sigma-Aldrich, P8139) for 48 h to induce macrophage differentiation.

treatment_protocol: CircARCN1 overexpression or knockdown was achieved by infecting lentivirus containing circARCN1 overexpression or knockdown vector, followed by puromycin selection.

value: monocyte isolated from peripheral blood

value: with circARCN1 overexpression

tag: disease

value: acute monocytic leukemia patient


title: WT_PN5_biol rep 2


title: Animal_A2X010_W0_D1

tag: animal

tag: week

tag: day

tag: regimen


title: Animal_A2X010_Baseline_D0


title: pash-1(mj100)I adult hermaphrodite 6 hrs after upshift to restrictive temperature, sample group 1 rep 2

tag: RNAi

tag: genotype

value: hermaphrodite


title: THP1-SH-FLASH

tag: cell line

value: with circARCN1 knockdown


title: pash-1(mj100)I adult hermaphrodite on cid-1 RNAi 0 hrs after upshift to restrictive temperature, sample group 2 rep 1

tag: strain

tag: replicate

tag: tissue

value: whole animal


title: WT_MII_biol rep 2

tag: cell type

tag: Stage


title: THP1-FLASH-2

value: wild type


title: Animal_A15N234_W27_D0

tag: treatment

tag: group


title: pash-1(mj100)I adult hermaphrodite 6 hrs after upshift to restrictive temperature, sample group 1 rep 1

tag: sample

tag: time point

tag: sample group

tag: dev stage


title: WT_MII_biol rep 1


title: THP1-FLASH-1

tag: disease


title: Animal_A15N234_W24_D0

tag: animal

tag: week

tag: day


title: HO_GV_biol rep 3

tag: genotype

value: Nlrp14 knockout

value: GV


title: Animal_A2X010_W4_D0

tag: regimen


title: DICER-delHelicase rescue replicate 3

city: Hong Kong SAR

first: Truc

middle: Cong

last: LE

address: Clearwater Bay, Kowloon

department: Life Science

country: Hong Kong

institute: The Hong Kong University of Science and Technology

data_processing:
The sequencing reads of mRNA were also adapter-trimmed by cutadapt (Martin 2011) (-a AGATCGGAAGAGCACACGTCT for Read 1 and -a GATCGTCGGACTGTAGAACTCTGAAC for Read 2).
Processed pair-end reads were then joined by using fastq-join (Aronesty 2013), and low-quality reads were then discarded by using fastq_quality_filter (-q 30 -p 90) (http://hannonlab.cshl.edu/fastx_toolkit/index.html, version 0.0.13).
Reads are then mapped to human genome reference (GRCh38) using bowtie2 (bowtie2 --local --score-min L,-4,2 --ma 2 -k 5) (Langmead and Salzberg, 2012).
miRNA genomic coordination file was obtained from miRBase v22 (Kozomara et al., 2019), and annotation of the mapped reads was done by using bedtools intersect (Quinlan A.R. and Hall I. M., 2010).
Assembly: home-made reference shRNA sequences
Supplementary files format and content: Bed files of control samples contain the raw read count of each shRNA in the control library.
Supplementary files format and content: Bed files of the single cleavage and double cleavage samples contains the assigned cleavage sites, cleavage accuracy, positional cleavage efficiency, global cleavage efficiency.

source_name: HCT116 DICER-KO

growth_protocol: The HCT116 DICER-KO cells were cultured in McCoyʼs 5A medium (Gibco, 16600082) supplemented with 10% fetal bovine serum (FBS) (Gibco, 10270106) and 1% of  Penicillin-Streptomycin (Gibco, 15140122).

extract_protocol:
The total RNAs were isolated from the cells by using TRIzol Reagent (Invitrogen, 15596018) following the manufacturer's mannual.
Transfected cells were harvested 48 h post-transfection and total RNA was extracted using Trizol (Ambion, #15596018). Small RNA fractions were obtained from 10 µg of total RNA by using 12% urea-gel and IPA precipitation. The small RNA sequencing libraries were constructed by using the TruSeq Small RNA Library Prep Kits (Illumina). The DNA libraries of small RNAs were sequenced by Illumina Nextseq 6000. The concentration and size distribution of the DNA libraries were examined by Qubit dsDNA HS Assay Kit (Invitrogen, #Q32854) and Fragment Analyzer system, respectively. Finally, the examined DNA libraries were subjected to the next-generation sequencing (NGS).

treatment_protocol: Cells were transfected with pXG-DICER-WT, pXG-DICER∆Helicase using Lipofectamine 3000.

tag: cell line

value: HCT116 DICER-KO

value: culture cells

value: pXG-DICER-delHelicase plasmid rescue


title: HO_MII_biol rep 1


title: Animal_A15N234_W23_D1

value: PBMC


title: HO_GV_biol rep 2


title: pash-1(mj100)I adult hermaphrodite 48 hrs after upshift to restrictive temperature, sample group 1 rep 1

tag: strain

tag: RNAi

tag: replicate

value: adult

tag: Sex


title: DICER-delHelicase rescue replicate 2

tag: cell type

tag: treatment


title: Animal_A15N234_W23_D0

tag: tissue

tag: group


title: Animal_A15N234_W4_D0


title: WT_GV_biol rep 3

value: WT

tag: Stage


title: HO_GV_biol rep 1

value: oocyte


title: pash-1(mj100)I adult hermaphrodite 24 hrs after upshift to restrictive temperature, sample group 1 rep 1

tag: sample

tag: time point

tag: sample group

tag: dev stage


title: pash-1(mj100)I adult hermaphrodite 24 hrs after upshift to restrictive temperature, sample group 1 rep 2


title: pash-1(mj100)I adult hermaphrodite 0 hrs after upshift to restrictive temperature, sample group 1 rep 2


title: WT_GV_biol rep 2


title: DICER-WT_rescue replicate 2

value: pXG-DICER-WT plasmid rescue


title: DICER-delHelicase rescue replicate 1


title: Animal_A15N234_W0_D1

tag: animal

tag: week

tag: day


title: WT_MII_biol rep 3

tag: genotype

value: MII


title: DICER-WT_rescue replicate 3

tag: cell line


title: KO-12-3

city: Suzhou

first: Dapei

last: Li

address: NO100 Chongwen road

institute: Suzhou Institute of Systems Medicine,Chinese Academy of Medical Sciences & Peking Union Medical College

data_processing:
Reads were treated using fastp software with parameter '-n 10 -q 5 -u 50' to discard reads which are short or in poor quality
The treated reads then mapped to mm10 reference genome using CLC Genomic Workbench 12 to get expression of genes
Assembly: mm10

source_name: PMs

extract_protocol:
The cell samples were lysed in TRIzol and total RNA were extracted for RNA-seq
RNA libraries were prepared for sequencing using standard Illumina protocols

value: PMs

value: Mouse peritoneal macrophages

value: Usp5 KO

value: HSV-1 infection


title: Animal_A15N234_W1_D0

data_processing:
Reads were aligned using STAR 2.7.10a
Assembly: Mmul-10
Supplementary files format and content: Reads per transcript, tab-delimited text

tag: regimen


title: pash-1(mj100)I adult hermaphrodite 48 hrs after upshift to restrictive temperature, sample group 1 rep 2

tag: strain

tag: RNAi

tag: replicate

value: hermaphrodite

value: whole animal


title: WT_GV_biol rep 1

tag: cell type


title: KO-12-2

tag: treatment


title: HEK-293T, HS2-TRIM22_without_ABA

city: ShenZhen

first: Rui

last: Chen

state: GuangDong

address: Southern University of Science and Technology

data_processing:
The obtained sequencing data from the in situ ChIA-PET experiment were subjected to data processing using the ChIA-PIPE software. Visualization of the data was performed using the BASIC Browser. Chromatin Contacts within the regions of interest were plotted as violin plots, with the corresponding pet counts being aggregated on the top. Statistical analysis was conducted using a binomial test to determine the significance, and the resulting p-value was shown.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes track loop for each sample
Supplementary files format and content: tab-delimited text file includes peak for each sample

growth_protocol: HEK-293T cells were cultured in DMEM medium with addition of 10% FBS and 1% PS at 37°C and 5% CO2.

extract_protocol:
Cells was fixed by 1% Formaldehyde and chromatin was sonicated after cell lysis, nuclei permeabilization, is situ digestion & ligation.
Sequencing libraries were constructed following the established in situ ChIA-PET protocol using 10 million input HEK 293 cells co-expressing both ABI1-mCherry-dCas9-VP64-FUS with gHS2 and PYL1-BFP-dCpf1-VP64-FUS with crRNAs before and after ABA treatment, employing an antibody specifically targeting mCherry

value: Human embryonic kidney

value: Stably expressing ABI-mCherry-dCas9-VP64-FUS and PYL-BFP-dCpf1-VP64-FUS

value: Transfected by HS2 and TRIM22 gRNAs and treated by DMSO


title: Animal_A15N189_W24_D0

extract_protocol:
The blood Paxgene tubes were stored until all samples were collected. The whole blood samples were then subjected to RNA extraction using the Thermo Fisher “MagMAX™ for Stabilized Blood Tubes RNA Isolation Kit, compatible with PAXgene Blood RNA Tubes.”
Sample QC was performed with Agilent 2100 bioanalyzer to identify samples with RIN > 7. Qualified RNA from each sample was processed with non-stranded mRNAseq library prep (with globin mRNA removal). In brief, mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. Globin mRNA was depleted using globin mRNA probes. mRNA molecules were fragmented into small pieces using a fragmentation reagent, and the first-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. They were then end-repaired, followed by A-tailing and adapter ligation reactions. The library was subsequently PCR enriched and purified by the Ampure XP bead size selection method. All libraries are quantified by Agilent Technologies 2100 bioanalyzer. The double-stranded PCR products were heat-denatured and circularized by the splint oligo sequence. The single-strand circle DNA (ssCir DNA) was formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular. The DNBs were loaded into the patterned nanoarray and paired-end 150-base reads were generated by sequencing using the sequencer G400.

tag: tissue

tag: group


title: Animal_A15N234_Baseline_D0

value: Baseline


title: DICER-WT_rescue replicate 1

value: HCT116 DICER-KO

value: culture cells


title: wild type adult hermaphrodite, sample group 1 rep 3

data_processing:
Deep sequencing data were analyzed using the miTRATA web interface (https://wasabi.ddpsc.org/~apps/ta/) after preprocessing the data using miTRATA’s accompanying Python3-based preprocess.seq pipeline, installed on the NIH High Performance Computing Cluster in a dedicated miniconda environment. The matureC. elegansmiRNAs from miRBase Release 22.1 were used for miTRATA mapping. A custom C++ script reformatted the miTRATA output by consolidating read numbers for all reads meeting the following criteria into a tabular format: a tail:head ratio >0.12 and a tail length≤3nt. These reformatted tailing data were further analyzed in RStudio. (One non-unique miRNA pair was of sufficient abundance to be included in tailing analysis—mir-44/45-3p;mir-45-3pwas therefore culled from tabular data to avoid plotting this data twice). To calculate reads per million, reads were normalized by the number of genome-mapping reads in the library (Supplementary Table S3). The number of genome-mapping reads was determined using Bowtie to align to the C. elegans genome (WS215) with the arguments -v 3 -f -B 1 -a –best –strata. Alignments were then filtered based on the length of the reads and the number of mismatches as follows: for sequence lengths 16–17, 18–19, 20–24or >24: zero, one, twoor three mismatches were allowed, respectively. Reads passing this threshold were considered ‘genome-mapping reads’. A custom bash/R pipeline was used to calculate trimming relative to canonical miRNA length from the miTRATA output files.
Assembly: WBcel_235
Assembly: WS215
Supplementary files format and content: xlsx file containing sample metadata, normalized reads and percent tailing for microRNAs above minimum abundance threshhold

tag: sample

value: adult

value: wild type

tag: Sex


title: Animal_A15N189_W27_D0

value: PBMC


title: HEK-293T, HS2-TRIM22_treated_by_ABA

institute: Southern University of Science and Technology

value: Transfected by HS2 and TRIM22 gRNAs and treated by ABA


title: wild type adult hermaphrodite, sample group 1 rep 2

tag: time point

tag: sample group


title: wild type adult hermaphrodite, sample group 1 rep 1

tag: dev stage


title: WT-12-3


title: pash-1(mj100)I adult hermaphrodite 0 hrs after upshift to restrictive temperature, sample group 1 rep 1


title: HEK-293T, HS2-UBQLN3_without_ABA

value: Transfected by HS2 and UBQLN3 gRNAs and treated by DMSO


title: Animal_A15N189_W23_D1

tag: animal

tag: week


title: Animal_A15N189_W23_D0

tag: day


title: C-02

city: Harbin City

first: Chenghao

state: HeiLongJiang Province

address: No. 51 HeXing Road,Xiangfang District

department: College of Forestry

institute: Northeast Forestry University

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data).
The reference genomes and the annotation file were downloaded from the Populus genome (version3.0, https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa ). Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Genome_build: Populus trichocarpa v3.0 (https://phytozome.jgi.doe.gov/pz/portal.html#!info?alias=Org_Ptrichocarpa)
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include FPKM values.

organism: Populus ussuriensis

source_name: basal ends of stem cuttings

growth_protocol: Plantlets cultured on half-strength Murashige and Skoog (1/2 MS) medium (Duchefa) containing 20 g/L sucrose. Media used in experiments were adjusted to pH 5.8 before adding 3 g l-1 Gelrite (Duchefa). Cultures were performed in 150 ml Erlenmeyer flasks with 50 ml medium and incubated under a 16 h light/8 h dark photoperiod at 25°C under illumination with cool white fluorescent lights at 45 µmol m−2 s−1.

extract_protocol:
Basal ends of in vitro stem cuttings (0.5 cm) were harvested, flash frozen on dry ice, and RNA was isolated using Trizol reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Two-week-old seedlings were cutting.

value: Basal ends of stem cuttings

tag: age

value: Post-cutting day 14


title: C-01


title: WT-12-2

tag: cell line

value: PMs

value: Mouse peritoneal macrophages

tag: genotype


title: Animal_A15N189_W4_D0

tag: regimen


title: Animal_A15N189_W1_D0


title: HSV-PM-12-3

value: HSV-1 infection


title: patient55

city: Atlanta

first: Min

last: Huang

address: WMB, 101 Woodruff Circle

institute: Emory University

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_50D1_A1

data_processing:
Fastp was used to perform quality control and adapter trimming and the results were filtered by quality. HISAT2 (Version: 2.2.1) was used to map RNA sequencing reads prior to building the index using the human reference genome GRCh38. We then used indices to map our sequential reads to the human genome. We applied featureCounts (Version: 2.0.2) to generate a matrix of row counts of each of the genes in all the samples. Genes were kept in the analysis that had at least 10 reads in at least half of the samples.
Assembly: GRCh38
Supplementary files format and content: txt counts

source_name: blood

extract_protocol:
RNA was isolated from CD14+ monocytes using the Nucleospin RNA II kit with on-column genomic DNA digestion according to the manufacturer’s protocol (Takara, Mountain View, CA, USA)
cDNA was generated using the SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio), and the final RNA-seq library was generated using the Nextera XT kit (Illumina). RNA-seq libraries were sequenced on the Illumina NovaSeq 6000 with a sequencing depth of 30M PE100 reads per sample.

value: blood

value: primary human cell

value: Monocyte

tag: time

value: PARDS


title: patient54_d2

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_48D2_A1

tag: cell type


title: KO-12-1

value: Usp5 KO

tag: treatment


title: fetal-Kidney (bs-seq)

city: Hohhot

first: jing

last: wang

state: Nei Mongol

address: Zhaojun Road

institute: Inner Mongolia University

data_processing:
First of all, we use FastQC (fastqc_v0.11.5) to perform basic statistics on the quality of the raw reads. Then, those reads sequences produced by the Illumina pipleline in FASTQ format were pre-processed through Trimmomatic (Trimmomatic-0.36) software use the parameter (SLIDINGWINDOW: 4:15 ; LEADING:3, TRAILING:3 ; ILLUMINACLIP: adapter.fa: 2: 30: 10 ; MINLEN:36) The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC to perform basic statistics on the quality of the cleandata reads.
Bismark software (version 0.16.3; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to a reference genome (-X 700 --dovetail). The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2 (Langmead B, 2012). Sequence reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome in a directional manner. Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. The same reads that aligned to the same regions of genome were regarded as duplicated ones. The sequencing depth and coverage were summarized using deduplicated reads.
The results of methylation extractor (bismark_methylation_extractor, --no_overlap) were transformed into bigWig format for visualization using IGV browser. The sodium bisulfite non-coversion rate was calculated as the percentage of cytosine sequenced at cytosine reference positions in the lambda genome.
Differentially methylated regions (DMRs) were identified using the DSS software (Hao Feng HaoWu, 2014；Hao Wu，2015；Yongseok Park Hao Wu,2016 ) , The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.
Assembly: UCSC-BT9
Supplementary files format and content: cytosine_report

organism: Bos taurus

source_name: Kidney

growth_protocol: For tissues, we collected fetal tissues from four healthy pregnant Holstein cows at a slaughterhouse. After the slaughter, we extracted fetal tissues to examine their normal development and measured the crown-rump length (CRL) to estimate gestational age. The gender was identified based on the position of the gonads within the abdominal cavity, anatomical structures, and relationships with adjacent organs (mesonephros and/or kidneys). Two male and two female fetuses were identified (13-16 cm CRL), nine different tissues were collected, including the forebrain, hindbrain, heart, liver, lungs, skeletal muscle (hind limb), kidneys, rumen, and testes.

extract_protocol:
Genomic DNA degradation and contamination was monitored on agarose gels. DNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). DNA concentration was measured using Qubit® DNA Assay Kit in Qubit® 2.0 Flurometer (Life Technologies, CA, USA).
A total amount of 5.2 microgram genomic DNA spiked with 26 ng lambda DNA were fragmented by sonication to 200-300bp with Covaris S220, followed by end repair and adenylation. Cytosine-methylated barcodes were ligated to sonicated DNA as per manufacturer’s instructions. Then these DNA fragments were treated twice with bisulfite using EZ DNA Methylation-GoldTM Kit (Zymo Research), before the resulting single-strand DNA fragments were PCR amplificated using KAPA HiFi HotStart Uracil + ReadyMix (2X). Library concentration was quantified by Qubit® 2.0 Flurometer (Life Technologies, CA, USA) and quantitative PCR, and the insert size was assayed on Agilent Bioanalyzer 2100 system.

treatment_protocol: For pluripotent stem cells: The bovine embryonic stem cell line bESCs-F7 was established using the CTFR system. Two treatment methods were employed for bESCs-F7 using MM-102: one involved treating bESCs-F7 with a high concentration (50 μM) of MM-102 for 7 days, followed by normal culturing for 5 passages before characterization, labeled as bESCs-F7-102 (50). The other involved long-term treatment with a low concentration (5 μM) of MM-102, followed by characterization after 5 passages of culturing, labeled as bESCs-F7-102 (5). Bovine induced pluripotent stem cells and the bEPSCs-B18 cell line were established using the LCDM system. And bEPSCs-AGS was using a 500mL system, including 485mL of basic mTeSR1 medium, 5.0 mL of 100×Penicillin-Streptomycin Solution, 0.1 mM 2-mercaptoethanol, 1 μM GSK3β inhibitor CHIR99021, 0.3 μM Lck/Src inhibitor WH-4-023, 5 μM Tankyrase inhibitor XAV939, 5 μM classic WNT signaling pathway inhibitor IWR-1, 50 μg/mL Vitamin C, 10 ng/mL Leukemia Inhibitory Factor (LIF), and 20.0 ng/mL Activin A for culturing bovine Embryonic Pluripotent Stem Cells.

tag: tissue

value: Kidney

value: male

value: fetal

tag: crl

value: WT

value: no treatment


title: fetal-Liver (bs-seq)

source_name: Liver

value: Liver


title: patient53

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s069_MONOCY_AIR_47D1_A1


title: fetal-Heart (bs-seq)

source_name: Heart

value: Heart


title: patient55_d2

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_50D2_A1


title: fetal-Lung (bs-seq)

source_name: Lung

value: Lung


title: Animal_A15N189_W0_D1

city: Palo Alto

first: Dmitri

last: Kazmin

address: 240 Pasteur Dr

institute: Stanford University

value: PBMC

tag: group


title: HSV-PM-12-2

value: PMs

value: wild type


title: patient54

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_48D1_A1


title: Animal_A15N189_Baseline_D0

value: Baseline


title: HSV-PM-12-1

value: Mouse peritoneal macrophages

value: HSV-1 infection


title: Animal_A15N125_W24_D0


title: Animal_A15N125_W27_D0


title: WT-12-1


title: patient52_d2

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_46D2_A1

value: blood

value: primary human cell

value: Monocyte


title: patient52

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_46D1_A1

value: PARDS


title: HSV-PM-6-2


title: HEK-293T, HS2-UBQLN3_treated_by_ABA

value: Human embryonic kidney

value: Stably expressing ABI-mCherry-dCas9-VP64-FUS and PYL-BFP-dCpf1-VP64-FUS

value: Transfected by HS2 and UBQLN3 gRNAs and treated by ABA


title: HSV-PM-6-1


title: HSV-PM-0-3

value: mock


title: patient51_d2

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_45D2_A1


title: HSV-PM-6-3


title: patient51

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_45D1_A1


title: fetal-Muscle-2 (bs-seq)

source_name: Skeletal Muscle

value: Skeletal Muscle

value: male

value: fetal

value: WT

value: no treatment


title: fetal-Muscle-1 (bs-seq)


title: Animal_A15N125_W4_D0

value: PBMC


title: fetal-Testis (bs-seq)

source_name: Testis

value: Testis


title: HSV-PM-0-2

value: PMs

value: Mouse peritoneal macrophages

value: wild type


title: fetal-Rumen (bs-seq)

source_name: Rumen

value: Rumen


title: HSV-PM-0-1


title: fetal-Hindbrain-2 (bs-seq)

source_name: Hindbrain

value: Hindbrain


title: patient50_d2

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_44D2_A1

value: blood

value: primary human cell

value: Monocyte

value: PARDS


title: HCT116 cells, belinostat treated, invaded-layer, rep1

value: human colorectal cancer cells

value: Belinostat treated


title: Animal_A15N125_W0_D1

source_name: PBMC


title: patient50

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_44D1_A1


title: fetal-Hindbrain-1 (bs-seq)

value: male


title: Animal_A15N125_W1_D0


title: patient49_d2

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_42D2_A1


title: fetal-Forebrain-2 (bs-seq)

source_name: Forebrain

value: Forebrain

value: fetal


title: Animal_A15N125_W23_D1


title: GFP_tie2-cre-rep1

city: Guangzhou

first: He

last: Xiaosong

state: Guangdong

address: Xinzao Road

department: Department Of Anatomy

institute: Guangzhou Medical University

data_processing:
Reads were aligned to themouse Ensemble genome GRCm38 using bowtie2 aligner (v 2.3.5.1) under parameters: “--rna-strandness RF”. The reads mapped the genome were calculated using featureCounts (v1.6.3). Differential gene expression analysis was performed using the DESeq R-package.
Assembly: GRCm38
Supplementary files format and content: gene counts for each sample

source_name: endothelial cells

extract_protocol:
Isolated endothelial cells from three mice were collected. 10000 isolated endothelial cells were lysised and labeled by DRUG-seq RT primer and purified. After ExoI treatment, material was pre-amped with DRUG-seq PCR primers and purified. The pre-amplified matierals was quanity checked and quantified.
RNA libraries were prepared for sequencing using standard Illumina protocols performed by the Guangzhou epibiotek co .ltd.

tag: strain

value: endothelial cells

value: GFP


title: NeuroD1_tie2-cre-rep1


title: Animal_A15N125_W23_D0

value: PBMC


title: fetal-Forebrain-1 (bs-seq)

value: WT

value: no treatment


title: Animal_A15N125_Baseline_D0

value: Baseline


title: Animal_A14X078_W24_D0


title: patient49

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_42D1_A1


title: Animal_A14X078_W27_D0


title: LCDM-bEPSCs-B18-2 (bs-seq)

source_name: bovine embryonic stem cells

value: bovine induced pluripotent stem cells

value: Bovine induced pluripotent stem cells were established using the LCDM system


title: TEAD1_KO

city: Beijing

first: Ye-Guang

state: China

address: Haidian  District

institute: Tsinghua University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
ChIP-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to the UCSC hg38 genome using Bowtie version 2.2.5. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to Fragments Per Kilobase Million, fpkmm) and reformatted in the bigWig file format.
Peaks were called uing MACS v2.2.7.1 with the significance cut-off q-value <=0.01
bigWig files were generated using the deeptools v3.5.1. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: Intestinal organoids

growth_protocol: Advanced DMEM F12, B27, N2, 1x penicillin/streptomycin, EGF, R-Spondin1, Noggin. Intestinal organoids were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with EGS for 30 minutes and followed by 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

treatment_protocol: Intestinal organoids were treated with TGF-b1 for 12 hours before fixing

value: Intestinal organoids

value: Murine intestinal epithelium

tag: chip antibody

value: TEAD1 (ABclonal, #A5218)


title: Animal_A14X078_W23_D0


title: bEPSCs-AGS-2 (bs-seq)

value: bEPSCs-AGS

value: bovine expanded pluripotent stem cells

value: A 500mL system was prepared, including 485mL of basic mTeSR1 medium, 5.0 mL of 100×Penicillin-Streptomycin Solution, 0.1 mM 2-mercaptoethanol, 1 μM GSK3β inhibitor CHIR99021, 0.3 μM Lck/Src inhibitor WH-4-023, 5 μM Tankyrase inhibitor XAV939, 5 μM classic WNT signaling pathway inhibitor IWR-1, 50 μg/mL Vitamin C, 10 ng/mL Leukemia Inhibitory Factor (LIF), and 20.0 ng/mL Activin A for culturing bovine Embryonic Pluripotent Stem Cells


title: patient45

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s055_MONOCY_AIR_36D1_A1

value: blood

value: primary human cell

value: Monocyte


title: Animal_A14X078_W4_D0


title: Animal_A14X078_W23_D1


title: bovine-fetal-Rumen-2 (rna-seq)

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
For each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.18.1). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
Assembly: UCSC BT9
Supplementary files format and content: Tab-separated values file includes raw counts for each sample

extract_protocol:
Cells were collected by tryple-select enzyme  and the lyophilized cells were sent for sequencing. Transcriptome (RNA) sequencing was performed by Tianjin Nuohe Zhiyuan Biotechnology Co., LTD, Tianjin, China.
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each samp

value: Rumen

tag: Sex

value: male

value: 90 days fetus


title: bEPSCs-AGS-1 (bs-seq)

value: WT


title: Animal_A14X078_W1_D0

value: PBMC


title: patient44

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s054_MONOCY_AIR_34D1_A1

value: PARDS


title: patient43

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s052_MONOCY_AIR_32D1_A1


title: bovine-fetal-Rumen-1 (rna-seq)


title: Animal_A14X078_W0_D1


title: SMAD2/3_KO


title: patient46

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s056_MONOCY_AIR_38D1_A1


title: TEAD1_WT


title: bovine-fetal-Liver-2 (rna-seq)

value: Liver


title: patient42

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s050_MONOCY_AIR_28D1_A1


title: patient47

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s057_MONOCY_AIR_40D1_A1


title: bovine-fetal-Liver-1 (rna-seq)


title: patient40

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s048_MONOCY_AIR_25D1_A1


title: Animal_A14X077_W27_D0


title: bovine-fetal-Forebrain-2 (rna-seq)

value: Forebrain


title: Animal_A14X077_W24_D0


title: SMAD2/3_WT

value: Intestinal organoids


title: β cells, control4

city: BEIJING

address: Malianwa street

institute: China Agriculture University

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

source_name: pancreas islet

extract_protocol:
Trizol
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: pancreas islet

value: beta cell

value: wt


title: Animal_A14X077_W23_D1


title: patient41

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s049_MONOCY_AIR_27D1_A1


title: LCDM-bEPSCs-B18-1 (bs-seq)

value: bovine induced pluripotent stem cells

value: Bovine induced pluripotent stem cells were established using the LCDM system


title: β cells, Cko4

value: Cko


title: β cells, control3


title: Animal_A14X077_W23_D0


title: YAP_KO

value: Murine intestinal epithelium


title: YAP_WT


title: patient36

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s044_MONOCY_AIR_21D1_A1

value: blood

value: primary human cell

value: Monocyte


title: H3K27ac, fetal-Liver, 2 (cut&tag-seq)

data_processing:
First of all, we use FastQC (fastqc_v0.11.5) to perform basic statistics on the quality of the raw reads. Then, those reads sequences produced by the Illumina pipleline in FASTQ format were pre-processed through Trimmomatic (Trimmomatic-0.36) software use the parameter (SLIDINGWINDOW: 4:15 ; LEADING:3, TRAILING:3 ; ILLUMINACLIP: adapter.fa: 2: 30: 10 ; MINLEN:36) The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC to perform basic statistics on the quality of the cleandata reads.
Bismark software (version 0.16.3; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to a reference genome (-X 700 --dovetail). The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2 (Langmead B, 2012). Sequence reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome in a directional manner. Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. The same reads that aligned to the same regions of genome were regarded as duplicated ones. The sequencing depth and coverage were summarized using deduplicated reads.
The results of methylation extractor (bismark_methylation_extractor, --no_overlap) were transformed into bigWig format for visualization using IGV browser. The sodium bisulfite non-coversion rate was calculated as the percentage of cytosine sequenced at cytosine reference positions in the lambda genome.
Differentially methylated regions (DMRs) were identified using the DSS software (Hao Feng HaoWu, 2014；Hao Wu，2015；Yongseok Park Hao Wu, 2016 ) , The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.
Assembly: UCSC-BT9
Supplementary files format and content: bedGraph
Library strategy: CUT&Tag-seq

value: male

value: 90 days fetus

tag: antibody


title: Animal_A14X077_W1_D0

value: PBMC

tag: animal


title: patient48

description:
donor human monocyte exposed to tracheal aspirate airway fluid
MONOCY_AIR_41D1_A1

value: PARDS


title: β cells, Cko3


title: H3K27ac, fetal-Liver, 1 (cut&tag-seq)

value: Liver

value: WT


title: Animal_A14X078_Baseline_D0

tag: week

value: Baseline


title: patient35

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s043_MONOCY_AIR_20D1_A1


title: patient39

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s047_MONOCY_AIR_24D1_A1


title: Animal_A14X077_Baseline_D0

tag: day


title: Animal_A14X077_W0_D1


title: H3K4me1, fetal-Liver, 2 (cut&tag-seq)

tag: age


title: bovine-fetal-Forebrain-1 (rna-seq)

value: Forebrain


title: β cells, Cko1

value: pancreas islet

value: beta cell


title: patient38

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s046_MONOCY_AIR_23D1_A1

tag: cell line


title: Animal_A14X028_W24_D0


title: RNA-seq-Te-KO2

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

data_processing:
FastQC was used to identify features of the raw data that may indicate quality problems
Low quality bases were removed using Trim_galore
Reads were mapped to the mouse reference genome (mm10) with Tophat2
The reads counts were assigned to genes using Htseq
The fold change and p-value of the genes were estimated by DESeq2
Supplementary files format and content: mm10
Supplementary files format and content: xlsx format. Read counts for each gene

source_name: Spleen

extract_protocol:
Naïve (CD44−CD62L+) CD8+ T cells were sorted from Mettl3ΔCd4 and control mice (3 samples per group), effector (CD44+CD62L−EYFP+) CD8+ T cells  (2 samples per group), and memory (CD44+EYFP+) CD8+ T cells (2 samples from control donors and 3 samples from Mettl3ΔGzmb donors ) were sorted from recipient mice in adoptive transfer experiments. Total RNAs were extracted from indicated cells and then submitted to RNA-Seq protocol.
libraries are constructed according to the standard protocol for Smart-seq2

value: Spleen

value: Effector CD8

tag: genotype

value: 6~8 weeks


title: H3K4me1, fetal-Liver, 1 (cut&tag-seq)


title: β cells, control1

value: wt


title: patient37

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s045_MONOCY_AIR_22D1_A1

value: blood


title: Animal_A14X077_W4_D0

tag: regimen


title: H3K4me3, adult-rumen, 1 (chip-seq)

data_processing:
Illumina reads were first mapped to the UCSC bosTau9 reference using bwa-mem (version:0.7.17) with default parameters.
Next, Picard (http://broadinstitute.github.io/picard/, accessed on 12 June 2023, version 2.23.1) was used to mark up the PCR duplicates.
Then, we used macs2 (v2.2.7.1, -nomodel-broad-broad-cutoff 0.1-shift 0-gsize 2.7e9-keep-dup auto) to call the peaks.
H3K4me1 signals were normalized using the MA norm (version: 1.1.4) method for the quantitative comparison of ChIP-seq data, and the significant differential peaks were determined as log10(p-value) < 0 and M-value > 1. Subsequently, the differential peaks were annotated to UCSC bosTau9 using the R package ChIP seeker (version: 1.28.3) and TxDb.Btaurus.UCSC.bosTau9.refGene (version: 3.10.0).
Assembly: UCSC BT9
Supplementary files format and content: bigWig

extract_protocol:
Cells were collected by tryple-select enzyme  and the lyophilized cells were sent for sequencing. The sequencing was performed by Tianjin Nuohe Zhiyuan Biotechnology Co., LTD, Tianjin, China.
The Simple ChIP®Plus Enzymatic Chromatin IP Kit (Magnetic Beads) (9005, Cell Signaling) was utilized to extract DNA fragments from the cells.

value: Rumen

value: 2 years adult


title: RNA-seq-Tm-KO3

value: Memory CD8


title: Animal_A14X028_W23_D0


title: patient30

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s038_MONOCY_AIR_15D1_A1

value: primary human cell

value: Monocyte

tag: time


title: H3K27me3, adult-rumen, 1 (chip-seq)

value: male


title: H3K4me1, adult-rumen, 2 (chip-seq)


title: RNA-seq-Tm-KO2

tag: cell type


title: Animal_A14X028_W27_D0

value: PBMC

tag: treatment


title: H3K27me3, adult-rumen, 2 (chip-seq)

tag: tissue

value: WT


title: patient33

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s041_MONOCY_AIR_18D1_A1


title: H3K27ac, adult-rumen, 2 (chip-seq)


title: H3K4me3, adult-rumen, 2 (chip-seq)


title: RNA-seq-Tm-KO1


title: Animal_A14X028_W4_D0


title: patient32

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s040_MONOCY_AIR_17D1_A1

value: PARDS


title: Animal_A14X028_W1_D0


title: Animal_A14X028_W0_D1


title: patient34

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s042_MONOCY_AIR_19D1_A1


title: RNA-seq-Tn-KO2

value: Naive CD8


title: RNA-seq-Tm-WT1

value: control


title: Animal_A14X028_W23_D1


title: RNA-seq-Tm-WT2


title: RNA-seq-Te-WT2


title: patient29

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s037_MONOCY_AIR_14D1_A1


title: RNA-seq-Te-KO1


title: RNA-seq-Te-WT1


title: patient28

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s036_MONOCY_AIR_12D1_A1


title: RNA-seq-Tn-KO3


title: H3K27ac, adult-rumen, 1 (chip-seq)


title: patient27

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s035_MONOCY_AIR_11D1_A1


title: patient31

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s039_MONOCY_AIR_16D1_A1


title: Animal_A13L131_W9_D0


title: patient23

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s031_MONOCY_AIR_06D1_A1


title: H3K4me1, adult-rumen, 1 (chip-seq)


title: Animal_A14X028_Baseline_D0

value: Baseline


title: patient26

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s034_MONOCY_AIR_10D1_A1


title: H3K27me3, fetal-rumen, 2 (chip-seq)

value: 90 days fetus


title: RNA-seq-Tn-KO1

value: Spleen


title: patient25

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s033_MONOCY_AIR_08D1_A1


title: H3K4me3, fetal-rumen, 1 (chip-seq)


title: Animal_A13L131_W8_D0


title: Animal_A13L131_W12_D0


title: RNA-seq-Tn-WT2

value: 6~8 weeks


title: RNA-seq-Tn-WT3


title: H3K4me1, fetal-rumen, 2 (chip-seq)


title: H3K27me3, fetal-rumen, 1 (chip-seq)


title: patient21

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s029_MONOCY_AIR_02D1_A1


title: Animal_A13L131_W8_D1


title: H3K4me3, fetal-rumen, 2 (chip-seq)


title: patient24

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s032_MONOCY_AIR_07D1_A1


title: RNA-seq-Tn-WT1


title: patient20

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s028_MONOCY_AIR_01D1_A1


title: patient22

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s030_MONOCY_AIR_04D1_A1


title: Intestinal organoids, Smad4 KO+TGFb-2, 48h

data_processing:
Quality control was performed using FastQC v0.11.9.
The SAM files generated from HISAT2 2.1.0 were brought into BAM format using SAMtools v1.9.
We generated read counts with StringTie v1.3.3b.
Assembly: Sequencing reads were aligned using GRCm38/mm10 assembly of the mouse genome.
Supplementary files format and content: gene_count_matrix_organoids.csv: Comma-delimited text file includes reads counts for each sample.

growth_protocol: Intestinal organoids were cultured in the ENR culture medium (Advanced DMEM/F12 supplemented with Penicillin/Streptomycin, GlutaMAX-I, N2, B27 and N-acetylcysteine) containing EGF (50ng/ml, Invitrogen), Noggin (100 ng/ml, R&D) and R-spondin1 (500 ng/ml, R&D) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Total RNA was extracted and purified by using TRIZOL reagent (Thermo Fisher Scientific). 1ug of total RNA was used for the construction of sequencing libraries.
RNA integrity was measured using electrophoresis. Subsequently, First-strand cDNA was generated using random hexamer primers. Then, a second-strand cDNA was synthesized. A-Tailing Mix and RNA Index Adapters followed to subjected to the end of the cDNA. The cDNA fragments were amplified by PCR and the product was qualified by Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY) and the 2100 Bioanalyzer (Agilent). After it, the products were denatured and circularized to collect the final library.

treatment_protocol: Smad4-deficient spheroids were induced by treatment of TGFb for 48h at the concentration of 0.5nM. Smad4-deficient organoids were then fed with ENR medium supplemented with 0.5nM TGFb for 2 days, after which they were collected for RNA extraction.

value: Intestinal organoids

value: Intestinal epithelial cells

value: Smad4 KO+TGFb


title: adult-rumen, Input, 1 (chip-seq)

value: Rumen

value: 2 years adult


title: H3K27ac, fetal-rumen, 2 (chip-seq)


title: Intestinal organoids, Smad4 KO+TGFb-1, 48h


title: Animal_A13L131_W4_D0


title: Animal_A13L131_W0_D1


title: Intestinal organoids, Smad4 KO-2, 48h

value: Smad4 KO


title: H3K27ac, fetal-rumen, 1 (chip-seq)


title: patient19

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s027_MONOCY_PNA_53D1_A1

value: blood

value: primary human cell

value: Monocyte


title: H3K4me1, fetal-rumen, 1 (chip-seq)

value: male

value: WT


title: fetal-rumen, Input, 1 (chip-seq)


title: Intestinal organoids, Smad4 KO-1, 48h


title: Intestinal organoids, WT-2, 48h


title: patient17

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s025_MONOCY_PNA_51D1_A1

value: PARDS


title: Animal_A12X028_W12_D0

value: PBMC


title: adult-Rumen, 2 (atac-seq)

data_processing:
First of all, we use FastQC (fastqc_v0.11.5) to perform basic statistics on the quality of the raw reads. Then, those reads sequences produced by the Illumina pipleline in FASTQ format were pre-processed through Trimmomatic (Trimmomatic-0.36) software use the parameter (SLIDINGWINDOW: 4:15 ; LEADING:3, TRAILING:3 ; ILLUMINACLIP: adapter.fa: 2: 30: 10 ; MINLEN:36) The remaining reads that passed all the filtering steps was counted as clean reads and all subsequent analyses were based on this. At last, we use FastQC to perform basic statistics on the quality of the cleandata reads.
Bismark software (version 0.16.3; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to a reference genome (-X 700 --dovetail). The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2 (Langmead B, 2012). Sequence reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome in a directional manner. Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. The same reads that aligned to the same regions of genome were regarded as duplicated ones. The sequencing depth and coverage were summarized using deduplicated reads.
The results of methylation extractor (bismark_methylation_extractor, --no_overlap) were transformed into bigWig format for visualization using IGV browser. The sodium bisulfite non-coversion rate was calculated as the percentage of cytosine sequenced at cytosine reference positions in the lambda genome.
Differentially methylated regions (DMRs) were identified using the DSS software (Hao Feng HaoWu, 2014；Hao Wu，2015；Yongseok Park Hao Wu,2016 ) , The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.
Assembly: UCSC-BT9
Supplementary files format and content: narrowPeak


title: patient16

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s024_MONOCY_PNA_50D1_A1


title: Intestinal organoids, WT-1, 48h


title: Animal_A12X028_W9_D0


title: Smad4 KO2-DSS

data_processing:
Quality control was performed using FastQC v0.19.7.
The SAM files generated from HISAT2 2.1.0 were brought into BAM format using SAMtools v1.9.
We generated read counts with StringTie v1.3.3b.
Assembly: Sequencing reads were aligned using GRCm38/mm10 assembly of the mouse genome.
Supplementary files format and content: gene_count_matrix_DSS.csv: Comma-delimited text file includes reads counts for each sample.

source_name: Epithelial cells

extract_protocol:
Total RNA was extracted and purified by using TRIZOL reagent (Thermo Fisher Scientific). 1.5ug of total RNA was used for the construction of sequencing libraries.
RNA integrity was measured using electrophoresis. Subsequently, First-strand cDNA was generated using random hexamer primers. Then, a second-strand cDNA was synthesized. A-Tailing Mix and RNA Index Adapters followed to subjected to the end of the cDNA. The cDNA fragments were amplified by PCR and the product was qualified by Qubit 2.0 Fluorometer (Life Technologies, Grand Island, NY) and the 2100 Bioanalyzer (Agilent). After it, the products were denatured and circularized to collect the final library.

treatment_protocol: WT and epithelial Smad4 knockout mice (8-10 weeks old) were fed with 3.5% DSS (MW; 36–50 kDa; MP Biomedicals) dissolved in drinking water for consecutive 5 days followed by regular watering until sacrificed at the seventh day.

value: Epithelial cells

value: Colonic epithelial cells

value: DSS

value: 5 days


title: adult-Rumen, 1 (atac-seq)


title: Animal_A12X028_W8_D1


title: Smad4 KO1-DSS


title: patient15

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s023_PNA49D1_MONO_TA_A1

source_name: blood


title: patient14

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s021_PNA45D1_MONO_TA_A1


title: Animal_A13L131_W1_D0


title: fetal-Rumen, 2 (atac-seq)

value: 90 days fetus


title: CT3-DSS


title: Animal_A12X028_W8_D0


title: fetal-Rumen, 1 (atac-seq)


title: patient18

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s026_MONOCY_PNA_52D1_A1


title: Animal_A12X028_W4_D0


title: patient13

description:
donor human monocyte exposed to tracheal aspirate airway fluid
p23152_s020_PNA44D1_MONO_TA_A1


title: CT1-DSS


title: Animal_A13L131_Baseline_D0

value: Baseline