title: CAB2

city: Guangzhou

first: Tingjun

last: Liu

address: 56 Lingyuanxi Road

department: Hospital of Stomatology, Guanghua School of Stomatology

institute: Sun Yat-sen University

description: CAB(Fnp)_vs_Fnp.genes.read.txt, CAB(Sg)_vs_Sg.genes.read.txt

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36 http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic). Then clean reads were separately aligned to reference genome with orientation mode using Rockhopper (http://cs.wellesley.edu/~btjaden/Rockhopper/) software. Rockhopper was a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads generated by high-throughput sequencing technology. This software was used to calculate gene expression levels with default parameters.
To identify DEGs (differential expression genes) between the two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) was used for differential expression analysis. The DEGs between two samples were selected using the following criteria: i) the logarithmic of fold change was greater than 2 and the false discovery rate (FDR) should be less than 0.05.
To understand the functions of the differential expressed genes, GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do) respectively. DEGs were significantly enriched in GO terms and metabolic pathways when their Bonferroni-corrected P-value was less than 0.05.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample: values for S. gordonii DL1 in mono-species group (Sg) as well as in coaggregation group (CAB) were reported in the processed file "CAB(Sg)_vs_Sg.genes.read.txt"; values for F. nucleatum subsp. polymorphum (ATCC10953) in mono-species group (Fnp) as well as in the coaggregation group (CAB) were reported in the processed file "CAB(Fnp)_vs_Fnp.genes.read.txt".

organism:
Fusobacterium polymorphum
Streptococcus gordonii str. Challis substr. CH1

source_name: two bacterial species

growth_protocol: S. gordonii DL1 was grown in Brain Heart Infusion (BHI) broth (Difco, USA). F. nucleatum subsp. polymorphum (ATCC10953) was grown in BHI broth supplemented with 0.5% yeast extract (Difco, USA), 1 μg/mL vitamin K (Sigma-Aldrich, USA), and 5 μg/ml hemin (Sigma-Aldrich, USA). Both bacterial strains were grown under anaerobic conditions (85% N2, 10% H2, 5% CO2) at 37 °C.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Intergeneric coaggregation was performed in coaggregation buffer (CAB) (150 mM NaCl, 1 mM Tris pH 8, 0.1 mM CaCl2, 0.1 mM MgCl2) as previously described [37]. The optical density (OD600) of F. nucleatum subsp. polymorphum after 24-hour culture reached 0.85 (~109 CFU), and the OD600 of S. gordonii DL1 after 12-hour culture was assessed to be 0.7 (~109 CFU). Bacterial cells of each species were harvested, washed twice, and resuspended in CAB to a final concentration of ~2×109 cells/ml (OD600~1.0). Equal numbers of cells from each species were pooled together in a new sterile reaction tube. The reaction tube was vortexed for 20 seconds to maximize bacterial physical contact and incubated anaerobically at 37℃ for 30 min for coaggregation.

tag: f. nucleatum atcc#

tag: growth protocol

value: dual-species coaggregation treated

tag: gram status

value: Gram-positive species and Gram-negative species


title: day0.WT3

status: Public on May 20 2021

type: SRA

city: Beijing

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

country: China

institute: Tsinghua University

description: microbial DNA

library_source: genomic

data_processing:
Library strategy: 16S
Raw reads were filtered to remove adaptors and low-quality and ambiguous bases, and then paired-end reads were added to tags by the Fast Length Adjustment of Short reads program (FLASH, v1.2.11) to get the tags.
The tags were clustered into OTUs with a cutoff value of 97% using UPARSE software (v7 .0.1090) and chimera sequences were compared with the Gold database using UCHIME (v4.2.40) to detect.
OTU representative sequences were taxonomically classified using Ribosomal Database Project (RDP) Classifier v.2.2 with a minimum confidence threshold of 0.6, and trained on the Greengenes database v201305 by QIIME v1.8.0
The USEARCH_global was used to compare all Tags back to OTU to get the OTU abundance statistics table of each sample.
Alpha and beta diversity were estimated by MOTHUR (v1.31.2) and QIIME (v1.8.0) at the OTU level, respectively. Sample cluster was conducted by QIIME (v1.8.0) based on UPGMA.
Genome_build: Greengenes

molecule: genomic DNA

organism: Microbiota

source_name: microbiota

extract_protocol: microbial DNA was isolated from stools of indicated mice by using QiAamp DNA Stool Mini Kit (QIAGEN) according to manufacturer’s instructions.

treatment_protocol: WT and Il17d-deficient mice treated with or without colitis

tag: state

value: steady state

tag: mouse genotype

value: Wild type

tag: source

value: mouse feces


title: Trp53 MZ-KO late 2-cell rep #5

city: Salt Lake City

first: Edward

middle: John

last: Grow

state: UT

address: 2000 Circle of Hope Dr

department: Oncological Sciences

country: USA

institute: University of Utah

library_source: transcriptomic

data_processing:
Bbduk adapter Trimming
Tophat2 (--t --q --N1 --L 25 --X 2000 --no-mixed --no-discordant)
and counts for each transcript were generated using “Get datasets”
Differential expression analysis was performed using DESEq2.
Genome_build: mm10
Supplementary_files_format_and_content: 20200423-SMRT-seq-DESEq-FPKM-table.txt

molecule: total RNA

organism: Mus musculus

source_name: mouse embryo

growth_protocol: Animal experiments performed at the University of Utah were first approved by IACUC and Institutional approval, the protocol # is 18-07014. The Trp53 KO allele has already been described and was obtained as Trp53 flox allele flanking exons 2-10 and maintained on a mixed Bl6/C57 background. Trp53 flox/flox mice were mated to Ddx4::Cre driver to remove the flox cassette leaving the floxed allele. Male Trp53 KO mice were mated to female +/floxed Trp53 mice to generate Trp53 KO females. To generate Trp53 MZ-KO embryos, Trp53 KO females were mated to Trp53 KO males (which were previously confirmed to be fertile). The Trp53 WT control embryos were Trp53 flox/flox animals. Trp53 floxed KO alelles were detected using PCR before weaning of animals and confirmed after sacrifice of animals (see Supplementary Table X for genotyping primer sequences). For Trp53 MZ-KO embryos vs controls stained with DUX antibodies, females were injected with 5U of PSMG followed by 5U of hCG 48 hours later. Zygotes were harvested at 24 hours post hCG injection, washed in M2 media to remove cumulus cells, and then cultured in pre-equilibrated KSOM media under mineral oil. Early 2-cell stage embryos were harvested 2-3 hours after cytokinesis, typically 28-32 hours post hCG injection. Late 2-cell stage embryos were cultured cultured in KSOM after zygote harvest, confirmation of cytokinesis by 32 hours post hCG injection through visual inspection and collected for SMRT-seq libraries 48 hours post hCG

extract_protocol:
individual embryos or eggs were lysed in 5uL of lysis buffer (SMRT-seq v4)
SMRT-seq v4 library using 15 cycles of LD, followed by Nexterna DNA library prep tagmentation into ds-cDNA and PCR
RNAseq via Tn5 tagmentation of cDNA

treatment_protocol: embryos were cultured in KSOM prior to harvest

tag: genotype

value: Trp53 MZ-KO

tag: tissue

value: embryo

tag: tag

value: late 2-cell


title: E12.5 motor neurons rep2

first: Catarina

last: Catela

state: Illinois

address: Abbott Hall 402,

department: Neurobiology

institute: University of Chicago

data_processing:
Reads were analyzed for quality control
Reads were align to the mouse genome using HISAT program
Reads were counted using FeatureCounts algorythm
Differential expression data generated with DESeq2 program
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files with differential expression generated by DESeq2

source_name: Motor neurons

extract_protocol:
Spinal cords were isolated and dissociated with papain. Motor neurons were sorted by FACS (GFP and TdTomato). Motor neuron RNA was extracted using the Arcturus Picopure Extraction Buffer.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: Stage

value: Wildtype

tag: spinal cord region

value: Brachial


title: Trp53 MZ-KO late 2-cell rep #1


title: Sample022 [Rectal biopsy]

city: Atlanta

first: Angela

last: Mo

state: GA

address: 950 Atlantic Drive

department: School of Biological Sciences

institute: Georgia Institute of Technology

data_processing:
Using FastQC, the single end 150 bp reads were trimmed and adapters were removed.
Reads were mapped to human genome hg19 using hisat2.
The aligned reads were converted into read counts per gene with SAMtools and HTSeq in the default union mode.
The raw read counts were normalized via trimmed mean of M-values normalization with the edgeR R package.
Further adjustment and removal of batch effects was performed with SVA and (SNM).
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file with raw gene counts for each sample.
Supplementary_files_format_and_content: Tab-delimited text file with normalized gene expression for each sample.

organism: Homo sapiens

source_name: Rectal biopsy

extract_protocol:
Rectal biopsy specimens were obtained during diagnostic colonoscopy. RNA was extracted using Qiagen AllPrep DNA/RNA Mini Kit.
RNA sequencing libraries were prepared using the Lexogen QuantSeq 3' Library Prep Kit FWD for Illumina and sequenced on the Illumina NextSeq as single-end 150-bp reads.

tag: individual

tag: gender

value: F

tag: age at diagnosis

tag: time of sampling

value: Baseline

tag: initial treatment

tag: colectomy

tag: disease

value: pediatric ulcerative colitis


title: Sample017 [Rectal biopsy]

value: CS-IV


title: E12.5 motor neurons rep1


title: CAB1

tag: f. nucleatum atcc#

tag: growth protocol


title: Trp53 MZ-KO late 2-cell rep #4


title: Sample019 [Rectal biopsy]


title: Granulosa Hi-C rep1 (P23)

city: Minneapolis

first: Micah

last: Gearhart

state: MN

address: 6-160 Jackson Hall, 321 Church St.

department: Genetics, Cell Biology and Development

institute: University of Minnesota

description:
processed data file:
Granulosa_AB_Compartments_P23.bigWig
Supplementary_Table_2.xlsx

data_processing:
For each of the experiments, reads were trimmed using Trim Galore (v0.6.0) and cutadapt (v1.18) and assessed for quality with FastQC (v0.11.8). STAR (v2.7.2a), BWA mem (v0.7.12) and HiC-Pro (v2.11.4) were used to map transcriptomic (RNA-seq), genomic (ChIP-seq, ATAC-seq) and 3D (Hi-C) trimmed reads to the GRCm38 (mm10) genome respectively
The GENCODE M23 gene annotation set was used to estimate strand-specific gene expression data in the RNA-seq data with the Bioconductor package RSubread (v1.28.1) and to assign the locations of nearby genes in the ATAC-seq datasets. For ChIP-seq and ATAC-seq experiments, duplicated reads were removed with Picard MarkDuplicates (v2.17.10) and low quality reads (MAPQ < 55) or reads that mapped to the mitochondrial genome were removed with SAMtools (v1.0).
MACS2 (v2.1.1.20160309) was used to call peaks in the ChIP-seq and ATAC-seq datasets using the parameters ‘-call-summits -m 2 20’ and ‘--nomodel –broad’ respectively
Genome_build: GRCm38/mm10
Supplementary_files_format_and_content: Tables of expression values and fold changes in gene expression, bigWig Coverage files and called peaks.

source_name: Granulosa Cells

extract_protocol: Hi-C were performed for each cell type on  about 1 million primary granulosa cells using the Arima Hi-C Kit (#A510008).  Cells were fixed in 2% methanol-free formaldehyde in PBS at RT for ten min. with occasional mixing then quenched by addition of glycine to 0.125M with occasional mixing for 5 min.. Cells were placed on ice for 15 min. prior to washing with 1X PBS and stored at -80o C.  Hi-C was performed according to Arima Genomics (Document part # A160134 v00).  Sequencing libraries were prepared using the KAPA Hyper Prep Kit and xGen Duplex Seq adapters (Integrated DNA Techologies) according to Arima Genomics (Document part # A160139 v00).

tag: genoype

value: wild type

tag: strain background

value: Mixed 129Sv and C57Bl/6J

tag: tamoxifen time point

tag: antibody

tag: age

value: 23 days


title: Trp53 MZ-KO early 2-cell rep #6

tag: genotype

tag: tissue

tag: tag

value: early 2-cell


title: CAB3

value: dual-species coaggregation treated

tag: gram status

value: Gram-positive species and Gram-negative species


title: Sertoli Hi-C rep1 (P7)

description:
processed data file:
Sertoli_AB_Compartments_P7.bigWig
Supplementary_Table_2.xlsx

source_name: Sertoli Cells

extract_protocol: Hi-C were performed for each cell type on  about 1 million primary Sertoli cells using the Arima Hi-C Kit (#A510008).  Cells were fixed in 2% methanol-free formaldehyde in PBS at RT for ten min. with occasional mixing then quenched by addition of glycine to 0.125M with occasional mixing for 5 min.. Cells were placed on ice for 15 min. prior to washing with 1X PBS and stored at -80o C.  Hi-C was performed according to Arima Genomics (Document part # A160134 v00).  Sequencing libraries were prepared using the KAPA Hyper Prep Kit and xGen Duplex Seq adapters (Integrated DNA Techologies) according to Arima Genomics (Document part # A160139 v00).

value: CAG-Stopflox-tdTomato; Dhh-Cre

value: 7 days


title: Trp53 MZ-KO late 2-cell rep #2

value: Trp53 MZ-KO


title: SK-N-SH vector control Rep 3 [SK3_V_S7]

city: Aurora

first: Nikita

last: Pozdeyev

state: CO

address: 1890 N. Revere Court | Mailstop F600

department: Biomedical Informatics

institute: University of Colorado

data_processing:
Sequencing was performed on a NanoSeq 6000 (Illumina).
During analysis, adapter sequences were removed with the help of Trimmomatic trimmer.
The “Tuxedo” pipeline was used for transcript expression analysis.
RNAseq reads were aligned to the hg19 reference genome with HISAT2.
Stringtie was used for transcriptome assembly and transcript abundance estimation.
Raw transcript counts were extracted from ballgown object and summarized at the gene level
Genome_build: hg19

source_name: SK-N-SH vector control

growth_protocol: Three neuroendocrine tumor (NET) cell lines were utilized, SK-N-SH (neuroblastoma; ATCC), QGP-1 and BON-1 (both pancreatic NET; generous gift from Dr. Christopher Heaphy). SK-N-SH cells were grown in EMEM (Corning MT10010CV), QGP-1 cells were grown in RPMI (Gibco 11875093) and BON-1 cells were grown in DMEM/F12 (Corning MT10092CV), all supplemented with 10% FBS (Sigma F0926) and Gemini Antibiotic:Antimycotic (F77R001).

extract_protocol:
On day three post transfection, RNA was harvested using Trizol (Invitrogen).
1mcg total RNA was submitted to the Genomics and Microarray Core at the University of Colorado for library prep using an Illumina TruSeq mRNA library kit (Illumina, San Diego, CA, USA).

treatment_protocol: MAML3 plasmids were cloned using the pCMV6-AC vector from Origene (PS100020) using the full-length cDNA MAML3 sequence (FL) and the MAML3 cDNA sequence lacking the first exon (dEx1).  A C-terminal V5 tag was added to both constructs.  Transfection with the pCMV6-AC vector without either MAML3 sequence was used as the control. SK-N-SH, BON-1 and QGP-1 cells were transfected with Lipofectamine 3000 (Invitrogen L3000) reagent with vector control, FL MAML3 or dEx1 MAML3. Three biological replicates were plated in triplicate.

tag: cell line/type

value: SK-N-SH cells

tag: genotype/variation

value: Vector Control pCMV6-AC plasmid from Origene (PS100020)


title: CAG-Sox9 ATAC-seq rep 3 (6 DPTx)

description:
processed data file:
CAGSox9_Granulosa_Cells_ATACseq_6_DPTx.bigWig
Supplementary_Table_2.xlsx

source_name: Cultured Granulosa Cells

extract_protocol: ATAC-seq was performed using 50,000 freshly isolated cells.  Transposition and library prep were performed as described in PMID: 25559105.

treatment_protocol: Tamoxifen treatments began on day 2 of culture (24 hr after plating).  Immediately prior to treatment, 2 mM 4-hydroxytamoxifen (in ethanol; Sigma H7904) was diluted to 2 uM in serum-free McCoy 5A with 0.1% BSA, 1X ITSS supplement (Sigma I1884) and 1X Pen/Strep. Cells were tamoxifen-treated for 48 hours before replacing media with complete media. Thereafter, media was changed every 2-3 days until the indicated timepoint.

value: CAG-mRFP1 floxed-Sox9-eGFP; UBC-CreERT2

value: 6 DPTx


title: Granulosa Hi-C rep2 (P23)


title: Sample015 [Rectal biopsy]

tag: individual

tag: gender

value: F

tag: age at diagnosis

tag: time of sampling


title: Trp53 MZ-KO early 2-cell rep #3

value: embryo


title: Trp53 MZ-KO early 2-cell rep #4


title: Sample013 [Rectal biopsy]

value: M

value: Baseline

tag: initial treatment

value: CS-Oral

tag: colectomy

tag: disease

value: pediatric ulcerative colitis


title: Sample016 [Rectal biopsy]


title: Trp53 MZ-KO early 2-cell rep #5


title: CAG-Sox9 ATAC-seq rep 2 (6 DPTx)

tag: genoype

tag: strain background

value: Mixed 129Sv and C57Bl/6J


title: Trp53 MZ-KO early 2-cell rep #2

value: early 2-cell


title: SK-N-SH full length MAML3 overexpression Rep 3 [SK3_F_S8]

value: Full length MAML3 overexpression:full-length cDNA MAML3 with C-terminal V5 tag in pCMV6-AC plasmid from Origene (PS100020)


title: Sample014 [Rectal biopsy]

value: CS-IV


title: SK-N-SH delta exon 1 MAML3 overexpression Rep 3 [SK3_D_S9]

value: Delta exon 1 MAML3 overexpression:deletion of exon 1 cDNA MAML3 with C-terminal V5 tag in pCMV6-AC plasmid from Origene (PS100020)


title: SK-N-SH vector control Rep 2 [SK2_V_S4]


title: CAG-Sox9 ATAC-seq rep 1 (6 DPTx)

tag: tamoxifen time point

tag: antibody


title: Sample012 [Rectal biopsy]


title: SK-N-SH full length MAML3 overexpression Rep 2 [SK2_F_S5]


title: Control for CAG-Sox9 ATAC-seq rep 2 (6 DPTx)

description:
processed data file:
Control_for_CAGSox9_Granulosa_Cells_ATACseq_6_DPTx.bigWig
Supplementary_Table_2.xlsx

value: CAG-mRFP1 floxed-Sox9-eGFP

tag: age


title: SK-N-SH vector control Rep 1 [SK1_V_S1]


title: Sertoli ATAC-seq rep2 (P7)

description:
processed data file:
Sertoli_ATACseq_P7.bigWig
Supplementary_Table_2.xlsx

value: CAG-Stopflox-tdTomato; Dhh-Cre

value: 7 days


title: Sample011 [Rectal biopsy]


title: Sertoli ATAC-seq rep1 (P7)


title: Sample010 [Rectal biopsy]


title: Trp53 KO egg #3

source_name: mouse M-II egg

tag: genotype

value: Trp53 KO

tag: tissue

value: M-II egg


title: SK-N-SH delta exon 1 MAML3 overexpression Rep 2 [SK2_D_S6]

value: SK-N-SH cells


title: Control for CAG-Sox9 ATAC-seq rep 3 (6 DPTx)

value: 6 DPTx


title: SK-N-SH full length MAML3 overexpression Rep 1 [SK1_F_S2]


title: Sample009 [Rectal biopsy]


title: Trp53 KO egg #2


title: Trp53 KO egg #1


title: Sample008 [Rectal biopsy]


title: Sample007 [Rectal biopsy]

value: F


title: Granulosa ATAC-seq rep2 (P23)

description:
processed data file:
Granulosa_ATACseq_P23.bigWig
Supplementary_Table_2.xlsx

value: wild type

value: 23 days


title: SK-N-SH delta exon 1 MAML3 overexpression Rep 1 [SK1_D_S3]


title: Sample006 [Rectal biopsy]

value: Baseline


title: QGP-1 full length MAML3 overexpression Rep 3 [Q3_F_S17]

source_name: QGP-1 full length MAML3 overexpression

value: QGP-1 cells


title: CAG-Dmrt1 α-H3K27ac ChIP-seq rep2 (6 DPTx)

description:
processed data file:
CAGDmrt1_H3K27ac_ChIPseq_6_DPTx.bigWig
Supplementary_Table_2.xlsx

extract_protocol: Cells were fixed with 1% methanol-free formaldehyde in PBS (Thermo scientific #28906) for five minutes at RT with rotation.  Fixation was stopped by addition of glycine to 0.125M and rotation at RT for 10 min.  After pelleting, cells were washed in PBS and stored at -80o C until use.  Sertoli cell ChIP was performed with about 2.5 million cells and granulosa cell ChIP with about 1 million cells.  Nuclei were prepared from the fixed cells and chromatin was sheared to an average size of 300-400 bp in a Covaris S220 according to the manufacturer’s recommendations.  After shearing, the lysate was diluted 1:3 with complete DOC RIPA (37) and the sample was centrifuged at 21,000g for ten minutes at 4o C to pellet any insoluble material.  The supernatant was transferred to a fresh siliconized tube and the ChIP was initiated with the addition of ~1 ug of the relevant antibody and rotated at 4o C overnight.  Samples were then spun at 21,000g for 10 min. to pellet insoluble material and supernatant was mixed with 20 ul Protein A Dynabeads (Invitrogen, 10002D) previously blocked with BSA and yeast tRNA to inhibit non-specific binding.  After incubation at 4o C for 60 min. with rotation to allow association of protein A with the antibody, beads were applied to a magnet and washed sequentially as described previously (37).  After elution and cross link reversal, sequencing libraries were prepared using the Hyper Prep Kit (KAPA Biosystems, KK8502). Whole gonad ChIP-seq was performed essentially the same as for primary cells ChIP-seq except gonads from 2-3 animals were pooled and fixed in 1% paraformaldehyde (Electron Microscopy Sciences #15710) for 10 min. (ESR2 and FOXL2) or fixed in 2 mM disuccinimidyl glutarate (DSG, ThermoFisher Scientific #20593) at RT for 45 min. followed by 1% paraformaldehyde fixation at RT for 15 minutes (SOX9).  After quenching the fix with 0.125M glycine, chromatin was sheared to an average size of 300-500 bp using a tip sonicator.

value: CAG-Stopflox-Dmrt1-eGfp;  UBC-CreERT2

value: Mixed 129Sv and C57Bl/6J

value: Abcam ab4729


title: Granulosa ATAC-seq rep1 (P23)


title: QGP-1 vector control Rep 3 [Q3_V_S16]

source_name: QGP-1 vector control

value: Vector Control pCMV6-AC plasmid from Origene (PS100020)


title: P8 thoracic motor neuros rep1

tag: Stage

value: Wildtype

tag: spinal cord region

value: Thoracic


title: WT egg rep #1

value: WT


title: WT egg rep #3


title: Trp53 MZ-KO early 2-cell rep #1

value: Trp53 MZ-KO

value: embryo

tag: tag

value: early 2-cell


title: WT egg rep #2

value: M-II egg


title: Control for CAG-Sox9 ATAC-seq rep 1 (6 DPTx)

value: CAG-mRFP1 floxed-Sox9-eGFP

value: 6 DPTx


title: Sample005 [Rectal biopsy]

tag: individual

value: F

value: CS-Oral

value: pediatric ulcerative colitis


title: QGP-1- delta exon 1 MAML3 overexpression Rep 3 [Q3_D_S18]

tag: cell line/type

value: QGP-1 cells

tag: genotype/variation

value: Delta exon 1 MAML3 overexpression:deletion of exon 1 cDNA MAML3 with C-terminal V5 tag in pCMV6-AC plasmid


title: Sample004 [Rectal biopsy]

tag: gender

tag: age at diagnosis

tag: time of sampling

value: Baseline


title: CAG-Dmrt1 α-H3K27ac ChIP-seq rep1 ( 6 DPTx)

value: CAG-Stopflox-Dmrt1-eGfp;  UBC-CreERT2

value: Mixed 129Sv and C57Bl/6J

value: Abcam ab4729


title: QGP-1 vector control Rep 2 [Q2_V_S13]

value: Vector Control pCMV6-AC plasmid from Origene (PS100020)


title: Sample003 [Rectal biopsy]

value: M

tag: initial treatment

tag: colectomy

tag: disease


title: Control for CAG-Dmrt1 α-H3K27ac ChIP-seq rep 2 (6 DPTx)

description:
processed data file:
Control_for_CAGDmrt1_H3K27ac_ChIPseq_6_DPTx.bigWig
Supplementary_Table_2.xlsx

tag: genoype

tag: strain background

tag: tamoxifen time point


title: HB rep2_input for m6A

city: Nanning

first: Yixing

last: Li

address: Daxuedong Road, Xixiangtang District

department: Guangxi University

institute: Guangxi University

description: eight-week-old male mouse was fed high-fat diet plus Betaine for 8 weeks

data_processing:
For m6A-seq data sets, quality control of the paired-end reads was performed with Q30, which was followed by trimming of the three adaptors and removal of low-quality reads using cutadapt software (v1.9.3). Then, clean reads of all libraries were aligned to the reference genome (MM10) using Hisat2 software (v2.0.4). High quality reads of the input sample were used for RNA-seq analysis, the read count value of each transcript was calculated using HTSeq (version: 0.6.0), and then the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) value was estimated. MACS2 (version 2.1.0.20151222) was employed to perform m6A peak calling. Then HOMER (version: 4.8) was used to annotate the m6A peaks. The nucleotides in the m6A peaks regions were used to determine the consensus m6A motif by DREME (version: 4.11.1) and MEME (version: 4.11.1).
For both mRNA and RNC-mRNA sequencing data sets, high quality reads were mapped to a RefSeq mRNA reference sequence (mm10 25-Mar-2017) using the FANSe2 algorithm with the following parameters: –L80 –E5 –I0 –S14 –B1 –U0. Reads that mapped to alternative splice variants of one gene were merged. The mRNA and RNC-mRNA in each sample were normalized using RPKM (reads per kilobase per million reads), while the relative abundance between two groups was normalized using the edgeR package.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Supplementary_files_format_and_content: peak text files

source_name: Liver

extract_protocol:
In brief, RNA fragments were incubated with anti-m6A polyclonal antibody (202003; Synaptic Systems, Gottingen,Germany) in immunoprecipitation (IP) buffer for 2 h at 4◦C. Then, the mixture was immunoprecipitated byincubation with protein-A beads (Thermo Fisher Scientifific, MA, USA) for 2 h at 4◦C. Bound RNA was then eluted from the beads with m6A (BERRY & ASSOCIATES, PR3732, MI, USA) in IP buffer, and subsequentlyextracted with TRIzol reagent (Thermo Fisher Scientifific).Total RNA of a liver sample was extracted using the TRIzol reagent (Ambion, Inc., Austin, TX, USA). RNC isolation was performed in accordance with a previously reported procedure with some modifications. Briefly, 90 mg liver tissue was treated with 200 μl lysis buffer. An additional 700 μl lysis buffer was added to the samples, followed by incubation in an ice-bath for 30 min. After centrifuging at 16,200 x g for 20 min at 4°C, supernatants were added to the surface of 5 ml of sucrose buffer (30% sucrose in ribosome buffer), and the RNC complex was pelleted by ultra-centrifugation at 330,000 x g for 3 h at 4°C. RNC-mRNA was extracted from the RNC complex using TRIzol.
The final library product (m6A)  was assessed with Agilent 2200 TapeStation and Qubit®3.0 and then sequenced on Illumina HiSeq X Ten platform platform and run pair end standard sequencing program. Adaptor and low-quality bases were trimmed with Trimmomatictools (version: 0.36), and the clean reads underwent rRNA deletion through RNAcentral to acquire effective reads. Genomic alignment (version from UCSC genome browser) was performed using Tophat (version:2.0.13) to obtain unique reads.   The quality of the total RNA and RNC was determined by electrophoresis using a 2.5% agarose gel. A pooled sample from two independent experiments was used for subsequent RNA-seq assessing mRNA and RNC-mRNA. RNA libraries were prepared according to the VAHTS mRNA-seq v.3 Library Prep Kit for Illumina protocol (Vazyme Biotech Co., Ltd, Nanjing, Jiangsu, China), and the raw sequencing reads were generated on an Illumina HiSeqX Ten sequencer.

tag: strain

value: liver

tag: treatment

value: high-fat diet plus Betaine

tag: age

value: 16 weeks

tag: rip antibody


title: Control for CAG-Dmrt1 α-H3K27ac ChIP-seq rep 1 (6 DPTx)

tag: antibody


title: HB rep2_m6A

tag: tissue

value: anti-m6A antibody (Synaptic Systems, Gottingen,Germany;202003 )


title: Sertoli α-SOX9 ChIP-seq rep 2b (P7)

description:
processed data file:
Sertoli_SOX9_ChIPseq_P7.bigWig
Supplementary_Table_2.xlsx

value: CAG-Stopflox-tdTomato; Dhh-Cre

value: 7 days


title: HB rep1_input for m6A


title: QGP-1 full length MAML3 overexpression Rep 2 [Q2_F_S14]

tag: cell line/type

value: Full length MAML3 overexpression:full-length cDNA MAML3 with C-terminal V5 tag in pCMV6-AC plasmid


title: Sample002 [Rectal biopsy]

tag: individual

value: F


title: Sertoli α-SOX9 ChIP-seq rep 2a (P7)


title: Sample001 [Rectal biopsy]

tag: gender

value: CS-IV

value: pediatric ulcerative colitis


title: Sertoli Input rep 2 (P7)

description:
processed data file:
Supplementary_Table_2.xlsx


title: QGP-1 vector control Rep 1 [Q1_V_S10]

value: QGP-1 cells

tag: genotype/variation


title: HF rep2_input for m6A

description: eight-week-old male mouse was fed high-fat diet for 8 weeks

value: high-fat diet


title: HB rep1_m6A


title: Sertoli α-DMRT1 ChIP-seq rep 2 (P7)

description:
processed data file:
Sertoli_DMRT1_ChIPseq_P7.bigWig
Supplementary_Table_2.xlsx


title: HF rep2_m6A


title: QGP-1 full length MAML3 overexpression Rep 1 [Q1_F_S11]

value: Full length MAML3 overexpression:full-length cDNA MAML3 with C-terminal V5 tag in pCMV6-AC plasmid from Origene (PS100020)


title: HF rep1_input for m6A


title: BON-1 vector control Rep 3 [B3_V_S25]

source_name: BON-1 vector control

value: BON-1 cells


title: QGP-1- delta exon 1 MAML3 overexpression Rep 1 [Q1_D_S12]

value: Delta exon 1 MAML3 overexpression:deletion of exon 1 cDNA MAML3 with C-terminal V5 tag in pCMV6-AC plasmid from Origene (PS100020)


title: Sox8-/-;Sox9-/-;CAG-Dmrt1 6 DPTx rep2

description:
processed data file:
Supplementary_Table_3.xlsx
Supplementary_Table_4.xlsx

molecule: polyA RNA

extract_protocol: Cells or tissues were harvested into 1 ml Trizol reagent and stored at -80o C.  Total RNA was prepared according to Trizol reagent manufacturer’s protocols and further cleaned up using RNAeasy kit protocols and reagents (Qiagen).  RNA was quantified via Qubit RNA assay, and 500 ng total RNA per sample were used in stranded mRNA-seq library preparation (KAPA Biosystems, KK8481) for Illumina sequencing.

value: Mixed 129Sv and C57Bl/6J

value: 6 DPTx


title: QGP-1- delta exon 1 MAML3 overexpression Rep 2 [Q2_D_S15]


title: HF rep1_m6A

value: liver


title: Recombinant anti-thrombin treated mouse 2 30 hours after LPS

type: RNA

city: Gifu

first: Hideshi

last: Okada

address: 1-1 Yanagido

department: Emergency and Disaster Medicine

country: Japan

institute: Gifu University Graduate School of Medicine

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent-028005 SurePrint G3 Mouse GE 8x60K Microarray for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: Lung tissue

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

growth_protocol: Ten week-old male C57BL6 mice were obtained from Chubu Kagaku Shizai Co. Ltd. (Nagoya, Japan).

extract_protocol: Total RNA was extracted using a RNeasy kit (Qiagen, TX, USA) according to the manufacturer’s protocol. cDNAs were synthesized using a SuperScript III First-Strand Synthesis Kit (Life Technologies, Inc., MD, USA).

treatment_protocol: Following 16-h starvation, mice were intraperitoneally injected with LPS (20 mg/kg; MilliporeSigma, Burlington, MA), and in some assays, with saline or recombinant anti-thrpombin (rAT; 750 IU/kg; Kyowa Kirin Co., Ltd, Tokyo, Japan) at 3 and 24 h post-LPS injection.

value: recombinant anti-thrombin after  LPS administration

value: Male

value: 10 weeks old


title: Recombinant anti-thrombin treated mouse 1 30 hours after LPS


title: BON-1 full length MAML3 overexpression Rep 3 [B3_F_S26]

source_name: BON-1 full length MAML3 overexpression


title: Sox8-/-;Sox9+/-;CAG-Dmrt1 6 DPTx rep2


title: Sox8-/-;Sox9-/-;CAG-Dmrt1 6 DPTx rep1


title: HB rep2_RNC

value: high-fat diet plus Betaine

value: 16 weeks


title: BON-1 delta exon 1 MAML3 overexpression Rep 3 [B3_D_S27]

source_name: BON-1 delta exon 1 MAML3 overexpression


title: Saline treated mouse 3 30 hours after LPS

value: saline after LPS administration


title: Saline treated mouse 2 30 hours after LPS


title: HB rep1_RNC


title: Sox8-/-;Sox9+/-;CAG-Dmrt1 6 DPTx rep1


title: BON-1 vector control Rep 2 [B2_V_S22]

value: Vector Control pCMV6-AC plasmid from Origene (PS100020)


title: Recombinant anti-thrombin treated mouse 3 30 hours after LPS


title: BON-1 delta exon 1 MAML3 overexpression Rep 2 [B2_D_S24]


title: BON-1 full length MAML3 overexpression Rep 2 [B2_F_S23]


title: germcells_KO4

city: La Jolla

first: Kun

last: Tan

state: CA

address: 2880 Torrey Pines Scenic Dr. Room 4812

department: Department of Obstetrics, Gynecology, and Reproductive Sciences

institute: UCSD

data_processing:
Reads were filtered for quality and aligned with STAR (2.5.2b) against Mus musculus, release-101, Ensembl genome (GRCm38).
The exon counts were aggregated for each gene to build a read count table using SubRead function featureCounts.
DEGs were defined using DESeq2.
Genome_build: Mus musculus, release-101, Ensembl genome (GRCm38).
Supplementary_files_format_and_content: featurecounts

source_name: purified germ cells

extract_protocol:
Total RNA was extracted using the RNeasy Plus Micro Kit (Qiagen), following the manufacturer’s protocol.
1 ng of total RNA was used to make the library using the SMARTer® stranded total RNAseq kit v2 - pico input system (Takara Bio USA), as per manufacturer's instructions.

value: testis

tag: cell type

value: purified germ cells

tag: genotype


title: germcells_KO2


title: U87, DMSO_2

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Genome_build: hg19
Supplementary_files_format_and_content: bigWig

source_name: glioblastoma

growth_protocol: U87 cells was maintained in DMEM High Glucose supplemented with 10% heat-inactivated fetal bovine serum.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol.DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina .Paired-end sequencing was performed with Illumina instrument.

treatment_protocol: U87 cells were pre-incubated with or without JQ1 (100 nM) for 30 min, and then incubated with control T or EGFR CAR-T cells at a ratio of 1 to 1 for 48 h. When cells were stimulated with IFNγ, U87 cells were incubated with or without IFNγ (10 ng/mL) for 48 hrs.

tag: cell line

value: DMSO


title: germcells_KO1


title: U87, JQ1


title: U87, JQ1_EGFR-CAR-T


title: HF rep2_RNC

value: high-fat diet


title: HF rep1_RNC


title: U87, EGFR-CAR-T

value: EGFR-CAR-T


title: U87, DMSO


title: germcells_WT3

value: wild-type


title: germcells_WT4


title: germcells_KO3


title: germcells_WT2


title: iPSC-day8-SMC-rep2

first: Jie

state: Beijing

address: Tsinghua University

department: Basic Medical Sciences, School of Medicine

description:
cultured cells
fpkm_EC_SMC.xlsx

data_processing:
Illumina Casava software was used for basecalling.
Sequenced reads were trimmed for adaptor sequences, and masked for low-complexity or low-quality sequences, then mapped to hg38 genome using RSEM.
Fragments Per Kilobase per Million mapped reads (FPKM) of Refseq genes were caculated.
Genome_build: hg38
Supplementary_files_format_and_content: Table of gene names and FPKM values for each sample.

source_name: human iPSCs from CD34 cord blood

growth_protocol: Undifferentiated hESCs was cultured in E8 medium without feeders.

extract_protocol:
Total RNA was extracted using RNeasy Plus Mini Kit (Qiagen) and treated with Rnase-free DNase.
RNA-seq library was prepared following the Smart-seq2 protocol (Picelli, 2014)

treatment_protocol: For monolayer based EC and SMC differentiation, pluripotent stem cells were first cultured in E8 medium, after replating, E8 medium was changed to RPMI1640 medium with AATS supplement with or without insulin, and with BMP4 and CHIR99021. After 3 days of induction, cells were replated and cultured in RPMI1640 medium with AATS supplement and VEGF and FGF. On differentiation day 8, CD31+ and SM22a+ cells were sorted and subjected to RNA-seq analysis.

value: induced pluripotent stem cells (iPSCs)

tag: passage number


title: 2829

city: Boston

first: Christina

last: Codden

state: MA

address: 800 Washington Stree

department: Molecular Cardiology Research Institute

institute: Tufts Medical Center

data_processing:
Demultiplexing, read alignment, and read counting, and nuclei calls were done with Cellranger 3.0
Quality control (QC) filtering, clustering, dimensionality reduction, visualization, and differential gene expression was performed using the development version of the R package Seurat in R 3.5.0
Genome_build: GRCh38-1.2.0
Supplementary_files_format_and_content: tab separated values files with barcode sequences corresponding to column indices, features corresponding to row indices.  For each feature, its feature ID and names are stored in the first and second column of the features.tsv file.  The third column of this file indentifies that it is a gene expression feature.  The actual gene cell matrix, .mtx file, is stored in the Market Exchange Format (MEX) for sparse matrices.

molecule: nuclear RNA

source_name: Adult human myectomy tissue

extract_protocol:
Nuclei were released from the tissue via dounce homogenization and then nuclei were processed using 10x genomics Chromium Single Cell 3' reagent V2 kit
10x Genomics Chromium Single Cell 3' reagent v2 kit

value: adult heart IVS

value: Female


title: HB rep2_mRNA

value: liver


title: BON-1 vector control Rep 1 [B1_V_S19]

value: BON-1 cells


title: STIM1KO HEK293-ACE2 cells - SARS-CoV-2 infected rep2

city: Irvine

first: Arunachalam

last: Ramaiah

address: McGaugh Hall

department: Ecology and Evolutionary Biology

institute: University of California, Irvine

data_processing:
Illumina reads from all the samples were mapped to human and SARS-CoV-2 reference genomes by STAR v2.27a and read counts per gene were quantified using human Ensembl GRCh38.98 and SARS-CoV-2 GTF file to generate raw reads counts . Differential expression analysis was performed using DESeq2 v1.28.1 in R v4.0.3
Genome_build: hg38 & SARS-CoV-2 ASM985889
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: HEK293-ACE2 cells

growth_protocol: Cells were cultured in DMEM+10%FBS+1% Pen-Strep + 1% HEPES +1%Glutamine

extract_protocol:
Samples were harvested in TriZol and RNA was extracted using the Direct-zol RNA Mini prep kit
Libraries for RNA-Seq were prepared with TruSeq Stranded mRNA Library Prep Kit (Illumina). The workflow consisted of mRNA enrichment and fragmentation. Cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP, followed by second strand cDNA synthesis using DNA Polymerase I and RNase H. cDNA generation is followed by A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

treatment_protocol: 3 types of cells described above were either uninfected or infected with SARS-CoV-2 at MOI 1.0 for ~20 hrs

tag: infection

value: Infected


title: STIM1KO HEK293-ACE2 cells - SARS-CoV-2 infected rep3


title: HF rep1_mRNA


title: iPSC-day8-SMC-rep1

description:
cultured cells
fpkm_EC_SMC.xlsx


title: HB rep1_mRNA


title: BON-1 full length MAML3 overexpression Rep 1 [B1_F_S20]

value: Full length MAML3 overexpression:full-length cDNA MAML3 with C-terminal V5 tag in pCMV6-AC plasmid from Origene (PS100020)


title: HF rep2_mRNA


title: STIM1KO HEK293-ACE2 cells - SARS-CoV-2 infected rep1


title: U87, IFNγ

value: IFNγ


title: xanthophore rep4

city: Charlottesville

first: Delai

last: Huang

state: VA

address: University of Virginia

institute: UVA

data_processing:
Reads were aligned to Danio rerio reference genome GRCz11 using Kallisto (Bray et al., 2016) and analyzed using DESeq2 (Love et al., 2014) (Love et al., 2014).
Genome_build: GRCz11
Supplementary_files_format_and_content: tsv files with estimated counts (est_counts) and transcripts per million (tpm) for each gene

organism: Danio albolineatus

source_name: anal fin

extract_protocol:
Adult male Danio albolineatus were euthanized, anal fins were dissected and tissue collected from proximal erythrophore or distal xanthophore regions in PBS. RNA was extracted using TRIzol and Direct-zol RNA MiniPrep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: anal fin

tag: region

value: distal

tag: Stage

value: adult


title: 2934

value: Male


title: xanthophore rep3


title: Saline treated mouse 1 30 hours after LPS

value: saline after LPS administration

tag: strain

value: 10 weeks old


title: xanthophore rep2


title: ORAI1KO HEK293-ACE2 cells - SARS-CoV-2 infected rep2


title: ORAI1KO HEK293-ACE2 cells - SARS-CoV-2 infected rep3


title: BON-1 delta exon 1 MAML3 overexpression Rep 1 [B1_D_S21]

value: Delta exon 1 MAML3 overexpression:deletion of exon 1 cDNA MAML3 with C-terminal V5 tag in pCMV6-AC plasmid from Origene (PS100020)


title: erythrophore rep2

value: proximal


title: iPSC-AATSI-rep2

description:
cultured cells
RNA-seq FPKM1.xlsx


title: 2828


title: iPSC-AATSI-rep1

description:
cultured cells
RNA-seq FPKM1.xlsx


title: erythrophore rep3


title: germcells_WT1

value: testis

value: purified germ cells

value: wild-type


title: iPSC-AATS-rep2

description:
cultured cells
RNA-seq FPKM1.xlsx

value: induced pluripotent stem cells (iPSCs)


title: U2OS_KO_PARGi_R3

city: Leicester

first: Michael

last: Tellier

state: Select State

address: Lancaster Road

department: Department of Molecular and Cell Biology

country: United Kingdom

institute: University of Leicester

description: RNA-seq U2OS ADPRS KO cells, PARGi treated, replicate 3

data_processing:
Adapters were trimmed with Cutadapt v1.18
Removal of rRNA reads and mapping to the hg38 genome were performed with STAR v2.7.3a
Extraction of properly paired and properly mapped reads and Bam files sorting and indexing were done with SAMtools v1.9
Differential gene expression analysis was performed with htseq-count v0.11.3 and DESeq2 v3.12
Bigwig files were generated with the Deeptools2 v3.4.2 bamCoverage tool
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files: genome-coverage files for all samples

source_name: U2OS ADPRS KO cells

growth_protocol: DMEM (Sigma) supplemented with 10% FBS (Gibco) and penicillin-streptomycin (100 U/mL, Gibco)

extract_protocol:
RNA was extracted using Direct-zol RNA MiniPrep Plus kit (Zymo Research) according to the manufacturer’s instructions. The quality of the RNA was measured spectrophotometrically using NanoDrop 2000c (Thermo Scientific) and quality was analysed by RNA ScreenTape Assay and 4200 TapeStation System (Agilent).
For RNA-seq, libraries were prepared using Illumina's TruSeq Stranded Total RNA library Preparation Kit according to Illumina's instructions

treatment_protocol: DMSO or 25µM PARGi inhibitor (PDD00017273, Sigma) for 4 days

value: U2OS ADPRS KO cells

tag: treatment

value: PARGi


title: iPSC-day8-EC-rep2

description:
cultured cells
fpkm_EC_SMC.xlsx


title: 2839

value: adult heart IVS

tag: age


title: STIM1KO HEK293-ACE2 cells - mock rep3

value: mock


title: iPSC-day8-EC-rep1

description:
cultured cells
fpkm_EC_SMC.xlsx


title: ORAI1KO HEK293-ACE2 cells - mock rep1


title: AqSCr_LB_Cr(VI)_adapted_rep3

city: Mexico

first: Leticia

last: Vega

state: Mexico

address: Circuito Ext s/n

country: Mexico

institute: Universidad Nacional Autonoma de Mexico

data_processing:
Illumina bcl2fastq software were used for basecalling
Reads were aligned to the SAMN05730075 genome assembly using bowtie
The number of reads falling in the genes  were counted using coveragebed software and normalized with DESeq2 software
Genome_build: SAMN05730075
Supplementary_files_format_and_content: tab-delimited text files include the differential expression results of edgeR, DESeq2, limma and NOISeq. Additionally, each file contains the raw and normalized counts  for each sample.

organism: Klebsiella sp. AqSCr

growth_protocol: AqSCr strain was grown aerobically at 30°C and subcultured twice in LB pH8 with and without 11mM of Cr(VI), when the cultures reached an optical density (600 nm) of 0.64 ± .05 and 1.05 ± .05 respectively (exponential growth phase) they were harvested. Experiments were conducted by triplicate

extract_protocol:
Total RNAs were extracted from each sample using the RNeasy Mini Kit (QIAGEN). After, total RNA was digested with DNase I (Thermo Fisher Scientific) and consecutively digested with the enzyme Terminator™ 5´-Phosphate-Dependent Exonuclease (Epicentre) to eliminate the ribosomal RNA. RNAs were examined with an Agilent 2100 Bioanalyzer and quantified using NanoDrop 200c (Thermo Scientific).
Illumina sequencing was performed at the UUSMD (UNAM, Mexico). The mRNA-enriched RNA was chemically fragmented to 150~200 bp. Based on these cleaved RNA fragments, cDNA was synthesized using a random hexamer primer and reverse transcriptase. After end reparation and ligation of adaptors, the products were amplified by PCR, further purified, and used to create the final cDNA library. Libraries were sequenced on an Illumina Genome Analyzer IIx.

treatment_protocol: RNA Later (Ambion) was added to cultures before harvesting cells

value: AqSCr

tag: medium/metal

value: LB pH 8/Cr(VI) 11mM


title: iPSC-AATS-rep1

description:
cultured cells
RNA-seq FPKM1.xlsx


title: 2841


title: erythrophore rep4

value: anal fin


title: U2OS_KO_DMSO_R2

description: RNA-seq U2OS ADPRS KO cells, DMSO treated, replicate 2

value: DMSO


title: STIM1KO HEK293-ACE2 cells - mock rep2


title: 2843

value: Male


title: AqSCr_LB_Cr(VI)_adapted_rep2


title: H1-AATSI-rep2

description:
cultured cells
RNA-seq FPKM1.xlsx

source_name: human embryonic stem cell line H1

value: Embryonic stem cells


title: STIM1KO HEK293-ACE2 cells - mock rep1


title: scr HEK293-ACE2 cells - SARS-CoV-2 infected rep3

value: Infected


title: U2OS_KO_DMSO_R1

description: RNA-seq U2OS ADPRS KO cells, DMSO treated, replicate 1


title: H1-day8-SMC-rep1

description:
cultured cells
fpkm_EC_SMC.xlsx


title: AqSCr_LB_Cr(VI)_adapted_rep1


title: scr HEK293-ACE2 cells - SARS-CoV-2 infected rep2


title: scr HEK293-ACE2 cells - SARS-CoV-2 infected rep1


title: H1-day8-EC-rep2

description:
cultured cells
fpkm_EC_SMC.xlsx


title: H1-day8-EC-rep1

description:
cultured cells
fpkm_EC_SMC.xlsx


title: H1-day8-SMC-rep2

description:
cultured cells
fpkm_EC_SMC.xlsx


title: AqSCr_LB_control_rep2

value: LB pH 8


title: MDA-MB-231_CART

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using Tophat version 2.1.1.
Genome_build: hg19

source_name: breast

growth_protocol: MDA-MB-231 was maintained in DMEM High Glucose supplemented with 10% heat-inactivated fetal bovine serum .

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. For xenograft experiment,mice were sacrificed and tumor tissue were resected for RNA extraction.Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol.DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina NovaSeq 6000 at AMOGENE Co., Ltd

treatment_protocol: MDA-MB-231 cells were incubated with control T or EGFR CAR-T cells at a ratio of 2 to 1, and treated with or without THZ1 (250 nM) for 48 hours (hrs). When cells were stimulated with IFNγ, MDA-MB-231 cells were incubated with or without IFNγ (10 ng/mL) in the presence or absence of THZ1 (250 nM) for 48 hrs.

value: CART


title: ORAI1KO HEK293-ACE2 cells - SARS-CoV-2 infected rep1


title: MDA-MB-231_THZ1-IFNγ


title: Undiff-iPSC-rep2

description:
cultured cells
RNA-seq FPKM1.xlsx


title: U2OS_KO_PARGi_R2

description: RNA-seq U2OS ADPRS KO cells, PARGi treated, replicate 2


title: 2812

value: Female


title: xanthophore rep1

value: distal

value: adult


title: Fnp2

first: Tingjun

address: 56 Lingyuanxi Road

data_processing:
The raw paired end reads were trimmed and quality controlled by Trimmomatic with parameters (SLIDINGWINDOW:4:15 MINLEN:75) (version 0.36 http://www.usadellab.org/cms/uploads/supplementary/Trimmomatic). Then clean reads were separately aligned to reference genome with orientation mode using Rockhopper (http://cs.wellesley.edu/~btjaden/Rockhopper/) software. Rockhopper was a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads generated by high-throughput sequencing technology. This software was used to calculate gene expression levels with default parameters.
To identify DEGs (differential expression genes) between the two different samples, the expression level for each transcript was calculated using the fragments per kilobase of read per million mapped reads (RPKM) method. edgeR (https://bioconductor.org/packages/release/bioc/html/edgeR.html) was used for differential expression analysis. The DEGs between two samples were selected using the following criteria: i) the logarithmic of fold change was greater than 2 and the false discovery rate (FDR) should be less than 0.05.
To understand the functions of the differential expressed genes, GO functional enrichment and KEGG pathway analysis were carried out by Goatools (https://github.com/tanghaibao/Goatools) and KOBAS (http://kobas.cbi.pku.edu.cn/home.do) respectively. DEGs were significantly enriched in GO terms and metabolic pathways when their Bonferroni-corrected P-value was less than 0.05.
Genome_build: Beta_vulgaris.GCF_000511025.2_RefBeet-1.2.2
Supplementary_files_format_and_content: tab-delimited text files include counts values for each Sample: values for S. gordonii DL1 in mono-species group (Sg) as well as in coaggregation group (CAB) were reported in the processed file "CAB(Sg)_vs_Sg.genes.read.txt"; values for F. nucleatum subsp. polymorphum (ATCC10953) in mono-species group (Fnp) as well as in the coaggregation group (CAB) were reported in the processed file "CAB(Fnp)_vs_Fnp.genes.read.txt".

organism: Fusobacterium polymorphum

source_name: single species

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: f. nucleatum atcc#

tag: growth protocol

value: monoculture

tag: gram status

value: Gram-negative species


title: ORAI1KO HEK293-ACE2 cells - mock rep3


title: MDA-MB-231_DMSO


title: erythrophore rep1

tag: tissue

value: proximal


title: miRNA in high ALDH activity 4T1 cells

city: fukuoka

first: naoya

last: matsunaga

address: maidashi 3-1-1, higashi-ku

institute: kyushu university

hyb_protocol: biotin labeled miRNA was hybridized to Affymetrix GeneChip miRNA 4.0 array, washed and stained according to the manufacturer's instructions.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner

data_processing: Arrays were RMA and quantile normalized by Affymetrix Expression Console 1.4.1 software. After the normalization, the probes designed for Mouse were extracted from normalized data.

label: biotin

source_name: High ALDH activity 4T1 cells

label_protocol: 130ng of total RNAs were labeled  using the FlashTag™ Biotin HSR RNA Labeling Kit (Affymetrix), following the manufacturer’s instructions (User manual of the FlashTag™ Biotin HSR RNA Labeling Kit, Affymetrix)

extract_protocol: Total RNAs including miRNAs were isolated and purified from cells using miRNeasy Mini Kit  (Qiagen)　according to the manufacturer's instructions.

value: BALBc

value: 4T1 cells


title: scr HEK293-ACE2 cells - mock rep1

value: mock


title: ORAI1KO HEK293-ACE2 cells - mock rep2


title: MEF G9Gl-2 RNA-seq

status: Public on May 19 2021

city: Freiburg im Breisgau

first: Galina

last: Erikson

address: Stübeweg 51

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

data_processing:
Reads were aligned to the GRCm38 genome from Ensembl using STAR (Dobin et al., 2013) version 2.5.2b, with settings as recommended by TEtranscripts (Jin et al., 2015). Both genes and repeats were then quantified using TEtranscripts version 2.0.3 and differentially expressed repeat elements and genes determined using DESeq2
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts uploaded

source_name: MEF deficient for 2 KMTs (G9a and Glp)

growth_protocol: The growth protocols have been described in our study (Montavon et al). MEFs are grown in standard medium

extract_protocol:
RNA was extracted with trizol and ethanol precipitation, Dnase treated and column-purified
RNA libraries were prepared using standard TruSeq Stranded Total RNA (Gold) protocol

value: Mouse Embryonic Fibroblasts

value: G9a/Glp KO


title: MEF G9Gl-1 RNA-seq


title: MEF S1S2-2 RNA-seq

source_name: MEF deficient for 2 KMTs (Suv39h1 and Suv39h2)

value: Suv39h1/Suv39h2 KO


title: U2OS_KO_PARGi_R1

description: RNA-seq U2OS ADPRS KO cells, PARGi treated, replicate 1

value: U2OS ADPRS KO cells

value: PARGi


title: Fnp1

city: Guangzhou

last: Liu

institute: Sun Yat-sen University


title: miRNA in low ALDH activity 4T1 cells

source_name: Low ALDH activity 4T1 cells


title: U2OS_KO_DMSO_R3

description: RNA-seq U2OS ADPRS KO cells, DMSO treated, replicate 3

value: DMSO


title: MEF WT H3K9me3-2

description: ChIP for H3K9me3 (abcam ab8898)

data_processing:
Reads were aligned to mm10 (GRCm38)  with bwa version 0.7.1. (Heng et. al 2009). Peaks were called using histoneHMM (Heinig et.al 2009).
Genome_build: GRCm38
Supplementary_files_format_and_content: peak files (BED)

source_name: wild type MEF

extract_protocol:
ChIP-seq protocol has been described in our study (Montavon et al).
NEBNext Ultra II DNA library for Illumina

value: wild type


title: MEF WT H3K9me3-1

description: ChIP for H3K9me3 (abcam ab8898)


title: MEF WT H3K9me1-1

description: ChIP for H3K9me1 (abcam ab8896)


title: MEF WT input-2

description: fragmented (sonication) input DNA


title: MEF WT-1 RNA-seq


title: MEF WT H3K9me2-1

description: ChIP for H3K9me2 (abcam ab1220)


title: shKmt2f_4

city: Bunkyo-ku

first: Toshiro

last: Iwagawa

state: Tokyo

address: 7-3-1 Hongo

department: Tokyo University Hospital

institute: University of Tokyo

data_processing:
Illumina Casava1.8 software was used for basecalling
Sequenced reads were processed by salmon 0.11.3 with its default parameters to quantify transcript expression level
Downstream analysis including TPM calculation, differentially expressed gene detection, and visualization were performed using wasabi 0.3 and sleuth 0.30.0
Genome_build: GRCm38.p6
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each samples.

source_name: Explant retina

growth_protocol: Electroporated retinas were culture on a chamber filter (Millicel) with medium (50% MEM with Hepes, 25% Hank's solution, 25% heat-inactivated HS, 200 mM L-glutamine, and 5.75 mg/ml glucose, penicillin and streptomycin) at 34ºC in 5% CO2.

extract_protocol:
Retinas were trypsinized and EGFP positive cells were sorted out using a cell sorter (FACS AriaII, BD). Total RNA was extracted using Sepasol RNA I super G reagent (nacalai). SMART-Seq v4 (Illumina) was used fro cDNA synthesis with 1 ng of toal RNA.
Nextera DNA Flex Library Prep Kit (Illumina) was used for libraries preparation.

treatment_protocol: Retinas at E17.5 were electroporated with control or shKmt2f-expressing plasmid together with EGFP-expressing plasmid and cultured for 2 days.

value: ICR

value: retina

value: embryonic day 17.5 day in vitro 2

value: electroporation shKmt2f


title: H1-AATSI-rep1

city: Beijing

institute: Tsinghua University

description:
cultured cells
RNA-seq FPKM1.xlsx

value: Embryonic stem cells


title: AqSCr_LB_control_rep3

value: AqSCr

value: LB pH 8


title: MDA-MB-231_THZ1-CART


title: H1-AATS-rep2

description:
cultured cells
RNA-seq FPKM1.xlsx


title: control_1

value: electroporation control


title: scr HEK293-ACE2 cells - mock rep3


title: MEF G9Gl-3 RNA-seq


title: AqSCr_LB_control_rep1


title: scr HEK293-ACE2 cells - mock rep2


title: ATAC-seq_B1A6 oht1

description: Eset1/Eset2/Suv39h1/Suv39h2/G9a/Glp KO

data_processing:
Unprocessed reads were first quality and adapter trimmed using fastp (Chen S. et al., 2018) version 0.19.4, using a mean window quality threshold of 3 and excluding low complexity sequences. These were then aligned to the mouse genome from Ensembl using STAR (Dobin et al., 2013) version 2.6.0c allowing no spliced alignments and with other options as described be TEtranscripts (Jin Y. et al. 2015).
 For visualization, bigWig tracks were constructed using deepTools and IGV (Robinson et al., 2011).
Genome_build: GRCm38
Supplementary_files_format_and_content: bigWigs files uploaded

source_name: Eset1/Eset2/Suv39h1/Suv39h2/G9a/Glp KO

growth_protocol: The growth protocols have been described in our study (Montavon et al). MEFs are grown in standard medium, in presence or absence of 4-hydroxytamoxifen (4-OHT)

extract_protocol: Extract protocol not provided.

treatment_protocol: 4-OHT (1 uM) in culture medium

value: Eset1/Eset2/Suv39h1/Suv39h2/G9a/Glp KO


title: ATAC-seq_E2 oht2

description: Eset1/Eset2/G9a/Glp KO

source_name: Eset1/Eset2/G9a/Glp KO

value: Eset1/Eset2/G9a/Glp KO


title: MDA-MB-231_THZ1


title: Fnp3

value: monoculture

value: Gram-negative species


title: MDA-MB-231_IFNγ

value: IFNgamma


title: ATAC-seq_B1 oht2

description: Eset1/Suv39h1/Suv39h2 KO

source_name: Eset1/Suv39h1/Suv39h2 KO

value: Mouse Embryonic Fibroblasts

value: Eset1/Suv39h1/Suv39h2 KO


title: ATAC-seq_B1 oht1

description: Eset1/Suv39h1/Suv39h2 KO


title: Undiff-H1-rep2

description:
cultured cells
RNA-seq FPKM1.xlsx


title: H1-AATS-rep1

description:
cultured cells
RNA-seq FPKM1.xlsx


title: ATAC-seq_E2F4 oht1

description: Eset1/Eset2/G9a/Glp/Suv39h1/Suv39h2 KO

source_name: Eset1/Eset2/G9a/Glp/Suv39h1/Suv39h2 KO

value: Eset1/Eset2/G9a/Glp/Suv39h1/Suv39h2 KO


title: Undiff-H1-rep1

description:
cultured cells
RNA-seq FPKM1.xlsx


title: Undiff-iPSC-rep1

description:
cultured cells
RNA-seq FPKM1.xlsx

source_name: human iPSCs from CD34 cord blood

value: induced pluripotent stem cells (iPSCs)


title: MEF S1S2-3 RNA-seq

value: Suv39h1/Suv39h2 KO


title: MEF S1S2-1 RNA-seq


title: ATAC-seq_A4 ctr2

description: Eset2 KO

source_name: Eset2 KO

value: Eset1cKO Eset2 KO


title: MEF WT-3 RNA-seq

value: wild type


title: ATAC-seq_A4 ctr1

description: Eset2 KO


title: ATAC-seq_E25 oht1


title: MEF WT-2 RNA-seq


title: MEF WT H3K9me2-2

description: ChIP for H3K9me2 (abcam ab1220)


title: MEF WT H3K9me1-2

description: ChIP for H3K9me1 (abcam ab8896)


title: E2F4 oht1

description: Eset1/Eset2/G9a/Glp/Suv39h1/Suv39h2 KO

data_processing:
Unprocessed reads were first quality and adapter trimmed using cutadapt (Martin M., 2011) version 1.8.1 using a quality threshold of 20. Reads were then aligned to the GRCm38 genome from Ensembl using STAR (Dobin et al., 2013) version 2.5.2b, with settings as recommended by TEtranscripts (Jin Y. et al., 2015).
Genome_build: GRCm38
Supplementary_files_format_and_content: raw counts in .tsv file

source_name: MEF

extract_protocol:
RNA was extracted with trizol and ethanol precipitation, Dnase treated and column-purified
RNA libraries were prepared for sequencing using standard Illumina protocols


title: MEF WT input-1

description: fragmented (sonication) input DNA


title: E2 oht3

description: Eset1/Eset2/G9a/Glp KO


title: B1A6 oht1

description: Eset1/Eset2/Suv39h1/Suv39h2/G9a/Glp KO


title: shKmt2f_3

value: ICR

value: retina

value: embryonic day 17.5 day in vitro 2

value: electroporation shKmt2f


title: shKmt2f_2


title: shKmt2f_1


title: E2 oht1

description: Eset1/Eset2/G9a/Glp KO


title: B1 oht3

description: Eset1/Suv39h1/Suv39h2 KO


title: control_3

value: electroporation control


title: Ctrl_S11_23

city: New York

first: Weijia

last: Zhang

state: NY

address: 1 Gustave L. Levy Pl

department: Renal

institute: Icahn School of Medicine at Mount Sinai

data_processing:
The reads with good quality were firstly aligned to several mouse reference databases including mm10 mouse genome, exon, splicing junction segment and contamination database including ribosome and mitochondria sequences using BWA alignment algorithm. After filtering reads mapped to contamination database, the reads that are uniquely aligned to the exon and splicing-junction segments with a maximal 2 mis-matches for each transcript were then counted as expression level for corresponding transcript.  After filtering out of the transcripts with low read (<100) across all samples, the read counts were log2 transformed and quantile-normalized at an equal global median value in order to compare transcription level across samples.
Genome_build: mm10
Supplementary_files_format_and_content: text file of raw counts

source_name: Control (baseline)

extract_protocol:
Glomeruli were extracted following intracardiac perfusion of magnetic Dynabeads. Total RNA was then isolated using the RNeasy mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: For induction of type I diabetes with STZ, mice were injected over 5 consecutive days with low-dose STZ (50 μg/g per day intraperitoneally)

tag: strain background

value: control

value: Control (baseline)

value: Glomeruli


title: Ctrl_S10_30

tag: genotype/variation


title: B1 oht1

description: Eset1/Suv39h1/Suv39h2 KO


title: control_2


title: KO_STZ_S8

source_name: Podocyte-specific DACH1 KO + STZ

value: Podocyte-specific DACH1 KO

value: STZ injection


title: ATAC-seq_E2F4 oht2

description: Eset1/Eset2/G9a/Glp/Suv39h1/Suv39h2 KO

value: Mouse Embryonic Fibroblasts


title: ATAC-seq_B1A6 oht2

description: Eset1/Eset2/Suv39h1/Suv39h2/G9a/Glp KO

value: Eset1/Eset2/Suv39h1/Suv39h2/G9a/Glp KO


title: B1 oht2

description: Eset1/Suv39h1/Suv39h2 KO

value: Eset1/Suv39h1/Suv39h2 KO


title: A4 oht2

description: Eset1/Eset2 KO

value: Eset1/Eset2 KO


title: ATAC-seq_E2 oht1

description: Eset1/Eset2/G9a/Glp KO

value: Eset1/Eset2/G9a/Glp KO


title: ATAC-seq_A4 oht2

description: Eset1/Eset2 KO

source_name: Eset1/Eset2 KO


title: ATAC-seq_A4 oht1

description: Eset1/Eset2 KO


title: A4 ctr1

description: Eset2 KO

value: Eset1cKO Eset2 KO


title: ATAC-seq_E25 oht2


title: ATAC-seq_E25 ctr2

description: control

source_name: control

value: Eset1 cKO


title: 2D2 WT CNS Th17 cells_rep4

city: Arlington

first: Vanja

last: Lazarevic

address: 1820 N Tuckahoe Street,

department: National Cancer Institute

institute: National Institutes of Health

data_processing:
Illumina RTA 1.18.64 software used for basecalling
Bcl2fastq v2.17 software was used for demultiplexing
Reads of the samples were trimmed for adapters and low quality bases using Trimmomatic 0.36 software before the algnment with the reference genome (Mouse - mm10)
The annotated transcripts were aligned to the reference genome (Mouse - mm10) using STAR2.6.1
Mapping statistics and duplication statistics was calculated using Picard 2.4.1 software
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each sample
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: CNS (day 20 after adoptive transfer)

growth_protocol: Naïve sorted (CD4+ CD62Lhi CD25-) CD4+ T cells were activated and differentiated under non-pathogenic (Th17(b)) or pathogenic (Th17(23), Th17(alt)) differentiation conditions. Within 24 hours of activation, CD4+Tcells were transduced with empty control retrovirus or Egr2-expressing retrovirus.

extract_protocol:
RNA was extracted from splenic and CNS-infiltrating CD4+ T cells at the peak of disease, and from Th17 cells transduced with empty virus control or Egr2-expressing retrovirus under non-pathogenic [Th17(b)] or pathogenic [Th17(23) and Th17(alt)] conditions after brief 4-hr PMA and ionomycin restimulation, using QIAshredder columns and RNase Plus Mini kit (Qiagen).
26 mRNA-Seq samples were pooled and sequenced on HiSeq4000 using Illumina TruSeq Stranded mRNA Library Prep and paired-end sequencing.

treatment_protocol: Emtpy control retrovirus or Egr2-expressing retrovirus

value: WT

tag: treatment (culture conditions)

value: IL-6+TGFb1 (aIFN-g + aIL-4) --> IL-23

tag: treatment (retroviral transduction)


title: 2D2 WT CNS Th17 cells_rep2

tag: genotype


title: ATAC-seq_E25 ctr1

description: control


title: E2F4 oht3

description: Eset1/Eset2/G9a/Glp/Suv39h1/Suv39h2 KO

value: Eset1/Eset2/G9a/Glp/Suv39h1/Suv39h2 KO


title: B1A6 oht3

description: Eset1/Eset2/Suv39h1/Suv39h2/G9a/Glp KO


title: E25 oht1


title: 2D2 WT CNS Th17 cells_rep1


title: KO_S11_45

source_name: Podocyte-specific DACH1 KO (baseline)

value: Podocyte-specific DACH1 KO (baseline)


title: B1A6 oht2

description: Eset1/Eset2/Suv39h1/Suv39h2/G9a/Glp KO


title: KO_S11_13


title: E2 oht2

description: Eset1/Eset2/G9a/Glp KO


title: KO_S10_24


title: 2D2 Egr2-/- CNS Th17 cells_rep1


title: 2D2 WT Spleen Th17 cells_rep4

source_name: Spleen (day 20 after adoptive transfer)


title: E2F4 oht2

description: Eset1/Eset2/G9a/Glp/Suv39h1/Suv39h2 KO


title: Ctrl_S11_12


title: A4 oht3

description: Eset1/Eset2 KO


title: KO_STZ_S6


title: KO_STZ_S4


title: A4 oht1

description: Eset1/Eset2 KO


title: ZH-02-QG-Exo_S2

city: Louisville

first: Huang-Ge

state: KY

address: 505 S Hancock Street

department: James Graham Brown Cancer Center

institute: University of Louisville

data_processing:
Illumina Casava v1.8.4 software used for basecalling.
Raw fastqs were adapter and quality score trimmed with cutadapt v1.10. with a minimum length of 15 nt.
MicroRNAs were identified using the sRNABench Pipeline (version 05/14).
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Zingiber officinale

source_name: Ginger nanoparticle

extract_protocol:
Total RNA exptracted with miRNeasy Mini Kit (Qiagen)
Small RNA libraries were generated with 100ng of total RNA and QIAseq miRNA Library Kit (Qiagen) according to the manufacturer’s instructions. Equal amounts of libraries were pooled and sequenced on the Illumina HiSeq 2500 using NextSeq Sequencing Kit (illumina).

value: Ginger root


title: ZH-01-QG-Tis_S1

source_name: Ginger tissue


title: Healthy lung tissue, patient 17

type: genomic

city: Trieste

first: Sara

last: Patrizi

address: via dell'Istria 65

country: Italy

institute: University of Trieste

hyb_protocol: 1 ug of genomic DNA was bisulphite-converted, amplified, fragmented and hybridised to Illumina Infinium Human EPIC 850K according to manufacturer's instructions

scan_protocol: Arrays were imaged using Illumina IScan and Illumina IScan Control Software

data_processing:
Raw data was loaded and normalized using standard parameters of R package ChAMP
Normalized matrix: Normalized (with method BMIQ) Average Beta

label: Cy5 and Cy3

source_name: Healthy lung tissue

label_protocol: Samples were labeled with Cy5 and Cy3 according to standard Illumina Protocol

extract_protocol: Genomic DNA was extracted as previously described by Miller et al., 1988

tag: histological type

value: healthy

tag: barcode

value: normal

tag: Sex

value: male


title: 2D2 WT Spleen Th17 cells_rep1


title: hetN_STZ_S3

source_name: Control + STZ

value: control

value: Glomeruli


title: 2D2 Egr2-/- Spleen Th17 cells_rep3


title: hetN_STZ_S2

value: STZ injection


title: hetN_STZ_S1


title: Healthy lung tissue, patient 13


title: A4 ctr3

description: Eset2 KO

value: Mouse Embryonic Fibroblasts


title: E25 oht3


title: Th17(alt) EV_rep3

source_name: In vitro differentiated Th17 cells

value: Empty control retrovirus


title: 2D2 Egr2-/- Spleen Th17 cells_rep1


title: A4 ctr2

description: Eset2 KO


title: 2D2 WT CNS Th17 cells_rep3


title: Healthy lung tissue, patient 11

value: female


title: Healthy lung tissue, patient 10


title: E25 ctr3

description: control


title: 2D2 Egr2-/- CNS Th17 cells_rep3


title: Th17(alt) EV_rep1


title: E25 ctr2

description: control


title: Pleuropulmonary Blastoma tissue, patient PM23

source_name: Pleuropulmonary Blastoma

value: PPB

value: cancer


title: E25 oht2


title: 2D2 Egr2-/- CNS Th17 cells_rep2


title: Th17(23) EV_rep3


title: E25 ctr1

description: control

value: Eset1 cKO


title: Th17(23) EV_rep2

value: WT


title: Th17(23) EV_rep1

value: IL-6+TGFb1 (aIFN-g + aIL-4) --> IL-23


title: Congenital Pulmonary Malformation, patient 18, malformation A

source_name: Congenital Pulmonary Malformation

value: ELS

value: malformed


title: 2D2 WT Spleen Th17 cells_rep3


title: 2D2 WT Spleen Th17 cells_rep2


title: Healthy lung tissue, patient 14


title: Congenital Pulmonary Malformation, patient 17

value: ILS


title: ZH-03-QG-MP_S3

value: Ginger root


title: Healthy lung tissue, patient 12

value: healthy

value: normal


title: 2D2 Egr2-/- Spleen Th17 cells_rep2


title: Congenital Pulmonary Malformation, patient 15

value: CPAM 1


title: Congenital Pulmonary Malformation, patient 14

value: CPAM 2


title: Congenital Pulmonary Malformation, patient 12


title: Striatum 3m, repl 3

city: London

last: Lattke

address: Hammersmith Hospital Campus, Du Cane Road

department: Brain Sciences

institute: Imperial College London

description: This library was run on 11 lanes to acquire the required sequencing depth.

data_processing:
The resulting data was demultiplexed using the 10x cellranger mkfastq function according to manufactuer’s instructions. Reads from individual samples were mapped to the mouse genome (mm10) and quantified with the cell ranger count function (v3.0.2, option --expect-cells=3500).
The generated count matrices were imported into Seurat (v3.1.1) (Stuart et al., 2019) and aggregated using the Seurat “merge” function.
The metadata file contains key metadata for all cells retained after QC filtering, including UMAP coordinates for whole dataset and UMAP and PCA coordinates for subclustered astrocytes, as well as pseudotime values and bins from Slingshot analysis described in the related manuscript
Genome_build: mm10
Supplementary_files_format_and_content: csv files with raw read counts for each gene for each cell from all samples merged (extracted from Seurat); and key cell metadata from downstream analysis

source_name: striatal astrocytes (MACS-purified)

extract_protocol:
cell suspensions of striatal astrocytes were prepared by anti-ACSA2-MACS. Samples were prepared using the 10x Chromium Next GEM Single Cell 3ʹ v3.1 kit.
Following GEM recovery, cDNA was amplified and final libraries prepared according to the manufactuer’s instructions.

value: striatum

value: 3 months

value: wild type

tag: cell type

value: striatal astrocytes (MACS-purified)

value: male

tag: internal sample name in raw data

tag: internal sample name in analysis (processed data)

tag: experimental group

tag: experiment type

value: scRNA-Seq


title: Striatum P3, repl 3

tag: strain

tag: age

value: post natal day 3


title: Healthy lung tissue, patient 9

value: female


title: Striatum 3m, repl 2


title: Striatum P3, repl 2


title: Healthy lung tissue, patient PM21


title: Congenital Pulmonary Malformation, patient 18, malformation B


title: Congenital Pulmonary Malformation, patient 8


title: Striatum P3, repl 1


title: Congenital Pulmonary Malformation, patient 6

value: CPAM 3


title: Th17(b) Egr2_rep3

value: WT

value: IL-6+TGFb1 (aIFN-g + aIL-4)

value: Egr2-expressing retrovirus


title: Congenital Pulmonary Malformation, patient 4

value: malformed


title: Th17(b) Egr2_rep2


title: Th17(alt) EV_rep2

value: Empty control retrovirus


title: Congenital Pulmonary Malformation, patient 2

value: ILS


title: Congenital Pulmonary Malformation, patient 16


title: normal diet 2

city: Shanghai

first: FEI

last: XU

state: Shanghai

address: 1609 Xietu Road

institute: Zhongshan Hospital, Fudan University

data_processing:
Cutadapt was used to remove the reads that contained adaptor contamination, low-quality bases or undetermined bases. The sequence quality was then verified with Fast QC.
CIRCExplorer and CIRI were used to assemble the mapped reads to circular RNAs, and the back-splicing reads were identified in the unmapped reads by TopHat-fusion.
The differentially expressed circRNAs were selected with log2 (fold change) > 1 or log2 (fold change) < -1 and with statistical significance (p value < 0.05).
Supplementary_files_format_and_content: srpbm, count, log2FoldChange

source_name: aorta

extract_protocol:
Total RNA was isolated and purified from cell or tissue samples using TRIzol reagent (Invitrogen, USA) following the manufacturer's protocol. RNase R (Lucigen, USA) was used to isolate circRNA from total RNA.
We reverse-transcribed the cleaved RNA fragments into cDNA and synthesized U-labeled second-strand DNA with reverse-transcribed cDNA, E. coli DNA polymerase I, RNase H and dUTP. An A-base was then added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Single- or dual-index adapters were ligated to the fragments, and AMPureXP beads were used for size selection. After heat-labile UDG enzyme treatment of the U-labeled second-strand DNA, the ligated products were amplified by PCR. The average insert size for the final cDNA library was 300 bp (±50 bp). Finally, we performed paired-end sequencing on an Illumina HiSeq 4000 (LC Bio, China) following the manufacturer’s recommended protocol.

tag: group

value: normal diet fed


title: normal diet 1


title: Th17(b) Egr2_rep1


title: Ctlmethy_C056_Batch2

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Raw Illumina BeadChip data (i.e. IDAT files) were imported into R and normalized using  minfi version 1.30.0.  IDAT files were normalized using functional normalization (FunNorm). probes located on X and Y chromosomes and probes closer than 3 bp to a SNP were excluded.
Average Beta normalized using functional normalization (FunNorm)

label_protocol: Standard Illumina Protocol

extract_protocol: DNA were isolated from duodenal biopsies obtained during diagnostic esophagogastroduodenoscopy using the Qiagen AllPrep RNA/DNA Mini Kit (Qiagen, Valencia, CA)

tag: diagnosis

value: CONTROL

tag: gender

value: Male

tag: age (month)

value: Duodenum

tag: pid


title: Congenital Pulmonary Malformation, patient 13

value: CPAM 2


title: Th17(b) EV_rep3

tag: treatment (culture conditions)

tag: treatment (retroviral transduction)


title: Th17(b) EV_rep2

tag: genotype


title: Congenital Pulmonary Malformation, patient 10, malformation A

tag: histological type

tag: barcode


title: Congenital Pulmonary Malformation, patient 10, malformation B

value: ELS

tag: Sex


title: Congenital Pulmonary Malformation, patient 11


title: Congenital Pulmonary Malformation, patient 5

value: male


title: Congenital Pulmonary Malformation, patient 7


title: Striatum 3m, repl 1

tag: tissue

value: striatum

value: 3 months

value: wild type

tag: cell type

value: striatal astrocytes (MACS-purified)

tag: internal sample name in raw data

value: scRNA-Seq


title: high fat diet 3

value: high fat diet fed


title: Th17(b) EV_rep1

value: WT

value: IL-6+TGFb1 (aIFN-g + aIL-4)


title: high fat diet 2


title: Ctlmethy_C027_Batch2


title: Ctlmethy_C043_Batch2

value: Female


title: EEDmethy_51_Batch2

value: EED


title: EEDmethy_52_Batch2


title: Congenital Pulmonary Malformation, patient 9

value: ILS

value: malformed

value: female


title: normal diet 3

value: normal diet fed


title: Congenital Pulmonary Malformation, patient 3


title: high fat diet 1


title: EEDmethy_50_Batch2

value: Duodenum


title: death 1_D-P-2 mRNA

city: Hangzhou

first: Shanshan

last: Ms

state: Zhejiang

address: No.79 Qingchun Road

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

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

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

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

source_name: peripheral blood mononuclear cells

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

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

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

tag: disease

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

value: whole blood

tag: survival state of 28-day

value: dead


title: death 2_D-P-3 mRNA

value: male

tag: age


title: EEDmethy_48_Batch2

value: Male


title: Congenital Pulmonary Malformation, patient 1


title: death 4_D-P-5 mRNA


title: death 3_D-P-4 mRNA


title: Ctlmethy_C055_Batch2

value: CONTROL


title: Ctlmethy_C052_Batch2


title: survival 6_97P1 mRNA

value: survivial


title: EEDmethy_45_Batch2


title: EEDmethy_44_Batch2


title: death 6_99P1 mRNA


title: death 8_N16P1 mRNA


title: survival 5_93P1 mRNA


title: Ctlmethy_C050_Batch2


title: Ctlmethy_C025_Batch2


title: Ctlmethy_C017_Batch2


title: death 5_B141 mRNA


title: EEDmethy_42_Batch2


title: T2-S3-b (Fig5) (+) BSseq

city: Los Angeles

first: Colette

middle: L

last: Picard

state: California

address: 610 Charles E Young Dr East, Room 4045

department: Molecular, Cell and Developmental Biology

institute: University of California - Los Angeles

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

organism: Arabidopsis thaliana

source_name: rosette leaf

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

extract_protocol:
CTAB-based method was used to extract DNA
75 to 150 ng of DNA was used to prepare WGBS libraries using the Ovation Ultralow Methyl-seq kit (NuGEN)

tag: strain

tag: genetic background

value: fwa

tag: transgene present

value: yes (SunTag-MQ1v)

tag: developmental stage

value: rosette stage


title: T2-S2-d (Fig5) (-) BSseq

tag: generation


title: EEDmethy_49_Batch2

tag: diagnosis

tag: gender

tag: age (month)

tag: pid


title: EEDmethy_37_Batch2


title: EEDmethy_47_Batch2


title: survival 8_100P1 mRNA


title: T2-S1-d (Fig5) (-) BSseq


title: EEDmethy_35_Batch2


title: death 7_115P1 mRNA


title: T2-S1-b (Fig5) (+) BSseq


title: T2-S1-a (Fig5) (+) BSseq


title: survival 2_S-P-3 mRNA


title: survival 7_98P1 mRNA


title: survival 4_S-P-5 mRNA


title: EEDmethy_33_Batch2


title: survival 3_S-P-4 mRNA


title: T2-S3-d (Fig5) (-) BSseq


title: T2-S3-c (Fig5) (-) BSseq


title: Col (Fig5) rep 2 BSseq

value: wild-type

value: no transgene


title: T2-S2-b (Fig5) (+) BSseq


title: EEDmethy_41_Batch2

value: EED

value: Female


title: Col (Fig5) rep 1 BSseq


title: EEDmethy_43_Batch2


title: T2-S3-a (Fig5) (+) BSseq


title: fwa (Fig5) rep 2 BSseq


title: EEDmethy_40_Batch2


title: EEDmethy_39_Batch2


title: T2-S2-c (Fig5) (-) BSseq


title: survival 1_S-P-1 mRNA


title: EEDmethy_29_Batch2


title: EEDmethy_38_Batch2


title: EEDmethy_36_Batch2


title: MQ1v T1-R3 BSPCR [P3_T1_R3]

source_name: MQ1v T1-R3 BSPCR

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

tag: ecotype background

value: fwa drm1 drm2

value: yes (MQ1v)

value: rosette leaf


title: MQ1v T1-R4 BSPCR [P3_T1_R4]

source_name: MQ1v T1-R4 BSPCR


title: EEDmethy_24_Batch2

value: Duodenum


title: T2-S2-a (Fig5) (+) BSseq


title: EEDmethy_27_Batch2


title: EEDmethy_34_Batch2


title: T2-S1-c (Fig5) (-) BSseq


title: EEDmethy_26_Batch2


title: MQ1v T1-R2 BSPCR [P3_T1_R2]

source_name: MQ1v T1-R2 BSPCR


title: MQ1v T1-R5 BSPCR [P3_T1_R5]

source_name: MQ1v T1-R5 BSPCR


title: EEDmethy_32_Batch2


title: EEDmethy_31_Batch2


title: EEDmethy_16_Batch2


title: EEDmethy_14_Batch2


title: dMQ1 T1-R1 BSPCR [P3_T1_R1]

source_name: dMQ1 T1-R1 BSPCR

value: yes (dMQ1)


title: dMQ1 T1-R6 BSPCR [P3_T1_R6]

source_name: dMQ1 T1-R6 BSPCR

value: fwa rdr6


title: fwa (Fig5) rep 1 BSseq


title: EEDmethy_30_Batch2


title: EEDmethy_22_Batch2


title: EEDmethy_12_Batch2


title: MQ1v T1-R8 BSPCR [P3_T1_R8]

source_name: MQ1v T1-R8 BSPCR


title: EEDmethy_10_Batch2


title: Col (Fig4) BSseq [P4_Col]

source_name: Col  BSseq

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


title: Ctlmethy_C041_Batch1


title: Ctlmethy_C043_Batch1


title: EEDmethy_17_Batch2


title: Ctlmethy_C037_Batch1


title: Ctlmethy_C026_Batch1


title: SunTag-MQ1v T1-S2 BSseq [P4_T1_2]

source_name: SunTag-MQ1v T1-S2 BSseq


title: SunTag-MQ1v T1-S3 BSseq [P4_T1_3]

source_name: SunTag-MQ1v T1-S3 BSseq


title: liver tissue_t-PBS_rep2

first: Qixin

last: HAN

address: NO.845 Lingshan Road

institute: Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University

data_processing:
Raw reads were filtered by Seqtk
Hisat2 (version:2.0.4) was employed to map the cleaned reads to Rattus norvegicus Rnor_6.0.
The fragments of genes were counted using Stringtie (version:1.3.0) followed by FPKM normalization.
Genome_build: Rnor_6.0
Supplementary_files_format_and_content: Matrix table with FPKM values and raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: liver tissue

growth_protocol: specific pathogen-free barrier facility

extract_protocol:
RNeasy mini kit (Qiagen, Germany) was used to extract total RNA from snap-frozen rat liver tissue.
TruSeq® RNA Sample Preparation Kit (Illumina, USA) was employed to construct paired-end libraries.

treatment_protocol: fecal microbiota transplantation

value: liver

tag: treatment

value: FMT recipient from PBS treated donor rat

value: Sprague Dawley


title: Ctlmethy_C025_Batch1

value: CONTROL

value: Male


title: MQ1v T1-R7 BSPCR [P3_T1_R7]

source_name: MQ1v T1-R7 BSPCR

tag: tissue


title: Ctlmethy_C036_Batch1


title: Ctlmethy_C040_Batch1


title: liver tissue_t-DHEA_rep2

value: FMT recipient from DHEA treated donor rat


title: liver tissue_t-DHEA_rep3


title: Ctlmethy_C027_Batch1


title: liver tissue_t-DHEA_rep1


title: liver tissue_t-PBS_rep3


title: Ctlmethy_C024_Batch1


title: Ctlmethy_C022_Batch1


title: Ctlmethy_C020_Batch1


title: Ctlmethy_C019_Batch1


title: AR3419_03: organoid-momlayer

city: Suita

first: Tomoki

last: Yamashita

state: Osaka

address: 1-6 Yamadaoka

department: Graduate School of Pharmaceutical Sciences

institute: Osaka University

description: organoid-derived monolayer

hyb_protocol: 0.6 μg of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Human GE 8x60K Microarray Ver3.0 (Agilent Technologies) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent Technologies) and 1 minute with 37°C GE Wash buffer 2 (Agilent Technologies).

scan_protocol: Slides were scanned immediately after washing on the Agilent SureScan Microarray Scanner (G2600D) using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with Feature Extraction Software 12.0.3.1 (Agilent Technologies) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities.
Processed signal intensities were normalized by the global scaling method. A trimmed mean probe intensity was determined by removing 2% of the lower and the higher end of the probe intensities in order to calculate the scaling factor. Normalized signal intensities were then calculated from the target intensity on each array using the scaling factor, so that the trimmed mean target intensity of each array was arbitrarily set to 2500.

source_name: duodenal organoid-derived monolayer

label_protocol: Cyanine3 (Cy3) labeled cRNA was prepared from 0.1 μg Total RNA using the Low Input Quick Amp Labeling Kit (Agilent Technologies) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: Duodenal biopsy; The human duodenal biopsy was performed during upper gastrointestinal endoscopy in patients from Sapporo Medical University Hospital. Under endoscopic observation, 2–4 biopsy samples were obtained from the noninflammatory lamina propria mucosae of the duodenum. The obtained samples were stored in ice-cold PBS containing 1× antibiotic-antimycotic (15240062; Thermo Fisher Scientific, MA, USA) until the procedures to establish the organoids. Establishment of human duodenal organoids; We established human duodenal organoids based on the methods described in several previous reports with some modifications (Miyoshi and Stappenbeck, 2013; Sato et al., 2009, 2011a; Sugimoto and Sato, 2017; VanDussen et al., 2015). Briefly, obtained samples were incubated in 2.5 mM EDTA at 4℃ for 30 min, and vigorously pipetted up and down to isolate crypts. The crypts were resuspended in Matrigel (354230; Corning, NY, USA), and 25-40 μL of the crypt suspension was applied to the center of each well of a 24-well plate (142475; Thermo Fisher Scientific). The Matrigel was polymerized for 10 min at 37℃, and 500 μL/well of the organoid culture medium (IntestiCult Organoid Growth Medium (Human), ST-06010; STEMCELL Technologies, BC, Canada) containing 1× antibiotic-antimycotic was overlaid. According to the manufacturer, the composition of the organoid culture medium is based on two reports (Jung et al., 2011; Sato et al., 2011a). Maintenance of human duodenal organoids; In order to maintain human duodenal organoids, the medium was changed every 2 days and organoids were passaged 1:3–1:10 every week. The procedure for passaging human duodenal organoids was mainly based on the report of Miyoshi et al. with some modifications (Miyoshi and Stappenbeck, 2013). Each well was washed with 0.5 mM EDTA, and the organoid cultures were scraped and suspended in TrypLE Select (12563029; Thermo Fisher Scientific). The suspension was incubated at 37℃ for 5–7 min to dissolve the Matrigel. After incubation, the organoids were pipetted up and down 2–5 times, then resuspended with Matrigel to the desired concentration. Then, 25–40 μL of the organoid suspension was applied to the center of each well of a 24-well plate. The Matrigel was polymerized for 10 min at 37℃, and 500 μL/well of the organoid culture medium containing 1× antibiotic-antimycotic was overlaid. Caco-2 cells; Caco-2 cells (HTB-37; ATCC, VA, USA) were cultured with minimum essential medium (M4655; Merck, Hessen, Germany) containing 10% fetal bovine serum, 1× MEM-NEAA (11140050; Thermo Fisher Scientific), 1× GlutaMAX-I (35050061; Thermo Fisher Scientific), and 1× antibiotic-antimycotic. For differentiation of Caco-2 cells, the cells were cultured on Transwell filter insert for 21 days after they reached confluence.

extract_protocol: RNA was extracted using RNeasy Mini Kit.

treatment_protocol: Human duodenal organoid-derived monolayer; To maximize seeding efficiency, the culture surface was coated with Matrigel in advance. Organoids were collected and incubated in TrypLE Select following the passaging protocol described above. After incubation, the organoids were pipetted up and down to dissociate organoids into single cells. The cells were resuspended with the organoid culture medium containing 10 μM Y-27632 (036-24023; FUJIFILM Wako Pure Chemical, Osaka, Japan). The cell suspension was applied to the Matrigel-coated culture surface. The culture medium was replaced with the organoid culture medium every 1–2 days until assay.

tag: sample type

value: cultured cell


title: AR3419_02: organoid

description: organoid

source_name: duodenal orgaonid, biopsy-derived


title: liver tissue_t-PBS_rep1


title: EEDmethy_30_Batch1


title: Ctlmethy_C001_Batch1


title: EEDmethy_28_Batch1


title: Ctlmethy_C015_Batch1


title: AR3419_01: adult duodenum

description: biopsy

source_name: biopsy samples, noninflammatory lamina propria mucosae, duodenum

value: tissue


title: Ctlmethy_C017_Batch1


title: EEDmethy_24_Batch1


title: Ctlmethy_C018_Batch1


title: Ctlmethy_C016_Batch1


title: EEDmethy_22_Batch1


title: EEDmethy_20_Batch1


title: Ctlmethy_C013_Batch1


title: Ctlmethy_C011_Batch1


title: EEDmethy_31_Batch1


title: EEDmethy_16_Batch1


title: EEDmethy_15_Batch1


title: EEDmethy_29_Batch1


title: EEDmethy_25_Batch1


title: EEDmethy_05_Batch1


title: EEDmethy_11_Batch1


title: EEDmethy_04_Batch1


title: EEDmethy_21_Batch1


title: EEDmethy_03_Batch1


title: EEDmethy_19_Batch1


title: EEDmethy_46_Batch2


title: AR3419_04: Caco-2

description: colon cancer-derived cell line

source_name: Caco-2 cells, HTB-37, ATCC


title: EEDmethy_02_Batch1


title: EEDmethy_27_Batch1


title: wildtype, mRNA_N2_30

city: Basel

first: Jadiel

last: Wasson

address: Klingelbergstrasse 50/70

department: Zell Biologie

country: Switzerland

institute: Biozentrum, University of Basel

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to WBcel235 using BWA alignment tool.
featureCounts was used to count all alignments. Multi-read correction was used on all mRNA read counts. mRNA read counts from each library were normalized to the total number of mapped reads
variance stabilizing transformation was utilized and each library was analyzed for differential expression using Deseq2
Genome_build: WBcel235
Supplementary_files_format_and_content: tab-delimited text files include raw count values for each Sample …
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Caenorhabditis elegans

source_name: early embryos

extract_protocol:
Early embryos were isolated from C. elegans mothers when 1-2 eggs were present, flash frozen in liquid nitrogen, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on an Illumina instrument following the manufacturer's protocols.

tag: genotype

value: wildtype

value: early embryos


title: flp-21 mutant, mRNA_21_30


title: EEDmethy_26_Batch1

value: EED


title: flp-21 mutant, mRNA_21_11


title: EEDmethy_17_Batch1