title: Sample II con

city: Salt Lake City

first: Monica

last: Vetter

institute: University of Utah

data_processing:
Aligned reads to the mm10 reference from 10X genomics (version 2020-A from Ensembl 98) and generated feature-barcode matrices using cellranger count 3.1.0 with expected-cells set to 6000. Spliced and unspliced transcripts counts were also generated from batch II single cell samples with velocyto v0.17.17. Total transcripts were used for all analyses unless specified otherwise.
Filtered feature matrices from cellranger were further filtered with the aid of Seurat v4.0.3. High quality cells were identified by a mitochondrial percentage < 7.5 and a high number of genes/features. The feature cut-off was determined independently for each sample by the local minimum cell density between 200 and 2000 features (con I = 1490, cKO I = 1845, con II = 1367, cKO II = 1481). Each sample was run, individually, through Seurat’s SCTransform pipeline, regressing out mitochondrial percentage, to generate unsupervised cell clusters. DoubletFinder v2.0.3 identified likely doublets assuming 0.8% doublets in 1000 cells, adjusted for homotypic doublets. Doublets were excluded from downstream analysis.
Batch I and batch II were combined into a single dataset using the Seurat’s integration anchor pipeline with principal components set to 30 and cluster resolution to 2. Clusters were manually annotated using expression of known cell markers: Vsx2, Lhx2, and Pax6 for RPCs, Neurog2 and Olig2 for neurogenic cells, Crx for photoreceptor precursors, Thrb for cones, Nrl for rods, Rbpms for retinal ganglion cells, Tfap2a for amacrine cells, and Lhx1 for horizontal cells. Using batch II samples only, the SCTranform pipeline was run on spliced transcripts, regressing out cell cycle scores, to obtain a UMAP representing mature transcriptional state. Cell type annotation was carried over from the integrated dataset.
Assembly: mm10
Supplementary files format and content: matrix.mtx, barcodes.tsv, featrures.tsv: Filtered feature count matrix, generated by cellranger, stored as a sparse numeric matrix and tab separated values for row and column names.
Supplementary files format and content: jarid2_sc_counts_normalized.tsv: scaled gene expression data from the integrated dataset
Supplementary files format and content: jarid2_spliced_counts_normalized.tsv: SCTransformed spliced counts
Supplementary files format and content: jarid2_sc_meta_data.tsv: meta data for all cells including cell type and UMAP coordintes.

extract_protocol:
Cells for single cell sequencing were obtained from two tamoxifen-treated littermates with the genotypes Jaridfl/fl; Rax-CreERT2 (cKO) and Jaridfl/fl (control). Two freshly dissected retinas from an individual animal were pooled for each sample and dissociated in PBS, 50 mM HEPES, 0.05 mg/ml DNase I (Sigma D4513) and 0.025 mg/ml Liberase (Sigma 5401119001) for 35 min with intermediate trituration. Cells were passed through a 70 mm nylon cell strainer, washed with washing buffer (1X PBS, 2 % BSA, 0.1% sodium azide, 0.05% EDTA), and red blood cells were lysed in RBC lysis buffer (eBioscience 00-4333-57). Cell counts were determined using a Countess (Invitrogen C10228). 1x 106 cells was resuspended in 1mL DPBS and provided to the High Throughput Genomics Core for library prep. This protocol was repeated on two different days to provide cells for batch I and batch II.
Single cell libraries were generated with Single Cell 3’ Gene Expression Library Prep v3 reagents for batch I and Next GEM Single Cell 3’ Gene Expression Library prep v3.1 with UDI for batch II, according to manufacturer’s protocol (10X Genomics PN-1000092 and PN-1000128). Sequencing libraries were applied to a NovaSeq flow cell using XP chemistry workflow v1 and v1.5 for batch I and batch II samples respectively (Illumina 20021664 and 20043131). A 150 x 150 cycle paired end sequence run was performed using an Illumina NovaSeq 6000 instrument and NovaSeq S2 reagent Kit for batch I or S4 reagent Kit v1.5 for batch II (Illumina 20012860 and 20028312). Batch I libraries were sequenced in two separate runs to a read depth of > 600 million reads per sample. Batch II libraries were sequenced to > 200 million reads per sample in a single run.

value: retina

value: embryonic day 18.5

value: Jarid2 fl/fl


title: Hippocampus, young, chow, rep1

status: Public on Feb 15 2023

type: SRA

city: Columbus

first: Michael

last: Butler

state: OH

address: 460 Medical Center Drive

country: USA

institute: Ohio State University

library_source: transcriptomic

data_processing:
FASTQ files were aligned to the rat Rnor 7.1 reference genome using the STAR (spliced transcripts to a reference) aligner.
Data were normalized and differential expression was determined using DESeq2 in R.
Assembly: Rnor 7.1

molecule: total RNA

organism: Rattus norvegicus

source_name: Brain - Hippocampus

extract_protocol:
RNA extraction was performed with Trizol and molecular biology grade isopropanol
NEBNext® Ultra™ II Directional (stranded) RNA Library Prep Kit for Illumina (NEB #E7760L); NEBNext Poly (A) mRNA Magnetic Isolation Module (NEB #E7490); NEBNext Multiplex Oligos for Illumina Unique Dual Index Primer Pairs (NEB #6444S/L); Library input amount 200ng total RNA (quantified using Qubit Fluorometer); Fragmentation: 10 minutes; Libraries were sequenced with Novaseq SP Paired-End 150bp format

tag: tissue

value: Brain - Hippocampus

tag: gender

value: male

tag: genotype

value: F344 X BN

tag: treatment

value: Young, Chow


title: uninduced MCF10A YAP5SA cells pSer2 Pol II

city: Wuerzburg

first: Carsten

middle: P

last: Ade

address: Am Hubland

department: Lehrstuhl Biochemie und Molekularbiologie

country: Germany

institute: University of Wuerzburg

library_source: genomic

data_processing:
Galaxy was used to analyze NGS data (https://usegalaxy.org).
Reads were mapped to the human genome (hg19 assembly) using Bowtie2 (for ChIP-seq and ATAC-seq) and HISAT2 (for RNA-seq) with default parameters (Langmead and Salzberg, 2012).
For ATAC-seq, ATAC-peaks were called using Genrich (https://github.com/jsh58/Genrich).
Differential peak analysis and RNA-seq analysis was performed within Galaxy with Limma-voom (Liu et al., 2015).
Nucleosome calling was carried out with NucleoATAC (Schep et al., 2015).
Genome_build: hg19
Supplementary_files_format_and_content: For ATAC-seq and ChIP-seq, the provided processed files are bigWig files for data display in a genome browser. For RNA-seq, a normalized count-matrix and a differential expression analysis file are provided, both in text-format (*.txt).

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: MCF10A stably expressing doxycycline inducible YAP5SA or ER-YAP2SA and MY-COMP were grown in were cultured in DMEM/F-12 supplemented with 5% horse serum, 1% penicillin/ streptomycin, 10 µg/ml insulin, 500 ng/ml hydrocortisone, 20 ng/ml EGF and 100 ng/ml cholera toxin.

extract_protocol:
For ChIP-seq, cells were cross-linked with 1% formaldehyde (Sigma) for 10 min at room temperature. The reaction was stopped by adding 125 mM glycine (Sigma). After cells were lysed for 10 minutes on ice [5 mM PIPES pH 8.0, 85 mM KCl, 0.5% NP40, 1 mM PMSF, protease inhibitor cocktail (Sigma)], nuclei were resuspended in RIPA buffer [50 mM HEPES pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.1% SDS, 1 mM PMSF, protease inhibitor cocktail (Sigma)].
Chromatin was fragmented to an approximate length of 150 to 300 bp using a Branson sonifier. Antibodies (9 µg) were coupled to protein G dynabeads (Thermo Fisher Scientific) for 6 hours at 4°C and then incubated with fragmented chromatin over night at 4°C. Beads were washed in total twelve times with wash buffer I (50mM Tris-HCl pH8, 0.15M NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), wash buffer II (50mM Tris-HCl pH8, 0.5M NaCl, 1mM EDTA, 0.1% SDS, 1% Triton X-100, 0.1% sodium deoxycholate), wash buffer III (50mM Tris-HCl pH8, 0.5M LiCl2, 1mM EDTA, 1% Nonidet P-40, 0.7% sodium deoxycholate) and wash buffer IV (10mM Tris-HCl pH8, 1mM EDTA).
1mM PMSF and protease inhibitor cocktail (Sigma ) was added freshly to all buffers. Chromatin was eluted in (10mM Tris-HCl pH8, 0.3M NaCl, 5mM EDTA, 0.5% SDS, 10µg/ml RNAseA) and crosslink was reversed at 65°C over night. Proteins were digested by adding 200 µg/ml proteinase K at 55°C for 2 hours. DNA was purified using the QIAquick PCR Purification Kit (QIAGEN) and eluted in 50 µl EB buffer.
For ChIPseq, DNA libraries were generated using 10ng purified ChIP-DNA and the NEBNext®Ultra II DNA Library Prep Kit for Illumina® (New England Biolabs) according to the manufacturer’s instructions. DNA library was amplified by 15-18 PCR cycles and quality was analyzed using the Fragment Analyzer (Advanced Analytical). Libraries were sequenced on the NextSeq 500 platform (Illumina).

treatment_protocol:
ATAC-seq and ChIP-seq: YAP5SA was induced with 0.5µg/ml doxycycline for 48 hours.
RNA-seq: Cells were induced with 0.5 µg/ml doxycycline for 45 hours and with 1µM OHT for 14h.

tag: dox-treatment (yap5sa)

value: uninduced

tag: chip antibody

value: p-S2 RNA Pol II (Abcam, ab5095)


title: uninduced MCF10A YAP5SA cells pSer5 Pol II

value: p-S5 RNA Pol II (Abcam, ab5131)


title: uninduced MCF10A YAP5SA cells unphosphorylated Pol II

value: Pol II (8WG16) (Santa Cruz, sc-56767 )


title: Sample I cko

middle: L.

state: UT

department: Neurobiology & Anatomy

library_source: transcriptomic single cell

organism: Mus musculus

tag: strain

tag: age

value: Jarid2 fl/fl, Rax CreERT2/+


title: E14_IgG

data_processing:
Unique Molecular Indexes (UMIs) were sequenced to identify PCR duplicates, and the UMIs were handled by scripts written by the Huntsman Cancer Institute Bioinformatics Core. UMIs were added as a SAM flag to fastq files using merge_umi_fastq.pl. Samples were aligned to mouse genome build mm10 with Novoalign (v4.02.02) using standard Illumina TruSeq adapters. Samtools fixmate (v1.10) removed unmapped reads and added mate scores, then bam files were sorted and indexed. PCR and optical duplicates were removed by bam_umi_dedup.pl with optical distance threshold at 2500.
Peak calling was done with a Macs2-based pipeline, MultiRepMacsChIPSeq (v17.7), developed by the Huntsman Cancer Institute Bioinformatics Analysis Shared Resource. Briefly, multirep_macs2_pipeline.pl was run with no deduplication, expected fragment size of 200, and mappable genome size 2500000000, to obtain log2 fold enrichment tracks of H3K27me3 relative to IgG at E14.5 and P0.
Supplementary files format and content: dedup.fragment.bw files are tracks showing fragment coverage for each sample.
Supplementary files format and content: log2FE.bw files are tracks showing enrichment of H3K27me3 at each age compared to IgG control.
Assembly: mm10
Library strategy: CUT&RUN

source_name: retina

extract_protocol:
Single cells were obtained from female littermates. Freshly dissected retinas were pooled and dissociated in PBS, 50 mM HEPES, 0.05 mg/ml DNase I (Sigma D4513) and 0.025 mg/ml Liberase (Sigma 5401119001) for 35 min with intermediate trituration. Cells were passed through a 70 mm nylon cell strainer, washed with washing buffer (1X PBS, 2 % BSA, 0.1% sodium azide, 0.05% EDTA), and red blood cells were lysed in RBC lysis buffer (eBioscience 00-4333-57). Cell counts were determined using a Countess (Invitrogen C10228), and cells were split into technical replicates before performing CUT&RUN.
P0 H3K27me3 and P0 IgG samples were run in technical triplicate, E14.5 H3K27me3 was run in duplicate, and E14.5 IgG was a single sample. CUT&RUN was performed using a CUT&RUN Assay Kit (Cell Signaling 86652) according to manufacturer’s protocol. 2 µl rabbit anti-H3K27me3 antibody was used for H3K27me3 Immunoprecipitation and 5 µl Rabbit I (DA1E) mAb IgG XP Isotype Control provided by the kit was used as a negative control. Samples were purified on DNA spin column (cell signaling #14209) eluted with 35ul elution buffer. 5ul was used for PCR to validate sample quality and the rest used for library preparation. PCR showed specific bands with positive control primers for H3K27me3.
DNA was quality was confirmed by PCR, libraries were created with the NEBNext UItra II DNA Library Prep Kit (New England Biolabs E7645S) and 150 bp paired-end sequencing was performed with the NovaSeq S4 Reagent Kit v1.5.

value: IgG

value: embryonic day 14.5

value: wild type


title: Sample I con


title: G523 FLAG-mH2A2 IP 3

city: Calgary

first: Marco

last: Gallo

state: AB

address: 2500 University Dr NW

department: Biochemistry and Molecular Biology

country: Canada

institute: University of Calgary

description: FLAG-mH2A2 ChIP

data_processing:
Samples were aligned using bwa 0.7.17 with the mem algorithm to the GRCh38 (hg38) human reference genome.
Additional filtering was applied using samtools to remove reads mapping to blacklist regions and reads with  q  < 30.
Duplicates were marked and removed using Picard. Peaks were called using sicer with default parameters and using an input sample as reference.
Peaks from different replicates were merged to create a consensus peaklist using bedtools merge.
Assembly: hg38
Supplementary files format and content: Bed file of consensus FLAG-macroH2A2 peaks

growth_protocol: Cells were grown under standard culture conditions in 10 cm PLO-laminin coated Primaria plates.

extract_protocol:
In brief, cells were resuspended in warm media, then fixed in fresh PFA to a final  concentration of 0.5% for 5 minutes  with agitation, followed by quenching with 750 mM Tris-HCl pH 8.1. Nuclei were then extracted on ice with  nuclear extraction buffer (10 mM Tris-HCl pH  7.5; 10 mM NaCl; 0.3% Igepal CA630; 3 mM MgCl2, Roche protease inhibitors), and cells were spun to isolate nuclei. Nuclei were lysed in lysis buffer (1% SDS; 10 mM EDTA; 50 mM Tris-HCl pH 8.1), then sheared on a Diagenode Bioruptor for 40 minutes at high power  and 30 seconds on, 30 seconds off. Immunoprecipitation was performed overnight on an equivalent of 1-2 million cells, with 20 uL of protein A Dynabeads (Invitrogen) with 8 uL of anti-FLAG antibody (Cell Signalling Technologies #14793). Samples were washed on a rotator at 4C for 5 minutes each with low-salt (20 mM Tris-HCl pH 8.0, 2 mM EDTA; 150 mM NaCl, 1% Tx100, 0.1% SDS), high-salt (20 mM Tris-HCl pH 8.0, 2 mM EDTA; 500 mM NaCl, 1% Tx100, 0.1% SDS), 250 mM RIPA-LiCl (50 mM HEPES pH 7.4, 1 mM EDTA; 0.7% Na deoxycholate, 1% NP-40, 250 mM LiCl) and TE buffers supplemented with protease inhibitors (Roche). Samples were eluted in elution buffer (1% SDS; 10 mM Tris-HCl pH 8.0, 5 mM EDTA pH 8, 300 mM NaCl) with RNAse (20 mg/mL) and Proteinase K (20 mg/mL) in a  dry bath for 6 hours at 65 C with agitation. DNA was purified using SPRI beads (Beckman-Coulter) with a 1.8X ratio and eluted in 10 mM Tris-HCl pH 8.0.
Libraries were constructed at the Center for Genomics and Health Informatics (CHGI) using the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs).
Sequencing was performed at the CHGI using a Illumina NovaSeq 6000 on an SP flow cell with 200 cycles (2x100 bp).

tag: cell line

tag: cell type

value: primary culture


title: G523 FLAG-mH2A2 IP 2

description: FLAG-mH2A2 ChIP


title: E14_H3K27me3_2


title: Sample II cko


title: induced MCF10A YAP5SA cells Input DNA

value: induced


title: induced MCF10A YAP5SA cells pSer5 Pol II


title: M medium (differentiation medium), scaffold, Day28, rep 3

city: Palo Alto

first: James

last: Dunn

state: California

address: 453 Quarry Road, Office 454H

institute: Stanford University

data_processing:
STAR (v. 2.6.0.a).
Reads were mapped against the mouse genome GRCm38 (mm10) using STAR (v. 2.6.0.a).
Assembly: mm10
Supplementary files format and content: raw_counts.csv: Comma-separated text file includes raw counts for each sample.

source_name: Primary cells isolated from the intestinal muscle layers

growth_protocol: Primary cells were isolated from freshly collected intestinal muscle layers. Cells were cultured in the P medium (DMEM plus 10% FBS and 1x ABAM) on a well-plate, or in the M medium (Advanced DMEM/Ham's F-12 with 1x N2, 1x B27 (minus vitamin A), 1 mM N-acetylcysteine, 10 mM HEPES, 2 mM GlutaMAX, 100 ng/mL recombinant murine Noggin, 1 μg/mL recombinant human R-spondin1, 10 μMY27632 and 1x ABAM) on a well-plate, or in the M medium on an electrospun gelatin scaffold for 28 days.

extract_protocol:
Total RNA from cultured cells (28 days in culture) or muscle strips was isolated using a Qiashredder (Qiagen) and RNeasy kit (Qiagen).
RNA-seq libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina) following the manufacturer's protocols.

value: WT

tag: condition

value: 3D culture

tag: medium

value: M medium

tag: time point

value: Day 28


title: Intestinal muscle strips, rep 3

value: Primary cells isolated from the intestinal muscle layers

value: positive control

value: Native tissue


title: G523 FLAG-mH2A2 IP 1

description: FLAG-mH2A2 ChIP


title: E14_H3K27me3_1

value: retina


title: uninduced MCF10A YAP5SA cells Input DNA

value: uninduced


title: G523 FLAG  input

description: G523-FLAG input


title: M medium (differentiation medium), well plate, Day28, rep 3

value: 2D culture


title: P0_IgG_3

value: postnatal day 0


title: P medium (proliferation medium), well plate, Day28, rep 3

value: P medium


title: P0_IgG_2

value: IgG


title: uninduced MCF10A-YAP5SA replicate 2

extract_protocol:
For ATAC-seq, cells were washed with ice cold PBS and lysed in ATAC lysis buffer (10mM Tris pH 7.4, 10mM NaCl, 3 mM MgCl2, 0.1% Tween 20 and freshly added protease inhibitor cocktail (Sigma)) by incubating on ice for 10 minutes. Nuclei were collected by spinning at 500 g for 10 minutes at 4°C. The transposition reaction mix (25 μl 2X TD buffer, 2.5 μl TDE1 Nextera transposase (Illumina), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl of nuclease free water) was added to nuclei and incubated at 37°C for 30 mins. Next, the reaction was cleaned using the MinElute PCR purification kit (Qiagen).
For ATAC-seq, a PCR with 10-13 cycles was performed using the NEBNext High Fidelity 2X PCR Master Mix (NEB) and Ad1_noMX and Ad2.1–2.4 barcoded primers described in (Buenrostro et al., 2013). Size selection of the libraries was performed with Agencourt AMPure XP beads (Beckman Coulter). Library quality and fragment size distribution was analyzed on a Fragment Analyzer (Advanced Analytical). Paired end 2 x 75 bp sequencing was performed on the NextSeq 500 platform (Illumina).

value: non induced


title: uninduced MCF10A-YAP5SA replicate 1


title: P0_IgG_1

value: wild type


title: M medium (differentiation medium), scaffold, Day28, rep 2


title: induced MCF10A-YAP5SA replicate 2


title: Intestinal muscle strips, rep 2


title: induced MCF10A-YAP5SA replicate 1


title: P0_H3K27me3_3


title: HepG2_shYTHDF2.rep2_input

city: Chongqing

first: Yang

last: Yang

state: Chongqing

address: No. 1, Medical College Road

country: China

institute: Chongqing Medical University

data_processing:
Illumina Casava1.8 software used for basecalling.
fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter, and sequence quality of IP and Input samples were also verified using fastp.
We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome. Mapped reads of IP and input libraries were provided for R package exomePeak (https://bioconductor.org/packages/exomePeak). And Called called peaks were annotated by intersection with gene architecture using R package ChIPseeker (https://bioconductor.org/packages/ChIPseeker).
Then StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts from input libraries by calculating FPKM . The differentially expressed mRNAs were selected by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: homo sapiens Ensembl release-101
Supplementary files format and content: .xlsx files include gene expression and methylation level

molecule: polyA RNA

source_name: hepatoma cell

growth_protocol: HepG2 cells were mainted in DMEM(HyClone, Logan, UT, USA) with 10%FBS (Gibco, Rockville, MD, USA)

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification. The poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. Then the cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to create the final cDNA library in accordance with the protocol for the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, cat.e7530L, USA).

treatment_protocol: HepG2 cells were infected with AdHBV1.3 adenoviruses for 5 days and then transfected with a control or YTHDF2 shRNA lentivial for another 3 days

value: infected with HBV virus and transfected with YTHDF2 shRNA lentivirus

tag: ip antibody


title: HepG2_shYTHDF2.rep3_input


title: M medium (differentiation medium), well plate, Day28, rep 2


title: HepG2_shYTHDF2.rep1_input


title: HepG2_shControl.rep3_IP

value: infected with HBV virus

value: m6A antibody IP


title: P0_H3K27me3_2


title: HepG2_shControl.rep3_input


title: P medium (proliferation medium), well plate, Day28, rep 2

value: WT


title: P0_H3K27me3_1


title: Bulk_72h_sorted_J2-46049

city: Vancouver

first: Francis

middle: C

last: Lynn

state: BC

address: 950 28th Ave W

department: Surgery

institute: University of British Columbia

data_processing:
<scRNA-seq> Following sequencing, FASTQ files were generated from the raw sequencing data using cellranger mkfastq (10x Genomics), after which they were mapped to the build 38 of the Genome Reference Consortium human genome (GRCh38) to generate single-cell gene counts using cellranger count (10x Genomics). Low quality score sequences were filtered out. Cellranger aggr (10x Genomics) was used to combine data from multiple samples and ensure that all libraries had the same sequencing depth.
The Seurat R package (4.0.2 version), executed with default parameters unless otherwise specified, was used for quality control, filtering, data preprocessing, scaling and normalization of scRNA-seq raw data. High quality cells with mitochondrial gene content lower than 5%, feature total number higher than 200 and lower than 4000 and RNA count number higher than 2500 were extracted. The top 5000 most variable genes were selected based on their average expression and dispersion, and used to reduce the dimensionality of the data through principal component (PC) analysis. The top 50 PCs were selected for clustering. tSNE (REF) were applied to the selected PCs for visualization of the data. Cluster-specific markers were identified using the Seurat’s FindAllMarkers function. Differentially expressed genes between two clusters were identified using the Seurat’s FindMarkers function with both the parameters min.pct and logfc.threshold set to 0.2.
pySCENIC (0.11.2 version), executed with default parameters (SCENICprotocol: A Scalable SCENIC Workflow for Single-Cell Gene Regulatory Network Analysis n.d.), was applied on the pre-processed scRNA-seq data to identify potential important TFs and their targets. First, potential modules of TFs and targets were identified based on their co-expression using GRNBoost2 (Moerman et al. 2019). Then, each co-expression module underwent cis-regulatory motif analysis using RcisTarget to filter out indirect targets without motif support and retain modules with significant motif enrichment. These RcisTarget-processed modules are referred to as “regulons”. Next, the activity of each regulon in each cell was computed using AUCell (Aibar et al. 2017). The resulting AUC scores were further processed using SCopeLoomR (0.11.0 version) (SCopeLoomR: R Package (compatible with SCope) to Create Generic .loom Files and Extend Them with Other Data E.g.: SCENIC Regulons, Seurat Clusters and Markers, n.d.) and scFunctions (0.0.0.9 version) (Wuennemann n.d.) for downstream analysis and visualization.
<Bulk RNAseq> Transcripts were quantified using salmon (1.4.0 version) (Patro et al. 2017). and annotated using GENCODE (version 36) (protein-coding transcripts only). Differential expression analysis was performed using the limma (3.48.1 version) (Ritchie et al. 2015) and edgeR (3.34.0 version) (Robinson, McCarthy, and Smyth 2010) R packages. A gene was considered as differentially expressed if the absolute change in log2-fold expression was >2, and significant (the FDR was controlled at 5% using the BH method).
Genome_build: GRCh38

source_name: hESC-derived definitive endoderm cells

growth_protocol: H1 hESCs were differentiated using the protocol published by Nair et al. (Nair et al. 2019). For planar culture (Protocol 1), hESCs were plated onto Geltrex-coated 12-well plates at a density of 5x10^5 in StemFlex medium with 1 mM Y-27632. Differentiations began 24h post-seeding. Cells were treated with RPMI (Gibco) containing 0.2% FBS, 1:5,000 ITS (Gibco), 100 ng/ml Activin A and 3 µM CHIR99021 on day 1. On day 2-3, cells were treated with RPMI containing 0.2% FBS, 1:2,000 ITS and 100 ng/ml Activin A. Morphogens were replaced for specific experiments as described in the manuscript.

extract_protocol:
For scRNA-seq, the 10x Genomics ChromiumTM controller and Single Cell 3’ Reagent Kits v2 (Pleasanton, CA, USA) were used to generate single cell libraries. Briefly, cells were counted following FACS and cell suspensions were loaded for a targeted cell recovery of 1000-5000 cells per channel.The microfluidics platform was used to barcode single cells using Gel Bead-In-Emulsions (GEMs). For bulk RNA-seq, RNA was extracted using Trizol (Thermo).
For scRNA-seq, RT is performed within GEMs, resulting in barcoded cDNA from single cells. The full length, barcoded cDNA is PCR amplified followed by enzymatic fragmentation and SPRI double sided size selection for optimal cDNA size. End repair, A-tailing, Adaptor Ligation, and PCR are performed to generate the final libraries that have P5 and P7 primers compatible with Illumina sequencing. The libraries were pooled and sequenced using an Illumina NextSeq500 platform with a 150 cycle High Output v2 kit in paired-end format with 26 bp Read 1, 8 bp I5 Index, and 85 bp Read 2. For bulk RNA-seq, SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara) was used to generate cDNA libraries for sequencing. The libraries were pooled and sequenced using an Illumina NextSeq500 platform with a 150 cycle High Output v2 kit in single-end format with Read 1: 85 cycle, Read 2: 0 cycle, and single index: 8 cycle. Following sequencing, FASTQ files were generated from the raw sequencing data using the BaseSpace Onsite (Illumina).

tag: Stage

value: JNJ+CHIR-JNJ-JNJ

value: H1 hESC line

value: Sorted DE


title: M medium (differentiation medium), scaffold, Day28, rep 1

value: Primary cells isolated from the intestinal muscle layers

value: 3D culture

value: M medium

value: Day 28


title: HepG2_shControl.rep2_input


title: HepG2_shControl.rep2_IP


title: Intestinal muscle strips, rep 1

value: positive control

value: Native tissue


title: E16_foxp1_cko_2

data_processing:
Overlapping reads were grouped by BBTools (v38.34) clumpify script, specified to remove duplicate reads and optical duplicates at a max distance of 12000. Illumina adapters were trimmed with cutadapt (v2.8) using a minimum read length of 20 and minimum overlap between read and adaptor of 6, then aligned to mouse Ensembl genome annotation (release 102) with STAR (v2.7.6a) in two pass mode. Reads were assigned to the target that had the largest overlap and uniquely aligned, reverse stranded, reads were counted with featureCounts (v1.5.1). Genes with fewer than 5 counts in every sample were eliminated and differentially expressed genes were identified using DESeq2 (v1.32.0). In addition to the variable of interest: genotype, the additional variable: sex, was included in the DESeq2 design formula to mitigate its effect on the results.
Supplementary files format and content: foxp1_counts.txt is a tab deliminated file containing read counts for each sample.
Supplementary files format and content: mouse_retina_E16_foxp1_cKO_vs_contol.txt is a tab deliminated table containing DESeq2 results.
Assembly: mm10

extract_protocol:
For Foxp1 bulk RNA-seq analysis, retinas were dissected freshly at e16.5. Left and right eyes were combined, and total RNA was isolated using RNeasy Plus Mini Kit (Qaigen 74134) according to manufacturer’s protocol. Three biological replicates of each: Six3-Cre; Foxp1fl/fl animals and Foxp1fl/fl controls, all from the same litter, were used for RNA sequencing.
Library generation, sequencing, and alignment were performed by the Huntsman Cancer Institute High-Throughput Genomics and Bioinformatics Analysis Shared Resource. Total RNA concentration and quality were measured by RNA ScreenTape Assay (Agilent Technologies, 5067-5576, 5067-5577). All samples had a RIN value of 10. Total RNA samples (5-500 ng) were hybridized with NEBNext rRNA Depletion Kit v2 (Human, Mouse, Rat) (E7400) to substantially diminish rRNA from the samples. The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760L) was used to generate sequencing libraries which were qualified by D1000 ScreenTape Assay (Agilent Technologies, 5067-5582, 5067-5583) and quantified with a Kapa Library Quant Kit (Kapa Biosystems, KK4824). Samples were sequenced on an Illumina NovaSeq 6000 instrument using the NovaSeq XP workflow (20043131).  A 150 x 150 cycle paired end sequence run was performed using a NovaSeq 6000 S4 reagent Kit v1.5 (20028312).

value: retina

value: embryonic day 16.5

value: Foxp1 fl/fl, Six3-Cre

tag: Sex

value: male


title: E16_foxp1_cko_3


title: Bulk_72h_sorted_BLoA2-46053

value: BRD+LoAA+CHIR-BRD+LoAA-BRD+LoAA


title: Bulk_72h_sorted_BLoA1-46052


title: HepG2_shControl.rep1_IP

value: infected with HBV virus


title: E16_foxp1_cko_1

value: female


title: E16_control_3

value: Foxp1 fl/fl


title: E16_control_2


title: HepG2_IP

data_processing:
Illumina Casava1.8 software used for basecalling.
Trimmomatic was used to filter raw reads, and then clean reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing
The de-duplicated consensus sequences were mapped to the reference genome using STAR software (version 2.5.3a) with default parameters.
The exomePeak (Version 3.8) software was used for peak calling.
Assembly: homo sapiens Ensembl release-101
Supplementary files format and content: .txt files include gene expression and methylation level

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0.
Poly(A) RNA was purified from total RNA using Dynabeads Oligo (dT) by two rounds of purification. The poly(A) RNA used in immunoprecipitation reactions with anti-YTHDF2 (abcam,ab220163) as IP. The IP/input RNA were reverse-transcribed to create the final cDNA library by using Stranded mRNA Library Prep Kit for Illumina following the manufacturer’s instruction.

value: anti-YTHDF2 (abcam,ab220163)


title: Bulk_72h_sorted_B1-46050

value: BRD+CHIR-BRD-BRD

value: H1 hESC line


title: P medium (proliferation medium), well plate, Day28, rep 1

value: Primary cells isolated from the intestinal muscle layers

value: WT

value: 2D culture

value: P medium


title: HepG2_input


title: HepG2_shControl.rep1_input


title: RNA_KO_St2

city: Okazaki

first: Akira

last: Yamashita

address: Nishigonaka 38, Myodaiji

country: Japan

institute: National Institute for Basic Biology

data_processing:
Basecalling with Illumina Casava bcl2fastq2 (v2.20) program.
3' adapter trimming with Fastp.
Library sorting based on sample barcode sequence with custom script.
Random barcode trimming with custom script.
After removing noncoding RNA-mapped reads, the remaining reads were aligned to the mouse genome with STAR v2.7.0a.
Read quantitation using custom scripts. In RNA-seq, the reads from two raw files were summed for analysis.
Two replicates from 4 mice were analyzed in each group (each replicate consists of samples from two mice).
Assembly: mm10
Supplementary files format and content: Text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts

source_name: Amygdala

growth_protocol: To generate PrLD-deletion mice (Ilf3ΔPrLD/ΔPrLD mice), a stop codon at the 5' end of exon 20 in the Ilf3 gene was introduced by replacing c.2104C with T using CRISPR/Cas9.

extract_protocol:
The amygdala was isolated from the brains of control and stressed mice and quickly frozen in liquid nitrogen. The samples were lysed in ice-cold lysis buffer.
For RNA-Seq, TruSeq Stranded mRNA Library Prep Kit (Illumina) was used. For ribosome profiling, RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, and PCR amplification were conducted.

treatment_protocol: The mice in the stress group were placed in a 50 mL conical polypropylene centrifuge tube with holes for breathing and soaked in water at a level where the nose was not submerged for 3 hours a day during the light cycle over 14 days.

value: Amygdala

value: Ilf3 deltaPrLD/deltaPrLD

value: chronic stress


title: RNA_KO_St1


title: Bulk_72h_sorted_A2-46047

value: AA+CHIR-AA-AA

value: Sorted DE


title: RNA_WT_St1

value: Ilf3+/+ (wild-type)


title: E16_control_1

value: retina

value: embryonic day 16.5


title: Bulk_72h_sorted_J1-46048

value: JNJ+CHIR-JNJ-JNJ


title: Bulk_72h_sorted_A1-46046


title: Bulk_24h_unsorted_BwoC2-46057

value: BRD

value: Unsorted


title: Apc Min/+ mice, lamina propria, gavage atorvastatin, replicate 2

city: Shanghai

first: Ji-Xuan

last: Han

address: 145 Middle Shandong Road

institute: Renji Hospital, Shanghai Jiao-Tong University School of Medicine

data_processing:
The raw data was handled by Perl and data quality was checked by FastQC v0.11.2
Clean reads were aligned to the mouse genome from NCBI using Bowtie
The expression of the transcript was calculated by FPKM using Perl
Differentially expression transcripts were determined using the MA-plot-based method with Random Sampling (MARS) model in the DEGseq package
Function and signaling pathway enrichment analysis using GO and KEGG database
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

source_name: Colon

growth_protocol: Mice were housed in laminar flow cabinets under specific pathogen-free conditions with food and water provided ad libitum

extract_protocol:
Lamina propria cells were isolated from mice colon and total RNA was extracted by RNAiso Plus according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Adult male Apc Min/+ mice (5–6 weeks) were administered atorvastatin (20 mg/kg) or vehicle control (2% Tween 80) by oral gavage every other day.

value: Colon

value: Lamina propria cells

value: Apc Min/+

value: Atovastatin (20 mg/kg)


title: Apc Min/+ mice, lamina propria, gavage atorvastatin, replicate 1


title: RNA_KO_C2

value: control condtion


title: Apc Min/+ mice, lamina propria, gavage atorvastatin, replicate 3


title: RNA_KO_C1


title: Bulk_6h_unsorted_BwoC1-46054

value: H1 hESC line


title: Bulk_72h_sorted_B2-46051

value: BRD+CHIR-BRD-BRD


title: Bulk_6h_unsorted_BwoC2-46055


title: M medium (differentiation medium), well plate, Day28, rep 1

value: Primary cells isolated from the intestinal muscle layers

value: WT

value: 2D culture

value: M medium

value: Day 28


title: Apc Min/+ mice, lamina propria, gavage control, replicate 3

value: Vehicle control (2% Tween 80)


title: Apc Min/+ mice, lamina propria, gavage control, replicate 2


title: Bulk_24h_N2-38039


title: RNA_WT_St2

value: Amygdala

value: Ilf3+/+ (wild-type)

value: chronic stress


title: Apc Min/+ mice, lamina propria, gavage control, replicate 1


title: RNA_WT_C1


title: Bulk_24h_JC2-38045

value: JNJ+CHIR

value: Unsorted


title: Bulk_24h_unsorted_BwoC1-46056

value: BRD


title: Ribo_KO_St2

data_processing:
Basecalling with Illumina Casava bcl2fastq2 (v2.20) program.
3' adapter trimming with Fastp.
Library sorting based on sample barcode sequence with custom script.
Random barcode trimming with custom script.
After removing noncoding RNA-mapped reads, the remaining reads were aligned to the mouse genome with STAR v2.7.0a.
Read quantitation using custom scripts. In RNA-seq, the reads from two raw files were summed for analysis.
Two replicates from 4 mice were analyzed in each group (each replicate consists of samples from two mice).
Assembly: mm10
Supplementary files format and content: Text files contain three columns: 1. transcript name; 2. CDS region (nt) used for read counting; 3. read counts
Library strategy: Ribosome profiling

value: Ilf3 deltaPrLD/deltaPrLD


title: Ribo_KO_St1


title: Apc Min/+ mice, gavage atorvastatin, replicate 3

extract_protocol:
Epithelial Cells were isolated from mice colon and total RNA was extracted by RNAiso Plus according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Colon

value: Epithelial cells

value: Apc Min/+

value: Atovastatin (20 mg/kg)


title: Bulk_24h_JC1-38044

value: H1 hESC line


title: Ribo_WT_St2


title: Apc Min/+ mice, gavage atorvastatin, replicate 1


title: Ribo_WT_St1


title: Bulk_24h_C1-38040

value: CHIR


title: Bulk_24h_C2-38041


title: Apc Min/+ mice, gavage control, replicate 3


title: RNA_WT_C2

value: control condtion


title: Bulk_24h_BC2-38047

value: BRD+CHIR


title: Ribo_KO_C2


title: Ribo_KO_C1


title: Ribo_WT_C2


title: Bulk_24h_AC2-38043

value: AA+CHIR


title: Bulk_24h_BC1-38046


title: Th17 cells, GSK805+ILA, biological replicate 3

source_name: Spleen

growth_protocol: Naïve CD4+ mouse T cells were magnetically isolated, cultured in RPMI 1640 medium supplemented with CytoBox Th17, and activated with CD3/CD28 activation cocktail

extract_protocol:
Total RNA was extracted by RNAiso Plus according to the manufacturer's instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Cells were treated with vehivle control or ILA (200 uM) or GSK805 (0.5 uM) or combined

value: Spleen

value: Navie CD4+ T cells

value: WT

value: Th17 differentiation+GSK805+ILA


title: Apc Min/+ mice, gavage control, replicate 1

value: Vehicle control (2% Tween 80)


title: Ribo_WT_C1

value: Amygdala

value: Ilf3+/+ (wild-type)


title: Th17 cells, GSK805+ILA, biological replicate 2


title: Bulk_24h_N1-38038

value: Unsorted


title: Apc Min/+ mice, gavage atorvastatin, replicate 2

value: Colon


title: Th17 cells, GSK805+ILA, biological replicate 1


title: Th17 cells, GSK805, biological replicate 3

value: Th17 differentiation+GSK805


title: Th17 cells, GSK805, biological replicate 2


title: Apc Min/+ mice, gavage control, replicate 2

value: Epithelial cells

value: Apc Min/+


title: DAtfA-DAtfB MSB treated mycelium 2

city: Debrecen

first: Tamas

last: Emri

address: Egyetem ter 1

country: Hungary

institute: University of Debrecen

data_processing:
The FastQC package (http://www.bioinformatics.babraham.ac.uk/projects/fastqc) was used for quality control.
Reads were aligned to the genome of A nidulans FGSC A4 with hisat2 (version 2.1.0).
DESeq2 (version 1.24.0) (Love et al. 2014) was used to determine differentially expressed genes. Since conidial samples were originated in two separate experiments, the batch effect was taken into consideration during the identification of differentially expressed genes in this case.
RPKM values were calculated with the edgeR package (“rpkm” function).
Assembly: genome: http://www.aspergillusgenome.org/download/sequence/A_nidulans_FGSC_A4/current//A_nidulans_FGSC_A4_version_s10-m04-r14_chromosomes.fasta.gz; gff3:   http://www.aspergillusgenome.org/download/gff/A_nidulans_FGSC_A4/A_nidulans_FGSC_A4_version_s10-m04-r14_features_with_chromosome_sequences.gff.gz
Supplementary files format and content: Excel file includes count and RPKM values for each Sample

organism: Aspergillus nidulans

source_name: mycelium

growth_protocol: Barratt's agar plates, 37 °C

extract_protocol:
Total RNA was isolated from lyophilized samples with Trisol reagent.
RNA libraries for RNA-seq were prepared using TruSeq RNA Sample preparation kit (Illumina) following manufacturer's protocols.

treatment_protocol: 0.04 Mm menadion sodium bisulfite (MSB) treated and untreated

value: mycelium

value: DAtfB DAtfB double mutant

value: MSB treated

tag: batch

value: batch 3


title: DAtfA-DAtfB MSB treated mycelium 3

tag: tissue


title: Th17 cells, GSK805, biological replicate 1


title: Bulk_6h_N1-33033

value: H1 hESC line


title: DAtfA-DAtfB untreated mycelium 3

value: untreated


title: Th17 cells, ILA, biological replicate 3

value: Spleen

value: Navie CD4+ T cells

value: Th17 differentiation+ILA


title: DAtfA-DAtfB untreated mycelium 1


title: Th17 cells, ILA, biological replicate 2

value: WT


title: Bulk_6h_JC2-33040

value: JNJ+CHIR


title: Bulk_6h_C1-33035

value: CHIR


title: Bulk_6h_C2-33036

value: Unsorted


title: Bulk_6h_JC1-33039


title: DAtfA-DAtfB untreated mycelium 2


title: DAtfB MSB treated mycelium 2

value: DAtfB mutant


title: DAtfB MSB treated mycelium 1


title: Bulk_24h_AC1-38042

value: AA+CHIR


title: Th17 cells, ILA, biological replicate 1


title: Bulk_6h_BC1-33041

value: BRD+CHIR


title: Bulk_6h_BC2-33042


title: Th17 cells, vehicle control, biological replicate 2

value: Th17 differentiation


title: Th17 cells, vehicle control, biological replicate 3


title: Bulk_6h_AC2-33038


title: DAtfA-DAtfB MSB treated mycelium 1

value: mycelium


title: DAtfB untreated mycelium 3


title: Bulk_6h_N2-33034


title: Th17 cells, vehicle control, biological replicate 1


title: Bulk_6h_AC1-33037


title: DAtfB untreated mycelium 2


title: LPS_CLA_6

city: Wuhan, Hubei

first: Minghao

last: Dong

address: No. 1095, Jiefang Avenue

institute: Tongji Hospital

data_processing:
Illumina Casava 1.7 software used for basecalling.
To get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2  (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4[3] with “-rna-strandness RF” and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach.
Assembly: Ensembl_release104
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: Microglia in primary culture

growth_protocol: Primary microglia were isolated from the brain of neonatal C57BL/6J mice (aged 1-3 days) . In brief, mixed glia cells were obtained from cerebral cortices, and cultured in Dulbecco’s modified Eagle’s medium (DMEM)/F12 medium (HyClone, Logan, UT, USA) with 20% fetal bovine serum (FBS) for the first three days. And the medium was changed to high glucose DMEM medium with 20% FBS at the 4th day, refreshed every 3 days. After being cultured for 8-10 days, microglia were collected by shaking the mixed glia at 220 rpm for 1 h at 37°C.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
After total RNA was extracted, eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China).

treatment_protocol: Microglia were transfected using lipofectamine3000(Thermofisher) with 50nM Atg5 siRNA and relevant NC siRNAs for 48h, followed by treatments. Microglia were stimulated with 100ng/ml LPS (Sigma), 10nM BAF A1 (MCE), 50nM CLA (Cayman), 10nM T0070907 (Selleck) for 24 hours in combination or respectively.  After 24 hours treatment, the supernatants were collected.

value: Microglia

value: LPS+CLA


title: DAtfB untreated mycelium 1

value: batch 3


title: LPS_CLA_5


title: DAtfB MSB treated mycelium 3

value: MSB treated


title: DAtfA MSB treated mycelium 3

value: DAtfA mutant


title: DAtfA MSB treated mycelium 2


title: LPS_CLA_4


title: Single_cell_36h

source_name: hESC-derived primitive streak cells

value: AA+CHIR-AA

value: H1 hESC line


title: DAtfA MSB treated mycelium 1


title: LPS_CLA_2


title: DAtfA untreated mycelium 3

value: untreated


title: LPS_CLA_1


title: G523_DMSO 3

data_processing:
Samples were pseudoaligned to the human transcriptome (GRCh38.rel79) using kallisto, and differential analysis was performed using sleuth
Genome_build: hg38

source_name: glioblastoma G523

growth_protocol: Grown in serum-free conditions on laminin-PLO coated plates with FGF and EGF

extract_protocol:
Cells were harvested using Accutase and PBS; RNA was extracted from 1 million cells using the RNEasy Mini Kit (Qiagen) as per manufacturer instructions. RNA was quantified using the Nanodrop.
Libraries were constructed at the Center for Health Genomics and Informatics using the NEBNext Ultra II Directional RNA Library prep kit (New England Biolabs) with ribosomal RNA depletion
Samples were sequenced on a NextSeq 500 for 150 cycles  (paired end; 2x75 bp)

treatment_protocol: 200 nM MI-3 or equivalent volume of DMSO x 7 days

value: DMSO


title: G523_DMSO 2


title: DAtfA untreated mycelium 2


title: G523_DMSO 1


title: DAtfA untreated mycelium 1


title: G523_MI3 3


title: LPS_siATG5_4


title: G523_MI3 2


title: LPS_siATG5_5


title: Reference strain MSB treated mycelium 3

value: reference strain


title: LPS_siATG5_3


title: G523_MI3 1


title: LPS_siATG5_2


title: Reference strain MSB treated mycelium 2


title: Single_cell_Meso_72h

source_name: hESC-derived mesoderm cells

value: STEMdiff Mesoderm Induction


title: Single_cell_Endo_72h


title: G523_shH2AFY2bB [RNA-seq KD]

extract_protocol:
Cells were harvested using Accutase and PBS; RNA was extracted from 1 million cells using the RNEasy Mini Kit (Qiagen) as per manufacturer instructions. RNA was quantified using the Nanodrop.
Libraries were constructed at the Center for Health Genomics and Informatics using the NEBNext Ultra II Directional RNA Library prep kit (New England Biolabs) with ribosomal RNA depletion
Samples were sequenced on a NextSeq 500 for 150 cycles  (single-end; 1x75bp)

treatment_protocol: 2 ug/mL doxycycline x 7 days

tag: genotype/variation


title: LPS_CLA_3


title: LPS_dNC_3

value: LPS+dNC


title: G523_shH2AFY2bA [RNA-seq KD]


title: Reference strain untreated mycelium 3

tag: genotype


title: LPS_siATG5_1

tag: treatment


title: LPS_dNC_2


title: Reference strain untreated mycelium 2


title: Reference strain MSB treated mycelium 1


title: G523_shH2AFY2aA [RNA-seq KD]


title: Reference strain untreated mycelium 1


title: G523_ScrB [RNA-seq KD]

value: Scr


title: G523_shH2AFY2aB [RNA-seq KD]


title: DAtfA-DAtfB MSB treated conidium 2

source_name: conidium

value: conidium

value: DAtfB DAtfB double mutant

value: batch 1


title: G523_ScrA [RNA-seq KD]


title: LPS_BAFA1_5

value: LPS+Baf A1


title: LPS_BAFA1_3

value: Microglia


title: LPS_BAFA1_4


title: WGBS, Ws, biol rep 2

city: Bloomington

first: Craig

middle: S.

last: Pikaard

state: Indiana

address: 915 E. Third Street

department: Department of Biology and Department of Molecular and Cellular Biochemistry

institute: Howard Hughes Medical Institute, Indiana University

data_processing:
To analyze the whole-genome bisulfite sequencing data, 3’ adapters were removed by Cutadapt v1.18 with the following options: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -m 15 -q 20.
Trimmed reads were aligned to the Arabidopsis TAIR10 genome by bsmap2 with the following options: -w 100 -n 1 -p 3 -v 0.08. Methylation ratios at individual cytosine sites were calculated using methratio.py.
Arabidopsis genome was binned into 100 nt windows with CG, CHG, and CHH (where H represents any nucleotide except G) methylation calculated individually. To avoid regions with low sequencing coverage, only bins with at least 4 cytosines that were each covered by no less than 4 reads were included in this analysis.
Bins that have at least 10% less CHH methylation in the two independent replicates of ago4-4 compared to the two independent replicates of wild-type Ws ecotype plants were defined as differentially methylated bins.
Differentially methylated bins within 200 bp from each other were merged into differentially methylated regions (DMRs). Cytosine methylation levels at methylated regions were caculated.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files include chromosome, coordinates of cytosines, strandedness, sequence context, methylation ratio, effective total C counts, total C counts, total G counts on the reverse strand, total G+A counts on the reverse strand, lower bound of 95% confidence interval of methylation ratio, and upper bound of 95% confidence interval of methylation ratio

organism: Arabidopsis thaliana

source_name: Inflorescence

growth_protocol: All Arabidopsis thaliana plants were grown at 21 C with 16 h light and 8 h dark in a growth room

extract_protocol:
For each library, genomic DNA was extracted from the inflorescence tissues of a single plant using Nucleon Phytopure DNA Extraction Kit (Cytiva).
Whole-genome bisulfite sequencing libraries were prepared using Perkin Elmer’s Nextflex Bisulfite-Seq Kit per the manufacturer’s instruction. Approximately 500 ng DNA fragments were end-repaired, 3’ adenylated, and ligated with adapters. Unmethylated cytosines in the adapter-ligated DNA were chemically converted by EZ DNA Methylation-Gold Kit (Zymo Research Corp.) following the manufacturer’s instruction. The CT converted products were purified and subjected to 12 cycles of PCR amplification before single-ended Illumina sequencing.

value: Inflorescence

value: wild-type


title: G523_shH2AFY2cB [ATAC-seq]

data_processing:
Reads were aligned to hg38 using bwa mem
samtools was used to remove the mitochondrial and Y chromosome reads, and reads mapping to genome blacklists
Duplicates were removed using picard.
Peak assignments were generated using macs2 with the following parameters:  -g hs -q 0.05 --shift -100 --extsize 200 --nomodel -B --keep-dup all
Differential peak calls were performed by generating a pileup of counts of all consensus peaks from all samples, transforming the counts to counts per million using edgeR, and running these normalized counts through DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: TDF: fold enrichment pileup generated by macs2; narrowPeak - peak calls and quality metrics from macs2

extract_protocol:
Cells were harvested using Accutase and PBS
50,000 cells were harvested fresh from culture from two biological replicates, lysed on ice, spun at 4 C, and treated with Tn5 transposase (Illumina) for 30 minutes at 37 C. Libraries were amplified using the NebNext HiFi polymerase mastermix (New England Biolabs) and standard Illumina Nextera primers, and DNA was purified using the MinElute kit (Qiagen).
Sequencing was performed on a NextSeq 500 using 150 cycles of paired end 75 bp sequencing


title: G523_shH2AFY2cA [ATAC-seq]


title: LPS_BAFA1_2


title: DAtfA-DAtfB untreated conidium 3

value: batch 2


title: G523_shH2AFY2aB [ATAC-seq]


title: WGBS, Ws, biol rep 1


title: WGBS, ago4-4/AGO4, biol rep 2


title: DAtfA-DAtfB MSB treated conidium 1

value: MSB treated


title: DAtfA-DAtfB untreated conidium 2


title: WGBS, ago4-4/AGO4, biol rep 1


title: WGBS, ago4-4/AGO4-D742A, biol rep 2


title: LPS3

value: LPS


title: G523_ScrB [ATAC-seq]


title: LPS_dNC_1


title: G523_shH2AFY2aA [ATAC-seq]


title: DAtfB MSB treated conidium 3

value: DAtfB mutant


title: LPS2


title: DAtfA-DAtfB untreated conidium 1

value: untreated


title: G523_ScrA [ATAC-seq]


title: DAtfB MSB treated conidium 2


title: DAtfA-DAtfB MSB treated conidium 3


title: WGBS, ago4-4/AGO4-D742A, biol rep 1


title: LPS1


title: DAtfB MSB treated conidium 1


title: WGBS, ago4-4, biol rep 2


title: WGBS, ago4-4, biol rep 1


title: LPS_BAFA1_1


title: DAtfB untreated conidium 3


title: sRNA-seq, slicing-defective AGO4 immunoprecipitation, biol rep 2

data_processing:
The 3’ adapters were removed by Cutadapt v1.18 with the following options: -a TGGAATTC --discard-untrimmed -e 0 -m 8 -O 8.
Trimmed reads were aligned to the Arabidopsis thaliana TAIR10 genome using ShortStack v3.8 allowing no more than 2 mismatches.
Small RNA clusters were determined by analyzing two immunoprecipitated RNA sequencing replicates for both wild-type and slicing-defective AGO4 by the default setting of ShortStack.
The alignment files (BAM format) were loaded in JBrowse configured with ‘Small RNA plugin’ with modifications to allow customized small RNA alignment visualization.
Assembly: TAIR10
Supplementary files format and content: Tab-delimited text files include mapped RNA sequences, lengths, and raw counts

extract_protocol:
AGO4 proteins were immunoprecipitated from inflorescence tissues of transgenic plants stably expressing FLAG-tagged wild-type AGO4 or slicing-defective AGO4 in ago4-4 mutant background, or mock-IPed from non-transgenic wild-type plants. One gram of inflorescence tissues was ground to fine powder in liquid nitrogen and resuspended in 6 mL extraction buffer [50 mM Tris-HCl (pH 7.9), 75 mM sodium chloride, 5 mM magnesium chloride, 10% glycerol, 0.05% IGEPAL, 1 mM DTT, 1 mM PMSF and 1X plant protease inhibitor (Millipore Sigma)]. The homogenate was subjected to centrifugation at 16,000 g for 20 minutes at 4 ˚C. The supernatant was collected, filtered through CellTrics 30 um strainer (Sysmex), and subject to the second round of centrifugation at 16,000 g for 20 minutes at 4˚C. The supernatant was incubated with 50 μL of anti-FLAG M2 agarose resin (Sigma) for 3 hours in a rotating mixer at 4 ˚C, followed by 4 washes, each with 1 mL of extraction buffer without plant protease inhibitor. The resin was resuspended to a final volume of 100 μL. 25 μL of the slurry containing immunoprecipitated AGO4 was treated with 0.8 unit of proteinase K (New England BioLabs) followed by RNA extraction using TE saturated phenol/chloroform/isoamyl alcohol (pH 4.5). The RNA in the aqueous phase was ethanol precipitated, washed with 70% ethanol, and resuspended in nuclease-free water.
The libraries were prepared with Illumina’s TruSeq Small RNA Library Prep Kit per manufacturer’s instruction.


title: Female Hypoxia-3

city: Philadelphia

first: Jaslyn

last: Johnson

state: Pennsylvania

address: 3500 N. Broad Street

department: Cardiovascular

institute: Lewis Katz School of Medicine, Temple University

data_processing:
Raw data quality was evaluated with FastQC, reads were mapped onto Mus musculus GRCm39 reference genome with Salmon Software. Genome is available on GENCODE. Quant files were imported, and transcript-level abundance was estimated with R package Ttximport, 39210 genes were mapped.
Assembly: GRCm39
Supplementary files format and content: abundance, counts and length of genes

source_name: Heart

extract_protocol:
Total RNA was extracted from frozen cardiac tissue using miRNeasy Mini Kit (Qiagen 217004) following the manufacturer’s instructions.
The reagent used for RNA sequencing was NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (Cat #E4720L). Stranded mRNA-seq library:  100-1000ng total RNAs from each sample were used to make library according to the product guide of stranded mRNA library kit.

value: Heart

tag: gender

value: Female

value: Hypoxia


title: Female Hypoxia-2


title: Female Normoxia-3

value: Normoxia


title: Female Hypoxia-1


title: sRNA-seq, wild-type AGO4 immunoprecipitation, biol rep 2


title: DAtfB untreated conidium 2


title: DAtfB untreated conidium 1


title: DAtfA MSB treated conidium 3

value: DAtfA mutant


title: sRNA-seq, mock immunoprecipitation, biol rep 2


title: Female Normoxia-2


title: Female Normoxia-1


title: N2_2

first: qifei

last: liang

address: Medical building, 1239 Siping Road

department: Medical college

institute: Tongji University

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
GO and KEGG enrichment analysis of differentially expressed genes was tested by the clusterProfiler R package.
Assembly: WBcel235
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Caenorhabditis elegans

source_name: whole body

extract_protocol:
Total RNA was isolated using TRIzol (Invitrogen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: whole body

tag: developmental stage

value: wild type


title: glna_2

value: glna knockout


title: N2_3


title: glna_1


title: DAtfA MSB treated conidium 2

value: conidium

value: batch 1


title: sRNA-seq, slicing-defective AGO4 immunoprecipitation, biol rep 1

value: Inflorescence


title: Male Hypoxia-3

value: Male

tag: strain


title: sRNA-seq, wild-type AGO4 immunoprecipitation, biol rep 1


title: glna_3


title: BVD013B

first: Ashenafi

last: Bulle

state: Missouri

address: 660 S Euclid Ave

department: Molecular Oncology

institute: Washington University School of Medicine

data_processing:
Basecalling with Illumina RTA 1.9
Demultiplexing with Illumina bcl2fastq2
Fastq files were combined and aligned with STAR 2.0.4b
Gene counts quantitated with Subread:featureCount 1.4.5 with CPM and RPKM transformations added with custom Rscripting.
Assembly: Ensembl GRCh38.76
Supplementary files format and content: Gene counts with CPM and RPKM in tab-delimitted text format

source_name: Patient tumor

extract_protocol:
RNA was harvested using Trizol reagent. mRNA is extracted form total RNA using a Dynal mRNA Direct kit.
Ribo-Zero

treatment_protocol: Samples were collected from Pancreatic cancer patients before and after treatment with Ulixertinib (300ng/uL)

value: Patient tumor

tag: diagnosis

value: pancreatic cancer

value: Yes


title: DAtfA MSB treated conidium 1

value: MSB treated


title: N2_1

value: untreated


title: Male Hypoxia-2

value: Heart


title: DAtfA untreated conidium 3

value: batch 2


title: BVD013A

value: No


title: Male Hypoxia-1

value: Hypoxia


title: DAtfA untreated conidium 2

value: DAtfA mutant


title: BVD011B


title: DAtfA untreated conidium 1


title: BVD011A


title: Male Normoxia-3

value: Normoxia


title: Male Normoxia-2


title: Reference strain MSB treated conidium 3

value: reference strain


title: Male Normoxia-1


title: BVD010A


title: BVD010B


title: BVD009B


title: Reference strain MSB treated conidium 2


title: Reference strain untreated conidium 3


title: sRNA-seq, mock immunoprecipitation, biol rep 1

value: wild-type


title: BVD009A


title: P12#3

city: Be'er Sheva

first: Omri

last: Koren

address: David Ben Gurion Blvd 1

department: The Shraga Segal dept. of Microbiology, Immunology, and Genetics

country: Israel

institute: Ben-Gurion University of the Negev

data_processing:
Base calling- Illumina's bcl2fastq v2.17
Filter contaminants (Bowtie 2) - v2.2.5 Partek. Filter out rDNA,mtrDNA
Alignment: STAR v2.5.3a , default parameters, reference index: mm10 - Ensembl Transcripts release 92
Quantification to annotation model (Partek E/M)) reference index: mm10 - Ensembl Transcripts release 92
Differential-expression analysis DEseq2 v3.5
Assembly: mm10 - Ensembl Transcripts release 92
Supplementary files format and content: Normalized counts (after DEseq run)

source_name: Hematopoietic Stem Cells

growth_protocol: Mice were kept in the specific pathogen free (SPF ) unit at the Ben-Gurion University; all experiments were performed according to ethical committee approval and under local and state regulations, protocols IL01-01-2017D and IL29-05-2021C. Leukemia lines were previously described [Keinan et al; Cell Death & Disease (2021) 12: 193].

extract_protocol:
Treated mice where euthanized, femur and tibia extracted, crashed in sample medium (PBSx1, EDTA 2mM, serum 2%) and loaded on Histopaq1083. Antibodies of Biolegend: CD45.1 APC, CD45.2 pacific blue, Mac1 PE-Cy7, B220 APC-Cy7, CD3e PE, Lineage-PacificBlue (Including- anti Ter119, Mac1, Gr1, CD3e, CD4, CD8 and B220), c-Kit Alexa780 , Sca1- APC , CD150-PEcy7 , CD48- percp cy5.5 , CD9-APC, CD34-PE, CD84-PE. Cells were stained on ice for 1 hr, and washed. Flow cytometry analy-sis of the reporter expression frequencies (ZsGreen+), and the surface markers expression, was performed on the Gallios Flow Cytometer (Beckman Coulter). FACS data analysis was performed using Kaluza v1.2 (Beckman Coulter). Sorting was performed on FACSAr-ia III (BD), essentially as previously reported [Keinan et al; Cell Death & Disease (2021) 12: 193]. Library construction and sequencing was performed by the INCPM facility (Rehovot). in short - library preparation was done according to the Smart-seq2 protocol (Simone Picelli et al. Nature Protocols 2014) samples were pooled together and sequenced on one lane of the illumina HiSeq 2500 V4 instrument.
SMARTSeq-2 Ultra Low Input RNA V4 kit from Clontech (polyA based capture), with 14 cycles of cDNA amplification. The amplified cDNA was fragmented using the Covaris machine to around 450bp. Illumina libraries were constructed using the End repair, A base addition and adapter ligation (TruSeq like adapters:GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCGCCTTATCTCGTATGCCGTCTTCTG) and amplified using 13 PCR cycles. Performed by INCPM in the Weizmann institute of science.

treatment_protocol: ML23 leukemia line was generated as previously reported [Keinan et al; Cell Death & Disease (2021) 12: 193]. essentially, transgenic rtTA mice (Jax strein 6965) cells transformed using lentiviruses over expressing oncogenic factors. ML23 cells were passaged in C57BL/6 mice.

value: Jax strain 6965

tag: cell line


title: BVD007B


title: Reference strain MSB treated conidium 1

value: conidium

value: batch 1


title: P12#1


title: BVD007A


title: P11#2


title: P11#1


title: P12#2


title: Reference strain untreated conidium 1


title: BVD002A


title: BVD001B


title: P11#3


title: BVD001A


title: P10#2


title: Hepatocytes_with_Bezafibrate_Negative

city: 福岡市

first: Yuya

last: Yoshida

state: 福岡県

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

institute: Kyushu-university

data_processing:
Quality trimming and adapter clipping of the read data were performed using Trimmomatic version 0.36.
Trimmed reads were mapped to the transcript in the human  reference sequence mm10 using Bowtie2 aligner within RSEM.
Read count extraction and normalization were performed using edgeR program.
Assembly: mm10
Supplementary files format and content: tab-delimited text file. normalized CPM count matrix with GeneSymbol index.

source_name: Liver

extract_protocol:
The total RNA was isolated from cells using NucleoSpin® totalRNA FFPE (TAKARA bio, Japan) according to the manufacturer's instructions.
The sequencing libraries were prepared with MGIEasy rRNA Depletion Kit and MGIEasy RNA Directional Library Prep Set (MGI Tech Co., Ltd.) according to the manufacturer's instructions. The libraries were sequenced on the DNBSEQ-G400 FAST Sequencer (MGI Tech Co., Ltd.) with a paired-end 150-nt strategy.

value: ICR

tag: cell type

value: negative


title: Hepatocytes_with_Bezafibrate_Positive

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

value: positive


title: P10#3


title: Hepatocytes_Positive

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野

value: Hepatocytes


title: P10#1


title: Hepatocytes_with_Bezafibrate_High

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野


title: BVD002B

value: Patient tumor

value: pancreatic cancer

value: Yes


title: Reference strain untreated conidium 2

value: untreated


title: Hepatocytes_Negative

address: 東区馬出3-1-1 九州大学薬学部棟本館3F 薬剤学教室, 薬物動態学分野


title: P9#3


title: 674M

first: Jian

last: Sun

address: Quxi Road No.500

institute: Shanghai Ninth People's Hospital

description: Dlx2 CUT&Tag of E12.5 maxillary process tissue in wildtype mice

data_processing:
Raw data were trimmed from 3' end until the final base had a quality score > 30, using Trimgalore-0.4.5, discarding reads left with < 20 bp
Raw data were aligned to the UCSC mm10 genome using Bowtie version 1.1.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing MACS2 v2.2.7 with the significance cut-off q-value <=0.01
Assembly: mm10
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

source_name: maxillary process cells

growth_protocol: C57BL/6 mice were purchased from Shanghai Jihui Laboratory Animal Care Co.Ltd. All mice were maintained in SPF conditions at the Animal Center of the Ninth People’s hospital affiliated to Shanghai Jiaotong University School of medicine. Female and male mice between the ages of 8 to 12 weeks were used.

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). 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 the Illumina HiSeq X following the manufacturer's protocols.

value: maxillary process cells

tag: chip antibody


title: P65c3E_HIPCTX

city: Ann Arbor

first: Shigeki

last: Iwase

email: siwase@umich.edu, kbonefas@umich.edu

state: MI

address: 1241 E. Catherine St.

institute: University of Michigan

data_processing:
Mapped reads to mus musculus mm10 Gencode genome through STAR (v2.5.3a)
Counts file generated by featureCounts (Subread v1.5.0)
BAM files were convered to bigwigs using deeptools (v3.1.3) and visualized by the UCSC genome browser
Assembly: mm10
Supplementary files format and content: bigwig
Supplementary files format and content: counts table

organism: Mus

source_name: Forebrain

extract_protocol:
total RNA was purified by Qiagen RNEasy Midi Kit (75144)
cDNA library was generated from purified total RNA and prepared by poly-A enrichment

value: Forebrain

value: Postnatal day 6

value: Male

value: Kdm5c hemizygous deletion


title: P9#1


title: P65c1E_HIPCTX

value: Wild type


title: P65c2E_HIPCTX


title: B1471

description: Bulk RNA-Seq of maxillary process tissue in E10.5 Wnt1cre; Rosa26Dlx2/- mice

data_processing:
The PE150 raw reads of RNA-Seq libraries were filtered by removing adaptor sequences, contamination and low-quality (phred quality < 20) reads. Reads quality was assessed using FastQC.
Sequenced reads were then mapped to the mm10 genome using STAR aligner version 2.7.3a. Reads were counted using htseq-count version 0.12.4 at the union mode.
Assembly: mm10
Supplementary files format and content: counts

growth_protocol: Wnt1cre mice were obtained from the Jackson laboratory. The Rosa26CAG-LSL-Dlx2-3xFlag mice was constructed by Shanghai Model Organisms Center, Inc(Shanghai, China). To generate wnt1cre; Rosa26Dlx2/- mice, which can specifically overexpress Dlx2 in neural crest cells, we mated wnt1cre mice with Rosa26CAG-LSL-Dlx2-3xFlag mice.

extract_protocol:
Total RNA was extracted using Trizol from freshly dissected maxillary prominence tissues. Three independent RNA samples were prepared. RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For each sample, 2 μg total RNA was used as input material for the library preparations. Sequencing libraries were then generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and eluted with EB buffer, followed by terminal repair, A-tailing and adapter ligation. The ligated products were retrieved and PCR amplification was performed to generate sequencing libraries. RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurately quantified using a StepOnePlusTM Real-Time PCR System. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina HiSeq X ten platform and 150 bp paired-end reads were generated.

treatment_protocol: On E10.5 pregnant wnt1cre; Rosa26Dlx2/- female were euthanized via isoflurane and cervical dislocation. Embryos were dissected from uterus and transferred ice-cold PBS in a 6-cm Petri dish using a disposable glass pipette. Intact maxillary prominences were carefully dissected out from embryos using fine forceps under a stereomicroscope and used for library construction as described below.

value: Wnt1cre; Rosa26Dlx2/-

value: Surgical separation

tag: time


title: B1416


title: CTRP9_620

city: Mannheim

first: Joerg

last: Heineke

address: Ludolf-Krehlstr. 7-11 Tridomus B

department: Cardiovascular Physiology

institute: Medical Faculty of Mannheim Heidelberg University

description:
CTRP9_620
result_diff2_AAV_CTRP9vsLuc.xlsx

data_processing:
FastqCleaner was used for trimming
bowtie2 was used for mapping
Gene annotation was performed with bioMaRt
Read counts were normalized to counts per million
Differential expression analysis was performed using Deseq2 from R. Differentially expressed Genes were selected with (0.75<FC>1.5 and FDR<0.05).
Assembly: mm10
Supplementary files format and content: Excel files from differentially expressed genes

extract_protocol: Extraction of RNA samples was performed with Macherey-Nagel Extraction kit by following manufacturers' protocols, which at the end eluded in nuclease-free water. Library preparation for RNA sequencing was performed by BGI with DNBSEQ Transcriptome standard library preparation protocols.

value: Heart

value: WT

value: high fat diet + AAV CTRP9


title: P65c7D_HIPCTX


title: B1412


title: CTRP9_611

description:
CTRP9_611
result_diff2_AAV_CTRP9vsLuc.xlsx


title: E10.5 wt3_bulk rnaseq

description: Bulk RNA-Seq of maxillary process tissue in E10.5 wildtype mice

extract_protocol:
Total RNA was extracted using Trizol from freshly dissected maxillary prominence tissues from. Three independent RNA samples were prepared. RNA purity was checked using the kaiaoK5500®Spectrophotometer (Kaiao, Beijing, China). RNA integrity and concentration were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
For each sample, 2 μg total RNA was used as input material for the library preparations. Sequencing libraries were then generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and RNase H. Second strand cDNA synthesis was subsequently performed using buffer, dNTPs, DNA polymerase I and RNase H. The library fragments were purified with QiaQuick PCR kits and eluted with EB buffer, followed by terminal repair, A-tailing and adapter ligation. The ligated products were retrieved and PCR amplification was performed to generate sequencing libraries. RNA concentration of library was measured using Qubit® RNA Assay Kit in Qubit® 3.0 to preliminary quantify and then dilute to 1ng/μl. Insert size was assessed using the Agilent Bioanalyzer 2100 system (Agilent Technologies, CA, USA), and qualified insert size was accurately quantified using a StepOnePlusTM Real-Time PCR System. The clustering of the index-coded samples was performed on a cBot cluster generation system using HiSeq PE Cluster Kit v4-cBot-HS (Illumina) according to the manufacturer’s instructions. After cluster generation, the libraries were sequenced on an Illumina HiSeq X ten platform and 150 bp paired-end reads were generated.

treatment_protocol: On Embryo 10.5(E10.5) pregnant C57BL/6 female were euthanized via isoflurane and cervical dislocation. Embryos were dissected from uterus and transferred ice-cold PBS in a 6-cm Petri dish using a disposable glass pipette. Intact maxillary prominences were carefully dissected out from embryos using fine forceps under a stereomicroscope and used for library construction as described below.

value: wildtype


title: P65c5D_HIPCTX


title: E10.5 wt2_bulk rnaseq


title: P9#2

value: Jax strain 6965


title: P65c4D_HIPCTX


title: E10.5 wt1_bulk rnaseq


title: CTRP9_624

description:
Luc_624
result_diff2_AAV_CTRP9vsLuc.xlsx

value: high fat diet + AAV Luciferase


title: Control 8

type: genomic

city: Umeå

first: Ida Maria

last: Westin

address: NUS, 6M

department: Medical Biosciensces

country: Sweden

institute: Umeå University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850K Beadchip using standard Illumina protocol

scan_protocol: HiScan array reader (Illumina)

data_processing: Normalization was done with BMIQ version 1.3 (Teschendorff, A.E. et al. 2013) and annotation and pre-filtering was done in R version 3.6.2. The pre-filtering steps excluded CpGs with detection p-value > 0.05, CpG probes that aligned to multiple loci in the genome or were located less than 5 bp from a known single nucleotide polymorphism (Zhou, W. et al. 2017) and CpGs probes identified as meQTLs (Gaunt, T. R. et al. 2016, McClay, J. L. et al. 2015).

source_name: corneal endothelium

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA from human corneal endothelium was extracted using NucleoSpin Tissue XS (Macherey-Nagel, Düren, Germany)

treatment_protocol: EZ DNA Methylation kit (Zymo Research, Irvine, USA) was applied for bisulfite conversion of genomic DNA from corneal endothelium

tag: relative age

value: elderly

tag: disease

value: normal


title: P65c2D_HIPCTX


title: Control 11


title: Control 12

value: young


title: Control 10


title: CTRP9_615

description:
Luc_615
result_diff2_AAV_CTRP9vsLuc.xlsx


title: P65c6D_HIPCTX


title: P65c9E_HIPCTX

value: Female

value: Kdm5c heterozygous deletion


title: CTRP9_610

description:
CTRP9_610
result_diff2_AAV_CTRP9vsLuc.xlsx


title: E12.5DLX2

description: Single cell RNA-Seq of E12.5 maxillary process tissue in Wnt1cre; Rosa26Dlx2/- mice

data_processing:
After extracting read one without poly T tails, cell barcode or UMI, raw sequencing reads of scRNA-Seq libraries were trimmed by fastp V1 to remove adapters and poly A tails before aligning read two to GRCm38 with ensemble version 92 gene annotation (fastp 2.5.3a and featureCounts 1.6.2). The number of UMIs per gene per cell was estimated by counting the reads with the same cell barcode and UMI. The UMI count tables of each cellular barcode were imported for downstream analysis.
Cell type identification and clustering analysis was performed using Seurat program (http://satijalab.org/seurat/). Cell-by-gene counts expression matrices were imported to Seurat. Cells with <200 unique genes and 1500 unique molecular identifiers (UMI) or >3000 unique genes and 15,000 UMI were excluded from downstream analysis.
The expression data were then log transformed, normalized, and scaled for sequencing depth by following the standard Seurat processing pipeline. Clustering of maxillary cells was performed on 5291, 6522, and 5277 cells from E10.5, E11.5 and E12.5 maxillary prominences, respectively, in Seurat at a resolution of 0.8. The identities of the resultant clusters were inferred using literature-derived marker genes.
Cell cycle analysis was performed using the CellCycleScoring function in Seurat and a list of cell cycle markers from a previous study (Tirosh et al., Science, 2016). Due to the strong influences of cell cycle states on clustering. G1 stage mesenchymal cells at E10.5, E11.5 and E12.5 were selected for further clustering analysis using resolutions of 0.5, 0.6 and 0.6, respectively. The G1 mesenchymal cells from all stages were then combined and clustered at a resolution of 0.6. Marker genes associated with each mesenchymal cell subpopulation were identified using the FindAllMarkers function in Seurat.
Supplementary files format and content: mm10
Supplementary files format and content: rds

source_name: maxillary process

extract_protocol:
Fresh maxillary prominence tissues were conserved in the GEXSCOPE® Tissue Preservation Solution (Singleron) until library preparation. scRNA-seq libraries were constructed using a microwell-based system (Zhang K, et al., Nucleic Acids Research, 2018). Briefly, the specimens were washed 3 times with Hanks Balanced Salt Solution (HBSS, Gibco, Cat. No.14025-076), shredded into 1–2 mm pieces, and then digested with 2ml GEXSCOPE® Tissue Dissociation Solution (Singleron) at 37℃ for 15min in a 15ml centrifuge tube (Falcon, Cat. No.352095) with sustained agitation. After digestion, cells were filtered through 40-micron sterile strainers (Falcon, Cat. No.352340) and centrifuged (Eppendorf, 5810R) at 1,000rpm for 5 minutes. The supernatant was removed, and the pellets were resuspended in 1ml PBS (Hyclone, Cat. No.SA30256.01). To remove the red blood cells, 2 mL RBC lysis buﬀer (Roche, Cat. No. 11 814 389 001) was added to the cell suspension according to the manufacturer’s protocol. Cells were collected by centrifugation at 500g for 5 min and resuspend in PBS (Hyclone, Cat. No.SA30256.01). An aliquot from the cell mixture was stained with trypan blue (Bio-RAD, Cat. No.#1450013) and counted on an ECLIPSE Ts2 cellcounter (Nikon). The concentration of the single-cell suspension was adjusted to 1×105 cells/mL using PBS.
Single-cell suspensions were then loaded onto microfluidic devices and scRNA-seq libraries were constructed according to Singleron GEXSCOPETM protocol by GEXSCOPETM Single-Cell RNA Library Kit (Singleron Biotechnologies). Individual libraries were diluted to 4nM and pooled for sequencing. Pools were sequenced on Illumina HiSeq X with 150 bp paired end reads.

treatment_protocol: On Embryo 12.5 pregnant wnt1cre; Rosa26Dlx2/- female were euthanized via isoflurane and cervical dislocation. Embryos were dissected from uterus and transferred ice-cold PBS in a 6-cm Petri dish using a disposable glass pipette. Intact maxillary prominences were carefully dissected out from embryos using fine forceps under a stereomicroscope and used for library construction as described below.

value: maxillary process


title: Control 7


title: CTRP9_614

description:
Luc_614
result_diff2_AAV_CTRP9vsLuc.xlsx


title: Lens epithelial explants, 5 day in differentiation  media after D0 ATAC_D5_DM_B

city: OXFORD

first: Anil

last: Upreti

address: 501 E High St, Oxford, OH 45056

department: Biology

institute: Miami University

data_processing:
Raw reads were trimmed using Cutadapt 3.4 and Trim Galore 0.6.5-1 with the trimming parameters -q 20 --phred33 --length 20.
Alignment of raw reads to the Mus musculus genome GRCm39 was performed with Bowtie2 using the parameters -X 2000 --very-sensitive-local --no-mixed --no-discordant --no-dovetail.
Peaks were called for samples individually with MACS2 using parameters -f BAMPE -g mm -q 0.05. Peaks aligning to the mitochondrial chromosome were discarded.Differential expression testing of peak regions and peak summits was performed with DESeq2.
ATAC coverage tracks were visualized using the Integrative Genomics Viewer.Prior to visualization, BAM files were converted to BIGWIG format and normalized using the bamCoverage --binSize 1 and --scaleFactor parameter using the inverse of DESeq2 size factors.
Differential expression testing was performed with DESeq2.
Assembly: GRCm39 v.M27
Supplementary files format and content: ATAC_seq_normalized_count.csv

source_name: Lens Epithelium

growth_protocol: Lens epitheliall explants were maintained in 35mm culture dish with either pre-calibrated M-199 media supplemented with 1% antibiotic-antimycotic solution  and 0.1% bovine serum albumin  henceforth referred to as “culture medium (CM)” or cultured in vitreous, diluted by CM to 50% concentration, henceforth referred to as “differentiation medium (DM)”, for 1 day or 5 days at 37 °C and 5% CO2.

extract_protocol:
Chromatin was extracted using ATAC-seq kit from Active motif (53150) as per the manufacturers instructions.
ATAC-seq library preparation was performed using ATAC-Seq kit (53150) per the manufacturer’s instructions

value: Lens Epithelium

value: FVB/N

value: D5 DM


title: Control 2


title: P65c8E_HIPCTX

value: Forebrain

value: Postnatal day 6


title: Control 1


title: 661M

value: maxillary process cells


title: Lens epithelial explants, 5 day in differentiation  media after D0 ATAC_D5_DM_A


title: Control 5


title: FECD case 25

value: FECD


title: CTRP9HFD1019

description:
CTRP9HFD1019
results_diff_allsignificant WT vs KO.xlsx

value: Heart

value: KO

value: high fat diet


title: P65c6E_HIPCTX


title: CTRP9HFD1017

description:
CTRP9HFD1017
results_diff_allsignificant WT vs KO.xlsx


title: FECD case 12


title: P65c5E_HIPCTX

value: Wild type


title: FECD case 17

value: elderly


title: Lens epithelial explants, 5 day in culture media after D0 ATAC_D5_CM_A

value: D5 CM


title: Lens epithelial explants, 5 day in culture media after D0 ATAC_D5_CM_B


title: FECD case 15


title: CTRP9HFD1008

description:
CTRP9HFD1008
results_diff_allsignificant WT vs KO.xlsx


title: Lens epithelial explants, 1 day in differentiation  media after D0 ATAC_D1_DM_B

value: D1 DM


title: CTRP9HFD1007

description:
CTRP9HFD1007
results_diff_allsignificant WT vs KO.xlsx


title: FECD case 16


title: Control 3

value: normal


title: P65c4E_HIPCTX

value: Female


title: Control 4


title: Lens epithelial explants, 1 day in differentiation  media after D0 ATAC_D1_DM_A


title: FECD case 13


title: P65c9D_HIPCTX

value: Kdm5c heterozygous deletion


title: Control 6


title: P65c3D_HIPCTX


title: Lens epithelial explants, 1 day in culture media after D0 ATAC_D1_CM_B

value: Lens Epithelium

value: D1 CM


title: CTRP9HFD1003

description:
CTRP9HFD1003
results_diff_allsignificant WT vs KO.xlsx

value: WT


title: YH9,DA_3,Day21

city: HeFei

first: Yaohua

last: Cheng

address: Changjiang West Road 130

institute: Anhui  Agricultural University

description: Camellia. sinensis var. assamica cv. ‘Yinghong 9’

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: mm10

organism: Camellia sinensis var. assamica

source_name: tissue culture of tea seedlings(height of 4-5 cm)

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

tag: cultivar

value: CA-treated plants were exposed to normal temperature (25°C daytime, 20°C night)for 7 days


title: CTRP9HFD1027

description:
CTRP9HFD1027
results_diff_allsignificant WT vs KO.xlsx


title: Lens epithelial explants, 1 day in culture media after D0 ATAC_D1_CM_A

value: FVB/N


title: P65c1D_HIPCTX

value: Forebrain

value: Postnatal day 6

tag: Sex


title: CTRP9HFD998

description:
CTRP9HFD998
results_diff_allsignificant WT vs KO.xlsx

value: Heart


title: FECD case 10

value: FECD


title: CTRP9_609

description:
CTRP9_609
result_diff2_AAV_CTRP9vsLuc.xlsx

value: high fat diet + AAV CTRP9


title: Lens epithelial explants, 24 hrs in Culture media ATAC_D0_B

value: 25 hrs in media


title: whole body discarding last third from the cloaca, 37dph, rep2

city: Vigo

first: Laura

middle: Guerrero

last: Peña

state: Pontevedra

address: Eduardo Cabello, 8

department: Aquaculture and Biotecnology

country: Spain

institute: CSIC

data_processing:
Reads were mapped to turbot genome assembly using STAR alignment software
Number of aligned reads overlapping each gene was calculated using HTseq-count software
Count matrix was normalized using median of ratios methos with DESEq R package
Assembly: Turbot genome: http://ftp.ensembl.org/pub/release-107/fasta/scophthalmus_maximus/dna/
Supplementary files format and content: Gene counts from Htseq-count
Supplementary files format and content: bigWig format for displaying in a genome browser track

organism: Scophthalmus maximus

extract_protocol:
Total RNA of each developmental stage was isolated using Rneasy Mini Kit (Qiagen) with Dnase digestion treatment (Qiagen)
Library preparation was performed using the TruSeq Stranded mRNA Library Prep Kit (Illumina)

tag: developmental stages

value: 37 days post hatching


title: BJR_P0_KO33

city: Madrid

first: Mercedes

last: Ricote

address: Darwin 3

institute: CNB-CSIC

data_processing:
Fastq files containing reads for each library were extracted and demultiplexed using bcltofastQ (Illumina).
Sequencing adapter contaminations were removed using cutadapt, discarding those reads that were shorter than 30 nt after trimming.
Resulting reads were aligned against the GRCm38.76 mouse transcriptome, with RSEM v1.3.1, to obtain expression estimates at gene level.
Expected expression counts were then processed with an analysis pipeline that used Bioconductor package Limma for normalization (using TMM method), considering only those genes for which expression was at least 1 count per million (CPM) in at least 3 samples.
Genome_build: GRCm38.76
Supplementary_files_format_and_content: NormCounts.xlsx: TMM-normalized counts (CPM) for genes with expression level of at least 1 count per million (CPM) in at least 3 samples.

source_name: Perinatal heart

extract_protocol:
Total RNA from P0 hearts of wild type (WT) and cardiomyocyte-specific RXRab-/- newborns was prepared with RNeasy Mini kit (Qiagen) by standard protocols from 3-4 biological replicates.
cDNA was synthesized and amplified from total RNA (1-10 ng) using the Ovation® RNA-seq System v2 (NuGEN® Technologies). Sequencing was performed using the Illumina HiSeq-2500 system (1x61 reads).

tag: tissue

value: Total heart

value: edKO

tag: age


title: YH9,DA_1,Day21

value: tissue culture of tea seedlings(height of 4-5 cm)


title: FECD case 14

value: elderly


title: Lens epithelial explants, 24 hrs in Culture media ATAC_D0_A

tag: genotype

value: 24 hrs in media


title: YH9,DA_2,Day21

tag: treatment


title: BJR_P0_KO15


title: YH9,CA_3,Day14

value: Low temperature (10 °C during the day and 4 °C at night) treatment for 7 days. Subsequently, freezing acclimation was performed by 4°C daytime, 0°C night exposure for 7 days (CA-treated)


title: FECD case 8


title: whole body discarding last third from the cloaca, 23dph, rep2

value: 23 days post hatching


title: FECD case 11


title: FECD case 7


title: whole body discarding last third from the cloaca, 37dph, rep1


title: YH9,CA_2,Day14


title: Lens epithelial explants, Immediate collection ATAC_IMD_A

value: Lens Epithelium

value: Immediate Collection


title: BJR_P0_KO5


title: YH9,CA_1,Day14


title: BJR_P0_WT28

value: Wild-type