title: Embryo, E15.5, single nuclei ATAC

description: snATAC-seq

library_source: genomic single cell

data_processing:
Raw reads were pre-processed using 10X Genomics’ CellRanger ATAC pipeline (v2.0.0).
We obtained age-specific fragment files from ENCODE and merged them using GenomicRanges’s (v1.46.1) ´reduce()´ function.
Next, we calculated new count matrices for each sample separately using FeatureMatrix() function from Seurat (v4.1.0) and merged the data into a single dataset.
We normalized data and performed clustering following Signac (v1.6.0) standard workflow.
Assembly: mm10
Supplementary files format and content: h5 (feature-barcode matrix)
Supplementary files format and content: csv (metadata with spatial coordinates, sample, and clustering)
Supplementary files format and content: tsv (fragments)

extract_protocol:
We prepared single nuclei suspensions from fresh frozen embryos (E12.5, E13.5 and E15.5) that were littermates to those used for spatial ATAC. Three to five 70 µm frozen sections were obtained for each embryonic stage matching the anatomical landmarks from spatial ATAC sections. Frozen sections were then dissociated according to the 10X Chromium Single Nuclei Isolation kit (1000494) omitting the debris removal step to avoid cell loss.
Nuclei suspensions were stained with 7-AAD (Miltenyi; 1:50) and sorted on a BD Fusion flow cytometer with a 100 µm nozzle. Nuclei were then immediately processed according to the 10X Genomics’ Single Cell ATAC Next GEM kit v1.1


title: TFexp_H1_PU1_BC04_Rep2

status: Public on Nov 03 2022

type: SRA

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

country: USA

institute: The University of Pennsylvania

library_source: genomic

data_processing:
Array construction: the 162 bp Cx3cr1 mononucleosome sequence that corresponds to the genomic location: mm9 chr9:119946611-119946762 13 was extended on either side by 35 bp to incorporate linker DNA and BfuAI and XbaI flanking sequences: ACCTGCGTTACAGCATCCACTCAGTATCCCTTGAGCCCCGCGTGCAAAGCCCAGGAGCCCTTGCTTAGGTGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCTGAGTCTTAGCAATGATACTTCCCGATTCCCCTCACAAAAATAGGTCAGTCTGTCTG553 GCTAGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCTATTTTTCTAGCTCCCAGGCT TCTGTCTGCTTCCTTCGTTTAGTATGTCTA
The DNA sequence was generated by PCR of genomic mouse DNA with BfuAI and XbaI restriction sites cloned into the p208-10.N1N2 16 to generate p208-10-Cx3cr1. Mutant Cx3cr1 arrays were generated by infusion cloning using linearized BfuAI XbaI digested p208-10-Cx3cr1 plasmids. Geneblocks for cloning were obtained from IDT:
TF mutant motif Cx3cr1:
AAAATAACCTGCGTTACAGCATCCACTCAGTATCCCTTGAGCCCCGCGTGCAAAGCCCAGGAGCCCTTGCTTAGGTGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCTGAGTCCCGTATAGAGATCGTATAGCGTATAGAGCACAAAAATAGGTCAGTCTGTCTGGCTAGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCTATTTTTCTAGCTCCCAGGCTTCTGTCTGCTTCCTTCGTTTAGTATGTCTAGACTACAGTTATTGGTT
Swap1 Cx3cr1:
AAAATAACCTGCGTTACAGCATCCACTCAGTATCCCTTGAGCCCCGCGTGCAAAGCCCAGGAGCCCTTGCTTAGGTGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCTGAGTCTACTTCCCGAATTAGCAATGGTTCCCCTCACAAAAATAGGTCAGTCTGTCTGGCTAGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCTATTTTTCTAGCTCCCAGGCTTCTGTCTGCTTCCTTCGTTTAGTATGTCTAGACTACAGTTATTGGTT
Swap2 Cx3cr1:
AAAATAACCTGCGTTACAGCATCCACTCAGTATCCCTTGAGCCCCGCGTGCAAAGCCCAGGAGCCCTTGCTTAGGTGCAGGGCCTCTCGGCTGCTGATCTTCAGCTGGTTGCTGAGAGTTGCAGCATTGCTGAGTCTACTTCCCGAATTAGCAATGGTTCCCCTCACAAAAATAGGTCAGTCTGTCTGGCTAGTTCTGTACTTGCAGACACAGGGCATGTGGGGTTCCTATTTTTCTAGCTCCCAGGCTTCTGTCTGCTTCCTTCGTTTAGTATGTCTAGACTACAGTTATTGGTT
Transformation to FASTQ: the fast5 raw data files from the Nanopore sequencer were basecalled and converted to fastq format with Guppy Software (Oxford Nanopore Technologies).
Alignment: reads were mapped to the Cx3cr1 Array reference with minimap2, a mapping algorithm specifically designed to analyze nanopore sequencing reads.
Quality Control: BAM files produced by minimap2 were imported into R 44 then filtered and normalized using tidyverse packages 45 .Specifically, reads were excluded if they were identified as multimappers by minimap2 or were located entirely within the non- unique regions of the nucleosome array DNA sequence.
Track Creation: the ends of each read from an array digestion identify the precise nucleotide at which a nuclease was able to access and cleave the DNA in the array. We quantified the endpoints of each read using the hash package and then normalized each dataset to the total number of mapped reads, resulting in provided bigWigs.
Assembly: mm9
Supplementary files format and content: BigWig files represent pile-ups of fragment endpoints, indicating nuclease cleavage sites

molecule: genomic DNA

organism: Mus musculus

source_name: Plasmid-amplified sequence

growth_protocol: Plasmids were amplified in E.coli, purified, and digested with MluI, SmaI and HhaI to release array fragments. Fragments were purified by ethanol precipitation then labeled with579 dCTP-Cy5 (Cytiva PA55021) by end-repair with Klenow fragment DNA polymeraase (3’-5’ exo-) (NEB). Cy5-DNA labeling reactions were carried out at final concentrations of 1 μM DNA, 4 mM Cy5-dCTP and 0.5 U/μL Klenow fragment in the presence of excess 4mM dATP, 4 mM dTTP, and 4 mM dGTP in NEB buffer 2 (50mMNaCl, 10mM Tris-HCl, 10 mM MgCl 2 , 1 mM DTT). The reaction was incubated at 37C for 1 hr. Labeling reactions were purified by phenol:chloroform extraction followed by FPLC purification of the 2.7 kb MluI-SmaI fragment using a Capto HiRes Q anion exchange column (Cytiva 29275878).

extract_protocol: Partially MNase-digested chromatin retaining contiguous oligonucleosomes was used for generation of libraries for nanopore sequencing. Purified DNA was end-repaired and A-tailed with the NEBnext Ultra II end repair module (New England Biolabs), purified with Ampure XP beads (Beckman Coulter) and ligated to AMX adapter from the Oxford Nanopore 1D sequencing Kit (SQK-LSK108, Oxford Nanopore Technologies) using NEB Blunt/TA ligase master mix. Excess adapters were removed by adding 0.5 volumes of Ampure XP beads and washing with ABB buffer from the 1D sequencing kit. Purified library was eluted and loaded to a MinION R9.4 flowcell according to the manufacturer’s instructions and run for 24 h.

treatment_protocol:
Nucleosome Arrays: nucleosome arrays were assembled as previously described 16 . Assembly reactions containing 2 μg of end-labeled DNA fragments and core histones at a 1:1.0 molar ratio of octamers to nucleosomal sites, and 2 M NaCl in a total of 10 μl were incubated at 37°C for 15 min, serially diluted by adding 3.3, 6.7, 5, 3.6, 4.7, 6.7, 10, 30, and 20 μl of 50 mM HEPES (pH 7.5), 1 mM EDTA, 5 mM DTT, and 0.5 mM PMSF in 15 min incubation steps at 30°C, and brought to 0.1 M NaCl by adding 100 μl of 10 mM Tris·HCl (pH 7.5), 1 mM EDTA, IGEPAL, 5 mM DTT, 0.5 mM PMSF, and 20% glycerol, followed by incubation at 30°C for 15 min. Array saturation was determined by EcoRI digestion, performed with a concentration of 2 nM nucleosome array or free DNA in 20 mM HEPES (pH 7.5), 50 mM KCl, 1% glycerol, 5 mM DTT, 100 μg/ml BSA, and 2 U/μl EcoRI. Following a 2 hr incubation at 37°C, digestion products were resolved on 4% polyacrylamide 0.5X TBE gels and analyzed as described 16 . Cx3cr1 mononucleosomes were reconstituted by dialysis with the Cy5 end-labeled 162bp Cx3cr1 DNA fragment and recombinant human histones as described previously 13.
TF Binding: binding reactions for the DNase I digestion, MNase, and Restriction enzyme assays were carried out with 1 nM (1.5 ng/μl) of nucleosome array (13 nM of nucleosomes) in 6 mM HEPES (pH 7.5), 35 mM KCl, 1.5% glycerol, 2 mM DTT, 250 μg/ml BSA. In experiments with compacted nucleosome arrays, 13 nM purified histone H1 (Calbiochem) was incubated with the nucleosome arrays at room temperature for 1 hr. Purified transcription factors were then incubated with the nucleosome arrays at room temperature for 1 hr. For cBAF remodeling assays 10nM of indicated transcription factors were incubated with H1-compacted arrays at room temperature followed by incubation with cBAF (6 nM) and ATP (0.5mM) for 30 minutes at 30°C.
DNase digestions were carried out by 2.5-10 ug/mL of DNase I diluted in 50 mM MgCl 2 , followed by incubation at room temperature for 1 min. MNase digestion was performed by addition of .075-0.6 U/mL MNase diluted in 30 mM CaCl2, followed by incubation at room temperature for 1 min. XbaI restriction enzyme digestion was performed by incubation with 0.25- 1 U/mL XbaI for 45 minutes at 30°C. Reactions were terminated by addition of 1 volume of stop buffer (20 mM Tris pH 7.5, 50 mM EDTA, 1% SDS, 0.5 mg/mL tRNA, and 0.2 mg/mL proteinase K) and incubated at 50C for 15 min. Digestion products are purified by ethanol precipitation and electrophoresed on 1% Agarose 1X TBE gels.

tag: tissue

value: Plasmid-amplified sequence

tag: condition

value: Compacted Array with PU.1


title: NIPBL knockdown rep 2

first: Jennifer

middle: Mary

last: Luppino

state: Pennsylvania

address: 415 Curie Blvd., Room: 570

department: Genetics

institute: University of Pennsylvania

library_source: transcriptomic

data_processing:
All custom scripts described herein are available on the AdelmanLab Github (https://github.com/AdelmanLab/NIH_scripts). Using a custom script (trim_and_filter_PE.pl), FASTQ read pairs were trimmed to 41bp per mate, and read pairs with a minimum average base quality score of 20 retained. Read pairs were further trimmed using cutadapt 1.14 to remove adapter sequences and low-quality 3’ bases (--match-read-wildcards -m 20 -q 10). R1 reads, corresponding to RNA 3’ ends, were then aligned to the spiked in Drosophila genome index (dm3) using Bowtie 1.2.2 (-v 2 -p 6 --best --un), with those reads not mapping to the spike genome serving as input to the primary genome alignment step (using Bowtie 1.2.2 options -v 2 --best). Reads mapping to the hg38 reference genome were then sorted, via samtools 1.3.1 (-n), and subsequently converted to bedGraph format using a custom script (bowtie2stdBedGraph.pl). Because R1 in PRO-seq reveals the position of the RNA 3’ end, the “+” and “-“ strands were swapped to generate bedGraphs representing 3’ end position at single nucleotide resolution.
For promoter reads, annotated transcription start sites were obtained from Ensembl v99 for hg38. After removing transcripts with {immunoglobulin, Mt_tRNA, Mt_rRNA} biotypes, PRO-seq signal in each sample was calculated in the window from the annotated TSS to +150 nt downstream, using a custom script, make_heatmap.pl.
Given good agreement between replicates (Spearman's rho ≥0.95) and similar return of spike-in reads, bedGraphs were merged within conditions, and depth-normalized, to generate bigWig files binned at 10bp.
To determine differentially expressed genes in PRO-seq analyses, the 5' ends from all PRO-seq reads were used to identify active transcription start sites using a custom script, proTSScall available on the NascentTranscriptionCore GitHub (https://github.com/NascentTranscriptionCore/proTSScall). Briefly, PRO-seq 3’ read bedGraphs for “+” and “-“ strands were separately combined across samples and the composite read counts were assigned to TSS-proximal windows (TSS to +150nt) using the same filtered TSS annotation described above.  TSSs with ≤9 counts in this window are deemed ‘inactive’ and the remaining TSSs, deemed ‘active’, are collapsed to yield 1 dominant TSS per gene, defined as the one with the highest TSS-proximal read count -- if the highest read count is shared amongst multiple transcripts, the TSS furthest upstream, in a strand-aware fashion, is called dominant.  Dominant TSSs sharing the same start position are deduplicated as follows: (1) if start positions are equal, the TSS with the longest associated annotated transcript is called dominant, (2) if start positions and transcript lengths are both equal, the TSS associated with the lowest Ensembl gene ID (numerical portion) is dominant.
Differential expression analysis was performed in R v3.6.1 with DESeq2 v1.30.1 (Love et al., 2014). Read counts were obtained over whole genes from TSS to TES as defined by proTSScall, distal dREG peaks, TSS proximal regions (dominant TSS to TSS+150bp), and gene bodies (dominant TSS+250 to TSS+2250bp) using the featureCounts function from Rsubread v1.34.7 (Liao et al., 2019). Defaults were used with the following exceptions: minMQS=10; countChimericFragments=FALSE; isPairedEnd=FALSE; strandSpecific=2 (or strandSpecific=0 for distal dREG peaks); nthreads=8. DESeq2 was run with defaults using the nbinomWaldTest function. The size factors obtained from whole gene bodies were applied to all other groups. Log fold change shrinkage was performed using the ‘apeglm’ algorithm (Zhu et al., 2019). Significant differentially expressed genes were filtered for a minimum adjusted p-value of 0.01 or less, removing NA values.
Assembly: hg38
Supplementary files format and content: bw: bigWig
Supplementary files format and content: txt: tab-delimined file containing differential expression analysis

molecule: total RNA

organism: Homo sapiens

growth_protocol: Cells were cultured in McCoy’s 5A media supplemented with 10% FBS, 2 mM L-glutamine, 100 U/ml penicillin, and 100ug/ml streptomycin and filtered using a 0.22-μm PES membrane at 37°C with 5% CO2

extract_protocol:
RNAi was performed as previously described. Following 72 h knockdown, cells were rinsed with Dulbecco's phosphate buffered saline (DPBS) and treated with trypsin to detach them from the plate. Cells were resuspended in cold supplemented McCoy’s 5A media and three wells of a 6-well plate were pooled per replicate and placed on ice. From this point on, all steps were performed on ice, all buffers were pre-chilled, and samples were spun at 300xg for 10 min at 4ºC, unless otherwise noted. Cells were rinsed in PBS containing 1% Bovine Serum Albumin (BSA) to prevent cell clumping, and then resuspended in 1 ml Buffer W (10 mM Tris-HCl pH 8.0, 10 mM KCl, 250 mM sucrose, 5 mM MgCl2, 0.5 mM DTT, 10% glycerol, 1% BSA) then strained through a 35 μm nylon mesh filter. The tube was rinsed with an additional 1ml of Buffer W and passed through the same strainer. A 9X volume of Buffer P (Buffer W + 0.1% IGEPAL CA-630) was immediately added to each sample and nutated for 2 minutes at room temperature. Cells were resuspended in 500μl Buffer F (50 mM Tris-Cl pH 8.3, 40% glycerol, 5 mM MgCl2, 0.5 mM DTT, 1 μL/ml SUPERaseIn RNase inhibitor, 0.5% BSA) using a wide-bore P1000 tip and transferred to a low binding tube. The original tube was rinsed with another 500μl Buffer F and the samples were pooled. Samples were spun at 400xg and resuspended to 5 x 106 cells in 500μl Buffer F. Samples were flash frozen in liquid nitrogen and stored at −80°C
PRO-seq library construction and data analysis was performed by the Nascent Transcriptomics Core at Harvard Medical School, Boston, MA. Aliquots of frozen (-80°C) permeabilized cells were thawed on ice and pipetted gently to fully resuspend. Aliquots were removed and permeabilized cells were counted using a Luna II, Logos Biosystems instrument. For each sample, 1 million permeabilized cells were used for nuclear run-on, with 50,000 permeabilized Drosophila S2 cells added to each sample for normalization. Nuclear run on assays and library preparation were performed essentially as described in Reimer et al. (Reimer et al., 2021)  with modifications noted: 2X nuclear run-on buffer consisted of (10 mM Tris (pH 8), 10 mM MgCl2, 1 mM DTT, 300mM KCl, 40uM/ea biotin-11-NTPs (Perkin Elmer), 0.8U/μl SuperaseIN (Thermo), 1% sarkosyl). Run-on reactions were performed at 37°C. Adenylated 3' adapter was prepared using the 5' DNA adenylation kit (NEB) and ligated using T4 RNA ligase 2, truncated KQ (NEB, per manufacturers instructions with 15% PEG-8000 final) and incubated at 16°C overnight. 180μl of betaine blocking buffer (1.42g of betaine brought to 10ml with binding buffer supplemented to 0.6 uM blocking oligo (TCCGACGATCCCACGTTCCCGTGG/3InvdT/)) was mixed with ligations and incubated 5 min at 65°C and 2 min on ice prior to addition of streptavidin beads. After T4 polynucleotide kinase (NEB) treatment, beads were washed once each with high salt, low salt, and blocking oligo wash (0.25X T4 RNA ligase buffer (NEB), 0.3uM blocking oligo) solutions and resuspended in 5' adapter mix (10 pmol 5' adapter, 30 pmol blocking oligo, water). 5' adapter ligation was per Reimer but with 15% PEG-8000 final. Eluted cDNA was amplified 5-cycles (NEBNextµltra II Q5 master mix (NEB) with Illumina TruSeq PCR primers RP-1 and RPI-X) following the manufacturer's suggested cycling protocol for library construction. A portion of preCR was serially diluted and for test amplification to determine optimal amplification of final libraries. Pooled libraries were sequenced using the Illumina NovaSeq platform.

treatment_protocol: The following siRNAs (Dharmacon) were used: Non-targeting control (D-001210-05-05), NIPBL (J-012980-08; target sequence: 5’-CAACAGAUCACAUAGAGUU-3’), WAPL (L-026287-01-0005; target sequences administered as a pool: 5’-GGAGUAUAGUGCUCGGAAU-3’, 5’-GAGAGAUGUUUACGAGUUU-3’, 5’-CAAACAGUGAAUCGAGUAA-3’, 5’-CCAAAGAUACACGGGAUUA-3’), and CTCF (L-020165-00-0010; target sequences administered as a pool: 5’-GAUGAAGACUGAAGUAAUG-3’, 5’-GGAGAAACGAAGAAGAGUA-3’, 5’-GAAGAUGCCUGCCACUUAC-3’, 5’-GAACAGCCCAUAAACAUAG-3’). siRNAs were incubated for 20 minutes at room temperature with RNAiMAX Lipofectamine transfection reagent (ThermoFisher) in Opti-MEM reduced serum media (ThermoFisher) and seeded into wells. HCT-116 cells were trypsinized and resuspended in antibiotic free media (McCoy’s 5A media supplemented with 10% FBS and 2 mM L-glutamine), then plated onto siRNA for a final siRNA concentration of 50 nM (non-targetting control and WAPL), 100 nM (NIPBL), or 150 nM (CTCF). For CTCF knockdowns, cells were retreated with 150nM CTCF siRNAs 24 hours after initial treatment. After 72h (NIPBL, WAPL, non-targeting control) or 96h from the initial RNAi treatment (CTCF), cells were harvested for experiments.

tag: cell line

tag: treatment

value: NIPBL siRNA


title: TFexp_H1_PU1_BC03_Rep1


title: NIPBL knockdown rep 1


title: Grad-seq E. faecium fraction 1

city: Würzburg

first: Jörg

last: Vogel

address: Josef-Schneider-Straße 2

department: Institute for Molecular Infection Biology

country: Germany

institute: Würzburg University

data_processing:
Library strategy: Grad-seq
READemption 0.4.5
Genome_build: NC_004668.1  NC_004669.1  NC_004670.1  NC_004671.1  NC_017022.1  NC_017023.1  NC_017024.1  NC_017032.1
Supplementary_files_format_and_content: wig

organism: Enterococcus faecium Aus0004

source_name: bacterial culture, gradient fractionation

growth_protocol: E. faecalis V583 and E. faecium AUS004 were grown at 37°C in M17 medium supplemented with 0.5% glucose with one third of media and two thirds oxygen until logarithmic/early stationary phase at an OD600 of 2.0.

extract_protocol:
Gradient samples were denatured with 1% SDS and RNA was PCI extracted, and ethanol precipitated. 5 µl of the resulting samples were diluted in 45 µl DEPC-treated water. 10 µl were mixedwith 10 µl of a 1:100 diluted ERCC spike-in mix 2 (Thermo Fisher) and subjected to library preparation. In RIP-seq, RNA-protein interaction was denatured by 1% SDS and PCI extraction. RNA was precipitated with ethanol and submitted to library preparation.
The RNA samples were fragmented using ultrasound (4 pulses of 30 s at 4°C) followed by 3′-adapter ligation. First strand cDNA synthesis was performed using M-MLV reverse transcriptase. After purification, the 5′-Illumina TruSeq sequencing adapters were ligated to the 3′end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10–20 ng/µl by high-fidelity DNA polymerase and purified with Agencourt AMPure XP kit (Beckman Coulter). cDNA samples were pooled with according to input concentration, a size range of 200–550 bp was eluted from a preparative agarose gel. This size-selected cDNA pool was sequenced on an Illumina NextSeq 500 system using 75 ntsingle-end read length.

treatment_protocol: DNase I treatment, ERCC spike-in supplementation for Grad-seq. Two polyclonal rabbit antibodies against full-length KhpB were produced by Eurogentec and used for the RIP-seq experiment.

tag: genotype

value: wt

tag: growth state

value: OD 2


title: TFexp_H1_NOTF_BC02_Rep2

value: Compacted Array


title: Embryo, E13.5, single nuclei ATAC

city: Stockholm

first: Margherita

last: Zamboni

address: Solnavägen 9

department: Cell and Molecular Biology

country: Sweden

institute: Karolinska Institutet

description: snATAC-seq

source_name: Embryo

value: Embryo

tag: age

tag: strain

value: WT


title: K348_T_39

city: Atlanta

first: Haydn

last: Kissick

state: Georgia

address: 1462 Clifton Rd

institute: Emory University

data_processing:
Aligned with HISAT2
Reads counted with subread/featurecounts
normalization and differential expression with DESEQ2
Assembly: HG38
Supplementary files format and content: CSV file with raw counts for all genes and samples

source_name: Tumor

extract_protocol: Qiagen micro RNA/DNA all-prep column

value: Tumor

tag: cell type

value: CD8 T cell


title: Embryo, E12.5, single nuclei ATAC

description: snATAC-seq


title: K300_T_39


title: TFexp_H1_NOTF_BC01_Rep1


title: LIU-LSC-1 shRaptor rep3

city: Hefei

first: Dapeng

last: Li

country: China

institute: The First Affiliated Hospital of Anhui Medical University

description: shRaptor

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam)
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam).
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.Linux_x86_64).
Genome_build: mm9
Supplementary_files_format_and_content: 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 level for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with fold change > 2 or fold change < 0.5 and p value < 0.05 by R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html) or DESeq2(http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html),and then analysis GO enrichment and KEGG enrichment to the differentially expressed mRNAs.

growth_protocol: All cells were maintained and propagated in Dulbecco’s modified eagle’s  medium with 10% fetal bovine serum and 1% penicillin/  streptomycin in a humidified atmosphere of 5% CO2 at  37 °C.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: No special treatment

value: shRaptor


title: LIU-LSC-1 shRaptor rep2

description: shRaptor


title: K28_T_39


title: Embryo, E12.5, replicate 1, spatial ATAC

description: spatial ATAC-seq

data_processing:
Raw reads were pre-processed using 10X Genomics’ CellRanger ATAC pipeline (v2.0.0) using a custom ´barcode_whitelist´ specifying positional barcodes from the spatial arrays.
Using 10X Genomics’ Loupe Browser (v6.0.0), we manually selected barcodes belonging to capture spots overlaying tissue and filtered the feature matrices.
We obtained age-specific fragment files from ENCODE and merged them using GenomicRanges’s (v1.46.1) ´reduce()´ function. Next, we calculated new count matrices for each sample separately using FeatureMatrix() function from Seurat (v4.1.0) and merged the data into a single dataset.
We normalized data and performed clustering following Signac (v1.6.0) standard workflow.
Assembly: mm10
Supplementary files format and content: h5 (feature-barcode matrix)
Supplementary files format and content: csv (metadata with spatial coordinates, sample, and clustering)
Supplementary files format and content: tsv (fragments)
Supplementary files format and content: jpg (picture of the tissue section)

extract_protocol:
Crosslinked and permeabilized sections were tagmented d according to OMNI ATAC-seq 3 at 37°C for 1 h under gentle shaking (300 rpm every 5 minutes) using 2 μl Tn5 in tagmentation mix (25 μl 2x TD buffer, 16,5 μl DPBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20). To stop the tagmentation and strip the transposase from DNA, sections were incubated with 50 mM EDTA while ramping down to 30°C for 10 minutes. To hybridise the tagments to the barcoded surface oligonucleotides, we then incubated the sections with a 2 μM solution of splint oligonucleotide (in 3X SSC buffer containing 0.01% Triton-X100, 0.8 μg/μl Proteinase K and 2.5% PEG8000) overnight at 30°C. Next, the sections were rinsed in 2X NEB 2.1 buffer and subsequently incubated with ligation and polymerization solution (1X NEB2.1 containing 3U T4 DNA polymerase, 2000U T4 DNA ligase, 100 μM dNTPs, 1 mM ATP, all from NEB) and incubated at 18°C for 4h. Tissue removal was then performed using 2 mg/ml Proteinase K in PKD-buffer (Qiagen), and incubated at 56°C for 30 minutes (shaking at 300 rpm). The slides were then sequentially washed in 2X SSC 0.1% SDS, 0.2X SSC and 0.1X SSC and finally spin dried.
Spatially barcoded ssDNA fragments were released from the surface by denaturation with 0.08N KOH at room temperature for 10 minutes and then quenched in 10 μl of 1M Tris pH7. The denatured fragments were pH adjusted with sodium acetate and cleaned with MinElute Reaction Cleanup Kit (Qiagen, 28204). The eluted DNA was then amplified using PCR using Partial.R1 and Ad2.short oligonucleotides for 15 cycles using PrimeSTAR Max DNA Polymerase mix (Takara, R045B). The amplified products were purified using 0.9X SPRI beads and i7-indexed in a second PCR (4 cycles) using PE1.0 and Ad2.X (where X is the sample index from 4) oligonucleotides and KAPA HiFi HotStart Mix (Roche, KK2602). The final indexed libraries were cleaned up using 0.8X SPRI beads and adjusted to the desired molarity based on the concentrations measured using Qubit HS dsDNA Assay Kit (Thermo, Q32854) and the average fragment size from HS DNA Bioanalyzer kit (Agilent, 5067-4626).
Pooled libraries were then sequenced on Illumina Nextseq 550 or 2000 instrument using custom sequencing oligonucleotides for Read1 and Index2 (CustomR1 and CustomI2). We sequenced 65 bases for reads 1 and 2 (genomic sequence), 28 bases for i5 (spatial barcode and UMI), and 8 bases for i7 (sample index).


title: TFexp_H1_CEBPb_BC08_Rep2

value: Compacted Array with CEBPb


title: Control rep 2

value: Non-targeting siRNA


title: TFexp_H1_CEBPb_BC07_Rep1


title: Control rep 1


title: K300_T_28


title: K348_T_28


title: LIU-LSC-1 shRaptor rep1

description: shRaptor


title: TFexp_H1_CEBPa_BC06_Rep2

value: Compacted Array with CEBPa


title: Embryo, E12.5, replicate 2, spatial ATAC

description: spatial ATAC-seq


title: LIU-LSC-1 shSs rep3

description: shSc

value: shSc


title: K28_T_28


title: TFexp_H1_CEBPa_BC05_Rep1


title: LIU-LSC-1 shSc rep2

description: shSc


title: Embryo, E15.5, replicate 2, spatial ATAC

description: spatial ATAC-seq


title: Embryo, E13.5, replicate 1, spatial ATAC

description: spatial ATAC-seq


title: Embryo, E15.5, replicate 1, spatial ATAC

description: spatial ATAC-seq


title: K241_LN

source_name: LN

value: LN


title: LIU-LSC-1 shSc rep1

description: shSc


title: TFexp_free_DNA_MNase_digest_BC18_Rep2

value: Free DNA


title: TFexp_free_DNA_MNase_digest_BC17_Rep1

value: Plasmid-amplified sequence


title: K80_LN


title: Adult primary cortical Ecs treated with MS-275- 2  (biol rep 2)

city: Houston

first: Peeyush Kumar

last: Thankamani Pandit

state: TEXAS

address: 6431 Fannin St,

department: Neurosurgery

institute: University of Texas Health Science Center Houston

description: PD_State_MS275_vs_Control-Adult_MS275-Adult_Control_results

data_processing:
mRNA-seq reads were quality checked using FastQC [www.bioinformatics.babraham.ac.uk/projects/fastqc/] after removing adaptors with cutadapt. .
Raw reads were mapped with STAR read aligner and default parameters against build mm10 of the mouse reference genome and the latest annotation of mouse genome from the mouse GENCODE repository
We used featureCounts to count reads on each gene for gene expression quantification.
Differentially expressed genes were detected and ranked using DESeq2
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each Sample

source_name: Primary cortical endothelial cells

extract_protocol:
Direct-zol RNA MiniPrep (Zymo research R2052). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA with an integrity number of greater than 7 was used for library preparation. Libraries were prepared with KAPA mRNA HyperPrep (KK8581, Roche) and KAPA UDI Adapter Kit 15μM (KK8727, Roche) following the manufacturer’s instructions.

value: Primary cortical endothelial cells

tag: developmental stage

value: Adult


title: K42_LN


title: LIU-LSC-1 ITGA5-KO rep3


title: TFexp_array_MNase_digest_BC20_Rep2

value: Nucleosome Array


title: LIU-LSC-1 ITGA5-KO rep2


title: TFexp_array_MNase_digest_BC19_Rep1


title: Adult primary cortical Ecs treated with Wnt3a-2  (biol rep 2)

description: PD_State_WNT3a_vs_Control-Adult_WNT3a-Adult_Control_results

value: Wnt3a 200nM


title: BAL sample patient 12, covid neg

city: Zwijnaarde

first: Liesbet

last: Martens

address: Technologiepark 927

department: VIB Inflammation Research Center

country: Belgium

institute: VIB-University of Ghent

description: filtered_feature_bc_matrix_sampleName.h5 = count matrix of genes and antibodies; metaData_allBAL-umap.csv = metadata of umap in fig 2A; metaData_zoomMF-umap.csv = metadata of umap in fig 1B; metaData_zoomMF-diffMap.csv = metadata of diffusion map in fig1F; usedABs.csv = list of ABs used for TotalVI analysis

data_processing:
Pre-processing of sequencing results to generate count matrices (gene expression, ADT barcode counts) was performed using the 10x genomics Cell Ranger pipeline (v4.0) and aligning to the GRCh38 genome build. For more detail, see Loss of evolutionary conserved GM-CSF-dependent signature in pulmonary macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment. Cell Reports Medicine. 2022
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files:h5 files

source_name: Lung

extract_protocol:
Extraction method explained in Loss of evolutionary conserved GM-CSF-dependent signature in pulmonary macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment. Cell Reports Medicine. 2022
Library construction explained in Loss of evolutionary conserved GM-CSF-dependent signature in pulmonary macrophages in COVID-19 provides a rationale for inhaled GM-CSF treatment. Cell Reports Medicine. 2022
All samples are CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

value: Lung

value: Bronchoalveolar lavage

tag: covid status

value: negative

tag: sample type

value: citeSeq


title: HIST1H1B KO DAY0 NT biological replicate 3, technical replicate 1

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

description: RNA-Seq

data_processing:
Adapter trimming was performed with cutadapt (version 1.9.1) (Martin M, 2011) with parameters “--minimum-length=25 --quality-cutoff=20 -a AGATCGGAAGAGC”.
The RSEM package (version 1.2.31) (Li and Dewey, 2011) in conjunction with the STAR alignment algorithm (version 2.5.2a) (Dobin et al., 2013) was used for the mapping and subsequent gene-level counting of the sequenced reads with respect to hg19 RefSeq genes downloaded from the UCSC Table Browser (Karolchik et al., 2004) on 7th June 2017. The parameters used were “--star-output-genome-bam --forward-prob 1”.
Differential expression analysis was performed with the DESeq2 package (version 1.12.3) (Love et al., 2014) within the R programming environment (version 3.3.1). An adjusted p-value of <= 0.01 was used as the significance threshold for the identification of differentially expressed genes.
Genome_build: hg19
Supplementary_files_format_and_content: Tab-delimited text file containing raw counts and TPM values generated by RSEM where gene names are rows and columns represent all RNA-Seq samples generated in the study.

molecule: polyA RNA

source_name: Melanoma cells MEXF 2090

growth_protocol: Cells were grown in RPMI medium containing Tet-free 10% fetal bovine serum (FBS), 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2.

extract_protocol:
Total cell RNA was prepared from the cells using RNAeasy reagents (Qiagen).
3’ mRNA-Seq libraries were prepared with the Lexogen QuantSeq 3’ mRNA-Seq (FWD) kit.  Total RNA was quantified using via the RNA QuantiFluor RNA system E3310 on the GloMax (Promega) Multi Detection system following the maufacturer's guidelines.  RNA quality was checked via the High Sensitivity RNA ScreenTape using the TapeStation 4200 (Agilent).  RNA was normalised to 30 ng and used for cDNA synthesis and library preparation using the Lexogen QuantSeq 3’ mRNA-Seq (FWD) kit according to the manufacturer’s instructions.  Libraries were sequenced on the Illumina HiSeq 4000 with single ended reads

treatment_protocol: Cells were grown in the absence of glutamine (RPMI medium containing Tet-free 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 µg/ml streptomycin, at 37 °C in 5% CO2) for 12d

value: Melanoma cells MEXF 2090

value: HIST1H1B KO

tag: timepoint

value: DAY 0

value: NT


title: BF70_2

city: Armilla

first: Antonio

middle: M

last: Estevez

state: Granada

address: Avda. del Conocimiento 17

department: Lopez-Neyra

country: Spain

institute: CSIC

description:
NGS041-20-5_S5
processed data file: bfRBP33.tsv

data_processing:
TruSeq RNA Single Indexes (set A&B)
The resulting 75-nt paired end sequences were checked for quality using FastQC, and
mapped to the T. brucei genome using the ‘align’ program of the Subread package with option unique=TRUE
Reads assignment to mRNAs and counting were carried out using the ‘featureCounts’ program of the Subread package (options -t gene -B -C)
Replicates were compared using the edgeR package
Genome_build: 427 2018 version 4.9
Supplementary_files_format_and_content: edgeR output, tab-delimited text file

organism: Trypanosoma brucei brucei

source_name: Cultured trypanosomes

growth_protocol: Grown in HMI-9 medium at 37ºC (bloodstream) or SDM-79 medium at 27ºC (procyclic)

extract_protocol:
Cells were centrifuged and RNA was extracted using the RNeasy Mini Kit (Qiagen)
TruSeq Stranded mRNA® Illumina

treatment_protocol: ± 1 µg/ml tetracycline for RNAi induction

value: Bloodstream forms, S16 strain

value: trasfected with pGR70 (RNAi plasmid)

tag: sample group

value: RNAi induced


title: LIU-LSC-1 ITGA5-KO rep1


title: ISC1

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

data_processing:
The instrument model is BGISEQ-500
The original sequencing data contained reads with low quality, joint contamination and high unknown base N content. These reads needed to be removed before data analysis to ensure the reliability of the results
After clean reads were obtained, clean reads were aligned to the reference genome sequence using HISAT
Clean reads were aligned to the reference gene sequence using Bowtie2 to obtain alignment results.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: spleen

extract_protocol:
Total RNA from spleen
RNA libraries were prepared for sequencing using standard BGISEQ protocols

treatment_protocol: Oral dosing

value: spleen

tag: agent

value: Blank


title: Naive3

source_name: PBMC

value: PBMC

value: CD8 T cell


title: 3D7-Imp input

city: Barcelona

first: Lucas

last: Michel-Todó

state: Barcelona

address: Roselló, 149

department: Malaria Epigenetics

institute: ISGlobal

data_processing:
Quality check was perfomed using FastQC (v.0.11.9) and reads were trimmed and repetitive k-mers removed using BBDUK (v.36.99), with parameters ktrim = r, k = 22, and mink = 6
Reads were aligned to the reference genome (P. falciparum 3D7, plasmoDB release 28) using Bowtie2 (v.2.3.0)
Duplicated reads were excluded using PICARD suite (v.4.1.9.0) with the RemoveDuplicates command
Peak calling was performed using MACS2 (v.2.2.7.1) with parameters “-f BAMPE -B -g 2.41e7 --keep-dup all --fe-cutoff 1.5 -nomodel --extsize 150”.
Coverage as RPKMs was generated for each sample at 10 bp resolution, using DeepTools (v. 3.5.0) BamCoverage command with parameters “--normalizeUsing RPKM -bs 10 --smoothLength 200”
Normalized coverage of enrichment over input (log2-transformed) at 10 bp resolution, we used the DeepTools (v. 3.5.0) BamCompare command with parameters “--normalizeUsing RPKM -bs 10 --smoothLength 200 –pseudocount 10”
Assembly: P. falciparum 3D7, plasmoDB release 28
Supplementary files format and content: Bedgraph: Coverage as RPKMs
Supplementary files format and content: Bedgraph: Coverage as input normalized RPKMs (except input samples)
Supplementary files format and content: narrowPeak: Peaks called using MACS2 (except input samples)

organism: Plasmodium falciparum

source_name: Cell Culture

growth_protocol: Plasmodium falciparum parasites (3D7 line) were maintained at a 3% hematocrit with B+ erythrocytes in standard parasite culture medium with Albumax II and no human serum, in a 5% CO2, 3% 02, balance N2 atmosphere.

extract_protocol:
Sorbitol-synchronized cultures at the late trophozoite-early schizont stage were saponin lysated and formaldehyde cross-linked. Chromatin was extracted using the MAGnify Chromatin Immunoprecipitation System (Life Technologies) and sonicated using a Covaris M220 sonicator.
ChIP-seq libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 4 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 8-10 cycles on the thermocycler.

value: Cell Culture

tag: parental line

tag: subclone

value: No

tag: Stage

value: late trophozoite-early schizont stage

tag: chip antibody


title: K28_LN

tag: tissue

value: LN


title: Adult primary cortical Ecs treated with MS-275- 1  (biol rep 1)

value: Primary cortical endothelial cells

value: Adult

value: WT

tag: treatment


title: LIU-LSC-1 WT rep3

tag: cell line

tag: genotype

value: wild type


title: TFexp_H1_PU.1_CEBPb_BC11_Rep1

value: Plasmid-amplified sequence

tag: condition

value: Compacted Array with PU.1+CEBPb


title: BF70_3

description:
NGS041-20-6_S6
processed data file: bfRBP33.tsv

tag: strain

value: Bloodstream forms, S16 strain


title: Sample 51 (M-2H-3)

type: RNA

city: Ottawa

first: Sabina

last: Halappanavar

state: ON

address: 251 Sir Frederick Banting Driveway

country: Canada

institute: Health Canada

hyb_protocol: An equimolar amount of UMRR cRNA was mixed with each experimental cRNA and was hybridized to 8x60K Agilent SurePrint G3 Mouse Gene Expression v2 Microarray (Agilent Technologies, Inc., Santa Clara, USA) slides in a hybridization chamber for 17 h at 65°C rotating at 10 rpm.

scan_protocol: Microarray slides were washed according to manufacturer’s protocol and scanned on an Agilent G2505B scanner. Data was retrieved using the Feature Extraction 11.0.1.1 software (Agilent). Data analysis is described below.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 11.0.1.1). Non background subtracted median signal intensities were LOWESS normalized using the maanova library in R. Probes with technical replicates were averaged using the median.

source_name: Immortalized Lung Epithelial cells (FE1)

label_protocol: In brief, 200 ng of total RNA per cell pellet sample or Universal Mouse Reference RNA (UMRR; Agilent Technologies) were used to synthesise labelled cDNAs and cRNAs using the Linear Amplification Kit (Agilent Technologies). T7 RNA polymerase-transcribed cRNA from experimental samples were labelled with Cyanine-5 and UMRR was labelled with Cyanine-3.

growth_protocol: FE1 immortalized alveolar lung epithelial cells were cultured as described in Decan et al 2015, in Dulbecco’s Modified Eagle’s Medium Nutrient Mixture F-12HAM (DMEM F12HAM) supplemented with 2 % fetal bovine serum (FBS), 1 ng/mL epidermal growth factor (EGF), 100 U/mL penicillin G, and 100 µg/mL streptomycin and maintained at 37°C, with 5 % CO2.

extract_protocol: RNA extraction, quantification, and integrity analysis were conducted as in Decan et al., 2015. Following exposure and collection of cell pellets, TRIzol reagent was used to isolate RNA in conjunction with Direct-zol RNA Miniprep Kit (Zymo Research Corp, Irvine, USA) according to manufacturer’s protocol (with a 2 min incubation in water prior to elution). Total RNA concentration and purity was determined using a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc, Waltham, USA). RNA integrity and quality analysis was conducted using an Agilent 2100 Bioanalyzer system (Agilent Technologies, Inc., Santa Clara, USA). RNA samples with an RNA Integrity Number (RIN) of ≥5 were used for subsequent microarray experiments.

treatment_protocol: Cells were plated at a cell density of 130 000 cells/well in 6-well plates. Following overnight incubation, cells were exposed to 1.8 mL of 1, 5, 10, and 25 µg/mL CuO NPs, CuO MPs or 7 µg/mL CuCl2. For all exposures, blank media exposed cells served as negative controls. For CuCl2 experiments, cells treated with 5 µg/mL NaCl were also used as additional control to rule out the possible contribution of Cl ions to the observed cellular toxicity in CuCl2 exposures. Following 2, 24, and 48 h of exposure, cell supernatant was harvested, cells were washed with PBS, trypsinized and suspended in fresh cell culture media. An aliquot of cell suspension was used for Trypan Blue dye exclusion staining and the rest of the cells were pelleted by centrifugation (8000 rpm, 10 minutes, 4°C) and frozen at -80°C for microarray analysis. Three biological replicates were used for each condition.

value: MutaMouse

value: Immortalized Lung Epithelial cells

value: Blank Media

tag: time point

value: 2 Hour

tag: dose

value: 0 ug/mL

tag: biological replicate

source_name: Universal Mouse Reference RNA

value: 11 mouse cell lines


title: Sample 40 (NP-10-2H-2)

value: CuO Nanoparticle

value: 10 ug/mL


title: Adult primary cortical Ecs treated with Wnt3a- 1  (biol rep 1)

tag: cell type

tag: developmental stage

value: Wnt3a 200nM


title: 3D7-Imp H3K9ac

value: Cell Culture

value: No

value: late trophozoite-early schizont stage

value: Diagenode, C15410004


title: Naive2

value: PBMC

value: CD8 T cell


title: LIU-LSC-1 WT rep2

value: wild type


title: Sample 16 (NP-5-2H-3)

value: 5 ug/mL


title: E-13.5 cortical Ecs-3  (biol rep 3)

description: Condition_E135_vs_Adult-E135_Control-Adult_Control_results

value: Primary cortical endothelial cells

value: WT

value: control


title: LIU-LSC-1 WT rep1


title: Sample 19 (MP-5-24H-1)

value: MutaMouse

value: Immortalized Lung Epithelial cells

value: CuO Microparticle

value: 24 Hour


title: Oxa2

city: Shijiazhuang

first: Luyuan Ma

middle: Luyuan

last: Ma

address: No.68, Xiangjiang Road

institute: the Third Hospital of Hebei Medical University

data_processing:
Nova6000 software used for basecalling.
After analyzing the RNA integrity of the sample and whether there is DNA contamination, Nanodrop is used to quantify and detect the RNA concentration and purity, and then use the Agilent 2100 bioanalyze to accurately detect the RNA integrity.
After the library is constructed, Qubit 2.0 is used for preliminary quantification, then Agilent 2100 is used to detect the Insert size of the library, and then the effective concentration of the library is accurately quantified using the qRT-PCR method to ensure the quality of the library.
Perform Illumina PE150 sequencing after pooling according to the effective concentration of the library and data output requirements. After the sequencing is completed, it is mainly based on the statistics of sequencing error rate, data volume, comparison rate, etc., to evaluate that the sequencing of the library is up to the standard for subsequent analysis.
Genome_build: mm9

source_name: liver

growth_protocol: HepG2 cells were cultured in DMEM medium containing fetal bovine serum and antibiotics and placed in incubator with 5% carbon dioxide at 37 C

extract_protocol:
Different groups of HepG2 cell lines were flash frozen on dry ice, and RNA was harvested using Trizol reagent.We used 2 ug total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard nova6000 Illumina PE150 protocol.

value: liver hepatocellular carcinoma

value: liver

tag: phenotype

value: oxaliplatin resistant cells


title: Islet, PASHA, rep1

city: Boston

first: Jonathan

last: Dreyfuss

state: MA

address: 1 Joslin Pl

department: Bioinformatics & Biostatistics Core

institute: Joslin Diabetes Center

data_processing:
Reads were aligned to the mouse mRNA transcriptome (Ensembl version 98) using kallisto and transcript counts converted to gene counts using tximport. We filtered out low expressing genes defined as those having less than 0.25 counts per million (CPM) in at least 5 samples. We then normalized counts by weighted trimmed mean of M-values (TMM) and transformed to log2-counts per million (LogCPM) using Voom.
Assembly: Ensembl Mus musculus version 98
Supplementary files format and content: CSV of log2 counts-per-million

source_name: Pancreatic islet

extract_protocol:
Total RNA was extracted from islet cells using RNeasy Mini Kit (Qiagen). Four sets of samples each from islets pooled from 2 mice were used for RNAseq.
Library prep was completed using the NexteraXT kit

value: Pancreatic islet

value: Islet cells

tag: Sex

value: Female

tag: age

value: 10 weeks

value: NOD

value: PASHA


title: Islet, PASHA, rep4


title: Islet, Vehicle, rep5

value: Vehicle


title: Islet, PASHA, rep2


title: E-13.5 cortical Ecs-2  (biol rep 2)

value: Primary cortical endothelial cells


title: Naive1

value: PBMC

value: CD8 T cell


title: Oxa1


title: Normal2

value: wild type


title: Islet, Vehicle, rep4


title: Islet, Vehicle, rep3


title: Adult primary cortical Ecs control- 3  (biol rep 3)

value: Adult

value: WT

value: control


title: E-13.5 cortical Ecs-1  (biol rep 1)


title: Islet, PASHA, rep3


title: Aldh1l1;Ptbp1-HOM;Sun1-GFP, FACS-purified, Cortex [TKG5]

city: Baltimore

first: Dong Won

middle: Thomas

last: Kim

state: Maryland

address: 733 N.Broadway, MRB building (Rm 332)

department: Neuroscience

institute: Johns Hopkins University

description: scRNA-Seq

library_source: transcriptomic single cell

data_processing:
scRNA-Seq: Sequencing results were processed through the Cell Ranger pipeline (10x Genomics) with default parameters. Seurat V3 was used to perform downstream analysis following the standard pipeline.
Assembly: mm10
Supplementary files format and content: scRNA-Seq count matrix

source_name: scRNA-Seq - TKG5_CR7

extract_protocol: scRNA-Seq following 10x V3.1 guideline

value: Cerebral cortex

value: 2 months old

value: pooled male and female


title: Normal1

value: liver hepatocellular carcinoma

value: liver


title: Islet, Vehicle, rep1

value: Pancreatic islet

value: Islet cells

value: Female


title: Adult primary cortical Ecs control- 2  (biol rep 2)


title: Aldh1l1;Ptbp1-HOM;Sun1-GFP, FACS-purified, Striatum [TKG4]

description: scRNA-Seq

source_name: scRNA-Seq - TKG4_CR7

value: Striatum


title: Aldh1l1;Ptbp1-WT;Sun1-GFP, FACS-purified, Striatum [TKG7]

description: scRNA-Seq

source_name: scRNA-Seq - TKG7_CR7


title: Aldh1l1;Ptbp1-WT;Sun1-GFP, FACS-purified, Substantia Nigra [TKG6]

description: scRNA-Seq

source_name: scRNA-Seq - TKG6_CR7

value: Substantia Nigra


title: Aldh1l1;Ptbp1-WT;Sun1-GFP, FACS-purified, Cortex [TKG8]

description: scRNA-Seq

source_name: scRNA-Seq - TKG8_CR7


title: s, ESC, XHOM&PKRnull+MosIR, RSP.3

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

data_processing:
Small RNA-seq reads were trimmed using fastx 0.0.14 and cutadapt 1.8.3:  zcat ${FILE}.fastq.gz | fastx_trimmer -f 5 -i - -o ${FILE}.tmp.fastq  cutadapt --format="fastq" --front=GTTCAGAGTTCTACAGTCCGACGATCNNNN --adapter=NNNNTGGAATTCTCGGGTGCCAAGG --error-rate=0.075 --times=2 --overlap=14 --minimum-length=12 --max-n=0.1 --output="${FILE}.fastq" --trim-n --match-read-wildcards ${FILE}.tmp.fastq
Trimmed reads were mapped to mouse (mm10) genome using STAR 2.7.3a with following parameters:  STAR --readFilesIn ${FILE}.fastq.gz --genomeDir ${GENOME_INDEX} --runThreadN 12 --genomeLoad NoSharedMemory --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix ${FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMultimapNmax 99999  --outFilterMismatchNoverLmax 0.1 --outFilterMatchNminOverLread 0.66 --alignSJoverhangMin 999 --alignSJDBoverhangMin 999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.29.2 and wigToBigWig v 4 from UCSC:  genomeCoverageBed -ibam ${FILE} -bg -split > ${FILE}.bedGraph  wigToBigWig ${FILE}.bedGraph chrNameLength.txt ${FILE}.bw
Genome_build: mm10
Supplementary_files_format_and_content: coverage genome browser tracks files:  - .bigWig format  - generated in a non-stranded mode.   - not normalized for library size

source_name: mouse ESC

growth_protocol: Mouse ESCs were cultured in 2i-LIF media: KnockOut-DMEM (ThermoFisher) supplemented with 15% fetal calf serum (Sigma), 1x L-Glutamine (Sigma), 1x non-essential amino acids (ThermoFisher), 50 µM β-Mercaptoethanol (ThermoFisher), 1000 U/mL LIF (Isokine), 1 µM PD0325901, 3 µM CHIR99021 (Selleck Chemicals), penicillin (100 U/mL), and streptomycin (100 µg/mL). All plastic was coated with 1% gelatin (Sigma) in PBS.

extract_protocol:
Cells were washed with PBS, homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by Qiazol-chloroform extraction and ethanol precipitation method. RNA quality was verified by Agilent 2100 Bioanalyzer.
Small RNA libraries were constructed using NEBNext Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) according to the manufacturer’s protocol. Small RNA libraries were size selected on 6% PAAGE gel, a band of 140 - 150 bp was cut from the gel and RNA was extracted using Monarch® Genomic DNA Purification Kit. Quality of the libraries was assessed by Agilent 2100 bioanalyzer.

treatment_protocol: Cells were transfected with 2 μg/well of pCAG-EGFP-MosIR plasmid and cultured for 48 hours.

value: Dicer X/X & Pkr-/-

tag: transfection

value: MosIR

value: ESC

tag: fraction

value: small RNA

tag: replicate


title: Adult primary cortical Ecs control- 1  (biol rep 1)

source_name: Primary cortical endothelial cells

value: Primary cortical endothelial cells

value: Adult


title: Aldh1l1;Ptbp1-HOM;Sun1-GFP, FACS-purified, Substantia Nigra [TKG3]

description: scRNA-Seq

source_name: scRNA-Seq - TKG3_CR7

tag: tissue


title: Aldh1l1;Ptbp1-WT;Sun1-GFP, FACS-purified, Cortex [TKG2]

description: scRNA-Seq

source_name: scRNA-Seq - TKG2_CR7


title: Aldh1l1;Ptbp1-WT;Sun1-GFP, FACS-purified, Substantia Nigra [TKF9]

description: scRNA-Seq

source_name: scRNA-Seq - TKF9_CR7


title: s, ESC, XHOM&PKRnull+MosIR, RSP.2


title: s, ESC, XHOM+MosIR, RS10.3

value: Dicer X/X


title: s, ESC, XHOM&PKRnull+MosIR, RSP.1


title: Aldh1l1;Ptbp1-HOM;Sun1-GFP, FACS-purified, Cortex [TKF8]

description: scRNA-Seq

source_name: scRNA-Seq - TKF8_CR7

value: Cerebral cortex


title: Aldh1l1;Ptbp1-HOM;Sun1-GFP, FACS-purified, Substantia Nigra [TKF6]

description: scRNA-Seq

source_name: scRNA-Seq - TKF6_CR7

value: 2 months old


title: s, ESC, XHOM+MosIR, RS10.2


title: s, ESC, XHOM+MosIR, RS10.1


title: Aldh1l1-CreERT2;Ptbp1-HOM;Sun1-GFP, Substantia Nigra -tech replicate, CellRanger 7 [TKD4a_CR7]

description: scRNA-Seq

source_name: scRNA-Seq - TKD4a_CR7


title: Aldh1l1-CreERT2;Ptbp1-HOM;Sun1-GFP, Substantia Nigra, CellRanger 7 [TKD4_CR7]

description: scRNA-Seq

source_name: scRNA-Seq - TKD4_CR7


title: B11, timepoint 43-48 hpi

hyb_protocol: Hybridization performed as previously described (Painter, H. et al., 2013. PMID: 22990780).

scan_protocol: Microarrays images were obtained using the Agilent G2505C Microarray Scanner.

data_processing:
Normalized Cy5 and Cy3 values were obtained directly using Agilent Feature Extraction software. The rest of the analysis was performed using mainly the Bioconductor and the tidyverse suite libraries in an R environment (v. 3.6.3). IFor each channel, background signal intensity was calculated as the median signal of the 100 lowest signal probes in each array. Probes with a signal for both channels below three times the background were excluded from further analysis. For each probe, the expression value was defined as the log2(Cy5/Cy3) signal. Probes were collapsed into genes using median polish. For each array, estimated parasite age in hpi was calculated using a previously described maximum likelihood method [Lemieux et al., 2009, PMID: 19376968]. For each gene and subclone, expression plots where generated with gene expression values in the y-axis and estimated hpi in the x-axis. These plots were used to calculate the average fold-change (AFC) for each gene over four overlapping time intervals of half the estimated parasite age difference (in hpi) between the first and last analysis time points. The AFC was calculated for all possible pairwise comparisons among A7, E5 and B11. The maximum AFC (mAFC) was defined as the AFC at the time interval in which it had the highest absolute value.
The file processed_data_with_genename.txt includes all normalized data with gene annotations and which probes were excluded from analysis

label_protocol: Test sample, Cy5; reference pool, Cy3. As previously described (Painter, H. et al., 2013. PMID: 22990780)

growth_protocol: Samples for transcriptomic analysis of A7, E5 and B11 lines were obtain from tightly synchronized cultures (0-5 h window) achieved by Percoll purification of erythrocytes infected with mature stages followed by 5% sorbitol lysis 5 h later. RNA was extracted from samples collected at 10-15, 20-25, 30-35, 37-42, 40-45 and 43-48 h post-invasion (hpi) using the Trizol method. After reverse transcription and labelling, Cy5-labelled samples where hybridized against a Cy3-labelled reference pool. The reference pool consisted of a mixture of equal amounts of cDNA from rings, trophozoites and schizonts from 3D7-A and 3D7-B stocks. Samples were hybridized oncustom Agilent microarrays (AMADID no. 085763) modified from design  AMADID no. 037237.

extract_protocol: RNA was purified using the TRIzol method following the manufacturer instructions.

treatment_protocol: No treatment was applied.

tag: parental strain

tag: timepoint

tag: estimated age (hpi)

source_name: 3D7-A and 3D7-B mixed stage Reference Pool

value: 3D7-A and 3D7-B


title: B11, timepoint 30-35 hpi

value: mixture of equal amounts of cDNA from rings, trophozoites and schizonts from 3D7-A and 3D7-B


title: B11, timepoint 40-45 hpi


title: s, ESC, WT+MosIR, RS7.2

tag: genotype

value: Dicer wt/wt


title: B11, timepoint 20-25 hpi

tag: strain


title: Aldh1l1-CreERT2;Ptbp1-WT;Sun1-GFP, Substantia Nigra, CellRanger 7 [TKD2_CR7]

description: scRNA-Seq

source_name: scRNA-Seq - TKD2_CR7


title: B11, timepoint 37-42 hpi


title: B11, timepoint 10-15 hpi


title: E5, timepoint 43-48 hpi


title: Aldh1l1-CreERT2;Ptbp1-HET;Sun1-GFP, Substantia Nigra, CellRanger 7 [TKD3_CR7]

description: scRNA-Seq

source_name: scRNA-Seq - TKD3_CR7


title: E5, timepoint 40-45 hpi


title: s, ESC, WT+MosIR, RS7.1


title: Aldh1l1-CreERT2;Ptbp1-HET;Sun1-GFP, Striatum, CellRanger 7 [TKC9_CR7]

description: scRNA-Seq

source_name: scRNA-Seq - TKC9_CR7


title: Aldh1l1-CreERT2;Ptbp1-HET;Sun1-GFP, Cortex, CellRanger 7 [TKC6_CR7]

description: scRNA-Seq

source_name: scRNA-Seq - TKC6_CR7


title: Aldh1l1-CreERT2;Ptbp1-HOM;Sun1-GFP, Striatum, CellRanger 7 [TKD1_CR7]

description: scRNA-Seq

source_name: scRNA-Seq - TKD1_CR7


title: Aldh1l1-CreERT2;Ptbp1-WT;Sun1-GFP, Striatum, CellRanger 7 [TKC8_CR7]

description: scRNA-Seq

source_name: scRNA-Seq - TKC8_CR7


title: Aldh1l1-CreERT2;Ptbp1-WT;Sun1-GFP, Cortex, CellRanger 7 [TKC5_CR7]

description: scRNA-Seq

source_name: scRNA-Seq - TKC5_CR7


title: Aldh1l1-CreERT2;Ptbp1-HOM;Sun1-GFP, Cortex, CellRanger 7 [TKC7_CR7]

description: scRNA-Seq

source_name: scRNA-Seq - TKC7_CR7


title: E5, timepoint 20-25 hpi


title: E5, timepoint 37-42 hpi


title: E5, timepoint 30-35 hpi


title: E5, timepoint 10-15 hpi


title: A7, timepoint 43-48 hpi


title: A7, timepoint 30-35 hpi


title: A7, timepoint 40-45 hpi


title: A7, timepoint 37-42 hpi


title: Embryo, E13.5, replicate 2, spatial ATAC

description: spatial ATAC-seq

source_name: Embryo

value: Embryo

value: WT


title: A7, timepoint 20-25 hpi


title: A7, timepoint 10-15 hpi


title: HeLa_TRP24_1

city: New Haven

first: Eduardo

middle: A

last: Groisman

state: Connecticut

address: Boyer Center for Molecular Medicine, 295 Congress Ave

department: Department of Microbial Pathogenesis

institute: Yale School of Medicine

data_processing:
sequencing files from a given replicate were concatenated (usegalaxy.org)
fastp: filter low quality reads, trim reads, cut adaptors (usegalaxy.org)
HISAT2: alignment to reference genome (usegalaxy.org)
htseq-count: count reads aligned to features (usegalaxy.org)
DESeq2: differential gene expression analysis (R)
Genome_build: Chlamydia trachomatis L2 434/Bu ASM6858v1; Homo sapiens GRCh38
Supplementary_files_format_and_content: Normalized count values for each feature output by DESeq2

organism:
Homo sapiens
Chlamydia trachomatis L2/434/Bu

source_name: C. trachomatis-infected HeLa

growth_protocol: Cells were cultured in DMEM + 10% FBS + 2 mM L-Gln + 10 µg/mL gentamicin until treatments were applied

extract_protocol:
Total RNA was collected from cultured cells in Trizol, vortexed with zirconia beads, and phenol-chloroform extracted prior to isolation through a PureLink RNA Mini Kit with two on-column DNA digestion steps. To remove rRNA, 10 µg of total RNA was run in 5 µg parallel samples through the RiboMinus Transcriptome Isolation kit with 3 µL of pan-prokaryotic rRNA probe and 4 µL eukaryotic rRNA probe. Depleted RNA was subsequently concentrated in an RNA Clean and Concentrator Kit from Zymo.
TruSeq Stranded Total RNA library preparation kit (Illumina, San Diego, CA, USA) was used to generate RNA-sequencing libraries following manufacturer protocols with a starting amount of 100 ng rRNA-depleted RNA. Depletion of rRNA in the TruSeq kit was performed by the addition of 2.5 µL each of standard rRNA Removal Mix (RRM) or Prokaryotic RRM.

treatment_protocol: 100 µM 2,2-bipyridyl was added to complete medium as described above; complete media was replaced with defined tryptophan-depleted media: DMEM-F12 w/o L-Trp + 10% dialyzed FBS + 2 mM L-Gln + 10 µg/mL gentamicin

value: C. trachomatis-infected HeLa

tag: treatment

value: Tryptophan-depleted


title: s-E15.5-GNTHOM-9

source_name: mouse E15.5 embryos

extract_protocol:
Embryos were homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by Qiazol-chloroform extraction and ethanol precipitation method.
Small RNA libraries were constructed using Nextflex Small RNA-seq kit v3 for Illumina (Perkin Elmer) according to the manufacturer’s protocol; 3′ adapter ligation was performed overnight at 20 °C, 15 cycles were used for PCR amplification and NextFlex beads were used for size selection.

treatment_protocol: E15.5 embryos were removed from the uterus and washed in PBS. The yolk sac was taken for genotyping and embryos were transferred into RNAlater (Thermo Fisher Scientific)

value: Dicer GNT/GNT

value: embryo


title: s-E15.5-GNTHOM-4


title: HeLa_BPD24_1

value: Bipyridyl


title: Huh7.5.1 HCC cells_DMSO treated (48h), biological rep2

city: Beijing

first: Jun-Nian

last: Zhou

address: 27# Taiping Road

institute: Institute of Health Service and Transfusion Medicine

description:
Gene expression data from huh7.5.1 cells treated with DMSO (48 hours).
Huh7.5.1-con-2

hyb_protocol: Array hybridization and wash was performed using GeneChip® Hybridization, Wash and Stain Kit (Cat#900720, Affymetrix, Santa Clara, CA, US)in Hybridization Oven 645 (Cat#00-0331-220V, Affymetrix, Santa Clara, CA, US) and Fluidics Station 450 (Cat#00-0079, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions

scan_protocol: Slides were scanned by GeneChip® Scanner 3000 (Cat#00-00212, Affymetrix, Santa Clara, CA, US) and Command Console Software 3.1 (Affymetrix, Santa Clara, CA, US) with default settings.

data_processing: Raw data were normalized by MAS 5.0 algorithm, Gene Spring Software 11.0 (Agilent technologies, Santa Clara, CA, US).

label: Biotin

source_name: Huh7.5.1 cell line, treated with DMSO (48 hours) as controls

label_protocol: Total RNA were amplified, labeled and purified by using GeneChip 3’IVT Express Kit (Cat#901229, Affymetrix, Santa Clara, CA, US) followed the manufacturer’s instructions to obtain biotin labeled cRNA.

growth_protocol: The cells were maintained in DMEM (Sigma) or MEM (Sigma) containing 10% FBS (ExCell Biology, Shanghai, China) at 37°C with 5% CO2.

extract_protocol: Total cellular RNA was isolated from the cells using an RNeasy Mini Kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s protocol.

treatment_protocol: The cells were washed with PBS after removed medium, and the TriZol was added into the cell monolayer, gently mixed with the tips, and immmediately freezed with liquid N2, followed by stored in the -80 oC freezer.

tag: cell line

value: Liver cancer cells

tag: agent

value: DMSO


title: Huh7.5.1 HCC cells_CU27 treated (48h), biological rep2

description:
Gene expression data from huh7.5.1 cells treated with 10 μM CU27 (48 hours).
Huh7.5.1-cu27-2

source_name: Huh7.5.1 cell line, treated with 10 μM CU27 (48 hours)

tag: cell type


title: s-E15.5-GNTHOM-3

value: small RNA


title: HeLa_TRP16_1


title: hep3b HCC cells_CU27 treated (48h), biological rep3

description:
Gene expression data from hep3b cells treated with 10 μM CU27 (48 hours).
hep3b-CU27-3

source_name: hep3b cell line, treated with 10 μM CU27 (48 hours)


title: Huh7.5.1 HCC cells_CU27 treated (48h), biological rep1

description:
Gene expression data from huh7.5.1 cells treated with 10 μM CU27 (48 hours).
Huh7.5.1-cu27-1


title: Huh7.5.1 HCC cells_DMSO treated (48h), biological rep1

description:
Gene expression data from huh7.5.1 cells treated with DMSO (48 hours).
Huh7.5.1-con-1


title: s-E15.5-WT-14


title: s-E15.5-WT-16


title: HeLa_BPD16_1


title: s-E15.5-WT-11


title: hep3b HCC cells_DMSO treated (48h), biological rep3

description:
Gene expression data from hep3b cells treated with DMSO (48 hours).
hep3b-con-3

source_name: hep3b cell line, treated with DMSO (48 hours) as controls


title: HeLa_UTD24_1

value: Untreated


title: HeLa_Mock_1

source_name: HeLa

value: Mock-infected HeLa


title: LN_AMP-CpG_24h_3

status: Public on Nov 02 2022

first: Martin

middle: P

last: Steinbuck

state: Massachusetts

address: 451D Street, Ste 501

department: Research

institute: Elicio Therapeutics

description: AMP-CpG 24h - 3

hyb_protocol: Performed by Canopy Biosciences following the NanoString protocols.

data_processing: NanoString generated raw values of 24h samples were analyzed and compared to baseline (0h) samples using Rosalind software. Volcano plots show Rosalind-generated p-values (log2) and fold-changes (-log10). For heat maps, Z-scores were calculated for the raw expression data. These were then averaged among biological duplicates and mock-subtracted.

label: NanoString Probes

organism: Macaca mulatta

extract_protocol: Inguinal lymph node fine needle aspirates were obtained from immunized NHP at the indicated time points and lysed with RLT buffer (Qiagen, cat# 79216).

treatment_protocol: In vivo - vaccine injection into NHP.

value: Lymph node

tag: vaccine

value: AMP-CpG

tag: time

tag: subject


title: LN_AMP-CpG_24h_1

description: AMP-CpG 24h - 1

scan_protocol: Performed by Canopy Biosciences following the NanoString protocols.


title: LN_AMP-CpG_24h_2

description: AMP-CpG 24h - 2

label_protocol: Performed by Canopy Biosciences following the NanoString protocols.


title: hep3b HCC cells_CU27 treated (48h), biological rep2

description:
Gene expression data from hep3b cells treated with 10 μM CU27 (48 hours).
hep3b-CU27-2


title: LN_AMP-CpG_0h_3

description: AMP-CpG 0h - 3


title: 204339300067_R05C01 [Lis45Pp30]

type: genomic

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

description: no duplicate

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC array (850k probes) using standard Illumina protocol

scan_protocol: Arrays were imaged using the Illumina iScan system using standard recommended Illumina scanner setting

data_processing: data was normalized in R (v. 3.6.3) using the minfi package (v. 1.32.0)(Aryee et al., 2014) with the “funnorm” function. Following normalization, probes that were found to cross-reactive on the EPIC array, probes overlapping genetic variatants at targeted CpG sites, and probes overlapping genetic variatants at single base extension sites for Infinium Type I probes were filtered out (Pidsley et al., 2016) leaving a total of 811,063 probes.

label: Cy5 and Cy3

source_name: cultured hESC in primed conditions for defined passage

label_protocol: Standard Illumina Protocol

growth_protocol: Naïve conditions included culture on MEFs in a modification of the naïve human stem cell medium (NHSM) developed by the Hanna laboratory (Gafni et al., 2013), consisting of: 1:1 Neurobasal medium and DMEM/F-12 (Gibco); 1X Pen/Strep (Biological industries); 2 mM L-Glutamine (Biological industries); 1% non-essential amino acids (Biological industries); 0.7 mM sodium pyruvate (Biological industries); 2% ml B27 supplement (in house produced); 0.2% ml defined lipid concentrate (Gibco); 0.05 mM β-ME (Gibco); 12.5 µg/ml insulin (Sigma-Aldrich); 100 µg/ml apo-transferrin (Sigma-Aldrich); 0.02 µg/ml progesterone (Sigma-Aldrich); 16 µg/ml putrescine (Sigma-Aldrich); 30 µM sodium selenite (Sigma-Aldrich); 50 µg/ml L-ascorbic acid 2-phosphate (Sigma-Aldrich); 0.07% BSA (Gibco); 20 ng/ml human LIF (Peprotech); 5 µM IWR1 (Biotest); 20 ng/ml human activin A (Peprotech); 1.7 ng/ml FGF2 (Peprotech); 0.2 µM Chir99021 (Axon Medchem); 1 µM PD0325901 (Axon Medchem); 0.2 µM BIRB796 (Axon Medchem); 2 µM SP600125 (Tocris); 2 µM PKCi (Tocris); 0.4 µM Thiazovivin (Peprotech); and 1.5 µM CGP77675 (Axon Medchem). Primed conditions included culturing on mitotically inactivated mouse embryo fibroblast (MEF) feeder layers in primed hESC culture medium, consisting of: DMEM/F-12 with 20% Knockout Serum Replacement (Gibco); 2 mM L-glutamine (Biological industries); 0.1 mM β-ME (Gibco); 1% non-essential amino acids (Biological industries); 1X Pen/Strep (Biological industries) and 8 ng/ml FGF2 (Peprotech). For both naïve and primed cultures, the medium was changed daily, passaging was performed every 3-5 days using 0.05% trypsin + EDTA (Biological industries), and 5 μM of Y27632 ROCK inhibitor (Axon Medchem) were used for 24 hr before and after passaging. Both naïve and primed cultures were grown without MEFs for two passages prior to collection of cells for molecular analysis.

extract_protocol: Genomic DNA was extracted from samples using the DNeasy Blood & Tissue Kit (Qiagen).

tag: gender

value: Female

tag: passage age

value: early

tag: culture conditions

value: Primed

value: human embryonic stem cell


title: 1025609_12

city: Aurora

first: Sana

middle: D

last: Karam

state: CO

address: 1665 Aurora Ct.

department: Radiation Oncology

institute: CU Denver Anschutz

description: NanoString Canine IO (Item No. 115000456)

organism: Canis lupus familiaris

source_name: Lymph node

extract_protocol: RNA was extracted from frozen tumor tissues using Rneasy Plus Mini Kit (QIAGEN) following manufactures protocol. Depending on starting material, samples were eluted in 30-50L RNase-Free water. Samples were initially checked for quantity and purity on a Nanodrop ND-1000 Spectrophotometer (Thermo Fisher) prior to being stored at -80oC until further processing. Samples were additionally quantity and quality checked using the RNA High Sensitivity assays on the Qubit 2.0 Fluorometer (Invitrogen/LifeTechnologies) and 5200 Fragment Analyzer Automated CE System (Agilent), respectively. NanoString gene expression analysis was performed using the Canine IO 360 panel. Nanostring analysis was performed with the nCounter Analysis FLEX system at the University of Arizona Genetics Core. Gene expression count data was analyzed via nSolver software.

treatment_protocol: Dogs with sinonasal cancer were randomized for treatment with SBRT (10Gy x 3) targeted to primary tumor +/- RLNs (n=3 per treatment group). Tumor only irradiation was targeted to the sinonasal tumor (GTV+ 2mm PTV) without any nodal irradiation. Tumor + ENI, however, included the inonasal tumor (GTV+ 2mm PTV) plus bilateral submandibular and retropharyngeal LNs.

tag: irradiation status

value: Irradiated lymph node

tag: age at diagnosis (years)

tag: Sex

value: Male

tag: hormonal status

value: neutered

tag: tumor type

value: Carcinoma

tag: survival status

value: dead

tag: survival time (days)


title: hep3b HCC cells_DMSO treated (48h), biological rep2

description:
Gene expression data from hep3b cells treated with DMSO (48 hours).
hep3b-con-2


title: 204339300067_R03C01 [Lis45Np18]

description: no duplicate

source_name: cultured hESC in naive conditions for defined passage

value: virgin

value: Naive


title: LN_AMP-CpG_0h_1

description: AMP-CpG 0h - 1

tag: tissue


title: 1025609_06

data_processing: Nanostring analysis was performed with the nCounter Analysis FLEX system at the University of Arizona Genetics Core. Gene expression count data was analyzed via nSolver software.


title: 1024471_11

value: spayed

value: Sarcoma


title: 1024468_04

value: Non-irradiated lymph node


title: 1023635_02

value: Malignant tumor


title: 1024468_10

value: Lymph node


title: 204339300123_R01C01 [Lis46Np30]

description: no duplicate

tag: cell line


title: 1024198_09


title: 204339300067_R02C01 [Lis39Pp51_1]

description: duplicate

value: late


title: 1023635_08


title: 204339300067_R04C01 [Lis45Np31]

description: no duplicate

value: Female


title: 204339300067_R01C01 [LIs39Np51_1]

description: duplicate


title: 1024198_03


title: 204339300123_R07C01 [Lis45Np51_2]

description: duplicate


title: 204339300123_R02C01 [Lis46Pp31]

description: no duplicate

value: early


title: 1024471_05


title: 204339300067_R06C01 [Lis45Np51]

description: duplicate


title: 1021368_01


title: 204339300123_R05C01 [Lis39Np51_2]

description: duplicate


title: Intra-amoebael C. jejuni-3

city: LONDON

first: Fauzy

last: Nasher

address: Keppel Street,

institute: London School of Hygiene and Tropical Medicine

data_processing:
The paired-end reads were trimmed and filtered using Sickle v1.200. Bowtie2 was used to map the reads against the reference sequence: C. jejuni strains 11168H assembly GCA_900117385.1. Cufflinks suite was used to convert annotations from GFF to GTF format and Bedtools was used to generate transcript counts per samples. Statistical analysis was performed in R using the combined data generated from the bioinformatics as well as meta data associated with the study (multifactorial design). Adjusted p-value significance cut-off of 0.001 and log fold change cut-off of >1.5 was used for multiple comparison.
Assembly: GCF_000009085.1 (ASM908v1)
Supplementary files format and content: *_EDGE.out.rpkm_0.txt: Tab-delimited text files include #reads and RPKM.

organism:
Campylobacter jejuni
Acanthamoeba castellanii

source_name: Bacteria + Amoeba

extract_protocol: RNA was extracted using Triazole, quality was checked by agarose gel, library was prepared according to Illumina protocol and was sent for sequencing.

value: Bacteria + Amoeba

tag: c.jejuni strain

tag: c.jejuni genotype

value: WT

tag: a.castellanii genotype

tag: treatment

value: Intra-amoebal bacteria (25C)

value: 4 hrs


title: 204339300123_R08C01 [Lis45Pp54]

description: duplicate

value: Primed

tag: cell type

value: human embryonic stem cell


title: 1021368_07

value: Carcinoma

value: dead


title: 204339300123_R03C01 [Lis46Np51]

description: no duplicate

tag: gender

value: Male

value: Naive


title: 204339300067_R07C01 [Lis45Pp50]

description: duplicate

tag: passage age


title: Intra-amoebael C. jejuni-2

tag: time


title: FD2M1-monoiPSC-P25

city: McAllen

first: Satish

last: Kumar

state: Texas

address: 5300 North L Street (MBMRF-2.219)

department: Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine

institute: University of Texas Rio Grande Valley

data_processing:
Raw fastq sequence files were generated and demultiplexed using Illumina bcl2fastq software (Illumina, Inc., San Diego, CA, USA).
After pre-alignment QCs, sequences were aligned to M. domestica GCF_000002295.2 MonDom5 genome assembly and mapped to M. domestica RefSeq transcripts using StrandNGS software v4 (Strand Life Sciences Pvt. Ltd.).
The aligned reads were filtered based on read quality metrics and only high-quality aligned sequencing reads were retained and quantified using NGS software v4 (Strand Life Sciences Pvt. Ltd., Bangalore, India).
The gene expression values as raw counts of sequencing reads were obtained and log2 transformation and ‘DESeq’ normalization was applied.
Assembly: MonDom5 (GCF_000002295.2)
Supplementary files format and content: Tab-delimited text file of raw counts of sequencing reads formatted as genes-vs-samples matrix table .
Supplementary files format and content: Tab-delimited text file of log2 transformed and DESeq normalized abundance measurements formatted as genes-vs-samples matrix table .

organism: Monodelphis domestica

source_name: induced pluripotent stem cell (iPSC)

growth_protocol: Primary neonatal skin fibroblast (neoSF) cultures from two fully inbred M. domestica strains, FD2M1 and LSD1 were established and then expanded for 3-4 passages in Monodelphis fibroblast growth medium (MFGM) containing Iscove’s Modified Dulbecco’s medium (IMDM), 16% fetal bovine serum (FBS), 0.5% insulin, transferrin, selenite supplement (ITS-G supplement), 2 mM L-glutamine, 1X Antibiotic-Antimycotic solution and 2 mM CaCl2.

extract_protocol:
Total RNA was extracted from snap frozen cell pellets (~3-5 x 106 cells) of M. domestica neonatal skin fibroblasts and validated iPSC lines (at passage 15 and 25) using commercially available RNeasy Mini Kit (Qiagen, Germantown, MD, USA) and the manufacturer protocol. RNA quality and quantity were assessed using a NanoDrop 2000 Spectrophotometer (Thermo Fisher Scientific,Waltham, MA, USA) and an Agilent 2200 TapeStation system (Agilent, Santa Clara, CA, USA).
1µg of total RNA per sample was used to prepare mRNA sequencing libraries. The sequencing libraries were prepared using Illumina TruSeq RNA sample preparation kit v2 and following manufacturer protocol.

treatment_protocol: One million M. domestica neoSF cells in log growth phase were harvested and then nucleofected with 1 µg each of the purified OriP/EBNA episomal plasmids encoding human reprogramming factors OCT4, SOX2, NANOG, KLF4, LIN28 and cMYC.  The nucleofected cells were seeded on human embryonic stem cell (hESC) qualified Matrigel Matrix (Corning) coated six-well cell culture plates, allowed to recover in Monodelphis fibroblast growth medium (MFGM) for 18-24 hours, and then transitioned into commercially available TeSR-E7 medium for reprogramming (Stem Cell Technologies). From day 4 to day 6, when clusters of epithelial like cells with large nuclei started to appear, reprogramming medium was replaced with feeder-free iPSC medium (FF-iPSC-M) containing DMEM/F12, 1% N-2 supplement, 2% B-27 plus supplement, 2 mM GlutaMAX, 0.1 mM MEM NEAA, 10 mM HEPES buffer, 10 ng/ml human LIF, 50 ng/ml heat stable bFGF and 0.25 µM Y27632 ROCK inhibitor, and 0.1 mM 2-mercaptoethanol. Medium was changed daily. From day 14 to 16, iPSC colonies similar in morphology to human iPSCs were picked and expanded in feeder free condition in FF-iPSC-M

value: induced pluripotent stem cell (iPSC)

value: iPSC

tag: genotype

value: wild type

value: cellular reprogramming


title: LSD1-monoiPSC-P15


title: FD2M1-monoiPSC-P15


title: LSD1-neoSF

source_name: skin

value: skin

value: skin fibroblast


title: 204339300123_R04C01 [Lis46Pp51]

description: no duplicate

value: late

tag: culture conditions


title: FD2M1-neoSF


title: scRNAseq WT TBM rep2

city: Nanjing

first: Xi

last: Wang

address: Longmian Avenue 101, Jiangning District

institute: Nanjing Medical University

data_processing:
Illumina HD.3.4.0/RTA 2.7.7 software used for sequencing and basecalling.
RNA-seq: adapter trimming and low-quality read filtering by flexbar (v2.5),  read mapping by Bowtie 2 (v2.2.9) and Tophat2 (v2.1.1), read counting by HTSeq-count (v 0.9.1).
scRNA-seq: 10x Genomics Cell Ranger v2.0.2/3.0.2 used for sequencing read alignment and UMI counting.
ChIP-seq: adapter trimming and low-quality read filtering by flexbar (v2.5), read mapping by Bowtie2 (v 2.2.9), duplicate read removal by Picard (v 2.17.3), peak calling by macs2 (v 2.1.1).
ATAC-seq: adapter trimming and low-quality read filtering by flexbar (v2.5), read mapping by Bowtie2 (v 2.2.9), duplicate read removal by Picard (v 2.17.3), peak calling by macs2 (v 2.1.1), heatmap by deeptoools (v3.4.3)
Assembly: mm10
Supplementary files format and content: RNA-seq: ; scRNA-seq; tar ball of mtx, tsv: UMI counts of individual genes in single cells; ChIP-seq:; ATAC-seq:

source_name: bone marrow

extract_protocol:
RNA-seq: RNA was extracted from sorted cells using the Arcturus PicoPure RNA Isolation Kit (Thermo Fisher Scientific).
ATAC-seq: 50,000 sorted LSK were lyzed and nuclei subjected to Tn5 mediated transposition for 30 minutes at 37°C. DNA was purified using Ampure XP beads and used for indexing PCR.
ChIP-seq: LSK were subjected to cross-linking in 1 % formaldehyde (in PBS) for 10 minutes at room temperature; chromatin was sheared to an average fragment size of 200-250 bp; pre-blocked magnetic Protein A beads were added; bead-bound chromatin fragments were separated on a magnetic tube rack and washed before they were subjected to tagmentation
scRNA-seq: Single cells were captured using the 10x Chromium system and further processed following the Chromium Single Cell 3’ Reagent Kit protocol.
RNA-seq: Sequencing libraries were prepared with the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina according to the manufacturer’s instructions.
ATAC-seq: Purified DNA was used for indexing PCR; Amplified libraries were purified by two-sided Ampure XP bead purification
ChIP-seq: Purified DNA was used for indexing PCR; Amplified libraries were purified by two-sided Ampure XP bead purification
scRNA-seq: cDNA library were fragmented and the sequencing library was generated according to the Single Cell 3’ Reagent Kit protocol.

value: bone marrow

value: Total bone marrow

tag: replicate


title: scRNAseq WT MPP rep2

value: MPP


title: scRNAseq cKO MPP rep2

value: Usp22 cKO


title: LSD1-monoiPSC-P25


title: scRNAseq WT LT-HSC rep2

value: LT-HSC


title: scRNAseq cKO ST-HSC rep2

value: ST-HSC


title: 204339300123_R06C01 [Lis39Pp51_2]

description: duplicate

value: Female

value: Primed

value: human embryonic stem cell


title: 204373110001_R02C01 [Lis38Np32]

description: no duplicate

value: Male

value: early

value: Naive


title: VG_5

city: Pamplona

first: Pablo

last: Sarobe

address: Avda. Pio XII, 55

institute: CIMA

description:
Vaccine+Gemcitabine-treated tumor
RNA-seq (mcSCRB-seq)
cDNA

data_processing:
The quality of the samples was verified using FastQC v0.11.8 software.
FASTQ files were mapped to GRCm38 mouse assembly using STAR v2.6.1c with default parameters.
featureCounts v1.6.0 software and Gencode M25 release were used to obtain read counts at gene level considering only those genes aligned to exonic regions.
Obtained gene counts were normalized using edgeR and voom function of limma.
Assembly: GRCm38
Supplementary files format and content: *.counts.txt: Tab-delimited text files include gene counts obtained with featureCounts for each sample.

source_name: LLC-OVA tumor sample

extract_protocol:
Tumors were collected and frozen in liquid nitrogen. Small sections were cut and RNA extracted using Maxwell RSC simplyRNA kit and Maxwell RSC.
Nextera XT library preparation protocol.

treatment_protocol: Mice were subcutaneously (s.c.) injected with OVA (0.5 mg/mouse; day 0) combined with topical application of Imiquimod cream (2.5 mg/mouse; days 0–2) or poly(I:C) (50 μg/ mouse; s.c.; day 0). Additionally, some mice received intraperitoneal (i.p.) injection of gemcitabine (30 mg/kg; day -1 and 0). Mice were sacrificed at day 7 after immunization.

value: LLC-OVA tumor

value: Vaccine+Gemcitabine

tag: sample collection

value: 20 days after cell inoculation

tag: strain

tag: Sex


title: scRNAseq cKO LT-HSC rep2


title: scRNAseq WT ST-HSC rep2

value: wild type


title: VAC_4

description:
Vaccine-treated tumor
RNA-seq (mcSCRB-seq)
cDNA

value: Vaccine


title: LN_AMP-CpG_0h_2

description: AMP-CpG 0h - 2

value: Lymph node

tag: vaccine

tag: subject


title: VAC_2

tag: tissue


title: 204373110001_R03C01 [Lis38Pp31]

description: no duplicate

tag: cell line


title: 204373110001_R01C01 [Lis38Np20]

description: no duplicate

value: virgin


title: scRNAseq cKO TBM rep2

value: bone marrow

value: Total bone marrow


title: 204339300067_R08C01 [Lis46Np19]

description: no duplicate


title: VG_2


title: HPX-plus-2-24h

city: London

first: Ioly

last: Kotta-Loizou

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

description: ΔkatE ΔkatG ΔahpC

data_processing:
Filtering using Trimmomatic ILLUMINACLIP:"adapters.fa":2:30:10 SLIDINGWINDOW:5:20 MINLEN:50.
Alignment using Bowtie2.
Generation of count table using HTSeq-count -m union -s yes -t exon -i Parent.
Genome_build: Escherichia_coli_str_k_12_substr_mg1655.ASM584v2.dna.chromosome.Chromosome.fa
Supplementary_files_format_and_content: *.txt: Tab-delimited text files include raw reads per transcript.

organism: Escherichia coli str. K-12 substr. MG1655

source_name: bacteria

growth_protocol: 37oC under shaking.

extract_protocol:
Total RNA was isolated from the cell pellets using a bead mill and the mirVana RNA isolation kit (Ambion) including DNase treatment.
Ribosomal RNA molecules were depleted using the Ribo-Zero rRNA Removal Kit for bacteria (Illumina). The rRNA depleted RNA samples were first fragmented using ultrasound (4 pulses of 30 s each at 4°C). Then, an oligonucleotide adapter was ligated to the 3' end of the RNA molecules. First-strand cDNA synthesis was performed using M-MLV reverse transcriptase and the 3’ adapter as primer. The first-strand cDNA was purified and the 5' Illumina TruSeq sequencing adapter was ligated to the 3' end of the antisense cDNA. The resulting cDNA was PCR-amplified to about 10-20 ng/μl using a high fidelity DNA polymerase. The cDNA was purified using the Agencourt AMPure XP kit (Beckman Coulter Genomics).

value: <delta>katE <delta>katG <delta>ahpC

value: Rtc inhibitor

tag: age


title: PK15, Mock, Input

city: Chengdu

first: Pei-Lun

last: Yu

address: No. 211, Huimin Road, Wenjiang District

institute: Sichuan Agricultural University

data_processing:
The original sequencing data were quality-analyzed by FastQC (v0.11.5).
Use Trimmomatic (v0.32) to remove low-quality sequences.
Use exomePeak (v2.13.2) to analyze the m6A peaks.
Assembly: Sscrofa11
Supplementary files format and content: Spreadsheet files include m6A peaks informations for each Sample
Supplementary files format and content: PK15-Mock-peaks.xlsx (m6A peaks of PK15 cell transcripts  uninfected with PRV) PRV-peaks.xlsx (m6A peaks of PRV transcripts) PK15-PRV-peaks.xlsx (m6A peaks of PK15 cell transcripts  infected with PRV)
Library strategy: MeRIP-seq

organism: Sus scrofa

growth_protocol: PK15 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% penicillin streptomycin  in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
Total RNA was extracted using the cell total RNA Isolation Kit (FORGENE). The purity and concentration of total RNA samples were determined with NanoDrop ND-1000 (Thermo Scientific). According to the manufacturer's protocol, the intact mRNA in the sample was captured with Seq-StarTM poly(A) mRNA Isolation Kit (AS-MB-006-01/02, ArrayStar, Rockville, MD, USA), and then the isolated mRNA was chemically fragmented into 300-nucleotide-long fragments by incubation in fragmentation buffer (10 mM Zn2+ and 10 mM Tris-HCl, pH 7.0). Fragmented mRNAs were immunoprecipitated with affinity purified anti-m6A rabbit antibody (202003, Synaptic Systems, Göttingen, Germanys), and one-tenth of the fragment mRNAs was retained as input. After immunoprecipitation, washing and elution, m6A mRNAs and input mRNAs were enriched respectively, and RNA-seq libraries were constructed by KAPA Stranded mRNA-seq Kit (Illumina) (KK8421, KAPA Biosystems, Boston, Massachusetts, USA). The completed libraries were qualified by Agilent 2100 Bioanalyzer Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The sequencing libraries was denatured in 0.1 M NaOH to generate single stranded DNA. DNA clusters were generated on Illumina cBot with NovaSeq 6000 S4 Reagent Kit (20012866, Illumina Inc., San Diego, CA, USA). Finally, clustered libraries were loaded onto reagent cartridge and forwarded to sequencing run on NovaSeq 6000 system (Illumina Inc.).

treatment_protocol: PK15 cells were infected with PRV (MOI = 1), after 1 h adsorption, cultured in DMEM  supplemented with 2% FBS  and 1% penicillin streptomycin  at 37 °C under 5% CO2 incubator.

value: Porcine kidney

value: Uninfected with PRV


title: VG_6

value: Female


title: PK15, PRV, Input

value: Infected with PRV


title: PK15, Mock, IP


title: PK15, PRV, IP


title: UT_3

description:
Untreated tumor
RNA-seq (mcSCRB-seq)
cDNA

value: Untreated


title: 204373110001_R05C01 [Lis38Pp50]

description: no duplicate

value: Male

value: late

value: Primed

value: human embryonic stem cell


title: GEM_3

description:
Gemcitabine-treated tumor
RNA-seq (mcSCRB-seq)
cDNA

value: LLC-OVA tumor

value: Gemcitabine

value: 20 days after cell inoculation


title: GEM_1


title: WT-plus-2-24h

value: wild-type


title: VAC_1

value: Vaccine


title: UT_5


title: d6_wt.4 [wgbs]

city: Rehovot

first: Amos

last: Tanay

address: Herzl

country: Israel

institute: Weizmann Institute of Science

data_processing: PE 150bp or 300bp reads were aligned to the mm9 reference genome  using an in-house script based on Bowtie2. In cases where the two reads ends were not aligned in a concordant manner, the reads were discarded. Reads that were mapped to the same genome coordinates where marked as duplicates and were used only once. We subsample methylation of single-cells to have only one methylation call per CpG.

source_name: J1 (SCRC1010, ATCC)

growth_protocol: Mouse embryonic stem cells (mESCs) were maintained under standard conditions. Cells were fed with fresh medium every day and were split every 2 days.

extract_protocol:
whole-genome single-cell PBAT DNA methlyation profiling: single cells were FACS sorted into 2 μl lysis buffer in  384-wells plates, before bisulfite-conversion and processing by the scPBAT protocol.Cells were lysed at 65C for 30 min and were subjected in to sequential process, performed by Bravo Automated Liquid Handling Platform (Agilent) combining with modified scaled down version of EZ-96 DNA Methylation-Lightning MagPerp kit (D5046, Zymo).
For PBAT in a  bulk Samples of 80 ng gDNA were suspended in 12 μl Tris pH 8 and bisulfate conversion was performed according to the EZ-96 DNA Methylation-Lightning MagPerp kit manufacture protocol with the following slight modifications. Mainly, half of the recommended amount of each reagent was used. CT reagent volume was reduced to 65 ml and 90 μl M-Binding buffer plus 10 μl MagBinding beads were added in to each sample. Bisulfate converted DNA samples were eluted in 38 ml elution buffer and were subjected the slightly modified PBAT protocol(Miura et al., 2012).
In solution sequence capture-PBAT:Pool of barcoded libraries (same molarity of each library), was concentrated by 0.7X beads to a volume of 10 μl and was subjected into Mybait capture reaction (MYcroarray Ann Arbor, Michigan, USA) https://arborbiosci.com/genomics/targeted-sequencing/mybaits/mybaits-custom/) according to the manufacture instructions with the following modifications.The amount of baits mix in the hybridization mix was changed to 2 μl and as a consequence the hybridization mix was in aliquot of 16 μl. The volume of the DNA library (125 ng to 2 μg) in the blockers mix was changed to 10 μl and the captured libraries were washed 4 times for 10 min with washing buffer 2.2. Following amplification the product was purify by 0.7X Agencourt Ampure XP beads, eluted in 10 μl elution buffer and was subjected to additional round of capture, four washes and 14 cycles of amplification. Libraries were pooled and sequenced on an iIllumina Nextseq or Navaseq system using the 150 bp high output sequencing kits or 300 bp SP1 kits respectively.

treatment_protocol: For the epigenetic reset, mESC were cultured in Neurobasal and DMEM-F12 (WITHOUT HEPES) medium (1:1), supplemented with N2B27, 20 ng/ml recombinant human LIF and 2i for two to three passages. Embryoid bodies were established in 25 μl hanging drops on a cover of low-adherent bacterial culture dish, allowing 500 cells/drop to aggregate for 48 hours. After two days 48-56 EBs were pooled into 10 cm low adherent bacterial culture dish.

tag: cell line/mouse line

value: J1 (SCRC1010, ATCC)


title: d6_wt.5 [wgbs]


title: GEM_4

tag: treatment


title: HPX-plus-1-24h

description: ΔkatE ΔkatG ΔahpC

value: <delta>katE <delta>katG <delta>ahpC


title: HPX-plus-1-8h

description: ΔkatE ΔkatG ΔahpC

value: Rtc inhibitor

value: 8 h


title: HPX-minus-2-24h

description: ΔkatE ΔkatG ΔahpC


title: 204373110001_R07C01 [Lis39Np30]

description: no duplicate

value: early

value: Naive

tag: cell type


title: d6_wt.2 [wgbs]


title: WT-plus-1-24h


title: d6_wt.1 [wgbs]


title: WT-minus-2-24h


title: HPX-minus-1-24h

description: ΔkatE ΔkatG ΔahpC


title: HPX-plus-2-8h

description: ΔkatE ΔkatG ΔahpC


title: d6_wt.6 [wgbs]


title: d6_wt.3 [wgbs]


title: HPX-minus-2-8h

description: ΔkatE ΔkatG ΔahpC


title: 204373110001_R08C01 [Lis39Pp31]

description: no duplicate

tag: gender

value: Female


title: Intra-amoebael C. jejuni-1

value: Bacteria + Amoeba

tag: c.jejuni strain

tag: c.jejuni genotype

value: WT

tag: a.castellanii genotype

value: Intra-amoebal bacteria (25C)

value: 4 hrs


title: d6_ko3b.3 [wgbs]

source_name: Cell Bank Riken BioResource Research Center)

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center


title: 204373110001_R06C01 [Lis39Np15]

description: no duplicate

tag: passage age

value: virgin

tag: culture conditions

value: human embryonic stem cell


title: d6_ko3a.3 [wgbs]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center


title: WT-minus-1-24h

tag: genotype

value: wild-type

value: Untreated


title: 204373110001_R04C01 [Lis38Np49]

description: no duplicate

value: Male

value: late


title: d6_ko3b.2 [wgbs]


title: WT-plus-1-8h

value: Rtc inhibitor


title: WT-plus-2-8h

value: 8 h


title: d6_ko3b.1 [wgbs]


title: d6_ko3a.1 [wgbs]


title: WT-minus-2-8h


title: ΔmazF2

description: ΔmazF

growth_protocol: 24 h at 37oC under shaking.

value: <delta>mazF


title: d5_wt.5 [PBAT_capture_V2]

value: J1 (SCRC1010, ATCC)


title: HPX-minus-1-8h

description: ΔkatE ΔkatG ΔahpC

value: <delta>katE <delta>katG <delta>ahpC


title: Δgor2

description: Δgor

value: <delta>gor


title: ΔmazF1

description: ΔmazF


title: d6_ko3a.2 [wgbs]


title: ΔsrmB2

description: ΔsrmB

value: <delta>srmB


title: ΔsrmB1

description: ΔsrmB


title: d5_wt.1 [wgbs]


title: d5_wt.4 [PBAT_capture_V2]


title: pif4-2_rep3

first: Xuncheng

address: 5 Yiheyuan Road

institute: Peiking University

description: polyA RNA isolated

data_processing:
We mapped RNA-seq reads to the TAIR10 genome using HISAT2 [39] . Only uniquely mapped reads were retained for subsequent analyses.  Differential expression between samples was statistically assessed using the R/Bioconductor package edgeR (V3.0.8) [65], and normalization was performed by trimmed mean of M values (TMM). Genes with FDR < 0.05 by edgeR were identified as differentially expressed.
Genome_build: TAIR10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.

organism: Arabidopsis thaliana

source_name: seedlings

growth_protocol: Col-0, bbx11-1 and pif4-2 mutant seedlings were grown in constant red (94 μmol/m2/s) light for 4 day

extract_protocol:
Total RNA was isolated from the whole Arabidopsis seedlings using RNeasy plant mini kits (Qiagen). mRNA was extracted from total RNA using Dynabeads oligo (dT) (Invitrogen Dynal).
First- and second-strand cDNAs were generated using SuperScript II reverse transcriptase (Invitrogen) and random hexamer primers. Double-stranded cDNAs were fragmented by nebulization and used for RNA-seq library construction following the NovaSeq protocol.

tag: strain

value: seedlings


title: WT2


title: Δgor1

description: Δgor


title: WT1


title: pif4-2_rep1

description: polyA RNA isolated


title: bbx11-1_rep3

description: polyA RNA isolated


title: d5_ko3b.2 [wgbs]


title: d5_ko3b.1 [wgbs]


title: bbx11-1_rep1

description: polyA RNA isolated


title: pif4-2_rep2

description: polyA RNA isolated


title: Col-0_rep2 (wt control for BBX11)

description: polyA RNA isolated


title: d5_wt.3 [PBAT_capture_V2]


title: Col-0_rep3 (wt control for BBX11)

description: polyA RNA isolated


title: d5_wt.2 [wgbs]


title: bbx11-1_rep2

description: polyA RNA isolated


title: Col-0_rep1 (wt control for BBX11)

description: polyA RNA isolated


title: Braco193

city: Guangzhou

first: Shunlun

last: Chen

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Spine Surgery

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

data_processing:
Illumina Casava software used for basecalling
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina NovaSeq 6000.
The 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.
Hisat2
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Rattus norvegicus

source_name: nucleus pulposus

growth_protocol: Gelatinous nucleus pulposus tissues were separated from discs and were then dissected. nucleus pulposus cells were released from the nucleus pulposus tissues and cultured in DMEM (Invitrogen, CA) containing 10% fetal bovine serum (Invitrogen, CA) and 1% penicillin/streptomycin (Invitrogen, CA) at 37 °C in presence of 5% CO2.

extract_protocol:
Nucleus pulposus cells were digested, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 1 μg RNA per sample was used as input material for the RNA sample  preparations.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Nucleus pulposus cells were seeded in 6-well plates for 24h and then treated with PDS, Braco-19 and Phen-DC3 separately for 24h.

value: Sprague Dawley

value: nucleus pulposus

value: 8 weeks


title: Braco192


title: control3

value: control


title: WT-minus-1-8h


title: control1


title: PhenDC33


title: control2


title: PhenDC31


title: Phencontrol3


title: Phencontrol2


title: PhenDC32


title: d4_wt.6 [PBAT_capture_V2]


title: d5_ko3a.1 [wgbs]

value: DNMT3A_KO_Cell Bank Riken BioResource Research Center


title: d4_wt.7 [PBAT_capture_V2]


title: d4_wt.8 [PBAT_capture_V2]


title: d5_ko3a.2 [wgbs]


title: d4_wt.5 [PBAT_capture_V1]


title: Braco191


title: Phencontrol1


title: d4_ko3b.6 [PBAT_capture_V1]

value: DNMT3B_KO_Cell Bank Riken BioResource Research Center


title: d4_ko3b.9 [PBAT_capture_V1]


title: d4_wt.3 [PBAT_capture_V1]


title: d4_wt.2 [PBAT_capture_V1]


title: d4_ko3b.8 [PBAT_capture_V1]


title: d4_ko3b.5 [wgbs]


title: d4_tko.1 [PBAT_capture_V1]

value: TKO_Cell Bank Riken BioResource Research Center


title: d4_wt.4 [PBAT_capture_V1]


title: d4_ko3b.12 [PBAT_capture_V2]


title: d4_ko3b.4 [wgbs]


title: d4_wt.1 [PBAT_capture_V1]


title: d4_ko3b.2 [wgbs]


title: d4_ko3b.3 [wgbs]


title: PDS2

value: PDS


title: d4_ko3b.1 [PBAT_capture_V1]


title: d4_ko3a.12 [PBAT_capture_V2]


title: PDScontrol3


title: PDScontrol1


title: PDScontrol2


title: d4_ko3b.10 [PBAT_capture_V2]


title: d4_ko3b.11 [PBAT_capture_V2]


title: PDS3


title: d4_ko3a.10 [PBAT_capture_V2]


title: d4_ko3a.11 [PBAT_capture_V2]


title: d4_ko3b.7 [PBAT_capture_V1]


title: PDS1