title: mES_am_Ctrl_TBE_Pol2_rep2

growth_protocol: mESCs were cultured routinely in LIF and serum medium.

extract_protocol: Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

treatment_protocol: mESC were treated with  H2O or 100ug/ml α-amanitin for 27 h till embryos at late 2C stage.

value: Embryonic stem cell

value: wild-type

tag: developmental stage

value: Pol2(Active Motif 102660)


title: mES_am_TBE_Pol2_rep2

status: Public on Oct 28 2020

type: SRA

city: Beijing

first: Bofeng

last: Liu

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

library_source: genomic

data_processing:
Library strategy: Stacc-seq
Basecalls performed using CASAVA version 1.8
Stacc-seq reads were aligned to the mm9 genome using bowtie 2.2.2, replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome
Genome_build: mm9

molecule: genomic DNA

organism: Mus musculus

source_name: Embryonic stem cell

tag: tissue

tag: genotype

tag: antibody


title: PAO1_MIC/10_Exp3_t=48 (DNA-seq)

city: Adelaide

first: James

last: Breen

state: SA

address: 108 North Terrace (Ground Floor)

department: John Curtin School of Medical Research

country: Australia

institute: Australian National University

data_processing:
Library strategy: WGS
Quality control assessment using FastQC
Data processing (trimming using AdapterRemoval, Alignment using BWA, variant calling using snippy)
Genome_build: GCF_000006765.1_ASM676v1
Supplementary_files_format_and_content: Variant call format (VCF)

organism: Pseudomonas aeruginosa

source_name: bacteria

growth_protocol: Hydroponic experiment in Growth Minimal medium (Rathnayake, I. V. N.; Megharaj, M.; Krishnamurti, G. S. R.; Bolan, N. S.; Naidu, R., Heavy metal toxicity to bacteria – Are the existing growth media accurate enough to determine heavy metal toxicity? Chemosphere. 2013, 90, (3), 1195-1200.

extract_protocol: DNA was harvested using QIAamp® DNA Mini Kit QIAGEN

treatment_protocol: solution was removed by centrifugation and bacteria were stored at -20°C prior to DNA extraction

tag: strain

value: PAO1 (Wild Type)

tag: treatment

tag: time


title: mES_am_TBE_Pol2_rep1


title: OI-3

city: Tartu

first: Ene

last: Reimann

address: Riia 23b

department: Institute of Genomics

country: Estonia

institute: University of Tartu

library_source: transcriptomic

data_processing:
Sequencing was performed using a SOLiD 5500W platform and DNA sequencing chemistry (Life Technologies Corp., Carlsbad, CA, USA). Three-lane sequencing was applied and 12 libraries per lane with specification of 75bp from a forward direction were sequenced. Sufficient depth of sequencing and adequate mapping rate for evaluation of the expression pattern of the transcriptome was achieved with the average 30 million reads/sample across samples.
Raw reads were processed and mapped using Lifescope 2.5.1 software (Life Technologies Corp., Carlsbad, CA, USA). This whole transcriptome analysis workflow generated output, which including gene and exon counts, alternative splicing, and fusion transcripts. Raw read counts per gene were input for further statistical analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: total RNA

organism: Homo sapiens

source_name: Whole blood

growth_protocol: Whole blood was collected into Tempus Blood RNA Tubes (Applied Biosystems, Life Technologies Corp., Carlsbad, CA, USA).

extract_protocol:
Total RNA extraction was performed with a commercial Tempus Spin RNA Isolation Kit (Ambion, Life Technologies Corp., Carlsbad, CA, USA) following manufacturer’s protocol. A GLOBINclear™ Kit (Ambion, Life Technologies Corp., Carlsbad, CA, USA) was used to purify the samples of globin mRNA. The quality of total RNA was assesed using a capillary electrophoresis approach Agilent 2100 Bioanalyzer and RNA 6000 Nano kit
RNA-seq library construction and RNA sequencing analysis were performed with a SOLiD 5500W protocols
SOLiD 5500 Wildfire (W) System chemistry (Life Technologies Corp., Carlsbad, CA, USA) was applied to prepare the resulting cDNA for the DNA fragment library. Next, the 12 libraries were pooled together in equal amounts to construct two different library pools. The pooled libraries were converted to SOLiD 5500W libraries.

tag: disease state

value: Osteogenesis Imperfecta type III

tag: age

tag: family


title: PAO1_MIC/10_Exp3_t=24 (DNA-seq)


title: mES_am_Ctrl_TBE_Pol2_rep1


title: PAO1_control_Exp3_t=72 (DNA-seq)

value: control


title: C-2

value: Healthy


title: PAO1_control_Exp3_t=24 (DNA-seq)


title: 2cell_late_am_Ctrl_TBE_Pol2_rep2

source_name: Preimplantation embryo

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. PN2-3 embryos were harvested in M2 medium 23 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

treatment_protocol: Zygotes were obtained 23 h post hCG and cultured in KSOM containing either H2O or 100ug/ml α-amanitin for 27 h till embryos at late 2C stage.

value: Preimplantation embryo

value: late 2-cell


title: C-1


title: 2cell_late_am_TBE_Pol2_rep1


title: PAO1_control_Exp3_t=0 (DNA-seq)


title: PAO1_MIC_Exp3_t=48 (DNA-seq)

value: MIC


title: 2cell_late_am_TBE_Pol2_rep2


title: 2cell_late_am_Ctrl_TBE_Pol2_rep1


title: XEN41_MIC_Exp5_t=72 (RNA-seq)

data_processing:
Data processing (trimming using AdapterRemoval, Alignment using BWA, quantification using featureCounts/R)
Quality control assessment using FastQC
Data filtering for low counts and transcriptional profiling (Table of expression levels for all samples)
Differential gene expression across groups using edgeR and limma
Basic Gene Ontology Enrichment Analysis based on data from the [Pseudomonas Genome Database](https://www.pseudomonas.com/)
Genome_build: GCF_000006765.1 ASM676v1 genomic
Supplementary_files_format_and_content: countTable.tsv

extract_protocol: RNA was harvested using RNeasy® Mini Kit QIAGEN

treatment_protocol: solution was removed by centrifugation and bacteria+RNA stabilization solution (RNAlaterTM solution, invitrogen) were stored at -80°C prior to RNA extraction

value: Xen41 Tetracycline resistant


title: PA_PN5_am_TBE_Pol2_rep2

source_name: Parthenogenetic embryos

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. MII oocytes were harvested in M2 medium 13 h after hCG.
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

treatment_protocol: Without specific statement, all reagents were purchased from Sigma Aldrich. Calcium ion free CZB with few modifications: 81.62 mM NaCl, 4.83 mM KCl, 1.18 mM KH2PO4, 1.18mM MgSO4, 25.12 mM NaHCO3, 0.27mM sodium pyruvate (11360070, Gibco), 1x GlutaMAX (35050061, Gibco) 5 mg/ml bovine serum albumin (BSA). For parthenogenetic activation, unfertilized MII oocyte from 6-8 weeks B6D2F1/J or C57BL/6J mice were treated with Calcium ion free Chatot-Ziomek-Bavister (CZB) medium supplement with 2.5 mM SrCl2 6H2O and 2.5 μg/ml cytochalasin B for 6hr in 37℃ under 5% CO2 in air. Zygotes were treated with H2O or 100 ug/ml α-amanitin for 11 h before and in parallele with parthenogenetic activation. Then we collect PA zygote with two distinct pronuclei and transfer the zygote in to KSOM culture medium with a mouth pipette. Further culture, for 6hr, late zygotes (PN5) was collected base on the morphology. Zona pellucida were gently removed by the treatment with tyrode solution. Polar body was gently removed with a sharp glass.

value: Parthenogenetic embryos


title: XEN41_MIC_Exp5_t=48 (RNA-seq)


title: OI-4

value: Osteogenesis Imperfecta type IV


title: PA_PN5_am_Ctrl_TBE_Pol2_rep2


title: XEN41_MIC_Exp5_t=24 (RNA-seq)


title: OCI-AML3_bulk_cntr

city: Freiburg

first: Heiko

last: Becker

state: Baden-Württemberg

address: Breisacher Straße 115

department: Department of Medicine I

country: Germany

institute: University Medical Center

description:
bulk DNA
NEBNext Ultra II DNA Library Preparation with 50ng ng of fragmented OCI-AML3 cell bulk gDNA according to the manufacturer's recommendations with 50% reduction of reaction volumes.
This sample was only used to control for amplification bias.

data_processing:
For the extraction of DNA methylation from epi-gSCAR data, NGS reads were analyzed using a custom bioinformatic pipeline which was automated using Snakemake (version 5.3.0) in Python (version 3.6). After removal of Illumina adapters, overlapping paired-end reads were merged and non-overlapping reads were converted to singletons using BBMerge to obtain single-read information. Next, GAT-Adapter sequences were removed. The resulting pre-processed merged and unmerged reads were filtered for reads containing either 5´ poly(d)T or 3´ poly(d)A tailed HhaI scars separately (motif: GCGAAAAAA or TTTTTTCGC; Hamming distance = 1). Poly(d)T and poly(d)A tails were removed, resulting in reads containing 5´ or 3´ HhaI scars, respectively (5´-scar file and 3´-scar file). Separately, poly(d)T and poly(d)A tails were removed from GAT-Adapter trimmed reads (all-read file). All trimming and filtering steps were performed using BBDuk. Reads were subjected to quality control by FastQC and 5´ or 3´ HhaI scar-containing reads were mapped to the human assembly GRCh37 (hg19) with BWA-MEM separately with soft trimming enabled. Samtools was used to remove secondary and supplementary alignments and alignments with MAPQ smaller than 10. Alignment intervals were generated with the bamtobed command of bedtools and reduced to the outermost three 5´ or 3´ nucleotides, respectively. Scar intervals were filtered for nucleotide-precise overlap with HhaI sites and CpGs in the human genome and assigned as cut HhaI sites. In order to identify uncut (intact) HhaI sites, the all-read file was aligned accordingly, since all reads can potentially contain intact HhaI sites. Next, all HhaI sites of the human genome were expanded by 1 bp on either side as a safety margin and only completely covered intervals were assigned as uncut HhaI sites. Intact sites overlapping with cut HhaI sites (e.g. GCGCG(A)n-3’) were excluded from the output since complete digestion of sites close to DNA ends cannot be guaranteed. Overlap of uncut with cut sites revealed sites of heterozygous methylation. All other uncut and cut HhaI sites were assigned as methylated or unmethylated, respectively. All CpG or HhaI sites of the human genome, which were covered by WGBS datasets of Kasumi-1 or OCI-AML3, respectively, were defined as informative for epi-gSCAR datasets.
Genome_build: GRCh37 (hg19)
Supplementary_files_format_and_content: bedgraph files with methylation values for all covered sites for Kasumi-1 single cell 1-27 and OCI-AML3 single cell 1-20

source_name: acute myeloid leukemia cell line OCI-AML3

growth_protocol: Kasumi-1 and OCI-AML3 cells were cultured in RPMI medium plus 10% FBS and 1% penicillin/streptomycin in a humidified 5% CO2 atmosphere.

extract_protocol:
Genomic DNA for cell bulk controls was extracted from Kasumi-1 and OCI-AML3 cell bulk samples using the AllPrep DNA/RNA Kit (Qiagen)
NGS libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) with 20 ng of partially fragmented epi-gSCAR amplicons (Kasumi-1 single cell 1-7), 50ng ng of fragmented epi-gSCAR amplicons (Kasumi-1 single cell 8-27 and OCI-AML3 single cell 1-20) or 50ng ng of fragmented Kasumi-1 and OCI-AML3 bulk gDNA according to the manufacturer's recommendations with 50% reduction of reaction volumes.

tag: cell line


title: PA_PN5_am_TBE_Pol2_rep1


title: OCI-AML3_single-cell_20

description:
single-cell DNA
assay variant A


title: OCI-AML3_single-cell_19

description:
single-cell DNA
assay variant A


title: XEN41_MIC/10_Exp5_t=72 (RNA-seq)


title: PA_PN5_am_Ctrl_TBE_Pol2_rep1


title: PAO1_MIC_Exp3_t=24 (DNA-seq)


title: OI-2

value: Osteogenesis Imperfecta type I


title: KPT-330 (K) Treated JEKO-1 Cell Line Replicate #2

city: Rochester

first: Surendra

last: Dasari

state: MN

address: 200 First Street SW

department: Quantitative Health Sciences Research

country: USA

institute: Mayo Clinic

data_processing:
Sequenced reads were aligned to the hg38 reference using the previously published MAP-RSeq pipeline slightly modified to use the STAR aligner. Gene-level read counts based on Ensembl version 78 were analyzed using edgeR to find differentially expressed proteins. For this, gene counts were normalized using TMM method to remove batch effects. Normalized read counts were compared across experimental groups using a negative binomial generalized log-linear model. A total of four group comparisons were performed: KPT-330 vs. control, CS vs. control, K+CS vs. control and CS vs. KPT-300. For each comparison, genes with an adjusted p-value (Benjamini-Hochberg) ≤ 0.05 and an absolute log2 (fold change)>2.0 were considered as significantly differentially expressed and saved for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: Filename is "Raw_gene_count_matrix.txt". File has raw gene count data.

molecule: polyA RNA

source_name: KPT-330 (K) Treated JEKO-1 Cell Line

growth_protocol: Cell lines used in this study were purchased from the cell line repositories ATCC (Manassas, VA) or DSMZ (Braunschweig, Germany). Cell lines were cultured in RPMI-1640 supplemented with 10% fetal bovine serum. Cells used in experiments had viability counts of 90% or greater before treatment.

extract_protocol:
RNA was extracted using the AllPrep DNA/RNA FFPE kit (Qiagen, Germany).
Sequencing libraries were prepared using TruSeq RNA Library Prep kit V2 (Illumina, San Diego, CA) and analyzed on a HiSeq 4000 sequencer (Illumina, San Diego, CA).

treatment_protocol: KPT-330 purchased from Selleckchem (cat no: S7252) was dissolved in DMSO while CS (Santa Cruz, CAS 2016-36-6), sodium salicylate (Sigma-Aldrich, cat no: S3007), acetyl salicylate (Sigma-Aldrich, cat no: CAS 50-78-2) was diluted in PBS. The concentration range of KPT-330 was 0.05-1.0 µM while CS was 1-3mM were used for ex vivo treatment and incubation time ranged from 24h to 72h. For the PARP inhibitor assay, olaparib 10µM (SelleckChem, cat no: AZD2281 Ku-0059436) was used. Q-VD-OPh (MilliporeSigma, cat no: 551476) was used as the pan-caspase inhibitor to assess caspase induced cell death by K+CS.


title: KPT-330+CS (K_plus_CS) Treated JEKO-1 Cell Line Replicate #2


title: KPT-330 (K) Treated JEKO-1 Cell Line Replicate #3


title: KPT-330+CS (K_plus_CS) Treated JEKO-1 Cell Line Replicate #1


title: C-3


title: OCI-AML3_single-cell_18

description:
single-cell DNA
assay variant A


title: KPT-330+CS (K_plus_CS) Treated JEKO-1 Cell Line Replicate #3


title: XEN41_MIC/10_Exp5_t=48 (RNA-seq)


title: PN5_am_TBE_Pol2_rep2

treatment_protocol: Zygotes were obtained 23 h post hCG and cultured in KSOM containing either 0.1% H2O or 100 ug/ml α-amanitin for 10 h till embryos entering PN5.


title: OI-1


title: XEN41_MIC/10_Exp5_t=24 (RNA-seq)


title: PAO1_control_Exp3_t=48 (DNA-seq)


title: OCI-AML3_single-cell_17

description:
single-cell DNA
assay variant A


title: Choline salicylate (CS) Treated JEKO-1 Cell Line Replicate #2

value: CS


title: Choline salicylate (CS) Treated JEKO-1 Cell Line Replicate #3


title: PN5_am_TBE_Pol2_rep1


title: Choline salicylate (CS) Treated JEKO-1 Cell Line Replicate #1


title: XEN41_control_Exp5_t=72 (RNA-seq)


title: KPT-330 (K) Treated JEKO-1 Cell Line Replicate #1


title: OCI-AML3_single-cell_15

description:
single-cell DNA
assay variant A


title: PN5_am_Ctrl_TBE_Pol2_rep2


title: XEN41_control_Exp5_t=48 (RNA-seq)


title: DMSO Treated JEKO-1 Cell Line Replicate #3

source_name: DMSO Treated JEKO-1 Cell Line

value: DMSO


title: XEN41_control_Exp5_t=24 (RNA-seq)


title: OCI-AML3_single-cell_14

description:
single-cell DNA
assay variant A


title: PN5_am_Ctrl_TBE_Pol2_rep1


title: XEN41_control_Exp5_t=0 (RNA-seq)


title: DMSO Treated JEKO-1 Cell Line Replicate #1


title: DMSO Treated JEKO-1 Cell Line Replicate #2


title: OCI-AML3_single-cell_13

description:
single-cell DNA
assay variant A


title: OCI-AML3_single-cell_12

description:
single-cell DNA
assay variant A


title: HepG2 Input for CTCF

city: La Jolla

first: Yunjiang

last: Qiu

state: CA

address: 9500 Gilman Drive

institute: University of California, San Diego

description: Input for CTCF

data_processing:
Reads were aligned using BWA MEM with either single-end or pair-end model to the hg19 reference genome. Reads with low mapping quality (mapq<10) were filtered out, and PCR duplicates were removed using Picard tool.
MACS2 were then applied to call peaks and generate signals to view in the genome browser.
Genome_build: hg19
Supplementary_files_format_and_content: Peak files in narrowPeak format and signal files in bigWig format for each samples were provided.

growth_protocol: The HepG2 (ATCC, HB-8065) cells were cultured under normal condition with 5% CO2 at 37°C.

extract_protocol:
Briefly, the cells were crossed linked with 1% formaldehyde at ambient temperature for 10 min. The reaction was quenched by 125mM glycine for 5 min at room temperature. Cells were washed with PBS and treated with hypotonic buffer (20mM Hepes pH7.9, 10mM KCl, 1mM EDTA, 10% Glycerol and 1mM DTT with additional protease inhibitor (Roche)) to isolate nuclei. The nuclei were suspended with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate with protease inhibitor) and sonicated using Covaris S220 Focused-ultrasonicator. Fragmented chromatin was pre-cleared with protein G conjugated sepharose beads (GE). Antibodies were used to pull down the respective proteins and their associated chromatin. Washes with different concentration of NaCl were performed. The enriched protein-DNA complexes were reverse crosslinked at 65 C over night with proteinase K (NEB). DNA was purified with Qiagen MinElute kit.
Sequencing library was prepared using an in-house kit, including end-repair, “A” addition and adapter ligation. The library was sequenced with illumina HiSeq 4000 for 50bp single read or 100bp pair-end, acquiring 10-30 million reads.

tag: chip antibody


title: 2cell_late_DRB_TBE_Pol2_rep2

treatment_protocol: Zygotes were obtained 23 h post hCG and cultured in KSOM containing either 0.1% DMSO or 100mM DRB for 27 h till embryos at late 2C stage.


title: PAO1_MIC_Exp5_t=48 (RNA-seq)


title: HepG2 CTCF

value: CTCF


title: OCI-AML3_single-cell_11

description:
single-cell DNA
assay variant A


title: OCI-AML3_single-cell_16

description:
single-cell DNA
assay variant A


title: OCI-AML3_single-cell_10

description:
single-cell DNA
assay variant A


title: PAO1_MIC_Exp5_t=24 (RNA-seq)


title: 2cell_late_DRB_Ctrl_TBE_Pol2_rep2


title: PAO1_MIC_Exp5_t=72 (RNA-seq)


title: mES_DRB_Ctrl_TBE_Pol2_rep2

treatment_protocol: mESCs were treated with either 0.1% DMSO or 100mM DRB for 7 h

value: Embryonic stem cell


title: Donor1_5

city: Chicago

first: Alexander

middle: V

last: Misharin

state: Illinois

address: 303 E Superior

institute: Northwestern University

description:
Sequenced on Illumina HiSeq 4000
Donor1_5_filtered_feature_bc_matrix.h5
Donor1_5_raw_feature_bc_matrix.h5
04all-lineages.h5ad
01epithelial.h5ad

data_processing:
Reads were demultiplexed using with cellranger mkfastq command (v3.1.0). Reads were aligned to a custom built genome (human GRCh38.93 and SARS-CoV-2 NC_045512.2) and counted by gene by cell with cellranger count command (v3.1.0), producing raw and filtered gene expression matrices.
Data was processed using Scanpy v1.5.1, doublets were detected with scrublet v0.2.1 and removed, samples were integrated with BBKNN v1.3.12, cells were clustered with leiden algorithm, and clusters were manually annotated.
We trained scArches model on data from Haberman et al., 2020 (GSE135893) and used it to integrate our data from patients with COVID-19. We used cell type annotations from Habermann and our dataset to separate cells by lineages, and performed clustering independently in lineages using latent space coordinates as input. Metadata fields were manually merged for both datasets and used for cluster composition analysis and computing differentially-expressed genes.
genome build: custom (human GRCh38.93 and SARS-CoV-2 NC_045512.2)
processed data files format and content: gene expression count matrices

source_name: Sorted Epithelial population

extract_protocol: Libraries were prepared with 10x Genomics 3' V3 gene expression (GEX) reagents according to the manufacturer protocol (CG000183_RevB).

value: Negative

tag: tissue type

value: Bronchus

tag: cell type

value: Sorted Epithelial population


title: OCI-AML3_single-cell_9

description:
single-cell DNA
assay variant A


title: PAO1_MIC/10_Exp5_t=48 (RNA-seq)

value: PAO1 (Wild Type)


title: Donor1_6

description:
Sequenced on Illumina HiSeq 4000
Donor1_6_filtered_feature_bc_matrix.h5
Donor1_6_raw_feature_bc_matrix.h5
04all-lineages.h5ad
03stromal.h5ad

source_name: Sorted Stromal population

value: Sorted Stromal population


title: 2cell_late_DRB_Ctrl_TBE_Pol2_rep1

value: wild-type

value: Pol2(Active Motif 102660)


title: 2cell_early_DRB_TBE_Pol2_rep2

treatment_protocol: Zygotes were obtained 23 h post hCG and cultured in KSOM containing either 0.1% DMSO or 100mM DRB for 36 h till embryos at early 2C stage.

value: Preimplantation embryo

value: early 2-cell


title: mES_DRB_TBE_Pol2_rep2


title: PAO1_MIC/10_Exp5_t=24 (RNA-seq)


title: 2cell_early_DRB_Ctrl_TBE_Pol2_rep2


title: Donor1_4

description:
Sequenced on Illumina HiSeq 4000
Donor1_4_filtered_feature_bc_matrix.h5
Donor1_4_raw_feature_bc_matrix.h5
04all-lineages.h5ad
02immune.h5ad

source_name: Sorted Myeloid population

value: Sorted Myeloid population


title: Donor1_3

description:
Sequenced on Illumina HiSeq 4000
Donor1_3_filtered_feature_bc_matrix.h5
Donor1_3_raw_feature_bc_matrix.h5
04all-lineages.h5ad
03stromal.h5ad

value: Distal lung parenchyma


title: 2cell_early_DRB_TBE_Pol2_rep1


title: Donor1_2

description:
Sequenced on Illumina HiSeq 4000
Donor1_2_filtered_feature_bc_matrix.h5
Donor1_2_raw_feature_bc_matrix.h5
04all-lineages.h5ad
01epithelial.h5ad


title: PAO1_control_Exp5_t=48 (RNA-seq)

value: control


title: PAO1_control_Exp5_t=72 (RNA-seq)


title: 2cell_late_DRB_TBE_Pol2_rep1

value: late 2-cell


title: Donor1_1

description:
Sequenced on Illumina HiSeq 4000
Donor1_1_filtered_feature_bc_matrix.h5
Donor1_1_raw_feature_bc_matrix.h5
04all-lineages.h5ad
02immune.h5ad


title: PN5_DRB_TBE_Pol2_rep2

treatment_protocol: Zygotes were obtained 23 h post hCG and cultured in KSOM containing either 0.1% DMSO or 100mM DRB for 30 h till embryos at PN5 stage.


title: OCI-AML3_single-cell_5

description:
single-cell DNA
assay variant A


title: OCI-AML3_single-cell_4

description:
single-cell DNA
assay variant A


title: OCI-AML3_single-cell_3

description:
single-cell DNA
assay variant A


title: 2cell_early_DRB_Ctrl_TBE_Pol2_rep1


title: OCI-AML3_single-cell_8

description:
single-cell DNA
assay variant A


title: OCI-AML3_single-cell_2

description:
single-cell DNA
assay variant A


title: PAO1_MIC/10_Exp5_t=72 (RNA-seq)


title: PN5_DRB_Ctrl_TBE_Pol2_rep2


title: PAO1_control_Exp5_t=0 (RNA-seq)


title: PAO1_control_Exp5_t=24 (RNA-seq)


title: PN5_DRB_TBE_Pol2_rep1


title: OCI-AML3_single-cell_1

description:
single-cell DNA
assay variant A


title: OCI-AML3_single-cell_7

description:
single-cell DNA
assay variant A


title: XEN41_MIC_Exp4_t=72 (RNA-seq)

value: Xen41 Tetracycline resistant

value: MIC


title: XEN41_MIC_Exp4_t=48 (RNA-seq)


title: PN5_DRB_Ctrl_TBE_Pol2_rep1


title: Kasumi-1_bulk_cntr

description:
bulk DNA
NEBNext Ultra II DNA Library Preparation with 50ng ng of fragmented Kasumi-1 cell bulk gDNA according to the manufacturer's recommendations with 50% reduction of reaction volumes.
This sample was only used to control for amplification bias.

source_name: acute myeloid leukemia cell line Kasumi-1


title: XEN41_MIC_Exp4_t=24 (RNA-seq)


title: OCI-AML3_single-cell_6

description:
single-cell DNA
assay variant A


title: Kasumi-1_single-cell_27

description:
single-cell DNA
assay variant A


title: XEN41_MIC/10_Exp4_t=72 (RNA-seq)


title: mES_NoAb_rep1


title: Kasumi-1_single-cell_26

description:
single-cell DNA
assay variant A


title: mES_IgG_rep1

value: IgG (Santa Cruz sc-2025)


title: XEN41_MIC/10_Exp4_t=48 (RNA-seq)


title: Kasumi-1_single-cell_25

description:
single-cell DNA
assay variant A


title: mES_H3K27me3_rep2

value: Embryonic stem cell


title: XEN41_MIC/10_Exp4_t=24 (RNA-seq)


title: XEN41_control_Exp4_t=72 (RNA-seq)


title: Kasumi-1_single-cell_23

description:
single-cell DNA
assay variant A


title: Kasumi-1_single-cell_24

description:
single-cell DNA
assay variant A


title: mES_H3K27me3_rep1


title: mES_H3K4me3_rep2

value: H3K4me3(Home made)


title: Kasumi-1_single-cell_22

description:
single-cell DNA
assay variant A


title: XEN41_control_Exp4_t=24 (RNA-seq)


title: mES_250_spk_Pol2_rep1


title: Kasumi-1_single-cell_21

description:
single-cell DNA
assay variant A


title: XEN41_control_Exp4_t=48 (RNA-seq)


title: XEN41_control_Exp4_t=0 (RNA-seq)


title: Kasumi-1_single-cell_19

description:
single-cell DNA
assay variant A


title: mES_1k_spk_Pol2_rep1


title: mES_H3K4me3_rep1


title: mES_500_spk_Pol2_rep1


title: PAO1_MIC_Exp4_t=72 (RNA-seq)


title: S5_sequence_1

city: Shanghai

first: Zhou

last: haiwen

address: 500 Qu-xi Road, Shanghai

department: Oral Mucosal Diseases

institute: Shanghai Ninth People’s Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine

data_processing:
Basecalls performed using CASAVA version 1.8
circRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
High throughput sequencing service was provided by CloudSeq Biotech (Shanghai, China). Transcriptome high throughput sequencing and subsequent bioinformatics analysis were all done by Cloud-Seq Biotech (Shanghai, China). Briefly, total RNA was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, USA) following the manufacturer's instructions. RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, USA).Libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs. The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis.
Genome_build: hg19
Supplementary_files_format_and_content: Number of raw junction read

source_name: oral squamous carcinoma tissue

growth_protocol: Patients with previous histories of All tissue samples were immediately frozen in liquid nitrogen after resection and stored at -80℃ until RNA retraction

extract_protocol:
RNA extraction protocol
library construction protocol

value: oral squamous carcinoma

value: fresh


title: Kasumi-1_single-cell_18

description:
single-cell DNA
assay variant A


title: S6_sequence_1


title: PAO1_MIC_Exp4_t=24 (RNA-seq)

value: PAO1 (Wild Type)


title: PAO1_MIC_Exp4_t=48 (RNA-seq)


title: mES_2k_spk_Pol2_rep1


title: S4_sequence_1


title: Kasumi-1_single-cell_17

description:
single-cell DNA
assay variant A


title: PAO1_MIC/10_Exp4_t=48 (RNA-seq)


title: Kasumi-1_single-cell_16

description:
single-cell DNA
assay variant A


title: PAO1_MIC/10_Exp4_t=72 (RNA-seq)


title: kidney_Pol2_rep1

source_name: Tissue

extract_protocol:
The related tissue was isolated from 8-week old male C57BL/6 mice following a protocol that was previously described by ENCODE http://genome.ucsc.edu/ ENCODE/protocols/cell/mouse/
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: Tissue

value: lung


title: lung_Pol2_rep1

value: wild-type

value: Pol2(Active Motif 102660)


title: S1_sequence_1


title: S2_sequence_1


title: S3_sequence_1


title: PAO1_control_Exp4_t=72 (RNA-seq)


title: Kasumi-1_single-cell_20

description:
single-cell DNA
assay variant A


title: Kasumi-1_single-cell_14

description:
single-cell DNA
assay variant A


title: heart_Pol2_rep1

value: heart


title: cortex_Pol2_rep1

value: cortex


title: PAO1_MIC/10_Exp4_t=24 (RNA-seq)


title: N5_sequence_1

source_name: healthy oral mucosa tissue

value: healthy oral mucosa


title: Kasumi-1_single-cell_13

description:
single-cell DNA
assay variant A


title: PAO1_control_Exp4_t=48 (RNA-seq)

value: control


title: spleen_Pol2_rep1

value: spleen


title: Kasumi-1_single-cell_12

description:
single-cell DNA
assay variant A


title: PAO1_control_Exp4_t=24 (RNA-seq)


title: PA_PN5_Dnmt3l_KO_Pol2_rep2

treatment_protocol: Without specific statement, all reagents were purchased from Sigma Aldrich. Calcium ion free CZB with few modifications: 81.62 mM NaCl, 4.83 mM KCl, 1.18 mM KH2PO4, 1.18mM MgSO4, 25.12 mM NaHCO3, 0.27mM sodium pyruvate (11360070, Gibco), 1x GlutaMAX (35050061, Gibco) 5 mg/ml bovine serum albumin (BSA). For parthenogenetic activation, unfertilized MII oocyte from 6-8 weeks B6D2F1/J or C57BL/6J mice were treated with Calcium ion free Chatot-Ziomek-Bavister (CZB) medium supplement with 2.5 mM SrCl2 6H2O and 2.5 μg/ml cytochalasin B for 6hr in 37℃ under 5% CO2 in air. Then we collect PA zygote with two distinct pronuclei and transfer the zygote in to KSOM culture medium with a mouth pipette. Further culture, for 6hr, late zygotes (PN5) was collected base on the morphology. Zona pellucida were gently removed by the treatment with tyrode solution. Polar body was gently removed with a sharp glass.

value: Parthenogenetic embryos

value: Dnmt3l KO


title: Kasumi-1_single-cell_11

description:
single-cell DNA
assay variant A


title: N3_sequence_1


title: N4_sequence_1


title: Kasumi-1_single-cell_10

description:
single-cell DNA
assay variant A


title: Kasumi-1_single-cell_15

description:
single-cell DNA
assay variant A


title: PA_PN5_Pol2_rep3


title: N2_sequence_1


title: Kasumi-1_single-cell_9

description:
single-cell DNA
assay variant A


title: PA_PN5_Pol2_rep2


title: PA_PN5_Pol2_rep1


title: PAO1_control_Exp4_t=0 (RNA-seq)


title: XEN41_MIC_Exp3_t=48 (RNA-seq)

value: Xen41 Tetracycline resistant

value: MIC


title: N1_sequence_1


title: Kasumi-1_single-cell_8

description:
single-cell DNA
assay variant A


title: N0_sequence_1


title: XEN41_MIC_Exp3_t=24 (RNA-seq)


title: PB2_4

description:
Sequenced on Illumina NovaSeq 6000
PB2_4_filtered_feature_bc_matrix.h5
PB2_4_raw_feature_bc_matrix.h5
04all-lineages.h5ad
01epithelial.h5ad

value: Positive

value: Distal lung parenchyma

value: Sorted Epithelial population


title: XEN41_MIC/10_Exp3_t=48 (RNA-seq)


title: PB2_3

description:
Sequenced on Illumina NovaSeq 6000
PB2_3_filtered_feature_bc_matrix.h5
PB2_3_raw_feature_bc_matrix.h5
04all-lineages.h5ad
03stromal.h5ad

value: Sorted Stromal population


title: PA_PN5_Dnmt3l_KO_Pol2_rep1


title: mESC_500_Pol2_rep2

value: Embryonic stem cell


title: mESC_500_ab2_Pol2_rep1

value: Pol2(Active Motif 61668)


title: mES_500_Pol2_rep1

value: wild-type


title: mES_1k_Pol2_rep2

value: Pol2(Active Motif 102660)


title: PB2_1

description:
Sequenced on Illumina NovaSeq 6000
PB2_1_filtered_feature_bc_matrix.h5
PB2_1_raw_feature_bc_matrix.h5
04all-lineages.h5ad
02immune.h5ad

value: Sorted Myeloid population


title: XEN41_MIC/10_Exp3_t=24 (RNA-seq)


title: XEN41_control_Exp3_t=72 (RNA-seq)


title: mES_1k_Pol2_rep1


title: XEN41_MIC_Exp3_t=72 (RNA-seq)


title: mES_2k_Pol2_rep2


title: XEN41_control_Exp3_t=48 (RNA-seq)


title: TX_Recipient_3

description:
Sequenced on Illumina NovaSeq 6000
TX_Recipient_3_filtered_feature_bc_matrix.h5
TX_Recipient_3_raw_feature_bc_matrix.h5
04all-lineages.h5ad
03stromal.h5ad


title: TX_Recipient_4

description:
Sequenced on Illumina NovaSeq 6000
TX_Recipient_4_filtered_feature_bc_matrix.h5
TX_Recipient_4_raw_feature_bc_matrix.h5
04all-lineages.h5ad
02immune.h5ad
03stromal.h5ad

source_name: Sorted CD31 population

value: Sorted CD31 population


title: XEN41_control_Exp3_t=24 (RNA-seq)


title: XEN41_MIC/10_Exp3_t=72 (RNA-seq)


title: XEN41_control_Exp3_t=0 (RNA-seq)


title: mES_5k_Pol2_rep2


title: TX_Recipient_1

description:
Sequenced on Illumina NovaSeq 6000
TX_Recipient_1_filtered_feature_bc_matrix.h5
TX_Recipient_1_raw_feature_bc_matrix.h5
04all-lineages.h5ad
01epithelial.h5ad


title: PAO1_MIC_Exp3_t=72 (RNA-seq)

value: PAO1 (Wild Type)


title: mES_2k_Pol2_rep1


title: PAO1_MIC_Exp3_t=48 (RNA-seq)


title: mES_5k_Pol2_rep1


title: mES_1M_Pol2_rep2


title: TX_Donor_4

description:
Sequenced on Illumina NovaSeq 6000
TX_Donor_4_filtered_feature_bc_matrix.h5
TX_Donor_4_raw_feature_bc_matrix.h5
04all-lineages.h5ad
02immune.h5ad
03stromal.h5ad

value: Negative


title: PB2_2

description:
Sequenced on Illumina NovaSeq 6000
PB2_2_filtered_feature_bc_matrix.h5
PB2_2_raw_feature_bc_matrix.h5
04all-lineages.h5ad
02immune.h5ad
03stromal.h5ad


title: PAO1_MIC_Exp3_t=24 (RNA-seq)


title: mES_1M_Pol2_rep1


title: TX_Donor_3

description:
Sequenced on Illumina NovaSeq 6000
TX_Donor_3_filtered_feature_bc_matrix.h5
TX_Donor_3_raw_feature_bc_matrix.h5
04all-lineages.h5ad
03stromal.h5ad


title: TX_Donor_2

description:
Sequenced on Illumina NovaSeq 6000
TX_Donor_2_filtered_feature_bc_matrix.h5
TX_Donor_2_raw_feature_bc_matrix.h5
04all-lineages.h5ad
02immune.h5ad


title: PAO1_MIC/10_Exp3_t=72 (RNA-seq)


title: ICM_Pol2_rep3

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 98 h after hCG.
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: Preimplantation embryo

value: ICM


title: TX_Donor_1

description:
Sequenced on Illumina NovaSeq 6000
TX_Donor_1_filtered_feature_bc_matrix.h5
TX_Donor_1_raw_feature_bc_matrix.h5
04all-lineages.h5ad
01epithelial.h5ad


title: PAO1_MIC/10_Exp3_t=48 (RNA-seq)


title: ICM_Pol2_rep2


title: PAO1_MIC/10_Exp3_t=24 (RNA-seq)


title: PB1_4

description:
Sequenced on Illumina NovaSeq 6000
PB1_4_filtered_feature_bc_matrix.h5
PB1_4_raw_feature_bc_matrix.h5
04all-lineages.h5ad
02immune.h5ad
03stromal.h5ad

source_name: Sorted Stromal and Myeloid populations

value: Sorted Stromal and Myeloid populations


title: ICM_Pol2_rep1


title: PB1_3

description:
Sequenced on Illumina NovaSeq 6000
PB1_3_filtered_feature_bc_matrix.h5
PB1_3_raw_feature_bc_matrix.h5
04all-lineages.h5ad
02immune.h5ad


title: PAO1_control_Exp3_t=48 (RNA-seq)

value: control


title: 8cell_Pol2_rep2

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 65 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.


title: 8cell_Pol2_rep1


title: PB1_1

description:
Sequenced on Illumina NovaSeq 6000
PB1_1_filtered_feature_bc_matrix.h5
PB1_1_raw_feature_bc_matrix.h5
04all-lineages.h5ad
01epithelial.h5ad


title: PAO1_control_Exp3_t=24 (RNA-seq)


title: PAO1_control_Exp3_t=0 (RNA-seq)


title: PB1_2

description:
Sequenced on Illumina NovaSeq 6000
PB1_2_filtered_feature_bc_matrix.h5
PB1_2_raw_feature_bc_matrix.h5
04all-lineages.h5ad
03stromal.h5ad


title: 2cell_late_Pol2_rep1

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 48 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: late 2-cell


title: EN scRNAseq exp#1

city: Milan

first: Giulia

middle: Maria

last: Scotti

state: Milan

address: Viale Rita Levi Montalcini, 1

department: National Facility for Data Handling and Analysis

country: Italy

institute: Fondazione Human Technopole

description: Sample 4

data_processing:
R1 are technical reads containing Unique Molecular Identifiers and cell barcodes.
Barcodes corresponding to real living cells were detected by counting the number of Unique Molecular Identifiers associated to each cell barcode (Macosko-Nemesh pipeline for Samples 1,8,9; UMItool pipeline for Samples 2,3,4,5,6,7)
Reads were aligned to the reference human genome with STAR (version 2.5.3a)
Mapped reads were assigned to the annotated genomic features (Gencode genome version: GRCh38, basic annotation, release 27)
Genome_build: UCSC hg38
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

source_name: Induced pluripotent cells

growth_protocol: hiPSC were maintained in Essential 8 on 0.5 µg/cm2 Vitronectin Recombinant human protein and differentiated following pancreatic developmental stages (Pellegrini, Cell transplantation 2018). Islets were cultured in CMRL 1066 supplemented medium.

extract_protocol:
Cells were dissociated with trypsin, filtered with a 0.45 um filter and resuspended in PBS BSA 0.2% at a concentration of 2000 cells/ul
Single cells suspensions were loaded on Dropseq microfluidic platform for transcriptome capture and barcoding following Drop-Seq Laboratory Protocol version 3.1 (http://mccarrolllab.org/wp-content/uploads/2015/05/Online-Dropseq-Protocol-v.-3.1-Dec-2015.pdf)
libraries were prepared according the Dropseq protocol (specifically, Nextera XT from Illumina was used to produce sequencing-ready libraries afterwards)

value: iPSC-derived pancreatic endocrine cells

tag: differentiation day


title: iβ scRNAseq exp#1

description: Sample 6

value: iPSC-derived Beta cells


title: 2cell_late_Pol2_rep3


title: 2cell_late_Pol2_rep2


title: cerebrospnial fluid from Hydrocephalus patient WGBS NonTumorCSF4

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

data_processing:
For the WGBS analysis, raw FASTQ files were mapped to the NCBI Human Reference Genome Build GRCh37 (hg19) using BSMAP 53. MCALL module in MOABS54 software was used to calculate DNA methylation ratio and coverage for each CpG site. Differentially methylated CpGs and regions were identified using the MCOMP module considering variance among samples (--withVariacne 1) in the MOABS software 54. Bisulfite conversion efficiencies were estimated using spike-in unmethylated lambda phage DNA. The output bedGraph files from MCALL include single base resolution DNA methylation ratios, which were transformed to a bigwig file format. The bigwig files were uploaded to the UCSC genome browser for visualization.
For CMS-IP-seq analysis, raw FASTQ files were mapped to NCBI Human Reference Genome Build GRCh37 (hg19) using BSMAP 53. Only uniquely mapped non duplicated reads were kept as input for MACS2 55 to call 5hmC enriched regions (peaks). Differential hydroxymethylation regions (DHMRs) were identified using DESeq2 with default parameters 56. Bam files were transformed to bigwig format, which can be used to visualize 5hmC signals in the UCSC genome browser.
Genome_build: hg19

extract_protocol:
Total DNA containing cell-free tumor DNA (ctDNA) was isolated from 200-400 µL cerebral spinal fluid (CSF) using QIAamp Circulating Nucleic Acid Kit (Qiagen) according to manufacturer’s instructions. For MB tumor tissues, up to 20 mg of tumor tissues was snap frozen with liquid nitrogen and grinded. DNA was then isolated using an AllPrep DNA/RNA mini kit according to the manufacturer’s protocol. The isolated DNA concentration was measured by a Qubit 4 Fluorometer with the Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific).
The whole genome bisulfite sequencing (WGBS) analysis was used to measure the genome-wide DNA methylation status. The ctDNA WGBS libraries were generated using a Pico Methyl-Seq Library Prep Kit (Zymo Research). Briefly, ctDNA was mixed with 0.1% unmethylated λ-bacteriophage DNA (NEB) followed by sodium bisulfite conversion. Then the bisulfite converted DNA was annealed with random primers for initial amplification, followed by adaptor ligation and final amplification with Illumian TruSeq indices. Constructed libraries were run on 2% agarose gel to assess the size distribution and library concentration was measured by a Qubit 4 Fluorometer with a Qubit dsDNA high sensitivity assay kit (Thermo Fisher Scientific). Normalized libraries were then pooled in an equimolar ratio and sequenced on NextSeq 500 (Illumina) with a NextSeq 500/550 High Output Kit v2.5 (single-end reads, 75 Cycles) following the manufacturer’s protocols.  CMS-IP-seq was performed as described previously with some modifications. Briefly, purified MB tumor gDNA was sonicated to the 200-400 bp size range using Covaris M220 Focused-ultrasonicator (Covaris). The CSF ctDNA was directly treated with sodium bisulfite without sonication. The sheared gDNA and purified ctDNA were treated with sodium bisulfite using an EZ DNA methylation-lightning kit (Zymo Research) with manufacturer’s protocols to convert 5hmC to cytosine-5-methylenesulfonate (CMS). Next, CMS-containing DNA fragments were immunoprecipitated using a CMS-specific antiserum conjugated with protein A/G dynabeads. Enriched DNA fragments were purified using the conventional phenol/chloroform/isomyl-alcohol method, and amplified with random primers, followed by adaptor ligation and final amplification with illumine TruSeq index using a Pico Methyl-Seq Library Prep Kit (Zymo Research). DNA library sizes and concentrations were verified by Bioanalyzer. The DNA libraries were then sequenced in NextSeq 500 (Illumina) with NextSeq 500/550 High Output Kit v2.5 (single-end reads, 75 Cycles) following the manufacturer’s protocols.
WGBS and CMS-IP

tag: sample type

value: cerebrospnial fluid


title: 2cell_early_Pol2_rep2

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 36 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: early 2-cell


title: cerebrospnial fluid from Hydrocephalus patient WGBS NonTumorCSF3


title: cerebrospnial fluid from Hydrocephalus patient WGBS NonTumorCSF2


title: PN5_Pol2_rep2

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. PN5 embryos were harvested in M2 medium 30 h after hCG
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.


title: cerebrospnial fluid from Hydrocephalus patient WGBS NonTumorCSF1


title: SN_Pol2_rep2

source_name: Oocyte

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG. Oocytes were harvested in M2 medium 48 h after PMSG.
Antibody and pA-Tn5 (Vazyme Biotech, S603) or pG-Tn5 (Vazyme Biotech, S602) complex was prepared 20min ahead of sample lysis step. Add 1ul fully dissolved 5% digitonin into 1ml Buffer1 (10 mM Tris-HCl pH=7.4, 150mM NaCl, 0.5mM NaCl, 1x EDTA-free Roche complete protease inhitibor.) to prepare DB-1. Add 7μl DB-1, 0.5ul pA/G-Tn5 (choosing pA or pG depends on antibody species and affinity, we used pG-Tn5 for Pol II and pA-Tn5 for H3K4me3 and H3K27me3), 0.5ug antibody into 200ul low-binding tube and mix by vortex. Incubate at 4°C for 30min. Briefly, for Stacc-seq without wash step, fresh cells or embryos were prepared and put into 200ul low-binding tube (total volume with buffer should be less than 1μl). Add 6ul DB-1 into the sample and vortex. Incubate at 4°C for 10min, vortex each 2.5min for 3 times. Add 35μl DB-1 into the resulting samples, then add pA/G-Tn5 mixture and 12.5μl pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was purified by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing. For Stacc-seq with wash step, fresh cells or embryos were suspended in 50ul Buffer1 into 200ul low-binding tube. 10ul Concanavalin-coated magnetic beads (Polyscience, 86057) were washed by 200 ul Buffer2 (10 mM Tris-HCl pH=7.4, 10mM KCl, 1mM CaCl2, 1mM MnCl2) once and resuspended in 10ul Buffer2. Add beads to samples and incubate for 10mins at room temperature. Place the samples on magnet stand and remove the supernatant and then wash beads with 200ul Buffer1 twice. Add pA/G-Tn5 mixture and DB-1 to 50ul to samples and resuspend the beads. Place tube on 4°C Thermo mixer at 400 rpm for 2h. Place the tube on magnet and remove the supernatant. Wash beads twice with 200ul DB-1. Resuspend the beads with 50ul DB-1 and add 12.5ul pre-warmed (37°C) 5x TTBL (Vazyme Biotech, TD502). Incubate in Thermo mixer at 37 °C for 30 min at 400 rpm. DNA was directly purified without removing beads by phenol-chloroform with 40ng carrier RNA and 2ul spike-in DNA followed by ethanol precipitation 30min at -80°C or overnight at -20°C. PCR was performed to amplify the library for 16 cycles using the following PCR conditions: 72 °C for 3 min; 98 °C for 30s; and thermocycling at 98°C for 15s, 60°C for 30s and 72°C for 3min; followed by 72 °C 5 min. After the PCR reaction, libraries were purified with the 0.4x-1.7x AMPure (Beckman) beads size selection and were subjected to next generation sequencing.

value: Oocyte

value: Full-grown oocyte SN


title: PN5_Pol2_rep1

value: wild-type


title: RAW264.7 cells treated without LPS and IFNγ,replicate 3

type: RNA

city: Jinan

first: Xiaoxiao

last: Zhu

address: 18877 Jingshi Road

institute: Shandong First Medical University & Shandong Academy of Medical Sciences

description: miRNA expression of RAW264.7 treated without LPS and IFNγ

hyb_protocol: 0.6 μg of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/μg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 22.5μl containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers' instructions. On completion of the fragmentation reaction, 22.5μl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to  Agilent Mouse miRNA Microarray (8*60K) for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner (G2505C) using one color scan setting for 4x180k array slides (Scan Area 61x21.6 mm, Scan resolution 3um, Dye channel is set to Green and Green PMT is set  to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7.1.1  (Agilent) using default parameters to obtain background subtracted and spatially  detrended Processed Signal intensities as the raw data. Raw data were normalized  in quantile algorithm with Genespring 13.0(Agilent). Probe that at least 1 out of 2  samples flagged as Detected were maintained.

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.2 μg RNA using the One-ColorLow RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN,Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: DMEM containing 10% FBS and 1% penicillin/ streptomycin, 37 degree and 5% CO2.

extract_protocol: RNA was extracted by mirVanaTM RNA Isolation Kit (Applied Biosystem p/nAM1556 ) following the manufacturer's instructions.

treatment_protocol: After overnight culture in complete medium, cells were treat with 100 ng/ml LPS and 20ng/ml IFNγ for 24h.

tag: tag

value: cell line:RAW264.7


title: SN_Pol2_rep1

tag: developmental stage

value: Pol2(Active Motif 102660)


title: NSN_Pol2_rep3

tag: tissue

value: Full-grown oocyte NSN


title: RAW264.7 cells treated without LPS and IFNγ,replicate 2


title: PE scRNAseq exp#1

description: Sample 2

value: iPSC-derived pancreatic endoderm cells


title: sh-PGK1+DHT3

first: Xia

address: 910, Hengshan Road, Shanghai

institute: International Peace Maternity and Child Health Hospital

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Genome_build: GRCh38
Supplementary_files_format_and_content: TXT file contain counts for each sample

source_name: KGN cells

growth_protocol: KGN cells were cultured in DMEM/F12 medium

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

treatment_protocol: DHT was used at a concentration of 0.1uM

tag: shRNA


title: sh-PGK1+DHT2


title: RAW264.7 cells treated with LPS(100ng/ml) and IFNγ(20ng/ml) for 24h,replicate 3

description: miRNA expression of RAW264.7 treated with LPS(100ng/ml) and IFNγ(20ng/ml) for 24h

value: cell line:RAW264.7,treatment:LPS(100ng/ml) and IFNγ(20ng/ml) for 24h


title: RAW264.7 cells treated with LPS(100ng/ml) and IFNγ(20ng/ml) for 24h,replicate 2


title: sh-PGK1+DHT1


title: PAO1_control_Exp3_t=72 (RNA-seq)

source_name: bacteria

extract_protocol: RNA was harvested using RNeasy® Mini Kit QIAGEN

value: PAO1 (Wild Type)


title: ICM_mRNA_rep2

data_processing:
Basecalls performed using CASAVA version 1.8
RNA-Seq reads were aligned to the mm9 genome assembly using tophat 2.1.1,  transcript abundance (FPKM) were calculated based on Reflat annotation using cufflinks version 2.1.1
Genome_build: mm9

source_name: Preimplantation embryo

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 98 h after hCG
The Smart-seq2 libraries of ICM were prepared as previously described (Picelli et al., 2014). ICM were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing.

value: Preimplantation embryo

tag: genotype

value: ICM


title: nc-3+DHT3


title: HepG2 CEBPA

data_processing:
Reads were aligned using BWA MEM with either single-end or pair-end model to the hg19 reference genome. Reads with low mapping quality (mapq<10) were filtered out, and PCR duplicates were removed using Picard tool.
MACS2 were then applied to call peaks and generate signals to view in the genome browser.
Genome_build: hg19
Peak files in narrowPeak format and signal files in bigWig format for each samples were provided.

value: CEBPA


title: HepG2 ATF3


title: nc-3+DHT2


title: 2cell_late_total_RNA_mTBE_rep1

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. Embryos were harvested in M2 medium 23 h after hCG
Total RNA-seq libraries were prepared as previously described (Brind'Amour, J., et al. 2018). Total RNA was isolated from about 100 mouse embryos using TRIzol (Thermo, 10296028), and ribosomal RNA was depleted using the NEB Next rRNA Depletion Kit (NEB, E6310S) according to the manufacturer’s instruction. Double-stranded cDNA was synthesized using NEB Next first-strand (NEB, E7771S) and second-strand synthesis modules (NEB, E7550S). Library preparation was performed using NEBNext UltraTM II DNA Library Prep Kit (NEB, E7645S) according to the manufacturer’s instruction. All libraries were sequenced by Illumina Hi-Seq Xten platform according to manufacturer’s instruction.

treatment_protocol: Zygotes were obtained at 23 h post hCG and cultured in KSOM containing either 0.1% DMSO or 60 uM DRB for 14 h. Embryos were released from DMSO or DRB when entering 2C stage and cultured for 12 h prior to the further experiment.

value: late 2-cell


title: nc-3+DHT1


title: NSN_Pol2_rep2

tag: antibody


title: HepG2 TGIF2LX

extract_protocol:
Briefly, the cells were crossed linked with 1% formaldehyde at ambient temperature for 10 min. The reaction was quenched by 125mM glycine for 5 min at room temperature. Cells were washed with PBS and treated with hypotonic buffer (20mM Hepes pH7.9, 10mM KCl, 1mM EDTA, 10% Glycerol and 1mM DTT with additional protease inhibitor (Roche)) to isolate nuclei. The nuclei were suspended with RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate with protease inhibitor) and sonicated using Covaris S220 Focused-ultrasonicator. Fragmented chromatin was pre-cleared with protein G conjugated sepharose beads (GE). Antibodies were used to pull down the respective proteins and their associated chromatin. Washes with different concentration of NaCl were performed. The enriched protein-DNA complexes were reverse crosslinked at 65 C over night with proteinase K (NEB). DNA was purified with Qiagen MinElute kit.
Sequencing library was prepared using an in-house kit, including end-repair, “A” addition and adapter ligation. The library was sequenced with illumina HiSeq 4000 for 50bp single read or 100bp pair-end, acquiring 10-30 million reads.


title: RAW264.7 cells treated with LPS(100ng/ml) and IFNγ(20ng/ml) for 24h,replicate 1


title: RAW264.7 cells treated without LPS and IFNγ,replicate 1


title: HepG2 HOXA13


title: ICM_mRNA_rep1


title: AIM_12

city: Boston

first: Cloud

middle: Peter

last: Paweletz

state: MA

address: 360 Longwood Avenue

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Sample-to-sample correlation heatmap was generated using VIPER (Visualization Pipeline for RNA-seq analysis) and displayed hierarchical clustering of spearman rank correlations across samples.
Differential expression analysis of bulk RNA-sequencing files was performed using the R package, DESeq2 (Love et al., 2014).  Volcano plots were generated using R with a log2 Fold Change cutoff of 1.5 and an adjusted p-value cutoff of 1e-10.
Pathway analysis of bulk RNA-sequencing was performed using the DEseq2 results and run through the R package, ClusterProfiler, using the Hallmark GeneSets from MSigDB (Broad Institute) (Yu et al., 2012). Plots of running enrichment score were generated with R.
Genome_build: mm9

source_name: cells after 6 days of ex vivo growth

growth_protocol: Fresh MC38 tumor specimens were dissociated, S2 fraction (40-100um) was re-suspended in a 2.8 mg/mL collagen matrix and loaded into the DAX-1 3-D cell culture chip (AIM Biotech).

extract_protocol:
After 6 day treatment in the microfluidic devices, RNA was lysed directly from the devices and isolated using the Agencourt RNAdvance Tissue isolation kit (with DNAse).
RNA libraries were prepared from 250 ng total RNA using the Illumina Exome Capture kit per manufacturer’s instructions.

treatment_protocol: Drug treatments were performed by diluting drugs in full media and adding 300 µL to each well of the chip.

tag: strain

value: C57BL/6 albino

tag: treatment

value: IFNg (R&D, 100ng/mL)


title: AIM_11

value: aPD-1 (clone RMP1-14, 10ug/mL)+CD8 (clone 53-6.7, 10ug/mL)


title: PN5_total_RNA_rep1

extract_protocol:
8-week-old female mice were intraperitoneally injected with PMSG and hCG. PN5 embryos were harvested in M2 medium 30 h after hCG
Total RNA-seq libraries were prepared as previously described (Brind'Amour, J., et al. 2018). Total RNA was isolated from about 100 mouse embryos using TRIzol (Thermo, 10296028), and ribosomal RNA was depleted using the NEB Next rRNA Depletion Kit (NEB, E6310S) according to the manufacturer’s instruction. Double-stranded cDNA was synthesized using NEB Next first-strand (NEB, E7771S) and second-strand synthesis modules (NEB, E7550S). Library preparation was performed using NEBNext UltraTM II DNA Library Prep Kit (NEB, E7645S) according to the manufacturer’s instruction. All libraries were sequenced by Illumina Hi-Seq Xten platform according to manufacturer’s instruction.


title: HepG2 IRF3


title: AIM_10

value: aPD-1 (clone RMP1-14, 10ug/mL)


title: AIM_9

value: IgG (clone 2A3, 10ug/mL)


title: AM0.25_3

city: Corvallis

first: Susan

middle: C.

last: Tilton

state: OR

address: 1007 ALS Bldg

department: AG Envr & Molec Toxicology

institute: Oregon State University

data_processing:
Cutadapt (version 1.8.1) to trim adapter sequences from the paired-end reads
The human genome assembly GRCh38.84 was indexed using bowtie2-build (version 2.2.3)
TopHat (version 2.1.1.) was used to index the transcriptome and to align the trimmed reads to indexed transcriptome and genome.
FeatureCounts, from the Subread package (version 1.6.0) was used to generate count tables.
Differential expression (q<0.05) was determined in DESeq2 (version 1.26.0) compared to vehicle control.
Genome_build: GRCh38.84

source_name: primary bronchial epithelial cells

growth_protocol: Primary HBEC differentiated on transwell inserts (EpiAirway™ 100, Mattek, Ashland, MA) were transferred to 6-well plates each well containing 1 ml of assay medium and equilibrated for 24 hours at 37°C, 5% CO2 followed by a change of fresh medium before treatment.

extract_protocol:
Total RNA was isolated from HBEC (n=4) using TRizol® reagent and was quantified on a Synergy HTX plate reader equipped with a Take3 module (BioTek).  RNA quality was evaluated based on 260/280 ratio (acceptable range 2.0-2.1) and by examining 18S and 28S peaks (Bioanalyzer 2100, Agilent, Santa Clara, CA). Acceptable RNA quality was based on RIN ≥ 8.5.
mRNA was poly-A selected, and libraries were prepared with the PrepXTM mRNA and Illumina sequencing workflow (Wafergen Biosystems, Fremont, CA).

treatment_protocol: Inserts were washed with phosphate buffered saline (PBS, pH 7.4) and then treated with PAHs in acetone vehicle on apical surface for up to 48 hrs, BAP (10, 100 ug/ml), BAN (500 ug/ml), PHE (100 ug/ml), CTE (1500 ug/ml) and AM (250 ug/ml).

tag: Stage

value: differentiated at air-liquid interface

value: Air Mixture 0.25


title: HepG2 HLF

value: HLF


title: HepG2 HNF1B


title: AM0.25_4


title: HepG2 MAFF/G/K

value: MAFF/G/K


title: 2cell_late_total_RNA_Con_rep1

value: wild-type


title: AM0.25_2


title: AM0.25_1


title: CTE1.5_3

value: Coal Tar Extract 1.5


title: CTE1.5_4


title: HepG2 PEA3


title: AIM_8


title: AIM_7


title: AIM_6


title: KO_Bladder 780

city: Lund

first: Sebastian

last: Albinsson

address: BMC D12

country: Sweden

institute: Lund University

description: KO_Bladder 780

data_processing:
Demultiplexing: organized the FASTQ files based on the sample index information, and generated the statistics and reporting files. This task was performed using the bcl2fastq2 software with default settings
Raw Quality Control (QC): FastQC provided quality control analyses and checked on raw sequence data coming from the above Demultiplexing step of the pipeline.
Read Mapping: alignment of reads to the specified reference genome. This task was performed using the HISAT2 software package.
Mapping QC: mapping quality control checked such as evaluating the distribution of reads mapped by the above mapping step.
Expression counts: assembled the alignments into full transcripts and quantified  the expression levels of each gene and transcript. This task was performed using the StringTie software package.
DE analysis: Differentially expressed genes (DEG) analysis was performed using DESeq2.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-separated text files generated by StringTie software package; contains expression counts

source_name: Urinary Bladder

growth_protocol: Animal were used after weaning at age of 5-7 weeks

extract_protocol:
RNA was extracted using Qiagen RNAeasy kit
Library was prepared according to TruSeq® Stranded mRNA Sample Preparation Guide (Part # 15031047 Rev. E) Modification of “Enrich DNA Fragment” step: from 15 to 13 PCR cycles.

treatment_protocol: Wwtr1/Yap1 floxed, Myh11CreERT2 positive (KO) or negative (WT) mice were injected with Tamoxifen (1mg/mouse/day) for 5 consecutive days. Tissues were extracted 7 days after the first tamoxifen treatment

value: Urinary Bladder

tag: gender

value: Male

tag: modification

value: SMC specific, inducible Yap1/Wwtr1 KO

tag: age

value: 5-7 weeks


title: AIM_5

tag: cell line


title: AIM_4


title: CTE1.5_2


title: CTE1.5_1


title: KO_Bladder 783

description: KO_Bladder 783


title: HepG2 HOXB4

tag: chip antibody


title: AIM_3


title: PHE100_4

value: Phenanthrene


title: AIM_2


title: KO_Bladder 782

description: KO_Bladder 782


title: PHE100_3


title: AIM_1


title: TX_Recipient_2

description:
Sequenced on Illumina NovaSeq 6000
TX_Recipient_2_filtered_feature_bc_matrix.h5
TX_Recipient_2_raw_feature_bc_matrix.h5
04all-lineages.h5ad
02immune.h5ad

extract_protocol: Libraries were prepared with 10x Genomics 3' V3 gene expression (GEX) reagents according to the manufacturer protocol (CG000183_RevB).

value: Positive

tag: tissue type

value: Distal lung parenchyma

tag: cell type

value: Sorted Myeloid population


title: CTRL_Bladder 788

description: CTRL_Bladder 788

value: Cre negative Tamoxifen treated


title: CTRL_Bladder 785

description: CTRL_Bladder 785


title: PHE100_1


title: CTRL_Bladder 784

description: CTRL_Bladder 784


title: PHE100_2


title: BAN500_4

value: Benz[a]anthracene


title: KO_Colon 780

description: KO_Colon 780

source_name: Colon

value: Colon


title: MMTV-PyMT tumor_cGAMP rep1

city: Daejeon

first: Myung Jin

last: Yang

country: South Korea

institute: Institute for Basic Science

data_processing:
quality assessment of raw sequence data was performed using FastQC
Sequenced reads were aligned to mouse reference genome (mm10) with STAR (version 2.7), and the aligned reads were used to quantify mRNA expression by using HTSeq-count
Fragments Per Kilobase of transcript per million mapped reads (FPKM) were calculated
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values all samples

source_name: breast tumor

extract_protocol:
Endothelial cells were sorted with FACS aria II (BD bioscience). RNA was extracted with Rneasy mini kit (Qiagen).  NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England BioLabs) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: FVB

value: breast tumor

tag: time

value: post injection 3 hr

value: MMTV-PyMT


title: MMTV-PyMT tumor_cGAMP rep2

tag: tag


title: BAN500_3

value: differentiated at air-liquid interface


title: KO_Colon 783

description: KO_Colon 783


title: BAN500_2


title: MMTV-PyMT tumor_cGAMP rep3


title: KO_Colon 759

description: KO_Colon 759


title: BAN500_1


title: CTRL_Colon 787

description: CTRL_Colon 787


title: MMTV-PyMT tumor_PBS rep2


title: MMTV-PyMT tumor_PBS rep1


title: Acet_5

value: Acetone


title: 12704_RN017

type: genomic

city: Pittsburgh

first: Anita

last: Bansal

state: PA

address: Biomedical Science Tower

department: Immunology

institute: University of Pittsburgh

hyb_protocol: Standard Illumina Protocol

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

data_processing: Data was processed using ChAMP

label: Cy5 and Cy3

source_name: Genomic DNA from Control cells

label_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation27 Beadchip using standard Illumina protocol

growth_protocol: Both non-diabetic and diabetic proximal tubule epithelial cells in renal epithelial cell growth media from Lonza

extract_protocol: Standard Illumina Protocol

treatment_protocol: Cells were treated with TGFB1 for 24 hours, 72 hours and 96 hours

value: Proximal Tubule Epithelial Cells

tag: disease state

value: non-diabetic Control

value: untreated


title: CTRL_Colon 786

description: CTRL_Colon 786

tag: tissue

value: Male

value: 5-7 weeks


title: Implanted tumor_cGAMP rep3

value: wild type


title: Acet_4


title: CTRL_Colon 788

description: CTRL_Colon 788


title: 12707_RN020

source_name: Genomic DNA from Control cells treated with TGFB1 for 24 hours

value: TGFB1 24 hours


title: Implanted tumor_cGAMP rep2


title: 12700_RN013

source_name: Genomic DNA from diabetic cells

value: Type 2 Diabetes


title: 12702_RN015

source_name: Genomic DNA from diabetic cells treated with TGFB1 for 24 hours


title: RL-20-Control-RprY-7_S20

city: Louisville

first: Richard

last: Lamont

state: Kentucky

address: 501 S. Preston St

department: Oral Immunology and Infectious Diseases

institute: University of Louisville

data_processing:
Fastq files were downloaded from Illumina's BaseSpace for analysis.
Quality control was perfomed using FastQC (version 0.10.1). After examining the results of QC it was determined that no sequence trimming was required due to the sequences having a sufficiently high enough quality.
Reads were mapped to the P. gingivalis ATCC 33277 genome (NCBI accession # AP009380) using STAR (version 2.6) to generate alignment files in bam format.
HTSeq was used to generate raw gene counts for every sample from aligned bam files produced from STAR.  HTSeq was set to include reads aligned to up to ten locations.
DESeq2 was used to perform differential gene expression analysis using the recommened guidelines.
Performed a regularized log transformation on raw count data as outlined in Love et al. 2014 (DOI: 10.1186/s13059-014-0550-8) for principal component analysis.
Genome_build: NCBI Accession AP009380
Supplementary_files_format_and_content: Matrix tables with raw gene counts for every gene and every sample

organism: Porphyromonas gingivalis

source_name: Culture

growth_protocol: Porphyromonas gingivalis ATCC 33277 and isogenic mutants were cultured anaerobically at 37℃ in trypticase soy broth (TSB) supplemented with 1 mg/mL yeast extract, 5 µg/mL hemin, and 1 µg/mL menadione.

extract_protocol:
Total RNA was isolated from the cells using the Qiagen RNAeasy kit (Qiagen) with DNase treatment.
Ribosomal RNA depletion and library construction were performed using the Universal Prokaryotic RNA-Seq kit (Tecan).

value: [delta]rprY


title: 14993_RN048

source_name: Genomic DNA from diabetic cells treated with TGFB1 for 48 hours

value: TGFB1 72 hours


title: 12705_RN018


title: 14997_RN052

source_name: Genomic DNA from diabetic cells treated with TGFB1 for 96 hours

value: TGFB1 96 hours


title: miRNA-CH2

city: Beijing

first: Ying

last: Zhang

address: Haidian District, Yuanmingyuan West Road 2

institute: China Agricultural University

data_processing:
Illumina Hiseq used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-quality sequence, then aligned to the chicken reference genome (Gallus gallus 6.0) using HISAT2 (version 2.0.9) software
FPKM and TPM were calculated using the StringTie, Differential expression analysis comparing TC and CH was performed with the DESeq2 software.
Genome_build: Gallus-gallus-6.0 (ftp://ftp.ensembl.org/pub/release-96/fasta/gallus_gallus/dna)
Supplementary_files_format_and_content: bam profiles

organism: Gallus gallus

source_name: Chorioallantoic membrane (CAM) of embryos

extract_protocol:
Chorioallantoic membrane tissues were removed, frozen on liquid nitrogen, and total RNA was harvested using Trizol reagent. Illumina HiSeq RNA Sample Prep Kit (Cat.#RS-122-2002; Illumina, San Diego, CA, USA) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: embryo

value: Chorioallantoic membrane

value: 11-day of embryo

value: Chahua chicken


title: 12703_RN016


title: 12706_RN019


title: miRNA-CH1

tag: genotype


title: 14991_RN046

source_name: Genomic DNA from Control cells treated with TGFB1 for 48 hours


title: Implanted tumor_cGAMP rep1

value: FVB

value: breast tumor

value: post injection 3 hr


title: Acet_3

value: differentiated at air-liquid interface

value: Acetone


title: Acet_2


title: 14995_RN050

source_name: Genomic DNA from Control cells treated with TGFB1 for 72 hours

value: Proximal Tubule Epithelial Cells

value: non-diabetic Control


title: 14994_RN049


title: miRNA-CH3


title: 14992_RN047


title: RL-18-Control-RprY-3_S18


title: miRNA-TC2

value: Tibetan chicken


title: 14996_RN051


title: MMTV-PyMT tumor_PBS rep3

value: MMTV-PyMT


title: miRNA-TC3


title: Implanted tumor_PBS rep2

value: wild type


title: BAP100_4

value: Benzo[a]pyrene


title: RL-19-Control-RprY-6_S19

value: [delta]rprY


title: 12701_RN014

value: Type 2 Diabetes

value: untreated


title: 14990_RN045

value: TGFB1 72 hours


title: Acet_1


title: Implanted tumor_PBS rep1


title: BAP100_3


title: 14988_RN043

value: TGFB1 24 hours


title: RL-16-Control-RprY-1_S16


title: Normal_cGAMP rep3

source_name: mammary fat pad

value: mammary fat pad


title: LncRNA-CH3

value: Chorioallantoic membrane

value: 11-day of embryo

value: Chahua chicken


title: BAP100_2

value: differentiated at air-liquid interface


title: LncRNA-CH2


title: RL-05-Control-WT-7_S5

value: WT


title: Normal_cGAMP rep2

value: FVB

value: post injection 3 hr


title: Normal_cGAMP rep1


title: 14984_RN039

value: Proximal Tubule Epithelial Cells

value: non-diabetic Control


title: LncRNA-CH1


title: BAP10_4


title: 14989_RN044


title: RL-03-Control-WT-5_S3


title: Normal_PBS rep3

value: wild type


title: 14985_RN040


title: BAP10_3

value: Benzo[a]pyrene


title: RL-17-Control-RprY-2_S17

value: [delta]rprY


title: RL-04-Control-WT-6_S4


title: RL-02-Control-WT-4_S2


title: BAP100_1


title: 14983_RN038


title: LncRNA-TC2

value: Tibetan chicken


title: Normal_PBS rep2


title: LncRNA-TC3


title: BAP10_2


title: RL-01-Control-WT-1_S1


title: LncRNA-TC1


title: Normal_PBS rep1


title: BAP10_1


title: 14986_RN041

value: Type 2 Diabetes

value: untreated


title: miRNA_fibrosis_Pigmentary PXF

status: Public on Oct 27 2020

city: Bhubaneswar

first: Munmun

last: Chakraborty

state: Odisha

address: MTC campus,Patia

department: Reasearch

country: India

institute: L.V Prasad Eye Institute

description:
Test
miRNA
SAMPLE 3

data_processing:
The normalization and all the data analysis were performed according to the manufacturers instructions using their web-based software package: https://www.qiagen.com/in/shop/genes-and-pathways/data-analysis-centre-overview-page/
For the normalization it uses the average of four housekeeping miRNA's: RNU6-6P, SNORD61, SNORD68 and SNORD95
Target gene signals normalized to housekeeping genes; 2^-deltaCt, where deltaCt = (Ct_Target − Ct_HKG)]
The web-based software package automatically performs all deltadeltaCt based fold-change calculations from the uploaded raw threshold cycle data.
Fold Change file reports test/control.

label: SYBR Green

source_name: Human Peripheral mononuclear cells

label_protocol: The total RNA obtained after PBMC isolation was purified of erythrocytes by PBS wash and used for miRNA extraction using the miRNA extraction kit (Qiagen, Hilden, Germany) This was reverse transcribed using the miScript II RT Kit (Qiagen) with 400ng of cDNA and later loaded onto human fibrosis/human miFinder The thermal cycling conditions used were as follows: Stage 1(1 cycle): 95°C for 15min, Stage 2 (40cycles): 94°C for 15seconds, 55°C for 30seconds and 70°C for 30seconds.

extract_protocol: PBMC was extracted using ficol and miRNA was obtained from PBMC using Trizol reagent and following steps as mentioned in Qiagen miRNeasy mini kit protocol

tag: diagnosis

value: Pigmentary PXF

value: Blood


title: miRNA_fibrosis_Psedoexfoliation (PXF)

description:
Control
miRNA
SAMPLE 1

value: Psedoexfoliation (PXF)


title: miRNA_fibrosis_Ocular Hypertension (OHT)

description:
Test
miRNA
SAMPLE 2

value: Ocular Hypertension (OHT)