title: Fly NSUN6 KO Male 1-3d tRNA BS

data_processing:
Adapters were first trimmed with Cutadapt (--max-n 1 -m 18 -e 0.25 --trim-n -q 20). Only reads containing adapters were retained.
Clean reads were first C-to-T (read 1) or G-to-A (read2) converted and mapped to C-to-T converted reference sequences containing tRNA (with CCA tail), mRNA, and rRNA with bowtie2 (--end-to-end --no-mixed --norc -k 50 -X 80). Read pairs were ranked by alignment scores (sum of AS and YS tags in the BAM file). Only read pairs with the highest alignment score and uniquely mapped to one tRNA type (multiple alignment on tRNA isodecoders was allowed) were used. For details, see github page: https://github.com/SYSU-zhanglab/tRNA-m5C
Original reads were recovered with a custom script and piled up to call m5C sites and calculate their methylation levels.
Genome_build: GtRNAdb Release 18.1 (hg19)
Supplementary_files_format_and_content: TXT, pileup file recording the tRNA position, coverage, methylation level of the samples

source_name: 1-3d Male, whole body

extract_protocol:
20 ug total RNA was first loaded into 15% denaturing TBE-Urea PAGE Gels and separated based on the molecular weight. The gel slice corresponding to 70-90 nucleotides was excised from the PAGE gel and the RNA fragments were recovered using ZR small-RNA™ PAGE Recovery Kit (Zymo Research) following the manufacturer’s protocol.
100ng-1μg of RNA was converted using the EZ RNA methylation kit (Zymo Research) with 3 cycles of [70 C 10 min, 64 C 45 min] and 37 C 30 min for desulfonation. End-repair was performed with T4 PNK (NEB) to phosphorylate 5’-hydroxyl termini and remove 2’,3’-Cyclic phosphate produced during the bisulfite/desulfonation reaction. The tRNA BS-seq library was generated using VAHTSTM Small RNA Library Prep Kit for Illumina (Vazyme) according to the manufacturer’s protocol.

value: NSUN6 knockout

tag: Sex

value: male

value: whole body

tag: molecule subtype

value: tRNA


title: ONLR [TJb3-5]

status: Public on Oct 29 2020

type: SRA

city: Boston

first: Tatjana

last: Jakobs

state: MA

address: 20 Staniford Street

department: Howe Laboratory of Ophthalmology

country: USA

institute: Massachusetts Eye and Ear Infirmary

description:
aged naïve mice
ONR1

library_source: transcriptomic

data_processing:
Transcriptome mapping to full genome sequences for Mus musculus (UCSC version mm10) was performed with STAR version 2.3.0 (Dobin et al., 2013)
Read counts for individual genes were produced using FeatureCounts (Liao et al., 2014)
Differential expression analysis was performed using the DESeq2 R package after normalizing read counts and excluding  those genes with normalized read counts equal 0  (Anders et al., 2013)
Genome_build: mm10
Supplementary_files_format_and_content: featureCounts_

molecule: total RNA

organism: Mus musculus

source_name: Optic nerve head

extract_protocol:
Optic nerve head were dissected. Qiagen microplus kit was used for total RNA extraction and Clontech SMARTer Ultra Low Input RNA Kit for Sequencing v3 (Takara, Kusatsu, Japan) was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Microbeads (experimental glaucoma) or saline solution (controls) were injected into right anterior chamber of young adult mice to induce high intraocular pressure in glaucoma group. In addition, 13 week old and 40 week old naïve C57bl/6 mice were also examined.

tag: strain

tag: tissue

value: optic nerve head

tag: age

value: 40 weeks

tag: genoptype

value: wild type

tag: group

value: 10 month, naive


title: YNLR [TJb3-3]

description:
young naïve mice
YNR3

value: 13 weeks

value: 3 month, naive


title: Fly testis rep2

city: Guangzhou

first: Rui

last: Zhang

address: No. 135, Xingang Xi Road

country: China

institute: Sun Yat-sen University

data_processing:
Adapters were trimmed with cutadapt-1.13 (-e 0.25 -q 25 –trim-n -a NNNNNNAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A NNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG). Adapter-trimmed reads were quality trimmed with Trimmomatic-0.36 (PE mode, HEADCROP:10 SLIDINGWINDOW:4:22 AVGQUAL:25 MINLEN:40).
Clean reads were mapped to Ensembl GRCh37.75 genome and transcriptome with hisat2-2.10 (-k 10, --fr, --rna-strandness FR --no-mixed), uniquely alignment only0. Unmapped reads were further mapped to transcriptome with bowtie2-2.2.9 (-end-to-end, --fr --gbar 5, --mp 5, -k 10, -R 2, -D 5). Unique alignments mapped to the same gene location were used. Transcriptome alignments were liftOver to genomic coordinates with a custom script. Hisat2 alignmets and bowtie2 alignmets were merged.
Pileup was performed using samtools API pysam to get base counts.
Custom scripts were used to call m5C sites from samples:  (i) C+T coverage >= 20; (ii) C count >= 3; (iii) m5C level >= 0.1; (iv) signal ratio >= 0.9 at certain C-cutoff (mostly at 2-5) and (v) one-side binomial P value < 0.001
Genome_build: BDGP5.78
Supplementary_files_format_and_content: CSV for the position, coverage, and methylation level for the samples

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Testis

extract_protocol:
Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit; for cytoplasm/nuclear fractions, cells were fractionated using the PARIS kit (Ambion) according to the manufacturer’s instructions. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with 3 cycles of [70 C 10 min, 64 C 45 min] and 37 C 30 min for desulfonation. The converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8 minutes in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

tag: genotype

value: Wildtype

value: Testis


title: Adult human cardiomyocytes_Mock_1

city: New York

first: Shuibing

last: Chen

state: NY

address: A 827B, 1300 York Ave

department: Surgery

institute: Weill Cornell Medical College

data_processing:
Illumina bcl2fastq2 v2.20 was used for basecalling.
Sequenced reads were trimmed for low-quality bases and for adapter sequences using cutadapt; then mapped to the human hg19 reference genome plus SARS-CoV-2 genome using STAR v2.5.2b.
Raw reads counts were extracted using htseq-count v0.11.2.
Genome_build: hg19
Supplementary_files_format_and_content: txt files storing raw read counts per gene per sample

organism: Homo sapiens

source_name: Adult human cardiomyocytes

growth_protocol: For monolayer-based cardiomyocyte (CMs) differentiation, hESCs were passaged at a density of 3x105cells/well of 6-well plate and grown for 48 hours to 90% confluence in a humidified incubator with 5% CO2 at 37℃. On day 0, the medium was replaced with RPMI 1640 supplemented with B27 without insulin and 6 µM CHIR99021. On day 1, the medium was changed to RPMI 1640 supplemented with B27 without insulin for 48 hr. Day 3, medium was refreshed to RPMI 1640 supplemented with B27 without insulin and 2 µM C59 for another 48 hr. On day 5, the medium was changed back to RPMI-B27 without insulin for 48 hr, and then switched to RPMI 1640 plus normal B27 until day 12 with a medium change every 2 days. On day 12, the medium was transiently changed to RPMI 1640 without D-glucose containing ascorbic acid, human albumin and DL-Lactate for two days to allow metabolic purification of CMs. From that day on, fresh RPMI 1640-B27 was changed every two days. On day 21, cells were dissociated with Accutase at 37℃ followed by resuspending with fresh RPMI 1640-B27 plus Y-27632 and reseeding into 96-well plates. After 24 hr, then switched to RMPI 1640-B27 without Y-27632 for following virus confection tests.

extract_protocol: Libraries were prepared using Illumina TruSeq RNA Sample Preparation (Non-stranded and Poly-A selection).

treatment_protocol: hPSC-derived cardiomyocytes were dissociated with Accutase at 37℃ followed by resuspending with fresh RPMI 1640-B27 plus Y-27632 and reseeding into 96-well plates. After 24 hr, the medium was switched to RMPI 1640-B27 without Y-27632. After 24h recovery, macrophages were added into hPSC-derived cardiomyocytes and co-cultured for another 24 hr before following analysis. Adult cardiomyocytes were also seeded into plates for 48-96 hr and co-cultured with macrophages for 24 hr before following analysis.

value: Adult human cardiomyocytes


title: F2: Stem FZB-treated 2

city: Frankfurt am Main

first: Lukas

last: Jost

address: Altenhöferallee 3

country: Germany

institute: GenXPro GmbH

data_processing:
Library strategy: Massive Analysis of cDNA ends (MACE-Seq)
Illumina bcl2fastq software used for basecalling.
Sequenced reads were trimmed for adaptor sequence and bad quality as well as MACE specific polyA stretches; PCR artifacts were deduplicated based on Unique Molecular Identifier sequences
Cleaned reads were mapped onto SolTub_3.0 genome using bowtie2 and raw counts were obtained using HTSeq
Genome_build: SolTub_3.0
Supplementary_files_format_and_content: tab-delimited text files include TPM values for each group
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Solanum tuberosum

source_name: Stem

growth_protocol: Plants were clonally propagated from potato 'Golden Wonder'. Cuttings were placed in polyurethane foam imbibed with 50 ml autotrophic M+S media. Photoperiod was 18/6 hours light/dark. Growth room temperature was ~ 23 degrees Celsius. Total growth time was 6 weeks.

extract_protocol:
Plants were harvested under aseptic conditions and RNA extractions from stem tissue were carried out using the QIAGEN® RNeasy™ plant extraction kit according to the manufacturer’s specifications. To eliminate genomic DNA contamination the Ambion® TURBO™ DNAse kit was used according to manufacturer’s specifications (Life Technologies, Carlsbad, CA, USA). RNA quantification was measured using a Nanodrop™ 2000c spectrophotometer (Thermo Fisher Scientific, Waltham, MA, USA). Samples were immediately stored at -80°C to prevent degradation of RNA.
MACE seq Kit was used (GenXPro-GmbH, Frankfurt Germany) for 3' end sequencing of poly-adenylated mRNAs. Sequences are generated fromm the 5' end of average 350 bp 3' mRNA fragemnts.

treatment_protocol: Plants were exposed to bacterial VOCs by dropping 20 µl of either bacterial culture, LAC2 (L) or FZB24 (F) at OD 600nm = 1.0 on the centre of a 50 mm petri dish containing either Methyl Red Voges Proskeur (MR-VP) broth (Sigma Aldrich) supplemented with 14 g agar (Sigma Aldrich) per litre

value: Stem

tag: cultivar

value: Golden Wonder

tag: treatment

value: Bacterial Volatile Organic Compounds


title: C3: Stem Control 3


title: Fly WT Male 1-3d tRNA BS

value: wildtype


title: Fly testis rep1


title: F1: Stem FZB-treated 1


title: hESC-derived cardiomyocytes+macrophages+SARS-CoV-2 Pseudo-entry virus

data_processing:
The sequencing data were primarily analyzed by the 10X cellranger pipeline (v3.0.2)
cellranger mkfastq was used for sample demultiplexing and fastq generation.
cellranger count was used to align reads to the 10X pre-built human reference genome (GRCh38 v3.0.0) plus virus genes and fluoresence genes, and to extract gene expression UMI counts matrix.
Genome_build: GRCh38
Supplementary_files_format_and_content: UMI counts matrix generated by 10X cellranger count; matrix.mtx.gz stores UMI counts per gene per cell; features.tsv.gz stores gene annotations; barcodes.tsv.gz stores cell barcodes.

source_name: hESC-derived cardiomyocytes

extract_protocol: Library was constructed according to the user manual of Chromium Single Cell 3’ Library & Gel Bead Kit v2

value: hESC-derived cardiomyocytes


title: YNLR [TJb3-2]

description:
young naïve mice
YNR2


title: hESC-derived cardiomyocytes+SARS-CoV-2 Pseudo-entry virus


title: C2: Stem Control 2


title: YNLR [TJb3-1]

description:
young naïve mice
YNR1


title: hESC-derived cardiomyocytes


title: Fly Body 5d rep2

description:
processed data file:
AdM_5days.csv

data_processing:
Basecalls performed using illumina bcl2fastq 2.17.
Adapters were trimmed with cutadapt. Adapter-trimmed reads were quality trimmed with Trimmomatic.
Clean reads were firstly mapped to the genome and then transcriptome with hisat2-2.10
Pileup was performed using samtools API pysam.
Customized scripts were used to call m5C sites from samples
Genome_build: BDGP5.78
Supplementary_files_format_and_content: CSV files recording the coverage, m5C level, P-value for m5C sites

source_name: male body

extract_protocol:
500-1,000 embryos, ~50 larvae, ~50 pupa, ~50 ovaries, and ~50 adult flies were used for RNA isolation in each stage.  Total RNA was isolated with TRIzol reagent and Direct-zol RNA MiniPrep kit. Polyadenylated RNA was separated from total RNA using Oligo dT Magnetic Beads (Vazyme).
100ng-1μg of polyadenylated RNA was converted using the EZ RNA methylation kit (Zymo Research) with modified high-stringency conversion conditions. The quantity of the converted RNA was determined by Qubit. 20ng converted RNA was fragmented into 150~200 nt fragments by incubation at 94 °C for 8min in fragmentation buffer (NEBNext Ultra II Directional RNA Library Prep Kit, NEB). The fragmented RNA was then used for library construction, following the manufacturer’s protocol (NEBNext Ultra II Directional RNA Library Prep Kit, NEB).

tag: developmental stage

value: Adult, male 5 days

value: Wild type


title: Fly Body 5d rep1

description:
processed data file:
AdM_5days.csv


title: C1: Stem Control 1


title: Group3-Asc-TMDKOAsc-3

status: Public on Oct 28 2020

city: Los Angeles

first: David

last: Casero

state: CA

address: 610 Charles Young Drive East

department: Pathology and Laboratory Medicine

institute: UCLA

description:
16S  rDNA sequencing
Pro-Group3-KO_3

library_source: genomic

data_processing:
Library strategy: 16S rNA sequencing
Data quality check was done on an Illumina SAV. Demultiplexing was performed with the Illumina Bcl2fastq2 v 2.17 program.
Raw data were processed using DADA2 in R and quality-filtered reads (~50862 reads per sample) were used to identify amplicon sequence variants (ASV), with taxonomy assigned based upon the Silva database.
Data in supplementary file ProDis_ASVcounts.txt was generated by the DADA2 pipeline: tab delimited file with 1) #OTU: nucleotide sequence of the exact amplicon sequence variant (ASV), 2) per-sample ASV counts, and 3) full phylogeny of the ASV (species level)
Genome_build: SILVA microbial database
Supplementary_files_format_and_content: Tab delimited: 1) #OTU: nucleotide sequence of the exact amplicon sequence variant (ASV), 2) per-sample ASV counts, and 3) full phylogeny of the ASV (species level)

molecule: genomic DNA

organism: mouse gut metagenome

source_name: Gut microbiome - Ascending colon

growth_protocol: To produce mice with induced deficiency of O-glycans specifically in colon, C1galt1-floxed (C1galt1f/f);C3GnT-/- females were crossed with previously generated C1galt1f/f;VillinCre-ERT2 (TM-IEC C1galt1f/f) mice on a C3GnT+/- background to generate C1galt1f/f;VillinCre-ERT2;C3GnT-/- (TM-DKO) and WT littermates. All mutant mice and WT littermates were on a C57BL/6J (BL/6) and 129/SvImJ (129/Sv) mixed background. Inbred WT mice (BL/6, Balb/c, and 129SvJ mice) were obtained from the Jackson Laboratory. Outbred WT CD1 mice and Swiss Webster (SW) mice and Sprague Dawley rat were bred in house. Animals were fed standard chow (PicoLab Rodent Diet 20; LabDiet 5053). Animals were housed in a specific pathogen free facility (SPF). All animal experiments were approved by the Institutional Animal Care and Use Committee of Oklahoma Medical Research Foundation.

extract_protocol:
DNA extraction and sequencing of the 16S ribosomal RNA gene was performed for mouse fecal samples as previously described (Tong et. al, PMID: 25367129). In brief, bacterial DNA was extracted using the ZymoBIOMICS DNA kit (cat#D4300) with bead beating.
The V4 region of the 16S gene was amplified and barcoded using 515f/806r primers then 250x2 bp sequencing was performed on an Illumina HiSeq 2500.

treatment_protocol: To generate mice with induced O-glycan deficiency in either the ascending or descending colon, mutant or WT littermates were injected intraperitoneally with 0.5 mg tamoxifen (TM, or ~20 mg/kg, MP Bio-medicals) in an ethanol/sunflower seed oil mixture (1:9 (v/v)) daily for 5 consecutive days, and mice were analyzed for deletion 5 or 10 days post final TM treatment. The dosage of TM was determined after serial titrations and characterization of different TM dosages in different mutant models.

tag: strain description

value: Mixed BL/6-129SvJ Cage C

value: TM-DKOAsc

value: F

tag: sample code


title: Group3-Asc-TMDKOAsc-2

description:
16S  rDNA sequencing
Pro-Group3-KO_2


title: Group3-Asc-TMDKOAsc-1

description:
16S  rDNA sequencing
Pro-Group3-KO_1


title: YNLR [TJb3-4]

description:
young naïve mice
YNR4

value: optic nerve head

value: wild type


title: Group3-Asc-Control-2

description:
16S  rDNA sequencing
Pro-Group3-Control_2

value: Control


title: Group2-Asc-Control-3

description:
16S  rDNA sequencing
Pro-Group2-Control_3

value: Mixed BL/6-129SvJ Cage B


title: Group2-Asc-TMDKOAsc-2

description:
16S  rDNA sequencing
Pro-Group2-KO_2


title: Group3-Asc-Control-1

description:
16S  rDNA sequencing
Pro-Group3-Control_1


title: Group2-Asc-Control-2

description:
16S  rDNA sequencing
Pro-Group2-Control_2


title: Group2-Asc-Control-1

description:
16S  rDNA sequencing
Pro-Group2-Control_1


title: Group2-Asc-TMDKOAsc-1

description:
16S  rDNA sequencing
Pro-Group2-KO_1


title: Group1-Asc-TMDKOAsc-3

description:
16S  rDNA sequencing
Pro-Group1-KO_3

value: C57BL/6 Background; Cage A


title: Group1-Asc-TMDKOAsc-1

description:
16S  rDNA sequencing
Pro-Group1-KO_1


title: Group1-Asc-TMDKOAsc-2

description:
16S  rDNA sequencing
Pro-Group1-KO_2


title: Group2-Desc-TMDKOAsc-2

description:
16S  rDNA sequencing
Dis-Group2-KO_2

source_name: Gut microbiome - Descending colon


title: Group1-Asc-Control-1

description:
16S  rDNA sequencing
Pro-Group1-Control_1


title: Group2-Desc-TMDKOAsc-1

description:
16S  rDNA sequencing
Dis-Group2-KO_1


title: Group1-Asc-Control-2

description:
16S  rDNA sequencing
Pro-Group1-Control_2


title: Group3-Desc-TMDKOAsc-3

description:
16S  rDNA sequencing
Dis-Group3-KO_3


title: Group3-Desc-TMDKOAsc-2

description:
16S  rDNA sequencing
Dis-Group3-KO_2


title: Group3-Desc-TMDKOAsc-1

description:
16S  rDNA sequencing
Dis-Group3-KO_1


title: Group2-Desc-Control-3

description:
16S  rDNA sequencing
Dis-Group2-Control_3


title: Group3-Desc-Control-2

description:
16S  rDNA sequencing
Dis-Group3-Control_2


title: Group2-Desc-Control-2

description:
16S  rDNA sequencing
Dis-Group2-Control_2


title: Group1-Desc-TMDKOAsc-3

description:
16S  rDNA sequencing
Dis-Group1-KO_3


title: Group2-Desc-Control-1

description:
16S  rDNA sequencing
Dis-Group2-Control_1


title: Group1-Desc-TMDKOAsc-2

description:
16S  rDNA sequencing
Dis-Group1-KO_2


title: Group1-Desc-TMDKOAsc-1

description:
16S  rDNA sequencing
Dis-Group1-KO_1


title: Group1-Desc-Control-2

description:
16S  rDNA sequencing
Dis-Group1-Control_2


title: Group1-Desc-Control-1

description:
16S  rDNA sequencing
Dis-Group1-Control_1


title: YTN16 anti-IL-17

city: Osaka

first: Koji

last: Nagaoka

address: 377-2 Ohno-Higashi, Osaka-Sayama

department: Department of Immunology

country: Japan

institute: Kindai University Faculty of Medicine

data_processing:
Cell Ranger Software v.3.0.0 was used to aligned, quality filtered, and aggregated the samples.
Genome_build: mm10
Supplementary_files_format_and_content: barcodes.tsv.gz
Supplementary_files_format_and_content: features.tsv.gz
Supplementary_files_format_and_content: matrix.mtx.gz

source_name: gastric cancer

extract_protocol:
CD45+ cells were sorted from day 10 untreated or anti-IL-17 mAb-treated YTN16 tumors. After sorting, cells were resuspended at 1000 cells/μl in 0.04%BSA/PBA and loaded onto the Chromium Controller.
cDNA libraries were generated using Chromium Single Cell 3’ Reagent Kits v2 (10X Genomics) according to manufacturer’s protocol.

tag: agent


title: Group3-Desc-Control-1

description:
16S  rDNA sequencing
Dis-Group3-Control_1


title: Single-cell RNA-Seq of Tumor-infiltrating T cells

data_processing:
CEL-Seq2 was used for UMI counting. UMI count data for each micro-chamber was normalized with UMIs for spked cRNA of luciferase.
Supplementary_files_format_and_content: Normalized UMI counts

source_name: Tumor-infiltrating T cells in YTN2 and YTN16

extract_protocol: The single-cell libraries were prepared using the Flow-cell devices composed of multiple vertical flow array chips) (VFACs, Shirai et al, Scientific Reports, 6, srep36014, 2016). VFAC (1 mm square) contains 100 microchambers packed with 1~2 x105 magnetic beads (1 µm in diameter) immobilized 7.5~15 x109 RT probes. RT probes consisted of 18nt of poly-T sequence, 6 nt of cell identifier (Cell-ID), 7nt of random sequence as UMIs(Unique Molecular Identifiers), and 30nt of common sequence (CS) for amplification (Supplementary Table 2). The procedures from cell captureing to cDNA synthesis were performed in the flow-cell device. In brief summary, FACS-sorted tumor-infiltrating lymphocytes isolated from YTN2 and YTN16 tumor tissues were washed once with PBS, and resuspended in PBS containing 90 copies/μL of spiked cRNA to a final concentration of 80 cells/μL. After adding 80 cells per a VFAC, the flow-cell device was connected to a vacuum pump (Ulback KOKI, Inc.) for appling negative pressure to the rear side of the VFACs, and single-cells were captured onto laser 4-micro-meter holes in diameter fabricataed at top of the microchambers respectively. Following cell lysis reagent, 4.5 μL of RT reagent (a mixture of 1.0 μL of 5 x FS buffer, 1.0 μL of 100 mM DTT, 1 μL of 10 mM dNTPs, 0.3 μL of 10 % Tween20, 0.4 μL of RNase OUT, and 0.4 μL of Super Script III (Thermo Fisher Scientific)) was added per a VFAC in the flow-cell device, and reverse transcription was performed for 50 minutes at 50 ℃ in a thermostatic incubator. Each VFAC was took out from the flow-cell device into a 0.2 mL tube containing 100 μL of resuspension buffer (50 mM Tris (pH 8.0) containing 0.1% Tween 20). Magnetic beads on which single-cell cDNA libraries were constructed were collected from microchambers of VFAC using a neodymium magnet, and washed twice with 50 μL of resuspend buffer. After exonuclease I treatment, 1st PCR was performed with primers listed in Supplementary Table 3, and the product was purified with Ampure XP (Beckman Coulter). Following 2nd PCR was performed with primers listed in Supplementary Table 4, the product was purified with Ampure XP. 3rd PCR was performed with primers containing illumina-tag sequences and index (chip-ID) listed in Supplementary Table 5, and the product was purified with Ampure XP. The single-cell libraries were analyzed with 2100 Bioanalyzer high sensitivity DNA kit (Agilent), to confirm a fragment distribution within a size range of 461–667 bp.  More than 3M reads for each chip was assigned to get sufficient deep sequencing data. Libraries of 3 or 4 chips were pooled before sequencing. Infomations of cells on each chip were shown in Supplementary Table 6. The final concentration of each 3rd PCR product should be diluted with 10 mM Tris:HCl (pH7.5) with 0.1 % tween20 to be 3.2 nM. According to the user manual of Miseq, denature is carried out. Phi X control is mixed at 10%. Paired-end sequencing (read 1 = 60bp, read 2 = 90bp) was carried out using Miseq (150 cycle (v3) reagents).

tag: tumor type

value: gastric cancer

tag: cell type

value: T cells


title: mouse embryonic stem cells - TX1072 - day 2 - replicate 2

city: Berlin

first: Guido

last: Pacini

address: Ihnestraße 63

department: Otto-Warburg-Laboratory

institute: Max Planck Institute for Molecular Genetics

data_processing:
SNPsplit version 0.3.2 (Krueger and Andrews 2016,  F1000Res. 5, 1479.), was used to N-mask the mm10 genome using high confidence SNPs. [SNPsplit_genome_preparation --nmasking]
STAR version 2.5.2b (Dobin et al. 2013, Bioinformatics, 29(1), 15-21.), was used to align the R2 reads to the masked mm10 genome and the 96 ERCC spike-in sequences, allowing for unique alignments and a maximum of two mismatches. [ star --outFilterMismatchNmax 2 --outFilterMultimapNmax 1]
featureCounts R function (Rsubread version 1.34.7) (Yang et al. 2014, Bioinformatics, 30(7), 923-930), was used for gene-wise read counting for the TX1072 (TX1072_CountMatrix.txt.gz) and the deletion (dXic_CountMatrix.txt.gz) cell lines. [countMultiMappingReads = FALSE, strandSpecific = 2]
The gene counting procedure was repeated for the two parental alleles (dXic_B6_CountMatrix.txt.gz, dXic_Cast_CountMatrix.txt.gz, TX1072_B6_CountMatrix.txt.gz, TX1072_Cast_CountMatrix.txt.gz), using SNPsplit to assign reads overlapping a SNP locus to their parental genomes. [SNPsplit --SNPs_B6_CAST.txt]
The allele specific gene counting procedure was repeated using only two SNPs (chrX:103,482,240 & chrX:103,482,895 mm10), to quantify the 5'-biased allelic expression for the Xist gene (ENSMUSG00000086503, chrX:103,460,366-103,483,254 mm10).
Genome_build: GRCm38

source_name: mouse embryonic stem cells (mESCs)

growth_protocol:
[TX1072] The female TX1072 cell line (clone A3) is a F1 hybrid ESC line derived from a cross between the 57BL/6 (B6) and CAST/EiJ (Cast) mouse strains that carries a doxycycline-responsive promoter in front of the Xist gene on the B6 chromosome and an rtTA insertion in the Rosa26 locus21. TxdXic_A1 [TXdXicB6] and TxdXic_A6 [TXdXicCast] lines were generated by deleting a 773 kb region around the Xist locus. TxdXic_A1 carries the deletion on the B6 chromosome (chrX:103,182,701-103,955,531, mm10) and TxdXic_A6 on the Cast allele (chrX:103,182,257-103,955,698, mm10). To generate these cell lines, a total of 4 guides flanking the region to be deleted (2 on each side) were cloned into the pX459-v2 vector (Addgene #62988). Four separate transfections were performed, each combining one guide upstream and downstream of  the targeted region and a single-stranded repair oligo with 50bp homology flanking each cut site (IDT). In each transfection, 2*106 TX1072 mESCs were electroporated with 2µg of each guide plasmid and 30pmol of the single stranded repair oligo using the P3 Primary Cell 4D-Nucleofector X Kit (V4XP-3024) with the Amaxa 4D Nucleofector system (Lonza, program CP-106) and plated on gelatin-coated 10cm dishes. Starting 30h after transfection, cells were selected with puromycin (1ng/µl) for 16h. After 4 days equal cell numbers from all 4 transfections were pooled and plated at a density of 2-3 cells/well in gelatin-coated 96-well plates. Genomic DNA was extracted and screened for the presence of the deletion with primers VM21 and VM24. Cells from wells showing the presence of the deletion were seeded at clonal density (100 cells/cm2) in 10cm plates. Individual clones were picked and screened for the presence of the deletion and the wild type allele and the absence of inversions or duplications of the targeted region. For all PCR reactions the Phusion HotStart Flex DNA Polymerase (NEB) was used with an annealing temperature of 55°C, an elongation time of 45sec and 35 cycles. To determine which allele carried the deletion, the PCR products were sequenced and annotated SNPs between Cast and B6 alleles were used to assign the deletion and the wild type allele. Correct karyotype of clones was verified with metaphase spreads.
Mouse embryonic stem (ES) cells were grown on gelatin-coated flasks in serum-containing ES cell medium (DMEM (Sigma), 15% FBS (Gibco), 0.1mM β-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF, Millipore)), supplemented with 2i (3 μM Gsk3 inhibitor CT-99021, 1 μM MEK inhibitor PD0325901).

extract_protocol:
Cells were lysed directly in the plate by adding 1 ml of Trizol (Invitrogen). RNA was isolated using the Direct-Zol RNA Miniprep Kit (Zymo Research) following the manufacturer’s instructions with on-collumn DNAse digestion.
[TX1072] Bulk RNA-seq libraries were prepared with the TruSeq-Stranded-Total-RNA-kit (Illumina) following the protocol. Around 1µg of totalRNA was used for rRNA-depletion and further steps, and final library-PCR was made with 15 cycles. The libraries were sequenced on a HiSeq2500 instrument (Illumina) in rapidrun mode with paired-end sequencing (Read1: 50bp, Read2: 50bp). Each sample was sequenced with at least 50M fragments, with 1% PhiX. [dXicB6, dXicCast] Bulk RNA-seq libraries were prepared with the KAPA-RNA Hyper Prep-Kit with RiboErase (Roche) following the protocol. 500ng total RNA were used for rRNA-depletion. For samples dXicCast_d0_r1, dXicCast_d0_r2 and dXicCast_d0_r3 fragmentation was adjusted to 85°C/5min instead of 94°C/8min, because these RNAs showed degradation. Nextflex unique dual-index-adaptors (PerkinElmer) were used, and final library-PCR was made with 10 cycles. The libraries were sequenced on a NovaSeq6000 instrument (Illumina) with paired-end sequencing (Read1: 100bp, Read2: 100bp). Each sample was sequenced with at least 50M fragments, with 1% PhiX.

treatment_protocol: Differentiation was induced by 2i/LIF withdrawal in DMEM supplemented with 10% FBS and 0.1mM β-mercaptoethanol at a density of 1.5*104cells/cm2 in fibronectin-coated (10 μg/ml) tissue culture plates

value: C57BL6/J x Cast/EiJ

value: female mESC

value: 2 days after 2i/Lif withdrawal

tag: cell line


title: mouse embryonic stem cells - TX1072 - day 0 - replicate 3

value: 0 days after 2i/Lif withdrawal


title: mouse embryonic stem cells - TX1072 - day 3 - replicate 1

value: 3 days after 2i/Lif withdrawal


title: mouse embryonic stem cells - TX1072 - day 2 - replicate 3


title: mouse embryonic stem cells - TX1072 - day 1 - replicate 2

value: 1 days after 2i/Lif withdrawal


title: mouse embryonic stem cells - TX1072 - day 4 - replicate 3

value: 4 days after 2i/Lif withdrawal


title: mouse embryonic stem cells - TX1072 - day 1 - replicate 3


title: mouse embryonic stem cells - TX1072 - day 4 - replicate 2


title: mouse embryonic stem cells - TX1072 - day 4 - replicate 1


title: mouse embryonic stem cells - dXic on Cast allele - day 1 - replicate 3

value: TXdXicCast:Xic deletion on Cast allele [chrX:103,182,257-103,955,698]


title: mouse embryonic stem cells - dXic on Cast allele - day 0 - replicate 3


title: mouse embryonic stem cells - TX1072 - day 3 - replicate 3


title: mouse embryonic stem cells - TX1072 - day 3 - replicate 2


title: mouse embryonic stem cells - dXic on Cast allele - day 4 - replicate 3


title: mouse embryonic stem cells - dXic on Cast allele - day 2 - replicate 3


title: mouse embryonic stem cells - TX1072 - day 1 - replicate 1


title: mouse embryonic stem cells - TX1072 - day 0 - replicate 2


title: mouse embryonic stem cells - TX1072 - day 2 - replicate 1


title: mouse embryonic stem cells - dXic on Cast allele - day 3 - replicate 3


title: mouse embryonic stem cells - dXic on B6 allele - day 3 - replicate 3

value: TXdXicB6:Xic deletion on B6 allele [chrX:103,182,701-103,955,531]


title: mouse embryonic stem cells - TX1072 - day 0 - replicate 1


title: mouse embryonic stem cells - dXic on B6 allele - day 1 - replicate 3


title: mouse embryonic stem cells - dXic on B6 allele - day 0 - replicate 3


title: mouse embryonic stem cells - dXic on B6 allele - day 2 - replicate 3


title: mouse embryonic stem cells - dXic on B6 allele - day 4 - replicate 3


title: mouse embryonic stem cells - dXic on Cast allele - day 4 - replicate 2


title: YTN16 untreated


title: mouse embryonic stem cells - dXic on Cast allele - day 2 - replicate 2


title: mouse embryonic stem cells - dXic on Cast allele - day 3 - replicate 2


title: mouse embryonic stem cells - dXic on Cast allele - day 1 - replicate 2


title: output CTRL group, sample2

city: Lausanne

first: Sylvain

last: Pradervand

address: Genopode

department: CIG

country: Switzerland

institute: UNI Lausanne

data_processing:
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.3)
Remaining reads were further filtered for low complexity seq_crumbs (v. 0.1.8)
Reads were aligned to the Mus musculus.GRCm38.82 genome using STAR (v. 2.4.2a)
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7)
The number of read counts per gene locus was summarized with htseq-count (v. 0.6.1)
Genome_build: Mus musculus GRCm38.82
Supplementary_files_format_and_content: Tab-separated .txt files with gene-level read count estimates, computed by the htseq-count software package

source_name: Immunoprecipitated RNA from SF1 cells

growth_protocol: Mouse fed with regular chow, after over-night fast

extract_protocol:
Translating Ribosome Affinity Purification (TRAP) was performed to obtain RNA from SF1 cells, followed by Nucleospin RNA mini kit (Macherey-Nagel) extraction
Linear amplification system Ovation RNA-Amplification System V2 (NuGEN) was used to amplify all samples.

treatment_protocol: AAV coding for AMPK dominant negative injected in the VMN of the mice and an AAV coding for GFP-L10 ribosomal fusion protein

tag: immunoprecipitated

value: Yes

tag: dominant-negative ampk mutant

value: No


title: mouse embryonic stem cells - dXic on B6 allele - day 4 - replicate 2

tag: strain


title: input CTRL group, sample1

source_name: Dissected VMN, input


title: mouse embryonic stem cells - dXic on B6 allele - day 2 - replicate 2


title: input CTRL group, sample2


title: mouse embryonic stem cells - dXic on B6 allele - day 2 - replicate 1


title: mouse embryonic stem cells - dXic on B6 allele - day 4 - replicate 1


title: mouse embryonic stem cells - dXic on Cast allele - day 0 - replicate 1


title: mouse embryonic stem cells - dXic on Cast allele - day 1 - replicate 1


title: mouse embryonic stem cells - dXic on B6 allele - day 3 - replicate 2


title: mouse embryonic stem cells - dXic on Cast allele - day 0 - replicate 2


title: mouse embryonic stem cells - dXic on B6 allele - day 1 - replicate 2


title: mouse embryonic stem cells - dXic on B6 allele - day 0 - replicate 2


title: output DN group, sample3


title: output CTRL group, sample3


title: mouse embryonic stem cells - dXic on B6 allele - day 3 - replicate 1


title: input CTRL group, sample3


title: output CTRL group, sample1


title: mouse embryonic stem cells - dXic on B6 allele - day 1 - replicate 1


title: mouse embryonic stem cells - dXic on Cast allele - day 2 - replicate 1


title: output DN group, sample2


title: mouse embryonic stem cells - dXic on B6 allele - day 0 - replicate 1


title: output DN group, sample1


title: input DN group, sample3


title: input DN group, sample1


title: mouse embryonic stem cells - dXic on Cast allele - day 4 - replicate 1


title: mouse embryonic stem cells - dXic on Cast allele - day 3 - replicate 1


title: FastATAC_NK_Toxo_d7_Liver_rep2

city: Bethesda

first: Hong-wei

last: Sun

state: MD

address: 9000 Rockville Pile

department: Office of Science & Technology

institute: NIAMS

data_processing:
FastATAC-seq reads from two biological replicates for each sample were mapped to the mouse genome (mm9 assembly) using Bowtie 0.12.8.
FastATAC-seq: Redundant reads were removed using fastquniq (Xu et al., 2012). Only one mapped read to each unique regions of the genome that was less than 175 base pairs was kept and used  in peak calling. Regions of open chromatin were identified by MACS (version 1.4.2)(Zhang et al., 2008) using a P-value threshold of 1 x 10-5. Only regions called in both replicates were used in downstream analysis.
RNA-Seq: Raw sequencing data were processed with CASAVA 1.8.2 to generate FastQ files. Reads of sequentially varying length were mapped to the mouse genome mm9 using TopHat 2.0. Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.0.
RNA-Seq: Gene expression values (RPKM, reads per kilobase exon per million mapped reads) were calculated with Cufflinks 2.0.
ChIP-seq: Reads of 50 bases were aligned to the mouse genome build mm9 with Bowtie 0.12.8, allowing two mismatches. Uniquely mapped and non-redundant reads were retained and used for peak calling.
ChIP-seq: Peak detection was performed with SICER (Zang et al, 2009 Bioinformatics, 25:1952-1958).
scRNA-seq: Sequence reads from all samples were processed and aggregated using Cell Ranger. Aggregated data was further analyzed by Seurat(Macosko et al., 2015).Downstream analyses and heatmap generation were performed with R using Rstudio. To
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files for ATAC-seq, RNA-seq and transcription factor ChIP-seq; bedgraph for histone modification ChIP-seq

growth_protocol:
cell isolation protocol: Cells from spleen were obtained by mechanical disruption. Peritoneal cells were obtained by  washing of the peritoneal cavity with cold PBS. Isolated cells were further sorted as based on their surface markers.
in vitro culture protocol: All cells were stimulated in RPMI medium with 10% (vol/vol) FCS (Invitrogen), 2 mM glutamine (Invitrogen), 100 IU/ml penicillin (Invitrogen), 0.1 mg/ml streptomycin (Invitrogen), and 20 mM HEPES buffer, pH 7.2–7.5 (Invitrogen), and 2 mM β-mercaptoethanol (Sigma-Aldrich). NK cells were treated with 1000 U/ml IL-2 and 10 ng/ml IL-12 (R&D) for 6 hours; ILC2 cells were treated with 50 ng/ml IL-25 (BioLegend) and 50 ng/ml IL-33 (Biolegend) for 4 hours; NCR+ILC3 were treated with 50ug/ml of IL-23 (R&D Systems) for 6 hours.

extract_protocol:
FastATAC-Seq: FastATAC-Seq was performed according to a published protocol(Corces et al., 2016)
RNA-Seq: RNA-seq was performed as described previously with slight modification (Hirahara et al., 2015). Total RNA was prepared from approximately 30-50,000 cells by using TRIzol  following manufacture’s protocol (Life Technologies).
RNA-Seq: Total RNA was subsequently processed to mRNA-seq library using TruSeq SR mRNA sample prep kit (FC-122-1001, Illumina).
RNA-Seq: The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
ChIP-seq: Cells were chemically cross linked by 1% formaldehyde. Cell lysates were made by appropriate sonication and protein-DNA complexes were isolated with antibody.
ChIP-seq: Libraries were prepared according to Illumina's instructions. Briefly, DNA was end-repaired and the blunt, phosphorylated ends were treated with Taq polymerase and dATP to yield a protruding 3- 'A' base for ligation of NEBNext adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation, DNA was PCR amplified with NEBNext index primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel, and quantitated by Qubit (Invitrogen).
ChIP-Seq (size fractionation). The purified libraries were multiplexed and captured on an Illumina flow cell for cluster generation. Libraries were sequenced for 50 single read cycles on HiSeq 2000 or 2500 following the manufacturer's protocols.
scRNA-seq: Freshly sorted NK cells (13,000 cells each) were encapsulated into droplets, and libraries were prepared using Chromium Single Cell 3’ Reagent Kits v2 according to manufacturer’s protocol (10X Genomics). Indexed libraries were multiplexed and sequenced on Illumina HiSeq 3000 instruments according to the manufacturer's instructions.
scRNA-seq: The generated scRNA-Seq libraries were sequenced using a 50 cycle (paired-end) with a HiSeq 3000 (Illumina).

treatment_protocol: Toxoplasma gondii infection protocol: Mice of at least 8 weeks of age were inoculated with an average of 15 cysts of type II avirulent T.gondii strain ME-49 by intraperitoneal injection

tag: tissue

value: Spleen

value: Natural killer cells

tag: surface marker

tag: culture condition

value: ex vivo

tag: description for exp id


title: FastATAC_NK_Toxo_d7_Liver_rep1


title: FastATAC_NK_Toxo_d0_Liver_rep1


title: FastATAC_NK_Toxo_d0_Spl_rep3


title: FastATAC_NK_Toxo_d7_Spl_rep1


title: input_NK_WT_2_12_6h


title: Tbet_NK_WT_exvivo_rep2

tag: chip antibody

value: anti-Tbet

tag: chip antibody vendor

value: Santa Cruz

tag: chip antibody cat. #

tag: chip antibody lot/batch#


title: FastATAC_NK_Toxo_d3_Spl_rep1


title: p300_NK_WT_IL2_12_6h_rep2


title: STAT4_NK_WT_exvivo_rep1


title: FastATAC_NK_Toxo_d3_Spl_rep3


title: input DN group, sample2


title: p300_NK_WT_exvivo_rep2


title: STAT5_NK_WT_IL2_12_6h_rep2

value: mix of 1. anti-STAT5A,  2. anti-STAT5b

value: R&D

value: mix of 1. PA-ST5A,  2. PA-ST5B


title: input_NK_WT_exvivo_rep1


title: K27m3_NK_WT_IL2_12_6h_rep2

value: Millipore


title: FastATAC_NK_Toxo_d0_Spl_rep2


title: FastATAC_NK_Toxo_d3_Spl_rep2


title: K27Ac_NK_WT_IL2_12_6h_rep2

value: Abcam


title: K36m3_NK_WT_2_12_6h


title: K4m1_NK_WT_2_12_6h


title: K27Ac_NK_WT_exvivo_rep2


title: K27m3_NK_WT_exvivo_rep2


title: K36m3_NK_WT_exvivo


title: FastATAC_NK_Toxo_d0_Spl_rep1


title: STAT4_NK_WT_IL2_12_6h_rep2


title: Tbet_NK_WT_exvivo_rep1

value: Miltenyi NK isolation Kit


title: K4m3_NK_WT_exvivo_rep2


title: FastATAC_NK_Toxo_d3_Liver_rep1


title: STAT4_NK_WT_IL2_12_6h_rep3


title: K4m3_NK_WT_IL2_12_6h_rep2


title: Tbet_NK_WT_IL2_12_6h_rep1


title: STAT5_NK_WT_IL2_12_6h_rep1


title: 2cell_mTBE_Pol2_rep2

city: Beijing

first: Bofeng

last: Liu

address: Haidian District

department: School of Life Science

institute: Tsinghua University

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

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 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: Preimplantation embryo

tag: genotype

value: wild-type

tag: developmental stage

value: late 2-cell

tag: antibody

value: Pol2(Active Motif 102660)


title: 2cell_mTBE_Pol2_rep1


title: 2cell_mTBE_Ctrl_Pol2_rep1


title: Normal-3_(BBN_10251)

city: Riverside

first: Junchao

last: Shi

address: 900 University Ave

department: Division of Biomedical Sciences, School of Medicine

institute: University of California, Riverside

data_processing:
For each RNA library, around 36 million reads (raw data) were generated by Illumina Hi-Seq 2000. Sequence reads that fit any of the following parameters were removed with following standard quality control criteria: 1) The reads with N; more than 4 bases whose quality score is lower than 10 or more than 6 bases whose quality score is lower than 13. 2) The reads with 5’ primer contaminants or without 3’ primer. 3) The reads without the insert tag. 4) The reads with ploy A. 5) The reads shorter than 15nt. The clean reads were obtained after data filtration.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include sequences, length of sequences and sequence counts.

source_name: Prefrontal cortex

extract_protocol:
Total RNAs were extracted by Trizol (Invitrogen).
Small RNA libraries were constructed according to BGI sandard protocol.

treatment_protocol: The brian tissue was harvest about 35hour PMI(postmortem interval).

value: Prefrontal cortex

tag: disease state

value: normal


title: NSN_Pol2_rep1

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 NSN


title: 2cell_early_Pol2_rep1

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: Normal-1_(BBN_9354)


title: AD-5_(BBN_9338)

value: Alzheimer’s disease


title: AD-4_(BBN_9336)


title: Normal-2_(BBN_9422)


title: mES_DRB_Ctrl_TBE_Pol2_rep1

source_name: Embryonic stem cell

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

value: Embryonic stem cell


title: Normal-4_(BBN_24325)


title: AD-6_(BBN_24326)


title: mES_DRB_TBE_Pol2_rep1


title: K4m1_NK_WT_exvivo

value: Spleen

tag: cell type

value: Natural killer cells

value: ex vivo


title: AD-3_(BBN_9296)


title: AD-1_(BBN_9076)


title: AD-2_(BBN_9274)


title: 2cell_mTBE_Ctrl_Pol2_rep2


title: HEp2 - 24hr - MOI 10 - rRNA + PolyA depletion

city: Wurzburg

first: Regan

last: Hayward

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

data_processing:
Sequenced reads were trimmed and quality checked using Trim Galore, FastQC and FastQ-Screen
Host reads were aligned to the human genome (GRCh 38.87) using STAR, while chlamydial reads were aligned to the Chlamydia trachomatis genome using Bowtie2. Samtools was used to remove duplicate reads in addition to only keeping mapped reads in both the host and chlamydial BAM files. To remove reads that mapped to both genomes, we first extracted the mapped reads back into paired-end fastq files using bedtools. Reads were then aligned using the initial mapping software to the reciprocal genomes. Any reads that mapped to both genomes were removed from the originating BAM files using the “FilterSamReads” command from Picard tools.
Features (genes) were counted for both host and chlamydial samples using featureCounts with additional parameters of “-Q 10 -p -C”.
Genome_build: Genome Reference Consortium Human Build 38 patch release 87 (GRCh38.p87)
Supplementary_files_format_and_content: Count matricies generated from each of the raw BAM files using FeatureCounts

source_name: Epithelial cells (HEp2)

growth_protocol: Human epithelial type 2 (HEp-2) cells (American Type Culture Collection, ATCC No. CCL-23) were grown as monolayers in 6x 100 mm tissue culture dishes until cells were 90% confluent. To harvest EBs for the subsequent infections, additional monolayers were grown and infected with C. trachomatis serovar E in sucrose phosphate glutamate (SPG) as previously outlined (Tan et al. 2009). The resulting EBs and cell lysates were then harvested and used to infect new HEp2 monolayers.

extract_protocol:
Ribo-Zero rRNA Removal kits (Human/Mouse/Rat and Gram-negative) were used to deplete samples of both human and gram-negative bacterial rRNA. Equivalent volumes from each kit were combined, thereby allowing the removal of bacterial and human rRNA simultaneously within each sample. Each sample was equally separated, with one half subjected to polyA depletion by the Poly(A) Purist Mag purification kit (Ambion), whereby removing host-based polyA transcripts to allow the enrichment of bacterial transcripts. Magnetic beads were used to bind to polyA mRNAs and were extracted from the solution with a magnet. Samples with combined depletion methods were further purified using Zymo-Spin IC columns (Zymo Research) before being re-combined for library construction.
The mRNA libraries were prepared from depleted samples as previously stated at 1 and 24 hours post infection, using the TruSeq RNA Sample Prep kit (Illumina, San Diego, CA) per the manufacturer's protocol with IGS-specific optimisations. Adapters and indexes (6 bp) were ligated to the double-stranded cDNA, which was subsequently purified with AMPure XT beads (Beckman Coulter Genomics, Danvers, MA) between enzymatic reactions and size selection steps (∼250 to 300 bp). The resulting libraries were sequenced on an Illumina HiSeq2000 using the 100 bp paired-end protocol

treatment_protocol: Infections for each dataset used the previously prepared HEp2 monolayers, infecting with C. trachomatis serovar E in 3.5 mL SPG buffer as previously outlined (Tan et al. 2009); infections were synchronised using centrifugation. EBs were introduced into monolayers from three MOIs (0.1, 1 and 10) using 1:10 dilutions beginning from an MOI of 10. EBs were quantified as previously described (Humphrys et al. 2013). To remove non-viable or dead EBs, each sample was incubated at 25ºC for 2 hours, and washed twice in SPG. Cell monolayers were incubated at 37ºC with 5% CO2, including the addition of 10 mL fresh medium (DMEM+10% FBS, 25 μg/ml gentamycin, 1.25 μg/ml Fungizone). After each infection time point, the infected and uninfected dishes were harvested by scraping and resuspending in 150 μL sterile PBS. Any resuspended samples were stored at −80°C.

value: Epithelial cells (HEp2)

tag: hours post infection

tag: multiplicity of infection

tag: depletion type

value: rRNA + PolyA

tag: chlamydial species

value: Chlamydia trachomatis - Serovar E


title: HEp2 - 1hr - MOI 10 - rRNA depletion

tag: tissue

value: rRNA


title: HEp2 - 1hr - MOI 1 - rRNA + PolyA depletion


title: HEp2 - 24hr - MOI 10 - rRNA depletion


title: HEp2 - 24hr - MOI 0.1 - rRNA + PolyA depletion


title: HEp2 - 24hr - MOI 1 - rRNA + PolyA depletion


title: HEp2 - 24hr - MOI 1 - rRNA depletion


title: HEp2 - 1hr - MOI 1 - rRNA depletion


title: HEp2 - 1hr - MOI 10 - rRNA + PolyA depletion


title: HEp2 - 24hr - MOI 0.1 - rRNA depletion


title: HEp2 - 1hr - MOI 0.1 - rRNA + PolyA depletion


title: RN084

city: Pittsburgh

first: Anita

last: Bansal

state: PA

address: Biomedical Science Tower

department: Immunology

institute: University of Pittsburgh

data_processing:
Illumina Casava1.7 software used for basecalling.
For RNA-seq: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using STAR
For ATAC-seq: Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38  using bowtie and peak calls was performed using MACS2.
Genome_build: hg38
Supplementary_files_format_and_content: adundance measurements showing readcounts for RNA-seq and NarrowPeaks files for ATAC-seq

source_name: Primary Proximal Tubule Epithelial Cells

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

extract_protocol:
For RNA-seq: RNA was harvested from cells from non-diabetic and diabetic donors without and with TGFB1 (24hours) treatment, and tloal RNA was harvested using Qiagen RNeasy kit. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries. For ATAC-seq: 50,000 cells from non-diabetic and diabetic donors without and with TGFB1 (24hours) treatment were processed using Illumina Nextra DNA prep kit.
RNA libraries were prepared for sequencing using standard paired-end Illumina protocols

treatment_protocol: Cells were treated with TGFB1 for 24 hours

tag: disease

value: diabetic donors

tag: treatment

value: Treated with TGFβ1 24 hours

tag: replicate-donor

value: Donor 2 - Replicate 2


title: RN082

value: Primary Proximal Tubule Epithelial Cells

value: no treatment


title: HEp2 - 1hr - MOI 0.1 - rRNA depletion


title: RN083

value: Donor 1 - Replicate 1


title: RN079

value: non-diabetic donors


title: RN078


title: RN080


title: RN035

value: Donor 2 - Replicate 3


title: RN033


title: RN077


title: RN032

value: Donor 2 - Replicate 4


title: RN036


title: RN081


title: RN031


title: RN030


title: RN012

value: Donor 1 - Replicate 2


title: RN029


title: RN011


title: RN010


title: RN009


title: RN008


title: RN006


title: 24hrs mock-infected

data_processing:
Base calls were performed using the bulit in Illumina basecaller
Sequenced reads were trimmed and quality checked using Trimmomatic, FastQC and FastQ-Screen
Trimmed reads were aligned to the human genome (GRCh 38.87) using Bowtie2 (2.3.2) with additional parametres of no mismatches and –very-sensitive-local. Duplicate reads and unmapped reads were removed using Picard Tools
Peak calling was performed using MACS2 (2.1.1) in paired-end mode, with additional parameters of –no-model –broad -q 0.05 and MACS2 predicted extension sizes. All infected and mock-infected replicates were passed separately, with significant peaks determined against software-predicted background signal . Any peaks that fell within the ENCODE blacklisted regions or were located on non-standard chromosomes such as (ChrMT and ChrUn) were removed.
Genome_build: Genome Reference Consortium Human Build 38 patch release 87 (GRCh38.p87)
Supplementary_files_format_and_content: Peak files were generated using MACS2 as outlined above

growth_protocol: HEp-2 cells (American Type Culture Collection, ATCC No. CCL-23) were grown as monolayers in 6 x 100mm TC dishes until 90% confluent. Fresh monolayers were infected with Chlamydia trachomatis serovar E in 3.5 mL SPG buffer for an MOI ~ 1, using centrifugation  to synchronize infections. Infections and subsequent culture were performed in the absence of cycloheximide or DEAE dextran. A matching number of HEp-2 monolayers were also mock-infected using uninfected cell lysates. Each treatment was incubated at 25°C for  2h and subsequently washed twice with SPG to remove dead or non-viable EBs. 10 mL fresh medium (DMEM + 10% FBS, 25μg/ml gentamycin, 1.25μg/ml Fungizone) was added and cell monolayers incubated at 37°C with 5% CO2.

extract_protocol:
FAIRE analysis of Chlamydia trachomatis-infected and mock-infected HEp-2 cells was performed according to the protocol published by Simon et al (Simon JM, Giresi PG, Davis IJ, Lieb JD: Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to  isolate active regulatory DNA. Nat Protoc 2012, 7(2):256-267), including crosslinking with formaldehyde, cell lysis, phenol-chloroform extraction, reverse-crosslinking, and purification prior to library construction.
FAIRE-Seq libraries were prepared from 10-100ng crosslinked DNA with the NEBNext Ultra II DNA Library Prep Kit (New England Biolabs) as per the manufacturer's protocol

treatment_protocol: Chlamydia trachomatis serovar E infections of HEp-2 cells and matched mock infections proceeded to 1, 12, 24, and 48 hours post-infection before application of the FAIRE protocol

tag: condition

value: Mock-infected


title: RN005


title: 48hrs mock-infected


title: RN034


title: 24hrs infected

value: Infected


title: RN007


title: 48hrs infected


title: Kasumi-1_single-cell_3

city: Freiburg

first: Heiko

last: Becker

state: Baden-Württemberg

address: Breisacher Straße 115

department: Department of Medicine I

institute: University Medical Center

description:
single-cell DNA
assay variant A

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

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: Kasumi-1_single-cell_5

description:
single-cell DNA
assay variant B


title: Kasumi-1_single-cell_7

description:
single-cell DNA
assay variant B


title: 1hr mock-infected


title: Kasumi-1_single-cell_6

description:
single-cell DNA
assay variant B


title: Kasumi-1_single-cell_2

description:
single-cell DNA
assay variant A


title: 12hrs infected


title: Kasumi-1_single-cell_4

description:
single-cell DNA
assay variant A


title: shUVSSA ONLY INPUT REP2

city: NewYork

first: Zhaoqi

state: New York

address: ICRC Building 8th Floor, Office 803B 1130 St. Nicholas Ave

department: Systems Biology

institute: Columbia university

data_processing:
Function ‘featureCounts’ from package ‘Subread’ was used to count the reads located in two regions for all expressed genes, where “transcription start sites (TSS)” regions were defined as 300 bp upstream and downstream of the TSS, and “gene body (GB)” regions were defined as 301 to 3000 bp downstream of the TSS. These counts are used for the calculation of Stalling indices.
Genome_build: hg19 for human samples

source_name: MCF10A-MYC-ER cells

growth_protocol: MCF10A-MYC-ER cells were cultured in DMEM/F12 (Invitrogen) supplemented with 5% horse serum (Invitrogen), 20ng/ml EGF (Peprotech), 0.5micrograms/ml hydrocortisone (Sigma), 100ng/ml cholera toxin (Sigma), 10micrograms/ml insulin (Sigma), and antibiotics, and were incubated at 37 degrees Celsuis with 5% carbon dioxide. Cells were typically passaged every 2-3 days and treated with or without 200nM 4-hydroxytamoxifen (Sigma) to induce MYC-ER.

extract_protocol:
Lysates were clarified from sonicated nuclei and input DNA was recovered (INPUT), then, RNAPII-bound DNA was isolated with antibody (IP).
20ng of ChIP or Input DNA were processed for end repair, adaptor ligation, and gel purification using the Illumina TruSeq ChIP Library Preparation Kit (IP-202-1012, Illumina), then quantified with the KAPA SYBR FAST Universal qPCR Kit (KAPA Biosystems, Wilmington, MA, USA). Fragment sizes were analyzed using the BioAnalyzer (Agilent, Santa Clara, CA, USA), and samples were pooled together to a final concentration of 20nM.

value: MCF10A-MYC-ER cells

value: MCF10A-MYC-ER-shUVSSA with shUVSSA induction only (shUVSSA ONLY)

tag: chip antibody


title: MYC ONLY INPUT REP2

value: MCF10A-MYC-ER-shCONTROL with MYC-ER and shCONTROL induction  (MYC ONLY)


title: CONTROL INPUT REP2

value: MCF10A-MYC-ER-shCONTROL with shCONTROL induction only (wild type/control)


title: shUVSSA ONLY IP REP2

value: RNAPII antibody N-20 (Santa Cruz Biotechnology, sc-899, lot#A2813)


title: MYC ONLY IP REP2


title: CONTROL IP REP2


title: 12hrs mock-infected

value: Epithelial cells (HEp2)


title: shUVSSA ONLY INPUT REP1


title: MYC+shUVSSA INPUT REP1

value: MCF10A-MYC-ER-shUVSSA with MYC-ER and shUVSSA induction  (MYC+shUVSSA)


title: MYC ONLY INPUT REP1


title: MYC+shUVSSA IP REP1


title: 1hr infected

value: Chlamydia trachomatis - Serovar E


title: CONTROL INPUT REP1


title: shUVSSA ONLY IP REP1


title: MYC ONLY IP REP1


title: CONTROL IP REP1


title: Kasumi-1_single-cell_1

description:
single-cell DNA
assay variant A


title: MYC+shUVSSA INPUT REP2


title: MYC+shUVSSA IP REP2


title: PitNET01

city: Riga

first: Raitis

last: Peculis

address: Ratsupites str 1 k-1

country: Latvia

institute: Latvian Biomedical Research and Study Centre

data_processing:
Torrent Suite 5.10.1 was used for basecalling
Adapter removal performed with Cutadapt (Galaxy Version 1.16.5)
Quality trimming performed with Trimmomatic (Galaxy Version 0.36.5) with sliding window with average quality across 5 bases set to 15
Alignment was performed using RNA-STAR (Galaxy Version 2.6.0b-1)
To account for batch effects, surrogate variables (SVA) were calculated using the sva (v3.34.0) package (Bioconductor project) and added to the design matrix.
Read counts were first filtered based on read count frequency in all samples. Genes with at least ten reads in at least three samples were included in the analysis. To detect sample outliers, read count data were transformed with variant stabilizing transformations (VST), considering the design of the experiment, and visualized with sample distance heat mapping, PCA and MDS methods. Read count density visualization was used to check for problematic samples. Counts were replaced with trimmed mean values for genes which were marked as outliers based on their dispersion Cook`s distance values, which were calculated as the .99 percentile of the F (p, m - p) distribution for each gene.
Differentially expressed genes were obtained using the DESeq2 (v1.26.0) package from the Bioconductor (v3.10) project and R (v3.6.1) software.
Genome_build: GRCh38.p12
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Twenty to 30 mg of PitNET tissues was homogenised using a FastPrep-24™ homogenizer in RLT Plus buffer in Lysing Matrix D 1.5 ml tubes (MP Biomedicals, USA), and total RNA was extracted with AllPrep DNA/RNA Mini Kit (Qiagen, Germany) and stored at -80 °C. Total RNA quality control was carried out using Agilent 2100 bioanalyzer and an Agilent RNA 6000 Pico Kit (Agilent Technologies, USA) and concentration was measured using Qubit 2.0 fluorometer and Qubit™ RNA HS Assay Kit (Thermo Scientific, USA).
Transcriptome libraries were prepared with the Low Input RiboMinus™ Eukaryote System v2 and Ion Total RNA-Seq Kit v2 (Thermo Fisher Scientific, USA) following the manufacturer’s instructions. Input amount for the transcriptome library preparation was 500 ng. The preparation of transcriptome libraries was carried out in relation to 1:1 based on patient samples, who had, or had no medical therapy before PitNET resection, to reduce any batch effects. Libraries were sequenced using the Ion Proton™ System for Next-Generation Sequencing (Ion OneTouch and Ion PI™ Hi-Q™ OT2 Reagents 200 Kit for emulsion PCR and Ion PI™ Hi-Q™ Sequencing 200 Solutions kit and Ion PI™ Chip V3 chips for sequencing, all from Thermo Fisher Scientific, USA). Libraries were sequenced 3 - 4 times to acquire at least 20 M reads per sample and at least 10 M would represent uniquely mapped reads, so that the rRNA content would not reach 50 % of the sample.

tag: subject status

value: patient with somatotrophinomas

tag: Sex

value: female

value: receiving SSA/DA treatment before surgery

value: Pituitary neuroendocrine tumor (PitNET)


title: PitNET09

value: untreated; naïve


title: PitNET06

value: treated 3months


title: PitNET02


title: PitNET05


title: PitNET11

value: male


title: PitNET07


title: RNA-seq-Panc-1-3P2_NTS rep2

city: Wakayama

first: Shogo

last: Ehata

state: Wakayama

address: Kimiidera 811-1

department: School of Medicine

institute: Wakayama Medical University

description:
Panc-1-3P2 cells treated with NTS
4

data_processing:
RNA-seq reads were trimmed down to 100 bases and processed by Tophat2 (version 2.0.10) and Bowtie2 (version 2.1.0) using hg19 version of index files. Parameters used are as follows: -a 6 --segment-length 25 --no-coverage-search --read-realign-edit-dist 0 -G.
FPKM calculation was performed by using Cuffdiff (cufflinks version 2.1.1, with option -u).
Genome_build: hg19
Supplementary_files_format_and_content: Expression data of the 4 samples were summarized into genes_.fpkm_tracking.

growth_protocol: Panc-1-3P2 cells were cultured in 6 well plate.

extract_protocol:
Total RNA was isolated with RNeasy (Qiagen).
cDNA libraries were prepared using Dynabeads mRNA DIRECT Purification Kit (Life Technologies) and Ion Total RNA-Seq Kit v.2 (Life Technologies).

treatment_protocol: Cells were seeded into 6-well plates. After 3 days, cells were treated with or without NTS (100 nM) for 4.5 hs.

tag: nts treatment

value: NTS (100 nM)

tag: histology

value: pancreatic adenocarcinoma


title: RNA-seq-Panc-1-3P2_no_treatment rep2

description:
untreated Panc-1-3P2 cells
3

value: no treatment


title: RNA-seq-Panc-1-3P2_NTS rep1

description:
Panc-1-3P2 cells treated with NTS
2


title: RNA-seq-Panc-1-3P2_no_treatment rep1

description:
untreated Panc-1-3P2 cells
1


title: Input genomic DNA of OS5K #3

description: input genomic DNA used for peak calling by HOMER

data_processing:
Reference files of the human reference sequence assembly (NCBI Build 37/hg19, February 2009). (http://support.illumina.com/sequencing/sequencing_software/igenome.html)
ChIP-seq reads were trimmed down to 50 bp and were aligned using Bowtie (version 1.2.2) (Langmead et al., 2009) with the command “-S -a --best --strata -n 1 -m 1”.
BAM files were sorted using SAMtools (http://samtools.sourceforge.net/).
H3K27ac binding regions were identified using HOMER software with findPeaks program (-style histone (for TE) and -style superhistone (for SE)).
Genome_build: hg19
Supplementary_files_format_and_content: BigWig files were generated using UCSC bedGraphtoBigWig program and HOMER software (version 4.9.1) (Heinz et al, 2010) with makeTagDirectory (-tbp1) and makeUCSCfile (-norm 1e6 -normLength 50) programs.

source_name: OS5K #3

growth_protocol: OS-RC-2 was obtained from RIKEN Cell Bank (Tsukuba, Japan) and cultured at 37℃ and 5% CO2 in RPMI 1640 medium (Thermo Fisher Scientific, Waltham, MA) containing 10% (v/v) foetal bovine serum (FBS) (GE Healthcare Life Sciences, Piscataway, NJ).

extract_protocol:
ChIP was performed using 5 μg of anti-H3K27ac antibody (#MABI0009, MCA, Nagano, Japan) or anti-BRD4 antibody (#A301-985A, Bethyl Laboratories, Montgomery, TX) as described previously (Koinuma D et al, Mol cell biol, 2009).
The libraries were constructed as described (Murai et al, Cell Discov, 2015), using IonXpress Plus Fragment Library Kit (Thermo Fisher Scientific). Adaptor-ligated samples were amplified by 15 cycles of PCR and purified by E-Gel SizeSelect (Thermo Fisher Scientific).

treatment_protocol: Cells were treated with JQ1 (ChemScene, Monmouth Junction, NJ) for 24 h.

value: clear cell renal cell carcinoma

tag: in vivo passaging status

value: repeated inoculation into subrenal capsule, five times

tag: introduced gene

value: Luc2, mCherry

value: untreated


title: BRD4 binding region in JQ1-treated OS5K #3, replicate 2

description: anti-BRD4 ChIP-seq


title: Input genomic DNA of OSPa

source_name: OSPa


title: PitNET12


title: BRD4 binding region in OSPa, replicate 2

description: anti-BRD4 ChIP-seq


title: BRD4 binding region in OS5K #3, replicate 2

description: anti-BRD4 ChIP-seq

value: DMSO


title: BRD4 binding region in OS5K #3, replicate 1

description: anti-BRD4 ChIP-seq


title: PitNET10


title: PitNET04


title: H3K27ac binding region in OS5K #3, replicate 2

description:
anti-H3K27ac ChIP-seq
H3K27ac_ChIPseq_OS5K_3_TE.bed
H3K27ac_ChIPseq_OS5K_3_SE.bed


title: H3K27ac binding region in OS5K #3, replicate 1


title: BRD4 binding region in OSPa, replicate 1

description: anti-BRD4 ChIP-seq


title: PitNET08


title: PitNET03


title: YTN2 cell line

type: RNA

description: Gene expression of cell line

hyb_protocol: 0.6ug of Cy3-labelled cRNA was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturer’s instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Mouse GE 8x60K Microarray (Agilent) 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).

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

data_processing: The scanned images were analyzed with Feature Extraction Software 11.5.1.1(Agilent) using default parameters.

source_name: Gastric cancer cell line

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.1ug Total RNA using the Low Input Quick Amp Labeling Kit(Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

growth_protocol: YTN2 and YTN16 cell lines were cultured in DMEM supplemented with 10% FBS, 100U/ml penicillin, 100 μg/ml streptomycin and MITO+ serum extender (Corning) on Type I collagen coated dish. Cells were harvested by treatment with trypsin.

extract_protocol: Total RNA was extracted from T cells using TRIzol (Life technologies) and RNeasy spin columns (Qiagen) according to manufacturers' protocols.

tag: strain

value: Gastric cancer cell line


title: H3K27ac binding region in OS5K #2, replicate 1

description:
anti-H3K27ac ChIP-seq
H3K27ac_ChIPseq_OS5K_2_TE.bed
H3K27ac_ChIPseq_OS5K_2_SE.bed

source_name: OS5K #2


title: YTN16 cell line

description: Gene expression of cell line


title: H3K27ac binding region in OS5K #1, replicate 2

description:
anti-H3K27ac ChIP-seq
H3K27ac_ChIPseq_OS5K_1_TE.bed
H3K27ac_ChIPseq_OS5K_1_SE.bed

source_name: OS5K #1


title: H3K27ac binding region in OSPa, replicate 1

description:
anti-H3K27ac ChIP-seq
H3K27ac_ChIPseq_OSPa_TE.bed
H3K27ac_ChIPseq_OSPa_SE.bed


title: RNA-seq_OS5K_1

description: RNA-seq of cultured OS5K #1

data_processing:
Reads per kilobase of exon permMegabase of library size (RPKM) were calculated by CLC Genomics Workbench (Qiagen).
Genome_build: hg19
Supplementary_files_format_and_content: Expression data of the four samples were summarized into a processed file.

extract_protocol:
Total RNA was isolated from cultured cells with RNeasy (Qiagen, Venlo, Netherlands).
cDNA libraries were prepared using Dynabeads mRNA DIRECT Purification Kit (Thermo Fisher Scientific) and Ion Total RNA-Seq Kit v.2 (Thermo Fisher Scientific).

treatment_protocol: untreated


title: RNA-seq_OS5K_3

description: RNA-seq of cultured OS5K #3


title: BRD4 binding region in JQ1-treated OS5K #3, replicate 1

description: anti-BRD4 ChIP-seq


title: H_0937_BA9_mRNASeq_ribo

city: Boston

first: Adam

last: Labadorf

address: 72 East Concord Street E301

department: Neurology

institute: Boston University Medical School

data_processing:
Sequencing adapters and low quality bases were trimmed from the sequencing reads of each sample using trimmomatic.
The trimmed sequencing reads were assessed to be high quality using fastqc.
Trimmed reads from above were aligned against the human reference genome hg38 using STAR allowing each read to align to at most 20 locations.
Multimapped reads were resolved to a single alignment location using the MMR software packag.
Bin counts from each sample were concatenated together into a counts matrix where features are bins and columns are samples.
Bins where more than half of the samples had zero reads were filtered out of the analysis.
Bin counts from each sample were concatenated together into a counts matrix where features are bins and columns are samples.
Filtered bin counts were normalized with DESeq2 prior to downstream analysis.
Genome_build: hg38

extract_protocol:
An average of 0.8 g of cortical ribbon tissue from prefrontal cortex (Brodmann Area 9) was dissected from each brain on a dissection block over dry ice. RNA was extracted from the tissue using the Qiagen RNeasy Kit according to manufacturer supplied protocols.
Paired end RNA sequencing libraries were prepared using a KAPA Stranded RNA-Seq Kit with RiboErase from Roche according to manufacturer supplied protocols.
2x76bp paired end stranded ribo-depleted RNA-Seq libraries with an average library size of 50M reads

tag: death

value: M

tag: cag

tag: grade

tag: duration


title: H_0923_BA9_mRNASeq_ribo


title: H_0916_BA9_mRNASeq_ribo

tag: onset


title: H_0915_BA9_mRNASeq_ribo


title: H_0884_BA9_mRNASeq_ribo

value: F


title: H_0921_BA9_mRNASeq_ribo


title: H_0876_BA9_mRNASeq_ribo


title: H_0896_BA9_mRNASeq_ribo


title: H_0904_BA9_mRNASeq_ribo


title: H_0882_BA9_mRNASeq_ribo


title: H_0865_BA9_mRNASeq_ribo


title: H_0873_BA9_mRNASeq_ribo


title: H_0864_BA9_mRNASeq_ribo


title: H3K27ac binding region in OS5K #2, replicate 2

tag: treatment


title: H_0862_BA9_mRNASeq_ribo


title: H_0861_BA9_mRNASeq_ribo


title: H_0847_BA9_mRNASeq_ribo


title: H_0843_BA9_mRNASeq_ribo


title: RNA-seq_OS5K_2

description: RNA-seq of cultured OS5K #2


title: RNA-seq_OSPa

description: RNA-seq of cultured OSPa


title: H3K27ac binding region in OS5K #1, replicate 1


title: H_0859_BA9_mRNASeq_ribo


title: H_0836_BA9_mRNASeq_ribo


title: H_0835_BA9_mRNASeq_ribo


title: H_0822_BA9_mRNASeq_ribo


title: H_0819_BA9_mRNASeq_ribo


title: H_0839_BA9_mRNASeq_ribo


title: H_0812_BA9_mRNASeq_ribo


title: H_0821_BA9_mRNASeq_ribo


title: H_0842_BA9_mRNASeq_ribo


title: H3K27ac binding region in OSPa, replicate 2


title: H_0804_BA9_mRNASeq_ribo


title: H_0794_BA9_mRNASeq_ribo


title: H_0799_BA9_mRNASeq_ribo


title: H_0815_BA9_mRNASeq_ribo


title: H_0793_BA9_mRNASeq_ribo


title: H_0805_BA9_mRNASeq_ribo


title: H_0802_BA9_mRNASeq_ribo


title: H_0788_BA9_mRNASeq_ribo


title: H_0792_BA9_mRNASeq_ribo


title: H_0791_BA9_mRNASeq_ribo


title: H_0787_BA9_mRNASeq_ribo


title: H_0758_BA9_mRNASeq_ribo


title: H_0780_BA9_mRNASeq_ribo


title: H_0757_BA9_mRNASeq_ribo


title: H_0826_BA9_mRNASeq_ribo


title: H_0830_BA9_mRNASeq_ribo


title: H_0776_BA9_mRNASeq_ribo


title: H_0785_BA9_mRNASeq_ribo


title: H_0789_BA9_mRNASeq_ribo


title: H_0750_BA9_mRNASeq_ribo


title: H_0784_BA9_mRNASeq_ribo


title: H_0749_BA9_mRNASeq_ribo


title: H_0747_BA9_mRNASeq_ribo


title: H_0744_BA9_mRNASeq_ribo


title: H_0746_BA9_mRNASeq_ribo


title: H_0733_BA9_mRNASeq_ribo


title: H_0739_BA9_mRNASeq_ribo


title: H_0740_BA9_mRNASeq_ribo


title: H_0743_BA9_mRNASeq_ribo


title: H_0720_BA9_mRNASeq_ribo


title: H_0723_BA9_mRNASeq_ribo


title: H_0707_BA9_mRNASeq_ribo


title: H_0709_BA9_mRNASeq_ribo


title: H_0704_BA9_mRNASeq_ribo


title: H_0706_BA9_mRNASeq_ribo


title: H_0702_BA9_mRNASeq_ribo


title: H_0701_BA9_mRNASeq_ribo


title: H_0700_BA9_mRNASeq_ribo


title: H_0698_BA9_mRNASeq_ribo


title: H_0695_BA9_mRNASeq_ribo


title: H_0699_BA9_mRNASeq_ribo


title: H_0682_BA9_mRNASeq_ribo


title: H_0697_BA9_mRNASeq_ribo


title: H_0683_BA9_mRNASeq_ribo


title: H_0670_BA9_mRNASeq_ribo


title: H_0672_BA9_mRNASeq_ribo


title: H_0689_BA9_mRNASeq_ribo


title: H_0681_BA9_mRNASeq_ribo


title: H_0657_BA9_mRNASeq_ribo


title: H_0656_BA9_mRNASeq_ribo


title: H_0726_BA9_mRNASeq_ribo


title: H_0627_BA9_mRNASeq_ribo


title: H_0620_BA9_mRNASeq_ribo


title: H_0619_BA9_mRNASeq_ribo


title: H_0648_BA9_mRNASeq_ribo


title: H_0590_BA9_mRNASeq_ribo


title: H_0539_BA9_mRNASeq_ribo


title: H_0231_BA9_mRNASeq_ribo


title: H_0589_BA9_mRNASeq_ribo


title: H_0565_BA9_mRNASeq_ribo


title: H_0513_BA9_mRNASeq_ribo


title: H_0012_BA9_mRNASeq_ribo


title: H_0008_BA9_mRNASeq_ribo


title: H_0014_BA9_mRNASeq_ribo


title: H_0658_BA9_mRNASeq_ribo


title: H_0010_BA9_mRNASeq_ribo


title: H_0007_BA9_mRNASeq_ribo


title: H_0009_BA9_mRNASeq_ribo


title: H_0003_BA9_mRNASeq_ribo


title: H_0001_BA9_mRNASeq_ribo


title: ZNF354C_1

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 5 nucleotides.  Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Ensembl human genome version hg38 (GRCh38) using STAR 2.6.1d with the parameter “--outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.18.1
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers.
Genome_build: hg38
Supplementary_files_format_and_content: library-size normalized counts

source_name: HMEC

growth_protocol: Immortalised human microvascular endothelial cells (HMEC) (#98247) were acquired from the CDC (Atlanta, GA, USA). HMECs were cultivated in a humidified atmosphere of 5% CO2 at 37°C.  Endothelial growth medium (EGM), consisting of endothelial basal medium (EBM) supplemented with human recombinant epidermal growth factor (EGF), EndoCGS-Heparin (PeloBiotech, Germany), 8% fetal calf serum (FCS) (#S0113, Biochrom, Germany), penicillin (50 U/ml) and streptomycin (50 µg/ml) (#15140-122, Gibco/ Lifetechnologies, USA) was used.

extract_protocol:
Total RNA Isolation was performed with the RNA Mini Kit according to the manufacturer’s protocol (Bio&Sell)
2µg of total RNA was used as input for VAHTS Stranded mRNA-seq Library preparation following manufacture’s protocol (Vazyme).

treatment_protocol: Overexpression of pCMV6-ZNF354C (NM_014594, #RC209312, Origene) in HMEC was performed for 24h by electroporation with the Neon™ Transfection System (ThermoFisher), according to the instructions provided. The pCMV6-entry vector (#PS100001, Origene) served as negative control.

value: ZNF354C vector


title: ZNF354C_3


title: H_0002_BA9_mRNASeq_ribo


title: H_0006_BA9_mRNASeq_ribo


title: ZNF354C_2


title: CTRL_3

value: empty vector


title: CTRL_2


title: CTRL_1


title: H_0601_BA9_mRNASeq_ribo


title: HI scRNAseq donor#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 8

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: Pancreatic islets

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)

tag: cell type

value: Human islets from organ donor


title: iPSC scRNAseq

description: Sample 1

source_name: Induced pluripotent cells

value: Induced pluripotent cells (iPSC)

tag: differentiation day


title: iβ scRNAseq exp#2

description: Sample 7

value: iPSC-derived Beta cells


title: EN scRNAseq exp#2

description: Sample 5

value: iPSC-derived pancreatic endocrine cells


title: HI scRNAseq donor#2

description: Sample 9


title: PE scRNAseq exp#2

description: Sample 3

value: iPSC-derived pancreatic endoderm cells


title: stomach4_RNA

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to hg19 reference genome by HISAT2 with uniquely mapped reads retained for the following analyses.
Normalization were performed by Deeptools.
Reads count was generated by featureCounts.
Normalized RPKM values were generated by edgeR.
Genome_build: hg19
Supplementary_files_format_and_content: RPKM matrix

source_name: stomach

extract_protocol:
Total RNA was isolated from tissue samples with TRIZOL reagent. Poly-adenylated RNA was enriched by using FastTrack MAG Maxi mRNA isolation kit (Invitrogen).
RNA-seq libraries were constructed using illumina Truseq stranded mRNA kit.

tag: technology

value: RNA-seq


title: testis4_RNA

source_name: testis


title: skin2_RNA

source_name: skin


title: stomach5_RNA


title: testis5_RNA


title: stomach3_RNA


title: testis2_RNA


title: skin4_RNA


title: skin3_RNA


title: testis3_RNA


title: prostate5_RNA

source_name: prostate


title: skin5_RNA


title: skin1_RNA


title: prostate4_RNA


title: testis1_RNA


title: stomach1_RNA


title: stomach2_RNA


title: prostate3_RNA


title: prostate2_RNA


title: prostate1_RNA


title: placenta4_RNA

source_name: placenta


title: placenta5_RNA


title: placenta3_RNA


title: pancreas5_RNA

source_name: pancreas


title: placenta1_RNA


title: pancreas3_RNA


title: placenta2_RNA


title: pancreas4_RNA


title: pancreas2_RNA


title: ovary5_RNA

source_name: ovary


title: ovary4_RNA


title: ovary3_RNA


title: pancreas1_RNA


title: ovary2_RNA


title: lymphnodes4_RNA

source_name: lymph nodes


title: lymphnodes3_RNA


title: lymphnodes5_RNA


title: ovary1_RNA


title: lymphnodes1_RNA


title: lung1_RNA

source_name: lung


title: lung3_RNA


title: lung2_RNA


title: liver4_RNA

source_name: liver


title: liver3_RNA


title: liver1_RNA


title: lung4_RNA


title: liver5_RNA


title: lung5_RNA


title: liver2_RNA


title: kidney3_RNA

source_name: kidney


title: kidney4_RNA


title: hypothalamus2_RNA

source_name: hypothalamus


title: hypothalamus4_RNA


title: hypothalamus3_RNA


title: kidney1_RNA


title: lymphnodes2_RNA


title: heart5_RNA

source_name: heart


title: heart4_RNA


title: hypothalamus1_RNA


title: colontransverse6_RNA

source_name: colon (transverse)


title: heart1_RNA


title: heart2_RNA


title: kidney5_RNA


title: heart3_RNA


title: colontransverse4_RNA


title: breast5_RNA

source_name: breast


title: colontransverse5_RNA


title: colontransverse2_RNA


title: colontransverse1_RNA


title: colonsigmoid1_RNA

source_name: colon (sigmoid)


title: colonsigmoid3_RNA


title: kidney2_RNA


title: breast4_RNA


title: colonsigmoid2_RNA


title: colonsigmoid4_RNA


title: breast3_RNA


title: breast2_RNA


title: brain3_RNA

source_name: brain


title: brain4_RNA


title: brain2_RNA


title: colontransverse3_RNA


title: bonemarrow5_RNA

source_name: bone marrow


title: bonemarrow4_RNA


title: brain1_RNA


title: colonsigmoid5_RNA


title: bonemarrow2_RNA


title: colonsigmoid6_RNA


title: bladder5_RNA

source_name: bladder


title: bladder3_RNA


title: bonemarrow3_RNA


title: bladder4_RNA


title: bladder2_RNA


title: testis5

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to hg19 reference genome by Bowtie with uniquely mapped reads retained for the following analyses.
PCR duplicates were removed by Samtools.
Normalization were performed by Deeptools.
Peak calling was performed with MACS2.
Genome_build: hg19
Supplementary_files_format_and_content: MACS2 output narrowPeak file

source_name: testis

extract_protocol:
DNA was purified using Qiagen's Puregene kit and sonicated to about 200 bp.
Fragmented DNA was purified by Zymo DNA Clean and Concentration Kit. Then, the selective 5hmC chemical labeling was performed in glucosylation buffer (50 mM HEPES buffer pH 8.0, 25 mM MgCl2) containing above fragmented DNA, βGT, N3-UDP-Glc, and incubated at 37°C for 2 hr. After DNA purification in ddH2O, DBCO-PEG4-Biotin (Click Chemistry Tools) was added and incubated at 37°C for 2 hr. The biotin labeled DNA was pulled down by C1 Streptavidin beads (Life Technologies) for 15 min at room temperature. Next, the captured DNA fragments were subjected to PCR amplification using Nextera DNA sample preparation kit. The resulting amplified product was purified by 1.0X AMPure XP beads. Input library was made by direct PCR from fragmented DNA directly without labeling and pull-down. The libraries were quantified by a Qubit fluorometer (Life Technologies) and sequenced on NextSeq 500.


title: bonemarrow1_RNA


title: testis1


title: brain5_RNA


title: testis4


title: testis2


title: testis3


title: stomach3

source_name: stomach


title: stomach4


title: stomach2


title: stomach5


title: bladder1_RNA


title: breast1_RNA


title: skin4

source_name: skin


title: skin5