title: HEK293, ICI-SNC80, 1.5h, nA

value: HEK293 stably expressing DOR

value: Human embryonic kidney

tag: treatment


title: Healthy control 2, week 0

status: Public on Apr 24 2023

type: SRA

city: Taichung

first: Kuo Tung

last: Tang

address: No. 1650, Sec. 4, Taiwan Blvd.

department: Division of Allergy, Immunology and Rheumatology

country: Taiwan

institute: Taichung Veterans General Hospital

library_source: transcriptomic

data_processing:
Bases with low quality and sequences from adapters in raw data were removed using program Fastp (version 0.20.0).
Filtered reads were aligned to the reference genomes using the HISAT2 software (version 2.1.0).
The software FeatureCounts (v2.0.1) in Subread package was applied to quantify the gene abundance.
Assembly: GRCh38
Supplementary files format and content: *.xlsx: Excel spreadsheet files include counts and TPM values for each Sample.

molecule: total RNA

organism: Homo sapiens

source_name: blood

extract_protocol:
Total RNAs were extracted from isolated neutrophils using the TRIzol Reagent (Thermo Fisher Scientific) and purified using a GENEzol TriRNA Pure kit (Geneaid, Taiwan R.O.C.).
The purified RNA was used for the preparation of the sequencing library using the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA).

treatment_protocol: Subcutaneous tocilizumab every 2-4 weeks.

tag: disease state

value: healthy

tag: tissue

value: blood

tag: cell type

value: neutrophils

tag: time point

value: week 0

tag: donor

value: control 2


title: Healthy control 4, week 0

value: control 4


title: W_S3

city: Zhengzhou

first: Liu

last: Xiaoting

address: 100 Science Avenue

country: China

institute: Zhengzhou University

data_processing:
Total RNA was isolated and purified using TRIzol reagent following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000. The RNA integrity was assessed by Bioanalyzer 2100.
The cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase. Then, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.
Cutadapt software was used to remove the reads that contained adaptor contamination. And After removed the low quality bases and undetermined bases ,we used HISAT2 software to map reads to the genome (http://www.wheatgenome.org/).
The mapped reads of each sample were assembled using StringTie with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software. After the final transcriptome was generated, StringTie and ballgown were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM .
Assembly: International Whaet Genome Sequencing Consortium(http://www.wheatgenome.org/)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Triticum aestivum

source_name: white grain wheat

growth_protocol: The white grain wheat and purple grain wheat were grown in pots containing a soil: vermiculite mixture (3:1) in a controlled artificial climatic chamber (16 h light/8 h dark photoperiod at 20°C/18 °C).

extract_protocol:
The stems and buds were collected,and RNA was harvested using Trizol reagent. 5–10 μg total RNA was used as the template for constructing RNA-seq libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: grain

tag: age

value: 30 days after flowering


title: Healthy control 1, week 0

value: control 1


title: RNA_OboxKO_FGO_rep1

city: Beijing

first: Fengling

last: Chen

state: Beijing

address: 30 Shuangqing Rd.

institute: Tsinghua University

description:
OboxKO_FGO_rep1
Obox_RNASeq_FPKM.xlsx

data_processing:
ATAC-Seq and Stacc-seq reads were aligned to the mm9 genome with the parameters: -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant by Bowtie2 v2.3.5. Aligned reads were filtered with a minimum MAPQ of 20, and PCR duplicates were removed using Picard MarkDuplicates v1.119. Read coverages over mm9 genome were estimated by bamCoverage from deepTools v3.3.1 with parameters --binSize 100 --normalizeUsing RPKM.
RNA-seq reads were trimmed by Trim Galore v0.6.6 then mapped to mm9 genome by HISAT2 v2.2.1(Kim et al., 2019). StringTie v2.1.2(Pertea et al., 2016) was used to calculate the FPKM per gene based on mm9 refFlat from UCSC genome annotation database.
Assembly: mm9
Supplementary files format and content: Bigwig for Stacc-seq and ATAC-Seq signals
Supplementary files format and content: gene expression FPKM table for RNA-seq data

organism: Mus musculus

source_name: FGO oocytes

growth_protocol: 2i ESCs were cultured on 0.1% gelatin pre-coated dishes in DMEM medium (Gibco, 11995-065) containing leukemia-inhibiting factor (LIF) (Millipore, ESG1107), 15% fetal bovine serum (FBS; Hyclone, SH30396.03), GlutaMAX (Gibco, 35050-061), penicillin/ streptomycin (Millipore, TMS-AB2-C), nucleosides (Millipore, ES-008-D), non-essential amino acids (Gibco, 25-025-CIR), and β-mercaptoethanol (Gibco, 21985- 023). Naïve mESCs (2i) mESCs were cultured on feeder-free dishes coated with 0.1% gelatin in the N2B27 medium supplemented with 1 μM PD035901, 3 μM Chir99021, and 1 × 103 units/mL LIF. The cells were passaged 1:10-1:20.

extract_protocol:
For embryos, the zona pellucida was gently removed by treatment with Tyrode’s solution (Sigma, T1844). Then the embryos were lysed in lysis buffer containing RNase inhibitor. 2i ESCs were lysed in lysis buffer containing RNase inhibitor. The following steps followed the Smart-seq2 protocol as previously described (Picelli et al., 2014). For whole genome sequence, the tail tip DNA were extracted with isopropanol precipitation method.
The Smart-seq2 libraries of embryos were prepared as previously described (Picelli et al., 2014). Embryos were lysed in lysis buffer containing RNase inhibitor according to the user manual. The library was quantified using Qubit and Agilent 2100 before being subjected to sequencing. For stacc-seq, the library was prepared following the protocol as descripted before (Liu et al., 2020). For ATAC-seq,  the library was prepared following the protocol as descripted before (Buenrostro et al., 2013; Wu ET AL., 2016).
The Smart-seq2, WGS (Picelli et al., 2014) and stacc-seq (Liu et al., 2020) library strategies were followed the protocols described.

treatment_protocol: siRNAs (25 uM for each) were injected into FGOs for maternal Obox KD and zygotes for zygotic Obox KD. For stacc-seq, Obox mRNA was injected into zygotes.

value: FGO oocytes

tag: genotype

value: Obox KO


title: RNA_WT_BL_rep2

description:
WT_BL_rep2
Obox_RNASeq_FPKM.xlsx

source_name: blastocyst mouse embryos

value: blastocyst mouse embryos

value: wild type


title: W_S2


title: FM patient 4, week 0

value: fibromyalgia

value: patient 4


title: FM patient 5, week 0

value: patient 5


title: HEK293, ICI, 1.5h, nF

city: Geneva

first: Miriam

last: Stoeber

state: GE

address: Rue Michel Servet 1

department: PHYM

country: Switzerland

institute: University of Geneva

data_processing:
1.5h: Libraries generated for the 1.5 h treatment were sequenced using the Illumina NextSeq 500 or HiSeq 4000 devices with a single-end read length of 80-90 nucleotides yielding at least 3 millions mapped reads per sample. Sequences were mapped to the human genome GRC h38.12 using GENCODE v28 annotation with STAR v. 2.6.0c. Generated raw counts were normalized and genes with low expression were filtered out leaving 15,946 genes. Differential expression analyses and related statistics between control and treated conditions were conducted using the Limma-voom R package 3.38.2.
6h: libraries were sequenced using the Illumina HiSeq 4000 device with a single-end read length of 50 nucleotides yielding around 30 million mapped reads per sample. Fastq files were generated using Illumina bcl2fastq v. 2.20.0 and mapped to the human genome UCSC hg38 using STAR v. 2.7.0f. Aligned reads were quantified with the Python software htseq-count v. 0.9.1. Genes were filtered down to 14,467 after removal of low expressers and normalized using the R package EdgeR 3.28.1. Differential gene expression between control and DPDPE or ICI and ICI/SNC80 conditions was computed and statistics were performed using the General Linear Model, quasi-likelihood F-test (QL F-test) with FDR and Benjamini & Hochberg correction.
Assembly: GRC h38.12 (1.5h), UCSC hg38 (6h)
Supplementary files format and content: 1.5h: tab delimited text files including ensembl, hgnc, Log2FC, p-value, adj. p-value, description
Supplementary files format and content: 6h: tab delimited text file including hgnc, description, FC, p-value, adj. p-value, raw counts, normalized counts

source_name: HEK293 stably expressing DOR

growth_protocol: HEK293 cells were maintained in DMEM supplemented with 10%FBS and geneticin

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), genomic DNA was removed using the RNase-free DNase kit (Qiagen) and samples analyzed using a bioanalyzer.
Multiplexed libraries for the 1.5 h samples were generated using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit and for the 6 h samples using TruSeqHT Stranded Total RNA Library Prep protocol (Illumina).

treatment_protocol: HEK293 cells stably expressing DOR were treated with vehicle control or DPDPE 100 nM or SNC80 100 nM or ICI 174, 864 100 uM + SNC80 100 nM for 1.5h or 6h (ICI preincubated for 5 min)

tag: cell line

value: HEK293 stably expressing DOR

value: Human embryonic kidney


title: HEK293, ICI, 1.5h, nE


title: RNA_WT_BL_rep1

description:
WT_BL_rep1
Obox_RNASeq_FPKM.xlsx


title: HEK293, ICI, 1.5h, nD


title: FM patient 3, week 0

value: blood

value: patient 3


title: HEK293, ICI, 1.5h, nC


title: RNA_WT_L2C_rep3

description:
WT_L2C_rep3
Obox_RNASeq_FPKM.xlsx

source_name: late 2-cell mouse embryos

value: late 2-cell mouse embryos


title: FM patient 2, week 12

value: neutrophils

value: tocilizumab

value: week 12

value: patient 2


title: RNA-seq-swi3d-1-bio2

city: Guangzhou

first: yaoguang

last: yu

address: No. 135, Xingang Xi Road

institute: SUN YAT-SEN UNIVERSITY

data_processing:
After removal of adapters and low-quality reads, the clean reads were mapped to the TAIR10 Arabidopsis genome using TopHat (v2.1.1) with default settings (Kim et al., 2013), except that a minimum intron length of 20 base pairs (Snelders et al.) and a maximum intron length of 4,000 bp were required.
Mapped reads were then assembled according to the TAIR10 version of genome annotation using Cufflinks (v.2.1.1) with default settings (Trapnell et al., 2012).
For analysis of differential expression, the assembled transcripts from three independent biological replicates in WT and other mutants (syd-5 and swi3d-1) were included and compared using Cuffdiff (v.2.1.1) with default settings (Trapnell et al., 2012).
Finally, genes with at least 1.5-fold change in expression (P < 0.05) were considered differentially expressed
Assembly: TAIR10
Supplementary files format and content: EXCEL

organism: Arabidopsis

source_name: 14-day-old seedlings

extract_protocol:
Total RNA was extracted from 14-day-old Arabidopsis seedlings grown under long-day conditions using the HiPure Unviersal RNA Mini Kit (MAGEN, Cat. No. R4130) according to the manufacturer’s instructions.
For RNA-seq analyses, RNA from three biological replicates were sequenced separately at Novogene (sequencing method: nova-seq PE150).

value: 14-day-old seedlings

tag: time


title: RNA-seq-swi3d-1-bio1


title: RNA-seq-syd-5-bio3


title: HEK293, ICI, 1.5h, nB


title: FM patient 2, week 0

value: week 0


title: RNA_WT_E2C_rep2

description:
WT_E2C_rep2
Obox_RNASeq_FPKM.xlsx

source_name: early 2-cell mouse embryos

value: early 2-cell mouse embryos


title: RNA_WT_L2C_rep1

description:
WT_L2C_rep1
Obox_RNASeq_FPKM.xlsx


title: FM patient 1, week 12

value: patient 1


title: HEK293, ICI, 1.5h, nA


title: ThO w/ SHH at day 12-20

city: NEW HAVEN

first: Bilal

last: Cakir

state: Connecticut

address: 10 Amistad Street, Ste 214J

country: USA

institute: Yale University

description: 10X Genomics

library_source: transcriptomic single cell

data_processing:
Reads were aligned to hg19 human genome by Cellranger (v3.0.2).
Assembly: hg19
Supplementary files format and content: Read count matrix was formated by mtx. Barcodes and genes were provided by tsv format.

source_name: Thalamic organoid

extract_protocol: Library was constructed by the manufacter's protocol (Chromium reagent 3' v2, 10X Genomics)

value: Thalamic organoid

value: H1 hESCs

value: 72 days

value: 100ng/ml SHH at day12-20


title: ThO w/ SHH at day 14-22

description: 10X Genomics

value: 100ng/ml SHH at day14-22


title: RNA_WT_E2C_rep1

description:
WT_E2C_rep1
Obox_RNASeq_FPKM.xlsx

value: wild type


title: RNA_WT_MII_rep2

description:
WT_MII_rep2
Obox_RNASeq_FPKM.xlsx

source_name: MII oocytes

value: MII oocytes


title: W_S1

value: grain

value: 30 days after flowering


title: RNA-seq-syd-5-bio1


title: RNA_WT_MII_rep1

description:
WT_MII_rep1
Obox_RNASeq_FPKM.xlsx


title: M28z-KITv CAR, Stimulated, Rep 3

city: New York

first: Navin

middle: K

last: Chintala

state: NY

address: 417 E 68th Street, 4th Flr, Room 427D

department: Surgery

institute: MSKCC

data_processing:
CutAdapt version cutadapt-1.6 was used to trim and filter reads. Adapters were trimmed with minimum overlap of 10 bases and reads of less than half original read length were filtered out.
STAR version STAR-STAR_2.5.0a was run using the 2-pass method. First pass was run with the following parameters: --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMattributes All --outSAMunmapped Within. Genome database was then generated using the minimum read length of half desired read length and second pass was run against the new genome file with the same parameters as pass 1.
Expression count matrix was computed using HTSeq version HTSeq-0.5.3. Parameters set were: -m intersection-strict -s reverse -t exon
Raw count matrix was processed using the R/Bioconductor package DESeq, version [UNKNOWN], which is used to both normalize the full dataset and analyze differential expression between sample groups.
Assembly: hg19
Supplementary files format and content: tab-delimited file containing normalized counts

source_name: CAR T cells

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen) in accordance with the manufacturer’s instructions.
After RiboGreen RNA quantification and quality control using an Agilent Bioanalyzer, libraries were prepared using TruSeq RNA Library Prep Kit v2 (Illumina)

treatment_protocol: M28z and M28z-KITv CAR T cells were unstimulated or stimulated with irradiated 3T3-MSLN for 24 h, followed by magnetic selection of CD8+ cells (Miltenyi Biotec).

value: CAR T cells

value: CD8+ T cells

value: CAR transduced

value: Antigen Stimulated


title: ThO w/o SHH

description: 10X Genomics


title: RNA-seq-WT-bio2

value: 14-day-old seedlings

value: WT


title: RNA_WT_L2C_rep2

description:
WT_L2C_rep2
Obox_RNASeq_FPKM.xlsx

value: late 2-cell mouse embryos


title: M28z-KITv CAR, Stimulated, Rep 1


title: M28z-KITv CAR, Stimulated, Rep 2


title: RNA-seq-swi3d-1-bio3


title: ThO w/ SHH at day 8-16

description: 10X Genomics

value: 100ng/ml SHH at day8-16


title: RNA-seq-WT-bio3


title: LMU_Pat_72

city: Munich

first: Kristian

last: Unger

address: Marchioninistr. 15

department: Department of radiation oncology

country: Germany

institute: LMU University Hospital

data_processing:
The resulting fastq files were subjected to alignment against the human reference genome (GRCh38.87) using the STAR short read aligner (2.5.3a) followed by quantification using Salmon in quantification mode.
The quality of unmapped and mapped reads was assessed using FastQC and the resulting reports summarized by MultiQC.
Assembly: GRCh38.87
Supplementary files format and content: Text file with raw counts per tumour.

source_name: head and neck squamous cell carcinoma

extract_protocol:
After histopathological review, simultaneous DNA and total RNA extraction of serial formalin-fixed and paraffin-embedded tissue sections was performed using the AllPrep DNA/RNA FFPE Kit RNA isolation (Qiagen, Hilden, Germany). Isolated RNA was quantified using a Qubit Fluorometer and RNA integrity was assessed determining DV200 values (percentage of fragments >200 nucleotides) using the 2100 Bioanalyzer followed by categorization into low, medium, and good quality samples.
For whole RNA sequencing, sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, Inc., USA). Input quantity and initial RNA fragmentation time was adjusted to the respective RNA quality. After library preparation, library quality and quantity were evaluated using the Quanti-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, MA, USA) and the Bioanalyzer High Sensitivity DNA Analysis Kits (Agilent Technologies).

value: head and neck squamous cell carcinoma

tag: hpv-status

value: head and neck


title: RNA-seq-WT-bio1


title: RNA_WT_FGO_rep1

description:
WT_FGO_rep1
Obox_RNASeq_FPKM.xlsx

value: FGO oocytes


title: M28z CAR, Stimulated, Rep 3


title: RNA_WT_FGO_rep2

description:
WT_FGO_rep2
Obox_RNASeq_FPKM.xlsx


title: RNA-seq-syd-5-bio2


title: FM patient 1, week 0

value: fibromyalgia

value: blood

value: neutrophils

value: week 0

value: patient 1


title: M28z CAR, Stimulated, Rep 2


title: LMU_Pat_71


title: microglia, WT

first: Insup

last: Choi

address: 1 Gustave L. Levy Pl

department: Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Count matrix was generated by Cell Ranger
Low-quality cells with either too few genes (<200), an excessive number (>4000) of genes, or more than 5% mitochondrion reads detected, were removed.
The UMIs data was first normalized by sequencing depth and log-transformed using the LogNormalize method implemented in Seurat.
Genome_build: mm10
Supplementary_files_format_and_content: matrix, features, barcodes

source_name: microglia

extract_protocol:
Brains were homogenized with Dounce homogenizer and microglia were enriched with Percoll solution (30%/70%). CD11bHigh/CD45Low) were collected using FACSDiva v8.0.1 (BD Biosciences)
Single-cell RNA sequencing was performed on these samples using the Chromium platform (10x Genomics, Pleasanton, CA) with the 3’ gene expression (3’ GEX) V3 kit, using an input of ~10,000 cells. In short, Gel-Bead in Emulsions (GEMs) were generated on the sample chip in the Chromium controller, then barcoded cDNA was extracted from the GEMs by Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly A-tailing, adapter ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using Bioanalyzer (Agilent) and QuBit (Thermofisher) analysis and then sequenced in paired end mode on a NovaSeq instrument (Illumina, San Diego, CA) targeting a depth of 50,000-100,000 reads per cell.
single cell RNA seq / Chromium Single Cell 3' Reagent Kits

value: FACS-sorted CD11b+CD45Low microglia

value: brain (forebrain)

tag: strain

value: 1.5mg of tamoxifen at 2-months-old


title: ChIPseq-SWI3D-GFP swi3d-1 syd-5-bio1

library_source: genomic

data_processing:
Raw data was trimmed by fastp with following parameters: “-g -q 5 -u 50 -n 15 -l 150”.
The clean data was mapped to the Arabidopsis thaliana reference genome (TAIR10) using Bowtie2 with the default settings (Langmead and Salzberg, 2012). Only perfectly and uniquely mapped reads were used for further analysis.
MACS 2.0 (Feng et al., 2012) was used for peak calling with the following parameters: “gsize = 119,667,750, bw = 300, q = 0.05, nomodel, extsize = 200.”
The aligned reads were converted to wiggle (wig) formats, and bigwig files were generated by bamCoverage with “-bs 10” and “-normalize using RPKM (reads per kilobase per million)” in deepTools (Ramirez et al., 2016).
To annotate peaks to genes, ChIPseeker was used with default settings (Yu et al., 2015).
ComputeMatrix and plotProfile (Ramírez et al., 2016) were used to compare the mean occupancy density (details are shown in each corresponding figure legends).
Assembly: TAIR10
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

source_name: 14-day-old seedling

growth_protocol: Arabidopsis seeds were sterilized with 20% sodium hypochlorite solution for 15 mins, washed with sterile water five times, and then stratified at 4 °C in darkness for three days. Seeds were then sown on ½ Murashige and Skoog (MS) medium containing 1% sucrose and 0.6% agar.

extract_protocol:
In brief, 14-day-old seedlings (0.5 g for each biological replicate) grown on ½-strength MS medium under long-day  conditions were fixed using 1% formaldehyde under a vacuum for 15 min and then ground into a fine powder in liquid nitrogen. The chromatin was sonicated into 300-500 bp fragments using a Bioruptor sonicator with a 30/45-s on/off cycle (27 total on cycles). Immunoprecipitation was performed using 1 μl of anti-GFP (Abcam, Cat. No. ab290) plus 40 μl Agarose beads (Abcam, Cat. No. 16-157) at 4°C overnight.
For ChIP-seq, 1 g of seedlings was used, and the ChIPed DNA was purified using the MinElute PCR purification kit (Qiagen, Cat. No. 28004). Libraries were constructed with 2ng of ChIPed DNA using the VAHTS Universal DNA Library Prep Kit for Illumina V3 (Vazyme Biotech, Cat. No. ND607), VAHTSTM DNA Adapters set3-set6 for Illumina (Vazyme Biotech, Cat. No. N805) and VAHTS DNA Clean Beads (Vazyme Biotech, Cat. No. N411-02) according to the manufacturer's protocol. High-throughput sequencing was performed at Novagene (sequencing method: NovaSeq-PE150).

value: 14-day-old seedling

value: SWI3D-GFP swi3d-1 syd-5

tag: chip antibody

value: Anti-GFP (ab290)


title: ChIPseq-SWI3D-GFP swi3d-1 syd-5-bio2


title: ChIPseq-SWI3D-GFP swi3d-1-bio3

value: SWI3D-GFP swi3d-1


title: M9-WT

city: Indianapolis

first: Lei

last: Yang

state: Indiana

address: 1044 W Walnut Street, R4 272

department: Department of Pediatrics

institute: Indiana University School of Medicine

data_processing:
Quality control for raw mRNA-seq data was generated by FastQC v0.11.5
Illumina adapter sequences and low-quality bases were trimmed by Trim Galore v0.4.5
High-quality paired-end reads was mapped to human genome (hg38) with the aligner STAR v2.7.2b
bam-filter in ngsutilsj v0.4.8 (https://compgen.io/ngsutilsj) was used to keep only properly and uniquely mapped paired reads (MAPQ ≥ 10) for downstream analysis
FeatureCounts from package subread v1.6.5 was employed for quantification of gene expression by summarizing mapped reads to corresponding genes according to GENECODE v31 annotation.
Analysis of differential expression genes (DEGs) was performed by edgeR v3.32.1
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: tab-delimited text files include with raw read counts for every gene and every sample by featureCounts

source_name: Heart

growth_protocol: iPSC derived cardiomyocytes were culutred in DMEM high glucose plus 10% FBS.

extract_protocol: Human RNA was extracted by using Qiagen RNeasy Mini Kit (Cat. 74104). Mouse heat tissue were homogenized by beadsbug homogenizer in Trizol, and then RNA was extracted by using Qiagen RNeasy Mini Kit (Cat. 74104).

treatment_protocol: iPSC derived cardiomyocyte were differentiated using Stem-pro 34 medium for 20 days, then iPSC-CMs cultured in high-glucose DMEM plus 10% FBS for 20 days, total 40 days culture, cells were harvested. Six-week old WT or LIPTER tg mice were fed with HFD for 7 months and Heat tissue were collected.

value: Heart tissue

value: WT


title: LMU_Pat_69

value: head and neck squamous cell carcinoma


title: M28z-KITv CAR, unstimulated, Rep 3

value: CAR T cells

value: CD8+ T cells

value: CAR transduced

value: Unstimulated


title: LMU_Pat_68

value: head and neck


title: M8-KI

value: LIPTER Transgenic


title: M28z-KITv CAR, unstimulated, Rep 2


title: M5-KI


title: ChIPseq-SWI3D-GFP swi3d-1-bio2


title: LMU_Pat_67


title: M28z-KITv CAR, unstimulated, Rep 1


title: M3-WT


title: LMU_Pat_66


title: M28z CAR, unstimulated, Rep 3


title: LMU_Pat_65


title: microglia, ATG7CKO


title: LMU_Pat_70


title: M28z CAR, Stimulated, Rep 1

value: Antigen Stimulated


title: LMU_Pat_64


title: M2-WT


title: M2G-KI


title: M28z CAR, unstimulated, Rep 2


title: ChIPseq-SWP73B-GFP swp73b-1-bio1

value: SWP73B-GFP swp73b-1


title: M28z CAR, unstimulated, Rep 1


title: ChIPseq-SWI3D-GFP swi3d-1-bio1


title: LMU_Pat_63


title: ChIPseq-SWP73A-GFP swp73a-2-bio1

value: SWP73A-GFP swp73a-2


title: LMU_Pat_62


title: ChIPseq-SWI3C-GFP -bio1


title: ChIPseq-BCL7B-GFP bcl7b-1-bio1

value: BCL7B-GFP bcl7b-1


title: ATAC_HNF1B_CRISPRi_enh3

city: St. Louis

first: Yasuhiro

last: Yoshimura

state: MO

address: 660. S Euclid Ave., CB 8118

department: Medicine / Nephrology

institute: Washington University in St. Louis

data_processing:
Fastq files were trimmed with Trim Galore and aligned with Bowtie2 with --very-sensitive -X 2000 using hg38. PCR duplicates were removed with Picard's MarkDuplicates function.
Assembly: hg38
Supplementary files format and content: bigwig format

source_name: primary RPTEC

growth_protocol: RPTECs were seeded at 5.0×104 cells per well on 6-well tissue culture plates one day before transfection. Culture media was then changed to the supernatants of lentivirus that contain dCas9-KRAB repression plasmid with sgRNAs supplemented with 3 µg/mL polybrene and transduced for 24 hours. After 48 hours from transduction, transduced cells were selected by 3 µg/ml of puromycin (InvivoGen, ant-pr-1) for 72 hours.

extract_protocol:
Adherent cells were scraped from culture dishes and centrifuged at 500 × g for 5 min. 10,000 cells were suspended in 50 μL of ice-cold lysis buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20, 0.1% Nonidet P40 Substitute, 0.01% Digitonin), followed by incubation on ice for 4 min. Subsequently, 450 μL of ice-cold wash buffer (10 mM Tris-HCl [pH 7.4], 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween-20) was added and centrifuged at 600 × g for 6 min. Pellets were resuspended in 25 μL of ATAC-seq transposition mix [12.5 μL 2× Illumina Tagment DNA (TD) buffer; 10.5 μL nuclease-free water; 2.0 μL Tn5 transposase (Illumina/Nextera, FC-121-1030)] and incubated at 37°C for 1 h on a thermomixer. The transposed DNA was purified with QIAGEN MinElute kit.
DNA samples were amplified with PCR ([72 °C; 5 min] and [98 °C; 30 s] followed by 9 cycles of [98 °C; 10 s, 63 °C; 30 s, 72 °C; 1 min] using unique 10-bp dual indexes and NEBNext High-Fidelity 2 × PCR Master Kit (M0541L). Following the first amplification, DNA size selection was performed using solid-phase reversible immobilization (SPRI) beads (AMPure XP [Beckman Coulter, A63881]) at an SPRI to DNA ratio of 0.5. The supernatant was further mixed with SPRI beads at a SPRI to DNA ratio of 1.2. The resulting supernatant was discarded, and the magnet-immobilized SPRI beads were washed twice with 80% ethanol. DNA was subsequently eluted in 20 μL of EB elution buffer (QUIAGEN, included in 28004). The size-selected DNA was amplified with an additional 9-cycle PCR. Subsequently, the amplified DNA was purified with Ampure XP (SPRI to DNA ratio of 1.7) and eluted with 25 μL of buffer EB elution buffer.

value: primary RPTEC


title: ATAC_HNF1B_CRISPRi_enh2


title: LMU_Pat_61


title: ChIPseq-BCL7A-GFP bcl7a-1-bio1

value: 14-day-old seedling

value: BCL7A-GFP bcl7a-1


title: LMU_Pat_60


title: ChIPseq-BSH-GFP bsh-bio1

value: BSH-GFP bsh

value: Anti-GFP (ab290)


title: ChIPseq-SWI3A-GFP swi3a-1-bio1

value: SWI3A-GFP swi3a-1


title: LMU_Pat_59

value: head and neck squamous cell carcinoma


title: ATAC_HNF1B_CRISPRi_enh1


title: ATAC_HNF1B_CRISPRi_prom


title: LMU_Pat_58


title: ChIPseq-MINU2-GFP minu2-1-bio1

value: MINU2-GFP minu2-1


title: ChIPseq-MINU2-GFP minu2-1-bio2


title: LMU_Pat_57


title: ChIPseq-SYD-GFP syd-5 brm-1-bio2

value: SYD-GFP syd-5 brm-1


title: LMU_Pat_56


title: LMU_Pat_55


title: tHIO, week 8, rep3

city: Cincinnati

first: Konrad

last: Thorner

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
counts_thio.txt
metadata_thio.txt

data_processing:
Cellranger 3.0.2 is used to perform alignment, filtering, barcode counting, and UMI counting for the snRNA reads. Alignment was against the human hg38 genome. The R library SoupX (v1.5.0) takes the resulting output to produce a counts matrix corrected for cell free mRNA
Assembly: hg38
Supplementary files format and content: Tab-separted matrix of raw counts, and table of metadata

molecule: nuclear RNA

source_name: tHIO

extract_protocol:
tHIOs were harvested, and a portion of the graft was flash frozen in liquid nitrogen. Single nucleus extractions were performed on flash frozen tHIOs using the Minute Detergent Free Single Nucleus Isolation Kit (Invent Biotechnologies, Inc.). The manufacturer’s instructions were followed, with a few modifications. Buffer A was supplemented with 100 Units of Protector RNAse Inhibitor (Roche), 1 μM DTT (Invitrogen), and 8x10-5 M Leptomycin B (Cell Signaling). Buffer B was supplemented with 110 Units of Protector RNAse Inhibitor and 8x10-5 M Leptomycin B. After the final spin in Buffer A, the nuclei were fixed in Riley’s Buffer (PBS supplemented with 1% BSA,146 mM NaCl, 10 mM Tris-HCl, 1 mM CaCl2, 21 mM Mg Cl2, 20 Units of SUPERaseIn (Invitrogen), and 8x10-5 M Leptomycin B) supplemented with 0.1% PFA. After fixation, the nuclei were centrifuged at 500g for four minutes, resuspended in Riley’s Buffer without PFA, and centrifuged again at 500g for four minutes. After centrifuging the nuclei in Buffer B as directed by the manufacturer’s protocol, the nuclei were resuspended in Nuclear Storage Buffer (PBS supplemented with 1% BSA, 200 Units of Protector RNAse Inhibitor, and 8x10-5 M Leptomycin B). An aliquot of the nuclei was stained with Trypan Blue, and nuclear concentration was determined using a TC20 Automated Cell Counter. Nuclei were assessed for intactness using a Nikon Eclipse Ti prior to submission to the Single Cell Genomics Core at CCHMC for 10x sequencing.
The scRNA-Seq assay was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Single Index*), 10x Genomics). Briefly, nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reverse transcribed to cDNA, adding an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The barcoded cDNA was then cleaned up with Silane DynaBeads and amplified using 18 PCR cycles. Full-length, barcoded cDNA was then enzymatically fragmented, sized-selected using SPRIselect reagent, adapter-ligated, and amplified for library construction. During the library construction, Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and sample index(es*) were added. Samples were pooled and run on the NovaSeq 6000 sequencer with S2 or S4 flow cells using the following sequencing parameters: R1: 28 cycles, i7: 8 cycles, i5: 0 cycles, R2: 91 cycles.
snRNA-seq

value: tHIO

value: Intestinal

tag: timepoint

value: 8 weeks


title: Duodenum, epithelial

description:
counts_epi_mes.txt
metadata_epi_mes.txt

source_name: Duodenum

extract_protocol:
Human duodenal surgical sample was dissected and flash frozen in liquid nitrogen. Single nucleus extractions was performed on flash frozen epithelial and mesenchymal cells using the Minute Detergent Free Single Nucleus Isolation Kit (Invent Biotechnologies, Inc.). The manufacturer’s instructions were followed, with a few modifications. Buffer A was supplemented with 100 Units of Protector RNAse Inhibitor (Roche), 1 μM DTT (Invitrogen), and 8x10-5 M Leptomycin B (Cell Signaling). Buffer B was supplemented with 110 Units of Protector RNAse Inhibitor and 8x10-5 M Leptomycin B. After the final spin in Buffer A, the nuclei were fixed in Riley’s Buffer (PBS supplemented with 1% BSA,146 mM NaCl, 10 mM Tris-HCl, 1 mM CaCl2, 21 mM Mg Cl2, 20 Units of SUPERaseIn (Invitrogen), and 8x10-5 M Leptomycin B) supplemented with 0.1% PFA. After fixation, the nuclei were centrifuged at 500g for four minutes, resuspended in Riley’s Buffer without PFA, and centrifuged again at 500g for four minutes. After centrifuging the nuclei in Buffer B as directed by the manufacturer’s protocol, the nuclei were resuspended in Nuclear Storage Buffer (PBS supplemented with 1% BSA, 200 Units of Protector RNAse Inhibitor, and 8x10-5 M Leptomycin B). An aliquot of the nuclei was stained with Trypan Blue, and nuclear concentration was determined using a TC20 Automated Cell Counter. Nuclei were assessed for intactness using a Nikon Eclipse Ti prior to submission to the Single Cell Genomics Core at CCHMC for 10x sequencing.
The scRNA-Seq assay was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index), 10x Genomics). Briefly, nuclei were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was reverse transcribed to cDNA, adding an Illumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The barcoded cDNA was then cleaned up with Silane DynaBeads and amplified using 18 PCR cycles. Full-length, barcoded cDNA was then enzymatically fragmented, sized-selected using SPRIselect reagent, adapter-ligated, and amplified for library construction. During the library construction, Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and sample index(es*) were added. Samples were pooled and run on the NovaSeq 6000 sequencer with S2 or S4 flow cells using the following sequencing parameters: R1: 28 cycles, i7: 10 cycles, i5: 10 cycles, R2: 90 cycles.
snRNA-seq

value: Duodenum

value: Epithelium

value: 19 years


title: Deodenum, mesenchymal

description:
counts_epi_mes.txt
metadata_epi_mes.txt

value: Mesenchyme


title: tHIO, week 8, rep2

description:
counts_thio.txt
metadata_thio.txt


title: tHIO, week 8, rep1

description:
counts_thio.txt
metadata_thio.txt


title: ChIPseq-SYD-GFP syd-5-bio4

value: SYD-GFP syd-5


title: LMU_Pat_54

value: head and neck


title: ChIPseq-SYD-GFP syd-5-bio3

value: 14-day-old seedling


title: tHIO, week 6

description:
counts_thio.txt
metadata_thio.txt

value: 6 weeks


title: ChIPseq-SYD-GFP syd-5 brm-1-bio1


title: LMU_Pat_52


title: tHIO, week 4, rep2

description:
counts_thio.txt
metadata_thio.txt

value: 4 weeks


title: ChIPseq-SYD-GFP syd-5 swi3d-1-bio2

value: SYD-GFP syd-5 swi3d-1

value: Anti-GFP (ab290)


title: tHIO, week 4, rep1

description:
counts_thio.txt
metadata_thio.txt


title: LMU_Pat_53

value: head and neck squamous cell carcinoma


title: ChIPseq-SYD-GFP syd-5 swi3d-1-bio1


title: tHIO, week 2

description:
counts_thio.txt
metadata_thio.txt

value: 2 weeks


title: ChIPseq-SYD-GFP syd-5-bio2


title: LMU_Pat_49


title: control 3h enteroid biol rep3

city: Uppsala

first: Staffan

middle: Gunnar

last: Svärd

address: Husargatan 3

department: Department of Cell and Molecular Biology

country: Sweden

institute: Uppsala University

description:
matrix column name:
253

data_processing:
Illumina NovaSeq 6000 , Demultiplexing and conversion to FASTQ performed using the bclfastq2 (2.20.0.422) software
FASTQ files were mapped to combined Giardia WB genome and human GRCh38 using STAR v2.7.10a. ReadsPerGene.out.tab output from STAR with specifying --quantMode GeneCounts were used as the raw counts input for downstream analysis
Gene differential expression analysis was carried out in R v4.0.1 using edgeR v3.32.1 workflow. Quasi-likelihood F test was used to determine significant differential gene expression.
Assembly: Giardia intestinalis WB C6,  GCA_000002435.2 UU_WB_2.1
Assembly: GRCh38, release 106, GCA_000001405.28
Supplementary files format and content: Tab-delimited text file containing count matrix of human raw counts from STAR mapping of all samples (counts_human.txt).
Supplementary files format and content: Tab-delimited text file containing count matrix of Giardia intestinalis raw counts from STAR mapping of all samples (counts_giardia.txt).

source_name: jenjunal enterocytes

growth_protocol:
Giardia intestinalis trophozoites were grown in TYDK at 37°C until 70% confluency. Trophozoites were washed twice in warm PBS and after incubated in either DMEM/F-12 supplemented with 10% FBS or with DMEM/F-12 for 1h at 37°C. After this preconditioning, trophozoites were detached, spun down, washed once in 1ml cold DMEM/F-12, spun down again and after resuspended in DMEM/F-12.
Human enteroids were maintained as 3D domes embedded in Matrigel in human Intesticult organoid growth media in humidified atmosphere with 5% CO2 at 37°C. For infections enteroids were grown as monolayers on PET-transwells and differentiated to an enterocyte phenotype by deprivation of WNT signaling for 4 to 5 days. 3h before the infection apical media was changed to DMEM/F-12 while the basal compartment was refreshed with differentiation media.

extract_protocol:
Total RNA extractions were performed using Trizol according to the manufactures instructions. RNA was then treated with DNaseI and extracted again by phenol chloroform extraction.
Sequencing libraries were prepared from 500ng total RNA using the TruSeq stranded mRNA library preparation kit (cat# 20020595, Illumina Inc.) including polyA selection. Unique dual indexes (cat# 20022371, Illumina Inc.) were used. The library preparation was performed according to the manufacturers’ protocol.

treatment_protocol:
Giardia intestinalis trophozoites were added apically to enterocytes for 1h and 3h. Uninfected enterocyte monolayers were collected after 1h and 3h as controls. Prior to infection preconditioned Giardia intestinalis trophozoites were collected as inoculum samples.
All samples were collected and lysed in Trizol reagent.

value: jenjunal enterocytes

value: uninfected


title: LMU_Pat_50


title: LMU_Pat_51


title: ChIPseq-BRM-GFP brm-1 syd-5-bio2

value: BRM-GFP brm-1 syd-5


title: ChIPseq-SYD-GFP syd-5-bio1


title: OESO_0138

type: genomic

city: Brisbane

first: Katia

last: Nones

state: QLD

address: 300 Herston Road

country: Australia

institute: QIMR Berghofer Medical Institute

description: public data

hyb_protocol: followed Illumina protocol

scan_protocol: Iscan following vendor instructions

data_processing: Raw idat files were imported using ChAMP (v.2.12.4).  Each data set, 450K and EPIC were imported and probes removed if the detected p-value >0.01 or or there were fewer than three beads in at least 5% of samples. Common probes to the two data sets (450K and EPIC arrays)  were normalized  using beta mixture quantile normalization (BMIQ) to account for probe type1 and type 2 biases, followed by a quantile normalisation (QN). Further filtering was performed to remove: 1) probes in non-CpG sites, 2) X or Y chromosome, 3) single-nucleotide polymorphism-related polymorphisms and 4) probes that map to multiple locations. A single value decomposition analysis determined a significant batch effect in the data sets. A batch correction was applied using removeBatchEffect from the limma package (v3.38.3) before any further analyses.

label: biotin

source_name: Tumour

label_protocol: followed Illumina protocol

extract_protocol: All prep DNA/RNA (Qiagen) following vendor protocol.

value: tumour


title: control 3h enteroid biol rep1

description:
matrix column name:
251


title: LMU_Pat_47


title: ChIPseq-BRM-GFP brm-1-bio2

value: BRM-GFP brm-1


title: OESO_6100

description: public data


title: OESO_6087

description: public data


title: control 3h enteroid biol rep2

description:
matrix column name:
252


title: LMU_Pat_46


title: OESO_0132

description: public data


title: OESO_6082

description: public data


title: ChIPseq-BRM-GFP brm-1 syd-5-bio1


title: ChIPseq-BRM-GFP brm-1-bio1


title: LMU_Pat_48


title: LMU_Pat_44


title: control 1h enteroid biol rep 2

description:
matrix column name:
240


title: OESO_6089

description: public data


title: OESO_6091

description: public data


title: LMU_Pat_45


title: U2OS33_T0h_Input_Rep1

city: Regensburg

first: Uwe

last: Schwartz

address: Universitätstraße 32

department: NGS Analysis Center

institute: University of Regensburg

data_processing:
Paired-end reads were mapped to the reference using bowtie2-aligner with following paramters: --very-sensitive-local, --no-discordant
Reads were filtered to mapping quality > 30 and only reads mapped in proper pair were kept using samtools.
CPM-normalized coverage tracks were generated using the bamCoverage script of the deepTools package
Assembly: hg19 and AY339865.1 (adapted)
Supplementary files format and content: bigwig files showing CPM normalized coverage

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and the reaction was quenched with glycine at a final concentration of 0.125 M. Chromatin was sheared using ultrasonication (Covaris S2). A total of 2.5 µg of antibody against H3K27ac (Abcam, ab4729), or FLAG (M2, Sigma Aldrich, F3165), was bound to 20 µl pre-washed Dynabeads Protein A (Thermo Fisher Scientific) in a total volume of 200 µl PBS containing 0.02% Tween-20 for 1h at room temperature rotating at 6 rpm. The buffer was removed on a magnet and antibody-coupled beads were resuspended in 120µl dilution buffer (20mM Tris pH7.4, 2mM EDTA, 100mM NaCl, 0.5% Triton x-100) containing proteinase inhibitors (cOmplete™, EDTA-free Protease Inhibitor Cocktail, 50x, Sigma). 80µl sonicated chromatin was added to the antibody-coupled Dynabeads (sonicated chromatin of approx. 1.7x106 cells) and incubated for 3h at room temperature rotating at 6 rpm. Beads were washed on a magnet and chromatin was eluted. After crosslink reversal, RNase A and proteinase K treatment, DNA was extracted with the Monarch PCR & DNA Cleanup kit (NEB).
Sequencing libraries were prepared with the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to manufacturer’s instructions

tag: integrated construct

value: H3.3 FLAG

tag: hours post_infection

value: Input


title: control 1h enteroid biol rep 1

description:
matrix column name:
239


title: OESO_6081

description: public data


title: LMU_Pat_42


title: LMU_Pat_41


title: OESO_6070

description: public data


title: U2OS33_T2h_Flag_Rep3

value: Flag


title: U2OS33_T4h_H3K27ac_Rep3


title: OESO_0115

description: public data


title: U2OS33_T4h_Flag_Rep3


title: LMU_Pat_43


title: LMU_Pat_39


title: HAP1,ATO biol rep1

city: guangzhou

first: Chen

last: Jun-Zhu

state: State...

address: 广州市越秀区中山二路58号中山大学附属第一医院

institute: Sun Yat-Sen University

data_processing:
Sequence artifacts, including reads containing adapter contamination, low-quality nucleotides and unrecognizable nucleotide (N), undoubtedly set the barrier for the subsequent reliable bioinformatics analysis. Hence quality control is an essential step and applied to guarantee the meaningful downstream analysis. we used Fastp (version 0.19.7) to perform basic statistics on the quality of the raw reads. The steps of data processing were as follows: (1) Discard a paired reads if either one read contains adapter contamination; (2) Discard a paired reads if more than 10% of bases are uncertain in either one read; (3) Discard a paired reads if the proportion of low quality (Phred quality
Assembly: hg38
Supplementary files format and content: tab-delimited text files include sgRNA counts for each Sample

source_name: Peripheral blood

growth_protocol: HAP1 cells were maintained in IMDM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
the genomic DNA was extracted by the TIANamp Genomic DNA Kit (#DP304, TIANGEN).
A total amount of 1μg DNA per sample was used as input material for the DNA sample preparations. Sequencing libraries were generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendationsandindexcodeswereaddedtoattributesequencestoeachsample. Briefly， the DNA samples were endpolished, A-tailed, and ligated with the full-length adapter for Illumina sequencing.After the DNA products were purified by AMPure XP system (Beckman Coulter, Beverly, USA), DNA concentration was measured by Qubit®3.0 Flurometer (Invitrogen, USA), libraries were analyzed for size distribution by Agilent 2100 Bioanalyzer and quantified by real-time PCR (>2 nM

treatment_protocol: Cells were treated with 2μM ATO or vehicle for 14 days.

value: Peripheral blood

value: Haploid Cells

value: WT

value: ATO


title: HAP1,ATO biol rep2

address: 广州市越秀区中山二路58号中山大学附属第一医院


title: OESO_6078

description: public data


title: OESO_6065

description: public data


title: HAP1, CTL biol rep2

address: 广州市越秀区中山二路58号中山大学附属第一医院

value: DMSO


title: HAP1, CTL biol rep1

address: 广州市越秀区中山二路58号中山大学附属第一医院


title: LMU_Pat_40

value: head and neck


title: U2OS33_T2h_H3K27ac_Rep3


title: LMU_Pat_37


title: F9

city: Montreal

first: Gustavo

last: Turecki

state: Quebec

address: 6875 Boulevard LaSalle

department: Psychiatry

country: Canada

institute: McGill University

description: Batch: 2F, Chemistry:  v2

data_processing:
10X Genomics Cellranger v3.1.0 mkfastq
10X Genomics Cellranger v5.0.1 count
Cell filtering as described in publication
Clustering and cell type annotation: Unsupervised clustering of nuclei was performed with the Seurat algorithm, after using highly variable genes for PCA and correcting for batch effects with the Harmony R package. Clusters were annotated to cell types based on the enrichment of expression of known marker genes.
Differential expression analysis between cases and controls was performed separately for males and females within each broad cell type and cluster, using the summed counts of every gene per subject and with the muscat and edgeR R packages.
Assembly: refdata-gex-GRCh38-2020-A,   https://support.10xgenomics.com/single-cell-gene-expression/software/release-notes/build
Supplementary files format and content: count matrix for filtered genes and barcodes for all samples combined. This includes, in Matrix Market format, female samples whose raw data is provided here and male samples from the previous study. The matrix row names (genes) and column names (barcodes and cell-type annotations) are also given in CSV format.

molecule: polyA RNA

source_name: Brain BA9 dlPFC

extract_protocol: Chromium Single Cell 3’ Reagent Kits v2 and v3.1

value: Brain BA9 dlPFC

tag: Sex

value: Female

tag: group

value: Case


title: U2OS33_T1h_Flag_Rep3


title: OESO_6067

description: public data


title: U2OS33_T0h_Flag_Rep3


title: F6

description: Batch: 8F, Chemistry:  v3


title: control 1h enteroid biol rep 3

description:
matrix column name:
241

value: jenjunal enterocytes

tag: treatment


title: LMU_Pat_38

tag: tissue

value: head and neck squamous cell carcinoma


title: U2OS33_T0h_H3K27ac_Rep3


title: U2OS31_T1h_H3K27ac_Rep3

value: H3.1 FLAG


title: F4

description: Batch: 6F, Chemistry:  v3


title: LMU_Pat_35

tag: cell type


title: LMU_Pat_36


title: U2OS31_T1h_Flag_Rep3


title: OESO_6028

description: public data

value: tumour


title: LMU_Pat_34


title: OESO_6032

description: public data


title: F37

description: Batch: 8F, Chemistry:  v3

value: Control


title: LMU_Pat_33


title: F38

description: Batch: 12F, Chemistry:  v3


title: F7

description: Batch: 7F, Chemistry:  v3


title: U2OS31_T0h_H3K27ac_Rep3


title: OESO_6027

description: public data


title: F36

description: Batch: 8F, Chemistry:  v3


title: U2OS31_T0h_Flag_Rep3


title: OESO_6064

description: public data


title: F35

description: Batch: 8F, Chemistry:  v3


title: U2OS33_T4h_Flag_Rep2

value: H3.3 FLAG


title: OESO_6039

description: public data


title: OESO_0044

description: public data


title: LMU_Pat_30


title: OESO_0034

description: public data


title: U2OS33_T1h_H3K27ac_Rep3


title: OESO_5007

description: public data


title: F34

description: Batch: 8F, Chemistry:  v3


title: OESO_6036

description: public data


title: U2OS33_T2h_H3K27ac_Rep2


title: F33

description: Batch: 6F, Chemistry:  v3


title: OESO_0041

description: public data


title: F32

description: Batch: 3F, Chemistry:  v2


title: LMU_Pat_31


title: sample 01032 genomic DNA from blasts at day 8 during course 2

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

hyb_protocol: Samples were hybridized according to manufacturer's protocol (Illumina).

scan_protocol: Samples were scanned according to manufacturer's protocol (Illumina).

data_processing:
preprocessRaw function from minfi (V1.36) R package
normalized data: Average Beta

label: Cy5 and Cy3

source_name: blasts

label_protocol: Samples were labeled with Cy5 and Cy3 according to manufacturer's protocol (Illumina).

growth_protocol: Mononuclear cells were isolated out of AML patients' whole blood samples by Pancoll density centrifugation. AML blasts were enriched by automated magnetic sorting using anti-CD34 and -CD117 beads.

extract_protocol: Genomic DNA was isolated with the DNeasy Blood & Tissue Kit (Qiagen, Hilden, Germany).

treatment_protocol: AML patients were treated within the DECIDER trial (NCT00867672) with decitabine ((Decitabine/DAC treatment, 20 mg/m2 intravenous 1-hour infusion over 5 days, with add-on drugs valproic acid and/or all-trans retinoic acid [ATRA] added at day 6).

tag: gender

value: male

value: blasts

tag: course

tag: day


title: sample 01777 genomic DNA from blasts at day 8 during course 2

value: female


title: U2OS33_T4h_H3K27ac_Rep2


title: LMU_Pat_28


title: LMU_Pat_29


title: U2OS33_T1h_H3K27ac_Rep2


title: F31

description: Batch: 6F, Chemistry:  v3


title: F8

description: Batch: 8F, Chemistry:  v3


title: LMU_Pat_27


title: sample 01031 genomic DNA from blasts at day 8 during course 2


title: U2OS33_T2h_Flag_Rep2

value: Flag


title: OESO-0017

description: public data


title: OESO_0023

description: public data


title: F30

description: Batch: 12F, Chemistry:  v3


title: LMU_Pat_26


title: OESO_0040

description: public data


title: U2OS33_T0h_H3K27ac_Rep2


title: F3

description: Batch: 6F, Chemistry:  v3


title: sample 01022 genomic DNA from blasts at day 8 during course 2


title: F29

description: Batch: 3F, Chemistry:  v2


title: sample 01027 genomic DNA from blasts at day 8 during course 2


title: OESO_0015

description: public data


title: sample 01004 genomic DNA from blasts at day 8 during course 2


title: LMU_Pat_24


title: OESO_0025

description: public data


title: LMU_Pat_25


title: F28

description: Batch: 3F, Chemistry:  v2


title: OESO_0014

description: public data


title: OESO_0013

description: public data


title: LMU_Pat_23


title: sample 01777 genomic DNA from blasts at day 0 during course 2


title: OESO_0009

description: public data


title: F27

description: Batch: 3F, Chemistry:  v2


title: sample 01032 genomic DNA from blasts at day 0 during course 2


title: F26

description: Batch: 3F, Chemistry:  v2


title: U2OS31_T2h_H3K27ac_Rep2


title: sample 01031 genomic DNA from blasts at day 0 during course 2


title: U2OS31_T4h_Flag_Rep2


title: LMU_Pat_22


title: LMU_Pat_21


title: OESO_0008

description: public data


title: U2OS31_T2h_Flag_Rep2


title: OESO_0031

description: public data


title: F25

description: Batch: 12F, Chemistry:  v3


title: LMU_Pat_32


title: sample 01027 genomic DNA from blasts at day 0 during course 2


title: OESO_0001

description: public data


title: LMU_Pat_19


title: F24

description: Batch: 3F, Chemistry:  v2


title: U2OS33_T1h_Flag_Rep2


title: U2OS31_T1h_H3K27ac_Rep2


title: sample 01022 genomic DNA from blasts at day 0 during course 2


title: F23

description: Batch: 2F, Chemistry:  v2


title: U2OS31_T0h_H3K27ac_Rep2


title: F22

description: Batch: 7F, Chemistry:  v3


title: U2OS31_T1h_Flag_Rep2


title: sample 26002 genomic DNA from T_cells at day 8 during course 1


title: sample 25002 genomic DNA from T_cells at day 8 during course 1


title: F21

description: Batch: 7F, Chemistry:  v3


title: LMU_Pat_17


title: LMU_Pat_16


title: U2OS33_T4h_H3K27ac_Rep1


title: LMU_Pat_20


title: F2

description: Batch: 7F, Chemistry:  v3


title: U2OS33_T4h_Flag_Rep1


title: sample 14005 genomic DNA from T_cells at day 8 during course 1


title: sample 02003 genomic DNA from T_cells at day 8 during course 1


title: LMU_Pat_14


title: LMU_Pat_15


title: LMU_Pat_13


title: sample 01999 genomic DNA from T_cells at day 8 during course 1


title: U2OS33_T2h_Flag_Rep1


title: U2OS33_T2h_H3K27ac_Rep1


title: F17

description: Batch: 7F, Chemistry:  v3


title: sample 01004 genomic DNA from blasts at day 0 during course 2


title: LMU_Pat_12


title: sample 01666 genomic DNA from T_cells at day 8 during course 1


title: U2OS33_T0h_Flag_Rep2


title: F16

description: Batch: 7F, Chemistry:  v3


title: LMU_Pat_11


title: U2OS33_T1h_H3K27ac_Rep1


title: U2OS31_T4h_H3K27ac_Rep2


title: sample 01032 genomic DNA from T_cells at day 8 during course 1


title: U2OS33_T1h_Flag_Rep1


title: sample 01030 genomic DNA from T_cells at day 8 during course 1


title: F15

description: Batch: 7F, Chemistry:  v3


title: F14

description: Batch: 12F, Chemistry:  v3


title: U2OS33_T0h_H3K27ac_Rep1


title: F18

description: Batch: 2F, Chemistry:  v2


title: sample 01027 genomic DNA from T_cells at day 8 during course 1


title: F13

description: Batch: 7F, Chemistry:  v3


title: sample 01021 genomic DNA from T_cells at day 8 during course 1


title: U2OS33_T0h_Flag_Rep1


title: U2OS31_T4h_H3K27ac_Rep1


title: F20

description: Batch: 3F, Chemistry:  v2


title: U2OS31_T0h_Flag_Rep2


title: LMU_Pat_07


title: LMU_Pat_08


title: sample 01016 genomic DNA from T_cells at day 8 during course 1


title: U2OS31_T4h_Flag_Rep1


title: F12

description: Batch: 12F, Chemistry:  v3


title: sample 01015 genomic DNA from T_cells at day 8 during course 1


title: F11

description: Batch: 8F, Chemistry:  v3


title: LMU_Pat_06


title: F10

description: Batch: 6F, Chemistry:  v3


title: sample 01012 genomic DNA from T_cells at day 8 during course 1


title: U2OS31_T2h_H3K27ac_Rep1


title: LMU_Pat_05


title: LMU_Pat_18


title: LMU_Pat_10


title: LMU_Pat_04


title: sample 01007 genomic DNA from T_cells at day 8 during course 1


title: F1

description: Batch: 8F, Chemistry:  v3


title: U2OS31_T2h_Flag_Rep1


title: sample 01004 genomic DNA from T_cells at day 8 during course 1


title: wk24-WT, replicate 1, scRNAseq

city: Daejeon

first: Jong-Eun

last: Park

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: Korea Advanced Institute of Science and Technology

description: 10x Genomics

data_processing:
Reads were aligned to the GRCh38 human reference genome and converted into count matrices by Cell Ranger 6.1.2 pipeline.
Count matrices were further processed by Seurat 4.0.6 (Hao et al., 2021). Cells with expressed genes less than 1000 or over 5500, unique molecular identifiers less than 2000 over 20000, mitochondrial transcript proportion over 20% were filtered out for the quality control. MALAT1 and mitochondrial gene expression was regressed out to avoid the bias in the expression variation.
Each dataset was log-normalized and linear transformed. Top 30 principal components (PCs) obtained by principal component analysis (PCA) with 2000 highly variable features, were subjected to further analysis. Nearest neighbors were calculated, and the cells were initially clustered with Louvain algorithm using a resolution of 0.5. Differentially expressed genes (DEGs) for each cluster was found by Wilcoxon test. Clusters displaying apoptosis-associated DEGs were excluded for the further analysis. 9 individual Seurat objects were integrated with Harmony package (Korsunsky et al., 2019) for the batch-correction. Integrated dataset was clustered and visualized by UMAP dimensional reduction. Clusters were annotated to their respective cell types using canonical cell type-specific marker genes.
Assembly: hg38
Supplementary files format and content: RDS file of integrated and processed single-cell RNA sequencing data from all 9 samples; found in total.rds
Supplementary files format and content: RDS file of integrated and processed single-cell RNA sequencing data from all 9 samples (excitatory neruon subset); found in excitatory.rds

source_name: iPSC

growth_protocol: hiPSCs were differentiated into cortical organoids as previously reported with minor modifications (Paşca et al., 2015). Briefly, hiPSC colonies were mechanically cut into four to nine clumps of approximately 0.5 mm x 0.5 mm in the size using syringe needle and treated with 10 mg/ml collagenase type IV (Gibco) for 4 min to detach. Detached clumps were cultured in suspension on low-attachment dishes in the EB medium supplemented with 10 μM Y-27632 (Cayman Chemical, Ann Arbor, MI, USA) for 1 day, and then changed daily with fresh EB medium without Y-27632 for 4 days. The EB medium is composed of the hiPSC medium without bFGF, supplemented with 10 μM SB431542 (Cayman Chemical) and 10 μM dorsomorphine (AG Scientific). The EB-derived spheres were further incubated in the neural medium containing Neurobasal™-A medium (Gibco), 2% B-27™ supplement minus vitamin A (Gibco), 1% GlutaMAX™ supplement (Gibco), 20 ng/ml bFGF, and 20 ng/ml recombinant human EGF (Peprotech, Cranbury, NJ) for 10 days with the medium change daily, and for 9 days with the medium change every other day. From day 25 to 43 of culture, cortical organoids were incubated in the neural medium supplemented with 20 ng/ml recombinant human BDNF (Peprotech) and 20 ng/ml recombinant human NT-3 (Peprotech) instead of EGF and FGF with the medium change every other day. For prolonged culture, cortical organoids were incubated in the neural medium without any growth factors with the medium change every other day. Morphology of cortical organoids was imaged on an inverted microscope (Olympus, Tokyo, Japan), and their surface areas were analyzed with ImageJ software (NIMH, Bethesda, MD)

extract_protocol:
Four individual cortical organoids having similar size were obtained from respective samples (WT, NS, and NS-Cor) at different developmental periods (week 8, 16, and 24) and subjected to the scRNA-seq library preparation. Each cortical organoid was dissected into small pieces using a 29G-syringe needle and dissociated using the papain dissociation system (Worthington Biochemical Corporation, Lakewood, NJ) according to the manufacturer’s protocol. Dissociated cells were suspended in 1ml of PBS solution supplemented with 0.04% BSA and 10μM Y-27632, counted with LUNA-II automated cell counter (Logos Biosystems, Anyang, Korea), and diluted at a concentration of 1x106 cells/ml.
scRNA-seq library was prepared by using Chromium single cell 3' reagent kits v3.1 chemistry (10x Genomics, Pleasanton, CA).

value: Brain organoid

value: iPSC

tag: time point

value: 24 wk

tag: genotype

value: WT-iPSCs


title: LMU_Pat_03

value: head and neck


title: U2OS31_T1h_H3K27ac_Rep1

tag: cell line


title: LMU_Pat_09

tag: hpv-status


title: sample 01001 genomic DNA from T_cells at day 8 during course 1


title: LMU_Pat_02


title: U2OS31_T0h_H3K27ac_Rep1


title: wk24-NS, replicate 1, scRNAseq

description: 10x Genomics

value: NS-iPSCs


title: wk24-Cor, replicate 1, scRNAseq

description: 10x Genomics

value: NS-Cor-iPSCs


title: U2OS31_T0h_Flag_Rep1


title: wk16-WT, replicate 1, scRNAseq

description: 10x Genomics

value: 16 wk


title: sample 26002 genomic DNA from T_cells at day 0 during course 1


title: sample 25002 genomic DNA from T_cells at day 0 during course 1


title: sample 14005 genomic DNA from T_cells at day 0 during course 1


title: wk16-NS, replicate 1, scRNAseq

description: 10x Genomics


title: wk08-WT, replicate 1, scRNAseq

description: 10x Genomics

value: 8 wk


title: Patient 6 Right Atria Tissue

city: London

first: Richard

middle: James

last: Mitter

state: LONDON

address: 1 Midland Road

department: Bioinformatics & Biostatistics

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
The nf-core rnaseq pipeline (release v3) was used to generate gene-level abundance estimates using RSEM-STAR (https://github.com/nf-core/rnaseq)
The pipeline was run with default options except for specifying the GRCh38 genome fasta, Ensembl release 95 GTF file and STAR aligner (--fasta Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa --gtf Homo_sapiens.GRCh38.95.gtf --aligner star_rsem)
Assembly: GRCh38 with Ensembl release 95 transcript annotations
Supplementary files format and content: RSEM gene abundance estimates

source_name: Heart tissue

extract_protocol:
RNA was isolated using the Qiagen Rneasy kit
KAPA mRNA (polyA) HyperPrep

tag: patient

tag: chamber

value: RA

value: Heart tissue


title: AF8

type: RNA

city: jinan

first: hai

middle: yan

last: liu

address: huaxianchanglu

institute: bohao

description: Exosomal miRNA expression in amniotic fluid derived from LPS-treated Premature births

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

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8 x 60k array slides (Scan Area 61x21.6 mm, Scan resolution 10um, Dye channel is set to Green and Green PMT is set to 100%).

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

source_name: Exosomes derived from amniotic fluid in mice of LPS-treated Premature births

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions

extract_protocol: Exosomes from amniotic fluid were isolated by size-exclusion chromatography using qEV original size exclusion column (IZON science, Oxford, UK). Firstly, the amniotic fluid was concentrated by centrifugal filter units (Millipore, Mass, US) through centrifugation at 1500 × g for 20 min. The sample were added into columns, and started to count the fraction, 0.5 ml/fraction, the seven to nine fractions were selected and concentrated.

treatment_protocol: LPS (100 μg/kg body weight) was intraperitoneally injected into the mice at 14 days of pregnancy. PTB has been found after approximately 48 h of treatment. When bleeding found in vagina, the uterus and other embryo without breaking water were selected in asepsis condition. The uterus, amnion, and amniotic fluid were analyzed for expression of specific genes compared with cesarean sections.

value: amniotic fluid

tag: developmental stage

value: 17 days of pregnancy


title: Patient 5 Right Ventricle Tissue

value: RV


title: AF5


title: AF7


title: sample 02003 genomic DNA from T_cells at day 0 during course 1

value: male


title: Patient 6 Left Ventricle Tissue

value: LV


title: sample 01999 genomic DNA from T_cells at day 0 during course 1

value: female


title: wk16-Cor, replicate 1, scRNAseq

description: 10x Genomics

value: Brain organoid


title: wk08-NS, replicate 1, scRNAseq

description: 10x Genomics

value: iPSC


title: U2OS31_T1h_Flag_Rep1

tag: integrated construct

value: H3.1 FLAG

tag: chip antibody

value: Flag


title: wk08-Cor, replicate 1, scRNAseq

description: 10x Genomics


title: sample 01032 genomic DNA from T_cells at day 0 during course 1


title: Patient 6 Right Ventricle Tissue


title: Patient 5 Right Atria Tissue


title: Patient 6 Left Atria Tissue

value: LA


title: Patient 5 Left Ventricle Tissue


title: H9_d7_snATAC-seq

library_source: genomic single cell

data_processing:
Raw sequencing reads were processed by CellRanger ARC (v2.0.0) with default setting.  Quality control, sample integration and analysis was performed using Seurat (v4.1.0) and Signac (v1.5.0) packages.
Assembly: hg38
Supplementary files format and content: The hdf5 files contain the count matrix generated by CellRanger ARC for each sample.
Supplementary files format and content: The fragments.tsv.gz and fragments.tsv.gz.tbi files contain unique ATAC-seq fragments captured by the assay and related information about the fragments.

source_name: Kidney organoid

growth_protocol: Kidney organoids were generated by Takasato et al., 2016 (PMID: 27560173) with slight modifications. Briefly, on the next day of passage, pluripotent stem cells were treated with 8 µM CHIR99021 in basal medium that were comprised APEL2 supplemented with 1.5% Protein Free Hybridoma Medium II and 1x antibiotic-antimycotic solution for 4 days. On day4, medium was switched to 200 ng/mL FGF9 and 1 μg/mL heparin in the basal medium. On day 7, cells were dissociated into single cells using Accutase and diluted 5-fold with the basal medium with 10 µM Y27632. 200,000 cells were spun down at 300 g for 2 minutes (twice with 180° flip) to make cell aggregates in a 1.5-ml low-cell-binding tube and transferred onto a 0.4-µm pore polyester membrane transwell. Pellets were incubated with 5 µM CHIR99021 in the basal medium for 1 hour, and then cultured with 200 ng/mL FGF9 and 1 µg/mL heparin in the basal medium for 5 days. From day 12 to day 26-28, organoids were grown in the basal medium. Medium were changed every other day.

extract_protocol:
To dissociate organoids into single cells, days 12, 16, 19, and 26 organoids were treated with 0.25% trypsin-EDTA at 37℃ for 8-10 minutes. Day 7 posterior intermediate cells were treated with Accutase at 37℃ for 6 minutes to obtain single cells. Dissociated cells were washed twice and filtered through 40-µm strainer. 1,000,000 cells were treated with chilled multiome lysis buffer on ice for 5 minutes to obtain nuclei. Isolated nuclei were washed with multiome wash buffer for a total of three times, then resuspended with chilled multiome nuclei buffer.
The snRNA-seq and snATAC-seq libraries were prepared using Chromium Next GEM Single Cell Multiome ATAC + Gene Expression kit following the manufacturer’s protocol.

value: Kidney organoid

value: H9 hESC

tag: time

value: day 7


title: LMU_Pat_01

extract_protocol:
After histopathological review, simultaneous DNA and total RNA extraction of serial formalin-fixed and paraffin-embedded tissue sections was performed using the AllPrep DNA/RNA FFPE Kit RNA isolation (Qiagen, Hilden, Germany). Isolated RNA was quantified using a Qubit Fluorometer and RNA integrity was assessed determining DV200 values (percentage of fragments >200 nucleotides) using the 2100 Bioanalyzer followed by categorization into low, medium, and good quality samples.
For whole RNA sequencing, sequencing libraries were prepared using the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, Inc., USA). Input quantity and initial RNA fragmentation time was adjusted to the respective RNA quality. After library preparation, library quality and quantity were evaluated using the Quanti-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, MA, USA) and the Bioanalyzer High Sensitivity DNA Analysis Kits (Agilent Technologies).

value: head and neck squamous cell carcinoma

value: head and neck


title: H9_d7_snRNA-seq


title: sample 01027 genomic DNA from T_cells at day 0 during course 1


title: AF3


title: A4

description: Exosomal miRNA expression in amniotic fluid derived from cesarean sections

source_name: Exosomes derived from amniotic fluid in mice of cesarean sections


title: sample 01666 genomic DNA from T_cells at day 0 during course 1


title: Patient 5 Left Atria Tissue

value: Heart tissue


title: sample 01021 genomic DNA from T_cells at day 0 during course 1


title: Patient 4 Right Ventricle Tissue


title: ABA_osfkbp20-1b_rep3

first: Haemyeong

last: Jung

address: 125 Gwahak-ro, Yuseong-gu

department: Plant Systems Engineering Research Center

institute: KRIBB

data_processing:
Raw sequencing data were filtered using standard RNA-seq parameters (Illumina pipeline).
The transcriptome short reads (< 25 bp) were filtered out using DynamicTrim and LengthSort of solexaQA package
The read counts were calculated by mapping the filtered reads that passed the pre-processing using HTSeq
The filtered reads were normalised using the DESeq library
The IR ratio was calculated by dividing the read depth of introns by the average read depth of two adjacent exons
The intron retention (IR) ratio was calculated by dividing the read depth of introns by the average read depth of two adjacent exons. AS occurred outside of IRs requiring junction reads, junction information was extracted using regtools
Genome_build: IRGSP-1.0 (Oryza sativa Japonica Group (Japanese rice) genome assembly)
Supplementary_files_format_and_content: Xlsx was processed data

organism: Oryza sativa Japonica Group

source_name: rice

growth_protocol: Rice seeds were sown on 1/2 MS gel for 3 days germination and transfer and growth the 50 mL conical ture 4 days in culture room (25℃, light/dart 16h/8h)

extract_protocol:
Total RNA was prepared from leaf using WizPrepTM Plant RNA Mini Kit (WIZBIOsolutions, Seongnam, South Korea)
Total RNA was extracted from the leaves, and cDNA was synthesized using PrimeScript™ RT reagent Kit (TaKara, Japan). The resultant cDNA fragments were purifed, end-reparided, polyA-tailed, and ligated to index adapters following the Illumina protocol.

treatment_protocol: 1-week-old rices were treated mock or ABA for 6 hours

value: Shoot

value: osfkbp20-1b mutant

value: 100uM ABA for 6 hr


title: ABA_osfkbp20-1b_rep2


title: sample 01030 genomic DNA from T_cells at day 0 during course 1

value: male


title: A2

value: amniotic fluid

value: 17 days of pregnancy


title: sample 01016 genomic DNA from T_cells at day 0 during course 1

value: female


title: AN1.1_d7_snRNA-seq

value: AN1.1 hiPSC


title: sample 01015 genomic DNA from T_cells at day 0 during course 1


title: H9_d12_snATAC-seq

value: day 12


title: ABA_osfkbp20-1b_rep1


title: A3


title: sample 01012 genomic DNA from T_cells at day 0 during course 1


title: ABA_WT_rep3

value: wild type


title: A1


title: Patient 4 Right Atria Tissue

value: RA


title: Patient 4 Left Atria Tissue

value: LA


title: Patient 4 Left Ventricle Tissue

value: LV


title: sample 01007 genomic DNA from T_cells at day 0 during course 1


title: sample 01004 genomic DNA from T_cells at day 0 during course 1


title: H9_d12_snRNA-seq

value: Kidney organoid

value: H9 hESC


title: AN1.1_d12_snRNA-seq


title: AN1.1_d12_snATAC-seq


title: Patient 3 Left Ventricle Isolated Cells

source_name: Ventricle Isolated Cells

value: Ventricle Isolated Cells


title: Patient 3 Right Ventricle Isolated Cells

value: RV


title: H9_d16_snATAC-seq

value: day 16


title: ABA_WT_rep1

value: Shoot


title: ABA_WT_rep2

value: 100uM ABA for 6 hr


title: AN1.1_d7_snATAC-seq

value: day 7


title: Patient 2 Right Ventricle Isolated Cells


title: Mock_osfkbp20-1b_rep3

value: osfkbp20-1b mutant

value: mock


title: Mock_osfkbp20-1b_rep2


title: H9_d16_snRNA-seq


title: Patient 2 Left Ventricle Isolated Cells


title: H9_d19_snATAC-seq

value: day 19


title: sample 01001 genomic DNA from T_cells at day 0 during course 1

value: female


title: sample 31001 genomic DNA from blasts at day 15 during course 1

value: male

value: blasts


title: H9_d19_snRNA-seq


title: sample 26004 genomic DNA from blasts at day 15 during course 1


title: sample 26002 genomic DNA from blasts at day 15 during course 1


title: Patient 1 Left Ventricle Isolated Cells


title: Mock_osfkbp20-1b_rep1


title: AN1.1_d19_snATAC-seq

value: AN1.1 hiPSC


title: Patient 1 Right Ventricle Isolated cells


title: Mock_WT_rep3

value: wild type


title: Mock_WT_rep2


title: sample 25005 genomic DNA from blasts at day 15 during course 1


title: Heart 42 Day 60 MLC2V

source_name: pluripotent stem cell line

growth_protocol: Cells were routinely passaged as sigle cells for differentiation. When cultures reached 80% confluency cells were differentiated in monolayer following the left ventricle cardiomyocyte differentiation protocol.

treatment_protocol: Cells were collected at specific time points and therefore were subject to different treatments in keeping with the left ventricle differentiation protocol

value: pluripotent stem cell line

tag: experiment number


title: AN1.1_d19_snRNA-seq

value: Kidney organoid


title: sample 16005 genomic DNA from blasts at day 15 during course 1


title: Heart 42 Day 40 MLC2V


title: Heart 42 Day 20 MLC2V


title: sample 14008 genomic DNA from blasts at day 15 during course 1


title: sample 14007 genomic DNA from blasts at day 15 during course 1


title: Heart 42 Day 15 MLC2V


title: AN1.1_d26_snATAC-seq

value: day 26


title: sample 14001 genomic DNA from blasts at day 15 during course 1


title: Heart 42 Day 10 MLC2V


title: Heart 42 Day 6 MLC2V


title: AN1.1_d26_snRNA-seq


title: sample 11011 genomic DNA from blasts at day 15 during course 1


title: sample 04012 genomic DNA from blasts at day 15 during course 1


title: BJFF.6_d26_snATAC-seq

value: BJFF.6 hiPSC


title: BJFF.6_d26_snRNA-seq


title: Heart 42 Day 4 MLC2V


title: Control 6

first: Yang

last: Fuming

address: 汉口路22号南园21舍

institute: 南京大学

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Bone marrow

extract_protocol:
1uM dexamethasone (Sigma), and 0.5mM isobutylmethylxanthine (Sigma) in the presence of 10% FBS until day 2. Cells were then fed with DMEM supplemented with 10% FBS and 10ug/ml insulin for 2 days, after which they were fed every other day with DMEM containing 10% FBS
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: After tumor resection, 4T1 female Balbc mice were treated with Onway by gavage for 2 weeks, while the Control mice were not. Bone marrow cells of the mice were havested after treatment. We then performed gene expression profiling analysis using data obtained from RNA-seq of bone marrow cells .

value: Bone marrow

value: Bone marrow cells

value: WT

value: Gene expression in bone marrow cells

tag: treatment

value: Day 0


title: Control 5

tag: tissue


title: Onway 1

tag: cell type


title: Onway 3


title: Heart 42 Day 2 MLC2V


title: Mock_WT_rep1

value: Shoot


title: H9_d26_snATAC-seq

value: H9 hESC


title: sample 03005 genomic DNA from blasts at day 15 during course 1

tag: gender


title: sample 01999 genomic DNA from blasts at day 15 during course 1

tag: course


title: Heart 42 Day 0 MLC2V

tag: day


title: ORG-PT_cut-and-run_H3K4me3

data_processing:
FASTQ files were trimmed with Trim Galore (Cutadapt [v2.8]) and aligned with Bowtie2 (parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -I 10 -X 700) using hg38.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: Kidney organoid-derived proximal tubule cells

growth_protocol: Kidney organoids were generated by Takasato et al., 2016 (PMID: 27560173) with slight modifications. Proximal tubular cells were sorted as an LTL-positive population by flow cytometry and filtered through a 40-μm cell strainer.

extract_protocol:
Frozen human adult kidney cortex was cut into < 1 mm pieces, homogenized using a dounce tissue homogenizer, and incubated on ice for 3 min in chilled Nuclei EZ lysis buffer supplemented with protease inhibitor cocktail. The homogenate was filtered through a 40-μm cell strainer and centrifuged at 500 g for 5 minutes at 4°C. The pellet was resuspended and washed with chilled lysis buffer, and further incubated on ice for 3 minutes. Following centrifugation, the pellet was resuspended in XL wash buffer, and filtered through a 5-μm cell strainer. 500,000 isolated nuclei were fixed with 0.5% formalin for one minute at room temperature, followed by addition of glycine.  Sorted kidney organoid-derived proximal tubular cells were fixed with 0.5% formalin for one minute at room temperature. After inactivating unreacted aldehyde by adding glycine, 100,000 cells were treated with chilled multiome lysis buffer on ice for 5 minutes to obtain nuclei.
Libraries were generated with the CUTANA™ ChIC/CUT&RUN Kit (EpiCypher, 14-1048). Fixed nuclei were incubated with Concanavalin A (ConA) conjugated paramagnetic beads and stained with 0.5 µg of antibodies. The remaining steps were performed according to manufacturer’s instructions. Library preparation was performed using the NEBNext Multiplex Oligos for Illumina with manufacturer’s instructions, including minor modifications indicated by CUTANA described above. CUT&RUN libraries were sequenced on a NovaSeq instrument (Illumina, 150 bp paired-end reads).


title: H9_d26_snRNA-seq


title: Onway 2


title: sample 01888 genomic DNA from blasts at day 15 during course 1


title: flag_siXRN2_2

city: South Birmingham

first: Anindya

last: Dutta

state: AL

address: 720 20th Street South, Kaul 230

department: Genetics

institute: University of Alabama at Birmingham

description: small RNA

data_processing:
For small RNA-seq, adapters were removed with cutadapt (cutadapt -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -j 24 -m 14). Sequencing reads were mapped using unitas version 1.7.5 ( -species homo_sapiens -threads 24 -quick -species_miR_only -tail 0).
Assembly: hg38
Supplementary files format and content: Processed data include DESeq2 results for siXRN1/2 small RNA-seq (SupplementalTable2.xlsx) and the average expression values from DESeq2 for FH-Ago2 RIPseq (SupplementalTable3.xlsx).

source_name: Human Embryonic Kidney

growth_protocol: HEK293T cells were obtained from ATCC and grown in Dulbecco’s High Glucose Modified Eagles Medium supplemented with 10% FBS and penicillin/streptomycin.

extract_protocol:
RNA was extracted using Trizol following manufacturer's protocol.
Small RNA-seq library preparation was similar to previously described (Su et al. 2019) with addition of spike-in. Briefly, 1 ul (500 ul total volume) of Qiaseq miRNA library QC spike-in (Qiagen #331535) were mixed with 1 ug total RNAs before library preparation. The resulting libraries were size selected for 15-50 nt inserts, and pooled for sequencing on Illumina NextSeq500.

treatment_protocol: Cells were initially reverse transfected with specified siRNA and forward transfected 24 hours later using RNAiMAX following manufacturer's protocol. RNA was collected after a total of 72hours incubation with siRNA.

tag: sirna

tag: antibody

value: Anti-Flag M2


title: flag_siGL2_2

description: small RNA

tag: cell line


title: ORG-PT_cut-and-run_IgG

value: Kidney organoid-derived proximal tubule cells

value: anti-IgG


title: Heart 18 Day 40 MLC2V


title: input_siXRN2_2

description: small RNA


title: sample 01777 genomic DNA from blasts at day 15 during course 1

value: female

value: blasts


title: sample 01039 genomic DNA from blasts at day 15 during course 1

value: male


title: input_siGL2_2

description: small RNA


title: sample 01033 genomic DNA from blasts at day 15 during course 1


title: HAK_cut-and-run_H3K4me3

source_name: Human adult kidney cortex

value: Human adult kidney cortex

tag: Sex

value: Female

tag: age

tag: serum creatinine


title: Heart 18 Day 20 MLC2V

value: pluripotent stem cell line


title: Heart 18 Day 15 MLC2V


title: Heart 18 Day 10 MLC2V


title: HAK_cut-and-run_IgG


title: flag_siXRN2_1

description: small RNA


title: Control 4

tag: genotype


title: flag_siGL2_1

description: small RNA


title: ORG-PT_cut-and-run_H3K27Ac

value: AN1.1 hiPSC


title: Heart 18 Day 6 MLC2V


title: sample 01032 genomic DNA from blasts at day 15 during course 1


title: input_siXRN2_1

description: small RNA


title: Heart 18 Day 60 MLC2V


title: input_siGL2_1

description: small RNA


title: Patient 7 (samples 7.1, 7.2, 7.3), scRNAseq, CITE-Seq

city: Essen

first: Jürgen

middle: C

last: Becker

state: NRW

address: Universitätsstraße 1

department: Translational Skin Cancer Research

institute: Deutsches Krebsforschungszentrum

description:
Multiplexed single cell RNA count matrix and HTO expression matrix containing samples 7.1, 7.2 and 7.3
Patient 7 - library a

data_processing:
Processing from FASTQ files towards the unfiltered count matrix (barcodes x genes) was performed using Cellranger Software Suite version 3.1.0 and the human reference genome build GRCh38, downloaded from 10x Genomics in version 3.0.0.  Cells were identified from the barcodes by evaluation of four quality criteria: (1) number of unique molecular identifiers (UMIs), (2) number of genes, (3) percentage of mitochondrial gene expression and (4) number of expressed housekeeper genes, derived from Tirosh et al. without the mouse gene PRPS1L3. Evaluating these quality criteria and their relationship was inspired by the best practices of Theis et al.. We defined cells by having a minimum number of 500 UMIs and excluded cells with mitochondrial gene expression above 10%. The count matrix was processed using Seurat version 4.0.1 and R version 4.0.5. Cells were normalized using SCtransform algorithm and the 3000 most variable genes were selected for principal component analysis (PCA) using a single value decomposition approximation implemented in Seurat. Based on the variance explained by each PC we chose the first 20 PCs for UMAP visualization and clustering based on a K-nearest neighbor (KNN) graph as implemented in Seurat using resolution 0.8 .Cell types were identified using marker gene expression and differential gene expression of clusters that were merged based on their proximity in the UMAP. Malignant cells were additionally identified by inferred CNVs using inferCNV software suite version 1.6.0.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: raw barcode x feature matrix from cellranger output, features.tsv.gz: raw barcode x feature matrix from cellranger output, matrix.mtx.gz: raw barcode x feature matrix from cellranger output.
Transcriptome.csv: samples x genes matrix with unnormalized gene counts from EdgeSeq Reveal output; celltype_metadata.csv: Table with barcodes identified as cells and respective celltype annotation used through the scripts.
celltype_metadata.csv: Barcode and respective celltype annotation

source_name: mouth base left (primary tumor tissue)

extract_protocol:
Samples were processed immediately after surgery and temporarily stored for transport at 4°C in tissue storage solution (Miltenyi Biotec, Bergisch Gladbach, Germany) as previously described. Briefly, samples were dissociated into single-cell suspensions using the gentleMACS Dissociator (Cat. No. 130-093-235, Miltenyi Biotec, Bergisch Gladbach, Germany) with program “h_tumor_01”, followed by 2x program “h_tumor_02” in 4.7 ml RPMI 1640 (Cat. No. P04-16500 , PAN-Biotech) and an enzyme mix consisting of 200µl Enzyme H, 100 µl Enzyme R and 25 µl Enzyme A (Cat. No. 130-095-929 Miltenyi Biotec). Afterwards, single-cell suspensions were reconstituted and washed thrice with 0.05 % BSA phosphate-buffered saline (PBS) and filtered through a 100 µl cell strainer.
In cases multiple samples of one patient had to be analyzed, antibody hashing for multiplexing of samples was performed according to manufacturer’s protocol. Briefly, 1 µg of the respective TotalSeq anti-human hashtag antibody was used to incubate a maximum of  ca. 2 million cells for 30 min at 4 °C (Cat. No. 394601, 394603, 394605 and 394661, 394663, 394665, respectively, Biolegend, San Diego, CA, USA). After 3 washes with PBS with 0.05 % BSA respective cell suspensions were mixed prior to single-cell RNA library preparation. In short, both unhashed and hashed single-cell suspensions were barcoded and processed with the microfluidic system of 10x Genomics Chromium v2.0 platform as described in the manufacturer’s protocols (10x Genomics, Leiden, Netherlands). Due to a change of system, both the 3’ technology including Chromium Single Cell 3’ Library & Gel Bead Kit version 2 (Cat. No. 120237), Chromium Single Cell A Chip Kit (Cat. No. 120236), Chromium i7 Multiplex Kit (Cat. No. 120262) as well as the 5’ technology including Chromium Single Cell 5’ Library & Gel Bead Kits version 2 (Cat. No. 1000263), Chromium Next GEM Chip K Single Cell Kit (Cat. No. 1000286), Dual Index Kit TT set A (Cat. No. 1000215) were used; for library construction the Chromium Single Cell 3’/5’ Library Construction Kit (Cat. No. 1000020) was applied. After library preparation, the library from patient one was sequenced with an Illumina HiSeq 4000 (Illumina, Berlin, Germany) at the DKFZ Genomics and Proteomics Core Facility in Heidelberg and all other libraries were sequenced on an Illumina NovaSeq 6000 (Illumina, Berlin, Germany) in three runs (Run 1: patient 2,4,5; Run2: patient 3, Run3: Patient 6 and 7) at the West German Genome Center in Cologne.

value: mouth base left


title: Patient 7 (samples 7.4, 7.5, 7.6), scRNAseq, CITE-Seq

description:
Multiplexed single cell RNA count matrix and HTO expression matrix containing samples 7.4, 7.5 and 7.6
Patient 7 - library b


title: Patient 6 (samples 6.4, 6.5, 6.6), scRNAseq, CITE-Seq

description:
Multiplexed single cell RNA count matrix and HTO expression matrix containing samples 6.4, 6.5 and 6.6
Patient 6 - library b

source_name: tongue base left (primary tumor tissue)

value: tongue base left


title: Heart 18 Day 4 MLC2V


title: sample 01016 genomic DNA from blasts at day 15 during course 1


title: Heart 18 Day 2 MLC2V


title: siXRN1/2 rep2

description: small RNA


title: HAK_cut-and-run_H3K27Ac


title: sample 01015 genomic DNA from blasts at day 15 during course 1


title: Heart 18 Day 0 MLC2V


title: Patient 4 (samples 4.1, 4.2, 4.3), scRNAseq, CITE-Seq

description:
Multiplexed single cell RNA count matrix and HTO expression matrix containing samples 4.1, 4.2 and 4.3
Patient 4

source_name: edge of tongue left (primary tumor tissue)

value: edge of tongue left


title: Heart 41 Day 20 H9


title: Heart 41 Day 40 H9


title: siGL2 rep1

description: small RNA


title: Patient 5 (sample 5), scRNAseq

description:
single cell RNA count matrix
Patient 5

source_name: cheek left (primary tumor tissue)

value: cheek left


title: sample 01012 genomic DNA from blasts at day 15 during course 1

source_name: blasts


title: sample 01027 genomic DNA from blasts at day 15 during course 1


title: Patient 3 (sample 3), scRNAseq

description:
single cell RNA count matrix
Patient 3

source_name: soft palate left (primary tumor tissue)

value: soft palate left


title: siGL2 rep2

description: small RNA


title: Heart 41 Day 15 H9


title: Heart 41 Day 10 H9


title: sample 01013 genomic DNA from blasts at day 15 during course 1


title: Patient 2 (samples 2.1, 2.2, 2.3), scRNAseq, CITE-Seq

description:
Multiplexed single cell RNA count matrix and HTO expression matrix containing samples 2.1, 2.2 and 2.3
Patient 2

source_name: anterior mouth base (primary tumor tissue)

value: anterior mouth base


title: sample 01010 genomic DNA from blasts at day 15 during course 1


title: sample 01007 genomic DNA from blasts at day 15 during course 1


title: sample 01025 genomic DNA from blasts at day 15 during course 1


title: Heart 41 Day 6 H9


title: HEK293, ISO, 1.5h, n3

city: Geneva

first: Miriam

last: Stoeber

address: Rue Michel Servet 1

institute: University of Geneva

data_processing:
1.5h: Libraries generated for the 1.5 h treatment were sequenced using the Illumina NextSeq 500 or HiSeq 4000 devices with a single-end read length of 80-90 nucleotides yielding at least 3 millions mapped reads per sample. Sequences were mapped to the human genome GRC h38.12 using GENCODE v28 annotation with STAR v. 2.6.0c. Generated raw counts were normalized and genes with low expression were filtered out leaving 15,946 genes. Differential expression analyses and related statistics between control and treated conditions were conducted using the Limma-voom R package 3.38.2.
6h: libraries were sequenced using the Illumina HiSeq 4000 device with a single-end read length of 50 nucleotides yielding around 30 million mapped reads per sample. Fastq files were generated using Illumina bcl2fastq v. 2.20.0 and mapped to the human genome UCSC hg38 using STAR v. 2.7.0f. Aligned reads were quantified with the Python software htseq-count v. 0.9.1. Genes were filtered down to 14,467 after removal of low expressers and normalized using the R package EdgeR 3.28.1. Differential gene expression between control and DPDPE or ICI and ICI/SNC80 conditions was computed and statistics were performed using the General Linear Model, quasi-likelihood F-test (QL F-test) with FDR and Benjamini & Hochberg correction.
Assembly: GRC h38.12 (1.5h), UCSC hg38 (6h)
Supplementary files format and content: 1.5h: tab delimited text files including ensembl, hgnc, Log2FC, p-value, adj. p-value, description
Supplementary files format and content: 6h: tab delimited text file including hgnc, description, FC, p-value, adj. p-value, raw counts, normalized counts

source_name: HEK293 stably expressing DOR

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen), genomic DNA was removed using the RNase-free DNase kit (Qiagen) and samples analyzed using a bioanalyzer.
Multiplexed libraries for the 1.5 h samples were generated using the Lexogen QuantSeq 3' mRNA-Seq Library Prep Kit and for the 6 h samples using TruSeqHT Stranded Total RNA Library Prep protocol (Illumina).

value: HEK293 stably expressing DOR

value: Human embryonic kidney

value: ISO

tag: time point


title: sample 01004 genomic DNA from blasts at day 15 during course 1


title: GBM_BS

city: Philadelphia

first: Rahul

middle: M.

last: Kohli

state: Pennsylvania

address: 3610 Hamilton Walk, 502B Johnson Pavilion

department: Department of Medicine

institute: University of Pennsylvania

description: The sample is predominantly human tumor gDNA. There are 3 spike in control genomes (1:100 dilution) added to estimate conversion efficiencies of our pipeline.

data_processing:
Reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: hg19
Supplementary files format and content: A tab-delimited text files (.txt) include genomic coordinates (chr, start, and end) and BS-Seq or DM-Seq analysis (signal [C/(C+T)], sequencing coverage, and strand) of all annotated CpG sites in the human genome as well as control DNA genomes (pUC19, methylated lambda, T4-hmC).

source_name: glioblastoma tumor

extract_protocol:
Agencourt FormaPure Kit for tumor gDNA.
10 ng of sheared gDNA ligated to 5pyC-containing adapters was used as input for DM-Seq when only comparing to BS-Seq. For DM-Seq, a methylated copy strand was created. 1 μM fully-methylated copy primer was annealed in a total volume of 10 μL in CutSmart Buffer and 1 mM final concentration (individually) of dATP/dGTP/dTTP (Promega) and dmCTP (NEB). 1 μl or 8 units Bst polymerase, large fragment (NEB) was added and incubated for 30 min at 65°C. The 5hmCs were then glucosylated with 40 μM UDP-Glucose and 1 μL or 10 units of T4 Phage β-glucosyltransferase (NEB) for 1 hour at 37°C in a final volume of 20 μL. Incompletely copied or uncopied fragments were degraded with 1 μL or 10 units Mung Bean Nuclease (NEB) for 30 min at 30°C. After SPRI magnetic bead purification (1.2x), libraries were mixed with 0.5 μM MBP-M.MpeI-N374K and 160 μM CxSAM in carboxymethylation buffer (50 mM NaCl, 10 mM Tris-HCl pH 7.9, 10 mM EDTA) and incubated overnight at 37°C followed by  denaturation for 5 min at 95°C. 1 μL or 0.8 units of Proteinase K (NEB) was subsequently added and incubated at 37°C for 15 min. The samples were purified using SPRI magnetic beads (1.2x) and eluted in 1 mM Tris-Cl, pH 8.0. DNA was then subjected to snap-cooling and A3A deamination in a final volume of 50 μL as previously described before SPRI magnetic beads purification (1.2x). DM-Seq libraries were amplified using indexing primers (IDT) and HiFi HotStart Uracil+ Ready Mix (KAPA Biosystems) before purification over SPRI magnetic beads (0.8X). Libraries were then characterized using a BioAnalyzer (High Sensitivity Kit, Agilent) and quantified (Qubit).
BS-Seq was performed on 10 ng of sheared gDNA ligated to 5mC-containing adapters (xGen, IDT), when only comparing to DM-Seq, with no added copy or DM-Seq specific steps, using manufacturer instructions (Diagenode). Purified BS-Seq libraries were amplified using indexing primers (IDT) and HiFi HotStart Uracil+ Ready Mix (KAPA Biosystems) before purification over SPRI magnetic beads (0.8X) and ultimate characterization using a BioAnalyzer (High Sensitivity Kit, Agilent) and quantified (Qubit).

value: glioblastoma tumor

tag: grade

value: grade IV glioma


title: GBM_DM

data_processing:
Reads were quality and length trimmed with Trim Galore! Reads were aligned with Bismark and deduplicated with Picard. All data was analyzed single-end. DM-Seq reads were filtered if 3 consecutive CpHs were non-converted using Bismark’s existing filter_non_conversion command. Only reads with MAPQ ≥ 30 were analyzed.
Assembly: hg19
Supplementary files format and content: A tab-delimited text files (.txt) include genomic coordinates (chr, start, and end) and BS-Seq or DM-Seq analysis (signal [C/(C+T)], sequencing coverage, and strand) of all annotated CpG sites in the human genome as well as control DNA genomes (pUC19, methylated lambda, T4-hmC).
Library strategy: DM-Seq


title: LIPTER_KO_n_2

first: Lei

last: Yang

address: 1044 W Walnut Street, R4 272

institute: Indiana University School of Medicine

data_processing:
Quality control for raw mRNA-seq data was generated by FastQC v0.11.5
Illumina adapter sequences and low-quality bases were trimmed by Trim Galore v0.4.5
High-quality paired-end reads was mapped to human genome (hg38) with the aligner STAR v2.7.2b
bam-filter in ngsutilsj v0.4.8 (https://compgen.io/ngsutilsj) was used to keep only properly and uniquely mapped paired reads (MAPQ ≥ 10) for downstream analysis
FeatureCounts from package subread v1.6.5 was employed for quantification of gene expression by summarizing mapped reads to corresponding genes according to GENECODE v31 annotation.
Analysis of differential expression genes (DEGs) was performed by edgeR v3.32.1
Genome_build: hg38 or mm10
Supplementary_files_format_and_content: tab-delimited text files include with raw read counts for every gene and every sample by featureCounts

source_name: Cardiomyocytes

extract_protocol: Human RNA was extracted by using Qiagen RNeasy Mini Kit (Cat. 74104). Mouse heat tissue were homogenized by beadsbug homogenizer in Trizol, and then RNA was extracted by using Qiagen RNeasy Mini Kit (Cat. 74104).

value: iPSC derived cardiomyocytes

value: LIPTER KO


title: LIPTER_KO_n_1


title: Heart 41 Day 4 H9


title: Patient 6 (samples 6.1, 6.2, 6.3), scRNAseq, CITE-Seq

description:
Multiplexed single cell RNA count matrix and HTO expression matrix containing samples 6.1, 6.2 and 6.3
Patient 6 - library a


title: WT_2

value: WT


title: HEK293, ISO, 1.5h, n2


title: siXRN1/2 rep1

description: small RNA


title: WT_1