title: SAM24410225_EZH2i_Rep2

city: South San Francisco

first: Marc

last: Hafner

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

data_processing:
ATAC-seq reads were analyzed using the ENCODE ATAC-seq pipeline v1.8
Reads were trimmed of adapters by cutadapt (version 1.9.1) and mapped to hg38 by Bowtie2 (version 2.2.6).
Bam files were converted to tagAlign format, which was then adjusted for Tn5 by shifting +4 bp for positive strand and by −5bp for negative strand.
TagAlign files were used to call peaks using MACS2 (version 2.1.0). Peaks with p<1e-6 were retained for differential analysis.
Assembly: GRCh38
Supplementary files format and content: narrowPeak

source_name: pancreatic

extract_protocol:
cells were trypsinized, washed with 1× PBS, counted and processed for library prep
About 100,000 cells were then lysed for 5 minutes on ice in 100 mL of Lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20 and 0.01% digitonin). 1 ml of wash buffer (10 mM Tris, pH7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20) was then added and the pellets were spun down at 500 g for 10 minutes at 4 °C. The supernatant was discarded, and the pellet was resuspended in 50 mL of tagmentation buffer (25 µL 2× TD buffer, 16.5 mL PBS, 0.5 mL 10% tween 20, 0.5 mL of 1% Digitonin, 2.5 µL Tn5 transposase and 5 mL H2O). The tubes were incubated at 37 °C for 30 minutes, followed by DNA isolation using the Qiagen MinElute Cleanup Kit (Cat. No. 28206). The DNA was then amplified using NEBNext 2× PCR Master mix (Cat. No. M0541L) and analyzed by Tapestation High Sensitivity DNA kit (Agilent Technologies) before submitting for sequencing.

value: pancreatic

value: pancreatic cells

value: wt

value: 2uM EZH2i


title: C. elegans gonad, Worm3, Diplotene Loop

status: Public on Jul 01 2024

type: SRA

city: Charlotte

first: Yangqi

last: Su

state: NC

address: 9201 University City Blvd

department: Bioinformatics

country: USA

institute: UNC Charlotte

library_source: transcriptomic single cell

data_processing:
Prior to mapping, raw reads were trimmed with Trim Galore, with parameters (quality >= 10, length > 35bp)
For differential gene expression analysis, trimmed reads were mapped to the genome using HISAT2, raw counts obtained via HTSeq
The trimmed reads were also mapped to the genome using Salmon with default settings to obtain transcript per million (TPM) estimates for both genes and transcripts
Assembly: WBcel235, GCA_000002985.3
Supplementary files format and content: tab delimited file containing HISAT aligned, HTSeq raw counts for all samples/genes
Supplementary files format and content: tab delimited file containing salmon estimated raw counts for all samples/genes
Supplementary files format and content: tab delimited file containing mapping and quality control metrics for all samples

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: gonad

extract_protocol:
a cut was made across the vulva using a 26G subcutaneous needle controlled by a micromanipulator (ROE-200, Sutter) under an inverted microscope (Olympus 1X71). This would release fertilized eggs and early-stage embryos from the uterus as well as sperms and at least portions of the two sides of the gonad. Each end of the gonad wrapped around by five pairs of sheath cells was completely isolated by pushing its distal end. The distal proliferative zone (S1) was cut off around the transition zone and harvested in about 10 nl bath solution by suction using a patch clamp pipette under controlled of another micromanipulator (ROE-200, Sutter). The pachytene zone (S2), the loop corresponding to the diplotene zone (S3) and diakinesis zone (S4) were sequentially cut off and similarly harvested. The -3 (F3), -2 (F2), and -1 (F1) oocytes were also isolated by cutting through their boundaries and similarly harvested. The zygote (fertilized oocyte) also known as P0 was similarly harvested when the two pronuclei were fused at its center.
We prepare a RNA-seq library for each harvested sample for Illumina platforms using a modified scRNA-seq method based on Tang et al or using the Smart-seq2 protocol

treatment_protocol: a well-fed gravid hermaphrodite was immobilized in the egg salt solution (ESS) with 10% tetramisole (Sigma, St. Louis)

tag: tissue

value: gonad

tag: section

value: Diplotene Loop

tag: group


title: 4T1, Day4, single cell 145

city: Beijing

first: Hanqiu

last: Zheng

address: Haidian District

country: China

institute: Tsinghua university

data_processing:
Raw reads were first analyzed for quality control using FastQC (v0.11.7) (Andrews, 2010). Adaptor sequences of raw reads were removed by using TrimGalore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore). Trimmed reads were mapped to a concatenated mouse genome (mm10) with STAR (v2.6.0c) with default parameters to result SAM format files (Dobin et al., 2013). Aligned reads stored in SAM format were transformed to generate BAM files using SAMtools (v1.7) (Danecek et al., 2021). The gene-level read count matrix was summarized from BAM files using FeatureCounts program (v1.6.2) (Liao et al., 2014). Subsequent data analysis was carried out in R 3.6.2 and the Seurat package (v3.1.2) (Stuart et al., 2019).
The gene counts per cell, the percentage of mitochondrial transcripts, the percentage of ERCC RNA spike-in, the percentage of α and β-globin genes were computed using the functions of the Seurat package. Quality controls were performed following: a. Cells with luciferase or GFP sequence detected were kept for further analysis. b. Cells with transcripts counts lower than 5 × 105 or higher than 1 ×107 were discarded. c. Single cell libraries with number of detected gene lower than 5,000, mapping rate lower than 40% or the percentage of mitochondrial transcripts higher than 10% were discarded before further analysis. d. Libraries with the percentage of α and β-globin genes higher than 1% were also discarded. 424 single cells passed quality controls, and were used for further analysis. The gene expression level was normalized as log2(TPM/10 + 1), in which TPM is the abbreviation for transcripts per million, and adding one to avoid negative expression values.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

extract_protocol:
Reverse transcription and cDNA amplification were carried out using a modified Smart-seq2 protocol (Picelli et al., 2014). Single cells were sorted by FACS as described above into 96-well plates containing 0.1 μl of RNase inhibitor (Clontech, Cat# 2313A), 1.9 μl of 0.2% Triton X-100 (Sigma, Cat# T9284), 1 μl of 10 µM oligo-dT primer (5′-AAGCAGTGGTATCA ACGCAGAGTAC T30VN-3′) and 1 μl of dNTP mix (10 mM each; Fermentas, Cat# R0192) in each well. Plates were either stored at -80 °C or processed immediately. Reverse transcription, PCR preamplification, PCR purification were performed following Picelli’s protocol (Picelli et al., 2014). As mRNA quality control, 1 ul of each PCR product was used as template for qPCR detection of mCherry expression and samples with Ct value higher than 30 will be discard. PCR products were purified with 1 × Agencourt Ampure XP beads (Beckman Coulter, Cat# A63881) and the final product was reconstituted in 20 µl TE buffer. The concentration of cDNA was measured by Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kit (Invitrogen, Cat# Q33230). Tagmentation and NGS library was carried out by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD503) following the manufacturer’s instructions. The purified library was qualify controlled by measuring the fragment size distribution with an Agilent HS DNA BioAnalyzer Chip and the concentration of library was measured with Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kits following the manufacturer’s instructions. Single cell cDNA libraries were sequenced on an Illumina HiSeq X Ten platform to obtain paired-end 150-bp reads.
SMART-Seq2 (Picelli et al., 2014)

tag: host

value: Female BALB/c mice

tag: cell line

tag: cell type

value: metastatic tumor cells


title: C. elegans gonad, Worm3, Diakinesis

value: Diakinesis


title: SKMEL28 cells, shLuc, day 3,  biological replicate 1

city: Istanbul

first: Tolga

last: Emre

address: Bogazici University, Kuzey Kampus, Kuzey Park Binasi, No 203

country: Turkey

institute: Bogazici University

library_source: transcriptomic

data_processing:
Reads were aligned with TopHat V2.0.8 and selection of uniquely mapped reads were done with samtools
To quantify mapped reads and determine differentially expressed gene Cuffdiff v2.1.1 software was used.
cuffdiff output was visualized using CummeRbund R package with R v3.0.1
Assembly: GRCh37/hg19 (Feb. 2009 )
Supplementary files format and content: tab-delimited text files include normalized counts for each sample

organism: Homo sapiens

growth_protocol: SKMEL28 and SKMEL5 cells were maintained in DMEM supplied with 10% FBS, non-essential amino acids, and antibiotics in an incubator at 37°C and 5% CO2

extract_protocol:
RNA was extracted using the Roche High Pure RNA Isolation kit. 1.1 mg total RNA  was used for generating RNA-seq libraries
TruSeq RNA Sample Preparation Kit was used for library preparation step. Briefly, library preparation starts with purification of mRNA by poly-A selection using oligo-dT attached magnetic beads. Following purification, mRNAs are fragmented and copied into first strand cDNA by using random hexamers. Then second strand cDNA synthesis is performed. End repair and addition of adenine base follows the procedure. At the end, adaptors with barcodes are ligated and products are enriched with PCR.

value: melanoma

tag: genotype

value: shLuc(Control)

tag: treatment

value: lentiviral transduction


title: SAM24410223_DMSO_Rep2

state: CA

library_source: genomic

molecule: genomic DNA

value: DMSO


title: C. elegans gonad, Worm3, Pachytene Zone

value: Pachytene Zone


title: SAM24410222_DMSO_Rep1


title: C. elegans gonad, Worm5, Mitotic Region and Transition Zone

value: Mitotic Region and Transition Zone


title: 4T1, Day4, single cell 144


title: C. elegans gonad, Worm3, Mitotic Region and Transition Zone


title: control 3

city: Yangzhou

first: Dunmin

last: She

state: CHINA

address: 98，Western Nantong

department: Endocrinology

institute: Northern Jiangsu People’s Hospital

description: single-cell RNA

data_processing:
Reads mapping, sample merge and single-cell counting was performed using the Cell Ranger Single-Cell Software Suite (10x Genomics).
Cell ranger count was used to align samples to the reference genome (GRCh38, download from 10xgenomics.com).
The Seurat package in R was used for subsequent analysis. For quality control, nuclei with mitochondrial content >15% were removed.
Principal component analysis was performed prior to clustering and the first 20 principal components were used based on the Elbow Plot.
Genome_build: GRCh38

molecule: total RNA

source_name: peripheral blood

extract_protocol:
PBMCs were isolated from PB using Ficoll Hypaque gradient centrifugation
PCR products were purified and library quality was assessed on the Agilent Bioanalyzer 2100 system. Then, the library preparations were sequenced on an Illumina platform and 125 bp /150 bp paired-end reads were generated.

value: peripheral blood

tag: disease state

value: Health control

value: untreated


title: control 2

description: single-cell RNA


title: SAM24409814_LACZ_Rep1

value: pancreatic

tag: stable cell_line_expressing_wt_brg1

value: pancreatic cells

value: stable cell line expressing LACZ


title: 4T1, Day4, single cell 143


title: control 1

description: single-cell RNA


title: 4T1, Day4, single cell 142


title: SAM24410224_EZH2i_Rep1

value: wt

value: 2uM EZH2i


title: C. elegans gonad, Worm2, -2 Oocyte

value: gonad

value: -2 Oocyte


title: SNU668 WT

type: RNA

city: Suwon

first: Tae Hoon

last: Kim

address: 206, World cup-ro, Yeongtong-gu

department: surgery

country: South Korea

institute: Ajou university

description: Gene expression data from human gastric cancer cell

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour.

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC).

label: biotin-labeled with TdT

source_name: Human gastric cancer cell

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit.

growth_protocol: SNU668 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C. CAFs were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C.

extract_protocol: RNA was harvested using Rneasy mini kit (Qiagen). 1ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: SNU668 cells were treated with recombinant human GAS6 protein.

value: human gastric cancer cell


title: FOP 3

description: single-cell RNA

value: fibrodysplasia ossificans progressiva


title: 4T1, Day4, single cell 140

value: Female BALB/c mice

value: metastatic tumor cells


title: SAM24409812_TM_Rep1

value: stable cell line expressing TM BRG1


title: C. elegans gonad, Worm2, Diplotene Loop

value: Diplotene Loop


title: C. elegans gonad, Worm2, -1 Oocyte

value: -1 Oocyte


title: SAM24409811_KR_Rep2

value: stable cell line expressing KR BRG1


title: 4T1, Day4, single cell 139


title: FOP 1

description: single-cell RNA

value: peripheral blood


title: FOP 2

description: single-cell RNA

value: untreated


title: SAM24409810_KR_Rep1

value: pancreatic


title: 4T1, Day4, single cell 138


title: C. elegans gonad, Worm2, Pachytene Zone

value: Pachytene Zone


title: SAM24409809_WT_Rep2

value: pancreatic cells

value: stable cell line expressing WT BRG1


title: C. elegans gonad, Worm2, Mitotic Region and Transition Zone

value: Mitotic Region and Transition Zone


title: SAM24409815_LACZ_Rep2

value: stable cell line expressing LACZ


title: C. elegans gonad, Worm2, Diakinesis

value: gonad

value: Diakinesis


title: SAM24409813_TM_Rep2


title: 4T1, Day4, single cell 137


title: 4T1, Day4, single cell 141


title: SAM24409808_WT_Rep1


title: C. elegans gonad, Worm2, Zygote

value: Zygote


title: NC1

data_processing:
RNA samples from three FOP patients and three health controls were sequenced using a standard Illumina protocol.
Reads were mapped to a human genome (hg19) by using hisat2 (v2.1).
Gene counts were estimated by HTSeq (0.11).
Genome_build: hg19
Supplementary_files_format_and_content: text with raw gene counts for every gene and every sample

extract_protocol:
1 ml whole blood from each subject was collected in the occipital sinus in EDTA tubes. After centrifugation, 250 μL of blood was diluted in a tube containing 750 μL of TRIzol® reagent (Sigma, USA, T9294). Total RNA was extracted according to the manufacturer's instructions and resuspended in 50 μL of H2O.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Healthy control


title: FOP3

value: fibrodysplasia ossificans progressiva


title: 4T1, Day4, single cell 136

value: Female BALB/c mice

value: metastatic tumor cells


title: SAM24406901_EZH2i_Rep2

value: wt

value: 2uM EZH2i


title: 4T1, Day4, single cell 135


title: SAM24406900_EZH2i_Rep1


title: FOP2

value: peripheral blood


title: C. elegans gonad, Worm1, Diakinesis


title: FOP1


title: C. elegans gonad, Worm1, -1 Oocyte

value: -1 Oocyte


title: C. elegans gonad, Worm1, Diplotene Loop

value: Diplotene Loop


title: 4T1, Day4, single cell 134


title: C. elegans gonad, Worm1, Pachytene Zone

value: Pachytene Zone


title: SAM24406898_DMSO_Rep1

value: pancreatic

value: pancreatic cells

value: DMSO


title: 4T1, Day4, single cell 132


title: RD-ES

city: Guangzhou

first: yang

last: yang

address: 58, Zhongshan Road II, Guangzhou

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.4
Filtering steps were as follows: 1) Remove reads with adapters; 2) Remove reads in which unknown bases were more than 10%; 3) Remove low quality reads (which were defined as reads having more than 50% bases with quality value <= 20).
ChIP-Seq reads were aligned to the NCBI human reference genome build 37 (GRCh37/assembly hg19) using soap2
Peaks were called using MACS (Model-based Analysis for ChIP-seq; version 1.4.2) with a p-value < le-05
Genome_build: GRCh37/assembly hg19
Supplementary_files_format_and_content: The result was stored in wiggle files

source_name: Ewing sarcoma cells

growth_protocol: RD-ES cells were cultured in high-glucose Dulbecco’s Modified Eagle Medium (DMEM; Gibco, USA) supplemented with 15% fetal bovine serum (FBS, Gibco) in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RD-ES cells were chemically crosslinked and sonicated to generate fractionated genomic DNA (gDNA) with fragment sizes of 100–500 bp. Sonicated chromatin was incubated with anti-HDGF antibody (Abcam, ab128921) coupled to Protein G beads (Dynabeads) overnight at 4°C.
For library preparation, the DNA fragments were blunt end-repaired, 3'-dA-tailed, and ligated to the Illumina adaptors according to the manufacturer’s instructions (Illumina DNA Sample Prep kit). After adapter ligation, DNA was PCR amplified, size selected (usually 100-300bp, including adaptor sequence), and sequenced on an Illumina HiSeq 2000 Genome Analyzer.

treatment_protocol: untreated

value: bone

value: untreated

tag: chip antibody

value: HDGF (Abcam, lot ab128921)


title: C. elegans gonad, Worm1, Mitotic Region and Transition Zone

value: gonad

value: Mitotic Region and Transition Zone


title: SAM24406792_EZH2i_Rep3

data_processing:
RNA-Seq reads were first aligned to ribosomal RNA sequences to remove ribosomal reads
remaining reads were aligned to the human reference genome (GRCh38) using GSNAP version 2013-11-1, allowing a maximum of two mismatches per 75 base sequence (parameters: ‘-M 2 -n 10 -B 2 -i 1 -N 1 -w 200000 -E 1 —pairmax-rna=200000—clip-overlap)
To quantify gene expression levels, the number of reads mapped to the exons of each RefSeq gene was calculated.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file that include gene counts for each sample

extract_protocol:
cells were trypsinized, washed with 1× PBS, counted and RNA was extracted using Qiagen RNeasy Plus Mini kit (Cat. No. 74034),
For sequencing library generation, the Truseq Stranded mRNA kit (Illumina) was used with an input of 100-1000 nanograms of total RNA. Libraries were quantified with Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific) and the average library size was determined using D1000 ScreenTape on TapeStation 4200 (Agilent Technologies). Libraries were pooled and sequenced on NovaSeq 6000 (Illumina) to generate 30 million single-end 50-base pair reads for each sample.

value: WT


title: 4T1, Day4, single cell 131

value: Female BALB/c mice


title: SAM24406791_EZH2i_Rep2


title: C. elegans gonad, Unkown Worm B, Zygote

value: Zygote


title: 4T1, Day4, single cell 130

value: metastatic tumor cells


title: C. elegans gonad, Unkown Worm A, Zygote


title: C. elegans gonad, WormJ, -3 Oocyte

value: -3 Oocyte


title: 4T1, Day4, single cell 128


title: 4T1, Day4, single cell 129


title: SAM24406790_EZH2i_Rep1

value: 2uM EZH2i


title: SAM24406789_DMSO_Rep3


title: SAM24406899_DMSO_Rep2

value: wt


title: SAM24406788_DMSO_Rep2


title: 4T1, Day4, single cell 133


title: Whole Blood, Lane 2, scRNAseq

city: Cambridge

first: Charles

middle: Ara

last: Demurjian

state: MA

address: 31 Ames Street

institute: BioMicro Center at MIT

description: scRNA - 10x genomics

data_processing:
LMO barcode and gene expression count matrices were analyzed using R (v4.0.3) and Seurat (v4.0.0). Cells were identified using emptyDrops (DropletUtils) were demuxed using HTODemux (Seurat) and hashedDrops (DropletUtils). Each lane was subject to demultiplexing and quality control separately then merged for downstream analyses. Cells with less than 300 unique genes detected were excluded. Additional cells were excluded based on the assessment of cluster-specific technical metrics (percent of mitochondrial reads per cell and number of UMIs per cell). Counts were normalized using the default parameters from NormalizeData (Seurat), i.e. scaling by 10,000 and log normalization. 3,000 variable features were used for PCA. SLM clustering was performed using FindClusters (Seurat) on the shared nearest neighbor graph generated from FindNeighbors (Seurat) using 30 principal components and k=20. Cell type annotation was based on expert annotation and predicted cell type labels from the PBMC dataset in Azimuth using FindTransferAnchors and TransferData (Seurat). Marker gene statistics were calculated using wilcoxauc (presto). Genes consistently increased following 24c5 SEHFST LS antibody treatment were defined as those: (i) with a Mann-Whitney p-value < 0.1 and a log2 fold change greater than 0.25 compared to either the 24c5 IgG1 or no Ab condition, (ii) detected in a minimum fraction of 0.1 cells in either of the two conditions, and (iii) with a log2 fold change greater than 0 compared to both the 24c5 IgG1 and no Ab conditions. Genes consistently decreased following 24c5 SEHFST LS antibody treatment were defined as those: (i)with a Mann-Whitney p-value < 0.1 and a log2 fold change less than -0.25 compared to either the 24c5 IgG1 or no Ab conditions, (ii) detected in a minimum fraction of 0.1 cells in either of the two conditions, and (iii) a log2 fold change less than 0 compared to both the 24c5 IgG1 and no Ab conditions.
Assembly: GRCh38
Supplementary files format and content: Tab separated values files and original H5 outputs

source_name: Blood

growth_protocol: Whole-blood from healthy 3 human donors was collected the day of the experiment in acid citrate dextrose anti-coagulant tubes.

extract_protocol:
Blood from each donor was added at a 1:9 ratio to ACK lysis buffer (Quality Biological, 10128-802) and incubated for 10min at RT. Cells were centrifuged at 400g for 5min, and the supernatant was discarded. 10mL of ACK lysis buffer was added to the cell pellet to repeat the lysis procedure. Cells were centrifuged at 400g for 5min, and the supernatant was discarded. Samples were washed twice with PBS buffer and counted before MULTI-seq barcoding
In brief, samples were barcoded with 2.5μM of the LMO anchor and barcode for 5min on ice in PBS before adding 2.5μM of the LMO co-anchor and incubating for an additional 5min. Samples were quenched with 1% BSA in PBS and washed once. Samples were pooled and 0.5U/μL RNase inhibitor (Roche) was added. Pooled samples were then loaded into two lanes using the 10X Genomics NextGEM Single Cell 3’ kit v3.1 per the manufacturer’s protocol. cDNA was inactivated at 95°C for 15min prior to biosafety level 3 removal for library construction. Libraries were sequenced on a NextSeq500 (Illumina). FASTQ files were processed using CellRanger v6.1.2 to generate gene expression count matrices and deMULTIplex to generate LMO barcode count matrices.

treatment_protocol: Blood was infected with Mtb and treated with antibodies.

value: Blood

value: Mix

value: 24c5 IgG1, 24c5 SEHFST LS, No Ab, and Uninfected


title: Whole Blood, Lane 1, scRNAseq

description: scRNA - 10x genomics


title: C. elegans gonad, WormJ, Diakinesis

value: Diakinesis


title: 4T1, Day4, single cell 127


title: SAM24406787_DMSO_Rep1

value: pancreatic

value: pancreatic cells

value: DMSO


title: C. elegans gonad, WormI, Diakinesis


title: 4T1, Day4, single cell 126


title: siSOX9 TGFB1 ATAC-seq

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer

data_processing:
All reads were mapped to the hg19/GRCh37 genome using the BWA-MEM aligner version 0.7.13.
BAM files were filtered using the encode_task_filter.py script from the ENCODE chip-seq-pipeline2.
MACS2 was used to call peaks using the parameters “-p 0.01 -f BAMPE  -g hs” for the CUT&RUN and CUT&Tag data, and “-p 0.01 -g hs --nomodel --shift -75 --extsize 150” for the ATAC-seq data.
Bigwig files were generated from the filtered BAM files using MACS2 bdgcmp using the fold enrichment option for the ATAC-seq data and deepTools bamCoverage with the options "--binSize 1 --normalizeUsing RPGC --effectiveGenomeSize 2864785220 --extendReads" for the CUT&Tag and CUT&RUN data
Assembly: hg19/GRCh37
Supplementary files format and content: tracks in BigWig file format

source_name: cell line

growth_protocol: A549 Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
For ChIP-seq 10 million cells per experiment were harvested and crosslinked with 1% formaldehyde. Crosslinked cells were lysed and homogenized using a Dounce homogenizer. Nuclei were lysed and sonicated to shear chromatin. Chromatin was incubated with antibody and beads. For ATAC-seq 100 000 cells per experiment were harvested and lysed and nuclei pelleted. Nuclei were incubated with Tn5 transposase.
For ChIP seq NEBnext DNA Ultra ii (New England Biolabs) was used to generate libraries according to the manufacturers protocol. For ATAC-seq libraries were generated generated using Ad1_noMX and Ad2.1–2.4 barcoded primers from Buenrostro et al. 2013 and NEBNext High-Fidelity 2X PCR Master Mix for a total of 10 cycles.

value: cell line

value: Lung adenocarcinoma

value: transfection siSOX9 and TGFB1 treatment


title: C. elegans gonad, WormH, Diakinesis

value: gonad


title: NC3

value: peripheral blood

value: Healthy control


title: 4T1, Day4, single cell 125

value: Female BALB/c mice

value: metastatic tumor cells


title: siSOX9 ATAC-seq

value: transfection siSOX9


title: SAM24402063_BRM_nodox

library_source: genomic single cell

data_processing:
Cell Ranger ARC (10X Genomics) was used to demultiplex BCL files into FASTQ files (cellranger-arc mkfastq command), align sequencing reads to the human genome (GRCh38), filter reads, call peaks, and generate counts for cell barcodes and UMIs (cellranger-arc count command).
Single cell ATAC data (fragment files) produced by Cell Ranger ARC were imported into ArchR version 1.0.2 for processing. Arrow files were created (using ArchR’s createArrowFiles function) for each sample, filtering for cells with a minimum transcription start site (TSS) enrichment score of 4 and a minimum of 1,000 unique mapped fragments. Computed gene scores were also generated for each Arrow file and stored in a GeneScoreMatrix. An ArchR project was created from the Arrow files for the two treatment groups of interest (naïve and dox-induced) for downstream analysis. Doublets were inferred and removed using ArchR’s addDoubletScores and filterDoublets functions. Iterative latent semantic indexing was performed with ArchR’s addIterativeLSI function to reduce dimensionality, and clusters were assigned with the addClusters function, which used the graph clustering approach implemented by Seurat. Doxycycline-treated cells were annotated by their BRM expression status assigned in the gene expression data, and uniform manifold approximation and projection (UMAP) results were generated by running the addUMAP and plotEmbedding functions of ArchR.
Pseudo-bulk replicates were generated using the addGroupCoverages function of ArchR for each cluster. Peaks were then called via MACS2 using ArchR’s addReproduciblePeakSet function, creating a PeakMatrix. Marker peaks were retrieved using the getMarkerFeatures function, accounting for bias from TSS enrichment and number of unique fragments per cell, as recommended by ArchR. Pairwise comparison of peaks between the naïve and doxycycline-treated samples was done via a Wilcoxon rank-sum test using the same getMarkerFeatures function, and peaks with abs(Log2FC) > 1 and FDR < 0.01 were visualized in color on volcano plots. P-values were adjusted for multiple hypothesis testing using the Benjamini-Hochberg method.
Assembly: GRCh38
Supplementary files format and content: The tsv files contain the unique ATAC-seq fragments and related index information.
Supplementary files format and content: The zipped folder contains the ArchR project, with Arrow files, for use with ArchR.

extract_protocol:
Cultured cells were trypsinized into single cell suspensions, counted using the Vi-CELL XR cell counter (Beckman Coulter) and nuclei were isolated based on the 10x demonstrated protocol (CG000365_DemonstratedProtocol_NucleiIsolation_ATAC_GEX_Sequencing_RevC.pdf).
The nuclei were processed and libraries were constructed using the Chromium Single Cell Multiome ATAC + Gene Expression Reagent Kit (10x Genomics, Cat. No. 1000285) as per the manufacturer’s recommendations. Accessibility and expression libraries were profiled using the Tapestation High Sensitivity DNA kit (Agilent Technologies) and quantified with the Kapa Library Quantification Kit (Kapa Biosystems).

value: stable cell line expressing dox-inducible BRM

value: untreated


title: SAM24402064_BRM_dox

value: 2ug/ml Doxycycline


title: 4T1, Day4, single cell 124


title: A549 replicate2

city: lille

first: frédéric

last: leprêtre

address: Boulevard du Pr Leclercq

department: CHU of Lille, CBP

country: France

institute: Lille University

description: CD43 expression consequences inA549 cells, replicate2

hyb_protocol: Agilent-026652 Whole Human Genome Microarray 4x44K were scanned on an Agilent G2505C scanner.

scan_protocol: Images were quantified using Agilent Feature Extraction Software (version V.10.7.3.1).

data_processing: Agilent Feature Extraction Software (v.10.7.3.1) was used for background subtraction and LOWESS normalization.

source_name: CD43 expression consequences in A549 cells

label_protocol: manufacturer's instructions

growth_protocol: A549 cells were grown as described by the American Type Culture Collection (Manassas, VA) with the addition of 0.5 mg/ml puromycin

extract_protocol: Total RNA extracted using manufacturer's instructions

treatment_protocol: A549 cells were infected with SMARTvector™ shRNA lentivirus particles constitutively expressing siRNA that did not target any known human gene. This non-targeting, control siRNA had the sequence CACACAACAUGUAAACCAGGGA  (Horizon Discovery, Ltd., Waterbeach, UK). A549 cells were also simultaneously infected with three lentiviruses that expressed siRNA targeting human CD43 mRNA at the coding sequence GUACACCACUUCAAUAACA and the 3' non-coding sequences GGCAGUUGGUAUUUCCCGA and AGAGCUGAGGAUUUGGCGA (Horozon Discovery, Ltd.). Since each siRNA gene contained within the lentiviruses was linked to a puromycin resistance gene, resistance to this antibiotic  was used to select for stable siRNA expression. The concentration of puromycin used for selection had previously been found to be the minimum required to kill 100% of parental A549 when added to actively growing cultures.  gcacuaccagaagcuaacucagauaguacu (OriGene Technologies, Inc., Rockville, MD). MDA-MB-231were also stably transfected with four linearized pRFP-C-RS plasmids expressing shRNA targeting human CD43 mRNA at the coding strand sequences acaccgugacagguggaaccauaacaacg, acgcucaccacuuucuuuggcagacggaa, gagccaacaaccuaccaggaaguuuccau and uggcaacugacucucuggagaccuccacu (OriGene Technologies, Inc.).

tag: knockdown


title: A549 replicate1

description: CD43 expression consequences inA549 cells, replicate1


title: C. elegans gonad, WormH, -3 Oocyte

value: -3 Oocyte


title: A549 replicate3

description: CD43 expression consequences inA549 cells, replicate3


title: siCtrl TGFB1 ATAC-seq

value: transfection siCtrl and TGFB1 treatment


title: A549 replicate4

description: CD43 expression consequences inA549 cells, replicate4


title: C. elegans gonad, WormH, -2 Oocyte

value: -2 Oocyte


title: SAM24402087_BRM_dox

data_processing:
Cell Ranger ARC (10X Genomics) was used to demultiplex BCL files into FASTQ files (cellranger-arc mkfastq command), align sequencing reads to the human genome (GRCh38), filter reads, call peaks, and generate counts for cell barcodes and UMIs (cellranger-arc count command).
Gene expression data produced by Cell Ranger ARC v2.0.1 were imported into Scanpy version 1.9.1, and data were filtered based on the following criteria: cells with a minimum of 200 genes expressed, genes detected in at least 3 cells, cells with minimum 5% and maximum 20% total counts from mitochondrial genes, and cells with a range of 1,000 to 10,000 genes with non-zero counts. Data were concatenated into a single AnnData object. Data was filtered for single cells using Scrublet version 0.2.3, with an expected doublet rate of 0.06 and threshold of 0.4 (https://github.com/swolock/scrublet). Data was logarithmized and normalized (counts per 1x104). Principal component analysis was then run on the highly variable genes. Data across samples were harmonized using Harmonypy version 0.0.6 (https://github.com/slowkow/harmonypy) before using the top 40 principal components to compute a neighborhood graph. Scores for the S and G2M cell cycle phases were calculated with the score_genes_cell_cycle function from Scanpy using canonical markers. These scores were used to regress out cell cycle phase expression signatures using Scanpy’s regress_out function. Leiden and Louvain clustering were performed using Scanpy’s implementation of Leiden community detection and the Louvain algorithm, both with a resolution of 0.5. Cells were scored for gene signatures using Scanpy’s tl.score_genes function. Due to doxycycline treatment inducing BRM overexpression in only a subset of cells, doxycycline-treated cells were subdivided by BRM expression status (“BRM_low” vs. “BRM_high” expressors) based on Louvain clusters for subsequent analysis of this subset. Louvain clusters were used for subdivision of cells in order to focus on the BRM-overexpressing cells which cluster away from the naïve cells.
Assembly: GRCh38
Supplementary files format and content: The tsv and mtx files contains the cell barcode and gene counts.
Supplementary files format and content: The NGS3789_BRM_expression_status.csv file contains the BRM expression status annotation per cell. NGS3789_cell_density.csv contains the density values per cell. NGS3789_umap_coordinates.csv contains the UMAP coordinates per cell. NGS3789_louvain_clusters.csv contains the louvain cluster assignment per cell.
Library strategy: single-cell multiomics

molecule: nuclear RNA

value: pancreatic

value: pancreatic cells


title: 4T1, Day4, single cell 123


title: C. elegans gonad, WormG, -2 Oocyte


title: siCtrl ATAC-seq

value: cell line

value: transfection siCtrl


title: SAM24402086_BRM_nodox


title: C. elegans gonad, WormG, -1 Oocyte

value: -1 Oocyte


title: A2780 cells,IgG,Jackson

city: Hefei

first: 丛蓉

last: 李

address: 安徽医科大学东校区弘毅楼1202室

institute: Nanjing Medical university

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System  using TruSeq PE Cluster Kit v3-cBot-HS (Illumina) according to the manufacturer’s instructions. The library preparations weresequenced on Illumina Novaseq platform at Tianjin Novogene  Bioinformatic Technology Co., Ltd. (Beijing, China) and 150 bp paired-end reads were generated.
Raw data (raw reads) of fastq format were firstly processed using fastp[2] (version 0.20.0). In this  step, clean data (clean reads) were obtained by removing reads containing adapter, reads  containing ploy-N and low-quality reads from raw data. At the same time, Q20, Q30 and GC  content of the clean data were calculated. All the downstream analyses were based on the clean  data
Briefly, paired-end reads were aligned to GRCh38p13 (https://ftp.ebi.ac.uk/pub/databases/gencode/ Gencode_human/release_40/GRCh38.p13.genome.fa.gz) using bowtie2 (v2.4.1).
Bigwig file, which is used for the display of dense, continuous data as a graph, was generated by the bam-Coverage command in deepTools (v3.3.0) software, during which the CPM normalization method was involved.
And , IGV (IGV: Integrative Genomics Viewer) was used for visualization.
Assembly: hg38
Supplementary files format and content: Bigwig , narrowPeak
Library strategy: CUT&Tag

growth_protocol: A2780 human ovary carcinoma cells were cultured in DMEM with 10% FBS and antibiotics in humidified atmosphere with 5%CO2 at 37°C

extract_protocol:
Take out the cryovial and shake it in 37°C water to quickly thaw it within 1-2min.Cells were  centrifuged for 5 min at 600×g at 4 ℃ Cell activity was detected with LUNA-FL and counted.
The Hyperactive Universal CUT&Tag Assay Kit for Illumina Pro (Vazyme, TD904) was used for the test. Illumina® (Catalog NO. DR08402, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction.

value: human ovary carcinoma cells


title: siSOX9 TGFB1 H3K27ac ChIP-seq

value: Lung adenocarcinoma

value: transfection siSOX9 and TGFB1 treatment


title: 4T1, Day4, single cell 122

value: Female BALB/c mice


title: 4T1, Day4, single cell 121

value: metastatic tumor cells


title: siSOX9 H3K27ac ChIP-seq

value: transfection siSOX9


title: C. elegans gonad, WormF, Diakinesis

value: gonad

value: Diakinesis


title: 4T1, Day4, single cell 120


title: siCtrl TGFB1 H3K27ac ChIP-seq


title: C. elegans gonad, WormF, -2 Oocyte


title: siCtrl H3K27ac ChIP-seq


title: C. elegans gonad, WormF, -1 Oocyte


title: SOX9 TGFB1 ChIP-seq

value: TGFB1 treatment


title: C. elegans gonad, WormE, Diplotene Loop

value: Diplotene Loop


title: 4T1, Day4, single cell 117


title: SOX9 ChIP-seq

value: No treatment


title: EPZ-6438_ IFN-γ, rep1

city: BEIJING

first: Qianqian

last: Yin

address: 49 North Garden Road, Haidian District

department: Center of Basic Medical Research

institute: Peking University Third Hospital

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through fastp software.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: hg38
Supplementary files format and content: txt file includes raw counts for each sample

growth_protocol: HCT116 cells were grown in IMDM supplemented with 10% fetalbovine serum (FBS, GIBCO, Cat # 10099141) and antibiotics were cultured at 37 °C in a humidified incubator in the presence of 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent，0.4 ug of  total RNA was used for sequencing libraries construction
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols

treatment_protocol: HCT116 cells were treated with 40μM EPZ-6438 for 24h, followed by an additional 24 hours of IFN-γ 40ng/ml treatment

value: human colon cancer cell line

value: EPZ-6438_ IFN-γ

value: EPZ-6438 40μM 24h, followed by an additional 24 hours of IFN-γ 40ng/ml


title: EPZ-6438_ IFN-γ, rep2


title: C. elegans gonad, WormE, Mitotic Region and Transition Zone

value: Mitotic Region and Transition Zone


title: 4T1, Day4, single cell 116


title: EndoC_HiChIP_replicate5

city: bethesda

first: Efsun

last: Arda

state: Maryland

address: 41 medlars drive

institute: National Institutes of Health

data_processing:
Raw reads Mapping: HiC pro
Loop calling: hichipper and FitHiChIP
Assembly: hg38
Supplementary files format and content: tab-delimited text file include reference loop coordinates with pair-ended tags (PETs) for each cell type
Library strategy: HiChIP

growth_protocol:
PANC1 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified CO2 (5%) incubator at 37C
EndoC bH1 cells were maintained in DMEM based media chemically defined as described in Ravassard et al. (PMID: 21865645) in humidified CO2 (5%) incubator at 37C

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes at room temperature, after quenching, cell lysis, in situ chromatin digestion and proximity ligation, the ligated chromatin was extracted from nuclei following the protocol described in Mumbach et al (PMID: 27643841)
custom DNA libraries were prepared following the protocol described in Mumbach et al (PMID: 27643841)

tag: sample origin

value: Pancreas

tag: source

value: human fetal pancreas

value: beta

tag: hichip antibody


title: DMSO_ IFN-γ,rep3

value: DMSO_ IFN-γ

value: DMSO 24h,followed by an additional 24 hours of IFN-γ 40ng/ml


title: 4T1, Day4, single cell 115

value: Female BALB/c mice


title: C. elegans gonad, WormE, -1 Oocyte

value: -1 Oocyte


title: C. elegans gonad, WormD, -1 Oocyte


title: A2780 cells,CTR,H3K27ac,CST

address: 安徽医科大学东校区弘毅楼1202室

value: human ovary carcinoma cells


title: 4T1, Day4, single cell 114

value: metastatic tumor cells


title: DMSO_ IFN-γ,rep2


title: DMSO_ IFN-γ,rep1


title: 4T1, Day4, single cell 119


title: EPZ-6438_ IFN-γ, rep3


title: A2780 cells,BPP,H3K27ac,CST

address: 安徽医科大学东校区弘毅楼1202室


title: C. elegans gonad, WormD, Pachytene Zone

value: gonad

value: Pachytene Zone


title: EndoC_HiChIP_replicate2


title: 4T1, Day4, single cell 113


title: EndoC_HiChIP_replicate3


title: 4T1, Day4, single cell 118


title: C. elegans gonad, WormC, -2 Oocyte

value: -2 Oocyte


title: 4T1, Day4, single cell 112


title: EndoC_HiChIP_replicate1


title: C. elegans gonad, WormC, -1 Oocyte


title: PANC1_HiChIP_replicate4

value: Pancreatic ductal  adenocarcinoma (PDAC)

value: duct


title: 4T1, Day4, single cell 110


title: x19shM7B_2

city: London

first: James

last: Nicholson

address: 4 Newark St

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

data_processing:
The Cell Ranger 2.0.1 pipeline was used to align reads to the GRCh38 human reference genome and produce count matrices
Downstream preprocessing and analysis using the Seurat v4.0 R package
Assembly: GRCh38 human reference genome
Supplementary files format and content: cellranger output series matrix files

source_name: cells

extract_protocol:
Selected mice for scRNAseq were culled by neck dislocation and the brains were dissected and placed into HBSS (Gibco, 14175095) in petri dishes. Brains were cut into small pieces with a surgical blade and then dissociated into single cell suspension using the Brain Tumour Dissociation Kit (P) (Miltenyi Biotec,130-095-942) following the manufacturer’s protocol. Cells were centrifuged at 300g x for 10 minutes, followed by cell debris removal using the Debris Removal Solution (Miltenyi Biotec, 130-109-398) as per protocol instructions. Mouse cells were removed using the Mouse Cell Depletion Kit (Miltenyi Biotec, 130-104-694) as per manufacturer instructions with minor adaptations. Cells were centrifugeds and manually counted. 30000 cells were isolated, centrifuged again at 300g x 5 minutes and re-suspended in 0.04% BSA in PBS at a concentration of 1000 cells/µl.
COs for single-cell RNA sequencing were processed with the same Neural Tissue Dissociation Kit (P) using the gentle MACS dissociator. 3-5 pooled day70 COs derived from gene-edited EPSC were harvested and washed with D-PBS without calcium and magnesium. The organoids were then transferred into a C-Tube containing the pre-heated enzyme mix 1 followed by the gentleMACS Program m_brain_01, 37⁰C incubations under slow continuous rotation, gentleMACS Program m_brain_02, addition of enzyme mix 2 and gentleMACS Program m_brain_03. Single-cell suspension was passed through a 70µm strainer and centrifuged at 300g x for 10 minutes. CO cells were then resuspended in 0.04% BSA in DPBS, and viability and cell number were assessed with the Countess® II FL Automated Cell Counter using trypan blue. 100,000 cells were aliquoted into a new tube in 100µl to achieve a cell density of 1000 cells/µl as required by the 10X Genomics Single-cell RNA sequencing protocol, followed by a final count to ensure the correct number of cells.
The Chromium Next GEM Single Cell 3’ Kit v3.1 (10X Genomics, 1000268) was used along with the Chromium Next GEM Chip G Single Cell Kit (10X Genomics, 1000120).

value: PDX-GIC-sample

value: METTL7B knockdown


title: 4T1, Day4, single cell 111


title: EndoC_HiChIP_replicate4


title: x19shM7B


title: C. elegans gonad, WormC, Pachytene Zone

data_processing:
Prior to mapping, raw reads were trimmed with Trim Galore, with parameters (quality >= 10, length > 35bp)
For differential gene expression analysis, trimmed reads were mapped to the genome using HISAT2, raw counts obtained via HTSeq
The trimmed reads were also mapped to the genome using Salmon with default settings to obtain transcript per million (TPM) estimates for both genes and transcripts
Assembly: WBcel235, GCA_000002985.3
Supplementary files format and content: tab delimited file containing HISAT aligned, HTSeq raw counts for all samples/genes
Supplementary files format and content: tab delimited file containing salmon estimated raw counts for all samples/genes
Supplementary files format and content: tab delimited file containing mapping and quality control metrics for all samples


title: PANC1_HiChIP_replicate3


title: C. elegans gonad, WormC, Mitotic Region and Transition Zone

value: Mitotic Region and Transition Zone


title: x19scr_2

value: Scr


title: PANC1_HiChIP_replicate1

value: Pancreas


title: 4T1, Day4, single cell 108

data_processing:
Raw reads were first analyzed for quality control using FastQC (v0.11.7) (Andrews, 2010). Adaptor sequences of raw reads were removed by using TrimGalore (v0.6.6) (https://github.com/FelixKrueger/TrimGalore). Trimmed reads were mapped to a concatenated mouse genome (mm10) with STAR (v2.6.0c) with default parameters to result SAM format files (Dobin et al., 2013). Aligned reads stored in SAM format were transformed to generate BAM files using SAMtools (v1.7) (Danecek et al., 2021). The gene-level read count matrix was summarized from BAM files using FeatureCounts program (v1.6.2) (Liao et al., 2014). Subsequent data analysis was carried out in R 3.6.2 and the Seurat package (v3.1.2) (Stuart et al., 2019).
The gene counts per cell, the percentage of mitochondrial transcripts, the percentage of ERCC RNA spike-in, the percentage of α and β-globin genes were computed using the functions of the Seurat package. Quality controls were performed following: a. Cells with luciferase or GFP sequence detected were kept for further analysis. b. Cells with transcripts counts lower than 5 × 105 or higher than 1 ×107 were discarded. c. Single cell libraries with number of detected gene lower than 5,000, mapping rate lower than 40% or the percentage of mitochondrial transcripts higher than 10% were discarded before further analysis. d. Libraries with the percentage of α and β-globin genes higher than 1% were also discarded. 424 single cells passed quality controls, and were used for further analysis. The gene expression level was normalized as log2(TPM/10 + 1), in which TPM is the abbreviation for transcripts per million, and adding one to avoid negative expression values.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: 4T1, Day4, single cell 109


title: C. elegans gonad, WormB, Mitotic Region and Transition Zone


title: CO61M7B

value: Cerebral Organoid 2months

value: METTL7B over expression


title: C. elegans gonad, WormB, Diplotene Loop

value: Diplotene Loop


title: x19scr


title: x19shM7B_3


title: 4T1, Day4, single cell 107

value: Female BALB/c mice


title: Huh7_Molidustat_48h_3

city: Lyon

first: Olivier

last: Diaz

address: Avenue Tony Garnier

department: Centre International de Recherche en Infectiologie (CIRI)

institute: INSERM U1111 – CNRS UMR5308 Université Lyon 1, ENS de LyonINSERM U1111 – CNRS UMR5308 Université Lyon 1, ENS de Lyon

data_processing:
Bcl2fastq v2.17.1.14 was used to demultiplex using 1 mismatch
Trimming was performed using cutadapt v1.9.1; Threshold quality score to 30; Minimum length of 25 bases after trimming; The maximum rate of undetermined bases (“N”s) was set to 0%; Adapters were trimmed with 3 bases overlap, a maximum error rate of 10%.
Reads were mapped using STAR 2.7.9a (splice aware mapping on genome; reference genome Homo spaiens, GRCh38, Ensembl release 103, type prmary assembly - all biotype
Tag counts were determined using HTSeq 0.11.2 (mode interesection-nonempty-nonunique all)
Normalization & Differential analysis was performed with DESeq2 R package v1.26.0 (Prior to differential analysis, a normalization step is performed by DESeq2 package : counts are divided by a sample-specific size factors determined by median ratio of gene counts relative to geometric mean per gene)
Assembly: GRCh38; Ensembl - release 103
Supplementary files format and content: Text files (.out) containing genes counts (raw values)

growth_protocol: Huh7 cells were cultured at 37°C and 5%CO2 in DMEM with Glutamax, 25 mM Glucose with 10% FCS and Penicillin/Streptomycin

extract_protocol:
Cells were washed with PBS and total RNA were extracted with Qiagen Rneasy kit
QIAseq UPX 3’ Transcriptome Kit, Qiagen

treatment_protocol: Cells were treated for 24h or 48h with Molidustat at 25 microM or DMSO alone

value: Molidustat

tag: time


title: C. elegans gonad, WormA, Mitotic Region and Transition Zone

extract_protocol:
a cut was made across the vulva using a 26G subcutaneous needle controlled by a micromanipulator (ROE-200, Sutter) under an inverted microscope (Olympus 1X71). This would release fertilized eggs and early-stage embryos from the uterus as well as sperms and at least portions of the two sides of the gonad. Each end of the gonad wrapped around by five pairs of sheath cells was completely isolated by pushing its distal end. The distal proliferative zone (S1) was cut off around the transition zone and harvested in about 10 nl bath solution by suction using a patch clamp pipette under controlled of another micromanipulator (ROE-200, Sutter). The pachytene zone (S2), the loop corresponding to the diplotene zone (S3) and diakinesis zone (S4) were sequentially cut off and similarly harvested. The -3 (F3), -2 (F2), and -1 (F1) oocytes were also isolated by cutting through their boundaries and similarly harvested. The zygote (fertilized oocyte) also known as P0 was similarly harvested when the two pronuclei were fused at its center.
We prepare a RNA-seq library for each harvested sample for Illumina platforms using a modified scRNA-seq method based on Tang et al or using the Smart-seq2 protocol


title: Huh7_Molidustat_48h_2


title: CO61CAS9PK


title: 4T1, Day4, single cell 106

extract_protocol:
Reverse transcription and cDNA amplification were carried out using a modified Smart-seq2 protocol (Picelli et al., 2014). Single cells were sorted by FACS as described above into 96-well plates containing 0.1 μl of RNase inhibitor (Clontech, Cat# 2313A), 1.9 μl of 0.2% Triton X-100 (Sigma, Cat# T9284), 1 μl of 10 µM oligo-dT primer (5′-AAGCAGTGGTATCA ACGCAGAGTAC T30VN-3′) and 1 μl of dNTP mix (10 mM each; Fermentas, Cat# R0192) in each well. Plates were either stored at -80 °C or processed immediately. Reverse transcription, PCR preamplification, PCR purification were performed following Picelli’s protocol (Picelli et al., 2014). As mRNA quality control, 1 ul of each PCR product was used as template for qPCR detection of mCherry expression and samples with Ct value higher than 30 will be discard. PCR products were purified with 1 × Agencourt Ampure XP beads (Beckman Coulter, Cat# A63881) and the final product was reconstituted in 20 µl TE buffer. The concentration of cDNA was measured by Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kit (Invitrogen, Cat# Q33230). Tagmentation and NGS library was carried out by using TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, Cat# TD503) following the manufacturer’s instructions. The purified library was qualify controlled by measuring the fragment size distribution with an Agilent HS DNA BioAnalyzer Chip and the concentration of library was measured with Qubit™ 1× dsDNA High Sensitivity (HS) Assay Kits following the manufacturer’s instructions. Single cell cDNA libraries were sequenced on an Illumina HiSeq X Ten platform to obtain paired-end 150-bp reads.
SMART-Seq2 (Picelli et al., 2014)


title: C. elegans gonad, Unknown Worm 4, Early Embryo

value: Early Embryo

value: Unknown


title: CO19M7B


title: Huh7_Molidustat_48h_1


title: CO19PK

value: PK


title: C. elegans gonad, Unknown Worm 3, Early Embryo

value: gonad


title: PANC1_HiChIP_replicate2


title: Huh7_DMSO_48h_2

value: DMSO


title: Huh7_DMSO_48h_3


title: 4T1, Day4, single cell 103

value: metastatic tumor cells


title: N19.M7Boe.4

data_processing:
Reads were quality trimmed using trimgalore v0.6.5
Counting of reads was performed with RSEM v1.3.1
Differential expression analysis was performed in DESeq2 using the Wald test
Gene set enrichment analysis was performed using R package fgsea and the ranked DESeq2 Wald statistic of all genes
Assembly: genome GRCh37 (hg19) using STAR v2.7.9a
Supplementary files format and content: comma separated values of log2RPKM of GIC samples
Supplementary files format and content: comma separated values of log2RPKM of NSC samples

growth_protocol: GIC were maintained in NeuroCult NS-A Proliferation kit medium, 1% Pen/Strep, 2µg/ml Heparin, 20ng/ml murine EGF and 10ng/ml human FGF. iNSC were cultured in 0.5X Advanced DMEM/F-12 , 0.5X Neurobasal medium, 1X Neurobasal Induction supplement and 1X pen/strep

extract_protocol:
Total RNA extraction with NORGEN Biotek DNA/RNA/Protein Purification Plus kit. 1ug of total RNA used for library construction
RNA library is formed by polyA capture (or rRNA removal) and reverse transcription of cDNA. Illumina PE150 technology

value: induced neural stem cells

value: METTL7B overexpression


title: C. elegans gonad, Unknown Worm 2, Early Embryo


title: C. elegans gonad, Unknown Worm 1, Zygote

value: Zygote


title: 4T1, Day4, single cell 101


title: Huh7_DMSO_48h_1


title: Huh7_Molidustat_24h_3


title: 4T1, Day4, single cell 100


title: N19.M7Boe.2


title: WD598 (mstr-1(on33)) biological replicate 2

city: Toronto

first: Matthew

last: Eroglu

state: ON

address: 686 Bay St

department: DSCB

institute: Hospital for Sick Children

data_processing:
Data processed by TCAG (SickKids, Toronto)
The quality of the data is assessed using FastQC v.0.11.2 (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Adaptors are trimmed using Trim Galore (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) v. 0.4.0. Trim Galore is running Cutadapt (https://cutadapt.readthedocs.org/en/stable/)
The raw trimmed reads are aligned to reference genome using Tophat v. 2.0.11 (http://ccb.jhu.edu/software/Tophat/index.shtml).
Tophat alignments are processed to extract raw read counts for genes using htseq-count v.0.6.1p2(HTSeq, http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html).
Raw gene counts are loaded and sample-normalized using DESeq v.1.18.0 (http://bioconductor.org/packages/release/bioc/html/DESeq.html).
Two-condition differential expression was done with the edgeR R package, v.3.16.5 using R v.3.3.2 (http://www.bioconductor.org/packages/release/bioc/html/edgeR.html).
Assembly: WBcel235
Supplementary files format and content: tab-delimited text files including: Entrez Gene ID, log2FC, logCPM, F value, P value, FDR, and RPKM

growth_protocol: 20oC on NGM with OP50, standard nematode growth protocol

extract_protocol:
Wash worms off the plate and collect into 1.5mL tubes, wash 3x with H2O, after last wash remove as much water as possible and freeze worm pellet at -80 until needed. Thaw pellet in Qiagen RLT buffer with DTT, agitate worms with narrow tip needle and follow Qiagen RNeasy mini kit instructions for extraction
NEBNExt Ultra II Directional RNA library prep kit (oligo dT to enrich for poly(A) mRNA during library prep)
stranded, paired end

value: whole worm

value: L4 stage


title: N19.M7Boe.1


title: N19.PK.4

value: WT


title: Huh7_Molidustat_24h_2


title: 4T1, Day4, single cell 105


title: Huh7_Molidustat_24h_1


title: WD598 (mstr-1(on33)) biological replicate 1


title: N19.PK.3


title: WT (N2) L4 stage biological replicate 3


title: 4T1, Day4, single cell 99


title: 4T1, Day4, single cell 98


title: Huh7_DMSO_24h_3


title: 4T1, Day4, single cell 104


title: N19.PK.1


title: WT (N2) L4 stage biological replicate 2


title: 4T1, Day4, single cell 97


title: WT (N2) L4 stage biological replicate 1


title: Huh7_DMSO_24h_2


title: 4T1, Day4, single cell 96


title: Huh7_DMSO_24h_1


title: N19.M7Boe.3


title: WD598 (mstr-1(on33)) biological replicate 3


title: 4T1, Day4, single cell 102


title: G19.shMETTL7B.4

value: Glioblastoma initiating cells

value: METTL7B knockdown


title: 4T1, Day4, single cell 95


title: KO Clone #69, 4-OHT positive (Ribo)

city: Dallas

first: Joshua

last: Mendell

state: TX

address: 6000 Harry Hines Blvd., NA6.200A

department: Molecular Biology

institute: UT Southwestern Medical Center

data_processing:
Adapter was trimmed
Reads that mapped to noncoding RNA were discarded
Reads were mapped to human reference genome using STAR
Uniquely mapped reads between 24 and 31nt were kept
Assembly: GRCh38
Supplementary files format and content: Table of normalized ribosome protected fragment counts from 4-OHT negative samples
Supplementary files format and content: Table of normalized ribosome protected fragment counts from 4-OHT positive samples
Library strategy: Ribo-seq

source_name: BJ

growth_protocol: BJ cells were cultured in DMEM (Invitrogen) supplemented with 20% Medium 199 (Gibco), 10% fetal bovine serum (Sigma-Aldrich) and 1X Antibiotic-Antimycotic (Gibco).

extract_protocol:
Ribosome protected fragments were isolated as described in McGlincy and Ingolia, Methods, 2017.
Ribosome profiling libraries were prepared as described in Ingolia et al., Nature Protocols, 2012, and McGlincy and Ingolia, Methods, 2017.

treatment_protocol: Cells were treated with 100 nM (Z)-4-Hydroxytamoxifen (sigma).

value: BJ

value: skin fibroblast

value: BJ-HRAS SNORA13 KO

value: (Z)-4-Hydroxytamoxifen treatment for 7 days


title: SIGAH12. replicate 2, scRNAseq

city: Munich

first: Eva

last: Hoermanseder

state: Bavaria

address: Feodor-Lynen-Str. 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Center Munich

description: 10x Genomics

data_processing:
The demultiplexing, barcode processing, gene counting and aggregation were made using the Cell Ranger software (v2.2.0 for 10x chemistry version 2 and v3.0.2 for 10x chemistry version 3)
Assembly: Xenopus laevis v9.1
Supplementary files format and content: Comma-separated UMI count matrix files

organism: Xenopus laevis

source_name: ectoderm

extract_protocol:
Ectodermal explants were isolated from IVF and NT embryos of stage 12 and shortly washed in Newport 2.0 dissociation buffer (100 mM sodium isethionate, 20 mM sodium pyrophosphate, 10 mM CAPS, 20 mM glucose, pH10.5 adjusted by NaOH) to remove calcium ions. Ectodermal explants were transferred into fresh dissociation buffer in BSA coated low bind microcentrifuge tubes and incubated for 30min at 18°C with agitation. During the period of incubation, tubes were inverted several times. Resulting single cell suspensions were resuspended in PBS-BSA solution and filtered through 30 µm cell strainers. Cells were washed 3-times with 1 ml PBS-BSA, counted and analyzed for viability. 2500 cells with viability more than 95% and not detectable RNA in supernatant were submitted for library preparation.
Libraries were constructed according to the manufacturer's instructions (single-cell 3' v2 and v3 protocols, 10x Genomics). GCs were resuspendend in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscribed to cDNA, which contains an Illumina R! primer sequence, Unique Molecular Identifier (UMI) and the 10x barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the appropriate sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Illumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: Nuclear transfer and IVF was  conducted according to Hormanseder et al. (https://pubmed.ncbi.nlm.nih.gov/28366589/). Only those NT embryos that were morphologically indistinguishable from IVF embryos at gastrula stage 12 were used for further analyses.

value: ectoderm

value: NT


title: KO Clone #66, 4-OHT positive (Ribo)


title: G19.shMETTL7B.3


title: G19.shMETTL7B.2


title: SIGAB2. replicate 1, scRNAseq

description: 10x Genomics


title: SIGAH5. replicate 2, scRNAseq

description: 10x Genomics

value: IVF


title: 4T1, Day4, single cell 94

value: Female BALB/c mice


title: 4T1, Day4, single cell 93

value: metastatic tumor cells


title: N19.PK.2

value: induced neural stem cells


title: SIGAA2. replicate 1, scRNAseq

description: 10x Genomics


title: WT Clone #15, 4-OHT positive (Ribo)

value: BJ-HRAS WT


title: 4T1, Day4, single cell 92


title: NNCSD-117.b

city: Herlev

first: Lauge

last: Kellermann

state: --- Select ---

address: Borgmester Ib Juuls Vej 1

department: Department of Gastroenterology

country: Denmark

institute: Herlev Hospital

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C. GeneChips were washed and stained on the Gene Titan platform (Affymetrix)

scan_protocol: The chips were scanned on the GeneTitan platform (Affymetrix).

data_processing: The Affymetrix raw data (.cel files) were normalized using the robust multichip average (RMA)  algorithm in R environment. Quality assurance was performed using the Bioconductor package  arrayQualityMetrics in R Probe set annotation files were obtained form from Affymetrix NetAffx website (NA35, available online: https: //www.affymetrix.com/analysis/index.affx). For four of the UC patients only one biopsy was analyzed due to quality issues, so in total 152 biopsies were analyzed: tow from each of the 19 healthy controls, tow from 55 UC patients and one biopsy from 4 UC patients, for at total of 152 .cel-files.

label: biotin

source_name: Sigmoid colonic tissue

label_protocol: 3'-IVT kit from Affymetrix according to standard protocol. Biotinylated cRNA were prepared from 100 ug total RNA

extract_protocol: RNA  was extracted by mechanical homogenization using a rotor-stator. RNA purification was performed by column purification (Nucleospin miRNA, Macherey–Nagel, Düren, Germany, ref: 740971.250) including DNAse I treatment according to the recommendations of the manufacturer. The RNA concentration was quantified using a NanoDrop spectrometer (Thermo Fisher Scientific, Wilmington, DE, USA). For samples with <10 ng/µL the Ribogreen® RNA assay Kit (Life Technologies, Carlsbad, CA, USA) was used. The Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) was used to assess RNA quality. Samples with a resulting RNA Integrity Number (RIN) value below 6 were excluded.

treatment_protocol: Colonic biopsies were kept in RNAlater (Ambion, Austin, TX, USA) 24–48 h before storage at -80C.

value: Sigmoid colonic tissue

tag: Sex

value: F

tag: uc or healthy control

value: UC - Active disease

tag: mayoscore

tag: diagnose duration (years)


title: 4T1, Day4, single cell 91

city: Beijing

first: Hanqiu

last: Zheng

institute: Tsinghua university

tag: host


title: NNCSD-117.a

tag: tissue


title: 4T1, Day4, single cell 90

tag: cell line

tag: cell type


title: G19.Scr.3

tag: genotype

value: WT


title: KO Clone #66, 4-OHT negative (Ribo)

tag: treatment


title: NNCSD-108.b

value: M

value: UC - Inactive disease


title: G19.Scr.2

value: Glioblastoma initiating cells


title: 4T1, Day4, single cell 89


title: WT Clone #54, 4-OHT negative (Ribo)

value: BJ

value: skin fibroblast


title: G19.Scr.1


title: KO Clone #69, 4-OHT negative (Ribo)

value: BJ-HRAS SNORA13 KO


title: NNCSD-107.b


title: G19.shMETTL7B.1

value: METTL7B knockdown


title: WT Clone #54, 4-OHT positive (Ribo)

value: (Z)-4-Hydroxytamoxifen treatment for 7 days


title: G19.Scr.4


title: NSC-4_INPUT_METTL7B

data_processing:
Quality and adapter trimming was performed using Trimgalore v0.6.5
Alignment to hg19 Genome was performed using Bowtie2 v2.4.5 with default parameters
samtools v1.9 was used to obtain bam from sam files that . Bam files were then sorted by cooirdinate and indexed
Bams were filtered to include only uniquely mapping reads (ie unmapped reads and multimapping were removed) using sambamba
Peak calling was performed with MACS2, BAM mode was used (-f BAM and also  -g 'hs’) and with the broad peak calling (--broad and --broad-cutoff 0.05) and 300bp fragment (shift) size ( –extsize 300)
Further quality assessment of peak calling was performed using R package ChIPQC
Differential peak analysis was performed with R package with DiffBind
Assembly: hg19
Supplementary files format and content: MACs2 output bedGraph files
Supplementary files format and content: bigWig files gnerated from bedGraphs

extract_protocol:
H3K27me3 ChIP was performed using ChIP-IT High Sensitivity kit (active Motif) as per manufacturer’s instructions. Briefly, cells were fixed with the formaldehyde-based fixing solution for 15 min at room temperature and lysed with provided lysis solution supplemented with proteases inhibitors. Next, nuclei pellets were lysed and chromatin sonicated with Bioruptor Plus sonication device (Diagenode) to obtain fragments within the recommended 200-1200 bp range. 5 µg of sheared chromatin was then incubated with 4 µg of antibody against H3K27me3 (Diagenode) overnight at 4 °C with rotation. Following incubation with Protein G agarose beads, bound chromatin was washed, eluted and purified following the manufacturer’s protocols. Validation by qPCR-ChIP on target genes was done before proceeding to sequencing.
ChIPed DNA was end-repaired, A-tailed and adapter-ligated before size selection and amplification. The obtained libraries were QC’ed and multiplexed before 150-bp paired-end sequencing on Illumina NovaSeq 6000


title: 4T1, Day4, single cell 87


title: NNCSD-107.a


title: NNCSD-108.a


title: 4T1, Day4, single cell 88


title: 4T1, Day4, single cell 86


title: 4T1, Day4, single cell 85


title: NSC-3_INPUT_METTL7B


title: BJ-HRAS-CRISPRi Clone b, D0

data_processing:
Raw data from machine are de-multiplexed and converted to fastq files using bcl2fastq
Galaxy: Clip adapter GTTTTAGA and CGGTGTTTC
Galaxy: Collapse sequences
Galaxy: FASTA-to-tabular
MAGeCK sgRNA enrichment
Assembly: GRCh38
Supplementary files format and content: Table of normalized read counts of sgRNAs
Library strategy: CRISPR screen

extract_protocol:
Genomic DNA was isolated using the MasterPure Complete DNA Purification kit (Lucigen).
Sequencing libraries were generated with two sequential rounds of PCR using Herculase II Fusion DNA polymerase (Agilent). 6.6 µg of genomic DNA was used in 100 µl reaction for the first round of PCR. A total of 40 reactions were performed per replicate and pooled following 18 cycles of PCR1 amplification. 5 µl from the pooled reaction product and primers containing barcodes and Illumina sequencing adaptors were used in the second round of PCR (11 – 12 cycles).
CRISPR screen custom DNA library

treatment_protocol: Transduced cells were selected with 2 µg/mL puromycin (Thermo Fisher Scientific) and then treated with 100 nM (Z)-4-Hydroxytamoxifen (sigma).

value: BJ-HRAS-CRISPRi Clone b


title: NSC4_INPUT_CTRL


title: NNCSD-106.a


title: BJ-HRAS-CRISPRi Clone a, D21

value: BJ-HRAS-CRISPRi Clone a

value: (Z)-4-Hydroxytamoxifen treatment for 21 days


title: NNCSD-106.b


title: BJ-HRAS-CRISPRi Clone b, D21


title: 4T1, Day4, single cell 84

value: Female BALB/c mice

value: metastatic tumor cells


title: NSC-3_INPUT_CTRL


title: NNCSD-104.b

value: Sigmoid colonic tissue


title: NSC-2_INPUT_METTL7B


title: BJ-HRAS-CRISPRi Clone a, D0


title: TH_9_N_str

city: daejeon

first: Seung-Jin

last: Park

address: gwahakro

institute: KRIBB

data_processing:
STAR mapping (2.9.10) with GeneCount function
Assembly: GRCh38
Supplementary files format and content: Genecounts as text formats

source_name: Thyroid

extract_protocol:
Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light.
Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR.

value: Thyroid

value: Normal

tag: cell subtype

value: PTC


title: NSC-2_INPUT_CTRL

value: WT


title: WT Clone #15, 4-OHT negative (Ribo)

value: BJ-HRAS WT


title: 4T1, Day4, single cell 82

address: Haidian District


title: 4T1, Day4, single cell 83


title: 4T1, Day4, single cell 81


title: TH_6_N_str


title: NSC-1_INPUT_CTRL

value: Glioblastoma initiating cells


title: NNCSD-102.b

value: F

value: UC - Active disease


title: NNCSD-104.a

value: UC - Inactive disease


title: NSC-1_INPUT_METTL7B

value: METTL7B knockdown


title: GIC-4_INPUT_shMETTL7B

value: induced neural stem cells

value: METTL7B overexpression


title: TH_8_N_str


title: NNCSD-101.b


title: TH_4_N_str


title: NNCSD-101.a


title: TH_3_N_str


title: NNCSD-102.a


title: GIC-4_INPUT_SCR


title: 4T1, Day4, single cell 79


title: 4T1, Day4, single cell 78


title: TH_297_N_str


title: 4T1, Day4, single cell 77


title: GIC-3_INPUT_SCR


title: NNCSD-100.b

value: M


title: NNCSD-098.b


title: TH_289_N_str


title: GIC-2_INPUT_shMETTL7B


title: 4T1, Day4, single cell 75


title: NNCSD-100.a


title: TH_285_N_str


title: 4T1, Day4, single cell 80


title: TH_284_N_str


title: GIC-1_INPUT_shMETTL7B


title: 4T1, Day4, single cell 74


title: GIC-2_INPUT_SCR


title: NNCSD-097.b

value: Healthy control


title: NNCSD-098.a


title: 4T1, Day4, single cell 72

value: Female BALB/c mice


title: GIC-1_INPUT_SCR


title: TH_298_N_str


title: TH_283_N_str


title: 4T1, Day4, single cell 73

value: metastatic tumor cells


title: NNCSD-097.a

value: Sigmoid colonic tissue


title: NSC-4_H3K27me3_METTL7B


title: GIC-3_INPUT_shMETTL7B


title: 4T1, Day4, single cell 71


title: TH_282_N_str

value: Thyroid


title: TH_281_N_str

value: Normal


title: NNCSD-096.b


title: NNCSD-096.a


title: 4T1, Day4, single cell 76


title: NNCSD-095.b


title: NSC-3_H3K27me3_METTL7B


title: TH_279_N_str

value: PTC


title: 4T1, Day4, single cell 70


title: TH_277_N_str


title: 4T1, Day4, single cell 69


title: NSC-3_H3K27me3_CTRL

value: WT


title: 4T1, Day4, single cell 68


title: TH_274_N_str


title: 4T1, Day4, single cell 67


title: NNCSD-094.a


title: NSC-2_H3K27me3_METTL7B


title: TH_272_N_str


title: NNCSD-094.b


title: 4T1, Day4, single cell 66


title: NSC-2_H3K27me3_CTRL


title: NNCSD-093.a


title: TH_268_N_str


title: NSC-1_H3K27me3_METTL7B


title: NNCSD-095.a


title: GIC-4_H3K27me3_shMETTL7B


title: TH_260_N_str


title: NSC4_H3K27me3_CTRL


title: TH_259_N_str


title: 4T1, Day4, single cell 64


title: NSC-1_H3K27me3_CTRL


title: NNCSD-092.b


title: 4T1, Day4, single cell 63


title: NNCSD-092.a


title: 4T1, Day4, single cell 62


title: TH_256_N_str


title: GIC-3_H3K27me3_shMETTL7B


title: NNCSD-091.b


title: GIC-4_H3K27me3_SCR


title: NNCSD-093.b


title: 4T1, Day4, single cell 65


title: 4T1, Day4, single cell 61


title: TH_255_N_str


title: NNCSD-091.a


title: NNCSD-090.b


title: TH_253_N_str


title: 4T1, Day4, single cell 59


title: TH_251_N_str


title: 4T1, Day4, single cell 60


title: GIC-3_H3K27me3_SCR


title: GIC-2_H3K27me3_shMETTL7B


title: NNCSD-089.b


title: 4T1, Day4, single cell 57


title: GIC-1_H3K27me3_SCR


title: 4T1, Day4, single cell 58


title: TH_247_N_str


title: TH_248_N_str


title: NNCSD-089.a


title: GIC-1_H3K27me3_shMETTL7B


title: GIC-2_H3K27me3_SCR


title: 4T1, Day4, single cell 56


title: TH_258_N_str


title: TH_245_N_str


title: NNCSD-087.b


title: 4T1, Day4, single cell 55


title: hfNSC

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

country: Italy

institute: San Raffaele Telethon Institute for Gene Therapy

data_processing:
Sample demultiplexing and quantification was done with Cell Ranger (v6.1.1) from 10X Genomics
Assembly: GRCh38
Supplementary files format and content: Tab-separated files of features and barcodes, and matrix counts

source_name: Fetal brain

extract_protocol:
hiPSC-NSC were enzymatically dissociated with Accutase while hfNSC were mechanically dissociated by pipetting. Cells were then checked for viability (>90%), counted, and resuspended at a concentration of 1,000 cells/μl
Single cells were processed using the Chromium Single Cell 3' Reagent Kit (v3.1 Chemistry) and the 10x Chromium Controller platform (10X Genomics). The target cell recovery was 2000 cells. Samples were processed following the manufacturer’s protocol. The resulting libraries were assessed for size distribution and concentration using the HS DNA assay (Agilent) on the TapeStation platform (Agilent)

value: Fetal brain

value: hfNSC

tag: condition

value: hfNSCs


title: NNCSD-087.a

value: F

value: UC - Active disease


title: hiPSC-NSC HD 1.1

source_name: Skin Fibroblast

value: Skin Fibroblast

value: hiPSC-NSCs


title: TH_243_N_str


title: NNCSD-086.b


title: TH_241_N_str


title: hiPSC-NSC HD 2.3


title: 4T1, Day4, single cell 52


title: NNCSD-090.a


title: 4T1, Day4, single cell 54


title: TH_240_N_str


title: NNCSD-081.b


title: NNCSD-081.a


title: 4T1, Day4, single cell 50


title: hiPSC-NSC HD 1.3


title: 4T1, Day4, single cell 49


title: NNCSD-080.b


title: 4T1, Day4, single cell 51


title: TH_238_N_str


title: tumor, liver meta, pat015, rep1

city: Seoul

first: Kitae

last: Kim

institute: Seoul National University

data_processing:
The raw paired-end sequencing data were aligned to the human reference genome (hg19) using the Spliced Transcripts Alignment to a Reference (STAR) aligner
RNA sequencing analysis was performed using the bcbio-nextgen pipeline
Gene expression quantification was carried out using the Salmon by tximport
Assembly: hg19
Supplementary files format and content: txt file for gene expression quantification

source_name: Gastric Cancer

extract_protocol:
Total RNA was extracted from the FFPE tissue samples using a commercially available extraction kit (RNeasy FFPE kit, Qiagen, Germany)
TruSeq Stranded Total RNA Library Prep Kit, IlluminaTM, CA, USA

value: Gastric Cancer


title: TH_235_N_str


title: tumor, primary T1, pat015, rep1


title: tumor, primary T3, pat015, rep1


title: tumor, primary T2, pat015, rep1


title: TH_244_N_str


title: TH_237_N_str


title: 4T1, Day4, single cell 48


title: TH_233_N_str


title: 4T1, Day4, single cell 53


title: NNCSD-086.a

value: M


title: NNCSD-080.a


title: tumor, perit meta, pat014, rep1


title: NNCSD-079.b

value: Healthy control


title: 4T1, Day4, single cell 47

value: Female BALB/c mice


title: 4T1, Day4, single cell 46

value: metastatic tumor cells


title: TH_232_N_str


title: NNCSD-079.a

value: Sigmoid colonic tissue


title: NNCSD-077.b

value: UC - Inactive disease


title: TH_230_N_str

value: Thyroid

value: Normal


title: 4T1, Day4, single cell 45


title: TH_227_N_str

value: PTC


title: tumor, ovary meta, pat014, rep1


title: tumor, ovary meta, pat014, rep2


title: TH_226_N_str


title: NNCSD-076.b


title: NNCSD-077.a


title: tumor, primary T1, pat014, rep1


title: 4T1, Day4, single cell 42


title: tumor, primary T2, pat014, rep1


title: 4T1, Day4, single cell 44


title: TH_224_N_str


title: 4T1, Day4, single cell 43


title: NNCSD-075.b


title: tumor, perit meta, pat013, rep1


title: NNCSD-076.a


title: tumor, ovary meta, pat013, rep2


title: NNCSD-075.a


title: 4T1, Day4, single cell 41


title: 4T1, Day4, single cell 40


title: tumor, ovary meta, pat013, rep1


title: TH_223_N_str


title: TH_222_N_str


title: NNCSD-074.b


title: tumor, primary T2, pat013, rep1


title: NNCSD-074.a


title: 4T1, Day4, single cell 38


title: TH_220_N_str


title: tumor, primary T1, pat013, rep1


title: tumor, perit meta, pat012, rep1


title: NNCSD-073.a


title: 4T1, Day4, single cell 37


title: tumor, ovary meta, pat012, rep2


title: TH_218_N_str


title: TH_219_N_str


title: tumor, ovary meta, pat012, rep1


title: 4T1, Day4, single cell 36


title: NNCSD-072.b


title: NNCSD-072.a


title: TH_225_N_str


title: TH_213_N_str


title: TH_215_N_str


title: tumor, primary T1b, pat012, rep1


title: 4T1, Day4, single cell 39


title: tumor, primary T1a, pat012, rep1


title: NNCSD-071.b


title: 4T1, Day4, single cell 33


title: NNCSD-071.a


title: TH_207_N_str


title: TH_221_N_str


title: 4T1, Day4, single cell 32


title: tumor, liver meta, pat010, rep1


title: TH_20_N_str


title: NNCSD-069.b


title: NNCSD-073.b


title: 4T1, Day4, single cell 31


title: TH_2_N_str


title: tumor, primary T2, pat012, rep1


title: tumor, primary T3, pat010, rep1


title: NNCSD-069.a


title: tumor, primary T2, pat010, rep1


title: 4T1, Day4, single cell 34


title: TH_198_N_str


title: 4T1, Day4, single cell 35


title: TH_19_N_str


title: 4T1, Day4, single cell 30


title: NNCSD-066.b


title: NNCSD-068.b


title: 4T1, Day4, single cell 27


title: 4T1, Day4, single cell 28


title: tumor, perit meta, pat009, rep1


title: NNCSD-066.a


title: 4T1, Day4, single cell 25


title: tumor, ovary meta, pat009, rep2


title: TH_18_N_str


title: TH_15_N_str


title: TH_17_N_str


title: tumor, primary T1a, pat010, rep1


title: 4T1, Day4, single cell 29


title: NNCSD-065.a


title: tumor, ovary meta, pat009, rep1


title: tumor, primary T1b, pat010, rep1


title: NNCSD-064.b


title: NNCSD-064.a


title: 4T1, Day4, single cell 26


title: 4T1, Day4, single cell 24


title: TH_14_N_str


title: 4T1, Day4, single cell 23


title: NNCSD-063.b


title: TH_12_N_str


title: 4T1, Day4, single cell 22


title: NNCSD-063.a


title: tumor, primary T1, pat009, rep1


title: 4T1, Day4, single cell 21


title: NNCSD-068.a


title: tumor, ovary meta, pat008, rep2


title: TH_16_N_str


title: TH_10_N_str


title: 4T1, Day4, single cell 19


title: 4T1, Day4, single cell 20


title: tumor, primary T3, pat008, rep1


title: TH_1_N_str


title: tumor, primary T3, pat009, rep1


title: 4T1, Day4, single cell 18


title: coloninc organoids_1,25(OH)2D3_6h_C

data_processing:
Raw reads were trimmed with Fastp (v0.21.0) using default settings ('--trim_poly_g --trim_poly_x --cut_tail --trim_front1 12  --trim_tail1')
The trimmed reads were aligned to the human genome (hg38 assembly) using the STAR aligner (v2.6.0c) in two-pass mode and guided by a RefSeq (UCSC,ncbiRefSeqCurated) gene annotation (default settings except: --sjdbOverhang 62 --twopassMode Basic --outSAMtype BAM SortedByCoordinate --outSAMattributes All --outSAMunmapped Within --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 25 --outFilterMismatchNmax 10)
After mapping the reads were assigned to genes with featureCounts (v1.5.1, settings: -s 0 -J).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include raw count values for each sample

source_name: colonic organoids

growth_protocol: Organoids were cultured as desribed in: kellermann et.al "Impaired vitamin D receptor signaling of crypt-top epithelial cells in flaring ulcerative colitis" - manuscript in preparation

extract_protocol:
RNA was extracted from intestinal organoids using NucleoSpin columns (Macherey-Nagel, Germany). For sequencing of RNA isolated from organoids the RNA integrity number (RIN) was measured at the Bioanalyzer 2100 All RIN-values were 9.7-10.
For library preparation, 500 ng of each sample was applied with the TruSeq RNA Sample Prep Kit v2 (Illumina).

treatment_protocol: Organoids were treated with 1uM 1,25(OH)2D3 (cat.no. 71820, Cayman Chemical) or vehicle control for 6h and 24.

value: colonic organoids


title: NNCSD-059.b


title: 4T1, Day4, single cell 17


title: NNCSD-059.a


title: tumor, primary T2, pat009, rep1


title: TH_13_N_str


title: tumor, primary T2, pat008, rep1


title: NNCSD-058.b


title: tumor, primary T1, pat008, rep1


title: coloninc organoids_1,25(OH)2D3_6h_B


title: TH_11_N_str


title: coloninc organoids_1,25(OH)2D3_6h_A


title: NNCSD-058.a


title: tumor, ovary meta, pat007, rep1


title: NNCSD-062.b


title: NNCSD-054.b


title: 4T1, Day4, single cell 15


title: 4T1, Day4, single cell 16


title: tumor, primary T3, pat007, rep1


title: NNCSD-062.a


title: tumor, ovary meta, pat008, rep1


title: 4T1, Day4, single cell 14


title: coloninc organoids_1,25(OH)2D3_24h_B


title: tumor, primary T2, pat007, rep1


title: tumor, primary T1b, pat007, rep1


title: 4T1, Day4, single cell 13


title: NNCSD-053.b


title: coloninc organoids_1,25(OH)2D3_24h_A


title: NNCSD-053.a


title: 4T1, Day4, single cell 12


title: coloninc organoids_vehicle_6h_C

value: Vehicle 6h


title: coloninc organoids_vehicle_6h_A


title: 4T1, Day4, single cell 10


title: NNCSD-052.b


title: coloninc organoids_1,25(OH)2D3_24h_C


title: tumor, primary T1a, pat007, rep1


title: coloninc organoids_vehicle_6h_B


title: 4T1, Day4, single cell 9


title: tumor, ovary meta, pat006, rep1


title: NNCSD-052.a


title: coloninc organoids_vehicle_24h_C

value: Vehicle 24h


title: tumor, primary T3, pat006, rep1


title: NNCSD-051.b

value: F


title: 4T1, Day4, single cell 8


title: NNCSD-051.a

value: UC - Active disease


title: tumor, primary T2, pat006, rep1


title: 4T1, Day4, single cell 7


title: coloninc organoids_vehicle_24h_A


title: NNCSD-049.b


title: tumor, primary T1b, pat006, rep1


title: tumor, ovary meta, pat006, rep2


title: coloninc organoids_vehicle_24h_B


title: 4T1, Day4, single cell 6


title: tumor, primary T1a, pat006, rep1


title: Colonic organoid, ChipB, sample, vitD

data_processing:
Raw ChIP-seq reads were trimmed with fastp with settings: --trim_poly_g --trim_poly_x --cut_tail --trim_front1 1
Trimmed reads were mapped to the hg38 canonical genome assembly with bowtie excluding multimapping reads (’-m 1’)
Each alignment bam file was sorted and duplicates marked with samtools
Peak calling was performed using MACS2 (v2.1.1.20160309) in two steps: first calling peaks against each samples own input control using 'macs2 callpeak' with the size estimates from SPP, and second calling differential peaks in contrast to other samples using 'macs2 bdgdiff' with the effective depth estimates from the first step.
mac2 callpeak produced the bigwig files
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: bed (’macs2 bdgdiff’ called peaks for the two samples for different treatments)

extract_protocol:
The 1,25(OH)2D3 / vehicle stimulated cells were fixed for 10 min in 1% formaldehyde (methanol free) and chromatin prepared for sheering at the Covaris M-220 sonicator using the truChIP Chromatin Shearing Kit (# 520154, Covaris) following manufacturer’s instruction. Chromatin sheering was continued until a product size of 150-300 bp was reached. The chromatin was prepared for IP with the rabbit IgG anti-VDR antibody (D2K6W, cat.no. 12550, Cell Signaling). The ChIP protocol are described in details in Kellermann et.al "Impaired vitamin D receptor signaling of crypt-top epithelial cells in flaring ulcerative colitis" - manuscript in preparation
ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Kit and NEBNext multiplex oligos for Illumina following manufacturer’s instruction as described in kellermann et.al "Impaired vitamin D receptor signaling of crypt-top epithelial cells in flaring ulcerative colitis" - manuscript in preparation

treatment_protocol: Organoids were treated with 1uM 1,25(OH)2D3 (cat.no. 71820, Cayman Chemical) or vehicle control for 2h.

tag: disease state


title: NNCSD-054.a


title: 4T1, Day4, single cell 5


title: Colonic organoid, ChipB, input, vitD


title: tumor, perit meta, pat005, rep2


title: 4T1, Day4, single cell 4


title: tumor, perit meta, pat005, rep1


title: NNCSD-048.b


title: 4T1, Day4, single cell 11


title: Colonic organoid, ChipA, sample, vitD


title: NNCSD-048.a


title: Colonic organoid, ChipA, input, vitD


title: NNCSD-046.b


title: 4T1, Day4, single cell 3


title: tumor, primary T3, pat005, rep1


title: 4T1, Day4, single cell 2


title: NNCSD-046.a


title: Colonic organoid, ChipB, sample, vehicle

value: vihecle (ethanol) for 2h


title: tumor, primary T2, pat005, rep1


title: Colonic organoid, ChipB, input, vehicle


title: 4T1, Day4, single cell 1


title: NNCSD-045.b


title: tumor, primary T1, pat005, rep1


title: NNCSD-049.a


title: YMHT3

first: Cuige

last: Shi

address: No.12, Dahuisi Road, Haidian District

institute: National Research Institute for Family Planning

data_processing:
Raw data (raw reads) were processed using Trimmomatic[1] . The reads containing ploy-N and the low quality reads were removed to obtain the clean reads. Then the clean reads were mapped to GRCm39 using hisat2.
FPKM value of each gene was calculated using cufflinks[4] , and the read counts of each gene were obtained by htseq-count.
DEGs were identified using the DESeq(2012) R package functions estimateSizeFactors and nbinomTest.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text filles include FPKM values for each Sample

source_name: hypothalamus tissue

growth_protocol: Mice were arranged for a regular light/dark cycle environment, providing free food and water throughout the study.

extract_protocol:
Total RNA from the hypothalamus was extracted using the the mirVana miRNA Isolation Kit (Ambion) according to the manufacturer's instructions.
Libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) following the manufacturer's requirements.

treatment_protocol: The animals were anesthetized and killed for spinal dislocation. Mice were anesthetized using sodium pentobarbital, followed by dislocation and euthanasia of the animals, and their heads were immediately placed on ice. The hypothalamus was removed via craniotomical and stored in liquid nitrogen.

value: hypothalamus tissue

tag: age

value: young mice, 12 weeks old


title: NNCSD-045.a

value: M


title: tumor, lung meta, pat004, rep1

value: Gastric Cancer


title: Colonic organoid, ChipA, input, vehicle

value: Healthy control


title: NNCSD-044.a


title: tumor, primary T3, pat004, rep1


title: NNCSD-044.b


title: tumor, primary T2, pat004, rep1


title: YMHT2


title: siRNA scrambled control bio rep 3

city: Brisbane

first: Brad

last: Balderson

state: QLD

address: Chemistry Bld, 68 Cooper Rd

department: The School of Chemistry and Molecular Bioscience

country: Australia

institute: The University of Queensland

description: Paired-end bulk RNA-seq of A2058 melanoma cells treated with a scrambled siRNA.

data_processing:
Raw sequencing data was converted to fastq files using bcl2fastq2 v2.18.0.
Paired-end bulk RNA-seq fastq file reads were mapped to the Hg19 reference genome using STAR v2.6.0.a with parameters “--outFilterMultimapNmax 2 --outSAMtype BAM Unsorted”.
Bam files were then sorted using samtools v1.10 with default settings
Gene counts were quantified using featureCounts v1.6.3 with parameters “-p -t exon”.
Genome_build: Hg19
Supplementary_files_format_and_content: counts.txt.gz,  sample_meta.txt

source_name: A2058_siRNA scrambled control

growth_protocol: Cells were seeded into 10cm dishes and cultured in DMEM at 70% confluency.

extract_protocol:
Overexpression and knockdown were confirmed using western blot prior to RNA isolation.  Once validated, RNA was extracted from these cells using an RNA extraction kit from Qiagen. Sample quality was confirmed using a Nanodrop and QC analysis was performed using a bioanalyzer to obtain RIN values.  Samples with appropriate RIN values were then chosen such that we had three independent triplicate samples for each condition.
RNA library preparation was performed using a Tru Seq stranded total RNA kit from Illumina. The library pool was diluted and denatured according to the standard NextSeq protocol (Document # 15048776 v02).
Sequencing was performed using the Illumina NextSeq 500 (NextSeq control software v2.1.0 / Real Time Analysis v2.4.11) to generate paired-end 76 bp reads using a 150 cycle NextSeq500/550 High Output reagent Kit v2 (illumina, FC-404-2002). Sequencing was performed at the Institute for Molecular Bioscience Sequencing Facility (University of Queensland).

treatment_protocol: Briefly, lentivirus was generated using Lenti-X 293 HEK cells. Two mastermixes were prepared: (1) 557μl reaction buffer (Clontech), 36μl (Clontech) and 7μg of pLVX vector-containing plasmid of interest; (2) 592.5μlreaction buffer (Clonetech) and 7.5μl polymer (Clontech). The two mastermixes were combined and incubated at room temperature for 20mins. The combined mastermix was added to the 10cm dish as droplets and incubated overnight at 37°C. The virus containing media was replaced by normal growth medium and incubated at 37°C for a further 48hrs. Virus particles were harvested by passing the media through a 0.45μm filter and were stored in -80°C until used. Lentiviral transduction was performed on cells grown in a 6-well plate at 70% confluency in media containing 8μg/ml polybrene. Viral particles were added into wells and centrifuged at room temperature at 2830rpm for 1 hr 30 minutes. media was replaced 24 hours post-centrifugation. Cells were then selected in media containing 1μg/μl puromycin prior to performing experiments.  siRNA transfection was performed using Lipofectamine 2000 as per the manufacturers protocol, with an siRNA concentration of 50 mM for 48 hours.

value: human melanoma cell line

value: siRNA scrambled


title: siRNA scrambled control bio rep 2


title: AMHT2

value: aging mice, 22 months old


title: AMHT3


title: NNCSD-043.a

value: Sigmoid colonic tissue

value: UC - Inactive disease


title: tumor, liver meta, pat003, rep2


title: tumor, primary T1, pat004, rep1


title: AMHT1


title: MITF siRNA bio rep 3

description: Paired-end bulk RNA-seq of A2058 melanoma cells treated with siRNA against MITF.

source_name: A2058_MITF siRNA

value: MITF siRNA


title: NNCSD-042.b


title: tumor, liver meta, pat003, rep1


title: Colonic organoid, ChipA, sample, vehicle

value: colonic organoids


title: MITF siRNA bio rep 2


title: tumor, primary T, pat003, rep1


title: Backfat, control diet, 5

city: Madrid

first: Patricia

last: Palma

address: Carretera de la Coruña, km 7,5

country: Spain

institute: INIA-CSIC

data_processing:
Quality analyses were performed on the reads using FastQC software (Babraham Bioinformatics, http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads were then mapped against the pig reference genome (Sscrofa11.1) using HISAT2. No additional trimming or filtering of reads was deemed necessary.
Reads counts were performed using HTSeq-count
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes counts per each sample

organism: Sus scrofa

source_name: Backfat

extract_protocol:
RNA was extracted using the RiboPureTM of High Quality total RNA kit (Ambion)
Library preparation and sequencing paired-end libraries were prepared using TruSeq SBS Kit v3-(Illumina)

value: Backfat

value: Iberian

value: control diet


title: Backfat, DOP diet, 5

value: DOP diet


title: NNCSD-042.a

value: F


title: MITF siRNA bio rep 1


title: tumor, liver meta, pat002, rep3


title: YMHT1

value: hypothalamus tissue


title: Backfat, DOP diet, 4


title: NNCSD-041.b

value: UC - Active disease


title: MITF bio rep 3

description: Paired-end bulk RNA-seq of A2058 melanoma cells treated with an LVX MITF vector.

value: LVX MITF vector


title: NNCSD-043.b

value: M


title: tumor, liver meta, pat002, rep2

value: Gastric Cancer


title: NNCSD-039.b


title: Backfat, DOP diet, 3


title: tumor, liver meta, pat002, rep1


title: siRNA scrambled control bio rep 1

value: human melanoma cell line


title: NNCSD-041.a


title: NNCSD-039.a


title: Backfat, DOP diet, 1


title: Backfat, DOP diet, 2


title: tumor, primary T2, pat002, rep1


title: LVX empty vector control bio rep 3

description: Paired-end bulk RNA-seq of A2058 melanoma cells treated with an LVX empty vector.

source_name: A2058_LVX empty vector control

value: LVX empty vector


title: tumor, primary T1, pat002, rep1


title: Backfat, WCOC diet, 5

value: WCOC diet


title: LVX empty vector control bio rep 2


title: MITF bio rep 1


title: NNCSD-037.b

value: Sigmoid colonic tissue


title: NNCSD-037.a


title: NNCSD-034.b


title: Backfat, WCOC diet, 4


title: tumor, primary T, pat001, rep1


title: LVX empty vector control bio rep 1


title: Backfat, WCOC diet, 3


title: MITF bio rep 2


title: NNCSD-034.a


title: Backfat, WCOC diet, 2


title: NNCSD-031B.b


title: HEK293T amplicon-seq

city: Guangzhou

first: Cheng

last: Chen

state: Guangdong

address: Kaiyuan Ave 190

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science

description: Amplicon-seq

data_processing:
library strategy:Amplicon-seq
Barcoding processing, read alignment, and gene counting were made using MGI-provided DNBelab_C_Series_HT_scRNA-analysis-software v1.0.
Normalization in Seurat ("LogNormalize")
Assembly: mm10
Supplementary files format and content: normalized UMI counts (mtx), gene names (tsv), and cellIDs (tsv); molecular table containing filtered lineage tracer calls.
Supplementary files format and content: Comma-separated value files and matrix files

growth_protocol: HEK293T cells were cultured in DMEM basic media supplemented with 10% FBS. mESCs were cultured on plates coated with 0.1% gelatin in DMEM high-glucose media containing 15% FBS, 1 mM sodium pyruvate, 1 mM non-essential amino acids (NEAA), 1% GlutaMAX, 0.1 mM 2-mercaptoethanol, 1000 U/ml leukemia inhibitory factor (LIF), 3 μM CHIR99021, and 1 μM PD0325901. All the cell lines were cultured in humidified incubators at 37℃ in 5% (v/v) CO2.

extract_protocol:
Embryoid bodies were dissociated by the Papain dissociation kit (Worthington). In brief, embryoid bodies were incubated in 1 ml Enzyme A along with 20 μl DnaseI at 37℃ for 20-25 min, followed by gentle blowing every 5 minutes with wide-bore tips.  HEK293T cells were dissociated using trypsin according to the user’s guide. After washing and filtering, a suitable volume of PBS with 0.04% BSA was added to resuspend the cells to achieve a cell concentration of 2x106 /ml.
Single-cell RNA libraries were prepared using DNBelab C4 kit (BGI-MGI) according to the user’s guide. The main steps of library preparation include droplet formation, demulsification, reverse transcription, second-strand synthesis, cDNA and oligo product amplification following size selection. Each obtained cDNA pool was divided into two parts. One part of cDNA was prepared by Single-cell RNA libraries were prepared using DNBelab C4 kit (BGI-MGI) according to the user’s guide. The main steps of library preparation include droplet formation, demulsification, reverse transcription, second-strand synthesis, cDNA and oligo product amplification following size selection. Each obtained cDNA pool was divided into two parts. One part of cDNA was prepared by fragmentation, end repair, adaptor ligation and PCR to get a cDNA library for scRNA-seq. Another part of cDNA was used for amplicon sequencing. Corresponding oligo libraries were generated by PCR amplification from oligo products.In order to better capture information on target site, we divided the obtained  cDNA into two portions. One portion was used for normal transcriptome sequencing, while the other portion was used for amplicon sequencing.fragmentation, end repair, adaptor ligation and PCR to get a cDNA library for scRNA-seq. Another part of cDNA was used for amplicon sequencing. Corresponding oligo libraries were generated by PCR amplification from oligo products.In order to better capture information on target site, we divided the obtained  cDNA into two portions. One portion was used for normal transcriptome sequencing, while the other portion was used for amplicon sequencing.

value: human embryonic kidney