title: Active; run2441

library_source: transcriptomic single cell

data_processing:
All scRNA-seq data were processed using Cell Ranger version 3.0.2 and hg19 reference.
Assembly: hg19
Supplementary files format and content: Matrix, feature barcode, cell barcode file containing gene read count per cell derived from Cell Ranger

extract_protocol:
For each sample, three biopsies from the distal esophagus of a donor were collected into RPMI medium with 10% FBS, kept on ice, and transported to the research laboratory within 30 minutes. The biopsies were then transferred into EDTA buffer (5 mM EDTA, 10% FBS, 1 mM HEPES in PBS) for 15 minutes in a 37ºC water bath, washed once with PBS, minced, and then subjected to collagenase A digestion (Roche, derived from Clostridium histolyticum, 2 mg/mL) in 10% FBS-RPMI at 37ºC for 30 minutes. The resulting suspension was diluted with 10 mL ice-cold PBS, passed through a 19-gauge needle 5 times, filtered through 2 layers of gauze, washed twice with ice-cold PBS (10 mL each), and then centrifuged at 450 g for 5 minutes, resulting in a visible, clear-edged, translucent pellet. Isolated cells were subjected to 10X Genomics sequencing in the CCHMC Gene Expression Core according to the manufacturer instructions.
Bulk population cells were directly subjected to the 10X mass genomics chip (10X Genomics, Inc.), targeting 10,000 simultaneously captured live events. Each cell was uniquely barcoded during the cDNA library generation by Single Cell 3’ Reagent Kits v2 per manufacturer instructions
10x scRNA-seq, Single Cell 3' v2

value: whole biopsy

tag: group

value: Active EoE


title: Remiss; run2442

status: Public on Jun 15 2022

type: SRA

city: Cincinnati

first: Hee-Woong

last: Lim

state: Ohio

address: 3333 Burnet Ave. MLC 7024

department: Division of Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital Medical Center

molecule: total RNA

organism: Homo sapiens

source_name: esophageal biopsy

tag: tissue

value: esophageal biopsy

tag: cell type

value: Remission EoE


title: Remiss; run2312


title: lesion_3

city: Grand Rapids

first: Gregory

last: Burns

state: MI

address: 400 Monroe Ave NW

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

library_source: transcriptomic

data_processing:
Adapter and quality trimming with TrimGalore (version 0.6.5)
Read quality assessment with FastQC (version 0.11.7)
Mapped with HISAT2 (version 2.1.0)
Reads overlapping Ensembl annotations (version 93) were quantified with featureCounts (version 1.6.2)
Genes with low expression were filtered with the edgeR filterByExpr function in edgeR (version 4.0.3)
Differential expression analysis using the edgeR-robust method (version 4.0.3)
Assembly: Panu_3.0
Supplementary files format and content: Tab separated text output from featureCounts with read counts per gene for each sample.

molecule: polyA RNA

organism: Papio anubis

source_name: Endometriotic Lesion

extract_protocol:
Trizol
NEBBext Ultra II RNA Library Prep kit for Illumina

tag: disease status

value: spontaneous


title: lesion_2


title: endo_1

source_name: Endometrium


title: endo_2


title: lesion_1


title: lesion_4


title: Normal; run2422

value: Healthy control


title: endo_3


title: (Rd): leg, collected 0h after amputation, adult animal 80, R side, distal part [Rd_0_R_80]

city: Lyon

first: Mathilde

last: PARIS

address: 32-34 Av. Tony Garnier

country: France

institute: CNRS

description: Regeneration dataset (Rd): leg, collected 0h after amputation, from adult animal 80, R side. distal part of the leg.

data_processing:
Reads were mapped to custom made gene models built on the Phaw_5.0 genome assembly, using kallisto v. 0.42.5 (Bray et al. 2016).
We noticed that some genes were erroneously split in our gene annotation (genes described in the gtf file and referred by 'gene_ID' in the correspondance table). The split genes we identified were kept unmodified in the gtf file because the exact positions of the exon junctions were not known. Merging was done after read mapping by simply adding up the read counts or tpm of the split genes. The list of those modified gene models are referred to by 'RNAseq_gene_ID' in the correspondance table. Count and tpm levels are provided for those merged genes only.
Genome_build: Phaw_5.0 (https://www.ncbi.nlm.nih.gov/assembly/GCA_001587735.2/)
Supplementary_files_format_and_content: Gene model annotation of the genome, on which the reads were mapped (gtf format)
Supplementary_files_format_and_content: Correspondance table between gene names from the annotation on which reads were mapped (column gene_ID) and gene names processed in the count and tpm matrices (column RNAseq_gene_ID)
Supplementary_files_format_and_content: Table of gene abundance measurements, in counts (1 value per gene per sample)
Supplementary_files_format_and_content: Table of gene abundance measurements, in tpm (1 value per gene per sample)

organism: Parhyale hawaiensis

source_name: Part of the adult T4 leg distal to the amputation plain: carpus

growth_protocol:
To grow animals prior to collecting embryonic limbs, Parhyale females of the Chicago-F inbred line (Kao et al. 2016) were collected after fertilization, and their embryos removed about 3 days post fertilization. Each brood was kept separately, in a temperature-controlled incubator set to 27˚C, in sterile 6-well plates (Costar, #3516), in filtered artificial seawater (FASW; salinity at 30 PSU) containing antibiotics (Gibco #15240-062, at 1X final concentration).
To grow adults prior to collecting regeneration limbs, adult males of the Chicago-F line (Kao et al. 2016) and the DistalDsRed line (Kontarakis et al. 2011), measuring ~1 cm in length and with no damaged appendages, were selected and kept individually in homogeneous conditions – photoperiod (12:12 hours light:dark cycle), temperature (25-26˚C) and medium (individual containers separated by mesh, sharing artificial seawater at 30 PSU) – for three months prior to experiment. The same conditions were kept during the course of sampling. Sampling was performed between 8:00 and 10:00 am.

extract_protocol:
For the embryonic samples, embryos were dissected in the lid of a 5 ml Protein LoBind Tube (Eppendorf, #0030108302), in 1% BSA in FASW (80 ul). The eggshell was removed with fine forceps (Fine Science Tools, #11254-20), and legs were dissected with borosilicate needles (pulled capillaries; Sutter, #B100-50-15). Samples were transferred in 100 ul of ice-cold lysis solution (Agilent Absolutely RNA Nanoprep kit, #400753), homogenized though brief pipetting, and flash-frozen in liquid nitrogen. RNA extraction was performed with the Agilent Absolutely RNA Nanoprep kit (#400753), following manufacturer's instructions, and eluted in 10 ul of elution buffer. RNA extraction was performed in randomized batches, to avoid shared batch effects in biological replicates.
For the adult samples, leg fragments were transferred immediately after dissection in 1.5 ml LowBind tubes with 500 ul of ice-cold lysis buffer (Reliaprep RNA Tissue MiniPrep System - Promega, #Z6111), vortexed, then transferred to a sterile multiwell plate for manual disruption of cuticle with a clean surgical blade. The sample was then re-transferred to the tube, vortexed, and frozen in liquid nitrogen, for then being stored at -80°C until further processing. RNA extraction was randomized, avoiding to process at the same time related samples. RNA was extracted with the Reliaprep RNA Tissue MiniPrep System (Promega, #Z6111), and eluted in 15 ul of nuclease-free water (Invitrogen, #AM9937).
1ng of RNA was used for cDNA synthesis. For samples from embryonic legs, RNA concentration was too low to be directly quantified, 9ul of RNA solution was used for cDNA synthesis over 15 cycles of LD-PCR, using the SMART-Seq v4 Ultra Low Input RNA kit for sequencing (Takara Bio, #634898) and the SeqAmp DNA Polymerase (Takara Bio, #638509); 1 ul of cDNA was then used for Qubit quantification (4.0 HS DNA), measuring in the range of 0.2- 0-7 ng/ul. Libraries were synthesized from 1 ng of cDNA, using the Nextera XT DNA Library Preparation Kit (Illumina, #FC-131-1096; with Dual indexing strategy, i7 and i5), and with a protocol that included an accelerated cooling step on ice after the 55°C step. Quantification and validation of libraries were done with both Qubit 4.0 (HS DNA kit, Thermofisher) and Tapestation D5000 equipment using the D5000 ScreenTape System (Agilent, #5067- 5588 and #5067- 5589).

tag: dissected part of the leg

value: distal

tag: collection time (hours post amputation)

tag: collection time (hours post fertilization)

tag: collection time (days relative to molting)

tag: animal id

tag: left or right leg

value: R


title: Active; run2326


title: Active; run2403


title: SOX9OE_H3S28PCUT&Tag

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer

library_source: genomic

data_processing:
Library strategy: CUT&TAG
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
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tracks in BigWig file format

molecule: genomic DNA

source_name: Umbilical vein endothelial cells

growth_protocol: HUVECs were cultivated in Medium 200 (Thermo Fisher Scientific) supplemented with 2% low serum growth supplement  and 1% Penicillin Streptomycin.

extract_protocol:
CUT&RUN, CUT&Tag, ATAC-seq
NEBnext DNA Ultra ii (New England Biolabs)

tag: cell line

value: HUVEC

tag: transduced with

value: SOX9 expression plasmid

tag: cut&run/tag antibody

value: H3S28P (ab5169, Abcam)


title: Active; run2233


title: Active; run2295


title: Remiss; run2242


title: SOX9OE_SOX9CUT&RUN_24h

data_processing:
Library strategy: CUT&RUN
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
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tracks in BigWig file format

value: SOX9 (AB5535, Millipore)


title: SOX9OE_SOX9CUT&RUN_96h


title: 011116 11RAP podo high ecadh high NL

data_processing:
RNA sequencing analysis was performed by BioWardrobe
Adapter sequences were trimmed from unaligned reads using TrimGalore.
Alignment of trimmed raw sequencing data to Homo sapiens (GRCh37/hg19) reference genome is done by STAR allowing maximum 5 mismatches and reporting only uniquelly mapped reads.
Mapped reads are then being sorted and indexed by Samtools sort and index utilities. Sorted reads are used for RPKM calculation.
Assembly: hg19
Supplementary files format and content: Excel file containing read counts per gene including RefSeq ID, gene symbol, raw read count, and RPKM-normalized read count

growth_protocol: Three biopsies collected from the distal esophagus typically yielded ~2,500–10,000 epithelial cells in each subpopulation, which were subsequently collected into RPMI-1640 media supplemented with 10% FBS and pelleted/centrifuged for immediate RNA isolation procedures

extract_protocol:
RNeasy Micro Kit (Qiagen).
Total RNA was amplified using the Ovation RNA-Seq System v2 assay (Tecan Genomics) according to the manufacturer’s protocol. The libraries were prepared with the Nextera XT DNA Sample Preparation kit (Illumina Technologies).

value: basal epithelium

tag: treatment

value: Healthy controls


title: DHA6_EXP

first: Rebekah

last: Karns

state: OH

address: 3333 Burnet Ave

department: Gastroenterology, Hepatology, & Nutrition

description: Mammary epithelial cells from milk fat globules obtained at 4 weeks postpartum in mother who delivered at 27.2 weeks who was treated postnatally with 1000mg DHA

data_processing:
Reads mapped to the human genome assembly hg19 using TopHat (http://tophat.cbcb.umd.edu) and NCBI’s Reference Sequence annotations.
Genome_build: hg19

source_name: milk fat globules containing mammary epithelial cell content

extract_protocol:
Fat layer containing mammary epithelial cell contents from fresh milk sample placed into a 2mL tube with 500 μL of TRIzol LS (Thermo Fisher Scientific, Waltham, MA)
To extract the mRNA, 200 μL of chloroform was added and samples were gently inverted by hand for 15 seconds and incubated for 5 minutes at room temperature.
The pure mRNA was isolated and purified using the PROMEGA Maxwell 16™ integrated system (Promega Corporation, Madison, WI)
The samples were checked for quality and quantity using the Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific, Waltham, MA) and the Agilent 2100 Bioanalyzer (Agilent, Santa Clara, CA).
Samples sequenced using the Illumina HiSeq 2000 (Illumina, Inc., San Diego, CA) and reads were trimmed for quality and aligned using BaseSpace RNA-seq Alignment v2.02. (Illumina, Inc., San Diego, CA) and STAR (Illumina, Inc., San Diego, CA). Salmon (Illumina, Inc., San Diego, CA) was used for quantification (TPM).
Standard poly-A RNA-seq SR 1x85bp, 50M reads

treatment_protocol: Randomly assigned to 1000mg/day or 200mg/day DHA during the first week postpartum

tag: gestational age

tag: time of milk sample

value: week 4 postpartum

value: 1000mg DHA


title: DHA7_STD

description: Mammary epithelial cells from milk fat globules obtained at 4 weeks postpartum in mother who delivered at 25.5 weeks and was treated postnatally with 200mg DHA

value: 200mg DHA


title: DHA10_EXP

description: Mammary epithelial cells from milk fat globules obtained at 4 weeks postpartum in mother who delivered at 25 weeks who was treated postnatally with 1000mg DHA


title: Empty_H3S28PCUT&Tag

value: Empty vector


title: Empty_SOX9CUT&RUN


title: DHA1_EXP

description: Mammary epithelial cells from milk fat globules obtained at 4 weeks postpartum in mother who delivered at 28.6 weeks who was treated postnatally with 1000mg DHA


title: DHA8_EXP


title: Z-138

city: Vancouver BC

first: Christian

last: Steidl

state: British Columbia

address: 675, West 10th Ave

department: Department of Lymphoid Cancer Research

data_processing:
RNA sequencing reads from each cell line were aligned to the hg19 reference using the STAR aligner (v2.5.2a), which also generated per-gene counts with HTSeq.
To compare the expression of the Ca2+ channel genes between different pathological groups, RNA sequencing counts from all samples were analyzed in R (v3.6.1) using the DESeq2 package (v1.26.0).
Counts from all cell lines were read into a merged DESeqDataSet object, and lowly expressed genes (1 or fewer counts across all samples) were removed. The count data were then normalized using a variance-stabilizing transformation (vst function). Pairwise t-tests were used to compare normalized counts of the Ca2+ channel genes between each combination of pathologies. For specific comparisons of interest, differential expression was also performed between pathological pairs (DESeq function), and the results for the Ca2+ channel genes (p value, adjusted p value (q value), and log2 fold change) were assessed.
Genome_build: hg19
Supplementary_files_format_and_content: DESEQeq output files (normalized abundance measurements): differential expression between (1) ABC-DLBCL vs GCB-DLBCL cell lines, (2) cHL vs other B-cell lymphoma cell lines, (3) PMBCL vs other B-cell lymphoma cell lines
Supplementary_files_format_and_content: Normalized abundance measurements (normalized with the DESeq2 variance stabilizing transformation)

source_name: Cell line

extract_protocol: RNA sequencing data were generated using standard Illumina protocols at the British Columbia Cancer Research Centre from 44 lymphoma cell lines representing multiple pathologies. These datasets were generated at multiple timepoints.

tag: pathology

value: Mantle Cell Lymphoma

tag: read length


title: DHA9_STD

description: Mammary epithelial cells from milk fat globules obtained at 4 weeks postpartum in mother who delivered at 26.1 weeks and was treated postnatally with 200mg DHA


title: Alb-vE8

city: Jacksonville

first: Yingxue

last: Ren

state: FL

address: 4500 San Pablo Rd S

institute: Mayo Clinic

data_processing:
The single cell sequence preprocessing was performed using the standard10X Genomics Cell Ranger Single Cell Software Suite v.3.0.0.
Raw sequencing data were demultiplexed, aligned to the mouse genome mm10, and the reads aligned to each gene were counted. Cell filtration, normalization, clustering and differential expression analyses were performed using Seurat v.4.0.
Assembly: mm10
Supplementary files format and content: matrix files

organism: Mus musculus

source_name: cortex

extract_protocol:
Mice were transcardially perfused with PBS and the cortical tissues were quickly dissected and enzymatically digested using the Neural Tissue Dissociation kit (P) (Cat#130-092-628, Myltenyi Biotec) at 37˚C in the gentleMACS™ Octo Dissociator with Heaters (Myltenyi Biotec). The myelin was then removed using magnetic bead separation (Myelin Removal Beads II, Cat#130-096-733, Myltenyi Biotec). After myelin removal and red blood cell removal (Cat.# 130-094-183, Miltenyi Biotec), microglia and debris were removed by magnetic separation using anti-CD11b+ microbeads (Cat. #130-049-601, Miltenyi Biotec), followed by a dead cell removal kit (Cat. #130-090-101, Miltenyi Biotec) according to the manufacturer’s instruction. The final cell pellet was suspended in Ca/Mg-free PBS supplemented with 0.5% FBS for downstream analysis. In all samples, more than 90% of the cells were viable based on trypan blue examination.
Single-cell RNA-seq (scRNAseq) was performed on the isolated cortical samples using the Chromium platform (10x Genomics, Pleasanton, CA) with the 3′ gene expression (3′ GEX) V3 kit, using a targeted input of ~ 3000 cells per sample. In brief, gel-beads in emulsions (GEMs) were generated on the sample chip in the Chromium controller. Barcoded cDNA was extracted from the GEMs using Post-GEM RT-cleanup and amplified for 12 cycles. Amplified cDNA was fragmented and subjected to end-repair, poly-A-tailing, adaptor ligation, and 10X-specific sample indexing following the manufacturer’s protocol. Libraries were quantified using the TapeStation (Agilent) analysis and then sequenced on a HiSeq 4000 instrument (Illumina, San Diego, CA) targeting a depth of ~50,000 reads per cell.

tag: background strain

tag: genotype

value: Cre+


title: U-HO1

value: Classical Hodgkin Lymphoma


title: SOX9OE_SOX9CUT&RUN_48h


title: Alb-vE6


title: Alb-vE9


title: Alb-vE5

value: Cre-


title: SOX9OE_SOX9CUT&RUN_72h


title: DHA5_EXP

description: Mammary epithelial cells from milk fat globules obtained at 4 weeks postpartum in mother who delivered at 26.2 weeks who was treated postnatally with 1000mg DHA


title: Toledo

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)


title: SUP-HD1


title: Alb-vE3


title: Stromal_cells_AML_1

type: RNA

city: Mainz

first: Pablo

last: Llavona

state: Rhineland-Palatinate

address: Institute of Molecular Biology gGmbH (IMB), Ackermannweg 4

country: Germany

institute: IMB

hyb_protocol: Hybridization to Mouse Gene ST 2.2 SST microarrays (Affymetrix, Santa Clara, CA) according to standard protocols.

scan_protocol: Scanned by GeneChip Scanner 3000 7G system (Affymetrix, Santa Clara, CA) according to standard protocols.

data_processing:
The primary microarray data was normalized and analyzed using R with limma and lumi packages.
False discovery rate (FDR, cut off analysis < 0.1) was used for multiple test correction.

label: GeneChip wild-type terminal labelling kit (Affymetrix)

source_name: Mus musculus with CML

label_protocol: Amplified cRNA was labelled with the GeneChip wild-type terminal labelling kit (Affymetrix, Santa Clara, CA).

growth_protocol: Primary sorted cells

extract_protocol: RNA was extracted using RNeasy Plus Micro Kit (Qiagen, Germantown, MD).

tag: tissue

value: bone marrow

tag: cell type

value: osteoblastic cells

value: Col2.3 GFP


title: Stromal_cells_CML_3


title: Stromal_cells_CML_2


title: Stromal_cells_AML_3


title: DHA4_STD

description: Mammary epithelial cells from milk fat globules obtained at 4 weeks postpartum in mother who delivered at 27.5 weeks and was treated postnatally with 200mg DHA


title: Normal; run2272

value: esophageal biopsy

value: whole biopsy

tag: group

value: Healthy control


title: Stromal_cells_CML_1


title: SU-DHL-5


title: U-2940

value: Primary Mediastinal B-cell Lymphoma


title: DHA2_STD


title: Alb-vE4


title: Alb-vE12


title: Alb-vE16


title: Alb-vE2


title: Alb-vE11


title: Stromal_cells_AML_2


title: Alb-vE7


title: SU-DHL-8

value: Diffuse Large B-cell Lymphoma (Activated B-cell-like)


title: Alb-vE10


title: Alb-vE1


title: Ramos

value: Burkitt’s Lymphoma


title: Alb-vE15


title: Alb-vE14


title: Raji


title: Pfeiffer


title: OCI-Ly3


title: Alb-vE13


title: SU-DHL-4


title: SC - OHT+DREADD replicate 10

city: Leuven

first: Lieve

last: Moons

state: Vlaams-Brabant

address: Naamsestraat 61

department: Biology

country: Belgium

institute: KU Leuven

data_processing:
Quality control of raw reads was performed with FastQC v0.11.7. [27] and adapters were filtered with ea-utils fastq-mcf v1.05.
Splice-aware alignment was performed with HiSat2 against the Mus musculus reference genome mm10 using the default parameters. Reads mapping to multiple loci in the reference genome were discarded. Resulting BAM alignment files were handled with Samtools v1.5.
Quantification of reads per gene was performed with HT-seq Count v2.7.14.
Differential gene expression analysis was performed with the R/Bioconductor EdgeR package (v3.14.) in R studio (v2021.09.1, build 372).
Non-expressed genes were filtered out by requiring that more than 5 reads should have been detected in at least 2 samples.
Assembly: mm10
Supplementary files format and content: Excel files including raw counts for all retinal ganglion (Raw counts_RGC samples) or superior colliculus (Raw counts_SC samples) samples

source_name: Superior colliculus

extract_protocol:
RNA was extracted using the DirectZol (Zymo Research) for RGC samples and using TRI reagent (Ambion, Life Technologies) and the RNeasy Micro kit (Qiagen) for collicular samples, according to the manufacturer’s instructions.
Libraries were prepared using the SmartSeq2 (RGC samples) or the Lexogen Quantseq (collicular samples) kits following manufacturer's protocols.

value: Superior colliculus

value: Neurons and glia

value: WT

value: Ocular hypertension + DREADD stimulation (hM3Dq, 5 weeks)


title: SC - OHT+DREADD replicate 7


title: Mino

value: Mantle Cell Lymphoma


title: SP-49


title: SC - OHT+DREADD replicate 6


title: REC-1


title: SU-DHL-10


title: SP-53


title: SC - OHT+DREADD replicate 9


title: SC - OHT+DREADD replicate 5


title: MD903


title: SC - OHT+DREADD replicate 8


title: OCI-Ly1


title: SC - OHT+DREADD replicate 4


title: MedB-1


title: SC - OHT+DREADD replicate 3


title: SC - OHT+DREADD replicate 2


title: L-540

value: Classical Hodgkin Lymphoma


title: SC - OHT+DREADD replicate 1


title: SC - SHAM+DREADD replicate 10

value: DREADD stimulation (hM3Dq, 5 weeks)


title: JVM2


title: Jeko-1


title: SC - SHAM+DREADD replicate 8


title: HBL-1


title: SC - SHAM+DREADD replicate 6


title: SC - SHAM+DREADD replicate 5


title: GRANTA519


title: SC - SHAM+DREADD replicate 7


title: RNA_ECM_No_ECM_15

city: Urbana

first: Zeynep

last: Madak Erdogan

state: IL

address: 1201 S Goodwin Ave

department: FSHN

institute: UIUC

description:
RNAseq_ECM
RNAseq_ECM_rnaseq_featurecounts.txt

data_processing:
Reads from the HiSeq 2000 were processed and analyzed through a series of steps. Base calling and de-multiplexing of samples within each lane were done with Casava 1.8.2.
For RNAseq, STAR (version 2.7.6a) was employed to map RNA-Seq reads to either version mm39 of the Mus musculus reference genome, GRCm39, from NCBI Genome Reference Consortium Mouse Build 39 or version GRCh38.p13 of the human reference genome from NCBI Genome Reference Consortium Human Build 38 patch release 13. For ChIPseq, Bowtie2 was employed to obtain BAM files.
For RNAseq, gene expression values (raw read counts) from BAM files were calculated using FeatureCounts function from the Subread module (version 2.0.0). For ChIPseq, gene expression values (raw read counts) from BAM files were calculated using BigWig and outputed as BW files.
DESeq normalization algorithm with DESeq2 module in R using default values was used.  Differentially expressed genes were then determined by fold-change and p-value for each gene for each treatment relative to the vehicle control.
Genome_build: mm39 for mouse, GRCh38.p13 for human

growth_protocol: MCF7 (ATCC HTB-22) (RRID:CVCL_0031) and T47D (ATCC HTB-133) (RRID:CVCL_0553) parental cells were cultured in RPMI-1640 medium with NEAA salts (Sigma, St Louis, MO, USA), 5% fetal bovine serum (FBS)  (HyClone, Logan, UT), 100 μg/mL penicillin/streptomycin (Invitrogen, Carlsbad, CA, USA) and 50 mg/mL Gentamicin (Gibco, Gaithersburg, MD). MCF7/ESR1D537S and - ESR1Y537S cells (RRID:CVCL_0031-citation needed) were cultured in Dulbecco’s Modified Eagle Medium (DMEM) with NEAA salts, 10% FBS, 100 μg/mL penicillin/streptomycin, and 50 mg/mL gentamicin. T47D ESR1D537S and T47D ESR1Y537S cells (RRID: CVCL_0553-citation needed) were cultured in Modified Eagle Medium (MEM) with NEAA salts, 10% FBS, 100 μg/mL penicillin/streptomycin, and 50 mg/mL gentamicin. Cell line authentication was performed by checking activity and expression of ERα, proliferative responses to ER agonists and antagonists for all cell lines, and sequencing of MCF7/ESR1Y537S and MCF7/ESR1D537G as described.

extract_protocol:
RNA extraction: For gene expression analysis, total RNA was extracted from at least 3 biological replicates for each ligand treatment using Trizol reagent and further cleaned using the RNAeasy kit from QIAGEN.                           ChIP-seq analysis was performed as described previously using MCF7-ESR1Y537S cells. ChIP: ERα–DNA or IgG–DNA complexes were immunoprecipitated using ERα- specific F10 and HC20 antibodies (Santa Cruz Biotech, 3:100 dilution).
Once the sample quality and replicate reproducibility was verified at least 2 samples from each group were subjected to sequencing. RNA at a concentration of 100 ng/µL in nuclease-free water was used for library construction.The RNAseq libraries were prepared with Illumina's 'TruSeq Stranded RNAseq Sample Prep kit.  The libraries were quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq2000  using a TruSeq SBS sequencing kit version 3. Fastq files were generated with the software Casava 1.8.2 (Illumina). Briefly, the poly-A containing mRNA was purified from total RNA, RNA was fragmented, double-stranded cDNA was generated from fragmented RNA, and adapters were ligated to the ends.                                                                                ChIP DNA was obtained from three pooled biological replicates. Libraries were prepared according to Illumina Solexa ChIP-Seq sample processing (San Diego, CA), and single-read sequencing was performed using the Illumina HiSeq 2000. Sequences generated were mapped uniquely onto the human genome (hg18) by Bowtie2 (RRID:SCR_016368). The MACS (model-based analysis of ChIP-seq) algorithm was used to identify enriched peak regions (default settings) with a P value cutoff of 6.0e−7 and FDR of 0.01, as we have described.

treatment_protocol: In vivo study: four-week-old, ovariectomized, NOD SCID gamma (NSG) immunodeficient female mice were obtained from The Jackson Laboratory (Bar Harbor, ME).After one week of acclimatization to the housing facility, we injected 1×106 MCF7-ESR1Y537S cells resuspended in 1% PBS via tail vein and randomized animals to indicated treatment groups.We randomized N=8 mice to one of the two treatments Vehicle (Veh) or Fulv in each diet group. Fulv (Sigma) was dissolved in 10% DMSO and 90% corn oil and administrated via intramuscular injection (100 mg/kg) twice a week (Monday, Friday) for four weeks. In vitro study, IN SITE Metastasis Kit (Xylyx Bio, Inc., NY) containing TissueSpec Bone (MTSBN101), Liver (MTSLV101), and Lung (MTSLG101) ECM Hydrogels, were used to model tumor microenvironments according to the manufacturer’s protocol. Briefly, 2×103 cells were encapsulated in corresponding extracellular matrix (ECM) hydrogels by mixing them with tissue culture matrix. A mixture volume of 100 uL/well was placed in 96-well plates in triplicate. Plates were incubated at 37°C in a humidified environment with 5% CO2 for at least 45 minutes to achieve gelation. Cells were treated with media containing Veh or 1μM Fulv every Monday and Friday for three weeks.

tag: Sex

value: female

value: 2D plastic vehicle

value: Human Breast cancer cell

tag: strain

value: ATCC HTB-22 (RRID:CVCL_0031)


title: HT

value: Diffuse Large B-cell Lymphoma (Germinal Centre B-cell-like)


title: HDLM-2


title: SC - SHAM+DREADD replicate 2


title: SC - SHAM+DREADD replicate 4


title: RNA_ECM_No_ECM_13


title: L-591


title: SC - SHAM+DREADD replicate 3


title: SC - SHAM+DREADD replicate 9


title: SC - OHT replicate 11

value: Ocular hypertension (5 weeks)


title: L-1236


title: RNA_ECM_No_ECM_14


title: RNA_ECM_Lung_1

value: Lung (MTSLG101) extracellular matrix hydrogel


title: RNA_ECM_Lung_3


title: RNA_ECM_Lung_2


title: SC - OHT replicate 9


title: RNA_ECM_Liver_3

value: Liver (MTSLV101) extracellular matrix hydrogel


title: RNA_ECM_Liver_1


title: RNA_ECM_Liver_2


title: SC - OHT replicate 10


title: SC - OHT replicate 8


title: SC - OHT replicate 7


title: RNA_ECM_Bone_3

value: Bone (MTSBN101) extracellular matrix hydrogel


title: RNA_ECM_Bone_2


title: SC - SHAM+DREADD replicate 1


title: SC - OHT replicate 5


title: SC - OHT replicate 4


title: 2D_serm_Vehicle3

description:
RNAseq_2Dserm
2D_Serm_rnaseq_featurecounts.txt

value: Vehicle


title: SC - SHAM replicate 10

value: Superior colliculus

value: Sham


title: SC - OHT replicate 2

value: Neurons and glia

value: WT


title: 2D_serm_TAM3


title: 2D_serm_Vehicle1


title: 2D_serm_Vehicle2


title: 2D_serm_TAM2


title: SC - OHT replicate 1


title: SC - SHAM replicate 9


title: SC - SHAM replicate 8


title: 2D_serm_TAM1


title: 2D_serm_Palb3

value: Palbociclib


title: SC - SHAM replicate 7


title: RNA_ECM_Bone_1


title: 2D_serm_Fulv3

value: Fulvestrant


title: SC - OHT replicate 6


title: SC - SHAM replicate 5


title: 2D_serm_Palb2


title: SC - SHAM replicate 6


title: 2D_serm_Palb1


title: 2D_serm_Fulv1


title: SC - SHAM replicate 4


title: SC - OHT replicate 3


title: SC - SHAM replicate 1

value: Ocular hypertension + DREADD stimulation (hM3Dq, 5 weeks)


title: ChIP_ECM_No_ECM_input

description:
ChIPseq_ECM
Refined_NO_ECM_PD_AGGTTCCT-TCGAACCT_L001.Q10.bw

value: female

value: ERα- specific F10 and HC20 antibodies


title: SC - SHAM replicate 2


title: RGC - OHT+DREADD replicate 10

source_name: Retina

value: Retina

value: Retinal ganglion cell


title: RGC - OHT+DREADD replicate 8


title: ChIP_ECM_Lung_input

description:
ChIPseq_ECM
Refined_LUNG_PD_CCACAACA-CATCCAAG_L001.Q10.bw

value: Human Breast cancer cell

value: ATCC HTB-22 (RRID:CVCL_0031)


title: RGC - OHT+DREADD replicate 9


title: RGC - OHT+DREADD replicate 5


title: ChIP_ECM_Liver_input

description:
ChIPseq_ECM
Refined_LIVER_PD_AAGTCCTC-AGCTACCA_L001.Q10.bw


title: ChIP_ECM_Bone_PD

description:
ChIPseq_ECM
Refined_BONE_PD_GAACCTTC-CAAGGTAC_L001.Q10.bw


title: ChIP_ECM_Bone_input


title: LNCaP-miR3622-KO rep1

city: Birmingham

first: Lizhong

last: Wang

address: 740 20th St S

institute: UAB

description:
Processed data file.txt
YZ-LN3622-1A

data_processing:
In our project, we sequenced 4 samples on BGISEQ-500 Platform in total
After reads filtering, we map clean reads to reference genome using HISAT
IGV(Integrative Genomics Viewer) tool can be used to review the mapping result.
we use StringTie to reconstruct transcripts, and with genome annotation information we identify novel transcripts by using Cuffcompare(a tool of Cufflinks ) and predict the coding ability of those new transcripts using CPC
After genome mapping, we use GATK to call  SNP  and  INDEL  variant for each sample.
Genome_build: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: prostate cancer cells

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

value: LNCaP

value: androgen-sensitive human prostate adenocarcinoma cells


title: RGC - OHT+DREADD replicate 4


title: ChIP_ECM_Liver_PD


title: RGC - OHT+DREADD replicate 2


title: SC - SHAM replicate 3


title: RGC - OHT+DREADD replicate 3


title: LNCaP-WT rep2

description:
Processed data file.txt
YZ-LN-2A


title: 2D_serm_Fulv2


title: RGC - OHT+DREADD replicate 6


title: LNCaP-miR3622-KO rep2

description:
Processed data file.txt
YZ-LN3622-2A


title: ChIP_ECM_No_ECM_PD


title: RGC - SHAM+DREADD replicate 10

value: DREADD stimulation (hM3Dq, 5 weeks)


title: ChIP_ECM_Lung_PD


title: RGC - SHAM+DREADD replicate 9


title: RGC - SHAM+DREADD replicate 7


title: RGC - OHT+DREADD replicate 1


title: RGC - SHAM+DREADD replicate 4


title: RGC - OHT+DREADD replicate 7


title: RGC - SHAM+DREADD replicate 6


title: RGC - SHAM+DREADD replicate 5


title: RGC - SHAM+DREADD replicate 3


title: RGC - SHAM+DREADD replicate 2


title: RGC - OHT replicate 11

value: Ocular hypertension (5 weeks)


title: RGC - OHT replicate 10


title: LNCaP-WT rep1

description:
Processed data file.txt
YZ-LN-1A


title: H19-13O

city: Utrecht

first: Onno

last: Kranenburg

address: Heidelberglaan 100

country: Netherlands

institute: UMC Utrecht

data_processing:
Mapping: Reads were aligned to GRCm38 using STAR v2.4.2a using the default parameters
ReadCounting: Readcounting was done with htseq-count v0.6.1p1 using the union mode with the GRCm38.70 version of  the GTF file as annotation
RPKM table was generated using EdgeR v3.8.6
Normalized counts table was generated using DESeq 1.18.0
Runs:https://github.com/UMCUGenetics/RNASeq
Workflow:https://github.com/UMCUGenetics/RNASeq/blob/develop/Workflow_RNASeq_pipeline.pdf
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text file with matrix of raw gene counts for every gene and every sample

source_name: peritoneal metastasis

extract_protocol:
Tumor samples were resected and snap frozen within one hour after resecting. RNA was harvested with RNeasy® Mini Kit; Qiagen. Generation of sequencing libraries was performed using the Truseq RNA stranded poly A Library Preparation Kit (Illumina, San Diego, CA, USA). Sequencing was performed on Illumina NextSeq500 with 75-bp reads (Illumina)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: patient

tag: tnmstage

tag: location primary tumor

value: sigmoid

tag: differentiation grade

value: moderate

value: unknown


title: RGC - SHAM+DREADD replicate 8

value: WT


title: RGC - OHT replicate 9


title: RGC - OHT replicate 7


title: H19-13P

source_name: liver metastasis


title: RGC - OHT replicate 3


title: H19-13F

source_name: primary tumor


title: RGC - OHT replicate 2


title: RGC - OHT replicate 6


title: H19-13M

source_name: lymph node metastasis


title: RGC - OHT replicate 8


title: H19-13N


title: H19-13I


title: H19-13H


title: H19-13D


title: H19-13G


title: RGC - SHAM replicate 10

value: Sham


title: RGC - OHT replicate 1


title: RGC - OHT replicate 4


title: RGC - SHAM replicate 9


title: H19-13C


title: H19-13E


title: H19-11M

value: coecum

value: mucineus

value: BRAF


title: RGC - SHAM+DREADD replicate 1


title: H19-11L


title: RGC - OHT replicate 5


title: H19-11K


title: RGC - SHAM replicate 6


title: RGC - SHAM replicate 7


title: H19-11J


title: H19-11I


title: RGC - SHAM replicate 5


title: H19-11H


title: RGC - SHAM replicate 4


title: H19-11F


title: RGC - SHAM replicate 1


title: RGC - SHAM replicate 2


title: H19-11E


title: cerebral cortices, PRPF6, MUT, 3

city: shanghai

first: sirui

last: zhang

address: yueyang road

country: China

institute: CAS

data_processing:
The RNA-seq reads were mapped to the mouse genome reference (UCSC genome browser mm10) using mapsplice with default parameters.
Differential splicing events were identified using the MISO pipeline, using as cut-off Bayes factor >5 to ensure the significant change. To find PRPF6-related splicing events, we used the cutoffs: delta PSI > 0.1 or < -0.1 and P value < 0.1(Student’s t-test) between PRPF6 mutant and wide type samples.
Gene expression levels were estimated using RSEM. Differentially expressed genes were identified using the cutoff: |log2FoldChange| > 1 and P value < 0.05.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes reads counts for each Sample

source_name: cerebral cortices

extract_protocol:
RNA was isolated using the PicoPure RNA Isolation Kit as per the manufacturer’s instructions (Arcturus).
library preparation using MicroPlex Library Preparation kit v2 (Diagenode)

value: cerebral cortices

value: electroporated with GFP + mutant PRPF6


title: RGC - SHAM replicate 8

value: Retina

value: Retinal ganglion cell


title: cerebral cortices, PRPF6, MUT, 2


title: H19-11B


title: RGC - SHAM replicate 3


title: cerebral cortices, PRPF6, WT, 3

value: electroporated with GFP + wild-type PRPF6


title: H19-11C


title: H19-09P

value: signet cell

value: PIK3CA (7% allele frequentie)


title: cerebral cortices, PRPF6, WT, 2


title: cerebral cortices, PRPF6, MUT, 1


title: H19-11A


title: H19-09M


title: H19-09N


title: H19-09K


title: H19-09J


title: AE4.14

data_processing:
Reads were mapped to the mouse genome mm10 using Tophat 2.1.0
Raw gene read counts, along with sequencing quality control, were generated using the Mayo Clinic RNA-Seq analytic pipeline: MAP-RSeq Version 2.1.1
Conditional Quantile Normalization (CQN) was performed on the raw gene counts to correct for GC bias and gene length differences, and to obtain similar quantile-by-quantile distributions of gene expression levels across samples.
Based on the bi-modal distribution of the CQN normalized and log2-transformed reads per kb per million (RPKM) gene expression values, genes with average log2 RPKM >= 0 in at least one genotype group were considered expressed above detection threshold.
One iE3 sample was determined as an outlier by Principal Component Analysis (PCA) and excluded from further analyses.
Genome_build: mm10
Supplementary_files_format_and_content: a tab-delimited text file containing covariates and CQN-normalized log2RPKM values for each sample.

source_name: Brain

extract_protocol:
Brain tissues were dissected and kept frozen at -80°C. RNAs were extracted via the Trizol (QIAGEN)/chloroform method, followed by DNase and Cleanup using RNase-Free DNase Set and RNeasy Mini Kit (QIAGEN).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Brain


title: AE4.13


title: AE4.16


title: AE4.15


title: AE4.12


title: H19-09H3


title: H19-09I


title: H19-09E


title: H19-09H1


title: H19-09H2


title: AE4.11


title: AE4.10


title: AE4.8


title: cerebral cortices, PRPF6, WT, 1


title: H19-09L


title: AE4.9


title: H19-09A


title: H19-09D


title: H1823J

value: ascending colon

value: NRAS


title: AE4.5


title: AE4.7


title: H1823K

value: moderate


title: H19-09C


title: AE4.6


title: H1823H


title: AE4.3


title: AE4.1


title: AE3.16


title: H1823F


title: H1823E


title: H1823G


title: AE3.15


title: AE4.2


title: H1823I


title: H1823B


title: AE4.4


title: H1817C


title: H1823A


title: H1817B2


title: AE3.10


title: AE3.13


title: AE3.12


title: AE3.8


title: AE3.7


title: H1817B1


title: H1817A


title: H1731D

value: lienal flexure

value: mucineus/SCD

value: KRAS


title: AE3.9


title: AE3.5


title: AE3.6


title: AE3.11


title: H1731E


title: H1731F


title: AE3.14


title: H1731G


title: H1729E

value: coecum

value: poor


title: AE3.2


title: AE3.1


title: H1729A

value: BRAF


title: H1729D


title: HRKD1

city: Zhanjiang

first: Zhe

last: Hu

state: Guangdong

address: 57 Renmin Avenue South, Xiashan District

institute: Guangdong Medical University

description: HUVECs under HR condition with SCIRT knockdown, replicate 1

data_processing:
Alignment was done by Bowtie2 (v2.3.4.3).
Sorting was done by name using Samtools (v1.9)
Count was done by Htseq (v0.11.2)
Normalization was done by using edgeR (v3.26.8)
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with normalized expression levels for every gene and every sample

source_name: HUVECs

growth_protocol: HUVECs were cultured at 37 ̊C, in a 95% O2 and 5% CO2 humidified atmosphere in DMEM supplemented with 10% fetal bovine serum, 100 μg/ml streptomycin, and100 IU/ml penicillin.

extract_protocol:
Total RNAs were extracted using Trizol according to the manufacturer's instructions.
Total RNAs were taken for the preparation of RNA-seq libraries and the massively parallel sequencing was perfomred with the Illumina HiSeq platform.  Paired-end 150 bp-length reads were produced.

treatment_protocol: The cultured HUVECs were incubated under hypoxic condition (5% CO2 and 95% N2) for 12 h, followed with reoxygenation (HR) for 4 h with knockdown control and lncRNA knockdown  to establish HR and HRKD samples, respectively. The negative control (NC) samples were cultured under normal condition.

value: human umbilical vein endothelial cells


title: H1730F

value: sigmoid

value: good


title: H1731C


title: H1730E


title: H1730C


title: NC1

description: HUVECs under normal culture condition, replicate 1

value: negative control replicate 1


title: H1731B


title: SNS-seq 2-4 kb

city: Cambridge

first: Guillaume

last: Guilbaud

address: Francis Crick Avenue

department: PNAC

country: United Kingdom

institute: Medical Research Council - LMB

description: SNS-seq 2-4kb fractions

data_processing:
Reads were map with Bowtie2 against hg38. Only reads mapped at a unique genomic position were kept. PCR duplicates were removed
Ini-seq 2 origins and efficency were called with a custum peak caller (https://github.com/Sale-lab)
SNS-seq orgins were called with MACS2, using EJ30_Input.fq.gz as Input  (same parameters as Akerman et al. Nature Communications volume 11, Article number: 4826 (2020))
Genome_build: hg38
Supplementary_files_format_and_content: Ini-seq 2: Origins position and effiency score (Z-score)
Supplementary_files_format_and_content: SNS-seq: Origins position and Unique origin identifier

source_name: Bladder carcinoma

extract_protocol:
Ini-seq2 Heavy-Light and Light-Light fraction were isolated by isopycnic centrifugation, desolted and precipitated.  SNS-seq samples were processed as descirbed in Akerman et al. Nature Communications volume 11, Article number: 4826 (2020).
Libraries were prepared with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (NEB, E7645S)

tag: cell line

tag: fraction

tag: method

value: SNS-seq


title: H1730B


title: AE3.4


title: H1729F


title: H1733I

value: rectum

value: unknown


title: H1733H


title: HRKD2

description: HUVECs under HR condition with SCIRT knockdown, replicate 2

tag: treatment


title: METTL18KO_WTrescue_rep2

city: Bunkyo-ku

first: Eriko

last: Matsuura

state: Tokyo

address: Yayoi

department: IQB

country: Japan

institute: The University of Tokyo

description:
Rnase I footprinting, ribosome pelleting, RNA extraction
Ribosome Profiling

data_processing:
Library strategy: Ribosome profiling
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with FastX-toolkit
Library sorting based on sample barcode sequence with custom script
random barcode triming with custom script
rRNA and other non-coding RNA alignment with STAR
Alignment with STAR
Read quantitation using custom scripts
Genome_build: hg38
Supplementary_files_format_and_content: text files contain three columns: 1. transcript name;2. CDS region (nt) used for read counting;3. read counts

source_name: HEK293T cell

extract_protocol: RNA extraction, preadenylated linker ligation, rRNA depeletion, reverse transcription, cDNA circularization, PCR amplification (for ribosome profiling)

value: embryonic kidney

value: mettl18 -/- with METTL18 wild-type


title: H1733F


title: H1729B


title: HR2

description: HUVECs under HR condition with knockdown control, replicate 2


title: AE3.3

value: Brain


title: METTL18KO_WTrescue_rep1


title: NC2

description: HUVECs under normal culture condition, replicate 2

value: negative control replicate 2


title: H1730A


title: H1733E

value: moderate


title: H1733D


title: H1733C


title: Naïve_rep2

value: wild type


title: H1905K

value: KRAS


title: HR1

description: HUVECs under HR condition with knockdown control, replicate 1


title: Naïve_rep1


title: Ini-seq2

description: Ini-seq2 Heavy-Light and Light-light fraction 3h reaction

value: Heavy-Light and Light-light


title: H1730D


title: H1905D

value: coecum


title: METTL18KO_VEC_rep2

value: mettl18 -/- with empty vector


title: H1729C

value: poor

value: BRAF


title: H1905B


title: CD69postive_G23

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

institute: Westlake university

description:
CD69positive_G23
processed data file: TCellActivation.TNTP.ratio.txt

data_processing:
The sequencing reads were firstly undergone adapter removal by “cutadapt”. The parameter to process the 1st GGA product NGS library is ”-n 1 -e 0.11 -O 15 -m 16”, and the parameter to process the other libraries are “-n 1 -e 0.11 -O 24 -m 16”.
Alignment was conducted using bowtie2 with “--np 0 --n-ceil L,0,0.2”.
The successfully aligned reads were assigned to the designed 4-gRNA combinations.
The G12 library and G23 library of each sample were treated as technical replicates. For each 4-gene combination, the log2 fold-change of the normalized read counts were calculated between the CD69+ and CD69- samples, and mean of replicates was used.
Genome_build: Customized references were used according to the sources of the NGS libraries.
Supplementary_files_format_and_content: txt

source_name: CD69+ (Top 25%) post-stimulation

growth_protocol: Jurkat-Cas9 cells were cultured in RPMI with 10% FBS and 1x Pen-Strep.

extract_protocol:
The plasmids were extracted using QIAGEN Plasmid Plus Midi Kit (QIAGEN, 12945) according to the manufacturer’s instructions.
The gDNA was extracted from cells using the QIAamp DNA Blood Mini kit (Qiagen, 51106).
For each of the NGS library, multiple 50 uL PCR reactions were performed. In each PCR reaction, we used template DNA, 0.25 uM forward primer, 0.25 uM reverse primer, 25 uL NEBNext Ultra II Q5 Master Mix (NEB, M0544S), and nuclease-free H2O up to 50 uL.

treatment_protocol: A total of 20×10^6 Jurkat-Cas9 cells were infected by the concentrated viral library at MOI≤0.3 in RPMI-1640 containing 8ug/ml polybrene. A ‘spinfection’ was conducted by centrifuging the culture plate at 700g, 32∘C for 2hrs. At 48-hrs post-transduction, cellular mKate2 expression, indicating the successful transduction, was verified by flow cytometry (Cytoflex, Beckman). In the next 6~10 days, cells grow under 2 ug/mL puromycin and 2 ug/mL blasticidin antibiotic selection, and the cell concentration was maintained at 5×105/mL. A total of 6×106 successfully infected Jurkat-Cas9 cells were collected as the starting reference (sample “Control”). Another 30×106 Jurkat cells were stimulated by 25μL/mL ImmunoCult™ Human CD3/CD28 T Cell Activator (STEMCELL, 10971) in RPMI with 10% FBS and 1x Pen-Strep at 5×106 per mL cell density. After 24hrs of stimulation, cells were stained by anti-CD69 (Biolegend, FN50), and CD69+ (Top 25%) and CD69- (Bottom 25%) cell population were sorted and collected using FACS (Fusion, BD). In total of 5×106 cells of each population were collected (sample “CD69+” and “CD69-”).

value: Jurkat cells with stable Cas9 expression

tag: surface cd69 expression

value: CD69+ (Top 25%) post-stimulation


title: Control_G12

description:
Control_G12
processed data file: Control.txt

source_name: before-stimulation (Control)

value: before-stimulation (Control)


title: CD69negative_G12

description:
CD69negative_G12
processed data file: TCellActivation.TNTP.ratio.txt

source_name: CD69- (Bottom 25%) post-stimulation

value: CD69- (Bottom 25%) post-stimulation


title: CD69negative_G23

description:
CD69negative_G23
processed data file: TCellActivation.TNTP.ratio.txt


title: H1804B

value: unknown


title: METTL18KO_rep2

value: embryonic kidney

value: mettl18 -/-


title: METTL18KO_VEC_rep1


title: HFHF-Old rat, replicate 1, scRNAseq

city: Beijing

first: Yue

last: Zhao

address: No. 1 Dahua Road, Beijing 100730, China

institute: Beijing Hospital

description: 10x Genomics

data_processing:
cat 2do form_letter > 2do_final; mv 2do form_letter DONE/; mv 2do_final 2do
Assembly: Rnor_6.0
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

organism: Rattus norvegicus

source_name: pancreas

extract_protocol:
Briefly, pre-cooled 0.5 mg/mL collagenase P solution was injected into the common bile duct to expand the pancreas, and then the pancreas was quickly extracted and transferred into a digestion bottle. After incubation at 38 °C for 10 min, the suspension was centrifuged at 1,200 × g for 2–3 min at 4 °C. The precipitate was washed twice with Hanks’ solution and resuspended in Histopaque-1077. After gently adding RPMI 1640 (containing 10% fetal bovine serum) solution to the liquid surface, the tube was centrifuged at 3,000 × g for 20 min at 4 °C. Granules scattered between the interfaces were collected and resuspended in 1 mL TrypLE (12604013; Thermo Fisher Scientific) for further digestion. DAPI staining was used to evaluate cell viability (Count Star, TANON SCIENCE & TECHONLOGY CO, Shanghai, China). When cell viability reached 80% and the proportion of doublets was less than 20%, an estimated 10,000 single cells per sample were suspended in phosphate-buffered saline solution (containing 0.04% bovine serum albumin)
Cell suspensions were loaded on a chromium single-cell controller (10x Genomics, San Francisco, CA, USA) to generate single-cell gel beads in emulsion (GEMs). According to the manufacture’ s introduction, single-cell RNA-seq libraries were constructed using Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (1000121; 10x Genomics, Pleasanton, CA, USA) and Single Cell B Chip Kit (1000127; 10x Genomics). The cDNA libraries were sequenced on an Illumina Novaseq6000 sequencer with a sequencing depth of at least 30,000 reads per cell and a pair-end of 150 bp.

value: pancreas

value: male

value: pancreatic cells

value: Wistar

value: 2-month-old rats were fed a high-fat high-fructose diet until 20 months old (HFHF group)


title: SNS-seq 0.5-2 kb

description: SNS-seq 0.5-2kb fractions

value: SNS-seq


title: Old rat, replicate 2, scRNAseq

description: 10x Genomics

value: fed a normal diet from 2 months old to 20 months old (control group)


title: CD69postive_G12

description:
CD69positive_G12
processed data file: TCellActivation.TNTP.ratio.txt


title: Old rat, replicate 1, scRNAseq

description: 10x Genomics


title: METTL18KO_rep1


title: H1905H

value: coecum

value: KRAS


title: H1905F


title: H1905J


title: H1703B2


title: young rat, replicate 1, scRNAseq

description: 10x Genomics

value: 2 months old (normal diet)


title: H1733B

value: rectum

value: moderate


title: H1905A


title: H1804D


title: H1724F


title: H1724D


title: H1905C


title: Control_G23

description:
Control_G23
processed data file: Control.txt

value: Jurkat cells with stable Cas9 expression

value: before-stimulation (Control)


title: H1703B1

value: unknown


title: H1804A


title: Input gDNA from EJ30

description: Input gDNA, used to call SNS-seq origins


title: H1703A

source_name: ovarium metastasis


title: HFHF-Old rat, replicate 2, scRNAseq

description: 10x Genomics


title: H1724C


title: Serum Impella rep6

first: Sayan

last: Bakshi

state: Alabama

department: Department of Pathology

institute: University of Alabama at Birmingham

data_processing:
Prior to alignment to the reference porcine genome, each sequence in the raw FASTQ files was trimmed on base call quality and sequencing adapter contamination using the Trim Galore! (v0.4.4) wrapper tool. Reads shorter than 20 base pairs were removed from the FASTQ files.
Trimmed reads were aligned to the reference genome using the open source short read aligner STAR (v2.4.2a) with settings according to log file.
Feature counts were determined using the R (v3.6.0) package “Rsubread” (v2.6.1). Only transcripts showing counts greater than 5 at least two times across all samples were considered for further analysis (data cleansing).
Gene annotation was performed using the R package “bioMaRt” (v2.48.0) with dataset 'sscrofa_gene_ensembl'.
Supplementary files format and content: excel spreadsheet file; include table with raw gene counts for every gene and each Sample

organism: Sus scrofa

source_name: Serum

extract_protocol:
Venous blood samples were collected at 3 time points and were immediately centrifuged at 2,000 g for 10 minutes at 4°C. The liquid supernatant was snap frozen in liquid nitrogen and stored at - 80 °C until subjected to further analysis.
The RNA sequencing library was generated from 100 ng of total RNA using the NEBNext® Single Cell/Low Input RNA Library Prep Kit (New England BioLabs, Frankfurt, Germany) according to manufacturer’s protocol.

value: Serum

tag: age

value: 5 months

value: Impella


title: young rat, replicate 2, scRNAseq

description: 10x Genomics

value: pancreas

value: male


title: WAS2425Q

value: BRAF


title: H1724E


title: WAS2425T


title: WAS2425P


title: H1724B


title: Serum Baseline rep6

value: Baseline


title: H1724A


title: H1804C


title: Serum Impella rep5


title: HR1

description: Gene expression of HUVECs under hypoxia/reoxygenation condition, replicate 1

hyb_protocol: To see manufacturer's website http://bioservices.capitalbio.com/fwpt/Agilentpt/15026.shtml

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Feature Extraction (11.5.1.1, Agilent Technologies, CA) software was used to extract all features of the data obtained from the scanned images and genespring software was used to analyze the raw data, which are normalized by percentile normalization.

source_name: HUVECs, hypoxia/reoxygenation , replicate 1

extract_protocol: RNA was prepared using the TRIzol reagent following the manufacturer's recommendations.

treatment_protocol: The cultured HUVECs were incubated under hypoxic condition (5% CO2 and 95% N2) for 12 h, followed with reoxygenation (HR) for 4 h to establish in vitro HR model, while negative control samples were untreated.

value: HUVECs

tag: condition

value: hypoxia/reoxygenation


title: Serum CS rep5

description: Card_Shock _5

value: Cardiogenic shock


title: HR2

description: Gene expression of HUVECs under hypoxia/reoxygenation condition, replicate 2

source_name: HUVECs, hypoxia/reoxygenation , replicate 2


title: NC2

description: Gene expression of HUVECs under normal condition, replicate 2

source_name: HUVECs, negative control, replicate 2

value: normal


title: HR3

description: Gene expression of HUVECs under hypoxia/reoxygenation condition, replicate 3

source_name: HUVECs, hypoxia/reoxygenation , replicate 3


title: NC1

description: Gene expression of HUVECs under normal condition, replicate 1

source_name: HUVECs, negative control, replicate 1


title: WAS2425R

source_name: primary tumor

value: coecum


title: Serum CS rep6

description: Card_Shock _6


title: WAS2425N

source_name: lymph node metastasis


title: WAS2425M

source_name: peritoneal metastasis


title: WAS2425O


title: NC3

description: Gene expression of HUVECs under normal condition, replicate 3

source_name: HUVECs, negative control, replicate 3


title: WAS2425L


title: WAS2425S


title: Serum Impella rep3


title: Serum CS rep4

description: Card_Shock _4


title: Serum Baseline rep4


title: Serum Impella rep4


title: Serum CS rep3

description: Card_Shock _3


title: WAS2425I


title: WAS2425J

source_name: liver metastasis


title: WAS2425H


title: Serum Baseline rep3


title: Serum CS rep2

description: Card_Shock _2


title: Serum Baseline rep2


title: WAS2425F


title: Serum Impella rep2


title: WAS2425E


title: WAS2425D


title: Serum Impella rep1


title: WAS2425B


title: WAS2425C


title: Serum CS rep1

description: Card_Shock _1


title: MB3W1 cells treated with OTX2 siRNA, replicate 3

city: Winnipeg

first: Tamra

last: Werbowetski-Ogilvie

state: Manitoba

address: 611-745 Bannatyne Avenue

department: Biochemistry & Medical Genetics

institute: University of Manitoba

description:
MB3W1_KD.3
Dietl et al., BMC Cancer 2016

data_processing:
Processed raw sequences with fastp to perform automatic adapter trimming, and default sequence quality filtering (>60% of bases with Q≥15, and no more than 5 'N' basecalls).
Quantified transcripts from GENCODE v35 with salmon v1.3.0 using --gcBias flag and genomic decoys in index.
Performed fold change analysis using DESeq2 as follows
Read transcript quantification data with tximport library and summarized to gene level quantification
Filtered to retain genes with at least 5 reads assigned in at least two samples
Constructed DESeqDataSet object with twelve samples (three replicates of two conditions in two cell lines), using the model ~condition (cell type/treatment)
Calculated fold changes between scr and siOTX2 in each cell line using the lfcShrink() function with the apeglm method.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_quant.sf: Salmon transcript quantification: Quantification of GENCODE v35 transcripts using salmon v1.3.0.
Supplementary_files_format_and_content: DESeq2 fold change results: Results from the DESeq2 lfcShrink() function comparing two conditions, including results for all genes retained after filtering.

source_name: MB3W1 cells treated with OTX2 siRNA

growth_protocol: Tumorspheres were grown in StemPro NSC Serum-Free Medium (HDMB03), Neural Precursor media (D283) and Stem Cell media (MB3W1) on ultra-low attachment tissue culture plates.

extract_protocol:
Total RNA was extracted from all samples using the Norgen RNA extraction kit (Norgen Biotek).
Library constructed with NEB Ultra II directional RNA library prep kit with poly-A selection module.

treatment_protocol: OTX2 levels were knocked down in HDMB03 and MB3W1 Group 3 MB cells (2X10^5 cells/well) as previously described (Zagozewski et al., Nature Comm, 2020; Stromecki et al., Molecular Oncology, 2018). Briefly, OTX2 was silenced using Silencer Select siRNAs 9931 or 9932 (Life Technologies) at a concentration of 30 nM. A non-silencing (scramble) served as the negative control. For RNA sequencing, OTX2 was knocked down in three independent biological replicates for each cell line and silencing was confirmed by Western blot (OTX2 ab21990 (Abcam) at 1:500) 72 hours following transfection.

value: Group 3 medulloblastoma cells

tag: sirna


title: WAS2425A

value: moderate


title: YM, Embryo 5, ICM

city: PALAISEAU

first: Emilie

last: Derisoud

state: Essonne

address: 26 Rue des Prés,

institute: INRAE

data_processing:
Demultiplexing has been done with bcl2fastq2 version 2.2.18.12 (Illumina) and adapters were trimmed with Cutadapt version 1.15, only reads longer than 10pb were kept.
A de novo assembly was made using StringTie version 2.1.2 following manufacturer instructions to identify XIST in equine embryo samples. The GTF output was aligned on Ensembl 99 EquCab3.0 assembly using IGV version 2.7.2. As XIST position and length on X chromosome was knew (thanks to Pablo Ross) and as XIST is annotated in human, the more similar contig was selected. Y chromosome is not assembly in the EquCab3.0 assembly but a nucleotide sequence of SRY is available on NCBI website.   Both sequences were added to FASTA file from Ensembl 99 EquCab3.0 assembly. Both genes were added to GTF from Ensembl 99 EquCab3.0 assembly as both unique chromosome with one gene composed of one transcript.
STAR version 2.6 was used for the alignment (2-pass mapping with GTF file using parameters: --alignSoftClipAtReferenceEnds No --alignEndsType EndToEnd --alignIntronMax 86545 --alignMatesGapMax 86545) on previously modified Ensembl 99 EquCab3.0 assembly. Genes were then counted with featureCounts from Subreads package version 1.6.1 (parameters: -p -B -C -M).
Genome_build: Ensembl 99 EquCab3.0 assembly + de novo XIST sequence + SRY sequence from NCBI
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample
Supplementary_files_format_and_content: gtf for de novo XIST gene and SRY gene from NCBI
Supplementary_files_format_and_content: fasta file for SRY gene from NCBI (GenBank: AB004572.1)
Supplementary_files_format_and_content: fasta file for XIST de novo annotated uing StringTie and IGV

organism: Equus caballus

source_name: Inner Cell Mass

growth_protocol: Saddlebred mares (French Anglo-Arabian and Selle Français breeds) were included in this study. They were raised in the “Institut Français du Cheval et de l’Equitation” experimental farm (Chamberet, France, 45° 34’55.17”N, 1°43’16.29”E, 442m). During the protocol period, mares were managed in herds in natural pastures 24h/day with free access to water. The experiments took place from April, the 1st until May 23rd, 2019. All mares remained healthy during this period. The mares’ estrus period was monitored by ultrasound with a 5MHz trans-rectal transducer. During estrus, ovulation was induced with a single 750-1500 IU IV injection of human chorionic gonadotropin (Chrorulon® 5000, MSD Santé animale) as soon as one ovarian follicle >35mm in diameter together with marked uterine edema were observed. At the same time, mares were artificially inseminated with fresh or refrigerated semen containing at least 1 billion motile spermatozoids from a single fertile stallion. Ovulation was confirmed within the next 48 hours by ultrasonography. Embryos were collected 10 days after the insemination (i.e., 8±0.5 days post-ovulation) by non-surgical uterine lavage using prewarmed (37°C) lactated Ringer’s solution (B.Braun) and EZ-Way Filter (IMV Technologies). All embryos were expanded blastocysts grade I or II according to the embryo classification of McKinnon and Squires. They were washed 4 times in commercially available Embryo holding medium (IMV Technologies) and then cut with a microscalpel under binocular magnifying glass to separate pure trophoblast (TE) and inner cell mass enriched hemi-embryo (ICM).

extract_protocol:
Each hemi-embryo was transferred to a DNA LoBind tube (Eppendorf) with extraction buffer from PicoPure RNA isolation kit (Applied Biosystems) and incubated for 30min at 42°C prior to storage at -80°C. The extraction of hemi-embryos RNA was performed using the PicoPure RNA isolation kit (Applied Biosystems), including a DNAse treatment, following the manufacturer’s instructions. RNA quality and quantity were obtained with 2100 bioanalyzer system using RNA 6000 Pico or nano kit (Agilent Technologies) according to the manufacturer's instructions. The RNA Integrity Number median was 9.8 (range from 8.7 to 10).
Five nanograms of total RNA were mixed with ERCC spike-in mix (Thermofisher) according to the manufacturer recommendations and then used for re-transcription and amplification using the SMART-Seq V4 ultra low input RNA kit (Clontech) according to the manufacturer recommendations. Nine PCR cycles were performed for each hemi-embryo. cDNA quality was assessed on an Agilent Bioanalyzer 2100, using an Agilent High Sensitivity DNA Kit (Agilent Technologies). Libraries were prepared from 0.15 ng cDNA using the Nextera XT Illumina library preparation kit (Illumina). Libraries were pooled in equimolar proportions and sequenced (Paired-end 50-34 pb) on NextSeq500 instrument, using a NextSeq 500 High Output 75 cycles kit (Illumina).

value: Blastocyst

tag: tissue

value: Inner Cell Mass

tag: maternal age

tag: maternal parity

tag: embryo size

tag: embryo sex

value: female


title: MB3W1 cells treated with OTX2 siRNA, replicate 1

description:
MB3W1_KD.1
Dietl et al., BMC Cancer 2016

tag: cell type


title: YM, Embryo 4, TE

source_name: Trophoblast

value: Trophoblast


title: YM, Embryo 4, ICM


title: YM, Embryo 5, TE


title: YM, Embryo 3, ICM


title: HDMB03 cells treated with OTX2 siRNA, replicate 3

description:
HDMB03_KD.3
T Milde et al., J Neurooncol 2012

source_name: HDMB03 cells treated with OTX2 siRNA


title: MB3W1 cells treated with scramble siRNA, replicate 2

description:
MB3W1_SCR.2
Dietl et al., BMC Cancer 2016

source_name: MB3W1 cells treated with scramble siRNA

value: scramble


title: MB3W1 cells treated with OTX2 siRNA, replicate 2

description:
MB3W1_KD.2
Dietl et al., BMC Cancer 2016


title: YM, Embryo 3, TE


title: MB3W1 cells treated with scramble siRNA, replicate 3

description:
MB3W1_SCR.3
Dietl et al., BMC Cancer 2016


title: YM, Embryo 2, ICM


title: MB3W1 cells treated with scramble siRNA, replicate 1

description:
MB3W1_SCR.1
Dietl et al., BMC Cancer 2016


title: YM, Embryo 2, TE


title: HDMB03 cells treated with OTX2 siRNA, replicate 2

description:
HDMB03_KD.2
T Milde et al., J Neurooncol 2012


title: YM, Embryo 1, ICM


title: HDMB03 cells treated with OTX2 siRNA, replicate 1

description:
HDMB03_KD.1
T Milde et al., J Neurooncol 2012


title: Serum Baseline rep1

value: Serum

value: 5 months


title: OM, Embryo 6, TE

value: male


title: HDMB03 cells treated with scramble siRNA, replicate 3

description:
HDMB03_SCR.3
T Milde et al., J Neurooncol 2012


title: OM, Embryo 6, ICM


title: YM, Embryo 1, TE


title: Serum Baseline rep5


title: OM, Embryo 5, TE


title: HDMB03 cells treated with scramble siRNA, replicate 1

description:
HDMB03_SCR.1
T Milde et al., J Neurooncol 2012


title: OM, Embryo 5, ICM


title: SOX9_rep1

first: Bettina

last: Fuglerud

address: 675 W 10th Ave

data_processing:
De-multiplexed read sequences were aligned to the reference genome using STAR_2.5.0b.
Assembly and differential expression was estimated using Cufflinks 2.2.1 through bioinformatics apps available on Illumina Sequence Hub.
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: Replicate FPKM table

source_name: Umbilical vein endothelial cells

extract_protocol:
RNA was extracted from cells using TRIzol (Thermo Fisher Scientific).
NEBnext Ultra ii Stranded mRNA (New England Biolabs)

value: HUVEC

tag: transduced with

value: SOX9 expression plasmid


title: OM, Embryo 4, TE


title: OM, Embryo 4, ICM


title: Empty_rep2

value: Empty vector


title: HDMB03 cells treated with scramble siRNA, replicate 2

description:
HDMB03_SCR.2
T Milde et al., J Neurooncol 2012


title: Empty_H3K27me3CUT&Tag

data_processing:
Library strategy: CUT&Tag
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
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tracks in BigWig file format

extract_protocol:
CUT&RUN, CUT&Tag, ATAC-seq
NEBnext DNA Ultra ii (New England Biolabs)

tag: cut&run/tag antibody


title: SOX9OE_H3K27me3CUT&Tag


title: OM, Embryo 3, TE


title: OM, Embryo 1, TE


title: OM, Embryo 3, ICM


title: OM, Embryo 1, ICM


title: Empty_H3K27acCUT&Tag

value: H3K27ac (ab4729, Abcam)


title: GSCLC_Laminb1_3

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description:
GSCLC_Laminb1_pool_log2ratio_1000.bw
GSCLC_LADs_pool.bed

data_processing:
Single-end reads were processed using Trim-Galore v0.4.1/cutadapt v1.9.1 to remove adaptor sequence.
The truncated reads were then aligned to (GRCm38p3) using Bowtie2 v2.3.4.1 with the “-very-sensitive” option.
The reads aligned to chromosome 1 to 19, X, Y were transformed to BAM format by SAMtools v1.7. BED files were obtained from the BAM files using the bamtobed command of BEDTools v2.29.2.
Genome_build: mm10
Supplementary_files_format_and_content: bw files are bigwig files generated from the BAM files using bamcoverage for raw count with the “--normalizeUsing CPM -bs 25” or bamcompare for IP/Input command with the “--pseudocount 1 -bs 1000” option of deepTools v3.5.0. In both cases, the blacklist regions (Amemiya et al, 2019) were excluded.
Supplementary_files_format_and_content: bed files describe peaks or domains files detected by macs2 or epic2, respectively

source_name: GSCLC

growth_protocol: The BDF1-2-1 mouse mESCs bearing Blimp1-mVenus and Stella-ECFP (BVSC) transgenes (Ohta et al., 2021) were cultured as described previously (Hayashi et al., 2011). Briefly, mESCs were maintained in N2B27 medium supplemented with PD0325901 (0.4 uM) (Stemgent), CHIR99021 (3 uM) (Bio Vision), and leukemia inhibitory factor (LIF) (1000 U/ml) (Merck Millipore) on a 12-well plate coated with poly-L-ornithine (0.01%) (Sigma) and laminin (10 ng/ml) (BD Bioscience). In this study, all cells were cultured at 37°C under an atmosphere of 5% CO2 in air. Induction of EpiLCs and PGCLCs was performed as described previously (Hayashi et al., 2011) with minor modifications. Briefly, the EpiLCs were induced by plating 8 x 104 mESCs on a well of 12-well plate coated with human plasma fibronectin (16.7 mg/ml) (Merck Millipore) in N2B27 medium containing activin A (20 ng/ml) (Peprotech), bFGF (12 ng/ml) (Invitrogen), and KSR (1%) (Gibco). PGCLCs were induced from d2 EpiLCs (2 days after induction) under a floating condition in wells of a low-cell-binding U-bottom 96-well plate in GMEM medium (Thermo Fisher Scientific) containing 15% KSR (Gibco), 0.1 mM NEAA (Thermo Fisher Scientific), 1 mM sodium pyruvate (Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Thermo Fisher Scientific) and 2mM L-glutamin (Thermo Fisher Scientific) supplemented with BMP4 (500 ng/ml) (RSD), LIF (1000 U/ml) (Merck Millipore), SCF (100 ng/ml) (RSD), EGF (50 ng/ml) (RSD). The expansion culture of PGCLCs was performed as previously described (Ohta et al., 2021). Briefly, following incubation in TrypLE™ Express (Gibco) for 10 min, the aggregates of d4 mPGCLCs (PGCLCs induced for 4 days) were dissociated into single cells by rigorous pipetting. Subsequently, BV-positive cells were sorted with a FACSAriaIII cell sorter. Purified d4 mPGCLCs were cultured on m220-5 cells as the feeder cells in GMEM (Gibco) containing 10% KSR (Gibco), 0.1 mM NEAA (Thermo Fisher Scientific), 1 mM sodium pyruvate (Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Thermo Fisher Scientific), 2 mM L-glutamin (Thermo Fisher Scientific), 2.5% FBS (Hyclone), SCF (100 ng/ml) (RSD), 10 uM forskolin (Sigma), 10 uM rolipram (abcam), 5 uM CsA (Sigma). Half of the culture medium was changed every two days. GSCs and GSCLCs bearing Acro/Act-EGFP (AAG) transgenes (Ishikura et al., 2016) were cultured as described previously (Ishikura et al., 2016). Briefly, cells were cultured in Stempro-34 SFM supplemented with Stempro Supplement (Gibco), with 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), 1% FBS (Hyclone), 1xMEM vitamin solution (Thermo Fisher Scientific), 5.0mg/ml AlbMAXI (Gibco), 0.1 mM NEAA (Thermo Fisher Scientific), 1 mM sodium pyruvate (Thermo Fisher Scientific), 0.1 mM β-mercaptoethanol (Thermo Fisher Scientific), 100 U/ml penicillin, 0.1 mg/ml streptomycin (Thermo Fisher Scientific), 2 mM L-glutamin (Thermo Fisher Scientific), 1x Insulin-Transferrin-Selenium (ITS-G) (Gibco), 10 ng/ml bFGF (Invitrogen), 20 ng/ml GDNF Rat Recombinant (RSD), 20 ng/ml EGF (RSD), and 1000 U/ml LIF (Merck Millipore) in a well of 6-well plate on mouse embryonic fibroblast cells (MEFs) as feeder cells. Half of the medium was replaced every two or three days.

extract_protocol:
The ChIP-seq library preparation was performed as previously described (Lee et al., 2006) with minor modifications. We used harvested mESCs and EpiLCs, and FACs-sorted BV-positive cells for d2 mPGCLCs and d4c7 mPGCLCs samples, and FACS-sorted AAG-positive cells for GSCs and GSCLCs samples. Briefly, the harvested cells were crosslinked with 1% formaldehyde (Thermo Fisher Scientific)/PBS for 10 min at RT and quenched with 125 mM glycine. Crosslinked cells were lysed consecutively using LB1 (50 mM HEPES-KOH pH 7.5, 1 mM EDTA, 140 mM NaCl, 10% glycerol, 0.5% NP-40, 0.25% Triton-100, protease inhibitors (Roche, 11873580001)), LB2 (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 200 mM NaCl, protease inhibitors), and LB3 (50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 mM EGTA, 100 mM NaCl, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, protease inhibitors) and then sonicated by picoruptor to achieve a mean DNA fragment size of around 200-400 bp. Sonicated chromatin was incubated with  Dynabeads M-280 Sheep anti Mouse IgG beads (Thermo Fisher Scientific) or Dynabeads ProteinA beads (Thermo Fisher Scientific) for 35 min at 4°C for preclear. Precleared chromatin was then incubated with antibody that was preincubated with the appropriate Dynabeads in 0.5% BSA (Gibco) in PBS as follows: chromatin equivalent of 5 x 105 cells with anti-H3K4me1 (rabbit monoclonal, CST, D1A9, 5 μl),  anti-H3K9me2 (mouse monoclonal, MBL, MABI0317, 5 μl), anti-H3K27me3 (mouse monoclonal, MBL, MABI0323, 5 μl); 1 x 106 cells with anti-H3K4me3 (mouse monoclonal, MBL, MABI0304, 5 μl), anti-H3K9me3 (mouse monoclonal, MBL, MABI0318, 5 μl), anti-H3K36me2 (rabbit monoclonal, CST, C75H12, 5 μl), anti-H2AK119ub1 (rabbit monoclonal, D27C4, 10 μl), anti-H3K36me3 (rabbit polyclonal, Active Motif, 61101, 2 μl); 1.5 x 106 cells with anti-H3K27ac (mouse monoclonal, MBL, MABI0309, 5 μl); 2 x 106 cells with anti-CTCF (rabbit monoclonal, CST, D31H2, 5 μl), anti-Laminb1 (rabbit polyclonal, Proteintech, 12987-1-AP, 10 μl); 3 x 106 cells with anti-Setdb1 (rabbit ployclonal, Proteintech, 11231-1-AP, 10 μl); 4 x 106 cells with anti-Ring1b (rabbit monoclonal, CST, D22F2, 10 μl); and 4.5 x 106 cells with anti-Rad21 (rabbit monoclonal, ab992, 5 μl). After incubation for 6 h at 4°C, the beads were washed 4 times in wash buffer 1 (20 mM Tris-HCl pH8.0, 2 mM EDTA, 150 mM NaCl, 1% TritonX-100, 0.1% SDS), 2 times in wash buffer 2 (20 mM Tris-HCl pH 8.0, 2 mM EDTA, 500 mM NaCl, 1% TritonX-100, 0.1% SDS), and 2 times in wash buffer 3 (10 mM Tris-HCl  pH 8.0, 1 mM EDTA, 250 mM LiCl, 1% Na-Deoxycolate, 1% NP-40). Then, the washed beads were eluted in 10 mM Tris-HCl pH 8.0, 5 mM EDTA, 300 mM NaCl, 1% SDS, and crosslinks were reversed overnight at 65°C. Input samples were treated in a similar manner. The following day, IP and Input samples were incubated with RNaseA (Thermo Fisher Scientific) and proteinase K (Thermo Fisher Scientific). IP or Input DNA was purified using QIA quick PCR purification kit (QIAGEN).
ChIP-seq libraries were prepared using KAPA Hyper Prep Kit (KAPA) following the manufacturer’s guidelines. An adaptor kit (Fastgene, FG-NGSAD24) was used for the sample indexes. The average size and concentration of libraries were analyzed using LabChIP GX (PerkinElmer) and KAPA library Quantification kit (KAPA), respectively.

value: GSCLC

tag: chip antibody

tag: controlled by

tag: genotype

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)

tag: strain


title: SOX9OE_H3K27acCUT&Tag

city: Vancouver

institute: BC Cancer

tag: cell line


title: GSCLC_Laminb1_2


title: SOX9OE_H3K4me1CUT&Tag

value: H3K4me1 (C15410037, Diagenode)


title: SOX9_rep3


title: Empty_H3K4me1CUT&Tag


title: GSCLC_Laminb1_1


title: GSCLC_H2Aub_2


title: SOX9OE_SOX9CUT&RUN

data_processing:
Library strategy: CUT&RUN
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
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tracks in BigWig file format

value: SOX9 (AB5535, Millipore)


title: GSCLC_Ring1b_3


title: GSCLC_H2Aub_1


title: SOX9_rep2


title: Empty_rep3


title: Empty_rep1


title: OM, Embryo 2, ICM


title: OM, Embryo 2, TE


title: GSCLC_Ring1b_2


title: Empty_SOX9CUT&RUN


title: GSCLC_Ring1b_1


title: GSCLC_K36me3_2


title: SOX9OE_ATAC

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
Genome_build: hg19/GRCh37
Supplementary_files_format_and_content: tracks in BigWig file format


title: DRG, AAV5-NIS V1 and V2, rep2

city: Newark

first: Yuan-Xiang

last: Tao

state: NJ

address: 183 S Orange Ave

department: Anesthesiology

institute: New Jersey Medical School, Rutgers, The State University of New Jersey

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

source_name: DRG

extract_protocol:
RNA was harvested using RNeasy Mini Kit  (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using TruSeq Stranded Total RNA Sample Preparation Kit (Illumina) following manufacturer's protocols.

value: DRG

value: WT

tag: treatment

value: AAV5-NIS V1 and V2


title: DRG, AAV5-NIS V1 and V2, rep1


title: DRG, AAV5-Gfp, rep1


title: Empty_ATAC


title: DRG, AAV5-NIS V1 and V2, rep3


title: GSCLC_K36me2_2


title: GSCLC_K36me2_1


title: GSCLC_K27me3_2


title: GSCLC_K27me3_1


title: GSCLC_K27ac_2


title: GSCLC_K9me2_2


title: KO NKT

city: Seoul

first: Jaemoon

last: Koh

address: Daehak-ro

country: South Korea

institute: Seoul National University Hospital

description: KO NKT

data_processing:
RNA data quality assessment was performed using FastQC v0.11.9
Adaptors were removed using Cutadapt v2.10.
Transcripts abundances were annotated against Mus musculus reference transcriptome GRCm38/mm10 ENSEMBL version 97 and summarized to the gene-level with tximeta v1.4.3.
Summarized gene level transcript abundances were imported into DESeq2 v1.26.0 and normalized by executing the DESeq function.
Genome_build: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). RNA quality and quantity were determined using an Agilent 2100 Bioanalyzer.
The extracted RNA samples were used for construction of cDNA libraries. The cDNA library preparation and RNA-Seq analysis were performed by Theragen Etex (Korea). The libraries were prepared for 100 bp paired-end sequencing using the TruSeq RNA Sample Preparation Kit (Illumina, San Diego, CA, USA). The quality of the cDNA libraries was evaluated using the Agilent 2100 BioAnalyzer (Agilent). The cDNA libraries were quantified using the KAPA Library Quantification Kit (Kapa Biosystems, Wilmington, MA, USA) according to the manufacturer's instructions.

value: liver

value: iNKT cell

value: ACC1 Knockout

value: CD3-CD28 stimulation


title: GSCLC_K27ac_1


title: WT NKT

description: WT NKT


title: GSCLC_K9me2_1


title: DFO_2

city: Shanghai

first: Yangshuo

last: Li

address: 168 Changhai Road

institute: Navy Medical University

data_processing:
Low-quality reads were filtered, and the reads with 5’ primer contaminants and poly (A) were removed. The reads without 3’adapter and insert tag, the reads shorter than 15 nt and longer than 41nt from the raw data were filtered, and the clean reads were obtained.
For primary analysis, the length distribution of the clean sequences in the reference genome was determined. Non-coding RNAs were annotated as rRNAs, tRNAs, small nuclear RNAs (snRNAs), and small nucleolar RNAs (snoRNAs).
These RNAs were aligned and then subjected to the BLAST search against Rfam v.10.1 and GenBank databases.
The known miRNAs were identified by aligning against miRBase v.21 database, and the known miRNA expression patterns in different samples were analyzed. Unannotated small RNAs were analyzed by mirdeep2 to predict novel miRNAs.
Based on the hairpin structure of a pre-miRNA and the miRBase database, the corresponding miRNA star sequence was also identified.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Ovarian granulosa cell

extract_protocol:
miRNAs of exosomes were extracted using the exoEasy Maxi kit (QIAGEN). 1 ug of micro RNA was used for the construction of sequencing libraries.
Small RNA sequencing was conducted using Illumina HiSeq 2500 with read lengths of 15–41 bp.

value: Ovarian granulosa cell

value: DFO

tag: molecule subtype

value: micro RNA


title: VE_2

value: VE


title: GSCLC_K4me1_1


title: VE_1


title: DFO_3


title: VE_3


title: GSCLC_K4me1_2


title: DRG, AAV5-Gfp, rep2


title: DFO_1


title: DRG, AAV5-Gfp, rep3


title: GSCLC_Input_4


title: GSCLC_K36me3_1


title: FAC_3

value: FAC


title: FAC_1


title: GSCLC_Input_3


title: FAC_2


title: GSC_Laminb1_4

description:
GSC_Laminb1_pool_log2ratio_1000.bw
GSC_LADs_pool.bed

source_name: GSC

value: GSC


title: GSC_Laminb1_2


title: CON_3

value: CON


title: GSC_Laminb1_1

value: Acrosin-EGFP; beta-Actin-EGFP (AAG)


title: GSC_H2Aub_2


title: CON_1


title: CON_2


title: GSC_H2Aub_1


title: GSC_Ring1b_3


title: S1-seq_activated.B.cells_adult_rep2_adaptor.swap.T

first: Shintaro

last: Yamada

state: --- Select a state ---

address: Yoshida Konoe, Sakyo-ku

department: Graduate School of Medicine

institute: Kyoto University

data_processing:
Library strategy: S1-seq
Base calls were perfomed using HiSeq Control Software v.2.0.10.0 for samples sequenced on Illumina HiSeq 2500  Reads were trimmed and filtered by Trim Galore version 0.4.5 with the arguments --paired --length 15 <http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/>
Sequence reads were mapped onto the mouse reference genome (mm10) by bowtie2 version 2.2.1 (ref. 1) with the arguments -N 1 -X 1000. (ref. 1) Langmead et al., Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).  Duplicated reads were removed by Picard <https://broadinstitute.github.io/picard/>. Uniquely and properly mapped reads (MAPQ ≥ 20) were extracted by samtools with the arguments -q 20 <http://www.htslib.org/>.
Reads for S1-seq were counted at which a nucleotide next to biotinylated adaptor DNA was mapped (this corresponds to a position of ssDNA). Adaptors were swapped for some samples (indicated by sample names), and reads were counted at which a nucleotide next to the other (unbiotinylated) adaptor DNA was mapped. Maps were analyzed using R versions 3.2.3 to 3.3.1 <http://www.r-project.org>.
Genome_build: mm10
Supplementary_files_format_and_content: bigWig files contain read counts at positions of ssDNA. Reads were not normalized to RPM (reads per million mapped). Letter "top" or "bottom" in sample names indicates that reads were mapped on top or bottom strand, respectively.

source_name: splenocytes

extract_protocol: Testis cells from 12-dpp juvenile mice were obtained as described previously (ref. 1). Splenic B cells were obtained from adult mice. Cells were embedded in plugs of low-melting point agarose to protect DNA from shearing, and DNA was liberated by treatment with SDS and proteinase K as described previously (ref. 2). In-plug overhang removal with nuclease S1 and adaptor ligation were performed as described previously (ref. 3, 4). After ligation to biotinylated adaptors, DNA was purified from the agarose, sheared by sonication, purified with streptavidin, ligated to second-end adaptors, amplified, and sequenced as described previously (ref. 2, 3, 4). (ref. 1) F. Cole et al., Mouse tetrad analysis provides insights into recombination mechanisms and hotspot evolutionary dynamics. Nat Genet 46, 1072-1080 (2014). (ref. 2) Yamada et al., Molecular structures and mechanisms of DNA break processing in mouse meiosis. Genes Dev 34, 806-818 (2020). (ref. 3) Mimitou et al., S. A global view of meiotic double-strand break end resection. Science 355, 40-45 (2017). (ref. 4) Mimitou et al., S1-seq Assay for Mapping Processed DNA Ends. Methods Enzymol 601, 309-330 (2018).

value: activated B cells

tag: age

value: 2 months


title: S1-seq_resting.B.cells_adult_rep3_adaptor.swap.T

value: resting B cells


title: S1-seq_resting.B.cells_adult_rep1_adaptor.swap.T


title: GSC_K36me3_1


title: GSC_K36me3_2


title: GSC_Ring1b_2


title: S1-seq_activated.B.cells_adult_rep1_adaptor.swap.T


title: S1-seq_Spo11.null_12dpp_rep1_adaptor.swap.F

source_name: Spermatocytes

value: testis

value: 12 days post partum


title: GSC_K36me2_2


title: Final_plasmid_G12

description:
Final_plasmid_G12
processed data file: Final_plasmid.GGA4.txt

organism: Escherichia coli

source_name: 4th GGA plasmid pool

tag: sample type

value: Plasmid

value: plasmid DNA


title: Final_plasmid_G23

description:
Final_plasmid_G23
processed data file: Final_plasmid.GGA4.txt


title: Lig1_plasmid

source_name: 1st GGA plasmid library


title: GSC_Laminb1_3


title: GSC_K36me2_1


title: GSC_K27me3_2


title: UMRC2_unt_n2

city: Cleveland

first: Treg

last: Grubb

email: grubbt@ccf.org, grubbt4@ccf.org

state: Ohio

address: 9500 Euclid Avenue

department: Cancer Biology

institute: Cleveland Clinic Foundation

description:
replicate 2
featureCounts_normalized.xlsx
featureCounts_RAW.xlsx

data_processing:
Base-called sequences were obtained using the DRAGEN Bio-IT Platform.
Reads with Phred scores <28 were trimmed using Cutadapt (v1.16).
Reads were aligned to the UCSC hg38 build of the human transcriptome using HISAT2 (v2.1.0).
Total read counts for genomic features (i.e., genes) were measured using featureCounts (v1.6.4).
Counts were filtered, normalized (Trimmed Mean of M-values), and differential expression was determined using EdgeR (v3.12).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: featureCounts_RAW.xlsx contains raw values obtained from featureCounts (v1.6.4) for each sample.
Supplementary_files_format_and_content: featureCounts_normalized.xlsx contains EdgeR (v3.12) normalized counts per million for each sample.

source_name: Renal cell carcinoma cell line

extract_protocol:
Total RNA was extracted using Trizol reagent.
DNA libraries were prepared using the Collibri Stranded RNA Library Prep Kit for Illumina with 50-100 ng of total RNA following the manufacturer’s protocol.

treatment_protocol: Cells were collected at baseline and following acute treatment using A-1331852 (6-16 hours).

value: Renal cell carcinoma


title: GSC_K27ac_2


title: UMRC2_A133_n2

value: A-1331852 (MedChemExpress HY-19741)


title: UMRC2_A133_n1

description:
replicate 1
featureCounts_normalized.xlsx
featureCounts_RAW.xlsx


title: S1-seq_activated.B.cells_adult_rep3_adaptor.swap.T


title: GSC_K27ac_1


title: OSRC2_unt_n2


title: UMRC2_unt_n1


title: GSC_K9me2_1


title: GSC_Ring1b_1


title: GSC_K4me1_2


title: S1-seq_resting.B.cells_adult_rep2_adaptor.swap.T


title: OSRC2_unt_n1


title: CAKI2_unt_n2


title: OSRC2_A133_n2


title: OSRC2_A133_n1


title: GSC_K27me3_1


title: CAKI2_A133_n1


title: CAKI2_unt_n1


title: GSC_Input_4


title: GSC_K4me1_1


title: GSC_Input_3


title: A498_unt_n2


title: GSC_K9me2_2


title: CAKI2_A133_n2


title: A498_unt_n1


title: d4c7PGCLC_Laminb1_1

description:
d4c7PGCLC_Laminb1_pool_log2ratio_1000.bw
d4c7PGCLC_LADs_pool.bed

value: Blimp1-mVenus reporter; Stella-ECFP reporter (BVSC)


title: d4c7PGCLC_Laminb1_2


title: d4c7PGCLC_H2Aub_2


title: A498_A133_n1


title: d4c7PGCLC_H2Aub_1


title: A498_A133_n2


title: d4c7PGCLC_Ring1b_1


title: d4c7PGCLC_K36me3_2


title: d4c7PGCLC_Laminb1_3


title: d4c7PGCLC_Ring1b_3


title: L8

city: Houston

first: Zejuan

state: Texas

address: 6565 Fannin St, MC227

department: Department of Pathology and Genomic Medicine

institute: Houston Methodist Hospital

data_processing:
Basecalls were converted using bcl2fastq2.
Sequencing quality of raw reads were evaluated using FastQC, and trimmed adaptors and low quality reads (Phred quality score < 15) using Trimmomatic
High quality reads were mapped to hg19  genome using bowtie2 with end-to-end mode
Duplicate reads were removed using samtools.
The reads were counted for overlap with gene bodies (annotated by the GENCODE Project) using featureCounts.
Genome_build: hg19
Supplementary_files_format_and_content: txt file for all sample with raw reads count summarised to genebody region.

source_name: Acute Myeloid Leukemia_Plasma

extract_protocol:
Plasma was separated from whole blood by centrifuge 1350 g for 10 minutes at 4 °C. Plasma cfDNA was extracted using QIAamp Circulating Nucleic Acid Kit (QIAGEN, Germantown, MD) following manufacturer’s instructions.
Briefly, cfDNA was ligated with barcode adaptors after end repair and A-tailing. Then cfDNA was purified and was incubated with 50 mM HEPES buffer (pH 8.0), 25 mM MgCl2, 100 μM N3-UDP-azide-glucose and 1 μM T4 Phage β-gulcosyltransferase at 37 °C for 1 hour. After purification, cfDNA was incubated with 1 μL DBCO-PEG4-DBCO (a click chemistry tool, 4.5 mM stock in DMSO) at 37 °C for 2 hours. Next, the cfDNA was purified and incubated with 5 μL pre-washed C1 Streptavidin beads (Thermo Fisher Scientific, Waltham, MA) for 15 min. The beads were subsequently washed for 5 minutes eight times. The captured DNA fragments were amplified with 15-18 cycles of PCR. The PCR products were purified with AMPure XP beads according to the manufacturer’s instructions. The concentration of DNA library was measured using a Qubit Fluorometer with dsDNA HS Assay Kit (Thermo Fisher Scientific, Waltham, MA) and Bioanalyzer 2100 with Agilent High Sensitivity Kit (Agilent Technologies, Santa Clara, CA).

tag: diagnosis

value: Acute Myeloid Leukemia

tag: training/validation group in diagnostic model

value: Test

tag: training/validation group in survival analysis

value: Train

tag: gender

value: male

tag: vital status (0

value: censored; 1:event):1

tag: survival (months)


title: L4


title: d4c7PGCLC_K36me3_1

tag: cell type


title: L38

value: female


title: L39


title: d4c7PGCLC_K36me2_2


title: L36


title: d4c7PGCLC_Ring1b_2


title: L25


title: L19


title: L18


title: L17

value: censored; 1:event):NA


title: BL93


title: d4c7PGCLC_K4me1_1


title: BL84


title: BL92


title: d4c7PGCLC_K9me2_1


title: d2PGCLC_Laminb1_3

description:
d2PGCLC_Laminb1_pool_log2ratio_1000.bw
d2PGCLC_LADs_pool.bed


title: BL83


title: d4c7PGCLC_Input_4


title: d2PGCLC_Laminb1_2


title: d4c7PGCLC_K27me3_1


title: BL67


title: d4c7PGCLC_K36me2_1


title: d4c7PGCLC_K27ac_2


title: d4c7PGCLC_K27me3_2


title: d4c7PGCLC_Input_3


title: BL66


title: d4c7PGCLC_K27ac_1


title: d4c7PGCLC_K9me2_2


title: d4c7PGCLC_K4me1_2


title: d2PGCLC_Laminb1_1


title: BL32


title: L13


title: d2PGCLC_H2Aub_2


title: BL29

value: censored; 1:event):0


title: L10


title: d2PGCLC_H2Aub_1


title: d2PGCLC_Ring1b_3


title: BL27


title: d2PGCLC_Ring1b_2


title: d2PGCLC_Rad21_2


title: d2PGCLC_Ring1b_1


title: BL2


title: BL111


title: BL117


title: BL13


title: BL57


title: BL15


title: 3B-8


title: d2PGCLC_Rad21_1


title: d2PGCLC_CTCF_2

value: CTCF


title: d2PGCLC_K27me3_1


title: d2PGCLC_K36me2_2


title: d2PGCLC_K27me3_2


title: d2PGCLC_K36me2_1


title: 3B-49


title: d2PGCLC_CTCF_1


title: d2PGCLC_K36me3_2


title: 3B-45


title: BL104


title: 3B-47


title: 3B-44


title: BL103


title: 3B-42


title: d2PGCLC_K36me3_1


title: d2PGCLC_K27ac_2


title: d2PGCLC_K27ac_1


title: 3B-40


title: d2PGCLC_K9me3_2

description:
d2PGCLC_K9me3_pool_log2ratio_1000.bw
d2PGCLC_K9me3_pool.bed


title: 3B-41


title: d2PGCLC_K9me3_1


title: 3B-36


title: 3B-34


title: d2PGCLC_K9me2_2


title: 3B-3


title: d2PGCLC_K9me2_1


title: 3B-27


title: d2PGCLC_K4me3_2


title: 3B-25


title: 3B-19


title: d2PGCLC_K4me3_1


title: 3B-22


title: 3B-20


title: d2PGCLC_K4me1_1


title: d2PGCLC_Input_2


title: d2PGCLC_K4me1_2


title: 3B-16


title: 3B-1


title: 3B-18


title: EpiLC_Laminb1_2

description:
EpiLC_Laminb1_pool_log2ratio_1000.bw
EpiLC_LADs_pool.bed

source_name: EpiLC

value: EpiLC


title: d2PGCLC_Input_4


title: 3B-14


title: L35

value: Training


title: d2PGCLC_Input_3


title: d2PGCLC_Input_1


title: EpiLC_H2Aub_2


title: 3B-30


title: BL30


title: EpiLC_H2Aub_1


title: L23


title: EpiLC_Ring1b_2


title: EpiLC_K36me3_2


title: L33


title: L27


title: EpiLC_K36me3_1


title: BL116


title: EpiLC_K36me2_2


title: EpiLC_K36me2_1


title: EpiLC_Laminb1_1


title: 3B-13


title: BL14


title: EpiLC_K27me3_1


title: EpiLC_K27ac_1


title: EpiLC_K9me2_2


title: L12


title: 3B-35


title: L6


title: EpiLC_K9me2_1


title: BL1


title: BL24


title: EpiLC_K4me1_1


title: EpiLC_K4me1_2


title: 3B-43


title: L15


title: EpiLC_Ring1b_1


title: 3B-11


title: EpiLC_Input_4


title: EpiLC_K27me3_2


title: BL101


title: 3B-28


title: EpiLC_K27ac_2


title: EpiLC_Input_3


title: 3B-17


title: ESC_Yy1_1

source_name: ESC

value: ESC


title: BL25


title: BL22


title: ESC_Laminb1_2

description:
ESC_Laminb1_pool_log2ratio_1000.bw
ESC_LADs_pool.bed


title: L28


title: ESC_Laminb1_1


title: ESC_H2Aub_2


title: ESC_Ring1b_2


title: ESC_H2Aub_1


title: L26


title: 3B-32


title: BL51


title: ESC_Ring1b_1


title: 3B-48


title: 3B-21


title: 3B-37


title: ESC_Laminb1_3


title: ESC_K36me2_1


title: ESC_K36me2_2


title: ESC_K36me3_1


title: 3B-39


title: ESC_K27me3_2


title: ESC_K27me3_1


title: BL7


title: 3B-38


title: 3B-9


title: ESC_K27ac_1


title: ESC_K27ac_2


title: BL26


title: ESC_Input_4


title: L31


title: ESC_K36me3_2


title: BL85


title: ESC_K9me2_1


title: ESC_K9me2_2


title: ESC_K4me1_1


title: BL114


title: ESC_K4me1_2


title: BL48


title: 3B-4


title: 3B-24


title: BL102


title: BL110