title: MOE_METATAC_220503-P3-Plate1

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P34)

value: mouse olfactory epithelium (P34)


title: JU03_AT_distant_Pz20

status: Public on Jan 15 2024

type: RNA

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

hyb_protocol: Standard Affymetrix hybridization protocol

scan_protocol: Standard Affymetrix scanning protocol

data_processing: The data were processed and normalised using RMA with Transcriptome analysis Console software

label: biotin

molecule: total RNA

organism: Homo sapiens

label_protocol: RNA from each sample was labeled according to the manufacturers recommendations (Thermo Fisher Scientific).

extract_protocol: RNA was extracted with QIAGEN RNeasy Lipid Tissue Mini kit in accordance with the prescribed protocol provided with the kit.

tag: subject status

value: patients subjected to mastectomy

tag: bmi

tag: age

tag: lymphnode positivity

value: pos

tag: hystotype

value: Ductal

tag: tumor grade

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos

value: IHC 3+):neg

tag: tumor ki67 positivity (pos

tag: tissue

value: Adipose tissues (AT)


title: MOE_METATAC_220503-P3-Plate2

type: SRA

city: Beijing

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

country: China

institute: Peking University

description: MOE_METATAC_peak files

library_source: genomic single cell

data_processing:
Cell barcodes and META sequences were identified for each pair of reads using a custom script. Reads from each cell were split according to their barcodes. Adapters were then trimmed using cutadapt (v4.0) with parameters “-e 0.22 -a CTGTCTCTTATACACATCT” followed by parameters “-e 0.22 -g AGATGTGTATAAGAGACAG”. Cleaned reads were then mapped to mm10 (GRCm38) reference genome using bowtie2 (v2.3.4.3) with parameters “-X 2000 --local --mm --no-discordant --no-mixed”. Duplicated reads were removed using custom script according to both their mapped location on the genome and META tags. Mapped paired reads were transformed into fragments, and a bias of “+4” or “-5” was added to each end of each fragment to center the Tn5 insertion sites.
10X scRNA-seq reads were processed and mapped to mm10 genome using Cell Ranger (v 5.0.1).
Assembly: mm10
Supplementary files format and content: count matrix (scRNA-seq)
Supplementary files format and content: bed (scATAC-seq)

molecule: genomic DNA

organism: Mus musculus

source_name: mouse olfactory epithelium (P35)

extract_protocol:
The main olfactory epithelium was dissected and minced to small pieces, then was dissociated into single cell suspension with the Papain Dissociation System (Worthington Biochemical, Cat. #LK003150) at 37°C for 15 min, during incubation, titration every 5 min with wide-bore pipette tip according to previously described2. Then filtered with 30 μm strainer (MACS), then wash twice with ice-cold 1 x PBS.
10X Genomics scRNA-seq and METATAC scATAC-seq

value: mouse olfactory epithelium (P35)

tag: cell type

value: mouse olfactory epithelium

tag: genotype

value: WT

tag: treatment

value: postnatal day 3


title: Mov10 KO_RNAseq input for Riboseq_1

city: Clayton

first: Partha

last: Das

state: VIC

address: 15 innovation walk

country: Australia

institute: Monash Biomedicine Discovery Institute, Monash University

description: Paired end 150bp

library_source: transcriptomic

data_processing:
Low quality reads were filtered out using trim galore (v0.6.5)
The 150bp paired end reads were mapped to the mm10 mouse genome assembly using Bowtie 2 (v2.3.2) and For RNAseq data, Filtered reads were aligned to the mm10 mouse genome assembly and the GENCODE version M23 mouse transcriptome using STAR RNA-seq alignment v2.6.3b
BigWig tracks were generated using the ‘bamCoverage’ program from the DeepTools software suite (v2.5.3), with reads extended to 300bp and tracks normalized using the  RPKM (Reads Per Kilobase per Million mapped reads) algorithm.
Peak calling was done with the ExomePeak and MACS2 program (v2.1.1.20160309). For mostRIP-seq datasets default MACS2 settings were used.  MACS2 was run with the “--nomodel” option. ExomePeak was used for m6A-RIP peak calling with deafult conditions.
Heatmap and plotprofile plots were generated using the 'plotHeatmap' and 'plotProfile' program respectively from the DeepTools software suite (v2.5.3)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

source_name: Embryonic Stem Cell

growth_protocol: Mouse ESCs (mESCs) were cultured in mouse ESC media that contains DMEM, supplemented with 15% fetal calf serum, 0.1mM b-mercaptoethanol, 2mM L-glutamine, 0.1mM NEAA, 1% of nucleoside mix , 1000 U/ml LIF/ESGRO, and 50U/ml Penicillin/Streptomycin. mESCs were cultured at 37ºC, 5% CO2.

extract_protocol:
Details of m6A-seq, Riboseq, RIPseq, RNAseq can be found in Methods section.
RNAseq, m6A-seq, RIPseq, Riboseq libraries were prepared using NEBNext Ultra Directional RNA Library Prep Kit and NEB NEXT Small RNA Library Prep Set for Illumina following the manufacturer’s instructions.

value: Mov10 KO

tag: strain

tag: antibody


title: SKOV3 cells, sgOTUD1_2

city: Wuhan

first: Yurou

last: Chen

address: Donghu Road

institute: Zhongnan Hospital of Wuhan University

data_processing:
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the edgeR software.
The KOBAS software analysis was used for KEGG pathway.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: ovarian cancer cells

growth_protocol: SKOV3 cells were maintained in DMEM (Sigma) supplemented with 10% fetal bovine serum (FBS) and at 37 °C in humid air with 5% CO2 condition.

extract_protocol:
Total amounts and integrity of RNA were assessed using Qubit fluorometer and the Agilent 2100 system (Agilent Technologies, CA, USA).
Sequencing libraries were constructed by NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA). Qubit2.0 Fluorometer, Agilent 2100 bioanalyzer and Quantitative real-time PCR (Q-PCR) were carried out successively to ensure the quality of the library.

tag: cell line

value: ovarian cancer cells

value: OTUD1 knockout


title: MOE_METATAC_210607-P3-Plate14

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P27)

value: mouse olfactory epithelium (P27)


title: SKOV3 cells, sgOTUD1_1


title: Wild-type_RNAseq input for Riboseq_3

description: Paired end 150bp

value: Wild-type


title: MOE_METATAC_210607-P3-Plate13

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P26)

value: mouse olfactory epithelium (P26)


title: SKOV3 cells, sgOTUD1_3


title: JU06_AT_adjacent_Pz21

tag: subject status

tag: bmi


title: Wild-type_RNAseq input for Riboseq_2

description: Paired end 150bp


title: JU05_AT_distant_Pz21

tag: age

tag: lymphnode positivity


title: JT98_AT_adjacent_Pz17

value: neg

tag: hystotype

tag: tumor grade


title: MOE_METATAC_210607-P3-Plate15

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P28)

value: mouse olfactory epithelium (P28)


title: JU01_AT_distant_Pz19

value: patients subjected to mastectomy

tag: tumor size (t)

tag: tumor er positivity (pos

value: IHC 3+):pos


title: MOE_METATAC_210607-P3-Plate12

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P25)

value: mouse olfactory epithelium (P25)


title: Wild-type_RNAseq input for Riboseq_1

description: Paired end 150bp


title: Mov10 KO_RNAseq input for Riboseq_2

description: Paired end 150bp


title: SKOV3 cells, sgNC_3

value: empty vector as negative control


title: JT97_AT_distant_Pz17

value: Ductal

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos

value: IHC 3+):neg

value: Adipose tissues (AT)


title: Mov10 KO_Riboseq_3

description: Single end 50bp

data_processing:
Library strategy: Ribo-Seq
Low quality reads were filtered out using trim galore (v0.6.5)
The 150bp paired end reads were mapped to the mm10 mouse genome assembly using Bowtie 2 (v2.3.2) and For RNAseq data, Filtered reads were aligned to the mm10 mouse genome assembly and the GENCODE version M23 mouse transcriptome using STAR RNA-seq alignment v2.6.3b
BigWig tracks were generated using the ‘bamCoverage’ program from the DeepTools software suite (v2.5.3), with reads extended to 300bp and tracks normalized using the  RPKM (Reads Per Kilobase per Million mapped reads) algorithm.
Peak calling was done with the ExomePeak and MACS2 program (v2.1.1.20160309). For mostRIP-seq datasets default MACS2 settings were used.  MACS2 was run with the “--nomodel” option. ExomePeak was used for m6A-RIP peak calling with deafult conditions.
Heatmap and plotprofile plots were generated using the 'plotHeatmap' and 'plotProfile' program respectively from the DeepTools software suite (v2.5.3)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig


title: SKOV3 cells, sgNC_2


title: MOE_METATAC_210607-P3-Plate11

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P24)

tag: tissue

value: mouse olfactory epithelium (P24)

value: mouse olfactory epithelium

value: WT


title: SKOV3 cells, sgNC_1

tag: cell type

value: ovarian cancer cells


title: Mov10 KO_Riboseq_2

description: Single end 50bp

tag: genotype

value: Mov10 KO


title: MOE_METATAC_210607-P3-Plate10

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P23)

value: mouse olfactory epithelium (P23)

tag: treatment

value: postnatal day 3


title: JT94_AT_adjacent_Pz14

value: pos

tag: tumor ki67 positivity (pos


title: JU02_AT_adjacent_Pz19


title: JT93_AT_distant_Pz14


title: Mov10 KO_Riboseq_1

description: Single end 50bp

tag: strain

tag: antibody


title: SKOV3 cells, Stem cells_3

data_processing:
FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0).
The GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp was used for GSEA independently.
Assembly: hg38
Supplementary files format and content: Excel file includes FPKM values for each Sample

growth_protocol: SKOV3 cells were seeded in ultra-low-attachment 96-well plates in DMEM/F12 medium supplemented with 2% B27 serum replacement to allow the formation of floating spheres. Then, these spheres were collected and recultured in a 6-well plate in DMEM with 10% FBS to allow the cells in the spheres to differentiate and attach to the bottom surface

extract_protocol:
Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
Sequencing libraries were constructed by NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA). Qubit2.0 Fluorometer, Agilent 2100 bioanalyzer and Quantitative real-time PCR (Q-PCR) were carried out successively to ensure the quality of the library.

tag: cell line

tag: growth protocol

value: floating sphere cells as stem cells


title: MOE_METATAC_210607-P3-Plate9

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P22)

value: mouse olfactory epithelium (P22)

tag: age


title: JT89_AT_distant_Pz11

tag: subject status

value: patients subjected to mastectomy

tag: bmi

tag: lymphnode positivity

value: neg


title: JT90_AT_adjacent_Pz11

tag: hystotype

tag: tumor grade

tag: tumor size (t)


title: Wild-type_Riboseq_3

description: Single end 50bp

value: Wild-type


title: SKOV3 cells, Stem cells_2


title: MOE_METATAC_210607-P3-Plate8

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P21)

value: mouse olfactory epithelium (P21)


title: SKOV3 cells, Stem cells_1


title: MOE_METATAC_210607-P3-Plate6

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P19)

value: mouse olfactory epithelium (P19)


title: Wild-type_Riboseq_2

description: Single end 50bp


title: SKOV3 cells, Adherent cells_3

value: floating sphere differentiated cells as Adherent cells


title: Wild-type_Riboseq_1

description: Single end 50bp


title: MOE_METATAC_210607-P3-Plate7

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P20)

value: mouse olfactory epithelium (P20)


title: m6A-RIPseq_Mov10 KO_2

description: Paired end 150bp

data_processing:
Library strategy: m6A-seq
Low quality reads were filtered out using trim galore (v0.6.5)
The 150bp paired end reads were mapped to the mm10 mouse genome assembly using Bowtie 2 (v2.3.2) and For RNAseq data, Filtered reads were aligned to the mm10 mouse genome assembly and the GENCODE version M23 mouse transcriptome using STAR RNA-seq alignment v2.6.3b
BigWig tracks were generated using the ‘bamCoverage’ program from the DeepTools software suite (v2.5.3), with reads extended to 300bp and tracks normalized using the  RPKM (Reads Per Kilobase per Million mapped reads) algorithm.
Peak calling was done with the ExomePeak and MACS2 program (v2.1.1.20160309). For mostRIP-seq datasets default MACS2 settings were used.  MACS2 was run with the “--nomodel” option. ExomePeak was used for m6A-RIP peak calling with deafult conditions.
Heatmap and plotprofile plots were generated using the 'plotHeatmap' and 'plotProfile' program respectively from the DeepTools software suite (v2.5.3)
Genome_build: mm10
Supplementary_files_format_and_content: bigWig

value: m6A:202 003 (Synaptic Systems)


title: SKOV3 cells, Adherent cells_2


title: m6A-RIPseq_Mov10 KO_1

description: Paired end 150bp


title: SKOV3 cells, Adherent cells_1


title: MOE_METATAC_210607-P3-Plate3

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P16)

value: mouse olfactory epithelium (P16)

value: mouse olfactory epithelium


title: RNA_ZR_28

city: Shanghai

first: Yuxuan

last: Zheng

address: 825 Zhangheng Rd.

institute: Fudan University

library_source: transcriptomic single cell

data_processing:
Procession of the 10× gene expression data, including barcode processing and single-cell gene counting, was performed using software CellRanger.
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: "barcodes.tsv" files include scRNA-seq barcode information, "features.tsv" files include scRNA-seq gene features and "matrix.mtx" files include scRNA-seq gene expression. "merge_BCR.xlsx" file include the single BCR information. "merge_TCR.xlsx" file include the single TCR information.

source_name: Peripheral blood mononuclear cell (PBMC)

extract_protocol:
Venous blood (20-30 mL) from study volunteers was collected in EDTA tubes. The tubes were centrifuged at 400 × g for 15 min to separate the cellular parts. The plasma-containing fraction was collected and centrifuged at 1200 × g for 15 min, and the plasma was aliquoted and stored at -20°C. The cellular fraction was reconstituted with phosphate-buffered saline (PBS) and subjected to Ficoll density gradient centrifugation (500 g, 30 min) according to the manufacturer’s instructions. After washing, PBMCs were resuspended in 90% foetal bovine serum (FBS) and 10% dimethyl sulfoxide (DMSO, Sigma Life Science) and then frozen at -80°C for one night before being stored in liquid nitrogen. PBMCs were thawed at 37°C and washed twice before use.
The appropriate numbers of cells to achieve a targeted cell input of 10,000 cells per condition were used to generate the GEMs (Gel Bead-In Emulsion). The Chromium Next GEM Single Cell 5' GEM, Library & Gel Bead Kit v3.1(10X Genomics, Pleasanton, CA, USA) was used for GEMs generation, cDNA synthesis and library preparation following the manufacturer’s instruction.

tag: library

value: scRNA-seq

tag: donor

value: ZR

tag: time point

value: Day 28


title: MOE_METATAC_210607-P3-Plate4

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P17)

tag: tissue

value: mouse olfactory epithelium (P17)

tag: cell type

tag: genotype

value: WT

value: postnatal day 3


title: JT86_AT_adjacent_Pz8

value: Ductal

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos

value: IHC 3+):neg

tag: tumor ki67 positivity (pos

value: Adipose tissues (AT)


title: RNA_ZR_0

value: Peripheral blood mononuclear cell (PBMC)

value: Day 0


title: JT83_AT_distant_Pz7

value: patients subjected to mastectomy

tag: age

value: neg


title: JT85_AT_distant_Pz8

tag: subject status


title: MOE_METATAC_210607-P3-Plate2

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P15)

value: mouse olfactory epithelium (P15)

tag: treatment


title: JT84_AT_adjacent_Pz7

tag: bmi

tag: lymphnode positivity


title: JT82_AT_adjacent_Pz6

tag: hystotype

tag: tumor grade


title: RNA_WJC_28

tag: library

value: WJC


title: Mov10 KO_RNAseq_2

description: Paired end 150bp

value: Mov10 KO

tag: strain

tag: antibody


title: MOE_METATAC_210607-P3-Plate5

description: MOE_METATAC_peak files

source_name: mouse olfactory epithelium (P18)

tag: tissue

value: mouse olfactory epithelium (P18)

value: mouse olfactory epithelium


title: m6A-RIPseq_Wild-type_1

description: Paired end 150bp

source_name: Embryonic Stem Cell

value: Wild-type

value: m6A:202 003 (Synaptic Systems)


title: Mov10 KO_RNAseq_1

description: Paired end 150bp


title: RNA_WJC_0

tag: cell type

value: scRNA-seq

tag: donor

tag: time point


title: MOE_10X_P28

molecule: polyA RNA

source_name: mouse olfactory epithelium (P14)

value: mouse olfactory epithelium (P14)

tag: genotype

value: WT

value: postnatal day 28


title: RNA_CCJ_0

value: CCJ


title: m6A-RIPseq_Wild-type_2

description: Paired end 150bp


title: MOE_10X_P14

value: postnatal day 14


title: Wild-type_RNAseq_1

description: Paired end 150bp


title: MOE_10X_P4-P7

source_name: mouse olfactory epithelium (P4, P7)

value: mouse olfactory epithelium (P4, P7)

value: postnatal day 4,7


title: NMΔasp23_RNA 2

status: Public on Jan 14 2024

city: Chongqing

first: Keting

last: Zhu

address: Shapinba Main Street

department: Department of Emergency Medicine

institute: Army Medical University

data_processing:
Illumina bcl2fastq 2.0 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using HISAT2
Transcript abundance values were obtained from gene-level count matrices were generated by StringTie
Gene counts were normalized using geometric mean (GEO) in DESeq2 package and log2 transformed. Removal of unwanted variation (RUV) was used to remove batch effects and genes with no counts in over 50% of the samples were removed.
Differential gene expression by limma voom was performed on normalized gene counts, using batch effects and the first two PCAs of aligning and sequencing as covariates.
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text file includes gene abundance for each sample

organism: Staphylococcus aureus

source_name: bacterial cells

growth_protocol: Overnight cultures of Newman and mutant NM∆asp23 were diluted 1:100 into fresh BHI and incubated at 37°C with shaking for 6 h.

extract_protocol: After quality control, library preparation and Illumina RNA sequencing was conducted by Shanghai Sangon Biotechnology (Shanghai, China).

treatment_protocol: Mid-log-phase cultures were firstly lysed with lysostaphin (Sigma-Aldrich, USA) and then total cellular RNA was isolated using RNAprep Pure Cell/Bacteria Kit (Promega, USA) according to the manufacturer’s protocol.

value: bacterial cells

tag: genotype/strain

value: mutant NM{delta}asp23


title: NM_RNA 2

value: NM


title: NM_RNA 3


title: JT79_AT_distant_Pz4

value: patients subjected to mastectomy

value: neg

value: Ductal

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos

value: IHC 3+):neg

tag: tumor ki67 positivity (pos

value: Adipose tissues (AT)


title: NMΔasp23_RNA 1


title: NM_RNA 1


title: MOE_METATAC_210607-P3-Plate1

description: MOE_METATAC_peak files

value: mouse olfactory epithelium

tag: treatment

tag: age

value: postnatal day 3


title: JT80_AT_adjacent_Pz4

tag: subject status

tag: bmi

tag: lymphnode positivity

tag: hystotype

tag: tumor grade


title: JT81_AT_distant_Pz6

tag: tissue


title: RNA-Seq, Pbrm1 cKO2

city: Bethesda

first: qiliang

last: Xin

state: MD

address: 50 South Dr

department: NIDDK

country: USA

institute: NIH

data_processing:
removing adapter sequences with cutadapt
aligning the reads with hisat2 against Mus musculus genome sequence
using featurecounts to estimate the number of gene reads
using a R script to perform differential expression analysis
Assembly: GRCm38.p5
Supplementary files format and content: featurecounts output  and fastq files

source_name: D4 primary uterine stromal cell Pbrm1 cKO

growth_protocol: The mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Uteru isolated from 8-12 weeks aged control and knockout mice.

extract_protocol:
5-10 pseudopregnant D4 WT mouse uterine horns were cut into small pieces (2–3 mm). Tissue pieces were first digested in 5 ml fresh medium (HBSS antibiotic; Gibco) containing 6 mg/ml dispase (Gibco) and 25 mg/ml pancreatin (Sigma), and then incubated in fresh medium (3 ml) containing 0.5 mg/ml collagenase (Sigma) at 37°C for 30 min. The digested cells were passed through a 70-lm filter to obtain the stromal cells. Cells were plated at 60-mm dishes, containing DMEM and Ham F-12 nutrient mixture (1:1) (Gibco) with 10% charcoal-stripped fetal bovine serum (FBS) and antibiotic. After 4 h, the medium was replaced with fresh medium (DMEM/F-12, 1:1) with 10% FBS. 2 hours later, wash twice with PBS gently for the preparation of RNA-Seq samples.
The libraries were constructed by using a Universal RNA-Seq Library Preparation Kit (TECAN) per the manufacturer’s protocol in which double-strand cDNA was generated using a mixture of random and poly(T) priming, followed by fragmentation of double-stranded cDNA, end repair, adaptor ligation, strand selection, targeted transcript depletion with AnyDeplete, and PCR amplification to produce the final library.

treatment_protocol: Mate with stud male for pregrancy.

tag: cell type

value: primary uterine stromal cell

value: Pbrm1 cKO

tag: time

value: Day 4 of pregrancy


title: RNA-Seq, Pbrm1 cKO3

tag: genotype


title: RNA_CCJ_28

value: Peripheral blood mononuclear cell (PBMC)

tag: library

value: scRNA-seq

tag: donor

value: CCJ

tag: time point

value: Day 28


title: RNA-Seq, Pbrm1 cKO1


title: RNA-Seq, WT3

source_name: D4 primary uterine stromal cell WT

value: WT


title: RNA-Seq, WT1


title: RNA-Seq, WT2


title: anti-FLAG - FLAG-Dsup 3R/3E - CUT&RUN

city: Durham

first: Michael-Christopher

last: Keogh

state: NC

address: 6 Davis Dr

institute: EpiCypher, Inc

library_source: genomic

data_processing:
*library strategy: CUT&RUN
Paired-end fastq files were aligned to thesacCer3reference genome using Bowtie2 (v2.2.5).
Duplicate reads were removed via SAMtools (v1.6).
Multi-aligned reads were removed via Picard (v2.26.2).
bigWig creation included both E. coli normalization and RPKM normalization via bamCoverage in deeptools (v3.5.1). Files were E. coli normalized by an E. coli scaling factor (1/%E. coli reads) and RPKM normalized ( --normalizeUsing option).
Assembly: sacCer3
Supplementary files format and content: bigWig

organism: Saccharomyces cerevisiae

growth_protocol: Yeast were grown in 500 mL of SC-ura media to OD of 0.6-0.8. Cells were spheroplasted using 500 μL of 2 mg/mL Zymolyase 100T at 37°C for approximately 30 mins (until a 50 μL aliquot mixed with 1 mL of 10% SDS had an OD approximately 10% of the starting value). See referenced text for further detail.

extract_protocol:
Nuclei from yeast cells expressing Dsup or mutant Dsup were purified according to published methods (doi:10.1007/978-1-0716-2257-5_9) with slight modifications described above. 1 mL aliquots containing approximately 5 x 107 nuclei were slow-frozen in an isopropanol chamber at  -80°C overnight. Immediately prior to an experiment, nuclei were thawed rapidly for 2-3 minutes at 37°C, then 100 μL of nuclei suspension was used per CUT&RUN reaction with the CUTANA™ ChIC/CUT&RUN Kit version 3 (EpiCypher). The protocol was carried out as directed by the version 3.2 user manual. MNase digestion of chromatin was performed for 2 hours at 4°C. See referenced text for further detail.
5 ng of DNA was used to prepare sequencing libraries with the Ultra II DNA Library Prep Kit (NEB #E7645L). Libraries were sequenced on an Illumina NextSeq 2000 platform. See referenced text for further detail.

treatment_protocol: Ramazzottius varieornatus plasmid pRS306-PTDH3-Dsup (carrying N-terminally His tagged and C-terminally FLAG tagged Dsup) was digested with MfeI and integrated into the yeast strain BY4741 3 at the site of the endogenous TDH3 promoter to make the “Dsup” strain, RGY002. Further mutations of the Dsup gene, including deletion of the C-terminus to make the “Dsup ΔC” strain (RAY136), addition of an NLS to make “Dsup ΔC-NLS” (RAY228), substitution of R363E/R364E/R367E to make “Dsup 3R/3E” (RAY153), and addition of a stop codon at codon 2 of Dsup to make the “Empty vector” strain (RAY149), were made after integration using CRISPR-Cas9 mediated genome editing. See referenced text for further detail.

tag: strain

tag: genetic modification

value: Plasmid pRS306-PTDH3-Dsup with substitution of R363E/R364E/R367E

tag: dsup strain

tag: antibody


title: JT76_AT_adjacent_Pz1

tag: age

tag: tumor size (t)

tag: tumor er positivity (pos

tag: tumor pgr positivity (pos

tag: tumor her2 positivity (pos

tag: tumor ki67 positivity (pos


title: NMΔasp23_RNA 3

value: bacterial cells

tag: genotype/strain

value: mutant NM{delta}asp23


title: anti-FLAG - FLAG-Dsup ΔC-NLS - CUT&RUN

value: Plasmid pRS306-PTDH3-Dsup with deletion of the C-terminus and addition of an NLS


title: anti-H3K4me3 - FLAG-Dsup 3R/3E - CUT&RUN


title: anti-FLAG - Empty Vector - CUT&RUN

value: Plasmid pRS306-PTDH3-Dsup with addition of a stop codon at codon 2


title: anti-FLAG - FLAG-Dsup - CUT&RUN

value: Plasmid pRS306-PTDH3-Dsup


title: anti-H3K4me3 - FLAG-Dsup ΔC-NLS - CUT&RUN


title: anti-H3K4me3 - Empty Vector - CUT&RUN


title: JT75_AT_distant_Pz1

tag: subject status

value: patients subjected to mastectomy

tag: bmi

tag: lymphnode positivity

value: neg

tag: hystotype

value: Ductal

tag: tumor grade

value: IHC 3+):neg

tag: tissue

value: Adipose tissues (AT)


title: JT78_AT_adjacent_Pz2


title: IgG Control - FLAG-Dsup - CUT&RUN

tag: strain


title: JT77_AT_distant_Pz2


title: IgG Control - Empty Vector - CUT&RUN

tag: genetic modification


title: IgG Control - FLAG-Dsup ΔC-NLS - CUT&RUN

tag: dsup strain


title: anti-H3K4me3 - FLAG-Dsup - CUT&RUN

tag: antibody


title: African Cheetah 45

type: genomic

city: Bloemfontein

first: Louis

middle: Stéphane

last: Le Clercq

state: FS

address: Genetics building, 205 Nelson Mandela Dr, Park West

department: Department of Genetics

country: South Africa

institute: University of the Free State

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850956
Source: SANBI Biobank, Location: South Africa

hyb_protocol: The EpiTYPER® Assay methylation analysis was run in three phases, starting with 1) PCR using T7-promoter tagged reverse primers to amplify the target regions while preserving the bisulfite-induced sequence changes and treatment of PCR product with Shrimp-Alkaline Phospatase. 2) In vitro transcription was performed, and 3) the resulting RNA transcripts were specifically cleaved at uracil residues. The resulting fragments differed in size and mass, depending on the sequence changes generated through bisulfite treatment, and through enzymatic cleavage of uracils. The resulting fragments were loaded onto a SpectroCHIP® Array (Chip) that was placed in the MASSarray (MALDI-TOF) mass spectrometer for data acquisition. Results showed individual peaks for the generated fragments.

scan_protocol: Fragmentation pattern was analysed for mass for each fragment (based on size) and the peak height, which corresponds to the percentage of methylation compared to an internal control. The output was automatically loaded into a database for data analysis with EpiTYPER® software.

data_processing: The EpiTYPER® software was used to call the β-value of methylation level for each peak corresponding to a specific CpG as a value between 0 and 1 indicating the percentage of methylation detected

label: Bisulfite converted

organism: Acinonyx jubatus

source_name: Captive African Cheetah

label_protocol: DNA was bisulfite converted using a commercial kit according to instructions

extract_protocol: Genomic DNA was extracted from whole blood samples using commercial DNA extraction kits according to instructions

value: Blood

tag: Sex

value: male

tag: age

value: 60 months

tag: developmental stage

value: Prime adult


title: African Cheetah 47

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850958
Source: SANBI Biobank, Location: South Africa

value: female

value: 1 months

value: Young cub


title: African Cheetah 49

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850960
Source: SANBI Biobank, Location: South Africa

value: 84 months


title: African Cheetah 46

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850957
Source: SANBI Biobank, Location: South Africa

value: 1.75 months


title: African Cheetah 48

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850959
Source: SANBI Biobank, Location: South Africa


title: African Cheetah 44

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850955
Source: SANBI Biobank, Location: South Africa

value: 42 months

value: Young adult


title: African Cheetah 39

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850950
Source: SANBI Biobank, Location: South Africa

value: 3 months


title: African Cheetah 42

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850953
Source: SANBI Biobank, Location: South Africa

value: 159 months

value: Very old adult


title: African Cheetah 35

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850946
Source: SANBI Biobank, Location: South Africa


title: African Cheetah 37

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850948
Source: SANBI Biobank, Location: South Africa

value: 120 months

value: Old adult


title: African Cheetah 38

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850949
Source: SANBI Biobank, Location: South Africa

value: 17.66 months

value: Adolescent


title: African Cheetah 40

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850951
Source: SANBI Biobank, Location: South Africa

value: Blood

value: 3.5 months


title: African Cheetah 36

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850947
Source: SANBI Biobank, Location: South Africa

value: 168 months


title: African Cheetah 30

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850941
Source: SANBI Biobank, Location: South Africa

value: female

value: 2.5 months


title: African Cheetah 34

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850945
Source: SANBI Biobank, Location: South Africa

value: male

value: 24 months

value: Newly indepenent


title: Wild-type_RNAseq_2

description: Paired end 150bp

tag: genotype

value: Wild-type


title: IgG Control - FLAG-Dsup 3R/3E - CUT&RUN

value: Plasmid pRS306-PTDH3-Dsup with substitution of R363E/R364E/R367E


title: African Cheetah 32

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850943
Source: SANBI Biobank, Location: South Africa

value: Young cub


title: African Cheetah 31

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850942
Source: SANBI Biobank, Location: South Africa


title: African Cheetah 33

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850944
Source: SANBI Biobank, Location: South Africa


title: African Cheetah 43

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850954
Source: SANBI Biobank, Location: South Africa

value: 3 months


title: African Cheetah 28

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850939
Source: SANBI Biobank, Location: South Africa


title: African Cheetah 29

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850940
Source: SANBI Biobank, Location: South Africa

value: 72 months

value: Prime adult


title: African Cheetah 41

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850952
Source: SANBI Biobank, Location: South Africa


title: African Cheetah 25

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850936
Source: SANBI Biobank, Location: South Africa


title: African Cheetah 23

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850934
Source: SANBI Biobank, Location: South Africa

value: 36 months

value: Young adult


title: African Cheetah 27

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850938
Source: SANBI Biobank, Location: South Africa


title: African Cheetah 24

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850935
Source: SANBI Biobank, Location: South Africa

value: 144 months

value: Old adult


title: African Cheetah 21

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850932
Source: SANBI Biobank, Location: South Africa

value: Blood


title: African Cheetah 20

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850931
Source: SANBI Biobank, Location: South Africa

value: 108 months


title: African Cheetah 22

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850933
Source: SANBI Biobank, Location: South Africa

value: female


title: African Cheetah 19

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850930
Source: SANBI Biobank, Location: South Africa

value: 27 months


title: African Cheetah 18

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850929
Source: SANBI Biobank, Location: South Africa

value: 27.96 months


title: African Cheetah 17

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850928
Source: SANBI Biobank, Location: South Africa

value: 13.92 months

value: Adolescent


title: African Cheetah 14

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850925
Source: SANBI Biobank, Location: South Africa

value: male

value: 96 months


title: African Cheetah 26

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850937
Source: SANBI Biobank, Location: South Africa


title: African Cheetah 16

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850927
Source: SANBI Biobank, Location: South Africa

value: 120 months


title: African Cheetah 06

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850917
Source: SANBI Biobank, Location: South Africa


title: African Cheetah 05

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850916
Source: SANBI Biobank, Location: South Africa

value: 4 months

value: Young cub


title: African Cheetah 15

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850926
Source: SANBI Biobank, Location: South Africa

value: 48 months


title: African Cheetah 07

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850918
Source: SANBI Biobank, Location: South Africa

value: 84 months

value: Prime adult


title: African Cheetah 13

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850924
Source: SANBI Biobank, Location: South Africa


title: African Cheetah 12

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850923
Source: SANBI Biobank, Location: South Africa

value: Young adult


title: African Cheetah 10

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850921
Source: SANBI Biobank, Location: South Africa


title: African Cheetah 11

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850922
Source: SANBI Biobank, Location: South Africa

value: Old adult


title: African Cheetah 08

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850919
Source: SANBI Biobank, Location: South Africa

value: Blood

value: 24 months

value: Newly indepenent


title: ATAC_iM2_1

city: Boulder

first: Sara

middle: L

last: Sawyer

state: CO

address: 3415 Colorado Ave.,

department: BioFrontiers Institute

institute: University of Colorado Boulder

data_processing:
Raw sequencing reads were first trimmed for low-quality reads and adapter sequences using BBDuk (BBMap v38.05). The trimmed reads were mapped to the human hg38 genome using Bowtie2 v2.2.9.
The resulting mapped reads were used to identify enriched open-chromatin peaks using the software package Genrich v0.6.1 in ATAC-seq mode, which automatically removes mitochondrial reads, PCR duplicates, and correct for read shifting caused by Tn5 transposition.
The identified narrow peaks were then merged across biological duplicates and experimental conditions. The number of reads mapped to each peak were counted using FeatureCount (Subread v1.6.2).
The read counts were then corrected for library size and Trimmed Mean of M-values (TMM) using edgeR v3.36.0. We then identified open chromatin regions that underwent significant accessibility changes during differentiation and/or polarization and clustered their accessibility profiles using hierarchical clustering. The motifs that are significantly enriched within each cluster were identified using Analysis of Motif Enrichment (AME, MEME suite 5.4.1) against the reference human motif database HOCOMOCO v11.
Assembly: hg38
Supplementary files format and content: GTF file containing ATAC-seq peaks merged from all samples
Supplementary files format and content: Tab delimited text file including raw read counts assgined to the peaks for each sample

source_name: IPSC-derived M2 macrophage

growth_protocol: The iPSC line is maintained in mTeSR Plus medium (STEMCELL Technologies #100-0276) using hESC-qualified Matrigel (Corning #CLS354277) coated plates. All cells were maintained at 37C and 5% CO2. All subcultures of iPSC were passaged using 0.5 M EDTA (Invitrogen # AM9260G). Additional culturing conditions for iPSC and blood-derived macrophages are listed in the treatment protocol.

extract_protocol:
iPSCs, along with blood- and iPSC-derived macrophages, were cultured in 6-well plates at 1x10E6 cells/well, each with biological duplicates. The cells were lifted via treatment with Accutase for 20 minutes at 37 ̊ C, and 5x10E4 cells were split for ATAC-seq library preparation.
The ATAC-seq libraries are constructed following the OmniATAC-seq protocol published in Corces et al. Nature Methods. 2017. The Illumina Nextera XT library preparation kit was used to construct the final sequencing library. The ATAC-seq library was further size-selected using a BluePippin machine with a 2% agarose gel cassette (Sage Science #RBF2010) to enrich for 100-1000 bp fragments.

treatment_protocol: Stem cell derived monocytes were differentiated from iPSCs using the STEMdiff Monocyte Kit (#05320; STEMCELL Technologies), following the manufacturer recommendations. Monocytes harvested from differentiation culture supernatants were collected via centrifugation at 300xg for 5 minutes and then transitioned to culture in ImmunoCult-SF macrophage medium (STEMCELL Technologies #10961) over a period of several days. We started iPSC-derived monocyte to macrophage differentiation 3 days after monocyte harvest by replacing medium with 100% ImmunoCult-SF macrophage medium containing 10 ng/mL M-CSF (R&D Systems #216-MC-010).  To obtain blood-derived monocytes, 50 mL of human blood from apparently healthy anonymous donors was collected on the day of purification. Within 1 hour of blood collection, 12 mL aliquots of blood were diluted 1:1 with Dulbecco’s Phosphate Buffered solution (PBS) (Caisson Labs # PBL02-500ML) + 2% FBS before being loaded onto 15 mL of Lymphoprep (STEMCELL Technologies #07801). The layered blood-Lymphoprep mixture was centrifuged at 800xg for 20 minutes at room temperature with the brake off. After the centrifugation, the upper plasma layer was gently removed and discarded. The buffy coat was collected and washed with PBS + 2% FBS three times with low-speed centrifugation at 180xg for 10 minutes at room temperature. Subsequently, monocytes were purified from the peripheral blood mononuclear cells (PBMCs) via Percoll (Sigma-Aldrich #P4937) gradient centrifugation as previously described. The purified monocytes were plated onto 6-well plates at 2x10E6 cells per well.  To differentiate both iPSC-derived and blood-derived monocytes into naïve macrophages, monocytes were plated at 1x10E6 cells per well of a 6-well plate in ImmunoCult-SF macrophage medium supplemented with 10 ng/mL M-CSF and cultured for 4 days. To polarize the naïve macrophages into M1 subtype, the M0 macrophages were incubated in ImmunoCult-SF macrophage medium supplemented with 50 ng/mL Interferon-gamma (R&D Systems #285-IF-100/CF) and 10 ng/mL lipopolysaccharide (Sigma-Aldrich #L2018) for 2 days. To polarize the naïve macrophages into M2 subtype, the M0 macrophages were incubated in ImmunoCult-SF macrophage medium supplemented with 10ng/mL Interleukin-4 (Sigma-Aldrich #H7291) for 2 days.

tag: cell line

value: IPSC-derived M2 macrophage

tag: cell type

value: M2 macrophage

value: WT


title: ATAC_iPSC_2

source_name: iPSC iCTR

value: iPSC iCTR

value: human induced pluripotent stem cells


title: ATAC_iPSC_1


title: ATAC_iM1_2

source_name: IPSC-derived M1 macrophage

value: IPSC-derived M1 macrophage

value: M1 macrophage


title: African Cheetah 09

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850920
Source: SANBI Biobank, Location: South Africa

value: male


title: African Cheetah 04

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850915
Source: SANBI Biobank, Location: South Africa

value: female

value: 60 months


title: African Cheetah 50

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850961
Source: SANBI Biobank, Location: South Africa

value: 96 months


title: African Cheetah 01

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850912
Source: SANBI Biobank, Location: South Africa

value: Prime adult


title: ATAC_iM2_2


title: ATAC_iM0_2

source_name: IPSC-derived M0 macrophage

value: IPSC-derived M0 macrophage

value: M0 macrophage


title: African Cheetah 02

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850913
Source: SANBI Biobank, Location: South Africa

value: Blood


title: African Cheetah 03

description:
Cheetah EDARADD.txt, Cheetah ELOVL2.txt, Cheetah FHL2.txt, Cheetah GRIA2.txt, Cheetah ITGA2B.txt, Cheetah PENK.txt
SAMN31850914
Source: SANBI Biobank, Location: South Africa

value: 24 months


title: ATAC_iM0_1


title: ATAC_bM2_1

source_name: blood monocyte derived M2 macrophage

value: blood monocyte derived M2 macrophage


title: ATAC_bM2_2


title: ATAC_bM1_2

source_name: blood monocyte derived M1 macrophage

value: blood monocyte derived M1 macrophage


title: ATAC_iM1_1


title: RNA_bM1_1

data_processing:
Sequencing reads were first trimmed for low-quality reads and adapter sequences using BBDuk (BBMap v38.05).
The trimmed reads were mapped to human hg38 genome using HISAT2 v2.1.0.
The number of reads were mapped to human RefSeq exons using FeatureCount (Subread v1.6.2).
The mapped reads were normalized by size factors and analyzed for differential expression using DESeq2 R package v1.34.0.
To visualize relative expression of genes, the fragments per kilobase of transcript per million mapped reads (FPKM) of size-factor normalized read counts were extracted to plot the heatmaps, and the expression level was subsequently scaled to row z-score. The gene ontology enrichment analysis was done using R package clusterProfiler v3.0.4.
Assembly: hg38
Supplementary files format and content: Tab delimited text file including raw counts for each sample

extract_protocol:
For RNA-seq, total RNA was harvested using Zymo Quick-RNA Microprep kit (Zymo #R1050), following manufactuere's protocol.
Following manufactuere's protocol, mRNA was enriched and prepared into sequencing library using KAPA mRNA HyperPrep kits (Roche #8098123702). The libraries were sequenced on the NovaSeq 6000 System using 2x151 cycles for a minimum of 20 million pair-end reads per library.


title: RNA_iPSC_2


title: RNA_iM1_1


title: RNA_bM1_2

value: M2 macrophage


title: RNA_iM2_1

value: IPSC-derived M2 macrophage

value: WT


title: ATAC_bM0_2

source_name: blood monocyte derived M0 macrophage

value: blood monocyte derived M0 macrophage


title: ATAC_bM0_1


title: RNA_bM2_2


title: RNA_iM1_2

value: IPSC-derived M1 macrophage


title: RNA_iM0_1


title: RNA_iM2_2


title: RNA_bM0_2


title: RNA_bM2_1

value: M1 macrophage


title: RNA_iM0_2


title: RNA_bM0_1


title: RNA_iPSC_1

value: iPSC iCTR

value: human induced pluripotent stem cells


title: T47D_24h_DMSO_rep_1

city: Dundee

first: Ralitsa

middle: Radostinova

last: Madsen

address: Dow Street

department: Medical Research Council Protein Phosphorylation and Ubiquitylation Unit

country: United Kingdom

institute: School of Life Sciences, University of Dundee

data_processing:
Nextflow (version 20.07.1) nf-core RNAseq pipeline (version 1.1), with Spliced Transcripts Aligment to a Reference (STAR) for read alignment to the human genome (Homo_sapiens.GRCh38.96.gtf) and featureCounts for counting of mapped reads (multimapped reads were discarded)
All subsequent analysis steps using the raw gene counts were performed in R. Filtering of low gene expression counts was performed with the TCGAbiolinks package with quantile value 0.75 (chosen empirically based on the observed count distribution).
Read count normalization was performed with the trimmed mean of M (TMM) method.
The mean-variance relationship was modelled with voom(), followed by linear modelling and computation of moderated t-statistics using the lmFit() and eBayes() functions in the limma package.
Experimental replicate was included as a batch effect term in the linear model. The associated p-values for assessment of differential gene expression were adjusted for multiple comparisons with the Benjamini-Hochberg method at false-discovery rate (FDR) = 0.05. Adjustments were performed separately for each contrast of interest.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing all raw gene counts for each sample

growth_protocol: Cells were obtained from ATCC and cultured in RPMI media supplemented with 10% heat inactivated fetal bovine serum without antibiotics at 37°C in the presence of 5% CO2. Cells were maintained in Corning tissue culture-treated 15-cm dishes (08-772-24) in 15 mL medium. Medium was replenished every 3 days, until cells reached 70-90% confluence. To passage, cells were washed once with 5 mL PBS and incubated for 5-10 minutes at 37°C with 0.25% Trypsin 0.1% EDTA and passaged up to 5 times in the same dish. Cells were maintained in culture for up to one month. Cells were routinely tested for mycoplasma using a Mycoplasma Detection Kit (Lonza cat. no. LT07-218).

extract_protocol:
Takara’s Nucleospin RNA Plus kit (cat. # 740984.50)
NEB Next® Ultra™ RNA Library Prep Kit (NEB #E7770)

treatment_protocol: Cells were treated with DMSO, AZD5363, or pitavastatin by spiking 3 µL of drug-containing media into 3 mL of media in 6-cm tissue culture-treated dishes.

tag: time

value: breast cancer, luminal

value: ERpos PRpos HER2neg

tag: treatment

value: DMSO


title: T47D_48h_Pitava_rep_3

value: Pitavastatin


title: T47D_48h_AZD5363_rep_3


title: T47D_48h_Combo_rep_3

value: Combination


title: M468_48h_Combo_rep_1

value: breast cancer, basal

value: ERneg PRneg HER2neg


title: M468_48h_AZD5363_rep_1


title: M468_48h_DMSO_rep_1


title: T47D_48h_DMSO_rep_3


title: T47D_24h_Combo_rep_3


title: T47D_24h_AZD5363_rep_3


title: T47D_24h_Pitava_rep_3


title: ATAC_bM1_1


title: M468_48h_Pitava_rep_1


title: T47D_24h_DMSO_rep_3


title: M468_48h_Pitava_rep_3


title: M468_48h_AZD5363_rep_3


title: M468_48h_Combo_rep_3


title: M468_24h_Combo_rep_3


title: M468_24h_Pitava_rep_3


title: M468_24h_DMSO_rep_3


title: T47D_48h_Combo_rep_2


title: M468_48h_DMSO_rep_3


title: M468_24h_AZD5363_rep_3


title: T47D_48h_AZD5363_rep_2


title: T47D_48h_DMSO_rep_2


title: T47D_24h_Pitava_rep_2


title: M468_24h_Pitava_rep_1


title: T47D_24h_AZD5363_rep_2


title: T47D_24h_Combo_rep_2


title: M468_24h_Pitava_rep_2


title: M468_48h_DMSO_rep_2


title: T47D_24h_DMSO_rep_2


title: M468_24h_AZD5363_rep_1


title: M468_48h_Combo_rep_2


title: M468_48h_Pitava_rep_2


title: M468_24h_DMSO_rep_2


title: M468_48h_AZD5363_rep_2


title: M468_24h_Combo_rep_2


title: M468_24h_AZD5363_rep_2


title: T47D_48h_Combo_rep_1


title: T47D_48h_Pitava_rep_1


title: T47D_48h_AZD5363_rep_1


title: T47D_48h_Pitava_rep_2


title: T47D_24h_Combo_rep_1


title: T47D_24h_Pitava_rep_1


title: M468_24h_DMSO_rep_1


title: T47D_24h_AZD5363_rep_1


title: THP1

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

data_processing:
For sequencing data with fastq files, read quality was assessed with FastQC (version 0.11.5). Illumina adapter sequences from raw fastq files were trimmed using Trimmomatic (version 0.39). The trimmed fastq files were aligned to the GRCh38 human reference genome (hg38, release 86) using HISAT2 (version 2.1.0) and gene counts were obtained using featureCounts, downloaded from Subread package. All downstream analyses were performed in R Studio (version, 1.4.1106) using the Bioconductor framework.
Assembly: GrCh38.86
Supplementary files format and content: .csv file contains raw counts for each gene per sample

source_name: Acute myeloid leukemia cell line

growth_protocol: Human AML cell lines were cultured as previously described (Pearson et al. Mol. Cancer Research, 2020).

extract_protocol:
Total RNA was isolated from AML patient PBMCs and AML cell lines by resuspending pellets in Trizol and purifying RNA with Direct-zol RNA Miniprep (Zymo Research # R2052). DNase treatment was done using RNase-Free DNase Set (Qiagen # 79254). RNA integrity was analyzed using the Agilent TapeStation system according to the manufacturer’s protocol. RNA samples with RIN scores higher than 5.3 were sent to Novogene for mRNA library prep and sequencing. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the second strand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.
100 ng total RNA isolated using trizol standard protocol (according to the manufacturer’s instructions) was used for sequencing using TruSeq Stranded Total RNA Ribo Zero kit (Human/Mouse/Rat) on NovaSeq6000 S4, 150 bp paired-end.

value: Acute myeloid leukemia cell line


title: UCSD-AML1


title: THP-1


title: TF1


title: PPBL9785

source_name: AML Primary sample

value: AML Primary sample


title: SKNO-1


title: TF-1


title: SET2


title: PBL10278


title: SKM-1


title: PPBL10173


title: PPBL9542


title: P934


title: P998


title: PBL10261


title: P933


title: P801


title: P218


title: P1356


title: T47D_48h_DMSO_rep_1


title: P1321


title: P1343


title: P1361


title: P136


title: PPBL8426


title: P1304


title: P1313


title: P1266


title: P850


title: P1316


title: P1257


title: P109


title: M468_24h_Combo_rep_1


title: GR_pred_1

city: Cincinnati

first: Mattia

last: Quattrocelli

state: OH

address: 240 Sabin Way

institute: Cincinnati Children's Hospital Medical Center

data_processing:
A quality control check on the generated fastq ﬁles was performed using FastQC.
Peak analysis was conducted using HOMER software (v4.10, 70; standard commands) after aligning fastq files to the mm10 mouse genome using bowtie2 71.
Assembly: mm10
Supplementary files format and content: bedgraph file of peaks (raw counts)

source_name: heart

extract_protocol:
Atria- and blood-deprived hearts were cryopowdered using a liquid nitrogen-cooled Retsch Cryomill. The cryopow-dered tissue was then fixed in 10 ml 1% PFA for 30 minutes at room temperature with gentle nutation. Fixation was quenched 1ml of 1.375M glycine (Cat # BP381-5, Fisher Scientific, Waltham, MA) with gentle nutation for 5 minutes at room temperature. After centrifugation at 3000g for 5 minutes at 4°C, the pellet was resuspended in cell lysis buffer as per reported conditions 69, supplementing the cell lysis buffer with 3mg/ml cytochalasin B and rotating for 10 minutes at 4°C.  Nuclei were pelleted at 300g for 10 min at 4°C, and subsequently processed following the reported protocol with the adjustment of adding 3µg/ml cytochalasin B into all solutions for chromatin preparation and sonication, antibody incubation, and wash steps.  Chromatin was then sonicated for 15 cycles (30 sec, high power; 30 sec pause; 500µl volume) in a water bath sonicator set at 4°C (Bioruptor 300; Dia-genode, Denville, NJ).  After centrifuging at 10000g for 10 minutes at 4°C, sheared chromatin was checked on agarose gel for a shear band comprised between ~150 and ~600bp. Two µg of chromatin was kept for pooled input controls, whereas ~50µg chromatin were used for each pull-down reaction in a final volume of 2ml rotating at 4°C overnight. Primary antibody: rabbit polyclonal anti-GR (ABclonal #A2164). Chromatin complexes were precipitated with 100µl Dynabeads M-280 (sheep anti-rabbit #11203D; Thermo Scientific, Waltham, MA).  After washes and elution, samples were treated with proteinase K (cat #19131; Qiagen, Hilden, Germany) at 55°C and cross-linking was reversed through overnight incubation at 65°C. DNA was purified using the MinElute puri-fication kit (cat #28004; Qiagen, Hilden, Germany), quantitated using Qubit reader and reagents.
Library preparation and sequencing were conducted at the CCHMC DNA sequencing Core. Up to 30 ng of post-Immunoprecipitation dsDNA as measured by Invitrogen™ Qubit™ high- sensitivity spectroﬂuorometric measurement was made into Illumina-compatible NGS libraries using the ThruPLEX® DNA-Seq kit from Takara Bio Inc.
Each created library was dual-indexed with 8-base molecular barcodes for high level mul5plexing. Libraries were made with 13 cycles of PCR ampliﬁcation.

value: heart

value: male

value: prednisone

tag: chip antibody

value: anti-GR (ABclonal #A2164)


title: GR_veh_3

value: WT

value: vehicle


title: P1021


title: P1044


title: P1065


title: GR_pred_2


title: GR_veh_2


title: P1006


title: GR_veh_1


title: GR, pooled inputs

value: pooled


title: OCIM2


title: OCIAML4


title: OCI1


title: Degron_ESC_-dtag_Rep2

city: Madison

first: Rupa

last: Sridharan

state: WI

address: 330 N. Orchard Street

department: Wisconsin Institute for Discovery

institute: University of Wisconsin

data_processing:
Libraries were sequenced to a depth of ~50 million reads/sample were sequenced PE150 by Novogene on an Illumina Novaseq 6000 platform.
Sequencing quality was assessed with FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Sequenced reads were processed using Trimmomatic (Bolger et al., 2014) with the following parameters: LEADING:3 TRAILING:3 CROP:135 HEADCROP:15 SLIDINGWINDOW:4:15 MINLEN:36
Reads were aligned to the mm9 genome using RSEM-1.2.4 (Li and Dewey, 2011) with a mismatch per seed set to 2 and seed length set to 28 (- bowtie-m 200 --bowtie-n 2 --forward-prob 0.5 --seed-length 28 --paired-end). RSEM-1.2.4 alignment yielded transcripts per million (TPM) for each gene
Differentially expressed (DE) genes were called with EBSeq (Leng et al., 2013). Differentially expressed genes were filtered to have a posterior probability DE greater than 0.95 and a 2 or 0.5 greater posterior fold change (PostFC). Expression changes reported are PostFC values determined by EBSeq unless otherwise noted to be TPM
Assembly: mm9
Supplementary files format and content: Output from RSEM is .results text file containing genes, transcript ID, length, counts, transcripts per million (TPM), and FPKM.

growth_protocol: ESCs were grown on 0.1% gelatin coated plates and maintained in ESC media (knock-out DMEM, 15% FBS, 1x non-essential amino acids, 1x glutamax, 1x penicillin/streptomycin, 2-Mercaptoethanol (4 μl/525ml), and leukemia inhibitory factor).

extract_protocol:
RNA was extracted with TRIzol and chloroform, cleaned using the Qiagen Rneasy Mini kit, and Dnase treated (Qiagen 79254) for 30 min.
1 ug of RNA was used for library construction. TruSeq RNA Sample Preparation kit V2 (RS-122-2002) was used to construct cDNA libraries

value: mESC

value: KDM3A:Degron/KO KDM3B:DEGRON/DEGRON


title: Degron_ESC_-dtag_Rep3


title: B16 tumor-associated macrophages, naïve, PirB-KO

city: Toronto

first: Tak

last: Mak

state: ON

address: 610 University Ave

department: The Campbell Family Institute for Breast Cancer Research

country: Canada

institute: Princess Margaret Cancer Centre, University Health Network

description: 10X Genomics

data_processing:
The raw sequencing reads were processed for quality control, mapping (to mouse genome build GRCm38), and UMI (unique molecular identifier) count matrix assembly using the CellRanger bioinformatics pipeline v2.0.1 provided by 10xGenomics.
Normalization, clustering, and gene expression analysis were carried out using the Seurat R Package v3.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: B16 tumor

growth_protocol: Standard housing at PMCC, Toronto

extract_protocol:
Mice were humanely euthanized utilizing CO2 displacement and cervical dislocation. Bone marrow-derived monocytes were recovered by flushing the bone marrow of femur plus tibia with ice-cold FACS buffer (PBS-/- supplemented with 2% heat-inactivated FCS and 2mM EDTA). To obtain splenocyte single-cell suspensions, spleens were crushed through a 70 µm filter using a syringe and suspended in 4 ml ice-cold FACS buffer. For peritoneal lavage, 5-7 ml ice-cold FACS buffer was injected into the peritoneal cavity followed by abdominal massage. Buffer containing peritoneal cells was aspirated by syringe equipped with a 20G needle. All cell suspensions were subjected to red blood cell (RBC) lysis using a commercially available buffer (Sigma). Cells were pelleted by centrifugation (300 x g, 5 min, 4˚C), resuspended in ice-cold FACS buffer, and subjected to cell count determinations.
Flow cytometry-based isolation of Lin-CD11b+CD115+Ly6G-Ly6C+ bone marrow (BM)-derived monocytes; Lin-F4/80+CD11bintMHCIIhi red pulp macrophages from digested spleens; Lin-F4/80+CD11b+Ly6Clo peritoneal macrophages; MerTK+CD64+ B16 tumor-associated macrophages; all cell populations were derived from WT and Pirb-/- (PirB KO) female littermate mice and immedeiately processed and subjected to scRNA-seq.
Single-cell suspensions were prepared according to the Chromium Single Cell 3’ Reagent Kits User Guide (v2 Chemistry). Samples were loaded onto a 10x Chromium instrument to produce sequencing libraries, which were processed according to methods provided by 10x Genomics. Cells were sequenced and processed to generate expression matrices using Cell Ranger (10x Genomics).
Libraries were prepared using the 10X Genomics Chromium Single Cell 3’ v4 Chemistry Reagent Kit, as per the parameters recommended by 10X Genomics.

treatment_protocol: naïve or B16-tumor-associated

value: B16 tumor

value: female, B16 tumor-associated macrophages, PirB-KO

value: PirB-KO

value: B16 tumor-associated


title: GR_pred_3


title: B16 tumor-associated macrophages, naïve, WT

description: 10X Genomics

value: female, B16 tumor-associated macrophages, WT


title: NCI-H1299, biological rep2

city: Shenyang

first: Qiuyue

last: Zhang

address: No. 103, Wenhua Road, Shenhe District

institute: Shenyang Pharmaceutical University

description: Gene expression data from NCI-H1299 cells

hyb_protocol: Following fragmentation, 5.2 ug of cRNA were hybridized for 16 hr at 45°C on GeneChip®Hybridization Oven 645. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneChip®Scanner 3000 7G

data_processing:
Probe cell intensity data from 3' Expression Array analyses is further analyzed in the Affymetrix® Expression Console™ software application using the MAS5, RMA, and PLIER algorithms to create CHP files. The *.CEL file (original chip data) was homogenized according to the RMA algorithm, and all database information was annotated to obtain the RMA data. Between-group statistical Moderated T-test comparison analyses were performed and screened based on >1.5-fold (or two-fold) differences between groups and between-group P-Value values ≤0.05
Moderated T-test comparison analyses

source_name: Non-small cell lung cancer cells

label_protocol: The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT) using the Affymetrix proprietary DNA Labeling Reagent that is covalently linked to biotin. 5.5 μg of single stranded cDNA is required for fragmentation and labeling

growth_protocol: NCI-H1299 and NCI-H1299 cells were cultured with RPMI 1640 medium containing 10% fetal bovine serum and 1% penicillin-streptomycin , then were incubated in 37 °C cell incubator containing 5% CO2.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: When the cell density reached 90-100%, the cells were collected and total RNA was extracted.

tag: disease

value: Non-small cell lung cancer


title: NCI-H1299, biological rep1


title: NCI-H1299/CDDP, biological rep2

description: Gene expression data from NCI-H1299/CDDP cells

source_name: Cisplatin-resistant non-small cell lung cancer cells


title: Degron_ESC_+dtag_4hrs_Rep3

value: +dTAG-13 4 hours


title: OCI-5

value: Acute myeloid leukemia cell line


title: Peritoneal macrophages, naïve, PirB-KO

description: 10X Genomics

source_name: Peritoneum

value: Peritoneum

value: female, peritoneal macrophages, PirB-KO

value: naïve


title: OCI-4


title: OCI-3


title: Peritoneal macrophages, naïve, WT

description: 10X Genomics

value: female, peritoneal macrophages, WT


title: OCI-2


title: Red pulp macrophages, naïve, PirB-KO

description: 10X Genomics

source_name: Spleen

value: Spleen

value: female, Red pulp macrophages, PirB-KO


title: Degron_ESC_+dtag_4hrs_Rep1


title: Degron_ESC_+dtag_4hrs_Rep2


title: Degron_ESC_-dtag_Rep1


title: Monocytes, naïve, PirB-KO

description: 10X Genomics

source_name: Bone marrow

value: Bone marrow

value: female, monocytes, PirB-KO


title: Monocytes, naïve, WT

description: 10X Genomics

value: female, monocytes, WT

value: WT


title: Red pulp macrophages, naïve, WT

description: 10X Genomics

value: female, Red pulp macrophages, WT


title: E14_ESC_+dtag_4hrs_Rep3

value: mESC

value: KDM3A:WT/WT KDM3B:WT/WT


title: CAOV3_STM3006_R1

city: Cambridge

first: Georgia

last: Tsagkogeorga

address: Moneta Building, Babraham Research Campus

institute: STORM Therapeutics Ltd

data_processing:
Analysis of CaOV3 samples (STM3006 n=3, DMSO n=3) was performed using nf-core/rnaseq bioinformatics pipeline (workflow container 3.0). Reads were mapped to the human genome GRCh38 using STAR aligner under default parameters.
Assembly: GRCh38
Supplementary files format and content: tab delimited text file with raw gene counts for each sample

source_name: ovary

extract_protocol:
For total RNA extraction, cells were homogenized in 700 μl Trizol (Thermo Fisher Scientific) followed by Chloroform addition and centrifugation. The aqueous phase was transferred to new tubes and RNA was precipitated using equal volumes of 100% Isopropanol followed by 2 washes with 80% Ethanol. RNA pellets were air-dried and resuspended in 25 μl nuclease-free water.
QuantSeq 3’ mRNA-Seq Library following manufacturer’s instructions

treatment_protocol: CaOV3 cells were treated with 500 nM STM3006 or 0.3% DMSO in triplicate for 48 hours

value: ovary

value: ovarian carninoma


title: CAOV3_DMSO_R3

value: DMSO


title: CAOV3_STM3006_R3


title: NOMO

description: NOMO

value: Acute myeloid leukemia cell line


title: CAOV3_STM3006_R2


title: CAOV3_DMSO_R2


title: E14_ESC_+dtag_4hrs_Rep2

value: +dTAG-13 4 hours


title: MV411


title: CAOV3_DMSO_R1


title: NCI-H1299/CDDP, biological rep1

value: Non-small cell lung cancer


title: MUTZ-2


title: CCRF-CEM cells - Input

city: Madrid

first: Javier

last: Redondo-Muñoz

state: Madrid

address: Ramiro de Maeztu,9

department: Molecular Biomedicine

country: Spain

institute: CIB-CSIC

data_processing:
Data filtering includes removing adaptor sequences, contamination and low-quality reads from raw reads. These reads were detected by BGI programs and data filtering parameters were: SOAPnuke filter -l 5 -q 0.5 -n 0.1 -Q 2 -c 50
After filtering, the Clean data was then mapped to the reference genome by SOAPaligner/SOAP2 (Version: 2.21t). No more than 2 mismatches are allowed in the alignment.
BWA (Burrows-Wheeler Aligner, Version: 0.7.10)is also used to do genome alignment after evaluating its performance. Align Parameter: bwa aln -t 4 -o 1 -e 49 -m 100000 -i 15 -q 10 -I
MACS (Model-based Analysis for ChIP -Seq, version: MACS-1.4.2) : The candidate Peak region was extended to be long enough for modeling. Dynamic Possion Distribution was used to calculated p-value of the specific region based on the unique mapped reads. The region would be defined as a Peak when p-value < le-05. Peak Calling Parameter: macs2 -g hs -s 49 -p 1e-5 -m 10 30 --broad -B --trackline
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files contain fragment densities along the genome determined as follows: the genome is divided into 10-nt bins and the number of fragments (aligned reads or tags) in each bin is normalized by reads per genomic content (normalizing coverage to 1x GRCh37 genome size).
Supplementary_files_format_and_content: peak Excel file

source_name: Jurkat cells

growth_protocol: CCRF-CEM cells were cultured in RPMI (supplemented with 10% FBS) at 37oC  and 5% CO2

extract_protocol:
Cells were washed, strained and fixed with 1% formaldehyde for 4 min and quenched with 0.125 M glycine.  Lysates were sonicated with a QSonica to shear the DNA. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. For each ChIP reaction, 30 ug of chromatin was precleared with protein A agarose beads (Invitrogen). ChIP reaction was set up using precleared chromatin and antibody and incubated overnight at 4º C. Protein A agarose beads were added and incubation at 4 C was continued for another 3 hr. Immune complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation.
(1)DNA-endrepair,3'-dAoverhangandligationofmethylatedsequencingadaptor. (2) PCR amplification and size selection (usually 100-300bp, including adaptor sequence). (3)Qualified library for next generation sequencing.

treatment_protocol: CCRF-CEM cells were cultured in suspension or in 3D conditions (a type I collagen matrix of 1,7 mg/mL) for 1 hour.

value: CCRF-CEM

value: untreated


title: E14_ESC_+dtag_4hrs_Rep1


title: CCRF-CEM cells - H3K4me3 - 3D - rep3

value: H3K4me3 (Cell signaling, Cat 9751S, Lot 14)

value: cultured in 3D conditions for 1 hour


title: CHIC-Seq, IgG-WT1-2

data_processing:
removing adapter sequences with cutadapt
aligning the reads with Bowtie2 against Mus musculus genome sequence
filter for uniquely mapped and non-duplicated reads
call peaks with macs2
Assembly: GRCm38.p5
Supplementary files format and content: peaks called in txt files
Library strategy: CHIC-seq

source_name: D4 WT primary uterine stromal cell IgG

growth_protocol: The mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Uteru isolated from 8-12 weeks aged .

extract_protocol:
5-10 pseudopregnant D4 WT mouse uterine horns were cut into small pieces (2–3 mm). Tissue pieces were first digested in 5 ml fresh medium (HBSS antibiotic; Gibco) containing 6 mg/ml dispase (Gibco) and 25 mg/ml pancreatin (Sigma), and then incubated in fresh medium (3 ml) containing 0.5 mg/ml collagenase (Sigma) at 37°C for 30 min. The digested cells were passed through a 70-lm filter to obtain the stromal cells. Cells were plated at 60-mm dishes, containing DMEM and Ham F-12 nutrient mixture (1:1) (Gibco) with 10% charcoal-stripped fetal bovine serum (FBS) and antibiotic. After 4 h, the medium was replaced with fresh medium (DMEM/F-12, 1:1) with 10% FBS. 2 hours later, wash twice with PBS gently for the preparation of  CHIC-Seq samples.
Small cell number ChIC-seq assays were performed as previous reported. ChIC-seq libraries were constructed using 50,000 mouse primary uterine stromal cells. Cells were fixed with 1% formaldehyde solution at RT for 5 minutes. Reaction was terminated by adding 1:10 volume of 1.25 M glycine. The fixed cells were kept in -80 ℃ after three washes with ice cold PBS. For ChIC reaction and library preparation, cells were incubated and rinsed with 500 ml antibody binding buffer (1xTE pH 7.5+150 mM NaCl+0.1% Trition X100) twice and re-suspended in 100 ml antibody binding buffer. To prepare ProteinA-MNase and antibody complex, Pbrm1 (Abcam,  ab196022), Brg1 (Abcam, ab110641), bounded PA-MNase (Ab+PA-MNase) and were incubated at a molecular ratio of 1:2 on ice for 30 min in 50 ml antibody binding buffer. This complex mixed with 50 ml resuspended cells and incubated for 1.5 h on ice. Cells were washed three times with 1 ml wash buffer (1xTE pH 7.5+400 mM NaCl+1% Triton X-100) and rinsed with 400 ml rinsing buffer (10 mM Tris pH 7.5+10 mM NaCl+0.1% Triton X-100). The MNase digestion was initiated by re-suspending rinsed cells in 40 ml reaction buffer (20 mM Tris, pH 7.4, 10 mM NaCl, 2 mM CaCl2, 0.1% Tx100) and incubated at 37 ℃ for 3 min. The reaction was stopped by adding 80 ml stop buffer (20 mM Tris, pH 8.0, 10 mM EGTA, 20 mM NaCl, 0.2% SDS) and 1 ml proteinase K, then incubated at 65 ℃ for overnight. DNAs were purified by phenol-chloroform extraction. The purified DNA was used for library preparation. For all ChIC-seq libraries, PCR was performed for 13-15 cycles and DNA fragments from 200 bp to 500 bp were isolated and sequenced on NovaSeq 6000 (Illumina).

value: primary uterine stromal cell

value: Day 4 of pregrancy

value: IgG


title: CCRF-CEM cells - H3K4me3 - 3D - rep2


title: MonoMac6


title: MOL16


title: CCRF-CEM cells - H3K4me3 - control - rep3


title: CCRF-CEM cells - H3K4me3 - control - rep2


title: MOL14


title: CHIC-Seq, IgG-WT1-1

value: WT


title: SEQ67

city: Indianapolis

first: Mithun

last: Sinha

state: IN

address: 340 West 10th Street

institute: Indiana University School of Medicine

data_processing:
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence using fastp version 0.20.1 with parameters "-l 17 --detect_adapter_for_pe -g -p", then mapped to GRCh38.p13 using Hisat2 version 2.1.0 with parameters "-q --rna-strandness F -mm".
Individual gene expression was quantified by counting the number reads mapping to the exon regions of each of the annotated genes using featureCounts tool of subread package version 1.6.4 with parameters "-O -M –primary -p –largetOverlap -s 2 -p -B" using Gencode v36 as the annotation.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Raw counts of reads mapped to genes using Gencode v36 as the annotation

extract_protocol:
RNA was extracted using Universal (DNA/RNA/microRNA) kit from Qiagen
The RNAseq libraries were generated using the TruSeq Stranded mRNA kit protocol. In brief, first the integrity of the RNA was checked with Agilent Tapestation, samples with RIN >7 were used for library preparation. The mRNA was purified from 1ug of total RNA for each sample, after cDNA synthesis and adapter ligation, the library was amplified with 12 rounds of PCR cycles.  The enriched and cleaned libraries were pooled and sequenced on the NextSeq500 using a 75 cycle high sequencing kit.

tag: group

value: BII

tag: race

value: Caucasian

value: Breast


title: SEQ66

tag: tissue


title: Mol13


title: SEQ64


title: CHIC-Seq, Brg1-WT1

source_name: D4 WT primary uterine stromal cell Brg1


title: CHIC-Seq, Brg1-WT2


title: ML2


title: CHIC-Seq, Pbrm1-WT3

source_name: D4 WT primary uterine stromal cell Pbrm1


title: SEQ59

value: non-BII

value: Asian


title: SEQ62


title: SEQ63


title: SEQ56


title: MKPL

description: MKPL


title: SEQ55

value: Not available


title: CHIC-Seq, Pbrm1-WT2


title: CCRF-CEM cells - H3K4me3 - 3D - rep1


title: SEQ52


title: ME-1

value: Acute myeloid leukemia cell line


title: SEQ53


title: CHIC-Seq, Pbrm1-WT1


title: CHIC-Seq, Brg1-WT3


title: CCRF-CEM cells - H3K4me3 - control - rep1


title: SEQ39


title: KG1ABTR


title: SEQ40

value: African American


title: SEQ38


title: SEQ29


title: SEQ37


title: SEQ30


title: KG1aABTR


title: SEQ28


title: SEQ27


title: SEQ25


title: KG1a


title: KG1


title: SEQ23


title: Stromal, ATAC-Seq, Pbrm1 cKO, 2

data_processing:
quality trim sequences and removing adapter sequences with cutadapt
aligning the reads with Bowtie2 against Mus musculus genome sequence
filter for uniquely mapped and non-duplicated reads
call peaks with macs2
IDR filter for conservertive peaks
Assembly: GRCm38.p5
Supplementary files format and content: conservertive reproduciable peaks in BED format

source_name: D4 primary uterine stromal cell Pbrm1 cKO

extract_protocol:
5-10 pseudopregnant D4 WT mouse uterine horns were cut into small pieces (2–3 mm). Tissue pieces were first digested in 5 ml fresh medium (HBSS antibiotic; Gibco) containing 6 mg/ml dispase (Gibco) and 25 mg/ml pancreatin (Sigma), and then incubated in fresh medium (3 ml) containing 0.5 mg/ml collagenase (Sigma) at 37°C for 30 min. The digested cells were passed through a 70-lm filter to obtain the stromal cells. Cells were plated at 60-mm dishes, containing DMEM and Ham F-12 nutrient mixture (1:1) (Gibco) with 10% charcoal-stripped fetal bovine serum (FBS) and antibiotic. After 4 h, the medium was replaced with fresh medium (DMEM/F-12, 1:1) with 10% FBS. 2 hours later, wash twice with PBS gently for the preparation of ATAC-Seq samples.
ATAC-seq libraries were constructed (Buenrostro et al., 2013) using 50,000 mouse primary uterine stromal cells. Cells were centrifuged (500 x g, 5 min, 4 °C), washed with 500 ml PBS and re-suspended in 50 ml of cold lysis buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.1% digitonin), incubated on ice for 3 min, and diluted with 1 ml wash buffer (10 mM Tris pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20). After centrifugation (500 x g, 10 min, 4 °C), pelleted nuclei were re-suspended in 50 µl of transposition reaction consisting of 2x tagmentation buffer (25 µl), water (5 µl), PBS (16.5 µl), 10% Tween-20 (0.5 µl), 1% digitonin (0.5 µl) and 2.5 ml Tn5 Transposase enzyme (Illumina). After incubation (45 min, 37 °C) with gentle mixing, DNA was purified using a phenol/chloroform extraction kit protocol (Sigma-Aldrich) and eluted with 10 ml of elution buffer. Transposed DNA was amplified using barcoded PCR primers and cycling conditions of 72 °C for 5 min and 98 °C for 30 s followed by 12 cycles of 98 °C for 10 s, 63 °C for 30 s, 72 °C for 1 min. DNA fragments of nucleosome free regions (between primer-dimers and mono-nucleosome bands) corresponding to sequence insert <100 bp or >1000 bp were removed by double-sided beads purification. Libraries were eluted with 15 ml elution buffer for analysis of size distribution and 50 bp paired-end sequencing was provided by the NIDDK Genomic Core Facility.

value: Pbrm1  cKO


title: Stromal, ATAC-Seq, Pbrm1 cKO, 3


title: ME1


title: SEQ21


title: KG-1


title: Stromal, ATAC-Seq, WT, 3

source_name: D4 primary uterine stromal cell WT


title: SEQ20


title: SEQ19


title: KAS-4


title: SEQ17


title: KAS-3


title: SEQ14


title: WBKO_heart_In

city: Harbin

first: Zheng

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

data_processing:
library strategy: meRIP-seq
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11).
Index of the reference genome was built using BWA v0.7.12 and clean  reads were aligned to the reference genome using BWA mem v 0.7.12.
exomePeak R package (version 2.16.0) was used for the m6A peak identification
The m6A-enriched motifs of each group were identified by HOMER (version 4.9.1).
GO enrichment analysis was implemented by the GOseq R package.
Assembly: mouse reference genome(GRCm39)
Supplementary files format and content: Processed data files; excel; WFF_peak; WCKO_peak

extract_protocol:
Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany)  from the hearts of Wtapflox/flox and Wtap-CKO mice at 4 days old.  A total of 300 μg RNAs were pooled from seven Wtapflox/flox mice and eight Wtap-CKO mice, respectively.
Fragmented RNA (~100 nt) was incubated for 2 hr at 4oC with anti-m6A polyclonal antibody (Merk Millipore) in the immunoprecipitation experiment. Then, immunoprecipitated RNAs or Input was used for library construction with Ovation SoLo RNA-Seq System Core Kit (NuGEN). The library preparations were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols.

value: heart

value: Wtap-CKO


title: SEQ13


title: WBKO_heart_IP

value: m6A antibody (Merk Millipore)


title: Stromal, ATAC-Seq, Pbrm1 cKO, 1


title: SEQ12


title: Stromal, ATAC-Seq, Pbrm1 cKO, 4


title: K562


title: liver, patient5, week 4

first: Adam

last: Gehring

address: 101 College St

institute: UHN

description:
barcodes.tsv.gz
genes.tsv.gz
matrix.mtx.gz
Seurat_metadata.tsv

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 (10x Genomics)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Tab-separated metadata information

source_name: liver

extract_protocol:
Liver FNA were performed by a hepatologist. A suitable location was determined using ultrasound and anesthetized with lidocaine. 25-gauge needles were used for puncture and cells were aspirated into a 10mL syringe containing 0.5mL of RPMI medium (Gibco). After collection, the needle was flushed with an additional 0.5mL RPMI to collect remaining cells. A total of four liver FNA passes were taken from each patient at each timepoint. The exact volume of each FNA pass was documented and the optical density (OD) of each pass was measured to assess for peripheral blood content. For scRNA-seq, red blood cells (RBC) were removed by 5 min. incubation with RBC Lysis Buffer (BioLegend) and subsequent 10x dilution with PBS.
Samples were prepared as outlined by 10x Genomics Single Cell 3’ Reagent Kits v2 user guide. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat sealed and incubated overnight in a Veriti 96-well thermos cycler (Thermo Fisher). The next day, sample cDNA was recovered using Recovery Agent provided by 10x and subsequently cleaned up using a Silane DynaBead (Thermo Fisher) mix as outlined by the user guide. Purified cDNA was amplified for 12 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen): cDNA) and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3’ Reagent Kits v2 user guide with modifications to the PCR cycles based on the calculated cDNA concentration.

value: liver

tag: subject id

tag: time point

value: week 4


title: Stromal, ATAC-Seq, WT, 4

value: primary uterine stromal cell

value: Day 4 of pregrancy


title: KASUMI1

source_name: Acute myeloid leukemia cell line


title: WFF_heart_In

last: Chen

value: Wtapflox/flox


title: liver, patient5, week 0

value: week 0


title: WFF_heart_IP


title: HL60VCR


title: HL60ABTR


title: Stromal, ATAC-Seq, WT, 1

value: WT


title: Stromal, ATAC-Seq, WT, 2


title: SEQ16

value: BII

value: Caucasian

value: Breast


title: SEQ9


title: SEQ8

value: non-BII


title: WCKO

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.20.0). In this step, clean data (clean  reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw  data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses  were based on the clean data.
Reference genome and gene annotation files were downloaded from genome website directly. Index of the reference  genome was built using BWA(v0.7.12) and clean reads were aligned to the reference genome using BWA mem.  Reads that were derived from mitochondrion  DNA and chloroplast DNA were discarded.These reads were then filtered for high quality (MAPQ ≥ 13),we also  removed reads that were not properly paired and with PCR duplicates. Only uniquely mapped(MAPQ ≥ 13) and  de-duplicated reads were used for further analysis.
All peak calling was performed with MACS2 (version 2.1.0) using ‘macs2 -q 0.05 -f AUTO --call-summits  --nomodel --shift -100 --extsize 200 --keep-dup all’. By default, peaks with q-value threshold of 0.05 was used for all  data sets.
Peaks were adjusted to the same size (500 bp) centered peak summits and motif discoveries of these loci sequences  were performed using findMotifsGenome.pl program in HOMER v4.11 software with ‘-len 8,10,12,14 -gc -size given  -homer2 -dumpFasta’.
The position of peak summit around transcript start sites of genes can predict the interaction sites between protein and  gene. ChIPseeker (Yu et al., 2015) was used to retrieve the nearest genes around the peak and  annotate genomic region of the peak. Peak-related genes can be confirmed by ChIPseeker, and then Gene Ontology  (GO) enrichment analysis was performed to identify the function enrichment results. GO enrichment analysis was  implemented by the GOseq R package, in which gene length bias was corrected. GO terms with corrected P-value  less than 0.05 were considered significantly enriched by peak-related genes. KEGG is a database resource for  understanding high-level functions and utilities of the biological system, such as the cell, the organism and the  ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome  sequencing and other high-throughput experimental technologies (http://www.genome.jp/kegg/). We used KOBAS  software to test the statistical enrichment of peak related genes in KEGG pathways.
Assembly: mouse reference genome(GRCm39)
Supplementary files format and content: Processed data files; excel; WCKO_vs_WFF_peak_compare_table

extract_protocol:
Each heart sample was pooled from six Wtap-CKO and seven Wtapflox/flox mice at 4 days old, respectively.Nuclei was extracted from heart samples.
Briefly, nuclei was extracted from samples, and the nuclei pellet was resuspended in the Tn5 transposase reaction mix.  The transposition reaction was incubated at 37℃ for 30 min. Equimolar Adapter1 and Adatper 2 were added after  transposition, PCR was then performed to amplify the library. After the PCR reaction, libraries were purified with the  AMPure beads and library quality was assessed with Qubit.
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE  Cluster Kit v3-cBot-HS (Illumina) according to the manufactuer’s instructions. After cluster generation, the library  preparations were sequenced on an Illumina platform and 150 bp paired-end reads were generated.


title: HL60-2

value: Acute myeloid leukemia cell line


title: SEQ15


title: WFF


title: SEQ7


title: KAS-1


title: liver, patient4, week 0


title: SEQ18


title: SEQ6


title: SEQ10


title: liver, patient3, week 4


title: SEQ5


title: liver, patient3, week 0


title: FKH

description: FKH


title: SEQ4


title: liver, patient2, week 4


title: SEQ3


title: liver, patient4, week 4


title: F36P


title: WFF_heart_3

data_processing:
The image data measured by the high-throughput sequencer are converted into  sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq  format were firstly processed through in-house perl scripts. In this step, clean data  (clean reads) were obtained by removing reads containing adapter, reads containing N  base and low quality reads from raw data. At the same time, Q20, Q30 and GC  content the clean data were calculated. All the downstream analyses were based on  the clean data with high quality.
Reference genome and gene model annotation files were downloaded from  genome website directly. Index of the reference genome was built using Hisat2  (v2.0.5) and paired-end clean reads were aligned to the mouse reference genome(GRCm39) using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each  gene. And then FPKM of each gene was calculated based on the length of the gene  and reads count mapped to this gene. FPKM, expected number of Fragments Per  Kilobase of transcript sequence per Millions base pairs sequenced, considers the  effect of sequencing depth and gene length for the reads count at the same time, and is  currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate padj<=0.05 and |log2(foldchange)| >= 0 were set as the threshold for significantly  differential expression.
Assembly: mouse reference genome(GRCm39)
Supplementary files format and content: Processed data files; excel; fpkm of each gene

extract_protocol:
Total RNA was extracted using Tripure Isolation Reagent (Roche, Mannheim, Germany) from the hearts of Wtapflox/flox and Wtap-CKO mice at 4 days old. Three independent biological replicates for each group were used for RNA-seq.
mRNA was purified from total RNA by using poly-T oligo-attached magnetic beads.  Fragmentation was carried out using divalent cations under elevated temperature in  First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using  random hexamer primer and M-MuLV Reverse Transcriptase, then use RNaseH to  degrade the RNA. Second strand cDNA synthesis was subsequently performed using  DNA Polymerase I and dNTP. Remaining overhangs were converted into blunt ends  via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA  fragments, Adaptor with hairpin loop structure were ligated to prepare for  hybridization. In order to select cDNA fragments of preferentially 370~420 bp in  length, the library fragments were purified with AMPure XP system (Beckman  Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by  AMPure XP beads, and the library was finally obtained.
After the library is qualified, the different libraries are pooling according to the  effective concentration and the target amount of data off the machine, then being  sequenced by the Illumina NovaSeq 6000. The end reading of 150bp pairing is  generated. The basic principle of sequencing is to synthesize and sequence at the same  time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase  and splice primers were added to the sequenced flowcell and amplified. When the  sequence cluster extends the complementary chain, each dNTP labeled by  fluorescence can release the corresponding fluorescence. The sequencer captures the  fluorescence signal and converts the optical signal into the sequencing peak by  computer software, so as to obtain the sequence information of the fragment to be  tested.


title: WCKO_heart_1


title: liver, patient2, week 0


title: WCKO_heart_2


title: CMK

description: CMK


title: WFF_heart_1


title: liver, patient1, week 0


title: liver, patient1, week 4


title: EOL


title: SEQ1


title: SEQ2


title: d25_Control

status: Public on Jan 13 2024

city: Kunming，Yunnan

first: Yang

last: Shao

address: Room 1405, Administration Building, No.727 Jingming South Road, Chenggong District, Kunming

institute: Kunming University of Science and Technology

description: 10 X Genomics

data_processing:
Cell Ranger v7.1.0
Assembly: Genome_build: hg19
Supplementary files format and content: Supplementary_files_format_and_content: tab-delimited text files include count values for each Sample

extract_protocol:
The mRNA in the cells is captured using Gel beads
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Mature Hepatocyte

value: genetic modification


title: d25_CDK5RAP3_null

description: 10 X Genomics


title: HL60-1


title: d10_Control

description: 10 X Genomics

value: Hepatic Edoderm cell


title: HEL

description: HEL


title: WCKO_heart_3

value: heart

value: Wtap-CKO


title: Batch 1 RNA

city: New York

first: Arnold

last: Han

state: New York

institute: Columbia University

description: Batch 1 RNA: 10x Genomics scRNA-seq of intestinal biopsies from "Batch 1" patients

data_processing:
Cell Ranger v5.0.0
Assembly: GRCh38
Supplementary files format and content: Raw processed files: Barcodes, features, and matrix for RNA and CITE. Metadata and processed RDS objects included.

source_name: Duodenum (Second part)

extract_protocol:
10X Genomics Chromium Platform
10X Genomics Chromium Single Cell 5’ V(D)J with Feature Barcoding Reagent Kits (CG000186) or Chromium Next GEM Single Cell V(D)J Reagent Kits v1.1 with Feature Barcode Technology for Cell Surface Protein (CG000208).

value: Duodenum (Second part)


title: Batch 6 RNA

description: Batch 6 RNA: 10x Genomics scRNA-seq of intestinal biopsies from "Batch 6" patients


title: HEK_RAF_ER_12h_R2_Targeted

city: Berlin

first: Nils

last: Blüthgen

address: Chariteplatz 1

department: Institute of Pathology

country: Germany

institute: Charite Universitätsmedizin Berlin

description: targeted enrichment using PCR of 140 transcripts

data_processing:
Raw sequences reads were analysed using cellranger-6.1.1 with feature calling using the guide sequences as in feature_ref.csv.gz; standard 10x gene expression libraries were processed alone and together with the targeted sequencing results
Effects of individual KO (represented by the CRISPR guides) on gene expression were assessed using pseudo-bulk analysis in R using the package glmGamPoi.
Assembly: GRCh38
Supplementary files format and content: *.h5 files contain the single cell gene expression matrices. Untargeted contain only data from the standard runs.
Supplementary files format and content: *.protospacer_calls_per_cell.csv.gz contain the guide / feature assignement of cells

source_name: HEK-RAF-ER

extract_protocol:
Approximately 20.000 cells were encapsulated in Gel Beads-in-emulsion (GEMs) and GEX and CRISPR libraries were generated using the 10x Chromium Single Cell 3' V3 with Feature Barcoding technology
Gene expression libraries were constructed as per manufacturers instruction. Targeted libraries were amplified with custom primers from the amplified cDNA library. Guide libraries were constructed using the direct capture method.
Direct Capture Perturb-seq: scRNA-seq, CRISPR-guides, targeted scRNA-seq

treatment_protocol: Cells were treated with tamoxifen to induce RAF/MAPK signalling for various times (6-18hrs)

value: HEK-RAF-ER

tag: library type

value: targeted enrichment

value: 4OHT (tamoxifen)

tag: replicate


title: WFF_heart_2

source_name: heart

value: Wtapflox/flox


title: HEK_RAF_ER_12h_R1_Targeted


title: HEK_RAF_ER_18h_R1_Targeted


title: HEK_RAF_ER_18h_R2_Targeted


title: HEK_RAF_ER_6h_R1_Targeted


title: HEK_RAF_ER_12h_R2_Guides

description: guides captured using the direct capture technique

data_processing:
Raw sequences reads were analysed using cellranger-6.1.1 with feature calling using the guide sequences as in feature_ref.csv.gz; standard 10x gene expression libraries were processed alone and together with the targeted sequencing results
Effects of individual KO (represented by the CRISPR guides) on gene expression were assessed using pseudo-bulk analysis in R using the package glmGamPoi.
Assembly: GRCh38
Supplementary files format and content: *.h5 files contain the single cell gene expression matrices. Untargeted contain only data from the standard runs.
Supplementary files format and content: *.protospacer_calls_per_cell.csv.gz contain the guide / feature assignement of cells
Library strategy: CHRISPR guide

value: CHRISPR guide


title: HEK_RAF_ER_18h_R2_Guides


title: HEK_RAF_ER_18h_R1_Guides


title: d10_CDK5RAP3_null

description: 10 X Genomics


title: HEK_RAF_ER_12h_R1_Guides


title: HEK_RAF_ER_6h_R2_Guides


title: HEK_RAF_ER_12h_R2_GE

description: Gene expression library

value: mRNA


title: HEK_RAF_ER_18h_R2_GE

description: Gene expression library


title: HEK_RAF_ER_18h_R1_GE

description: Gene expression library


title: HEK_RAF_ER_6h_R1_Guides


title: HEK_RAF_ER_6h_R2_GE

description: Gene expression library


title: HEK_RAF_ER_6h_R1_GE

description: Gene expression library


title: HEK_RAF_ER_6h_R2_Targeted


title: WT-clone_5-utr1-R1

data_processing:
poly-A sequences and adapters are trimmed with bbduk
Sequences are aligned using STAR aligner
Assembly: GRCh38
Supplementary files format and content: counts of reads per Gene

extract_protocol:
RNA was extracted using Qiagen RNAeasy kit following manufacturers recommendation, without removal of DNA
Library was constructed using QuantSeq 3’ mRNA-Seq V2 Library Prep Kit V2

treatment_protocol: Cells were treated with tamoxifen (4OHT) to activate RAF activity

value: WT

tag: clone

value: clone 5


title: WT-clone_4-utr1-R1

value: clone 4


title: WT-clone_5-utr2-R1


title: WT-clone_4-utr2-R2


title: WT-clone_5-12_hrs-R1

value: tamoxifen (4OHT)

value: 12 hrs