title: T.14.C2


title: T.17.C2

status: Public on Apr 24 2024

type: RNA

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

hyb_protocol: Hybridization was performed according to Nanostring manufacturer's protocol, overnight at 65°C, 18h in a thermocycler

scan_protocol: Cartridges were run on a nCounter Nanostring machine

data_processing: NanoStringNorm package for R software 4.1.2 (R Foundation for Statistical Computing, Vienna, Austria) was used to generate data and for quality check; the geometric mean of the counts relative to each sample, the mean plus two standard deviations and the total sum of counts options were used to correct the data for technical, background, and batch-effect issues, respectively.

molecule: total RNA

organism: Homo sapiens

source_name: CD3+ selected leukapheresis, patient

label_protocol: Probe labeling was performed according to Nanostring manufacturer's protocol

extract_protocol: RNA was extracted from CD3-positive selected cells with miRNeasy Mini kit (Qiagen) and 100 ng of total RNA were used for the transcriptomic analyses

treatment_protocol: Leukapheresis samples and donor lymphocyte infusions were quickly thawed and CD3+ cells were selected using magnetic anti-CD3 microbeads (Miltenyi Biotec) and the autoMACS Pro Separator (Miltenyi Biotec)

tag: disease state

value: large B-cell lymphoma

tag: model (1

value: EXP, 2:poor-EXP):1

tag: cell type

value: CD3+ selected leukapheresis, patient


title: T.13.C2

value: EXP, 2:poor-EXP):2


title: T.11.C1


title: T.12.C1


title: T.10.C1


title: Mn-N/C-TUMOR-rep2

type: SRA

city: Shanghai

first: Wen

last: Qiao

address: 1630 Dongfang Road, Pudong New Area, Shanghai

country: China

institute: 上海交通大学医学院

library_source: transcriptomic

data_processing:
We applied the reads filtering towards the raw reads after sequencing to achieve the clean data following the criteria: 1) 10% base quality<15 b) 13% base quality<20.
Hisat2 2.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: Excel file contain fpkms and counts for each sample

organism: Mus musculus

source_name: Tumor

growth_protocol: DMEM, 10% fetal bovine serum, 1x penicillin/streptomycin. MC38 tumor cells were cultured at 37C at 5% CO2, and were orthotopically injected into the right flank of male C57BL/6J mice subcutaneously.

extract_protocol:
The tumor tissues were harvested and snap frozen in the liquid nitrogen. RNA from tumor tissues was extracted using Trizol.  2 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Mice with palpable tumors were intratumorally injected with saline (50μl) or Mn-N/C (70mg/kg, 50μl) every 3 days. Mice were euthanized, and the tumor tissues were collected until the tumor volume reached 800-1000 mm3.

tag: tissue

value: Tumor

tag: cell line

value: colon cancer cells

tag: genotype

value: WT

tag: treatment

value: Mn-N/C


title: Mn-N/C-TUMOR-rep1


title: hCSF1_3

city: Irvine

first: Mathew

last: Blurton-Jones

state: CA

address: 845 Health Sciences Road

department: Neurobiology and Behavior

country: USA

institute: University of California, Irvine

description:
hCSF1x1882
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
NA
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv

data_processing:
FASTQ files were preprocessed using BBDuk to filter out ribosomal RNA and PhiX reads, trim Illumina adapters, quality trim any base pairs below a PHRED score of 28. and filter out reads less than 45bp after processing.
Reads were then aligned to a mixed species genome consisting of the unmasked top level FASTA files for the human GRCh38 (Ensembl release 99) and mouse GRCm39 (Ensembl release 107) DNA assemblies and aligned using HISAT2 using the -q, -1, and -2 options to align paired-end FASTQ files.
The output SAM files were then parsed using a modified version of the “byPrim.py” Python script from Song et al. (2022) which assigned each read to either mouse or human based on the species for which the primary alignment was specified by HISAT2.
Using the species assignments stored in the output of the “byPrim_MBJ.py” script, the “MBJ_FASTQSorter.py” script generated two sets of paired end reads for each original file, one pair consisting of the forward and reverse human reads and one pair consisting of the forward and reverse mouse reads.
Species-specific FASTQ files were then pseudoaligned to the human GRCh38 transcriptome (Ensembl release 107) or the mouse GRCm39 transcriptome (Ensembl release 107) using Kallisto v0.46.1.
Mouse transcripts were then summarized to the gene level via tximport and the dataset was filtered to retain only genes with 1:1 mouse to human gene homologues and then subsequently filtered to only retain genes with greater than 130 cumulative reads (average of 10 reads per sample). Human transcripts were then similarly summarized to the gene level, filtered to only retain genes with 1:1 homologues, and then both the mouse and human datasets were intersected to only retain genes present in both datasets.
Assembly: Ensembl GRCh38 and GCRm39
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts for the sorted human FASTQ files
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts for the sorted mouse FASTQ files
Supplementary files format and content: Tab-delimited text file containing VST normalized counts for the combined mouse and human samples

molecule: polyA RNA

source_name: Brain

extract_protocol:
Animals were perfused (20mL per minute) with 1X DPBS (4°C) for 3 min. Brains were surgically excised from each mouse and cut in half along the mid-sagittal plane. The left hemisphere was placed in 4% (wt/vol) paraformaldehyde (PFA) for 36 h at 4°C for subsequent immunohistochemistry (IHC) and the right hemisphere fresh-frozen on dry ice and stored at -80°C for biochemical analysis. Fresh frozen hemispheres were crushed on dry ice using mortar and pestle and total RNA was isolated using the Qiagen RNeasy Plus Micro Kit following manufacturer protocol.
350ng of total RNA was used as input for library construction using the Illumina TruSeq Stranded mRNA kit which utilizes oligo-dT beads to select and amplify mRNA. cDNA was synthesized using nine rounds of PCR and quality and concentrations of the DNA libraries were assayed using the Agilent 2100 bioanalyzer high sensitivity DNA assay and the DNA high sensitivity Qubit. The libraries were quantified by Kapa qPCR, normalized to 1.5nM and then multiplexed at equimolar concentrations for sequencing on the Illumina NovaSeq 6000 platform with paired-end read 100 base chemistry on an S4 flow cell.

value: Brain

tag: mouse strain

tag: injection

value: PBS


title: VEHICLE-TUMOR-rep2

value: Saline


title: T.18.C2


title: T.9.C1


title: VEHICLE-TUMOR-rep3


title: T.8.C1


title: CD8_GSK_rep3

city: Hangzhou

first: Wanqiang

last: Sheng

state: Zhejiang

address: 866 Yuhangtang Road

department: Department of Immunology

institute: Zhejiang University School of Medicine

data_processing:
Raw reads in fastq format were first processed using Trimmomatic and the low-quality reads were removed to obtain the clean reads. Only clean reads passing the QC were used for subsequent analyses.
The clean reads were mapped to the mouse reference genome (GRCm38) using hisat2 (version 2.1.0). FPKM of each gene was calculated using Cufflinks (version 2.2.1). The read counts of each gene were obtained by HTSeq-count (version 0.11.2).
Differential expression analysis was performed using R package DESeq2 (version 1.22.2). To be called DEGs, the fold change > 1.5 and q value < 0.05 were set as the cutoff. The reported statistical significances were corrected for multiple testing using the Benjamini-Hochberg procedure with a false discovery rate less than 0.05.
Assembly: GRCm38
Supplementary files format and content: Count table for each sample

source_name: mouse CD8+ T cells

growth_protocol: CD8+ T cells isolated from the spleens of OT1 mice were stimulated with plate-bound anti-CD3 (2μg/ml) and soluble anti-CD28 (2μg/ml) with the addition of 20 ng/mL IL-2 at a density of 1 million/ml for 48 h. Activated CD8+ T cells were expanded with IL2 in fresh medium for 3 days.

extract_protocol:
In vitro cultured CD8+ T cells under indicated treatment were directly lysed in 500 μl TRIzol reagent (TaKaRa, 9109). After incubation for 5 min, 100 μl chloroform was added and mixed by gentle inversion several times. Samples were incubated for 3 min at RT and then centrifuged for 15 mins at 12,000 g at 4 °C. The upper aqueous phase containing the RNA was collected and mixed with an equal volume of freshly prepared 70% ethanol, which was then loaded into a spin column from an RNA Clean ＆ ConcentratorTM-5 Kit (ZYMO Research, R1013) and subjected to RNA isolation according to the manufacturer’s instructions.
Total RNA was quantified by a NanoDrop 2000 spectrophotometer (Thermo Scientific) and RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies) with RIN > 9.0. The poly(A)+ RNA was enriched and subjected to library construction using a TruSeq Stranded mRNA LT Sample Prep Kit (Illumina, RS-122-2101) according to the manufacturer’s instructions. The libraries were sequenced on an Illumina Novaseq 6000 platform to generate 150 bp paired-end reads. Over 40 million raw reads for each sample were generated.

treatment_protocol: 0.5 μM GSK2879552 (GSK) or vehicle control was added to CD8+ T cells during in vitro activation and expansion.

tag: strain

value: Spleen


title: CD8_GSK_rep1


title: CD8_Veh_rep3


title: T.4.C1


title: CD8_Veh_rep2


title: T.6.C1


title: T.7.C1


title: VEHICLE-TUMOR-rep1


title: T.2.C1


title: GSK_Input1

library_source: genomic

data_processing:
All reads were mapped to unique genomic regions of mm10 using Bowtie2. PCR duplicates were removed manually. Bedtools genome coverage function was used to generate bedgraph files for further analysis. To compare changes in ChIP-seq signals, libraries were normalized by random picking to obtain the same numbers of reads. Normalized reads were used to generate bedgraph files for comparison in IGV. MACS2 was used to call peaks using default parameters with p value cutoff at 0.001. Differential peaks were found using the edgeR R package at p < 0.05, with changes over 20% up/down.
Enhancers were defined by merging H3K4me1 and H3K4me2 peaks in both conditions but excluding H3K4me3 peaks and TSS ± 2.5kb. Differential enhancers were found using the edgeR R package based on H3K27ac ChIP-seq signals with a p value cutoff at 0.05 and more than 3-fold changes in either condition. K-means clustering of enhancer heatmaps was done using Cluster3 on center ± 3 bins signals of H3K4me1 heatmaps, all heatmaps were plotted in this same order on center ± 1kb.
For deriving heatmaps of ChIP-seq signals, anchors plus flanking regions were binned equally to get a blank matrix (anchors × bins). To compare between samples, reads from the same antibody analysis were normalized by random pick. Normalized read pairs were mapped to each genomic bin with the bedtools intersect function to obtain read counts in each bin for the whole matrix. To normalize for sequencing depth, values in the matrix were divided by library sizes in millions to obtain reads per million per covered bin (RPMPCG or RPM), which was then visualized with Java TreeView to derive heatmaps. Average profiles of the ChIP-seq data were calculated and plotted using mean values of bins at the same distances from specific anchors. K-means clustering of ChIP-seq heatmaps was done using Cluster3 on center ± 3 bins signals of appropriate heatmaps. K-means clustering of promoter heatmaps was done using Cluster3 on TSSs ± 3 bins signals of H3K27ac heatmaps, all heatmaps were plotted in this same order on TSSs ± 1kb.
Assembly: mm10
Supplementary files format and content: bigwig files
Supplementary files format and content: peak files

molecule: genomic DNA

source_name: CD8+ T cell ChIP

extract_protocol:
In vitro cultured CD8+ T cells were fixed in 1% formaldehyde (Thermo Fisher Scientific, 28908) for 10 min at RT on a shaker, followed by quenching in 125 mM glycine. Next, cells were washed twice with ice-cold PBS and lysed in sonication buffer (50 mM HEPES pH7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 0.2% SDS and protease inhibitor), then sonicated to obtain DNA fragments mostly between 300-800 bp. Subsequent procedures were performed following the Epigenetics Protocols Database PROT-11 (https://www.epigenome-noe.net/researchtools/protocols.php.html). The following antibodies were used for immunoprecipitation: anti-LSD1 (Abcam, ab17721), anti-H3K4me1 (Abcam, ab8895), anti-H3K4me2 (EMD Millipore, 07-030), anti-H3K4me3 (Active Motif, 39060), anti-H3K27ac (Active Motif, 39034), anti-Pol II (Santa Cruz Biotechnology, sc-56767) and rabbit normal IgG (Proteintech, 30000-0-AP).
ChIP-seq libraries were prepared using the VAHTS Universal DNA Library Prep Kit (Vazyme, ND607-01) according to the manufacturer’s instructions. Library concentrations were quantified by Qubit (Invitrogen) and mixed equally for sequencing at Novaseq 6000 (Illumina) to generate 150 bp paired-end reads or at DNBSEQ-T7 (MGI Tech) to generate 100 bp paired-end reads.

tag: antibody


title: GSK_LSD1

value: LSD1 (Abcam, cat#17721)


title: T.3.C1


title: veh_H3K4me1

value: H3K4me1 (Abcam, cat#ab8895)


title: GSK_H3K4me1


title: CD8_Veh_rep1


title: veh_H3K4me2

value: H3K4me2 (EMD Millipore, cat#07-030)


title: T.1.C1


title: GSK_H3K4me2


title: veh_LSD1


title: veh_Input1


title: DSS+miR-146a mimics treated, miR-146a-/- 4

city: Yangpu

first: Changgeng

last: Peng

state: Shanghai

address: Siping Road 1239

department: School of Medicine

institute: Tongji University

description: miR-146a KO4_DSS+mimics_FPKM

data_processing:
CLC Genomics Workbench v 11.0.1
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to GrCM38/mm10 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Colon

extract_protocol:
Total RNA was extracted from colon tissues following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA) and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany).
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: Colon

value: miR-146a KO

value: DSS+miR-146a mimics


title: DSS+miR-146a mimics treated, miR-146a-/- 3

description: miR-146a KO3_DSS+mimics_FPKM


title: DSS+miR-146a mimics treated, miR-146a-/- 2

description: miR-146a KO2_DSS+mimics_FPKM


title: DSS+miR-146a mimics treated, miR-146a-/- 5

description: miR-146a KO5_DSS+mimics_FPKM


title: CD8_GSK_rep2


title: DSS+Saline treated, miR-146a-/- 6

description: miR-146a KO6_DSS_FPKM

value: DSS+saline


title: DSS+Saline treated, miR-146a-/- 3

description: miR-146a KO3_DSS_FPKM


title: DSS+miR-146a mimics treated, miR-146a-/- 1

description: miR-146a KO1_DSS+mimics_FPKM


title: DSS+Saline treated, miR-146a-/- 4

description: miR-146a KO4_DSS_FPKM


title: DSS+Saline treated, miR-146a-/- 2

description: miR-146a KO2_DSS_FPKM


title: DSS+Saline treated, miR-146a-/- 1

description: miR-146a KO1_DSS_FPKM


title: DSS treated, miR-146a-/- 3

description: miR-146a KO3+DSS_FPKM

value: DSS


title: DSS treated, WT2

value: wild type


title: DSS treated, miR-146a-/- 2

description: miR-146a KO2+DSS_FPKM


title: DSS treated, WT1


title: untreated, WT 3

value: non


title: DSS treated, WT3


title: untreated, WT 1


title: Mouse Nerve, Control,Nerve7

city: Minneapolis

first: David

last: Largaespada

state: MN

address: 515 Delaware St SE

department: Department of Pediatrics

institute: University of Minnesota

description:
Nerve7
raw_counts.txt

data_processing:
Quality Trimming via Trimmomatic 0.33
Read alignment via Hisat2 2.1.0
Count Quantification via Stringtie 1.3.4d
Assembly: GRCm39
Supplementary files format and content: Count Quantification via Stringtie 1.3.4d
Supplementary files format and content: Somatic Variant calling via Illumina Dragen

source_name: Nerve

growth_protocol: All in vivo procedures were approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Minnesota.

extract_protocol:
RNA was extracted utilizing RNeasy Mini Kit (Qiagen, 74106) per manufacturer instructions
TruSeq Stranded mRNA

treatment_protocol: To establish MPNST xenografts, equal number of male and female NOD-Rag1nullIL2rgnull (NRG) mice (The Jackson Laboratory; 6-7 weeks old) were inoculated with 2x106 human MPNST cells into flanks. Nodules reaching 200 mm3 were injected intratumorally with 1.0x1011 VP/tumor spread over 3 doses (3.30x1010 VP/dose every 48 hrs.) of either adenoviruses or vehicle.

value: Nerve


title: Mouse Nerve, Control,Nerve5

description:
Nerve5
raw_counts.txt


title: Mouse Nerve, Control,Nerve1

description:
Nerve1
raw_counts.txt


title: untreated, WT 2


title: Mouse Nerve, Control,Nerve6

description:
Nerve6
raw_counts.txt


title: Tumor, JW23, Virus, After 3rd Treatment, Male, M38_0_10

description:
JW23_T_V_M38_0_10
raw_counts.txt

value: Tumor

tag: time

value: After 3rd Treatment

tag: Sex

value: Male

tag: mouse

value: Virus


title: Mouse Liver, Control,Liver3

description:
Liver3
raw_counts.txt

source_name: Liver

value: Liver


title: Mouse Liver, Control,Liver1

description:
Liver1
raw_counts.txt


title: Mouse Liver, Control,Liver3_2

description:
Liver3_2
raw_counts.txt


title: Tumor, JW23, Control, After 3rd Treatment, Male, M38_0_03

description:
JW23_T_C_M38_0_03
raw_counts.txt

value: Control


title: Tumor, JW23, Virus, Endpoint, Male, M46_0_01

description:
JW23_T2_V_M46_0_01
raw_counts.txt

value: Endpoint


title: Tumor, JW23, Virus, Endpoint, Male, M44_0_01

description:
JW23_T2_V_M44_0_01
raw_counts.txt


title: DSS+Saline treated, miR-146a-/- 5

description: miR-146a KO5_DSS_FPKM


title: DSS treated, miR-146a-/- 1

description: miR-146a KO1+DSS_FPKM


title: Tumor, JW23, Control, Endpoint, Male, M45_0_03

description:
JW23_T2_C_M45_0_03
raw_counts.txt


title: Tumor, JW23, Control, Endpoint, Male, M45_0_01

description:
JW23_T2_C_M45_0_01
raw_counts.txt


title: Tumor, JW23, Control, Endpoint, Male, M44_0_03

description:
JW23_T2_C_M44_0_03
raw_counts.txt


title: Tumor, JW23, Control, After 2nd Treatment, Female, F41_0_10

description:
JW23_S_C_F41_0_10
raw_counts.txt

value: After 2nd Treatment

value: Female


title: Tumor, JW23, Virus, After 2nd Treatment, Male, M37_0_01

description:
JW23_S_V_M37_0_01
raw_counts.txt


title: Ramos-ctrl-1

city: Lanzhou

first: caiyue

last: que

state: 甘肃

address: 天水南路222号

institute: 兰州大学

data_processing:
Quality Control: In order to remove technical sequences, including adapters, polymerase chain reaction (PCR) primers, or fragments thereof, and quality of bases lower than 20, pass filter data of fastq format were processed by Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Alignment: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Expression analysis:In the beginning transcripts in fasta format are converted from known gff annotation file and indexed properly. Then, with the file as a reference gene file, HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <=0.05 to detect differential expressed ones.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text files includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Ramos

extract_protocol:
1 μg total RNA was used for following library preparation.The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.
Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina  Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

value: Ramos

value: B lymphocytes

value: WT


title: Sample 2 S63845

city: Frankfurt am Main

first: Meike

last: Vogler

address: Komturstrasse 3a

department: Institute for Experimental Pediatric Hematology and Oncology

country: Germany

institute: Goethe University Frankfurt

description: Novogene

data_processing:
Novogene
Assembly: hg18
Supplementary files format and content: fkpm count

source_name: B cell

growth_protocol: Standard culture in RPMI

extract_protocol:
RNA extraction
Poly A Enrichment

treatment_protocol: Treatment with S63845 (300 nM) and zVAD.fmk (20 uM) for 8h

value: B cell

value: lymphoma

value: wt


title: Ramos-ZEBRA-2

value: ZEBRA


title: Ramos-vector-1

value: Vector


title: Ramos-ctrl-2


title: Ramos-ZEBRA-1


title: Ramos-vector-2


title: Sample 2 S63845+zVAD

description: Novogene


title: Sample 1 S63845+zVAD

description: Novogene


title: Tumor, JW23, Virus, After 1st Treatment, Female, F41_0_00

description:
JW23_P_V_F41_0_00
raw_counts.txt

value: Tumor

value: After 1st Treatment


title: Sample 2 control

description: Novogene

value: control


title: Tumor, JW23, Virus, Endpoint, Male, M37_0_03

description:
JW23_E_V_M37_0_03
raw_counts.txt

value: Male

value: Virus


title: Tumor, JW23, Control, After 1st Treatment, Female, F41_0_30

description:
JW23_P_C_F41_0_30
raw_counts.txt

value: Control


title: A549 cells, ZBTB16, repeat3

city: jinan

first: Deyu

last: Guo

state: Shandong Province

address: Science and Education Park

department: Shandong Provincial Hospital

institute: Shandong University

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.0.5。
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: A549 cells were cultured in F12K (MAC GENE), and supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin (P/S) and were incubated at 37°C with 5% CO2.

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human lung adenocarcinoma

value: ZBTB16 overexpression


title: Tumor, JW23, Virus, Endpoint, Male, M46_0_03

description:
JW23_T2_V_M46_0_03
raw_counts.txt

value: Endpoint


title: Tumor, JW23, Virus, Endpoint, Male, M38_0_01

description:
JW23_E_V_M38_0_01
raw_counts.txt


title: A549 cells, ZBTB16, repeat2


title: Tumor, JW23, Virus, Endpoint, Female, F41_0_01

description:
JW23_E_V_F41_0_01
raw_counts.txt

value: Female


title: A549 cells, ZBTB16, repeat1


title: Tumor, JW23, Control, Endpoint, Male, M38_0_00

description:
JW23_E_C_M38_0_00
raw_counts.txt


title: A549 cells, pc3.1, repeat3


title: A549 cells, pc3.1, repeat2


title: Tumor, JW23, Control, Endpoint, Male, M37_0_10

description:
JW23_E_C_M37_0_10
raw_counts.txt


title: Tumor, JW23, Control, Endpoint, Female, F41_0_03

description:
JW23_E_C_F41_0_03
raw_counts.txt


title: Sample 1 S63845

description: Novogene


title: Tumor, JW23, Control, Endpoint, Female, F40_0_00

description:
JW23_EU_C_F40_0_00
raw_counts.txt


title: C_16_H03_6

city: Charlestown

first: Mariko

middle: Sidi

last: Takahashi

state: Massachusetts

address: 149 13th Street, Charlestown Navy Yard

department: Cancer Center

institute: MGH

data_processing:
Illumina Casava v.2.19 software used for basecalling.
Sequenced reads were aligned to hg19 genome using STAR v.2.4.0h with default settings.
The aligned fragments quantification was computed by featureCounts, and FPKM expression values were calculated for hg19 RefSeq genes
Assembly: hg19
Supplementary files format and content: tab-delimited text file include raw gene expression counts for each sample

source_name: skin

extract_protocol:
For Novogene sequencing total RNA was extracted with NucleoSpin RNA extraction kit (MACHEREY-NAGEL) according to manufacturer’s instructions, and 1500 ng/30 μL RNA was used for sequencing. For 96 well RNA sequencing libraries from each cell line were generated based on the Smart-seq2 protocol with modifications as described in the DrugMap publication.
Libraries were prepared with tagmentation using the Nextera XT Library Prep kit.
Libraries used custom barcode adapters and were combined for sequencing.

value: skin

value: melanoma


title: Tumor, JW18, Control, After 3rd Treatment, Male, M36_0_00

description:
JW18_T_C_M36_0_00
raw_counts.txt

value: After 3rd Treatment


title: Tumor, JW18, Virus, After 3rd Treatment, Male, M36_0_03

description:
JW18_T_V_M36_0_03
raw_counts.txt


title: C_13_F10_11


title: C_13_F10_12


title: A549 cells, pc3.1, repeat1

value: WT


title: C_16_H03_4


title: Sample 1 control

description: Novogene

value: B cell

value: lymphoma

value: wt


title: C_16_H03_5


title: Tumor, JW18, Virus, Endpoint, Male, M45_0_10

description:
JW18_T2_V_M45_0_10
raw_counts.txt

value: Tumor


title: Tumor, JW18, Virus, Endpoint, Male, M46_0_10

description:
JW18_T2_V_M46_0_10
raw_counts.txt


title: C_DMSO_3

value: DMSO


title: C_DMSO_2


title: Tumor, JW18, Control, Endpoint, Male, M45_0_00

description:
JW18_T2_C_M45_0_00
raw_counts.txt


title: Tumor, JW18, Control, Endpoint, Male, M44_0_00

description:
JW18_T2_C_M44_0_00
raw_counts.txt


title: C_13_F10_10


title: Tumor, JW18, Virus, After 2nd Treatment, Female, F40_0_03

description:
JW18_S_V_F40_0_03
raw_counts.txt

value: After 2nd Treatment


title: U_16_H03_6


title: Mouse Liver, Control,Liver2

description:
Liver2
raw_counts.txt

value: Liver


title: Tumor, JW18, Control, After 2nd Treatment, Male, M37_0_00

description:
JW18_S_C_M37_0_00
raw_counts.txt

value: Male


title: U_16_H03_5


title: Tumor, JW18, Virus, Endpoint, Male, M44_0_10

description:
JW18_T2_V_M44_0_10
raw_counts.txt

value: Virus


title: Tumor, JW18, Control, Endpoint, Male, M46_0_00

description:
JW18_T2_C_M46_0_00
raw_counts.txt

value: Control


title: Tumor, JW18, Virus, After 1st Treatment, Male, M35_0_00

description:
JW18_P_V_M35_0_00
raw_counts.txt

value: After 1st Treatment


title: Tumor, JW18, Control, After 1st Treatment, Male, M35_0_03

description:
JW18_P_C_M35_0_03
raw_counts.txt


title: U_13_F10_9


title: U_16_H03_4


title: Tumor, JW18, Virus, Endpoint, Male, M36_0_10

description:
JW18_E_V_M36_0_10
raw_counts.txt

value: Endpoint


title: C_DMSO_1


title: U_13_F10_7


title: U_13_F10_8


title: Tumor, JW18, Virus, Endpoint, Female, F40_0_10

description:
JW18_E_V_F40_0_10
raw_counts.txt

value: Female


title: Tumor, JW18, Virus, Endpoint, Female, F40_0_30

description:
JW18_E_V_F40_0_30
raw_counts.txt


title: mESC scRNA-seq

city: Nijmegen

first: Oscar

last: Garcia-Blay

state: Gelderland

address: Heyendaalseweg 135

department: Biophysical Chemistry

country: Netherlands

institute: Institute for Molecules and Materials (Radboud University)

description: processed data files include the matrix, barcodes and features files that correspond to the cell-to-gene matrix. Barcodes identify cells while features identify genes. Raw files include all fastq files corresponding to this sample.

library_source: transcriptomic single cell

data_processing:
Reads were processed with cellranger-4.0.0.
Assembly: mm10-2020-A transcriptome
Supplementary files format and content: Tab-separated files (barcodes, features) and matrix files

source_name: E14 mESCs (129/Ola background)

growth_protocol: Mouse embryonic stem cells (mESCs) were seeded with a density of 0.5E6 cells in a gelatinized 9.6cm2 well. mESC culture medium  consisted of Dulbecco's Modified Eagle Medium, supplemented with 0.1mM betamercaptoethanol, 1000 U/mL of Penicillin, 0.1 mg/mL of Streptomycin, 1mM of sodium pyruvate , 1000 U/mL of ESGRO recombinant Mouse Leukemia Inhibitory Factor and 15% of ES-qualified heat inactivated Fetal Bovine Serum (FBS)

extract_protocol:
Cells were washed with 1xPBS and dettached with 0.05% trypsin in EDTA for 2 minutes at 37C, followed by quenching with complete growth media. Proper viability of cells prior to freezing was quantified with propidium iodide/acridine orange staining in a LUNA-FL Dual Fluorescence Cell Counter. Cells were centrifuged at 200rcf for 3 minutes. The supernatant was discaded and the pellet was resuspended in 1mL freezing media (80% complete media, 10% heat-innactivated FBS, 10% DMSO), and frozen at -80C.
Cells were shipped to comercial company in dry ice for single-cell RNA barcoding (10x Genomics' Chromium) and sequencing (NextSeq 2000 instrument, Single Cell 3' v3 chemistry), according standard procedures.

treatment_protocol: Mouse embryonic stem cells (mESCs) were seeded with a density of 0.5E6 cells in a 9.6cm2 well. 24 hours post-seeding, cells were exposed to 0.007% EtOH in the media for 6 hours, to a total time of 30h.

value: E14 mESCs (129/Ola background)


title: Maslinic acid 2

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from1% Maslinic acid treated mice for 20 days

hyb_protocol: Following fragmentation, 250 ng of cRNA were hybridized for 16 hr at 45C on Calriom_S_Mouse. GeneChips were washed and stained in the Gene Atlas Fluidics Station 400

scan_protocol: GeneChips were scanned using the GeneAtlas Imaging Station

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways, tissue expression, and disease associations (Huang da et al., 2009). We also performed gene set enrichment analysis (GSEA) for the top DEGs.
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).
SST-RMA

label: biotin

source_name: C3H mouse skin treated with Maslinic acid

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 9.4 ug total RNA

growth_protocol: Seven-week-old C3H male mice (Charles River Laboratories, Japan Inc, Kanagawa, Japan) were used in the investigation of the hair growth effect of Tieghemelin and Maslinic acid.

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.

treatment_protocol: Following a seven-day acclimatization period, mice were randomly assigned to four groups: Control (n=8), 1% Minoxidil (n=8), 1% Tieghemelin (n=8), and 1% Maslinic acid (n=8). Anesthesia was administered using isoflurane (Wako Pure Chemical Industries, Tokyo, Japan) before trimming the hair in the dorsal area. Subsequently, depilation was carried out using a depilatory cream to expose the pink skin on the mice's back. Each mouse received a daily topical application of Tieghemelin, Maslinic acid, and Minoxidil for 20 days.

tag: gender

value: Skin


title: Maslinic acid 1


title: Tieghemelin 2

description: Gene expression data from1% Tieghemelin treated mice for 20 days

source_name: C3H mouse skin treated with Tieghemelin


title: Tumor, JW18, Virus, Endpoint, Female, F40_0_01

description:
JW18_E_V_F40_0_01
raw_counts.txt


title: U_DMSO_3

value: skin

value: melanoma


title: Tieghemelin 1


title: Minoxidil 1

description: Gene expression data from1% Minoxidil treated mice for 20 days

source_name: C3H mouse skin treated with 1% Minoxidil


title: Minoxidil 2

source_name: C3H mouse skin treated with 2% Minoxidil


title: U_DMSO_2


title: Tumor, JW18, Virus, Endpoint, Female, F39_0_10

description:
JW18_E_V_F39_0_10
raw_counts.txt


title: U_DMSO_1


title: Tumor, JW18, Control, Endpoint, Male, M36_0_01

description:
JW18_E_C_M36_0_01
raw_counts.txt


title: I_16_H03_24


title: Tumor, JW18, Control, Endpoint, Male, M35_0_01

description:
JW18_E_C_M35_0_01
raw_counts.txt


title: I_16_H03_23


title: Tumor, JW18, Control, Endpoint, Female, F39_0_30

description:
JW18_E_C_F39_0_30
raw_counts.txt


title: I_13_F10_27


title: Poly(I:C) + artLCMV-E7E6 treated tumor biological replicate 5 DAY7

city: Pamplona

first: Jose

last: Gonzalez

state: Navarra

address: C/PIO XII s/n

country: Spain

institute: FIMA

description:
d7E7PlyR6
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample

data_processing:
FastQC for quality control
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm39 using STAR
Quantification using FeatureCounts
Assembly: mm39
Supplementary files format and content: tab-delimited text files include log2CPM values for each Sample in day1 and day7

growth_protocol: Mice were subcutaneously injected with 1.5×105 TC-1/A9 cells in the right flank. Seven days later, tumor were treated.

extract_protocol:
On day 8 and day 14, mice were euthanized, and RNA from tumors was subjected to RNAseq analysis
TruSeq Stranded mRNA preparation

treatment_protocol: Seven days later, mice were intravenously treated with 1×105 RCV FFU artLCMV-E7E6 and received intratumoral injections of 50 μg of poly(I:C) in the right-sided tumor lesion on days 7, 10, and 13.

tag: tag

value: Poly(I:C) + artLCMV-E7E6 treated


title: Poly(I:C) + artLCMV-E7E6 treated tumor biological replicate 4 DAY7

description:
d7E7PlyR5
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: I_13_F10_26


title: I_13_F10_25


title: Control 1 (Tieghemelin and Maslinic acid control)

description: Gene expression data from water treated mice for 20 days

source_name: C3H mouse skin treated with Milli-q


title: I_16_H03_22


title: E12.5 Male Natural Placenta 7

type: genomic

city: Philadelphia

first: Eric

middle: Alejandro

last: Rhon Calderon

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Floor 9-175

department: Cell and Developmental Biology

institute: University of Pennsylvania

description:
Bisulfite treated
Male-Natural-C3F
Genomic DNA from E12.5 Male Natural Placenta 7

hyb_protocol: Bisulfite converted DNA was amplified, fragmented, and hybridized to Illumina Infinium Mouse285 Methylation BeadChip 12v1-0 using standard Illumina Protocol

scan_protocol: Illumina iScan System

data_processing:
SeSAMe R Package
Beta values of individual probe for each  sample. Probes that did not pass SeSAMe quality control pOOBAH approach are masked with NA

label: Cy5 and Cy3

source_name: E12.5 Placenta Male IVF Natural 7

label_protocol: Standard Illumina Protocol:

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Irradiated Rodent Diet 5LG4, LabDiet) ad libitum.

extract_protocol: Genomic DNA was extracted and purified from Placentas samples using Phenol:Chloroform according to lab protocols. Then samples were Bisulfite-treated using Qiagen EpiTect Bisulfite Conversion Kit.

treatment_protocol: Placentas were collected at E182.5, snap frozen in liquid nitrogen and stored at -80C for DNA extraction.

tag: group

value: Natural

value: placenta

tag: age


title: Control 2 (Tieghemelin and Maslinic acid control)


title: E12.5 Male Natural Placenta 5

description:
Bisulfite treated
Male-Natural-C2B
Genomic DNA from E12.5 Male Natural Placenta 5

source_name: E12.5 Placenta Male IVF Natural 5


title: Poly(I:C) + artLCMV-E7E6 treated tumor biological replicate 3 DAY7

description:
d7E7PlyR4
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample

source_name: Tumor

value: Tumor


title: E12.5 Male Natural Placenta 1

description:
Bisulfite treated
Male-Natural-C1B
Genomic DNA from E12.5 Male Natural Placenta 1

source_name: E12.5 Placenta Male IVF Natural 1


title: I_DMSO_21

value: DMSO


title: E12.5 Male Natural Placenta 3

description:
Bisulfite treated
Male-Natural-C1HN
Genomic DNA from E12.5 Male Natural Placenta 3

source_name: E12.5 Placenta Male IVF Natural 3


title: E12.5 Male IVF+TEBx Placenta 8

description:
Bisulfite treated
Male-IVFTEBx-B8A
Genomic DNA from E12.5 Male IVF+TEBx Placenta 8

source_name: E12.5 Placenta Male IVF+TEBx 8

value: IVF+TEBx


title: E12.5 Male Natural Placenta 2

description:
Bisulfite treated
Male-Natural-C1GO
Genomic DNA from E12.5 Male Natural Placenta 2

source_name: E12.5 Placenta Male IVF Natural 2


title: E12.5 Male Natural Placenta 8

description:
Bisulfite treated
Male-Natural-C5D
Genomic DNA from E12.5 Male Natural Placenta 8

source_name: E12.5 Placenta Male IVF Natural 8


title: I_DMSO_20


title: I_DMSO_19


title: E12.5 Male IVF+TEBx Placenta 7

description:
Bisulfite treated
Male-IVFTEBx-B3A
Genomic DNA from E12.5 Male IVF+TEBx Placenta 7

source_name: E12.5 Placenta Male IVF+TEBx 7


title: E12.5 Male IVF Placenta 8

description:
Bisulfite treated
Male-IVF-B13A
Genomic DNA from E12.5 Male IVF Placenta 8

source_name: E12.5 Placenta Male IVF 8

value: IVF


title: E12.5 Male IVF+TEBx Placenta 6

description:
Bisulfite treated
Male-IVFTEBx-B2B
Genomic DNA from E12.5 Male IVF+TEBx Placenta 6

source_name: E12.5 Placenta Male IVF+TEBx 6

value: Male


title: artLCMV-E7E6 treated tumor biological replicate 5 DAY7

description:
d7E7R6
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample

value: artLCMV-E7E6 treated


title: E12.5 Male IVF Placenta 6

description:
Bisulfite treated
Male-IVF-B11A
Genomic DNA from E12.5 Male IVF Placenta 6

source_name: E12.5 Placenta Male IVF 6


title: E12.5 Male Natural Placenta 6

description:
Bisulfite treated
Male-Natural-C2G
Genomic DNA from E12.5 Male Natural Placenta 6

source_name: E12.5 Placenta Male IVF Natural 6


title: E12.5 Male IVF+TEBx Placenta 3

description:
Bisulfite treated
Male-IVFTEBx-1888-1
Genomic DNA from E12.5 Male IVF+TEBx Placenta 3

source_name: E12.5 Placenta Male IVF+TEBx 3


title: Poly(I:C) + artLCMV-E7E6 treated tumor biological replicate 1 DAY7

description:
d7E7PlyR1
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: Tumor, JW18, Control, Endpoint, Female, F39_0_01

description:
JW18_E_C_F39_0_01
raw_counts.txt

value: Control


title: E12.5 Male IVF+TEBx Placenta 1

description:
Bisulfite treated
Male-IVFTEBx-1604-1
Genomic DNA from E12.5 Male IVF+TEBx Placenta 1

source_name: E12.5 Placenta Male IVF+TEBx 1


title: E12.5 Male IVF+TEBx Placenta 2

description:
Bisulfite treated
Male-IVFTEBx-1707-1
Genomic DNA from E12.5 Male IVF+TEBx Placenta 2

source_name: E12.5 Placenta Male IVF+TEBx 2


title: E12.5 Male Natural Placenta 4

description:
Bisulfite treated
Male-Natural-C1I
Genomic DNA from E12.5 Male Natural Placenta 4

source_name: E12.5 Placenta Male IVF Natural 4


title: E12.5 Male IVF+TEBx Placenta 5

description:
Bisulfite treated
Male-IVFTEBx-B14B
Genomic DNA from E12.5 Male IVF+TEBx Placenta 5

source_name: E12.5 Placenta Male IVF+TEBx 5


title: artLCMV-E7E6 treated tumor biological replicate 4 DAY7

description:
d7E7R4
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: C_16_H03_14

source_name: skin


title: Poly(I:C) + artLCMV-E7E6 treated tumor biological replicate 2 DAY7

description:
d7E7PlyR3
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample

source_name: Tumor


title: artLCMV-E7E6 treated tumor biological replicate 3 DAY7

description:
d7E7R3
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: E12.5 Male IVF Placenta 7

description:
Bisulfite treated
Male-IVF-B12A
Genomic DNA from E12.5 Male IVF Placenta 7

source_name: E12.5 Placenta Male IVF 7


title: E12.5 Male IVF Placenta 3

description:
Bisulfite treated
Male-IVF-1780-2
Genomic DNA from E12.5 Male IVF Placenta 3

source_name: E12.5 Placenta Male IVF 3


title: E12.5 Male IVF Placenta 5

description:
Bisulfite treated
Male-IVF-B10B
Genomic DNA from E12.5 Male IVF Placenta 5

source_name: E12.5 Placenta Male IVF 5


title: E12.5 Male IVF+TEBx Placenta 4

description:
Bisulfite treated
Male-IVFTEBx-B10C
Genomic DNA from E12.5 Male IVF+TEBx Placenta 4

source_name: E12.5 Placenta Male IVF+TEBx 4


title: E12.5 Male IVF Placenta 2

description:
Bisulfite treated
Male-IVF-1598-1
Genomic DNA from E12.5 Male IVF Placenta 2

source_name: E12.5 Placenta Male IVF 2


title: E12.5 Female Natural Placenta 8

description:
Bisulfite treated
Female-Natural-C4JO
Genomic DNA from E12.5 Female Natural Placenta 8

source_name: E12.5 Placenta Female Natural 8


title: E12.5 Female Natural Placenta 6

description:
Bisulfite treated
Female-Natural-C4H
Genomic DNA from E12.5 Female Natural Placenta 6

source_name: E12.5 Placenta Female Natural 6


title: artLCMV-E7E6 treated tumor biological replicate 2 DAY7

description:
d7E7R2
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: C_13_F10_18


title: C_16_H03_13


title: C_13_F10_17


title: E12.5 Female Natural Placenta 4

description:
Bisulfite treated
Female-Natural-C2I
Genomic DNA from E12.5 Female Natural Placenta 4

source_name: E12.5 Placenta Female Natural 4


title: Poly(I:C) treated tumor biological replicate 4 DAY7

description:
d7PlyR4
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample

value: Poly(I:C) treated


title: artLCMV-E7E6 treated tumor biological replicate 1 DAY7

description:
d7E7R1
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: E12.5 Female Natural Placenta 7

description:
Bisulfite treated
Female-Natural-C4IO
Genomic DNA from E12.5 Female Natural Placenta 7

source_name: E12.5 Placenta Female Natural 7


title: E12.5 Female Natural Placenta 5

description:
Bisulfite treated
Female-Natural-C3J
Genomic DNA from E12.5 Female Natural Placenta 5

source_name: E12.5 Placenta Female Natural 5


title: C_13_F10_16


title: C_16_H03_15


title: Poly(I:C) treated tumor biological replicate 3 DAY7

description:
d7PlyR3
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: C_DMSO_12_1


title: Poly(I:C) treated tumor biological replicate 2 DAY7

description:
d7PlyR2
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: C_DMSO_11_1


title: E12.5 Female Natural Placenta 3

description:
Bisulfite treated
Female-Natural-C2C
Genomic DNA from E12.5 Female Natural Placenta 3

source_name: E12.5 Placenta Female Natural 3


title: E12.5 Female Natural Placenta 2

description:
Bisulfite treated
Female-Natural-C1GN
Genomic DNA from E12.5 Female Natural Placenta 2

source_name: E12.5 Placenta Female Natural 2


title: Poly(I:C) treated tumor biological replicate 1 DAY7

description:
d7PlyR1
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: Vehicle (PBS) control treated tumor biological replicate 4 DAY7

description:
d7PBSR6
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample

value: Vehicle (PBS) control treated


title: C_DMSO_10_1


title: U257_siSOX10_E06


title: E12.5 Female IVF+TEBx Placenta 8

description:
Bisulfite treated
Female-IVFTEBx-B2A
Genomic DNA from E12.5 Female IVF+TEBx Placenta 8

source_name: E12.5 Placenta Female IVF+TEBx 8

value: Female


title: E12.5 Male IVF Placenta 1

description:
Bisulfite treated
Male-IVF-1520-2
Genomic DNA from E12.5 Male IVF Placenta 1

source_name: E12.5 Placenta Male IVF 1


title: U257_siSOX10_E05


title: Dsquame, Forehead, Volunteer 12

city: San Diego

first: Erica

last: Montano

address: 12340 El Camino Real

institute: DermTech

data_processing:
Samples underwent demultiplexing and were converted to FASTQ files using  BCL Convert version 2.4.0
Samples underwent splice aware mapping and alignment to human reference genome (hg38 No Alts, with decoys) using  Dragen RNA version 4.0.4.
Dragen RNA version 4.0.4. was used to generate mapping metrics files.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: normal epidermal tissue

extract_protocol:
All tapes collected from a single site were pooled into a single tube and underwent enzymatic digestion in a chaotropic buffer to extract genomic material from the adhesive. Nucleic acids were pricipatated and isolated using magnetic beads, automated on a KingFisher Apex instrument.
RNA libraries for RNA-seq were  prepared using NEBNext Low Input RNA Library Prep Kit following manufacturer's protocol.
Poly A Enrichment RNA-seq

value: normal epidermal tissue


title: Vehicle (PBS) control treated tumor biological replicate 2 DAY7

description:
d7PBSR3
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: Dsquame, Forehead, Volunteer 11


title: Vehicle (PBS) control treated tumor biological replicate 3 DAY7

description:
d7PBSR4
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: E12.5 Female IVF+TEBx Placenta 4

description:
Bisulfite treated
Female-IVFTEBx-1888-2
Genomic DNA from E12.5 Female IVF+TEBx Placenta 4

source_name: E12.5 Placenta Female IVF+TEBx 4


title: U257_siSOX10_E04

source_name: skin


title: E12.5 Female IVF+TEBx Placenta 5

description:
Bisulfite treated
Female-IVFTEBx-B10A
Genomic DNA from E12.5 Female IVF+TEBx Placenta 5

source_name: E12.5 Placenta Female IVF+TEBx 5


title: Dsquame, Forehead, Volunteer 10


title: Vehicle (PBS) control treated tumor biological replicate 1 DAY 7

description:
d7PBSR2
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample

source_name: Tumor


title: E12.5 Female Natural Placenta 1

description:
Bisulfite treated
Female-Natural-C1A
Genomic DNA from E12.5 Female Natural Placenta 1

source_name: E12.5 Placenta Female Natural 1


title: U257_siControl_E03

value: siControl


title: E12.5 Male IVF Placenta 4

description:
Bisulfite treated
Male-IVF-1860-2
Genomic DNA from E12.5 Male IVF Placenta 4

source_name: E12.5 Placenta Male IVF 4


title: Poly(I:C) + artLCMV-E7E6 treated tumor biological replicate 5 DAY1

description:
d1E7PlyR6
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: E12.5 Female IVF+TEBx Placenta 2

description:
Bisulfite treated
Female-IVFTEBx-1707-2
Genomic DNA from E12.5 Female IVF+TEBx Placenta 2

source_name: E12.5 Placenta Female IVF+TEBx 2


title: U257_siControl_E01

value: skin


title: E12.5 Female IVF+TEBx Placenta 1

description:
Bisulfite treated
Female-IVFTEBx-1598-2
Genomic DNA from E12.5 Female IVF+TEBx Placenta 1

source_name: E12.5 Placenta Female IVF+TEBx 1


title: E12.5 Female IVF+TEBx Placenta 6

description:
Bisulfite treated
Female-IVFTEBx-B11B
Genomic DNA from E12.5 Female IVF+TEBx Placenta 6

source_name: E12.5 Placenta Female IVF+TEBx 6


title: E12.5 Female IVF Placenta 7

description:
Bisulfite treated
Female-IVF-B42A
Genomic DNA from E12.5 Female IVF Placenta 7

source_name: E12.5 Placenta Female IVF 7


title: Poly(I:C) + artLCMV-E7E6 treated tumor biological replicate 4 DAY1

description:
d1E7PlyR5
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: SmartSticker, Forehead, Volunteer 10


title: SmartSticker, Forehead, Volunteer 9


title: U62_siSOX10_H06

value: melanoma


title: Dsquame, Forehead, Volunteer 8


title: E12.5 Female IVF+TEBx Placenta 3

description:
Bisulfite treated
Female-IVFTEBx-1710-1
Genomic DNA from E12.5 Female IVF+TEBx Placenta 3

source_name: E12.5 Placenta Female IVF+TEBx 3


title: SmartSticker, Forehead, Volunteer 8


title: Poly(I:C) + artLCMV-E7E6 treated tumor biological replicate 3 dAY1

description:
d1E7PlyR4
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample

value: Poly(I:C) + artLCMV-E7E6 treated


title: E12.5 Female IVF Placenta 2

description:
Bisulfite treated
Female-IVF-1544-3
Genomic DNA from E12.5 Female IVF Placenta 2

source_name: E12.5 Placenta Female IVF 2


title: E12.5 Female IVF Placenta 8

description:
Bisulfite treated
Female-IVF-B7A
Genomic DNA from E12.5 Female IVF Placenta 8

source_name: E12.5 Placenta Female IVF 8


title: U62_siSOX10_H04


title: E12.5 Female IVF Placenta 4

description:
Bisulfite treated
Female-IVF-1597-1
Genomic DNA from E12.5 Female IVF Placenta 4

source_name: E12.5 Placenta Female IVF 4


title: E12.5 Female IVF Placenta 3

description:
Bisulfite treated
Female-IVF-1576-1
Genomic DNA from E12.5 Female IVF Placenta 3

source_name: E12.5 Placenta Female IVF 3


title: E12.5 Female IVF+TEBx Placenta 7

description:
Bisulfite treated
Female-IVFTEBx-B1A
Genomic DNA from E12.5 Female IVF+TEBx Placenta 7

source_name: E12.5 Placenta Female IVF+TEBx 7


title: Dsquame, Forehead, Volunteer 7

source_name: normal epidermal tissue


title: SmartSticker, Forehead, Volunteer 11


title: E12.5 Female IVF Placenta 6

description:
Bisulfite treated
Female-IVF-B16A
Genomic DNA from E12.5 Female IVF Placenta 6

source_name: E12.5 Placenta Female IVF 6


title: SmartSticker, Forehead, Volunteer 7


title: Poly(I:C) + artLCMV-E7E6 treated tumor biological replicate 2 DAY 1

description:
d1E7PlyR3
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: U62_siControl_H03

source_name: skin


title: SmartSticker, Forehead, Volunteer 6


title: E12.5 Female IVF Placenta 1

description:
Bisulfite treated
Female-IVF-1520-1
Genomic DNA from E12.5 Female IVF Placenta 1

source_name: E12.5 Placenta Female IVF 1


title: E12.5 Female IVF Placenta 5

description:
Bisulfite treated
Female-IVF-1780-1
Genomic DNA from E12.5 Female IVF Placenta 5

source_name: E12.5 Placenta Female IVF 5


title: SmartSticker, Forehead, Volunteer 5


title: Dsquame, Forehead, Volunteer 9


title: artLCMV-E7E6 treated tumor biological replicate 4 DAY 1

description:
d1E7R4
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample

source_name: Tumor


title: Poly(I:C) + artLCMV-E7E6 treated tumor biological replicate 1 DAY1

description:
d1E7PlyR2
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: Dsquame, Forehead, Volunteer 5


title: SmartSticker, Forehead, Volunteer 4


title: Dsquame, Forehead, Volunteer 3


title: U62_siControl_H01


title: Dsquame, Forehead, Volunteer 6


title: Dsquame, Forehead, Volunteer 4


title: artLCMV-E7E6 treated tumor biological replicate 5 DAY 1

description:
d1E7R5
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: SK_MEL28_siSOX10_C05


title: SK_MEL28_siSOX10_C06


title: SK_MEL28_siSOX10_C04


title: artLCMV-E7E6 treated tumor biological replicate 2 DAY 1

description:
d1E7R2
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: SmartSticker, Forehead, Volunteer 2


title: Dsquame, Forehead, Volunteer 1


title: artLCMV-E7E6 treated tumor biological replicate 3 DAY1

description:
d1E7R3
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: SmartSticker, Forehead, Volunteer 1


title: artLCMV-E7E6 treated tumor biological replicate 1 DAY1

description:
d1E7R1
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: I79_p16_ICM_SMC1

city: Göttingen

first: Argyris

last: Papantonis

state: Goettingen

address: Robert-Koch-Str. 40

department: Institute of Pathology

institute: University Medical Center Göttingen

data_processing:
Read pairs were aligned to the human reference genome GRCh38 using Bowtie2 (v2.3.4.1),PCR duplicates were removed using the MarkDuplicates function in Picard tools (v2.20.7),
Read coverage tracks (BigWig) were generated and normalized with the RPCG parameter using the bamCoverage function of deepTools2 (v3.5.1)
Peaks were called using SEACR (1.3) with an FDR cutoff of <0.01.
Assembly: GRCh38
Library strategy: CUT&TAG

extract_protocol:
IMR90s were lifted from plates using accutase (Sigma-Aldrich). Typically, 0.5 million cells were processed using the CUT&Tag-IT kit (Active Motif) as per manufacturer’s instructions.
CUT&Tag-IT kit (Active Motif) as per manufacturer’s instructions.

value: human lung fibroblast

tag: assay

value: CUT&TAG


title: SK_MEL28_siControl_C01

tag: cell type


title: I79_p16_ctrl_SMC1


title: I79_p34_SMC1


title: SmartSticker, Forehead, Volunteer 3


title: Dsquame, Forehead, Volunteer 2


title: Poly(I:C) treated tumor biological replicate 4 DAY 1

description:
d1PlyR5
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample

tag: tissue

value: Tumor


title: Poly(I:C) treated tumor biological replicate 3 DAY 1

description:
d1PlyR4
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: SK_MEL5_siSOX10_D05

tag: cell line


title: SK_MEL5_siControl_D03


title: Poly(I:C) treated tumor biological replicate 1 DAY 1

description:
d1PlyR1
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample

tag: genotype


title: SK_MEL5_siControl_D01

tag: treatment


title: 16-cells embryos 5C

city: Québec City

first: Marc-André

last: Sirard

state: Quebec

address: Offfice 2732, 2440 Hochelaga Blvd.

department: Sciences Animales

country: Canada

institute: Université Laval

description: 16-cells embryos

data_processing:
Sequencing adapters were removed using Trimmomatic and base calls with low quality score were removed. Reads with a minimal length of 50 nucleotides were kept for analysis.
Read conversion, alignment to the bovine mitochondrial genome (NC_006853.1) and methylation calls were obtained using Bismark.
Differentially methylated cytosines (DMC) between 2 consecutive stages were identify using the MethylKit R package
For each C-site, a logistic regression model is fitted to calculate p-values that are then adjusted to control for false discovery rate using the BH method implemented in R 4.2.1 p.adjust function (R Core Team 2022).
Assembly: bostau9
Supplementary files format and content: xlsx file containing the results of differential methylation between consecutive stages
Supplementary files format and content: .txt files contain number of methylated and unmethylated reads per C-site

organism: Bos taurus

source_name: embryos

extract_protocol:
Bovine oocytes and embryos from all study groups were digested with proteinase K (50 mg/mL) in M-Digestion buffer 10X (Zymo Research) for 20 minutes at 50 oC to remove the zona pellucida. Then, they were submitted to total DNA extraction using QuickDNA Microprep Kit (Zymo Research; D3020) following the manufacturer protocol.
Library construction was performed using the Enzymatic Methyl-Sequencing kit from New England Biolabs (E7120S), following the manufacturer protocol.
Enzymatic Methyl-Sequencing

value: embryos


title: Poly(I:C) treated tumor biological replicate 2 DAY 1

description:
d1PlyR3
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: I79_p21_ctrl_CTCF

value: CTCF


title: blastocysts ICM 6B

description: blastocysts ICM


title: blastocysts ICM 6C

description: blastocysts ICM


title: I79_p34_CTCF


title: I79_p16_ICM6d_CTCF


title: SK_MEL28_siControl_C03


title: SK_MEL5_siSOX10_D04


title: SK_MEL2_siSOX10_B06


title: Vehicle (PBS) control treated tumor biological replicate 4 DAY1

description:
d1PBSR6
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: Vehicle (PBS) control treated tumor biological replicate 3 DAY1

description:
d1PBSR5
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: 4-cells embryos 4C

description: 4-cells embryos


title: SK_MEL2_siSOX10_B05


title: Vehicle (PBS) control treated tumor biological replicate 2 DAY1

description:
d1PBSR2
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: blastocysts ICM 6A

description: blastocysts ICM


title: 4-cells embryos 4A

description: 4-cells embryos


title: Vehicle (PBS) control treated tumor biological replicate 1 DAY 1

description:
d1PBSR1
NovaSeq6000 150PE (150 x 2bp) 80M total reads 12Gb/sample


title: SK_MEL2_siSOX10_B04


title: zygotes 3C

description: zygotes


title: zygotes 3A

description: zygotes


title: SK_MEL2_siControl_B03


title: zygotes 3B

description: zygotes


title: mature oocytes 2C

description: mature oocytes

source_name: gametes

value: gametes


title: Mewo_siSOX10_A06

value: MEWO


title: mature oocytes 2B

description: mature oocytes


title: hnRNPL_KO rep3

city: Montréal

first: Javier

middle: M

last: Di Noia

state: QC

address: 110 Pine Avenue West

institute: Institut de recherches cliniques de Montréal (IRCM)

data_processing:
Sequencing adapters were trimmed with fastp (0.23.1) with (parameter- --detect_adapter_for_pe).
Trimmed means were mapped to mm10 genome with STAR (2.7.9a) following manual instructions for multi-sample 2-pass mapping.
Gene expression counts were determined with featureCounts (Rsubread 2.12.2). DESeq2 (1.38.2) was used for differential gene expression. rMATS (4.2.2) was used for differential splicing analysis.
Mapped reads to mouse genome were filtered for mapping quality (MAPQ>=1) with using samtools (1.16.1) to generate bigwig files using bamCoverage and bamCompare from deepTools (3.5.0) with a bin size of 1bp.
Assembly: mm10
Supplementary files format and content: bigwig (forward and reverse strands)

source_name: spleen

growth_protocol: Cells were cultured in RPMI 1640 media (Wisent) supplemented with 10% fetal bovine serum (Wisent), 1% penicillin/streptomycin (Wisent) and 0.1 mM 2-mercaptoethanol (Bioshop), with 5μg/ml LPS + 5ng/ml IL-4.

extract_protocol:
RNA was extracted from  2 million cells per replicate using Qiagen RNeasy Mini kit.
mRNA was enriched using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and library was prepared using KAPA RNA HyperPrep kit (Roche Diagnostics) as per manufacturer's instructions.

value: spleen

value: activated B cells

value: hnRNPL F/F CD21-cre

value: LPS+IL4 (24h)


title: Mewo_siSOX10_A05


title: immature oocytes 1B

description: immature oocytes


title: 16-cells embryos 5B

description: 16-cells embryos


title: hnRNPL_KO rep1


title: immature oocytes 1C

description: immature oocytes


title: mature oocytes 2A

description: mature oocytes


title: SK_MEL2_siControl_B01


title: 16-cells embryos 5A

description: 16-cells embryos


title: SmartSticker, Forehead, Volunteer 12


title: hFIRE_HPC_4

description:
FIREx228
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_HumanOnly.tsv
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv

data_processing:
FASTQ files were preprocessed using BBDuk to filter out ribosomal RNA and PhiX reads, trim Illumina adapters, quality trim any base pairs below a PHRED score of 28. and filter out reads less than 45bp after processing.
Reads were then aligned to a mixed species genome consisting of the unmasked top level FASTA files for the human GRCh38 (Ensembl release 99) and mouse GRCm39 (Ensembl release 107) DNA assemblies and aligned using HISAT2 using the -q, -1, and -2 options to align paired-end FASTQ files.
The output SAM files were then parsed using a modified version of the “byPrim.py” Python script from Song et al. (2022) which assigned each read to either mouse or human based on the species for which the primary alignment was specified by HISAT2.
Using the species assignments stored in the output of the “byPrim_MBJ.py” script, the “MBJ_FASTQSorter.py” script generated two sets of paired end reads for each original file, one pair consisting of the forward and reverse human reads and one pair consisting of the forward and reverse mouse reads.
Species-specific FASTQ files were then pseudoaligned to the human GRCh38 transcriptome (Ensembl release 107) or the mouse GRCm39 transcriptome (Ensembl release 107) using Kallisto v0.46.1.
Mouse transcripts were then summarized to the gene level via tximport and the dataset was filtered to retain only genes with 1:1 mouse to human gene homologues and then subsequently filtered to only retain genes with greater than 130 cumulative reads (average of 10 reads per sample). Human transcripts were then similarly summarized to the gene level, filtered to only retain genes with 1:1 homologues, and then both the mouse and human datasets were intersected to only retain genes present in both datasets.
Assembly: Ensembl GRCh38 and GCRm39
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts for the sorted human FASTQ files
Supplementary files format and content: Tab-delimited text file containing raw gene-level counts for the sorted mouse FASTQ files
Supplementary files format and content: Tab-delimited text file containing VST normalized counts for the combined mouse and human samples

organism:
Homo sapiens
Mus musculus

source_name: Brain

extract_protocol:
Animals were perfused (20mL per minute) with 1X DPBS (4°C) for 3 min. Brains were surgically excised from each mouse and cut in half along the mid-sagittal plane. The left hemisphere was placed in 4% (wt/vol) paraformaldehyde (PFA) for 36 h at 4°C for subsequent immunohistochemistry (IHC) and the right hemisphere fresh-frozen on dry ice and stored at -80°C for biochemical analysis. Fresh frozen hemispheres were crushed on dry ice using mortar and pestle and total RNA was isolated using the Qiagen RNeasy Plus Micro Kit following manufacturer protocol.
350ng of total RNA was used as input for library construction using the Illumina TruSeq Stranded mRNA kit which utilizes oligo-dT beads to select and amplify mRNA. cDNA was synthesized using nine rounds of PCR and quality and concentrations of the DNA libraries were assayed using the Agilent 2100 bioanalyzer high sensitivity DNA assay and the DNA high sensitivity Qubit. The libraries were quantified by Kapa qPCR, normalized to 1.5nM and then multiplexed at equimolar concentrations for sequencing on the Illumina NovaSeq 6000 platform with paired-end read 100 base chemistry on an S4 flow cell.

value: Brain

tag: mouse strain

value: HPC


title: WT rep3


title: immature oocytes 1A

description: immature oocytes


title: Mewo_siControl_A03

value: siControl


title: 4-cells embryos 4B

description: 4-cells embryos


title: hFIRE_HPC_3

description:
FIREx165
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_HumanOnly.tsv
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv

tag: injection


title: WT rep2


title: Mewo_siControl_A01

value: skin


title: WT rep1


title: hFIRE_HPC_1

description:
FIREx119
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_HumanOnly.tsv
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv


title: HMCB_siSOX10_E10

value: HMCB

value: melanoma


title: hnRNPL_KO rep2


title: d+56_cDC1_IRF8_RNA-seq_rep3

city: Yokohama

first: Tomohiko

last: Tamura

address: 3-9 Fukuura, Kanazawa-ku

institute: Yokohama City University

data_processing:
The RNA-seq reads were aligned to a mouse reference genome (mm10/GRCm38) using STAR software (version 2.7.7a).
Duplicate reads were removed by using Picard tools (version 2.25.0).
The expression levels were quantified using RSEM software(version 1.3.3).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes expected counts for each sample

source_name: bone marrow

extract_protocol:
Total RNA was prepared using an RNeasy Micro Kit (QIAGENCat# 74004) from approximately 1,500 to 10,000 cells according to the manufactures' instructions.
cDNA was synthesized and amplified using a SMART-Seq HT Kit (Takara Bio Cat# 634437).  RNA-seq libraries were prepared using a Nextera XT Kit (Illumina Cat# FC-131-1096).

value: bone marrow

value: classical type 1 dendritic cells

tag: isolation

value: in vitro Flt3L culture

value: Irf8 +56 kb enhancer-deficient


title: d+32_cDC1_IRF8_RNA-seq_rep3

value: Irf8 +32 kb enhancer-deficient


title: WT_cDC1_MSCV_RNA-seq_rep3

value: Wild Type


title: LPS, Biol Rep 3

first: Peter

last: Kurre

state: PA

address: 3615 Civic Center Blvd

department: Pediatrics

institute: Children's Hospital of Philadelphia

data_processing:
RNA-seq data were preprocessed using the nf-core/RNAseq pipeline version 3.9 (1).  In brief, FastQC version 0.11.9 was used to assess the quality of 100 bp paired-end reads (2).  Trim Galore! version 0.6.7 was then used for adapter and quality trimming on the raw reads (3).  Reads were aligned to GRCm38 (mm10) using STAR version 2.7.10a (4) and quantified using RSEM version 1.3.1 (5).  Duplicates were removed using picard MarkDuplicates version 2.27.4-snapshot (6).    Following preprocessing, data were filtered using the R package WGCNA version 1.69 to remove genes with many missing entries or zero variance (7).  Differential expression between pairs of groups was estimated using DESeq2 version 1.38.3 (8).  Genes were considered to have significant differential expression if there was an adjusted p-value of less than 0.05.  Pathway enrichment analysis was performed using genes with significant differential expression between each group pairing ranked by their log2foldchange using the R package fGSEA version 1.24.0 (9).  We employed the Molecular Signatures Database (MSigDB) to include the following pathway databases in the analyses: Hallmark gene sets (H), Canonical pathways (C2CP) , Regulatory target gene sets (C3), and Cell type signature gene sets (C8) (10, 11, 12).
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-delimited text files for gene-level RSEM expected counts
Supplementary files format and content: Tab-delimited text files for transcript-level RSEM expected counts
Supplementary files format and content: Tab-delimited text files for gene-level RSEM TPM values
Supplementary files format and content: Tab-delimited text files for transcript-level RSEM TPM values

source_name: Bone Marrow

extract_protocol:
Mice were sacrificed 24 hours the last injection. Hind legs were dissected and bone marrow (BM) cells were harvested by flushing both femur and tibia. Whole bone marrow cells were subjected to RBC lysis and were lineage-depleted using magnetic-activated cell sorting (MACS)-based method with EasySep Mouse Hematopoietic Progenitor Cell Isolation Kit (StemCell Technologies). Lineage-depleted BM cells were stained and HSPCs were fluorescence-activated cell sorting (FACS)-sorted using the FACSAria Fusion sorter (BD). RNA were extracted from HSPCs using RNeasy Micro Plus kit according to manufactuer's protocol.
Library was constructed using the NEXTFLEX Rapid Directional RNA-Seq Kit v2.0 according to manufacturer's protocol

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells

value: LPS


title: d+32het_in vitro_pre-cDC1_RNA-seq_rep3

value: classical type 1 dendritic cell precurcers

value: Irf8 +32 kb enhancer-heterozygous deficient


title: d+56het_in vitro_pre-cDC1_RNA-seq_rep3

value: Irf8 +56 kb enhancer-heterozygous deficient


title: HMCB_siSOX10_D10


title: d+32_in vitro_pre-cDC1_RNA-seq_rep3


title: WT_in vitro_pre-cDC2_RNA-seq_rep3

value: classical type 2 dendritic cell precurcers


title: AF9-EV, Biol Rep 3


title: WT_in vitro_cDC1_RNA-seq_rep3


title: WT_in vitro_cDC2_RNA-seq_rep3

value: classical type 2 dendritic cells


title: LPS, Biol Rep 2


title: HMCB_siControl_H10

value: skin

value: siControl


title: LPS, Biol Rep 1


title: HMCB_siSOX10_C10

value: HMCB

value: melanoma


title: HMCB_siControl_G10


title: WT_in vitro_MDP_RNA-seq_rep3

value: bone marrow

value: monocyte-dendritic cell progenitors


title: WT_in vitro_CDP_RNA-seq_rep3

value: common dendritic cell progenitors

value: in vitro Flt3L culture


title: AF9-EV, Biol Rep 2


title: hFIRE_HPC_2

city: Irvine

first: Mathew

last: Blurton-Jones

address: 845 Health Sciences Road

institute: University of California, Irvine

description:
FIREx164
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_Mouse_Samples_Only.tsv
RawCounts_Sorted_0822I-02_BlurM_20230807_Analysis_HumanOnly.tsv
VSTCounts_Sorted_0822I-02_BlurM_20230807_Analysis_MergedMouse+Human.tsv

value: Brain

value: HPC


title: AF9-EV, Biol Rep 1

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells


title: WT_pre-cDC1_Spl_RNA-seq_rep3

value: spleen

value: classical type 1 dendritic cell precurcers

value: primary

value: Wild Type


title: H41_scRNA-seq

first: Kai

last: Tan

address: 3501 Civic Center Boulevard

description: 10x genomics

data_processing:
scRNA-seq data was demultiplexed, aligned, and count matrices generated using Cell Ranger v6.1.2 aligning to GRCh38 with intronic regions included
Cell Ranger matrices were directly imported into Seurat v4. We used DoubletFinder to remove doublets on a per-sample basis. Cells with 100-10,000 unique genes expressed and less than 10% mitochondrial reads were retained for the downstream analysis. Samples were combined without computational integration and subjected to dimension reduction and clustering. Cells were annotated by marker gene expression, and likely artifactual cells (only found in one sample or likely residual doublets) were removed from analysis using VisCello for interactive visualization and artifact selection and removal.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files
Supplementary files format and content: Seurat object

source_name: Bone marrow

extract_protocol:
Digested tissue samples were subjected to immunomagnetic RBC depletion followed by immunomagnetic CD45 depletion to isolate non-hematopoietic cells (using 67% of the remaining cells) or immunomagnetic CD34 enrichment (using 33% of the remaining cells). Following enrichment, each of the three cell fractions (RBC depleted, CD45 depleted, CD34 enriched) were resuspended at a concentration of 1000 cells / uL in PBS + 0.04% BSA.
Cells were pooled and loaded into the 10x Genomics Chip G. We used Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 and followed the protocol as provided by 10x Genomics.

value: Bone marrow


title: WT_cDC1_RNA-seq_rep3

value: classical type 1 dendritic cells


title: PB-EV, Biol Rep 3

value: Healthy Peripheral Blood EV


title: WT_pre-cDC1_BM_RNA-seq_rep3


title: H39_scRNA-seq

description: 10x genomics


title: PB-EV, Biol Rep 2


title: WT_CDP_RNA-seq_rep1


title: d+32_cDC1_IRF8_RNA-seq_rep2

value: Irf8 +32 kb enhancer-deficient


title: PB-EV, Biol Rep 1


title: H38_scRNA-seq

description: 10x genomics


title: d+56_cDC1_IRF8_RNA-seq_rep1

value: Irf8 +56 kb enhancer-deficient


title: d+32_cDC1_IRF8_RNA-seq_rep1

value: bone marrow


title: d+56_cDC1_IRF8_RNA-seq_rep2


title: H35_scRNA-seq

description: 10x genomics


title: PBS, Biol Rep 3

value: PBS


title: WT_cDC1_MSCV_RNA-seq_rep1


title: HMCB_siControl_F10

value: skin

value: HMCB

value: melanoma

value: siControl


title: H34_scRNA-seq

description: 10x genomics


title: H36_scRNA-seq

description: 10x genomics


title: d+32het_in vitro_pre-cDC1_RNA-seq_rep2

value: in vitro Flt3L culture

value: Irf8 +32 kb enhancer-heterozygous deficient


title: WT_MDP_RNA-seq_rep3

value: monocyte-dendritic cell progenitors


title: PBS, Biol Rep 2

value: Bone Marrow

value: Hematopoietic Stem and Progenitor Cells


title: PBS, Biol Rep 1


title: d+56het_in vitro_pre-cDC1_RNA-seq_rep2

value: classical type 1 dendritic cell precurcers

value: Irf8 +56 kb enhancer-heterozygous deficient


title: WT_in vitro_pre-cDC1_RNA-seq_rep3

value: Wild Type


title: 168_KMT2D_KO_input2_rep2

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

data_processing:
Fastq data was processed using CoBRA pipeline (https://bitbucket.org/cfce/cobra/src/master/).
Steps include alignment using BWA mem, filtering for uniquely mapped read and sorting bam files.
Peaks were called using macs2 with default settings (-broad mode for H3K4me1 and H3K27me3)
Output bedgraph files were then used to generate bigWig files.
Assembly: mm9
Supplementary files format and content: bigWig

source_name: breast cancer

growth_protocol: DMEM, 10% FBS, 1x Pen/Strep, 1x Glutamin, 1x Non-essential amino acids, 5% CO2, 37C

extract_protocol:
Cells were fixed with 1% formaldehyd for 10 minutes. Then, cells were collected, nuclei were isolated and lysed and chromatin was sheared with an ultrasonicator (Covaris E220)
ChIPseq libraries were prepared using xGen DNA library prep reagents (IDT) on a Biomek i7 (Beckman Coulter) liquid handling platform from approximately 1ng of DNA with 14 cycles of PCR amplification according to manufacturer’s protocol.

value: breast cancer

value: cell line

tag: chip antibody


title: d+56het_in vitro_pre-cDC1_RNA-seq_rep1


title: 168_KMT2D_KO_input2_rep1


title: d+32_in vitro_pre-cDC1_RNA-seq_rep2

value: Irf8 +32 kb enhancer-deficient


title: WT_cDC1_MSCV_RNA-seq_rep2

value: bone marrow

value: classical type 1 dendritic cells


title: H24_scRNA-seq

description: 10x genomics

value: Bone marrow


title: 168_KMT2C_KO_input2_rep2


title: WT_in vitro_cDC2_RNA-seq_rep2

value: classical type 2 dendritic cells


title: H32_scRNA-seq

description: 10x genomics


title: WT_in vitro_cDC2_RNA-seq_rep1


title: H23_scRNA-seq

description: 10x genomics


title: WT_in vitro_pre-cDC2_RNA-seq_rep2

value: classical type 2 dendritic cell precurcers


title: d+32_in vitro_pre-cDC1_RNA-seq_rep1


title: WT_in vitro_pre-cDC2_RNA-seq_rep1


title: 168_KMT2C_KO_input2_rep1


title: WT_in vitro_cDC1_RNA-seq_rep2


title: H21_scRNA-seq

description: 10x genomics


title: WT_in vitro_cDC1_RNA-seq_rep1


title: H33_scRNA-seq

description: 10x genomics


title: 168_WT_input2_rep1

value: WT


title: 168_KMT2D_KO_KDM6A_rep2

data_processing:
Fastq data was processed using CoBRA pipeline (https://bitbucket.org/cfce/cobra/src/master/), including alignment using BWA mem, filtering for uniquely mapped read and sorting bam files. Peaks were called using macs2 with default settings (-broad mode, -SPMR). Bedgraph files were then used to generate bigWig files.
Assembly: mm9
Supplementary files format and content: bigWig


title: WT_in vitro_pre-cDC1_RNA-seq_rep2

value: in vitro Flt3L culture


title: F2-AGVT c68 AGVT

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

description: F2-AGVT (1390G3-526) c68 AG(+) VT(+)

data_processing:
Paired-end reads were processed with Trim_Galore! V0.6.3 and mapped on the GRCh38.p12 genome using Bismark v0.22.1 and Bowtie2 v2.3.4.1 with the “-X 2000” option.  BAM files were, then, processed with deduplicate_bismark script to remove PCR duplicates, and bismark_methylation_extractor to count methyl- and unmehyl-Cytosine per at CpG or CpA sequences.
Assembly: GRCh38.p12
Supplementary files format and content: bismark report file
Library strategy: EM-seq, (Vaisvila, 2021)

extract_protocol:
Gemomic DNA extraction was integrated in "library construction protocol" process.
EM-seq libraries were generated as described previously (Gyobu-Motani, 2023).

value: differentiated hPGCLC

tag: transgene

value: TFAP2C-EGFP, DDX4-tdTomato knock-in

value: Expansion culture with BMP signalling


title: d+32het_in vitro_pre-cDC1_RNA-seq_rep1

value: Irf8 +32 kb enhancer-heterozygous deficient


title: WT_in vitro_CDP_RNA-seq_rep1

value: common dendritic cell progenitors


title: WT_in vitro_MDP_RNA-seq_rep2

value: monocyte-dendritic cell progenitors


title: WT_in vitro_pre-cDC1_RNA-seq_rep1

value: classical type 1 dendritic cell precurcers

value: Wild Type


title: WT_in vitro_CDP_RNA-seq_rep2


title: H14_MACS_scRNA-seq

description: 10x genomics


title: M2 c76

description: M2 (1383D6) c76 EpCAM(+) ITGA6(+)


title: M1-AGVT c82 AGVT

description: M1-AGVT (585B1-1375), c82 AG(+) VT(+)


title: WT_in vitro_MDP_RNA-seq_rep1


title: 168_KMT2D_KO_KDM6A_rep1

value: breast cancer

value: cell line


title: WT_pre-cDC1_Spl_RNA-seq_rep2

value: spleen

value: primary


title: PXGL,DOX,ATAC,Rep3

city: Paris

first: Claire

last: Rougeulle

address: 35 rue Helene Brion

department: Epigenetics and Cell Fate

country: France

institute: Université Paris Cité, CNRS

data_processing:
ATAC-seq raw data was processed using the atacseq pipeline (v1.2.1) (https://github.com/nf-core/atacseq/) from nf-core using the default parameters
Adapter trimming using Trim Galore
Reads were aligned using BWA aligner
Duplicates were marked by picard
bigWig tracks were generated by BEDTools.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
DNA was extracted using the MinElute PCR purification kit (QIAGEN).
Transposed DNA were pre-amplified for 5 cycles. The required number of additional cycles for each sample was determined by qPCR as described (Buenrostro et al., 2015). After the final amplification, double-sided bead purification was performed with AMPure XP beads.

value: human embryonic stem cell

value: DOX


title: 168_KMT2C_KO_KDM6A_rep1


title: 168_KMT2C_KO_KDM6A_rep2


title: 168_WT_input2_rep2


title: WT_pre-cDC1_BM_RNA-seq_rep2

value: bone marrow


title: PXGL,DOX,ATAC,Rep2


title: WT_MDP_RNA-seq_rep2


title: 168_WT_KDM6A_rep2

value: WT


title: WT_MDP_RNA-seq_rep1


title: PXGL,DOX,ATAC,Rep1


title: d+32_cDC1_IRF8_rep3

data_processing:
Single-end reads were mapped on a mouse reference genome sequence (mm10) using Bowtie2 software (version 2.3.5.1).
Mapped SAM format files were converted to TagDirectories using the makeTagDirectory module of the HOMER package (version 4.11) with the “-tbp 1” option to remove duplicate reads.
CUT&Tag signals in ±2 kb from center of each ATAC-seq peak were calculated by the HOMER annotatePeaks.pl module.
The bedGraph files were generated by the HOMER makeUCSCfile module.
Assembly: mm10
Supplementary files format and content: bedGraph
Library strategy: CUT&Tag

extract_protocol:
Nuclei were prepared from 5,000-7,200 FACS-sorted cells and incubated with anti-acetyl histone H3 (Lys27) antibody (Merck Cat# MABE647). The nuclei were further incubated with anti-rabbit IgG antibody (Antibodies-Online Cat# ABIN101961) and then treated with pAG-Tn5 enzyme (EpiCypher).
Tagmented DNA was amplified using a NEBNext High Fidelity 2 x PCR Master Mix (New England Biolabs) with indexed primers. Libraries were purified using SPRIselect beads (Beckman Coulter) .

value: classical type 1 dendritic cells

value: in vitro Flt3L culture

tag: first antibody

value: Irf8 +32 kb enhancer-deficient


title: 168_WT_KDM6A_rep1


title: d+32_cDC1_IRF8_rep2


title: d+32_cDC1_IRF8_rep1


title: 168_KMT2D_KO_input_rep2


title: 168_KMT2D_KO_input_rep3


title: d+56_cDC1_IRF8_rep1

value: Irf8 +56 kb enhancer-deficient


title: d+56_cDC1_IRF8_rep2


title: d+56_cDC1_IRF8_rep3


title: NaiveCult, XACTKO, Rep3

data_processing:
Reads were trimmed using trim_galore (v0.6.5) with a minimum length of 50 bp.
Reads were then mapped to the human genome (hg38) using bowtie 2 (version?) (Langmead and Salzberg 2012) with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -L 10 -X 700.
Reads were then deduplicated using MarkDuplicates from picard (v2.23.5)  with the following options: --CREATE_INDEX=true --VALIDATION_STRINGENCY=SILENT --REMOVE_DUPLICATES=true --ASSUME_SORTED=true.
Read counts were quantified for each gene with htseq-count from htseq (v0.13.5) (Anders et al., 2015) using the following options:  --stranded reverse  -a 10 -t exon -i gene_id -m intersection-nonempty. The annotation file used: Homo_sapiens.GRCh38.90.gtf.
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

extract_protocol:
RNA was extracted using RNeasy mini kit (QIAGEN) following the manufacturer's recommendation.
Libraries were prepared using the Illumina Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit according to the manufacturer’s recommendation

tag: hesc status

value: NaiveCult

value: XACTKO


title: NaiveCult, XACTKO, Rep1


title: NaiveCult, XACTKO, Rep2


title: WT_cDC1_MSCV_rep3


title: WT_pre-cDC1_Spl_RNA-seq_rep1


title: WT_cDC1_MSCV_rep2


title: WT_cDC1_MSCV_rep1


title: WT_pre-cDC1_BM_RNA-seq_rep1


title: 168_KMT2D_KO_input_rep1


title: d+32het_in vitro_pre-cDC1_H3K27ac_rep3

value: Irf8 +32 kb enhancer-heterozygous deficient


title: 168_KMT2C_KO_input_rep2


title: d+32het_in vitro_pre-cDC1_H3K27ac_rep2

value: classical type 1 dendritic cell precurcers


title: NaiveCult, WT, Rep2


title: d+32het_in vitro_pre-cDC1_H3K27ac_rep1


title: d+32het_cDC1_H3K27ac_rep3


title: NaiveCult, WT, Rep1


title: 168_KMT2C_KO_input_rep1


title: 168_WT_input_rep3


title: d+56het_in vitro_pre-cDC1_H3K27ac_rep3

value: Irf8 +56 kb enhancer-heterozygous deficient


title: d+32het_cDC1_H3K27ac_rep1


title: Primed, WT, Rep3

value: Primed


title: Primed, WT, Rep2


title: d+56het_in vitro_pre-cDC1_H3K27ac_rep2


title: Primed, WT, Rep1


title: 168_WT_input_rep2

value: breast cancer

value: cell line


title: d+56het_in vitro_pre-cDC1_H3K27ac_rep1


title: d+56het_cDC1_H3K27ac_rep3

value: spleen

value: primary


title: 168_WT_input_rep1


title: d+56het_cDC1_H3K27ac_rep2


title: 168_KMT2C_KO_input_rep3


title: PXGL, siSPEN2, Rep3

value: PXGL

value: human embryonic stem cell


title: 168_KMT2D_KO_H3K27me3_rep3


title: PXGL, siSPEN2, Rep2


title: NaiveCult, WT, Rep3

value: WT


title: WT_in vitro_cDC1_H3K27ac_rep3

value: bone marrow

value: classical type 1 dendritic cells

value: Wild Type


title: d+56het_cDC1_H3K27ac_rep1


title: WT_in vitro_cDC1_H3K27ac_rep2

value: in vitro Flt3L culture


title: WT_in vitro_cDC1_H3K27ac_rep1


title: 168_KMT2D_KO_H3K27me3_rep1


title: 168_KMT2C_KO_H3K27me3_rep3


title: PXGL, siSPEN2, Rep1


title: WT_in vitro_pre-cDC1_H3K27ac_rep3


title: WT_in vitro_pre-cDC1_H3K27ac_rep2


title: d+32het_cDC1_H3K27ac_rep2


title: PXGL, siSPEN1, Rep3


title: 168_KMT2C_KO_H3K27me3_rep1


title: WT_in vitro_CDP_H3K27ac_rep2

value: common dendritic cell progenitors


title: WT_in vitro_CDP_H3K27ac_rep3


title: 168_WT_H3K27me3_rep3


title: PXGL, siSPEN1, Rep2


title: Library_induced_500k_cells_G8_gate

city: Berkeley

first: Niklas

last: Hummel

address: 1 Cycloton Road

institute: Lawrence Berkeley National Laboratory

description: non_TF_activation_domains_from_yeast_plant_500k_G8

data_processing:
For basecalling we used  PEAR v0.9.11
After demultiplexing samples, we kept only the reads that contained a perfect match to a designed tile. For each set of 8 sorted samples, we performed two normalizations. We first normalized the reads by the total number of reads in each bin. Then, for each designed tile, we normalized across the 8 bins to calculate a relative abundance. We then converted relative abundances to an activity score for each tile by taking the dot product of the relative abundance with the median fluorescence value of each bin. This computation is a weighted average. Tiles with less than 10 reads were not included in the final dataset. Later, post hoc analysis suggested that tiles with at least 1000 reads were well measured.
Assembly: N/A

organism: Saccharomyces cerevisiae

extract_protocol:
We sorted 1e6/500k cells into each pool. We extracted genomic DNA from these cells with the Zymo YeaSTAR (#D2002) kit.
To ensure singular constructs per cell, we introduced our library into the URA3 locus of strain DHY211 (MATa, MKT1(30G,) RME1(INS-308A) TAO3(1493Q), CAT5(91M) MIP1(661T), SAL1+ HAP1+). Employing the established yeast transformation method (64), we subjected the transformation to 30 minutes at 30 °C followed by 60 minutes at 42 °C. To minimize potential PCR errors, we performed SalI and EcoRI digestion on the plasmid library, releasing the section encompassing the ACT1 promoter, the synthetic TF, and the KANMX marker. Simultaneously, PacI digestion was conducted to cleave plasmids devoid of an activation domain variant and barcode insert, thereby reducing the occurrence of transformants with inactive TFs. Directed integration into the URA3 locus was guided by 500 bp upstream homology spanning the URA3 and ACT1 promoters, along with a corresponding 500 bp downstream homology region spanning the TEF and URA3 terminators. These regions were PCR amplified from pMVS 295 (Strader 6161) and pMVS 296 (Strader 6768), a generous gift from Nick Moffy and Lucia Starder. Transformation utilized a molar ratio of 1:3 for linearized library to homology arms, with 28 μmol of linearized library per reaction. The transformed library was plated on YPD, followed by an overnight incubation at 30°C, and subsequent replica-plating onto freshly prepared SC G418 plates. Employing this process across 80 transformation reactions yielded an estimated >1,000,000 individual colonies. Subsequently, the transformants were collectively mated with an FY5 strain containing the reporter integrated into the uncertain ORF, YBR032w. Diploids were selected on YPD with G418 (200 µg/ml) and NAT (100 µg/ml) (strain MY436 YBR032w::P3_GFP NAT S288C), resulting in prototrophic diploids. These 110,000 yeast transformants were mated in batches, and prior to the final experiment, batches were pooled, and multiple aliquots were frozen.
beta-estradiol inducible library

treatment_protocol: We treated cells with ß-estradiol for 4hrs before cell sorting


title: 168_WT_H3K27me3_rep1


title: WT_in vitro_CDP_H3K27ac_rep1


title: Library_induced_500k_cells_G7_gate

description: non_TF_activation_domains_from_yeast_plant_500k_G7


title: Library_induced_500k_cells_G6_gate

description: non_TF_activation_domains_from_yeast_plant_500k_G6


title: WT_in vitro_MDP_H3K27ac_rep3

value: monocyte-dendritic cell progenitors


title: PXGL, siScr, Rep2

value: siScr


title: 168_KMT2D_KO_H3K27ac_rep2

value: H3K27ac (Diagenode, C15410196)


title: WT_in vitro_MDP_H3K27ac_rep1


title: Library_induced_500k_cells_G5_gate

description: non_TF_activation_domains_from_yeast_plant_500k_G5


title: WT_in vitro_MDP_H3K27ac_rep2


title: PXGL, siScr, Rep1


title: Library_induced_500k_cells_G4_gate

description: non_TF_activation_domains_from_yeast_plant_500k_G4


title: WT_in vitro_pre-cDC1_H3K27ac_rep1

value: classical type 1 dendritic cell precurcers


title: 168_KMT2D_KO_H3K27ac_rep1


title: PXGL, XIST KO, Rep2

value: XIST KO


title: WT_cDC1_H3K27ac_rep3


title: Library_induced_500k_cells_G3_gate

description: non_TF_activation_domains_from_yeast_plant_500k_G3


title: WT_cDC1_H3K27ac_rep2


title: PXGL, XIST KO, Rep3


title: 168_KMT2C_KO_H3K27ac_rep2

value: breast cancer


title: WT_cDC1_H3K27ac_rep1


title: 168_KMT2C_KO_H3K27ac_rep3

value: cell line


title: Library_induced_500k_cells_G2_gate

description: non_TF_activation_domains_from_yeast_plant_500k_G2


title: Library_induced_500k_cells_G1_gate

description: non_TF_activation_domains_from_yeast_plant_500k_G1


title: PXGL, siSPEN1, Rep1


title: PXGL, XIST KO, Rep1


title: 168_KMT2D_KO_H3K27ac_rep3


title: PXGL, WT, Rep3


title: PXGL, siScr, Rep3


title: 168_WT_H3K27ac_rep3


title: Library_induced_1mil_cells_G8_gate

description: non_TF_activation_domains_from_yeast_plant_1mil_G8


title: WT_CDP_H3K27ac_rep3


title: PXGL, WT, Rep2


title: PXGL, WT, Rep1


title: Library_induced_1mil_cells_G7_gate

description: non_TF_activation_domains_from_yeast_plant_1mil_G7


title: 168_WT_H3K27ac_rep2


title: WT_CDP_H3K27ac_rep1


title: 168_WT_H3K27ac_rep1


title: Library_induced_1mil_cells_G6_gate

description: non_TF_activation_domains_from_yeast_plant_1mil_G6


title: WT_MDP_H3K27ac_rep3


title: 168_KMT2D_KO_H3K4me1_rep3

value: H3K4me1 (abcam, ab8895)


title: PXGL, CRISPRi XIST Dox, Rep2

value: CRISPRi XIST Dox


title: WT_MDP_H3K27ac_rep2

value: primary


title: Library_induced_1mil_cells_G5_gate

description: non_TF_activation_domains_from_yeast_plant_1mil_G5


title: 168_KMT2D_KO_H3K4me1_rep2


title: Library_induced_1mil_cells_G4_gate

description: non_TF_activation_domains_from_yeast_plant_1mil_G4


title: 168_KMT2C_KO_H3K27ac_rep1


title: PXGL, CRISPRi XIST Dox, Rep1

value: PXGL

value: human embryonic stem cell


title: WT_MDP_H3K27ac_rep1

value: bone marrow


title: PXGL, CRISPRi XIST UT, Rep3

value: CRISPRi XIST UT


title: 50pg_rep2

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
Trimmed reads were mapped to mouse genome mm9 by bismark.
Only uniquely mapped reads were kept for down-stream analyses.
Calling of mC was performed by scripts in bismark.
Genome_build: mm9
Supplementary_files_format_and_content: bismark output cov files

source_name: mouse ESCs

extract_protocol:
DNA was purified using Qiagen's Puregene kit and sonicated to about 200 bp.
Methylated adapters were added with the NEBNext DNA library prep kit. Libraries were bisulfite converted with the Zymo EZ DNA Methylation Lightning kit.

tag: strain

tag: technology

value: ABS


title: 168_KMT2D_KO_H3K4me1_rep1


title: 168_KMT2C_KO_H3K4me1_rep2


title: 168_KMT2C_KO_H3K4me1_rep3


title: 50pg_rep1


title: PXGL, CRISPRi XIST UT, Rep2


title: Library_induced_1mil_cells_G2_gate

description: non_TF_activation_domains_from_yeast_plant_1mil_G2


title: WT_CDP_H3K27ac_rep2

value: Wild Type


title: PXGL, CRISPRi XIST Dox, Rep3


title: 20pg rep2


title: PXGL, CRISPRi XIST UT, Rep1


title: 168_KMT2C_KO_H3K4me1_rep1


title: run_2198_s_2_WTtreated_sequence.txt_TGAGGTT

first: Abigael

last: Cheruiyot

address: 1 Joslin Place

institute: Joslin Diabetes Center

data_processing:
A custom Perl script was used to determine the read counts for each sgRNA and map the sgRNAs to their gene IDs in the reference GeCKOv2 library
Supplementary files format and content: Raw read counts for each sgRNAs is provided in Read counts.xls with multiple tabs for different samples

source_name: Uterus; Cervix

growth_protocol: HeLa cells were cultured in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100 U/ml penicillin and 100 μg/ml streptomycin at 37°C with 5% CO2 in a humidified incubator.

extract_protocol:
Genomic DNA was extracted using PureLink Genomic DNA kit (ThermoFisher Scientific, K182001)
Two PCR reactions were used to prepare samples for Illumina Next-Gen sequencing. The first PCR was used to amplify sgRNA inserts in the cells, and the second PCR was used to add Illumina sequencing tags as well as index tags for sample identification. To improve the complexity of the library required for deep sequencing, a mixture of 5 forward primers with staggered nucleotides immediately upstream of the sgRNA sequences was used in the second PCR.
Survival screen after genome-wide KO of genes that may be important for survival under HU treatment, but not needed when Exo1 is also depleted

treatment_protocol: Exo1-KO cell lines were generated by transfection of  HeLa with pCRSIPRv2-sgRNA-expressing constructs with sgRNAs targeting human Exo1. Twenty-four hours after transfection, cells were selected withpuromycin(1.5μg/ml) for 2days. Single cells were grown in 96-well plates for amplification. Individual clones were verified bywestern blotto detect the depletion of Exo1. To carry out the screen, HeLa-Cas9 cells were infected with lentiviruses expressing the GeCKOv2 library (containing two sub-libraries) at a multiplicity of infection (MOI) of 0.3 with a 500x coverage of the library, selected 2 days post infection, and then cultured for 10 days. Cells were then treated with 4 mM HU for 24 hours and recovered in fresh DMEM medium for 3 days.

value: Uterus; Cervix

value: HeLa

value: epithelial cell

value: WT


title: 20pg rep1


title: 168_WT_H3K4me1_rep3


title: Naive, RAP XIST, Rep1

data_processing:
Reads were TM using trim_galore (v0.6.5) with a minimum length of 50 bp.
Reads were then mapped to the human genome (hg38) using bowtie 2 (Langmead and Salzberg 2012) with the following parameters: --local --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 -L 10 -X 700.
Reads were then deduplicated using MarkDuplicates from picard (v2.23.5) with the following options: --CREATE_INDEX=true --VALIDATION_STRINGENCY=SILENT --REMOVE_DUPLICATES=true --ASSUME_SORTED=true.
BigWig track files were generated with bamCoverage from deeptools (v3.5.0) using the following parameters: --normalizeUsing BPM --binSize 20 --smoothLength 40. normalizeUsing "BPM" --binSize 20 --smoothLength 40.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: RAP-seq

extract_protocol:
DNA was eluted by RNase H digestion, and crosslinking was reversed via proteinase K digestion at 65˚C for 1h. Finally, DNA was purified using the GeneJET Gel Extraction kit (Thermo Fisher Scientific).
Libraries were prepared using the TruSeq ChIP Library Preparation Kit from Illumina.

value: Naive

tag: fraction

value: RAP XIST


title: 10pg rep2


title: Naive, RAP XIST, Rep2


title: Library_induced_1mil_cells_G3_gate

description: non_TF_activation_domains_from_yeast_plant_1mil_G3


title: run_2198_s_1_WTuntreated_sequence.txt_TGAGGTT

value: untreated


title: 10pg rep1


title: Primed, RAP XIST, Rep2

value: Primed


title: run_2198_s_1_Exo1KOuntreated_sequence.txt_ATGACAG

value: Exo1 KO


title: 168_WT_H3K4me1_rep1

value: breast cancer

value: cell line

value: H3K4me1 (abcam, ab8895)


title: Primed, RAP XIST, Rep1

value: human embryonic stem cell


title: Library_induced_1mil_cells_G1_gate

description: non_TF_activation_domains_from_yeast_plant_1mil_G1


title: ApcDHep GFP+ J21

first: Angelique

last: Gougelet

address: 15 rue de l'école de médecine

institute: INSERM U1138

data_processing:
Illumina RTA 1.18.64 (Hiseq2500) and bcl2fastq Conversion Software v2.20 was used for basecalling and demultiplexing.
ATAC-seq reads were aligned to the mm9 genome assembly using bowtie2 the -X  2000 parameter
Bam were reordered and PCR duplicates removed using samtools
BigWig were generated using bamCoverage command from deepTools with the following parameters : --binSize 10 --normalizeUsing RPKM --extendReads
Assembly: Mus_musculus mm9
Supplementary files format and content: BigWIG

source_name: mouse ApcDHep hepatocytes

extract_protocol: Transposition was performed on 50,000 hepatocytes with 4,5 L Tn5 and digitonin 0.1%

treatment_protocol: ATAC-seq profiles from hepatocytes isolated from  ApcDHep livers by perfusion with collagenase in three-month old mice injected  with Ad5-Cre-GFP and sorted with ARIA3

tag: cell types

value: mouse  hepatocytes

value: Ad5-Cre-GFP 1,5x109 Vg


title: 168_KMT2D_KO rep3

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, feature counting and aggregation was done using cellranger v7.0.1.
Assembly: mm10
Supplementary files format and content: tsv files and matrix files

source_name: primary breast tumor

growth_protocol: Primary tumors were induced by injecting cells into mammary fat pads of Balb/c mice.

extract_protocol:
Whole tumors were disrupted using micropestles and digested for 1h at 37C on a shaker with digestion medium (2% w/v collagenase IV, 2% w/v hyaluronidase and 2% w/v BSA in DMEM). Cells were filtered through 500 µm meshes, washed with PBS and stored in freezing medium. Immediately before library preparation, dead cells and debris was removed using percoll purification (50%/40%/20% layers).
About 26,000 single cells were loaded onto a 10x Genomics ChromiumTM instrument (10x Genomics) according to the manufacturer’s recommendations. The scRNAseq libraries were generated using Chromium Next GEM Single Cell 5' HT Kit v2 (10x Genomics).

value: primary breast tumor

value: complete tumor suspensions

value: MFP injection