title: MG with CD177 WT N-2

city: Nanjing

first: Siming

last: Dai

address: No. 300, Guangzhou Road, Nanjing

department: Department of Orthopedic

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
fastp version 0.17.1
HISAT2 version 2.1.0
String Tie v1.3.4d
DESEQ2 v1.18.1
R version 3.4.3
Assembly: gencode v27
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: primary microglia

growth_protocol: To obtain primary microglia, C57BL/6 neonatal mice were used in this study. The whole brain was carefully extracted and minced into1 mm³ pieces. The minced tissue was then incubated in a mixed enzymatic solution containing 0.25% trypsin and DNase at 37°C for 20 minutes. Following centrifugation and washing, the cell suspension was transferred to a T75 culture flask coated with PLL for culture. Half of the culture medium was replaced every two days. On the 14th day, the culture flasks were placed on an orbital shaker at 37°C and agitated at 180 rpm for 4-6 hours to facilitate cell detachment.；To isolate neutrophils in the injured spinal cords, MACS was used.

extract_protocol:
Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) .  RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA).
Quality RNA samples were converted into cDNA libraries using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (NR601, Vazyme, NanJing, China). VAHTSTM DNA Clean Beads (Vazyme #N411) in this study was used to purify the fragments during the process of library constructing. The purified products were enriched with 12-15 cycles of PCR to create the final cDNA library. Finally, libraries were sequenced on the Illumina Hiseq X Ten according the manufacturer's protocols.

treatment_protocol: After co-cuturing for 24 h, microglia were isolated through FACS.

value: primary microglia

value: co-culture with CD177 WT neutrophils isolated from SCI lesion 3 dpi


title: MG with CD177 KO N-2

status: Public on Sep 10 2024

type: SRA

country: China

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: cell type

tag: genotype

value: WT

tag: treatment

value: co-culture with CD177 KO neutrophils isolated from SCI lesion 3 dpi


title: MG with CD177 KO N-3


title: MG with CD177 KO N-1


title: MG with CD177 WT N-1


title: BMM with CD177 KO N-2

source_name: BMM derived macrophages

growth_protocol: To obtain primary bone marrow-derived macrophages, bone marrow cells first underwent lysis of red blood cells and were then resuspended in complete RPMI-1640 medium consisting of 25 ng/ml macrophage colony-stimulating factor (M-CSF) and cultured for 7 days；To isolate neutrophils in the injured spinal cords, MACS was used.

treatment_protocol: After co-cuturing for 24 h, macropahges were isolated through FACS.

value: BMM derived macrophages


title: BMM with CD177 KO N-3


title: BMM with CD177 KO N-1


title: BMM with CD177 WT N-2


title: BMM with CD177 WT N-3


title: BMM with CD177 WT N-1


title: RNA_seq_2TX-3a-Het_2 HSC

city: SAINT LOUIS

first: Daofeng

last: Li

state: MO

address: 4515 McKinley Avenue

department: Genetics

country: USA

institute: Washington University in St. Louis

description: NovaSeq X Plus (300 cycles)

data_processing:
For RNA- seq, reads were sequenced using NovaSeq X Plus platform and aligned to mm10 using STAR and geen counts identified using subread:feature count. For WGBS, reads were sequenced using NovaSeq platform. Reads were aligned to mm10,  deduplicated and CpG methylation extracted using Bismark.
Assembly: mm10

source_name: HSC

growth_protocol: 250 CD45.2 HSCs of the indicated genotypes were competitively transplanted with competetive 250,000 CD45.1 whole bone marrow cells in lethally irradiated primary recipient mice.  Serial transplant was performed by repeating this process.

extract_protocol:
For RNA sequencing, 4000 HSC cells were sorted using Aurora cell sorter. And RNA was extracted using NucleoSpin RNA plus XS (Takara: 740990.50) . For WGBS, genomic DNA (gDNA) was prepared from the cells using PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific #K1820-02).
RNA librariers for RNA seq was preapred using Takara Clontech SMARTer mRNA library kit following manufactures protocol. For WGBS, using 200 ng of gDNA and 0.2% lambda DNA was bisulfite treated using EZ-96 DNA Methylation-Gold Mag Prep Kit (Zymo Research #D5042) and processed with xGen™ Methyl-Seq Library Prep (IDT, 10009824) to generate Illumina-compatible WGBS libraries.

tag: Stage

value: Secondary

value: HSC

value: Vav-Cre


title: LPS3

first: Yahao

last: Zhang

state: Jiangsu

address: 87 Dingjiaqiao

institute: Zhongda Hospital Southeast University

data_processing:
The raw reads were further processed with a bioinformatic pipelinetool,BMKCloud(www.biocloud.net) online platform.
Assembly: GRCm38_release95
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Spleen

extract_protocol:
Total RNA was extracted from spleen-derived monocytes following the instructions provided in the TRIzol Reagent (Life Technologies, California, USA) manual.
Sequencing libraries were prepared using the Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen Biotechnology, Shanghai, China) in accordance with the manufacturer’s instructions. Index codes were incorporated to assign sequences to each sample.

tag: tissue

value: Spleen

value: spleen-derived monocytes

value: low-dose LPS stimulation (40 ng/ml for 5 hours)


title: LPS-Oct2

value: low-dose LPS priming followed by octanal administration (20 µM for 19 hours)


title: LPS-Oct1

value: low-dose LPS priming followed by octanal administration (20 µM for 18 hours)


title: LPS2


title: RNA_seq_2TX-3a-Het_1 HSC

description: NovaSeq X Plus (300 cycles)


title: Untreat2

value: untreated control with DMSO (1:1001)


title: Untreat1

value: untreated control with DMSO (1:1000)


title: LPS1


title: Untreat3

value: untreated control with DMSO (1:1002)


title: KO sperm small RNA-seq_r2

city: Shanghai

first: Xinyu

last: Wang

address: Siping Road 1239

institute: Tongji University

description: KO sperm small RNA-seq replicate2

library_source: other

data_processing:
For raw paired-end transcriptome sequencing data, trim_galore v0.4.5 was used to remove low-quality bases and adapter sequences. STAR v2.6.1c was used to align the clean sequence data to the mouse reference genome (mm10), and RSEM v1.3.1 was used to quantify gene expression from the aligned sequences for each gene. The gene annotation file was obtained from the mouse GENCODE release (GRCm38.99). The R package DESeq2 v1.42.1 was used to identify differentially expressed genes between distinct Isca2 groups in mice. GSEA analysis was performed using the R package clusterProfiler v4.10.1, providing normalized enrichment scores and nominal p-values. KEGG functional annotation was conducted using the KOBAS online tool (http://bioinfo.org/kobas).
Assembly: mm10
Supplementary files format and content: aligned sequence file(bam) and gene expression quantification file(genes.results)

molecule: other

source_name: Sperm

growth_protocol: Animal welfare and the experimental procedures adhered to the ethical provisions on the Care and Use of Experimental Animals of Wenzhou Medical University and were approved and authorized by the Animal Experimental Committee of the University (No. xmsq2021-0068). Animals were maintained under a 12 h light/dark cycle and provided with food and water ad libitum in individually ventilated units.

extract_protocol:
To collected pre-implantation embryos, Isca2+/- female mouse intraperitoneal with 6.5 international unit of pregnant mares’ serum gonadotropin and, 45 to 47 h later, with 5 IU of human chorionic gonadotropin and crossed to Isca2+/- males. Embryos were isolated in M2 medium (Sigma: M7167) and cultured in potassium-supplemented optimised medium (Merck: MR-121-D) at 37℃ in 5% CO2.
The RNA-seq procedure was performed as previously described. Briefly, E4.5 blastocysts were washed three times in 0.5% BSA-PBS solution. cDNA was amplified using the single cell full length mRNA-amplification kit (N712, Vazyme). Library preparation was performed using the TruePrep DNA Library Prep Kit (TD501, Vazyme) according to the manufacturer’s instructions. All libraries were sequenced using the NovaSeq X Plus (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

value: Sperm

value: Isca2 -/-


title: KO sperm small RNA-seq_r1

description: KO sperm small RNA-seq replicate1


title: WT sperm small RNA-seq_r1

description: WT sperm small RNA-seq replicate1

value: wild type


title: MG with CD177 WT N-3

value: primary microglia

value: WT

value: co-culture with CD177 WT neutrophils isolated from SCI lesion 3 dpi


title: WT sperm small RNA-seq_r2

description: WT sperm small RNA-seq replicate2


title: WGBS_exp5_2TX-Control_2 WT BM Secondary

description: NovaSeq S4 300XP

library_source: genomic

molecule: genomic DNA

source_name: BM

value: Secondary

value: BM


title: E14 mESCs, sucrose cushion pellet, rep2

city: Singapore

first: Teodorus Theo

last: Susanto

address: 60 Biopolis St

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Adapter sequences were trimmed from the paired end reads using cutadapt v4.7 with parameters: "-j 0 --minimum-length=20 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT"
Genome index was build using STAR v2.7.11b with parameters: "--runThreadN 16 --runMode genomeGenerate --genomeDir <GRCm39_dir/> --genomeFastaFiles <GRCm39.primary_assembly.genome.fa> --sjdbGTFfile <gencode.vM34.primary_assembly.basic.annotation.gtf> --sjdbOverhang 149"
Reads were aligned using STAR v2.7.11b with --quantMode TranscriptomeSAM enabled
Meanwhile, transcriptome database was generated using gffread version 0.12.7, to parse out transcriptome data from GRCm39 primary assembly using GENCODE release M34 basic annotation.
Transcriptome was indexed using Salmon v1.10.3 with parameters: "-p 16 --gencode -t"
Transcript abundance was quantified using Salmon with parameters: "--gencode -t <transcriptome_from_genome.fa> -p 16 --gcBias -l ISR"
Output files from salmon (quant.sf) were subjected to differential gene expression analysis using DESeq2 v1.44.0. Cutoff for differentially enriched genes is: |FC| > 2, Benjamini-Hochberg adjusted p-value < 0.05.
Assembly: GENCODE release M34 (GRCm39)
Supplementary files format and content: tab-delimited text files of Salmon quant.sf output for each sample
Supplementary files format and content: comma-separated text file of differentially enriched genes (adj. pval < 0.05) between sucrose cushion alone and RAPIDASH using DESeq2 v1.44.0

molecule: polyA RNA

growth_protocol: E14 mESCs were maintained on cell culture dishes coated with 0.1% (w/v) gelatin (EmbryoMax® 0.1% Gelatin Solution, Millipore, ES-006-B) in sterile milliQ water in cell culture incubators at 5% CO2, 37 °C in mESC media containing KnockOutTM DMEM (Dulbecco’s Modified Eagle Media; Thermo Fisher Scientific, 10829-018) with 15% ES quality fetal bovine serum (FBS) (Millipore, ES-009-B), 2 mM EmbryoMax® L-glutamine (Millipore, TMS-002-C), 1x EmbryoMax® Penicillin/Streptomycin (Millipore, TMS-AB2-C), 1x EmbryoMax® MEM, non essential amino acids (Millipore, TMS-001-C), 0.055 mM 2-mercaptoethanol (Gibco, 21985023), and 103 U/mL mouse leukemia inhibitory factor (LIF) protein (Gemini, 400-495). Cells were typically passaged every other day at a 1:6 ratio for maintenance. On days where the cells were not split, the media was changed to fresh mESC media. Cells were harvested when when they were 50-60% confluent.

extract_protocol:
Each cell pellet was lysed in 300 µL lysis buffer A, and the lysates were subjected to sucrose cushion ultracentrifugation as in “Characterization of cysteine-charged sulfolink resin.” Each input sample for sucrose cushion ultracentrifugation contained approximately 75 µg of RNA. The pelleted material from each cushion, which contains ribosomes, was resuspended in 1 mL binding buffer. Half of each sample was subjected to total RNA extraction using TRIzol LS (Invitrogen, 10296010). To do this, 500 µL of sample was mixed with 1.5 mL TRIzol LS and then aliquoted into two 2 mL DNA lo bind tubes. Then, chloroform was added at one fifth of the volume of TRIzol LS, and the tubes were vigorously shaken by hand and then left at room temperature for 3 minutes. The tubes were then centrifuged at 12,000 ×g. The upper aqueous layers for the tubes deriving from one cell pellet were combined with an equal volume of ethanol and put onto one column from a Zymo RNA Clean and Concentrator-5 kit, and the RNA was purified following the manufacturer’s instructions. The final elution step in the recommended protocol was eluted for a combined total of 30 µL eluate for each sample.
The other half of each sample underwent chromatography with sulfhydryl-charged sulfolink resin. Each input sample consisted of 500 µL sucrose cushion pellet in binding buffer. Ribosomes were enriched using 1 mL cysteine-charged sulfolink resin, prepared as in "Methods: Characterization of cysteine-charged sulfolink resin.” Chromatography was performed as described above up until the elution step. To elute, 500 µL of elution buffer was added to the resin for each sample, and the resin was incubated on ice for 2 minutes. The eluate was collected by centrifuging into a clean tube for 1 minute at 1,000 ×g. This elution step was repeated. The RNA from the eluate was then extracted using the TRIzol LS and chloroform protocol above and subsequently purified using a Zymo RNA Clean and Concentrator-5 kit.
Samples were then submitted to Novogene for poly(A) enrichment of transcripts and library preparation. Libraries were then sequenced by Novogene on a NovaSeq X Plus Series instrument with paired-end 150 base pair reads.

treatment_protocol: The old media was changed with the fresh mESC media 1 hour prior to harvest and then supplemented with 100 µg/mL cycloheximide (CHX; Sigma Aldrich, C7698-1G) for 3 minutes. Subsequently, the cells were trypsinized and pelleted down as described in the "Methods: RNA-seq analysis of cysteine-charged resin input and eluate samples (related to Figure S2)"

tag: cell line

value: mouse embryonic stem cells


title: E14 mESCs, sucrose cushion pellet, rep1


title: E14 mESCs, sucrose cushion pellet, rep3


title: E14 mESCs, RAPIDASH eluate, rep1


title: E14 mESCs, RAPIDASH eluate, rep3


title: WGBS_exp5_2TX-Control_1 WT BM Secondary

description: NovaSeq S4 300XP

value: Vav-Cre


title: LPS-Oct3

value: Spleen

value: spleen-derived monocytes

value: low-dose LPS priming followed by octanal administration (20 µM for 20 hours)


title: E14 mESCs, RAPIDASH eluate, rep2


title: WGBS_exp5_2TX-3a-R832A_1 3aR832 BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp5_2TX-3a-KO_1 3aKO BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp5_2TX-3a-KO_2 3aKO BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp5_2TX-3a-E752A_1 3aE752 BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp5_2TX-3a-Het_1 3aHET BM Secondary

description: NovaSeq S4 300XP


title: WGBS_Exp4_Control_rep4 WT KSL Primary

description: NovaSeq S4 300XP

source_name: KSL

value: Primary

value: KSL


title: WGBS_exp5_2TX-3a-E752A_2 3aE752 BM Secondary

description: NovaSeq S4 300XP


title: WGBS_Exp4_3aR832A_rep4 3aR832 KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp4_3aR832A_rep1 3aR832 KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp4_3aKO_rep1 3aKO KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp4_3aKO_rep4 3aKO KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp4_3aHET_rep3 3aHET KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp4_3aE752A_rep4 3aE752 KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp4_3aHET_rep1 3aHET KSL Primary

description: NovaSeq S4 300XP


title: WGBS_exp5_2TX-3a-R832A_2 3aR832 BM Secondary

description: NovaSeq S4 300XP


title: WGBS_Exp4_3aE752A_rep3 3aE752 KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp4_3aE752A_rep1 3aE752 KSL Primary

description: NovaSeq S4 300XP


title: WGBS_exp3_2ndTX-R832A_rep1 3aR832 BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp5_2TX-3a-Het_2 3aHET BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp3_2ndTX-Het_rep2 3aHET BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp3_2ndTX-R832A_rep2 3aR832 BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp3_2ndTX-KO_rep1 3aKO BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp3_2ndTX-Het_rep1 3aHET BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp3_2ndTX-Control_rep1 WT BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp3_2ndTX-E752A_rep2 3aE752 BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp3_2ndTX-Control_rep2 WT BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp3_2ndTX-KO_rep2 3aKO BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp3_1stTX-E752A 3aE752 KSL Primary

description: NovaSeq S4 300XP


title: WGBS_exp3_1stTX-KO 3aKO KSL Primary

description: NovaSeq S4 300XP


title: WGBS_exp3_2ndTX-E752A_rep1 3aE752 BM Secondary

description: NovaSeq S4 300XP


title: WGBS_exp3_1stTX-Het 3aHET KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp4_3aKO_rep3 3aKO KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp4_Control_rep1 WT KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp4_3aHET_rep4 3aHET KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp2_KO_plus_WT 3aKO BM Primary

description: NovaSeq S4 300XP

value: Retrovirus


title: PBMC, Control Patient 1

status: Public on Sep 11 2024

city: New York

first: Justin

middle: J

last: Frere

state: NY

address: Alexandria Center for Life Sciences, West Tower, 430 E 29th St.

department: Microbiology

institute: NYU Langone Health

data_processing:
Samples were uplaoded to Illumina Basespace and aligned to either the Mesocricetus Auratus MesAur1.0 genome or Homo Sapiens GRCH38 as appropriate using the RNA Sequence Alignment application. The alignment was conducted using the Salmon alignment tool. The resulting quantifications of alignment were either utilized directly for analysis or were further processed using DESeq2.
Assembly: MesAur1.0; GRCH38
Supplementary files format and content: Salmon Files

organism: Homo sapiens

source_name: Peripheral Blood Mononuclear Cells

extract_protocol:
PBMCs were isolated from whole blood using Ficoll gradient and frozen in -80C. Frozen PBMC aliquots were thawed dropwise using 37C T-cell media. After thawing, PBMC were then incubated at 37C and 5% CO2 for 24 hours in tissue-culture treated 96 well plates in 250 uL of T-cell media. RNA was isolated using the Arcturus PicoPure RNA Isolation Kit per protocol (Life Technologies)
Libraries were poly-A enriched and constructed using TruSeq PolyA kits

value: Peripheral Blood Mononuclear Cells

tag: condition

value: Control

tag: timepoint


title: WGBS_Exp2_KO_plus_EV 3aKO BM Primary

description: NovaSeq S4 300XP


title: WGBS_exp3_1stTX-Control WT KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp2_KO_plus_E752A 3aKO BM Primary

description: NovaSeq S4 300XP


title: WGBS_Exp1_2-3A WT KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp2_WT_plus_EV 3aKO BM Primary

description: NovaSeq S4 300XP


title: WGBS_Exp2_KO_plus_V712G 3aKO BM Primary

description: NovaSeq S4 300XP


title: WGBS_Exp1_3-3L WT KSL Primary

description: NovaSeq S4 300XP


title: WGBS_Exp2_KO_plus_R832A 3aKO BM Primary

description: NovaSeq S4 300XP


title: WGBS_exp3_1stTX-R832A 3aR832 KSL Primary

description: NovaSeq S4 300XP


title: Ezh2-Y641F,activated,RNA-seq rep3

city: Berkeley

first: Janneke

last: Peeters

address: University Avenue and Oxford St

institute: University of California Berkeley

description:
Y641F_D4_r3
100 bp
Y641FD4_vs_Y641FN.tsv

data_processing:
Transcripts were quantified using Salmon (v1.9.0) with transcript definitions from ENSEMBL (release 102, Mus_musculus.GRCm38.cdna.all.fa.gz)
Salmon quantification was used directly in DESeq2 with four groups (three replicates each): naïve Ezh2WT, naïve Ezh2Y641F, activated Ezh2WT, and Ezh2Y641F Treg cells 116.
We then performed all six possible pairwise comparisons between the four groups to identify genes with significant log2 foldchange (adjusted p-value < 0.05). This superset of significantly changing genes was used in downstream analyses.
Assembly: mm10
Supplementary files format and content: DESeq2 output files for genes with significant log2 foldchange (adjusted p-value <0.05) and file containing superset of significantly changing genes
Supplementary files format and content: the rld_sig_up.txt" file with rlog normalized count data

source_name: Lymph node and spleen

extract_protocol:
RNA was extracted using the RNAeasy Micro kit (Qiagen) according to manufacturer’s instructions
Libraries were prepared using KAPAmRNA HyperPrep Kitaccording to manufacturer’s instructions with the following specifications. 120 ng RNA was used as starting material, mRNA fragmentation was performed for 7 minutes at 94 °C, 1.5 μM xGEN UDI-UMI adapters (Integrated DNA Technologies) were used for adapter ligation, and adapter-ligated libraries were amplified for 13 cycles.

treatment_protocol: For activation, Treg cells were cultured for 4 days with anti-CD3 and anti-CD28 coated beads at a ratio of 1:3 (cell:bead) in the presence of 2000 IU/mL recombinant human IL-2

value: Lymph node and spleen

value: Treg cell

value: activated (in vitro)


title: Ezh2-Y641F,activated,RNA-seq rep1

description:
Y641F_D4_r1
100 bp
Y641FD4_vs_Y641FN.tsv


title: Ezh2-Y641F,naïve,RNA-seq rep3

description:
Y641F_N_r3
100 bp
WTN_vs_Y641FN.tsv

value: naïve


title: WT,naïve, RNA-seq rep2

description:
WT_N_r2
100 bp
WTN_vs_Y641FD4.tsv

value: WT


title: Ezh2-Y641F,activated,RNA-seq rep2

description:
Y641F_D4_r2
100 bp
Y641FD4_vs_Y641FN.tsv


title: WT,naïve, RNA-seq rep3

description:
WT_N_r3
100 bp
WTN_vs_Y641FD4.tsv


title: Ezh2-Y641F,naïve,RNA-seq rep2

description:
Y641F_N_r2
100 bp
WTN_vs_Y641FN.tsv


title: Teff,activated,IgG

description:
150 bp
IgGTeff_A.bw

data_processing:
*library strategy: CUT&RUN
Sequencing reads were  trimmed using Cutadapt: Illumina adapter sequences were removed and reads trimmed to 140 bp. Reads less than 35 bp were discarded.
Trimmed reads were aligned to the mm10 version of Mus musculus genome using bowtie2.
Samtools and bedtools were used to process aligned reads from sam to bed files.
Coverage at 100 bp windows genome-wide was calculated as the number of reads that mapped at that window, normalized by the factor N:  N = 10,000/(Total number of spike-in reads) 10,000 was a number chosen arbitrarily. The spike-in normalized read counts were then smoothed with a running average spanning +/- 1000 bp around each 100 bp bin.
The distribution of normalized read counts in 100 bp windows genome-wide was generated and stored as a bigWig file
Assembly: mm10
Supplementary files format and content: The distribution of normalized read counts in 100 bp windows genome-wide was generated and stored as a bigWig file

extract_protocol:
Cells were immobilized on Con A beads (Bangs Laboratories) and permeabilized with wash buffer containing 0.01% w/v Digitonin (Sigma-Aldrich). Cells were incubated rotating for 2 hr at 4°C with 1 uL anti-tri-methyl-histone H3 (Lys27) (C36B11, Cell Signaling Technology) or normal rabbit IgG (#2729, Cell Signaling Technologies). Permeabilized cells were washed and incubated with pA-MNase (kindly provided by the Henikoff lab) at a concentration of 700 ng/mL for 10 min at room temperature, while rotating. After washing, cells were incubated at 0°C and MNase digestion was initiated by adding 2 mM CaCl2. After 30 min, the reaction was stopped by the addition of EDTA and EGTA and 2 pg/mL DNA from Saccharomyces cerevisiae micrococcal nuclease-treated chromatin (kindly provided by the Henikoff lab) was added ad spike-in DNA for calibration. Chromatin fragments were released by incubation at 37°C for 10 min, purified by overnight proteinase K digestion at a concentration of 150 μg/mL with 0.1% wt/vol SDS at 55°C. DNA was purified by phenol/chloroform extraction followed by PEG-8000 precipitation (final concentration of 20% wt/vol) using Sera-mag SpeedBeads (Fisher).
Libraries were prepared using the NEBNext Ultra II DNA library prep kit for Illumina (New England Biolabs) according to manufacturer’s instructions with the following specifications and modifications. The entire preparation of purified CUT&RUN fragments from a reaction were used to create libraries. NEBNext adaptor for Illumina from NEBNext Multiplex Oligos for Illumina (New England Biolabs) was diluted 25-fold in TBS buffer. Size selection was performed with AmpureXP beads (Agencourt), adding 0.4 X volumes to remove large fragments, after which supernatant was recovered and 0.6 X volumes of AmpureXP beads and 0.6 X volumes of PEG-8000 (20% wt/vol PEG-8000, 2.5 M NaCl) were added for recovery of smaller fragments. Adapter-ligated libraries were amplified for 15 cycles using NEBNext Ultra II Q5 Master Mix using the universal primer and an indexing primer provided with the NEBNext Multiplex Oligos for Illumina. Amplified libraries were further purified with the addition of 1.1 X volumes of AmpureXP beads to remove adapter dimer and eluted in 25 μL H2O.

value: CD4+ T effector cell

value: IgG (2729, Cell Signaling Technologies)


title: WT,activated,RNA-seq rep3

description:
WT_D4_r3
100 bp
WTD4_vs_Y641FN.tsv


title: WT,activated,RNA-seq rep1

description:
WT_D4_r1
100 bp
WTD4_vs_Y641FD4.tsv


title: Ezh2-Y641F,naïve,RNA-seq rep1

description:
Y641F_N_r1
100 bp
WTN_vs_Y641FN.tsv


title: Teff,activated,rep4

description:
150 bp
Teff_A.bw

value: H3K27me3 (C36B11, Cell Signaling Technology)


title: WT,activated,RNA-seq rep2

description:
WT_D4_r2
100 bp
WTD4_vs_WTN.tsv


title: WT,naïve, RNA-seq rep1

description:
WT_N_r1
100 bp
WTN_vs_Y641FN.tsv


title: Teff,naive,IgG

description:
150 bp
IgGTeff_N.bw


title: Teff,activated,rep3

description:
150 bp
Teff_A.bw


title: Teff,activated,rep1

description:
150 bp
Teff_A.bw


title: Teff,activated,rep2

description:
150 bp
Teff_A.bw


title: Teff,naïve, rep3

description:
150 bp
Teff_N.bw


title: Teff,naïve, rep4

description:
150 bp
Teff_N.bw


title: Teff,naïve, rep1

description:
150 bp
Teff_N.bw


title: Teff,naïve, rep2

description:
150 bp
Teff_N.bw


title: WGBS_Exp1_1-EV WT KSL Primary

description: NovaSeq S4 300XP


title: WT,naive,IgG

description:
150 bp
IGG_N.bw


title: Ezh2-Y641F,naïve,rep3

description:
150 bp
Ezh2-Y641F_N.bw


title: Ezh2-Y641F,activated,rep2

description:
150 bp
Ezh2-Y641F_A.bw


title: Ezh2-Y641F,naïve,rep2

description:
150 bp
Ezh2-Y641F_N.bw


title: Ezh2-Y641F,activated,rep1

description:
150 bp
Ezh2-Y641F_A.bw


title: Ezh2-Y641F,activated,rep3

description:
150 bp
Ezh2-Y641F_A.bw


title: WT,naïve, rep3

description:
150 bp
WT_A.bw


title: WT,activated,rep1

description:
150 bp
WT_N.bw


title: WT,activated,rep2

description:
150 bp
WT_N.bw


title: WT,activated,rep3

description:
150 bp
WT_N.bw


title: WT,naïve, rep1

description:
150 bp
WT_A.bw


title: XEN cells, Ctcf-degron, dTAG treated, RNA, rep1

city: Beijing

first: Zhenhai

last: Du

address: Qinghua Yuan, Haidian District

institute: Tsinghua University

data_processing:
Illumina Casava1.8 software was used for basecalling.
All reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then mapped to mm9 genome by HISAT2 (v.2.2.0) (Kim et al., 2019) under the parameters –dta --no-softclip.
The gene expression level was calculated by StringTie (v.2.1.1) (Pertea et al., 2015) using the refFlat database from the UCSC genome browser.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each allele of WT and mutant XEN cells

source_name: XEN

growth_protocol: XEN cells were cultured on 0.1% gelatin precoated dishes in MEM α medium (Invitrogen, #12561) containing 20% FBS (Invitrogen, #10439), 100mM Sodium Pyruvate (Invitrogen, #11360), 50ug/ml penicillin-streptomycin (Hyclone, #SV30010), 100uM β-mercaptoethanol (Sigma, #M6250) and 1x nonessential amino acids (Invitrogen, #11140). Cells were cultured at 37℃ at 5% CO2.

extract_protocol:
Cells were lysed in lysis buffer (0.2% (vol/vol) Triton X-100 and 2 U/μl RNase inhibitor). The polyadenylated mRNAs were captured by the oligodT primers,
mRNAs were subjected to the Smart-seq2 protocol as described previously (Picelli et al., 2014).

value: XEN

value: extraembryonic endoderm stem cells

value: 129S1/SvImj X JF1/Ms

value: Ctcf degron

value: dTAG 48hrs


title: XEN cells, Ctcf-degron, dTAG treated, RNA, rep2


title: XEN cells, Ctcf-degron, DMSO treated, RNA, rep1

value: DMSO 48hrs


title: XEN cells, Ctcf-degron, dTAG treated, rep2

data_processing:
Illumina Casava1.8 software was used for basecalling.
Hi-C reads were processed using HiCPro v2.11.1 and replicates of same stage were pooled together
Cmpartment and TAD analysis were done with  cooltools (v0.3.2) (Venev et al., 2020)
Hi-C data was visulalized with Juicebox (v1.11.08) (Durand et al., 2016)
Assembly: mm9
Supplementary files format and content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature (RT) for 10 min. Formaldehyde was then quenched with glycine for 10 min at RT.
sisHi-C libraries were produced as previously described (Du et al., 2017). Crosslinked embryos were washed with 1 × PBS and lysed in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 0.1mM EDTA, 0.5% NP-40 and proteinase inhibitor) on ice for 50 min, the chromatin was solubilized with 0.5% SDS at 62 °C for 5 min. The nuclei were digested with MboI at 37 °C overnight. After fill-in with biotin-14-dCTP (Invitrogen, #19518018), the fragments were ligated in a small volume. Reversal of cross-linking, DNA purification, and sonication were done sequentially. The biotin-labeled DNA was then pulled down with Dynabeads MyOne Streptavidin C1 (Thermo Fisher, #65001). The fragments that included a ligation junction were subjected to Illumina library preparation. 9-15 cycles of PCR amplification were performed with Kapa HiFi PCR mix (Roche, #KK2602), and the products were purified and size-selected with AMPure XP beads (Beckman Coulter, #A63881).


title: XEN cells, Ctcf-degron, DMSO treated, rep2


title: XEN cells, Rad21-degron, dTAG treated 8h, H3K27ac, clone1, rep1

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequencing reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then aligned to mm9 reference genome with random chromosome cleaned by Bowtie2 (version 2.3.4.1) under the parameters -t -q -N 1 -L 25 -X 700 --no-unal --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
Sequencing reads were assigned to two alleles with SNPsplit (v0.3.2) (Krueger and Andrews, 2016)
We normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome.
bigWig files were visualized with UCSC genome browser
Assembly: mm9
Supplementary files format and content: bigWig

growth_protocol: Cells were cultured on 0.1% gelatin precoated dishes in DMEM (Gibco, Cat #11995-073) containing 10% NBCS (Gibco, #16010159), 0.1 mM β-mercaptoethanol (Sigma, #M6250) and 50ug/ml penicillin-streptomycin (Hyclone, #SV30010). Cells were cultured at 37C at 5% CO2.

extract_protocol:
STAR ChIP-seq was performed as previously described (Zhang et al., 2021; Zhang et al., 2016). Briefly, cells were first lysed and then subjected to MNase digestion by incubating with MNase working buffer (50 mM Tris-HCl pH 8.0, 1 mM CaCl2 and 0.2% Triton X-100) containing diluted MNase (Sigma, #N3755-200UN) at 37 °C for exact 5 min. The reaction was terminated by stop buffer (110 mM Tris-HCl pH 8.0 and 55 mM EDTA). After adding cold 2× RIPA buffer (1.8% Triton X-100, 280 mM NaCl, 0.2% SDS, 0.2% sodium deoxycholate (DOC), 5 mM EGTA and proteinase inhibitor) and spinning at max speed in 4 °C for 10 min, the soluble chromatin containing supernatant was incubated with 1mg H3K27ac antibody (ActiveMotif, #39133) in RIPA buffer (10 mM Tris-HCl pH 8.0, 140 mM NaCl, 1% Triton X-100, 0.1% SDS, 0.1% DOC, 1 mM EDTA and proteinase inhibitor) at 4°C overnight with rotation. Protein A/G dynabeads (Thermo Fisher Scientific) were used to bind the antibody at 4°C for 2 to 3 hours with rotation. The beads were then washed five times with RIPA buffer and once with LiCl buffer (10 mM Tris-HCl pH 8.0, 250mM LiCl, 1 mM EDTA, 0.5% NP-40 and 0.5% DOC). Beads bound chromatin were then digested with proteinase K (NEB, #P8107S) at 55°C for 90 min, followed by incubation at 72°C for 40 min to inactivate the proteinase K.
STAR ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645S)  following manufacturer's protocols. The libraries were purified and size-elected with AMPure XP beads (Beckman Coulter, #A63881).

value: dTAG 8hrs

tag: chip antibody

value: H3K27ac (ActiveMotif, #39133)


title: XEN cells, Ctcf-degron, dTAG treated, H3K27ac, rep2


title: XEN cells, Ctcf-degron, DMSO treated, H3K27ac, rep2


title: WT,activated,IgG

description:
150 bp
IGG_A.bw


title: XEN cells, Rad21-degron, DMSO treated 8h, H3K27ac, clone1, rep2

value: DMSO 8hrs


title: XEN cells, Rad21-degron, DMSO treated 8h, H3K27ac, clone1, rep1


title: Ezh2-Y641F,naïve,rep1

description:
150 bp
Ezh2-Y641F_N.bw

value: Lymph node and spleen


title: XEN cells, Ctcf-degron, DMSO treated, H3K27ac, rep1


title: XEN cells, Ctcf-degron, DMSO treated, RNA, rep2


title: XEN cells, Ctcf-degron, dTAG treated, H3K27ac, rep1


title: XEN cells, Ctcf-degron, dTAG treated, rep1


title: XEN cells, Rad21-degron, dTAG treated 8h, H3K27ac, clone1, rep2


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo13

data_processing:
Illumina Casava1.8 software was used for basecalling.
All reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then mapped to mm9 genome by HISAT2 (v.2.2.0) (Kim et al., 2019) under the parameters –dta --no-softclip.
The gene expression level was calculated by StringTie (v.2.1.1) (Pertea et al., 2015) using the refFlat database from the UCSC genome browser.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each stage of embryos with replicates merged.

source_name: extraembryonic ectoderm

extract_protocol:
Embryos were lysed in lysis buffer (0.2% (vol/vol) Triton X-100 and 2 U/μl RNase inhibitor). The polyadenylated mRNAs were captured by the oligodT primers,
mRNAs were subjected to the Smart-seq2 protocol as described previously (Picelli et al., 2014).

value: extraembryonic ectoderm

value: Eedfl/fl;Gdf9-Cre X WT PWK/PhJ

value: EedmNull


title: XEN cells, Ctcf-degron, DMSO treated, rep1


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo10


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo11


title: WT,naïve, rep2

description:
150 bp
WT_A.bw

value: Treg cell

value: WT

value: naïve


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo8


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo6


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo5


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo4


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo7


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo3


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo2


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo12


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo6

data_processing:
Illumina Casava1.8 software was used for basecalling.
Hi-C reads were processed using HiCPro v2.7.1b and replicates of same stage were pooled together
Cmpartment and TAD analysis were done with  cooltools (v0.3.2) (Venev et al., 2020)
Hi-C data was visulalized with Juicebox (v1.11.08) (Durand et al., 2016)
Assembly: mm9
Supplementary files format and content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

extract_protocol:
Embryos were cross-linked with 1% formaldehyde at room temperature (RT) for 10 min. Formaldehyde was then quenched with glycine for 10 min at RT.
sisHi-C libraries were produced as previously described (Du et al., 2017). Crosslinked embryos were washed with 1 × PBS and lysed in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 0.1mM EDTA, 0.5% NP-40 and proteinase inhibitor) on ice for 50 min, the chromatin was solubilized with 0.5% SDS at 62 °C for 5 min. The nuclei were digested with MboI at 37 °C overnight. After fill-in with biotin-14-dCTP (Invitrogen, #19518018), the fragments were ligated in a small volume. Reversal of cross-linking, DNA purification, and sonication were done sequentially. The biotin-labeled DNA was then pulled down with Dynabeads MyOne Streptavidin C1 (Thermo Fisher, #65001). The fragments that included a ligation junction were subjected to Illumina library preparation. 9-15 cycles of PCR amplification were performed with Kapa HiFi PCR mix (Roche, #KK2602), and the products were purified and size-selected with AMPure XP beads (Beckman Coulter, #A63881).


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo3


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo1


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo13


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo7


title: MEF cells, PWK-Xi, NIPBL, rep2

description: nipbl pwkXi mef female rep2

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequencing reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then aligned to mm9 reference genome with random chromosome cleaned by Bowtie2 (version 2.3.4.1) under the parameters -t -q -N 1 -L 25 -X 700 --no-unal --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
Sequencing reads were assigned to two alleles with SNPsplit (v0.3.2) (Krueger and Andrews, 2016)
We normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome.
bigWig files were visualized withUCSC genome browser
Assembly: mm9
Supplementary files format and content: bigWig
Library strategy: CUT&RUN

source_name: immortal MEF

growth_protocol: Immortal MEF cells were cultured on 0.1% gelatin precoated dishes in DMEM (Gibco, Cat #11995-073) containing 10% NBCS (Gibco, #16010159), 0.1 mM β-mercaptoethanol (Sigma, #M6250) and 50ug/ml penicillin-streptomycin (Hyclone, #SV30010). Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were first resuspended in washing buffer (20mM HEPES-KOH pH 7.5, 150mM NaCl, 0.5mM spermidine and protease inhibitor) and then bound to the Concanavalin-coated magnetic beads (Polyscience, #86057) in binding buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM CaCl2 and 1mM MnCl2). The samples were incubated in antibody buffer (washing buffer plus 0.005%~0.01% digitonin and 2mM EDTA) with antibody diluted at ratio of 1:100 at 4°C on Thermomixer for 3 hrs at 300 rpm. Beads were then washed and incubated with protein A-MNase (pA-MNase) (to a final concentration of 400 to 700 ng/ml) at 4°C for 1-3 hrs on a thermomixer at 300 rpm. Targeted chromatin was digested for 30 min on ice after adding 2 ml of 100 mM CaCl2. The reaction was then terminated with 2× stop buffer (340mM NaCl, 20mM EDTA\, 4mM EGTA, 50μg/mL RNase A, 100μg/mL glycogen and 0.005%~0.01% digitonin). Samples were then incubated at 37°C for 20 min to release the targeted fragment.
CUT&RUN libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645S)  following manufacturer's protocols. The libraries were purified and size-elected with AMPure XP beads (Beckman Coulter, #A63881).

value: mouse embryonic fibroblast cells

value: immortal MEF

value: C57BL/6N X PWK/PhJ

value: NIPBL  (Bethyl laboratories, #A301-779A)


title: CUT&RUN XEN cells, NIPBL, WT, rep1

description: nipbl wt xen rep1

source_name: extraembryonic endoderm stem cells

value: XEN

value: extraembryonic endoderm stem cells

value: 129S1/SvImj X JF1/Ms


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo12


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo5


title: cKO_vehicle2, replicate 2, ATACseq

city: Philadelphia

first: Juan

middle: M.

last: Inclan-Rico

state: PA

address: 3800 Spruce St

department: Pathobiology

institute: University of Pennsylvania, School of Veterinary Medicine

data_processing:
FASTQ filese were checked with FASTQC v 0.11.9 (www.bioinformatics.babraham.ac.uk/projects) and sequence reads were trimmed for adaptor sequence with trimmomatic-0.39
Trimmed sequence reads were mapped to mm10 using R subread  version 2.10.1 R package. The mitochondrial reads  and  PCR duplicates were removed using SAMtools version 1.13 for the downstream analysis. The reads with high alignments (MAPQ score >30) .
Peak calling were performed using MACS2  v.2.7.4 with piling up of paired-end fragment mode (--format BAMPE).
bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate. narrowPeak files were generated using MACS v2 with default settings.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
Bone marrow (BM) cells from the femur and tibia were isolated and red blood cells were lysed. BM cells were cultured in DMEM-F12 media supplemented with 10%FBS and 20% supernatant derived from CMG14-12 (M-CSF producing) cell line for 5-7 days prior to experiments. BMDM polarization was assessed by cell morphology and later confirmed by cell surface expression of CD64, F4/80, CD11b, and CD11c
Libraries from cells were prepared using the Illumina Tagment DNA Enzyme and Buffer Small Kit (Ilumina) according to manufacturer’s protocol. Sequencing was performed using a third-party company (Novogene).

value: CD11c-specific IL-33KO

value: Illumina Tagment DNA Enzyme


title: MEF cells, PWK-Xi, NIPBL, rep1

description: nipbl pwkXi mef female rep1


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo1


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo9


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo10


title: WT_Vehicle, replicate 1, ATACseq

value: CD11c control


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo2


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo4


title: cKO_vehicle2, replicate 1, ATACseq


title: cKO_vehicle1, replicate 2, ATACseq


title: CD11CCRE, scRNAseq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Abdominal skin

extract_protocol:
Abdominal skin-resident myeloid cells from control or CD11-IL-33KO mice were sort-purified as Live CD45+ MHC-II+ CD11c+ cells using an BD FACS Aria II sorter. Sort-purified cells were resuspended in PBS supplemented with 10%FBS to achieve a target cell concentration of 700 to 1200 cells per μl. Cell viability was determined by trypan blue exclusion and only samples with >85% viability were processed.
Next-generation sequencing libraries were prepared using the 10x Genomics Chromium Single Cell 3’ Reagent kit v3 (10X Genomics) per manufacturer’s instructions. Libraries were uniquely indexed using the Chromium dual Index Kit, pooled, and sequenced on an Illumina NovaSeq 6000 sequencer in a paired-end, dual indexing run. Sequencing for each library targeted 20,000 mean reads per cell

value: CD45+ MHC-II+ CD11c+ cells

value: Abdominal skin

tag: gender

value: male

tag: age


title: RNA-seq Morula, Xp XRRa KO, female, rep4

data_processing:
Illumina Casava1.8 software was used for basecalling.
All reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then mapped to mm9 genome by HISAT2 (v.2.2.0) (Kim et al., 2019) under the parameters –dta --no-softclip.
The gene expression level was calculated by StringTie (v.2.1.1) (Pertea et al., 2015) using the refFlat database from the UCSC genome browser.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include FPKM values for each genotypes of embryos with replicates merged.

source_name: Morula embryo

value: Morula embryo

value: Xp XRRa KO


title: cKO_vehicle1, replicate 1, ATACseq


title: CD11CCREIL33KO, scRNAseq

description: 10x Genomics


title: E7.5 extraembryonic ectoderm, EedmNull, female, RNA, embryo9

value: extraembryonic ectoderm

value: Eedfl/fl;Gdf9-Cre X WT PWK/PhJ

value: EedmNull


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo11


title: RNA-seq Morula, Xp XRRa KO, female, rep3


title: CUT&RUN E6.5 visceral endoderm, female, NIPBL, rep1

description: nipbl E6.5 VE female rep1

source_name: visceral endoderm

extract_protocol:
Embryos were first resuspended in washing buffer (20mM HEPES-KOH pH 7.5, 150mM NaCl, 0.5mM spermidine and protease inhibitor) and then bound to the Concanavalin-coated magnetic beads (Polyscience, #86057) in binding buffer (20mM HEPES-KOH pH7.9, 10mM KCl, 1mM CaCl2 and 1mM MnCl2). The samples were incubated in antibody buffer (washing buffer plus 0.005%~0.01% digitonin and 2mM EDTA) with antibody diluted at ratio of 1:100 at 4°C on Thermomixer for 3 hrs at 300 rpm. Beads were then washed and incubated with protein A-MNase (pA-MNase) (to a final concentration of 400 to 700 ng/ml) at 4°C for 1-3 hrs on a thermomixer at 300 rpm. Targeted chromatin was digested for 30 min on ice after adding 2 ml of 100 mM CaCl2. The reaction was then terminated with 2× stop buffer (340mM NaCl, 20mM EDTA\, 4mM EGTA, 50μg/mL RNase A, 100μg/mL glycogen and 0.005%~0.01% digitonin). Samples were then incubated at 37°C for 20 min to release the targeted fragment.
CUT&RUN libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645S)  following manufacturer's protocols. The libraries were purified and size-elected with AMPure XP beads (Beckman Coulter, #A63881).

value: visceral endoderm


title: RNA-seq Morula, Xp XRRa KO, female, rep2

value: C57BL/6N X PWK/PhJ


title: E7.5 extraembryonic ectoderm, EedmNull, female, embryo8


title: RNA-seq Morula, Xp XRRa KO, female, rep1


title: RNA-seq Morula, control, female, rep3

value: wild type


title: RNA-seq Morula, control, female, rep1


title: RNA-seq Morula, control, male, rep3


title: DNA Morula, Xp XRRa KO, female, rep2

data_processing:
Illumina Casava1.8 software was used for basecalling.
Sequencing reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then aligned to mm9 reference genome with random chromosome cleaned by Bowtie2 (version 2.3.4.1) under the parameters -t -q -N 1 -L 25 -X 700 --no-unal --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
Sequencing reads were assigned to two alleles with SNPsplit (v0.3.2) (Krueger and Andrews, 2016)
We normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome.
bigWig files were visualized withUCSC genome browser
Assembly: mm9
Supplementary files format and content: bigWig

extract_protocol:
DNA from one part of each morula embryo was first amplified with a Discover-sc single cell WGA kit (Vazyme, #N603-01). The amplified DNA was then used for genomic DNA libraries.
Genomic DNA libraries were prepared with TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme, #TD502)  following manufacturer's protocols. The libraries were purified and size-elected with AMPure XP beads


title: DNA Morula, Xp XRRa KO, female, rep3


title: DNA Morula, Xp XRRa KO, female, rep1


title: CUT&RUN E6.5 visceral endoderm, reciprocal cross, female,  CTCF, rep1

value: PWK/PhJ X C57BL/6N

value: CTCF (Active motif, #61311)


title: DNA Morula, control, female, rep3


title: DNA Morula, control, male, rep1


title: RNA-seq Morula, control, male, rep4


title: DNA Morula, Xp XRRa KO, female, rep4


title: RNA-seq Morula, control, male, rep2


title: CUT&RUN XEN cells, XRRa KO, SMC3, rep2

data_processing:
library strategy: CUT&RUN
Illumina Casava1.8 software was used for basecalling.
Sequencing reads were first processed by TrimGalore (v.0.6.4) with default parameters to remove the reads of low quality and also the adapters.
The filtered reads were then aligned to mm9 reference genome with random chromosome cleaned by Bowtie2 (version 2.3.4.1) under the parameters -t -q -N 1 -L 25 -X 700 --no-unal --no-mixed --no-discordant. All unmapped reads, non-uniquely mapped reads, reads with low mapping quality (MAPQ < 20) and PCR duplicates were removed.
Sequencing reads were assigned to two alleles with SNPsplit (v0.3.2) (Krueger and Andrews, 2016)
We normalized the read counts by computing the numbers of reads per kilobase of bin per million of reads sequenced (RPKM) for 100-bp bins of the genome.
bigWig files were visualized withUCSC genome browser
Assembly: mm9
Supplementary files format and content: bigWig

value: XEN

value: extraembryonic endoderm stem cells

value: 129S1/SvImj X JF1/Ms

value: SMC3 (Abcam, #ab9263)


title: DNA Morula, control, male, rep3


title: DNA Morula, control, female, rep1


title: DNA Morula, control, male, rep2


title: CUT&RUN XEN cells, XRR KO, SMC3, clone2, rep1


title: CUT&RUN XEN cells, XRR KO, SMC3, clone1, rep1


title: DNA Morula, control, female, rep2


title: CUT&RUN XEN cells, XRRa KO, SMC3, rep1


title: RNA-seq Morula, control, male, rep1


title: CUT&RUN E6.5 visceral endoderm, reciprocal cross, female,  SMC3, rep1


title: RNA-seq Morula, control, female, rep2


title: CUT&RUN XEN cells, SMC3, WT, rep2


title: CUT&RUN XEN cells, XistpA, SMC3, rep1


title: CUT&RUN XEN cells, XRRa KO, CTCF, rep2


title: CUT&RUN XEN cells, XRR KO, CTCF, clone2, rep1


title: DNA Morula, control, male, rep4


title: CUT&RUN XEN cells, XRRa KO, CTCF, rep1


title: Post_Covid_6Months_BIS95

type: genomic

city: Cusano Milanino

first: Luciano

last: Calzari

state: MI

address: Via Zucchi 18

country: Italy

institute: IRCCS Istituto Auxologico Italiano

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation 850K EPIC Beadchip using standard Illumina protocol

scan_protocol: Fluorescence intensities were captured by using the fluorescent scanner Illumina HiScan SQ (Illumina).

data_processing:
Quality control, pre-processing and generation of β-values matrix were performed by using the ChAMP package (release 2.32.0) package, implemented R environment (version 4.3.1): after the quality control/pre-processing step, 12777 probes with a detection p-value above 0.01, 5179 probes with a beadcount <3 in at least 5% of samples, 2875 NoCG probes, 94318 probes with potential SNPs, 11 probes that align to multiple locations, and 16424 probes located on X, Y chromosome were filtered out. 734334 probes and 96 samples were retained.
The 'Post_COVID_Matrix_Processed.txt' contains the normalized (BMIQ Quantile) average beta and ComBat adjustment (with controls) data.
The 'Post_COVID_Matrix_Signal_Intensities.txt' contains unmethylated and methylated signal intensities

label: Cy3, Cy5

source_name: Post_Covid_6Months_whole blood

label_protocol: Standard Illumina protocol

extract_protocol: DNA was extracted from peripheral blood lymphocytes of individuals (Automated Extractor, Tecan Group Ltd. and Wizard Genomic DNA Purification Kit (Ref: A1125), Promega). Quality control and quantification of DNA was assessed by visualization of genomic DNA (gDNA) on 1% agarose gel electrophoresis and by using NanoPhotometer Pearl (Implen GmbH).

tag: Sex

value: M


title: CUT&RUN XEN cells, XistpA, CTCF, rep3


title: CUT&RUN XEN cells, SMC3, WT, rep1


title: Post_Covid_6Months_BIS93


title: CUT&RUN XEN cells, XRR KO, CTCF, clone1, rep1


title: Post_Covid_6Months_BIS96


title: CUT&RUN XEN cells, XistpA, CTCF, rep1


title: Post_Covid_6Months_BIS94


title: Post_Covid_6Months_BIS89

value: F


title: CUT&RUN XEN cells, XRRc XiKO, H3K27me3, rep2


title: Post_Covid_6Months_BIS88


title: CUT&RUN XEN cells, XRRc XiKO, H3K27me3, rep1


title: CUT&RUN XEN cells, CTCF, WT, rep1


title: Post_Covid_6Months_BIS90


title: Post_Covid_6Months_BIS92


title: CUT&RUN XEN cells, XistpA, SMC3, rep3


title: CUT&RUN XEN cells, CTCF, WT, rep2


title: CUT&RUN XEN cells, XRRc XaKO, H3K27me3, rep2


title: Post_Covid_6Months_BIS86


title: Post_Covid_6Months_BIS85


title: CUT&RUN XEN cells, XRRb XiKO, H3K27me3, rep2


title: Post_Covid_6Months_BIS91


title: Post_Covid_6Months_BIS82


title: Post_Covid_6Months_BIS81


title: CUT&RUN XEN cells, XRRb XaKO, H3K27me3, rep2


title: Post_Covid_6Months_BIS83


title: Post_Covid_6Months_BIS84


title: CUT&RUN XEN cells, XRRa KO, H3K27me3, rep2


title: CUT&RUN XEN cells, XRRa KO, H3K27me3, rep1


title: CUT&RUN XEN cells, XRRb XaKO, H3K27me3, rep1


title: Post_Covid_6Months_BIS80


title: CUT&RUN XEN cells, XistpA, CTCF, rep2


title: CUT&RUN XEN cells, XRRb XiKO, H3K27me3, rep1


title: Post_Covid_6Months_BIS87


title: Post_Covid_6Months_BIS77


title: Post_Covid_6Months_BIS75


title: Post_Covid_6Months_BIS76


title: CUT&RUN XEN cells, XRR KO, H3K27me3, clone2, rep1


title: Post_Covid_6Months_BIS79


title: CUT&RUN XEN cells, XistpA, H3K27me3, rep2


title: CUT&RUN XEN cells, H3K27me3, WT, rep2


title: Post_Covid_6Months_BIS74


title: Post_Covid_6Months_BIS73


title: Post_Covid_6Months_BIS78


title: CUT&RUN XEN cells, XRR KO, H3K27me3, clone1, rep1


title: CUT&RUN XEN cells, XistpA, H3K27me3, rep3


title: CUT&RUN XEN cells, XRRc XaKO, H3K27me3, rep1


title: Post_Covid_6Months_BIS72


title: ChIP-seq XEN cells, Rad21-degron, dTAG treated, H3K27ac, clone1, rep2

value: dTAG 24hrs

value: H3K27ac (ActiveMotif, #39133)


title: Post_Covid_6Months_BIS71


title: CUT&RUN XEN cells, XistpA, H3K27me3, rep1


title: ChIP-seq XEN cells, Rad21-degron, dTAG treated, H3K27ac, clone1, rep1


title: CUT&RUN XEN cells, H3K27me3, WT, rep1


title: ChIP-seq XEN cells, Rad21-degron, DMSO treated, H3K27ac, clone1, rep2

value: DMSO 24hrs


title: Post_Covid_6Months_BIS67


title: Post_Covid_6Months_BIS65


title: ChIP-seq XEN cells, XRRa KO, H3K27ac, rep1


title: Post_Covid_6Months_BIS70


title: Post_Covid_6Months_BIS69


title: ChIP-seq XEN cells, XRR KO, H3K27ac, clone1, rep1


title: Post_Covid_6Months_BIS66


title: ChIP-seq XEN cells, XRR KO, H3K27ac, clone2, rep1


title: Post_Covid_6Months_BIS62


title: ChIP-seq XEN cells, XistpA, H3K27ac, rep1


title: ChIP-seq XEN cells, XistpA, H3K27ac, rep2


title: ChIP-seq XEN cells, Rad21-degron, DMSO treated, H3K27ac, clone1, rep1


title: Post_Covid_6Months_BIS61


title: Post_Covid_6Months_BIS60


title: Post_Covid_6Months_BIS64


title: Post_Covid_6Months_BIS63


title: Post_Covid_6Months_BIS59


title: ChIP-seq XEN cells, H3K27ac, WT, rep2


title: ChIP-seq XEN cells, H3K27ac, WT, rep1


title: RNA-seq XEN cells, Rad21-degron, dTAG treated, clone2, rep2

description:
rna_dmso_dtag_Rad21_degron_xen_merged_chrX_allelic_FPKM.txt.gz
rna dTAG Rad21 degron xen clone2 rep2

extract_protocol:
Cells were lysed in lysis buffer (0.2% (vol/vol) Triton X-100 and 2 U/μl RNase inhibitor). The polyadenylated mRNAs were captured by the oligodT primers,
RNA-seq (Smart-seq2): mRNAs were subjected to the Smart-seq2 protocol as described previously (Picelli et al., 2014).


title: RNA-seq XEN cells, Rad21-degron, dTAG treated, clone2, rep1

description:
rna_dmso_dtag_Rad21_degron_xen_merged_chrX_allelic_FPKM.txt.gz
rna dTAG Rad21 degron xen clone2 rep1


title: Post_Covid_6Months_BIS58


title: RNA-seq XEN cells, Rad21-degron, dTAG treated, clone1, rep2

description:
rna_dmso_dtag_Rad21_degron_xen_merged_chrX_allelic_FPKM.txt.gz
rna dTAG Rad21 degron xen clone1 rep2


title: RNA-seq XEN cells, Rad21-degron, dTAG treated, clone1, rep1

description:
rna_dmso_dtag_Rad21_degron_xen_merged_chrX_allelic_FPKM.txt.gz
rna dTAG Rad21 degron xen clone1 rep1


title: Post_Covid_6Months_BIS56


title: RNA-seq XEN cells, Rad21-degron, DMSO treated, clone2, rep1

description:
rna_dmso_dtag_Rad21_degron_xen_merged_chrX_allelic_FPKM.txt.gz
rna dmso Rad21 degron xen clone2 rep1


title: Post_Covid_6Months_BIS68


title: Post_Covid_6Months_BIS57


title: Post_Covid_6Months_BIS53


title: Post_Covid_6Months_BIS52


title: Post_Covid_6Months_BIS54


title: RNA-seq XEN cells, XRRc XiKO, rep2

description:
rna_xrrb_xrrc_ko_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrrc xiko xen rep2


title: Post_Covid_6Months_BIS51


title: Post_Covid_6Months_BIS55


title: ChIP-seq XEN cells, XRRa KO, H3K27ac, rep2


title: RNA-seq XEN cells, Rad21-degron, DMSO treated, clone1, rep1

description:
rna_dmso_dtag_Rad21_degron_xen_merged_chrX_allelic_FPKM.txt.gz
rna dmso Rad21 degron xen clone1 rep1


title: RNA-seq XEN cells, Rad21-degron, DMSO treated, clone1, rep2

description:
rna_dmso_dtag_Rad21_degron_xen_merged_chrX_allelic_FPKM.txt.gz
rna dmso Rad21 degron xen clone1 rep2


title: RNA-seq XEN cells, Rad21-degron, DMSO treated, clone2, rep2

description:
rna_dmso_dtag_Rad21_degron_xen_merged_chrX_allelic_FPKM.txt.gz
rna dmso Rad21 degron xen clone2 rep2


title: RNA-seq XEN cells, XRRc XaKO, rep1

description:
rna_xrrb_xrrc_ko_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrrc xako xen rep1


title: Post_Covid_6Months_BIS50


title: RNA-seq XEN cells, XRRb XiKO, rep1

description:
rna_xrrb_xrrc_ko_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrrb xiko xen rep1


title: Post_Covid_6Months_BIS48


title: Post_Covid_6Months_BIS49


title: RNA-seq XEN cells, XRRb XaKO, rep1

description:
rna_xrrb_xrrc_ko_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrrb xako xen rep1


title: RNA-seq XEN cells, XRRb XiKO, rep2

description:
rna_xrrb_xrrc_ko_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrrb xiko xen rep2


title: Post_Covid_6Months_BIS46


title: Post_Covid_6Months_BIS45


title: RNA-seq XEN cells, XRRb XaKO, rep2

description:
rna_xrrb_xrrc_ko_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrrb xako xen rep2


title: Post_Covid_6Months_BIS47


title: Post_Covid_6Months_BIS44


title: Post_Covid_6Months_BIS43


title: RNA-seq XEN cells, XRRc XiKO, rep1

description:
rna_xrrb_xrrc_ko_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrrc xiko xen rep1


title: RNA-seq XEN cells, XRRa KO, rep3

description:
rna_wt_xistpA_xrrko_xrrako_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrra ko xen rep3


title: Post_Covid_6Months_BIS42


title: RNA-seq XEN cells, XRRa KO, rep2

description:
rna_wt_xistpA_xrrko_xrrako_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrra ko xen rep2


title: RNA-seq XEN cells, XRRa KO, rep1

description:
rna_wt_xistpA_xrrko_xrrako_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrra ko xen rep1


title: Post_Covid_6Months_BIS41


title: RNA-seq XEN cells, XRR KO, clone2, rep1

description:
rna_wt_xistpA_xrrko_xrrako_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrr ko xen clone2 rep1


title: WT_IFN_BR1

city: Stanford

first: Benjamin

middle: Rosenstock

last: Doughty

state: CA

address: 279 Campus Drive W

institute: Stanford University

data_processing:
Hisat2-build was used to build a reference transcriptome with a FASTA of the GRCh38 human reference genome and the accompanying GTF genome annotation file, and hisat2 was used to align the paired reads to the reference.
Output SAM files were converted to BAM files using samtools and differential expression analysis was performed in R with the Bioconductor DESeq2 package
Assembly: hg38
Supplementary files format and content: Comma-separated file with results from DE-seq2

growth_protocol: Cell culture was performed as described in61. Briefly, all experiments were performed in K562 cells (female, ATCC CCL-243). Cells were cultured in a controlled humidified incubator at 37C and 5% CO2, in RPMI 1640 (Gibco, 11-875-119) media supplemented with 10% FBS (Omega Scientific, 20014T), and 1% Penicillin-Streptomycin-Glutamine (Gibco, 10378016).

extract_protocol:
Cells were lysed and homogenized using QIAshredder columns (Qiagen #79654) and RNA was extracted with the RNeasy Mini Kit (Qiagen #74104).
500 ng of purified RNA for each sample was enriched for polyadenylated mRNA with the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490) and then used as input for the NEBNext Ultra II RNA Library Prep Kit (NEB #E7770S). Sample preparation was performed as per manufacturer’s specifications, with nine PCR cycles used for final library amplifications.

treatment_protocol: All interferon induction was performed by adding 10 ng/mL IFN-ꞵ (Peprotech, 300-02BC) for 6 hours unless specifically noted otherwise.

value: 10 ng/mL IFNb 24hr


title: RNA-seq XEN cells, XRRc XaKO, rep2

description:
rna_xrrb_xrrc_ko_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrrc xako xen rep2


title: WT_noTX_BR2


title: RNA-seq XEN cells, XistpA, rep4

description:
rna_wt_xistpA_xrrko_xrrako_xen_merged_chrX_allelic_FPKM.txt.gz
rna xistpA xen rep4


title: WT_IFN_BR2


title: Post_Covid_6Months_BIS40


title: WT_noTX_BR1


title: Post_Covid_6Months_BIS39


title: L2496-Michaela_NoDox_Pol2_4H8_rep2

data_processing:
Sequencing reads were aligned against a custom genome index containing the hg38 version of the human genome, the reporter sequence, and the mm10 version of the mouse genome using Bowtie (version 1.0.1)74 with the following settings: “-v 2 -k 2 -m 1 -t --best --strata -q X 1000”.
Duplicate alignments were removed using the MarkDuplicates function in PicardTools (version 1.99).
Peaks were called using MACS2 (version 2.1.0)75 with default settings (“-g hs”).
Assembly: hg38, mm10
Supplementary files format and content: narrowpeak calls, bigwig (hg38), bigwig (mm10)

extract_protocol:
For each ChIP reaction, 2x10^7 cells were used as input together with a spike-in of mouse chromatin used for orthogonal normalization. Cells were crosslinked with 1% formaldehyde for 15 min at room temperature, followed by quenching in glycine (final concentration 0.125 M). Cells were then centrifuged, resuspended in 1xPBS, centrifuged again, and stored at -80C. On the first day of the ChIP procedure, 10 uL Protein A Dynabeads (Thermofisher 10002D) were added to DNA Lo-Bind tubes and washed three times on a magnetic rack with 1 mL mg/mL BSA. Beads were resuspended in 1 mL BSA, 5 ug anti-H3K27ac (Abcam ab4729) or anti-Pol2-S5P (Abcam ab5408) antibody were added, and the antibodies were coupled to the beads overnight on a rotor at 4 °C. On the second day, crosslinked chromatin was resuspended in 1 mL Farnham Lysis Buffer (FLB; 5 mM HEPES pH 8.0, 85 mM KCl, 0.5% NP-40/IGEPAL, Roche Protease Inhibitor Cocktail), centrifuged, then resuspended in 1 mL FLB and centrifuged again, then resuspended in 880 uL RIPA buffer (1x PBS, 1% NP-40, 0.5% Sodium deoxycholate, 0.1% SGS, Roche protease inhibitor cocktail), and sheared using Covaris E220 Focused-Ultrasonicator. Beads were washed again three times with 1 mL BSA on a magnetic rack, resuspended in 100 uL BSA, and the chromatin in RIPA buffer was added to them, then incubated overnight at 4 °C on a rotor. On the third day, beads were washed five times with LiCl buffer (10mM Tris pH 7.5, 500 mM LiCl, 1% NP-40, 1% Sodium deoxycholate) for 10 minutes on a rotator at 4 °C followed by removal of the buffer using a magnetic rack, then washed once with 1 mL 1x TE buffer, and resuspended in 200 uL IP elution buffer (1% SDS, 0.1 M NaHCO3). Chromatin was eluted off the beads by incubation at 65 °C followed by centrifugation at max speed for 3 minutes, and transfer to fresh DNA Lo-Bind tubes. Crosslinks were reversed by addition of 2 uL Proteinase K (Promega) and incubation at 65 °C for 12-16 hours in a Thermomixer. DNA was purified by adding an equal volume (200 uL) 25:24:1 Phenol:Chloroform:Isoamyl alcohol, vortexing, and centrifugation for 3 minutes at max speed. The top phase was then purified using the MinElute kit (Qiagen), eluting in 50 uL 55°C EB buffer.
Sequencing libraries were prepared using the NEBNext Ultra II kit (NEB E7645) following the manufacturer’s instructions.

treatment_protocol: All doxycycline induction was performed by adding 1,000 ng/mL doxycycline (Fisher Scientific, 409050) for 24 hours unless specifically noted otherwise. CBP/p300 KAT inhibition was performed by adding 3 uM A-485 (Selleck Chemicals, S8740) as in65 for 30 minutes prior to doxycycline addition.

value: anti-Pol2-S5P (Abcam ab5408)

value: biorep 2, + 24 hr 1000ng/mL dox


title: L2495-Michaela_NoDox_Pol2_4H8_rep1

value: biorep 1, + 24 hr 1000ng/mL dox


title: RNA-seq XEN cells, XistpA, rep3

description:
rna_wt_xistpA_xrrko_xrrako_xen_merged_chrX_allelic_FPKM.txt.gz
rna xistpA xen rep3


title: Post_Covid_6Months_BIS37


title: L2494-Michaela_Dox_Pol2_4H8_rep2


title: RNA-seq XEN cells, XRR KO, clone1, rep1

description:
rna_wt_xistpA_xrrko_xrrako_xen_merged_chrX_allelic_FPKM.txt.gz
rna xrr ko xen clone1 rep1


title: RNA-seq XEN cells, WT, rep3

description:
rna_wt_xistpA_xrrko_xrrako_xen_merged_chrX_allelic_FPKM.txt.gz
rna wt xen rep3


title: Post_Covid_6Months_BIS35


title: ChIP_H3K27ac_dox_p300_inhibitor_A485_4xTetO_mESC_spike_rep2

value: anti-H3K27ac (Abcam ab4729)

value: biorep 2, + 24 hr 1000ng/mL dox + 24.5 hr 3uM A485


title: L2490-Michaela_NoDox_H3K27ac_rep2


title: ChIP_H3K27ac_dox_p300_inhibitor_A485_4xTetO_mESC_spike_rep1

value: biorep 1, + 24 hr 1000ng/mL dox + 24.5 hr 3uM A485


title: L2489-Michaela_NoDox_H3K27ac_rep1


title: ChIP_H3K27ac_dox_4xTetO_mESC_spike_rep1


title: RNA-seq XEN cells, XistpA, rep1

description:
rna_wt_xistpA_xrrko_xrrako_xen_merged_chrX_allelic_FPKM.txt.gz
rna xistpA xen rep1


title: JS_L184_ATAC_b2

data_processing:
Bulk ATAC-seq data processing of fastq files was performed with snakeATAC (https://github.com/GreenleafLab/snakeATAC_singularity) and alignment to hg38.
Assembly: hg38
Supplementary files format and content: Insertion bw, 100bp smoothed bw, narrowpeak calls

extract_protocol:
After the cells were counted, 50,000 cells were resuspended in 1 ml of cold ATAC-seq resuspension buffer (RSB; 10 mM Tris-HCl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 in water). Cells were centrifuged at 500 r.c.f. for 5 min in a pre-chilled (4 °C) fixed-angle centrifuge. After centrifugation, 900 μl of supernatant was aspirated, which left 100 μl of supernatant. This remaining 100 μl of supernatant was carefully aspirated by pipetting with a P200 pipette tip to avoid the cell pellet. Cell pellets were then resuspended in 50 μl of ATAC-seq RSB containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin by pipetting up and down three times. This cell lysis reaction was incubated on ice for 3 min. After lysis, 1 ml of ATAC-seq RSB containing 0.1% Tween-20 (without NP40 or digitonin) was added, and the tubes were inverted to mix. Nuclei were then centrifuged for 10 min at 500 r.c.f. in a pre-chilled (4 °C) fixed-angle centrifuge. Supernatant was removed with two pipetting steps, as described before, and nuclei were resuspended in 50 μl of transposition mix (25 μl 2× TD buffer, 2.5 μl transposase (100 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, and 5 μl water) by pipetting up and down six times. Transposition reactions were incubated at 37 °C for 30 min in a thermomixer with shaking at 1,000 r.p.m. Reactions were cleaned up with Zymo DNA Clean and Concentrator 5 columns.
Following purification, we amplified library fragments using 1× NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2, using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s and 72 °C for 1 min. To reduce GC and size bias in our PCR, we monitored the PCR reaction using qPCR in order to stop amplification before saturation. To do this, we amplified the full libraries for five cycles, after which we took an aliquot of the PCR reaction and added 10 μl of the PCR cocktail with Sybr Green at a final concentration of 0.6×. We ran this reaction for 20 cycles to determine the additional number of cycles needed for the remaining 45-μL reaction. The libraries were purified using a Qiagen PCR cleanup kit yielding a final library concentration of ∼30 nM in 20 μL. Libraries were amplified for a total of 10–12 cycles.

treatment_protocol: All doxycycline induction was performed by adding 1,000 ng/mL doxycycline (Fisher Scientific, 409050) for 24 hours unless specifically noted otherwise. All interferon induction was performed by adding 10 ng/mL IFN-ꞵ (Peprotech, 300-02BC) for 6 hours unless specifically noted otherwise. Brg1 and Brm ATPase inhibition was performed by adding 10 uM BRM014 (MedChem Express, HY-119374) to cells as in64 for 30 minutes prior to doxycycline addition. CBP/p300 KAT inhibition was performed by adding 3 uM A-485 (Selleck Chemicals, S8740) as in65 for 30 minutes prior to doxycycline addition. For interferon experiments, BAF and p300 inhibitors were added 24 hours prior to assaying unless specifically noted otherwise.

value: none biorep 2


title: Post_Covid_6Months_BIS36


title: JS_L183_ATAC_p300i_IFNb_b2

value: 24hr p300i, 6hr IFNb biorep 2


title: JS_L182_ATAC_IFNb_b2

value: 6 hr IFNb biorep 2


title: Post_Covid_6Months_BIS34


title: RNA-seq XEN cells, XistpA, rep2

description:
rna_wt_xistpA_xrrko_xrrako_xen_merged_chrX_allelic_FPKM.txt.gz
rna xistpA xen rep2

value: XEN

value: extraembryonic endoderm stem cells

value: 129S1/SvImj X JF1/Ms


title: L2487-Michaela_Dox_H3K27ac_rep1


title: ChIP_H3K27ac_dox_4xTetO_mESC_spike_rep2


title: L2493-Michaela_Dox_Pol2_4H8_rep1


title: Post_Covid_6Months_BIS33

value: M


title: RNA-seq XEN cells, WT, rep1

description:
rna_wt_xistpA_xrrko_xrrako_xen_merged_chrX_allelic_FPKM.txt.gz
rna wt xen rep1


title: Post_Covid_6Months_BIS32


title: Hi-C XEN cells, Rad21-degron, dTAG treated, clone2, rep3

value: Rad21 degron

value: dTAG 24hrs


title: Hi-C XEN cells, Rad21-degron, dTAG treated, clone2, rep2


title: Post_Covid_6Months_BIS38


title: Post_Covid_6Months_BIS31


title: CUT&RUN XEN cells, XistpA, SMC3, rep2

value: SMC3 (Abcam, #ab9263)


title: JS_L181_ATAC_BAFi_IFNb_b2

value: 24hr BAFi, 6hr IFNb biorep 2


title: L2488-Michaela_Dox_H3K27ac_rep2


title: RNA-seq XEN cells, WT, rep2

description:
rna_wt_xistpA_xrrko_xrrako_xen_merged_chrX_allelic_FPKM.txt.gz
rna wt xen rep2


title: Hi-C XEN cells, Rad21-degron, dTAG treated, clone1, rep7


title: JS_L173_ATAC_p300i_b1

value: 24hr p300i biorep 1


title: Hi-C XEN cells, Rad21-degron, dTAG treated, clone1, rep6


title: Post_Covid_6Months_BIS97


title: JS_L179_ATAC_BAFi_b2

value: 12hr BAFi biorep 2


title: JS_L180_ATAC_p300i_b2

value: 24hr p300i biorep 2


title: Post_Covid_6Months_BIS27


title: ATAC-6hr-IFN-b2

value: biorep 2, 6 hr 10 ng/mL IFN-b


title: ATAC-3hr-IFN-b2

value: biorep 2, 3 hr 10 ng/mL IFN-b


title: Hi-C XEN cells, Rad21-degron, dTAG treated, clone1, rep3


title: JS_L172_ATAC_BAFi_b1

value: 12hr BAFi biorep 1


title: ATAC-1hr-IFN-b2

value: biorep 2, 1 hr 10 ng/mL IFN-b


title: ATAC-24hr-IFN-b2

value: biorep 2, 24 hr 10 ng/mL IFN-b


title: JS_L177_ATAC_b1

value: none biorep 1


title: Post_Covid_6Months_BIS98


title: Post_Covid_6Months_BIS25

value: F


title: Hi-C XEN cells, Rad21-degron, dTAG treated, clone2, rep1

value: XEN

value: extraembryonic endoderm stem cells


title: JS_L175_ATAC_IFNb_b1

value: 6 hr IFNb biorep 1


title: Post_Covid_6Months_BIS29


title: JS_L176_ATAC_p300i_IFNb_b1

value: 24hr p300i, 6hr IFNb biorep 1


title: Hi-C XEN cells, Rad21-degron, dTAG treated, clone1, rep5

value: 129S1/SvImj X JF1/Ms

value: Rad21 degron

value: dTAG 24hrs


title: ATAC-12hr-IFN-b2

value: biorep 2, 12 hr 10 ng/mL IFN-b


title: Post_Covid_6Months_BIS26

value: M


title: Hi-C XEN cells, Rad21-degron, dTAG treated, clone1, rep4


title: ATAC-3hr-IFN-b1

value: biorep 1, 3 hr 10 ng/mL IFN-b


title: JS_L174_ATAC_BAFi_IFNb_b1

value: 24hr BAFi, 6hr IFNb biorep 1


title: Post_Covid_6Months_BIS24


title: Post_Covid_6Months_BIS21


title: Hi-C XEN cells, Rad21-degron, DMSO treated, clone2, rep1

value: DMSO 24hrs


title: Hi-C XEN cells, Rad21-degron, DMSO treated, clone2, rep2


title: Hi-C XEN cells, Rad21-degron, dTAG treated, clone1, rep1


title: Hi-C XEN cells, Rad21-degron, dTAG treated, clone1, rep2


title: ATAC-24hr-IFN-b1

value: biorep 1, 24 hr 10 ng/mL IFN-b


title: ATAC-12hr-IFN-b1

value: biorep 1, 12 hr 10 ng/mL IFN-b


title: Post_Covid_6Months_BIS23


title: ATAC-6hr-IFN-b1

value: biorep 1, 6 hr 10 ng/mL IFN-b


title: Hi-C XEN cells, Rad21-degron, DMSO treated, clone1, rep4


title: ATAC-1hr-IFN-b1

value: biorep 1, 1 hr 10 ng/mL IFN-b


title: ATAC_5xTetO_b2_biorep2

value: 24 hr 1000 ng/mL dox, biorep 2


title: Post_Covid_6Months_BIS22

value: F


title: ATAC-0hr-IFN-b2

value: biorep 2, no treatment


title: ATAC-0hr-IFN-b1

value: biorep 1, no treatment


title: ATAC_9xTetO_b1_biorep2


title: Post_Covid_6Months_BIS18


title: ATAC_8xTetO_b1_biorep2


title: Hi-C XEN cells, Rad21-degron, DMSO treated, clone1, rep3

value: XEN

value: extraembryonic endoderm stem cells


title: Post_Covid_6Months_BIS17


title: ATAC_6xTetO_b1_biorep2


title: ATAC_6xTetO_b2_biorep2


title: Post_Covid_6Months_BIS19


title: Hi-C XEN cells, Rad21-degron, DMSO treated, clone1, rep2

value: 129S1/SvImj X JF1/Ms

value: Rad21 degron


title: ATAC_2xTetO_b1_biorep2


title: ATAC_8xTetO_b1_biorep1

value: 24 hr 1000 ng/mL dox, biorep 1


title: ATAC_1xTetO_b1_biorep2


title: Hi-C XEN cells, Rad21-degron, DMSO treated, clone1, rep1


title: Post_Covid_6Months_BIS20

value: M


title: ATAC_4xTetO_b2_biorep2


title: Post_Covid_6Months_BIS14


title: Hi-C XEN cells, XRRc XiKO, rep2

value: XRRc XiKO


title: ATAC_5xTetO_b2_biorep1


title: ATAC_9xTetO_b1_biorep1


title: Post_Covid_6Months_BIS16


title: ATAC_7xTetO_b2_biorep2


title: ATAC_7xTetO_b2_biorep1


title: Hi-C XEN cells, XRRc XiKO, rep1


title: Hi-C XEN cells, XRRb XiKO, rep2

value: XRRb XiKO


title: ATAC_4xTetO_b2_biorep1


title: Post_Covid_6Months_BIS13


title: ATAC_6xTetO_b2_biorep1


title: Hi-C XEN cells, XRRc XaKO, rep1

value: XRRc XaKO


title: ATAC_2xTetO_b1_biorep1


title: ATAC_1xTetO_b1_biorep1


title: Hi-C XEN cells, XRRc XaKO, rep2


title: Post_Covid_6Months_BIS12


title: siSurf2-3

city: PARIS

first: Simon

last: Lebaron

address: 4 avenue de l'observatoire

country: France

institute: Université Paris Descartes

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using fastp v.0.23.1. UMI-based de-duplication was performed using fastp v.0.23.1 simultaneously
Trimmed and de-duplicated reads were then mapped to the Homo sapiens GRCh38 with ERCC genes reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences
BAM files were generated as a result of this step
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

source_name: Osteosarcomas

growth_protocol: U2OS cells were maintened in DMEM supplemented with 10% fetal bovine serum in humidified atmoshpere with 5% CO2 at 37°C.

extract_protocol:
RNAs were extracted by following Trizol procdure, 2ug of total RNA to constrcut polyA librairies.
Librairies were made by Genwiz using their in house protocol for PolyA

treatment_protocol: Cells were treated by siRNAs (2 shots, 49H intervals) for 96 hours.

value: Osteosarcomas

value: si Surf2


title: ATAC_0xTetO_b1_biorep1


title: Post_Covid_6Months_BIS15


title: Post_Covid_6Months_BIS11


title: ATAC_0xTetO_b1_biorep2


title: Hi-C XEN cells, XRRb XiKO, rep1


title: siSurf2-2


title: siSurf2-1


title: siSCR-2

value: si Scramble


title: siSCR-3


title: Post_Covid_6Months_BIS10


title: ATAC_6xTetO_b1_biorep1


title: Post_Covid_6Months_BIS09


title: Hi-C XEN cells, XRRb XaKO, rep1

value: XRRb XaKO


title: Hi-C XEN cells, XRRb XaKO, rep2


title: siSCR-1


title: Hi-C XEN cells, XRR KO, clone1, rep2

value: XRR KO


title: PD1FF2

first: Jianwei

last: Jiao

state: Beijing

address: 1 Beichen West Road

department: State Key Laboratory of Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

data_processing:
Illumina high-throughput sequencing results initially exist as Raw image Data files and are transformed bybcl2fastq software into Sequenced Reads, which are called Raw Data or Raw Reads
Raw Data was processed with Perl scripts to ensure the quality of data used in further analysis. The adopted filtering criteria are as follows：1) Remove the adaptor-polluted reads. 2) Remove the low-quality reads. Reads with the number of low quality bases (phred Quality value less than 19) accounting for more than 15% of total bases are regarded as low-quality reads; 3) Remove reads with number of N bases accounting for more than 5 %.
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was mapped to the reference genome using TopHat v2.0.12.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and RPKM (Reads Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: mm9
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Microglia

extract_protocol:
Collect total RNA with Trizol reagent and 2ug of total RNA was used to construct  sequencing libraries.
RNA libraries sequencing  was performed using standard Illumina protocols

value: Microglia


title: Post_Covid_6Months_BIS08


title: PD1CKO3


title: Hi-C XEN cells, XRR KO, clone2, rep2


title: Post_Covid_6Months_BIS06

value: F


title: PD1FF1


title: PD1CKO2


title: Hi-C XEN cells, XRR KO, clone1, rep1


title: Melanoma tumor, YKL-40 Overexpressing, 3

city: Weifang

first: Yubing

last: WANG

state: Shandong

address: no.7166 Baotong Street, Weicheng

institute: Weifang Medical University

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

source_name: Mus tumor

growth_protocol: B16F10 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using TruSeq RNA sample Preparation kit V2 (Illumina). 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:
Male C57BL/6 mice (6 weeks old) were implanted subcutaneously with cells (5×105 cells in 200 μL saline) in the lateral side of the left hind leg.
Tumor tissue was collected after 19 days.

value: Melanoma cells

value: WT

value: Subcutaneous injection

tag: time

value: Day 19


title: Melanoma tumor, Control, 3


title: Hi-C XEN cells, XRR KO, clone2, rep1

data_processing:
Illumina Casava1.8 software was used for basecalling.
Hi-C reads were processed using HiCPro v2.11.1 and replicates of same stage were pooled together
Cmpartment and TAD analysis were done with  cooltools (v0.3.2) (Venev et al., 2020)
Hi-C data was visulalized with Juicebox (v1.11.08) (Durand et al., 2016)
Assembly: mm9
Supplementary files format and content: The files including all the valid interaction pairs ( described as Servant et al., 2015). The valid pairs are stored using a simple tab-delimited text format: read name / chr_reads1 / pos_reads1 / strand_reads1 / chr_reads2 / pos_reads2 / strand_reads2 / fragment_size [/ allele_specific_tag]

extract_protocol:
Cells were cross-linked with 1% formaldehyde at room temperature (RT) for 10 min. Formaldehyde was then quenched with glycine for 10 min at RT.
sisHi-C libraries were produced as previously described (Du et al., 2017). Crosslinked embryos were washed with 1 × PBS and lysed in lysis buffer (10mM Tris-HCl pH7.4, 10mM NaCl, 0.1mM EDTA, 0.5% NP-40 and proteinase inhibitor) on ice for 50 min, the chromatin was solubilized with 0.5% SDS at 62 °C for 5 min. The nuclei were digested with MboI at 37 °C overnight. After fill-in with biotin-14-dCTP (Invitrogen, #19518018), the fragments were ligated in a small volume. Reversal of cross-linking, DNA purification, and sonication were done sequentially. The biotin-labeled DNA was then pulled down with Dynabeads MyOne Streptavidin C1 (Thermo Fisher, #65001). The fragments that included a ligation junction were subjected to Illumina library preparation. 9-15 cycles of PCR amplification were performed with Kapa HiFi PCR mix (Roche, #KK2602), and the products were purified and size-selected with AMPure XP beads (Beckman Coulter, #A63881).

value: XEN

value: extraembryonic endoderm stem cells

value: 129S1/SvImj X JF1/Ms


title: Melanoma tumor, YKL-40 Overexpressing, 2


title: Post_Covid_6Months_BIS04

value: M


title: Melanoma tumor, YKL-40 Overexpressing, 1


title: Post_Covid_6Months_BIS05


title: Hi-C XEN cells, XRRa KO, rep3

value: XRRa KO


title: Melanoma tumor, Control, 2


title: Melanoma tumor, Control, 1


title: Hi-C XEN cells, XRRa KO, rep2


title: Post_Covid_6Months_BIS03


title: tonsil_HTO_run2

first: Jean

last: Lim

address: 1468 Madison Ave

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw sequencing data output (BCL files) was converted to fastq files with CellRanger mkfastq v3.0.2 (10X Genomics).
Per cell gene count and hashtag antibody count matrices were generated with CellRanger count v3.0.2 (10X Genomics), using a human genome reference (GRCh38, Ensembl v96 transcript annotations) appended with the MeV-eGFP reference and corresponding transcript annotations (MeV-IC323-eGFP, Genbank: MW401770).
Data were read into the R statistical framework (v4.0.3) for additional analysis with Seurat(71, 72) (v4.0.1).
Hashtag antibody data were center log ratio normalized by feature, and individual samples were demultiplexed with the Seurat HTODemux function with the positive.quantile parameter set to 0.99.
Hashtag oligo assignments were as follows: Uninfected 1: {HBC21: ' AGGACCATCCAA'}, Uninfected 2: {HBC22: ' ACATGTTACCGT'}, Uninfected 3: {HBC23: 'AGCTTACTATCC'}, Uninfected 4: {HBC25: 'TCGATAATGCGA'}, Infected 1: {HBC26: 'GAGGCTGAGCTA'}, Infected 2: {HBC27: 'GTGTGACGTATT'}, Bystander 1: {HBC28: 'ACTGTCTAACGG'}, Bystander 2: {HBC29: 'TATCACATCGGT'}
Assembly: GRCh38, Genbank: MW401770
Supplementary files format and content: gene expression matrix in csv format
Supplementary files format and content: hash matrix in csv format

molecule: protein

source_name: tonsil

growth_protocol: Human tonsils from routine tonsillectomies performed at the Mount Sinai Hospital and the New York Eye and Ear Infirmary of Mount Sinai were collected under IRB-approved protocols within a few hours after surgery. Tonsils were cut into 2mm3 blocks, and 9 tissue blocks per well were placed on top of collagen gelfoams (Cardinal Health) in a 6-well plate, utilizing three wells per condition (a total of 27 blocks per experimental sample).

extract_protocol:
Single cell suspensions were generated by dissociating tissue (merged from the three technical triplicate wells) using Collagenase IV (Worthington Biochemical) incubated for 30 min at 37°C with gentle shaking as previously described (44). Samples were homogenized with mortar and pestle before filtration over a 100µm cell filter and washed once with cold PBS. Dead cells were depleted from samples using the EasySep™ Dead Cell Removal (Annexin V) Kit (Stemcell Technologies, #17899). Cells were blocked with Human TruStain FcXTM (Biolegend, #422302) as per the manufacturer’s protocol. Next, cells from the uninfected tonsil were split into 4 hashing groups (hash #1-4), and cells from the infected tonsil were split into two infected hashing groups (hash #5, 6) and two bystander hashing groups (hash #7, 8). Samples were stained with corresponding hashing antibodies for 30 min at 4°C and washed 3x in FACS buffer (PBS + 1mM EDTA + 2% BSA). Cell suspensions were filtered over a 70µm filter, stained with propidium iodide (PI) for viability, and live/GFP- cells were sorted from the uninfected condition, live/GFP+ cells were sorted from the infected condition, and live/GFP- cells were sorted from the bystander condition on a BD FACS Aria III.
Sorted cells were counted and 10,000 cells from the uninfected condition, 5,000 cells from the infected condition, and 5,000 cells from the bystander condition were pooled and processed for scRNA-Seq on the 10x Genomics Chromium platform, utilizing the 10x 3’ v3 kit. A scRNA-Seq library was generated as per the manufacturer’s protocol and sequenced on an Illumina NextSeq500 instrument. A corresponding library of barcoded hash antibody oligonucleotides was indexed with a standard Illumina D701 index and sequenced as above.

treatment_protocol: After an overnight incubation, individual tissue blocks were individually inoculated with 5μl containing 1,666 PFU MeV-GFP (for a final concentration of 5,000 PFU/ml) or left uninfected. Media was collected and replaced at days 3, 6, and 8 post-infection.

value: tonsil

tag: library type

value: HTO


title: Post_Covid_6Months_BIS07


title: Hi-C XEN cells, XRRa KO, rep1


title: tonsil_HTO_run1


title: Post_Covid_6Months_BIS02


title: Hi-C XEN cells, XistpA, rep3

value: XistpA


title: AVCM_rep2

city: Amsterdam

first: Alexandra

last: Wiesinger

state: Amsterdam

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

description: atrioventricular node cardiomyocytes at day 19 of differentiation

data_processing:
Libraries were sequenced on NextSeq500 using 1x75 bp read length kit
Mapping was performed using BWA-MEM against the (human) genome assembly GRCh38 (hg38). Count matrices were generated using MapAndGo, filtering reads with a minimum quality score of 60 and no alternative hits.
Assembly: hg38
Supplementary files format and content: transcript counts as .tsv files

source_name: hiPSC derived atrioventricular node cardiomyocytes

growth_protocol: hiPSCs were maintained in mTeSR medium on growth factor reduced Matrigel

extract_protocol:
Cells were singularzed and FACS sorted into 384-well plates (Muraro et al, 2016)
Preparation of single-cell libraries was performed using the CEL-Seq2 protocol (Muraro et al. 2016; Hashimshony et al., 2016)

treatment_protocol: Differentiation of hiPSCs towards MESP1+ mesoderm was initiated by activating Activin/Nodal, BMP and WNT signaling (Wiesinger et al, 2022; Li et al, 2022). To direct mesoderm towards AVCM, we treated mesoderm cultures with compounds that activated WNT and RA signalling for 72 hours.

value: wild type


title: Hi-C XEN cells, XistpA, rep2


title: T11 RNAseq

city: Jerusalem

first: Yotam

last: Drier

state: Israel

address: Faculty of Medicine, The Hebrew University, Ein Kerem

department: Immunology and Cancer Research

country: Israel

institute: The Hebrew University of Jerusalem

data_processing:
ChIP-seq reads were aligned to the reference genome (hg38) using BWA 0.7.17. Reads with mapping quality < 10 were not counted, and reads aligned to the same position and strand were only counted once. H3K27ac peaks were called using HOMER12, with style ‘histone’ for variable length. Density signals were calculated by deeptools’s bamCoverage.
RNA-seq reads were mapped to the hg38 reference genome using STAR 2.7.10a (Ref. 17) and Ensembl release 99 annotations. Reads were counted with featureCounts, discarding reads with mapping quality < 10. Density signals were calculated by deeptools’s bamCoverage11 with BPM normalization.
Assembly: hg38
Supplementary files format and content: bigwig

source_name: Lung neuroendocrine tumor

growth_protocol: NCI-H727, NCI-H1770 and NCI-H835 cell lines were acquired from ATCC. The cell lines were cultured in complete RPMI 1640 media (Gibco, Thermo Fisher Scientific, Massachusetts, USA) supplemented with 10% or 5% fetal bovine serum (FBS; HyClone, Utah, UK), 1% penicillin streptomycin (Diagnovum, Tilburg, Netherlands), 1% L-glutamine (Sartorius, Göttingen, Germany), 1% sodium pyruvate (Sartorius), and 1% non-essential amino acids (Diagnovum). LNET xenografts were established 5 days following the subcutaneous injection of 4*106 NCI-H727 cells to the back of athymic nude mouse (FOXN1NU NU/NU mouse).

extract_protocol:
2 mm tissue sample was homogenized in tri-reagent and RNA was extracted flowing the standard tri-reagent protocol. After precipitation RNA was resuspended in appropriate volume of Rnase free water supplemented with RNA inhibitors (New England Biolabs).
RNA-seq libraries were generated using the KAPA mRNA Hyperprep Kit according to the manufacturer's instructions. ChIP DNA was used to generate sequencing libraries using KAPA Hyper Prep Kit.

treatment_protocol: A51 treated cells were treated with 150nM BTX-A51.

value: Lung neuroendocrine tumor

value: Neuroendocrine


title: T12 RNAseq


title: AVCM_rep1

value: hiPSC derived atrioventricular node cardiomyocytes


title: Post_Covid_6Months_BIS01

value: F


title: tonsil_GEX_run2

value: mRNA


title: T9 RNAseq


title: NCI-H1770 RNAseq


title: T10 RNAseq


title: Hi-C XEN cells, Smchd1 KO, rep1

value: Smchd1 KO


title: T8 RNAseq


title: PB1_T677A infection #1

city: San Diego

first: Alistair

middle: Brian

last: Russell

address: 9500 Gilman Dr,

department: Biological Sciences

institute: University of California, San Diego

description: Circularized cDNA from influenza infection

data_processing:
Data were processed with a custom pipeline available at https://github.com/a5russell/ccRNA_miSeq
Assembly: A/WSN/1933
Supplementary files format and content: Counts and identities of 5' and 3' ends of each circularized cDNA, distance within each read of a set sequence, and distance to the template-switching oligo in commas-seperated tables.

growth_protocol: Samples were from infections of A549 cells at an MOI of 1 with the indicated A/WSN/1933 strain and harvested at 16hpi.

extract_protocol:
RNA was extracted using Monarch Total RNA Miniprep Kit from New England Biolabs (NEB #T2010)
cDNA conversion using ccRNA-specific primer and template-switching to append a 5' TSO. Samples circularized and amplified using custom primer pairs

value: Influenza A virus (A/WSN/1933(H1N1))


title: T6 RNAseq


title: PB1_T677A infection #3


title: PB1_T677A infection #2


title: Wild-type infection #3


title: T5 RNAseq


title: tonsil_GEX_run1


title: Wild-type infection #2


title: Hi-C XEN cells, WT, rep6


title: T2 RNAseq


title: T4 RNAseq


title: Hi-C XEN cells, WT, rep5


title: T3 RNAseq


title: Hi-C XEN cells, XistpA, rep1


title: Wild-type infection #1


title: NCI-H835 H3K27ac


title: Hi-C XEN cells, WT, rep4


title: RACE PB1_177_385 minimal replication with NS2 library #3

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library subjected to IAV minimal replication assays with NS2. Sequenced by 5' RACE
withNEP_3.tsv

data_processing:
Data were processed with a custom pipeline available at https://github.com/Russell-laboratory/NS2_sequence_specificity
Assembly: A/WSN/1933
Supplementary files format and content: Either barcodes from length variant libraries, and their relative amounts (see GSE183442 for assignment of barcodes to variant identity), or nucleotide at sites as they would map to full-length PB1.
Supplementary files format and content: All processed files are in a tab-seperated value format.
Library strategy: amplicon sequencing

organism: Influenza A virus (A/WSN/1933(H1N1))

growth_protocol: Samples were from transfections of HEK293T cells grown in D10 media and transfected with indicated libraries and minimal IAV replication components with, or without, NS2. Plasmid libraries rescued from E. coli.

extract_protocol:
RNA was extracted using Monarch Total RNA Miniprep Kit from New England Biolabs (NEB #T2010)
Custom amplicon sequencing, or custom 5' RACE using Template Switching RT Enzyme Mix (New England Biolabs, #M0466)

treatment_protocol: Transfection using BioT.

value: minimal replication assay with NS2


title: NCI-H727 H3K27ac


title: Hi-C XEN cells, Smchd1 KO, rep2

value: XEN


title: RACE PB1_177_385 minimal replication with NS2 library #2

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library subjected to IAV minimal replication assays with NS2. Sequenced by 5' RACE
withNEP_2.tsv


title: H727 xenograft H3K27ac rep2

value: PBS


title: Hi-C XEN cells, WT, rep2

value: extraembryonic endoderm stem cells

value: 129S1/SvImj X JF1/Ms


title: T12 H3K27ac


title: RACE PB1_177_385 minimal replication with NS2 library #1

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library subjected to IAV minimal replication assays with NS2. Sequenced by 5' RACE
withNEP_1.tsv


title: T11 H3K27ac


title: CUT&RUN E13.5 fibroblast, female, SMC3, rep1

description: smc3 E13.5 fibroblast female rep1

source_name: fibroblast

value: fibroblast

value: C57BL/6N X PWK/PhJ

value: SMC3 (Abcam, #ab9263)


title: Hi-C XEN cells, WT, rep1


title: T10 H3K27ac


title: T8 H3K27ac


title: PB1_177_385 minimal replication with NS2 library #3

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library subjected to IAV minimal replication assays with NS2
withNEP_3.tsv


title: PB1_177_385 minimal replication with NS2 library #2

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library subjected to IAV minimal replication assays with NS2
withNEP_2.tsv


title: T6 H3K27ac


title: T5 H3K27ac


title: T1 RNAseq


title: CUT&RUN E9.5 fibroblast, female, SMC3, rep1

description: smc3 E9.5 fibroblast female rep1


title: T4 H3K27ac


title: PB1_177_385 minimal replication with NS2 library #1

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library subjected to IAV minimal replication assays with NS2
withNEP_1.tsv


title: T3 H3K27ac


title: CUT&RUN E6.5 extraembryonic ectoderm, female, SMC3, rep2

description: smc3 E6.5 ExE female rep2

value: extraembryonic ectoderm


title: T2 H3K27ac


title: H727 xenograft H3K27ac rep1


title: Hi-C XEN cells, WT, rep3

value: wild type


title: RACE PB1_177_385 minimal replication no NS2 library #3

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library subjected to IAV minimal replication assays without NS2. Sequenced by 5' RACE
noNEP_3.tsv

value: minimal replication assay without NS2


title: T1 H3K27ac

value: Lung neuroendocrine tumor

value: Neuroendocrine


title: CUT&RUN E6.5 extraembryonic ectoderm, female, SMC3, rep1

description: smc3 E6.5 ExE female rep1


title: RACE PB1_177_385 minimal replication no NS2 library #2

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library subjected to IAV minimal replication assays without NS2. Sequenced by 5' RACE
noNEP_2.tsv


title: RACE PB1_177_385 minimal replication no NS2 library #1

description:
Defective PB1 (PB1_177_385) mutated by error-prone PCR. Initial plasmid library subjected to IAV minimal replication assays without NS2. Sequenced by 5' RACE
noNEP_1.tsv