title: WI-38, nomal, RNA-seq, Rep1

first: Zixin

state: 广东

address: Dongchuan Road

institute: Guangdong General Hospital

description:
WI-38_RNAseq_counts.txt
WI-38_Y_1_RNAseq

data_processing:
After obtaining raw data, paired-end reads were harvested and trimmed by fastp (version 0.20.1) to remove adaptor sequences and low-quality nucleotides.
High-quality reads were then aligned to ENSEMBL GRCh38 or GRCm39 reference genome using HISAT2 (version 2.2.1) with default parameters
For RNA-seq, featureCounts (version 2.0.1) software was used to count reads mapped to RefSeq genes, and differential gene expression analysis was conducted using DESeq2 R package (version 1.38.3).
m6A peaks on RefSeq transcripts and differentially m6A peaks were analyzed using exomePeak2 R package (version 1.10.0).
Assembly: GRCh38 and GRCm39
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 diffpeaks of Senescence vs nomal cells

extract_protocol:
RNA was extracted using Dynabeads® mRNA DIRECT (Thermo Fisher) to deplete ribosomal RNA and avoid DNA contamination. The purified product was divided into two parts, one for RNA-seq and the other for MeRIP-seq.
The fragmented mRNA underwent m6A IP using the EpiMark® N6-Methyladenosine Enrichment Kit (NEB) following the manufacturer's protocol. RNA libraries were prepared for both input RNA and m6A-enriched mRNA after IP using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) according to the manufacturer's instructions.

value: Human fetal lung fibroblast cells


title: WI-38, replicative senescence, MeRIP, Rep1

status: Public on Apr 18 2025

type: SRA

city: Guangzhou

last: Chen

country: China

library_source: transcriptomic

data_processing:
After obtaining raw data, paired-end reads were harvested and trimmed by fastp (version 0.20.1) to remove adaptor sequences and low-quality nucleotides.
High-quality reads were then aligned to ENSEMBL GRCh38 or GRCm39 reference genome using HISAT2 (version 2.2.1) with default parameters
For RNA-seq, featureCounts (version 2.0.1) software was used to count reads mapped to RefSeq genes, and differential gene expression analysis was conducted using DESeq2 R package (version 1.38.3).
m6A peaks on RefSeq transcripts and differentially m6A peaks were analyzed using exomePeak2 R package (version 1.10.0).
Assembly: GRCh38 and GRCm39
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 diffpeaks of Senescence vs nomal cells
Library strategy: MeRIP-seq

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type


title: WI-38, nomal, MeRIP, Rep2


title: U251ecDNA- WGS

city: Shenzhen

first: haiyun

last: gan

address: xueyuan lu 1068

institute: Shenzhen Institute of Advanced Technology

library_source: genomic

data_processing:
Sequence reads were mapped back to the human reference genome (hg38) using BWA-MEM (WGS) or Bowtie2 (END-seq) software. Only consistent pair-end reads were chosen for further analysis.
For END-seq, the sequence reads mapped to the Watson and Crick strands of the reference genome were separated by in-house Perl programs and then genome-wide reads coverage was calculated by BEDTools and in-house Perl  programs.
To calculate the genome-wide read coverage BEDTools and self-developed Perl programs was performed.
Bedtools was used to generate BigWig files and counting matrices in bins around peak summits, and bedGraphToBigWig was used for visualization.
Assembly: hg38
Supplementary files format and content: bigwig files were generated for Watson and Crick strand or merged, scores represent the normalization reads density.

molecule: genomic DNA

growth_protocol: Both the human glioblastoma cell line U251 and the human embryonic kidney cell line 293T were cultured in Dulbecco’s modified Eagle’s medium (DMEM, Procell, PM150210) containing 10% fetal bovine serum (FBS, Excell, FSP500), supplemented with 100 U ml-1 penicillin, 100 mg ml-1 streptomycin, and 2 mM L-glutamine, at 37 ℃ under 5% CO2. COLO320DM and COLO320HSR cells were maintained in RPMI-1640 (VivaCell, C3010-0500) with the same supplements as above. All cell lines tested negative for mycoplasma contamination.

extract_protocol:
For WGS, entirely digestion (2 hour) with proteinase K (0.5 mg/ml) and RNase A (0.2 mg/ml) in PBS at 65 ℃, genomic DNA was extracted from cells with phenol:chloroform:isoamyl alcohol (25:24:1, PH 7.8) and precipitated with ethanol. The genomic DNA was resuspended in TE buffer and sonicated (Covaris M220) in AFA milliTUBEs (Covaris. 520045) to obtain 200~500 bp fragments. Sonication parameters: PIP 50, duty factor 10%, cycles 200, processing time 170 s. Then, the DNA was purified using the DNA Clean & Concentrator™-5 (ZYMO, D4004) kit. For END-seq, plugs making, DSB end blunting, A-tailing, ligation of END-Seq adapter 1, DNA shearing and extractio and streptavidin capture of labeled DSB ends, blunting, and A-Tailing ligation of END-Seq adapter 2 were implemented in sequence.
The WGS libraries were prepared with the fragmented DNA (1 µg) using the VAHTS® Universal DNA Library Prep Kit for Illumina V3 (Vazyme, ND607). The WGS libraries were sequenced for at least 50 G data with PE150 on NovaSeq 6000. The END-seq library PCR was performed using standard Illumina Nextera Dual Indexing primers. Samples were pooled and sequenced using paired-end (2×150 bp) sequencing on an Illumina Novaseq or HiSeq X Ten platform by Annoroad Gene Technology Co. Ltd.

value: ecDNA-

tag: genotype

value: WT


title: WI-38, nomal, MeRIP, Rep1


title: WI-38, replicative senescence, RNA-seq, Rep2

description:
WI-38_RNAseq_counts.txt
WI-38_S_2_RNAseq


title: WI-38, nomal, RNA-seq, Rep2

description:
WI-38_RNAseq_counts.txt
WI-38_Y_2_RNAseq


title: WI-38, replicative senescence, RNA-seq, Rep1

description:
WI-38_RNAseq_counts.txt
WI-38_S_1_RNAseq


title: Uterine immune cells, E13.5, SMC-specific Il18 cKO_2

city: Tokyo

first: Hajime

last: Ino

address: 1-1-5, Sendagi, Bunkyo-ku

country: Japan

institute: Nippon Medical School

description:
Library name: Sample5
Column name in raw_counts.csv: cko_2

data_processing:
The quality of the raw sequence reads was assessed with FastQC (Version 0.11.7). Adapter sequences and low quality (< 20) bases were trimmed by Trimmomatic software (Version 0.38). The trimmed reads were aligned to the reference genome using RNA-seq aligner HISAT2 (Version 2.1.0) and mapped to GRCm38/m10.
Assembly: GRCm38/m10
Supplementary files format and content: csv file includes trimmed raw counts for each sample

organism: Mus musculus

source_name: Uterine myometrium

extract_protocol:
Female mice (8 – 12 weeks old) were mated overnight with Balb/cJ wild-type male mice. The presence of a vaginal plug was designated as embryonic day (E) 0.5. At E13.5, pregnant mice were euthanized by cervical dislocation, and the myometrium was isolated from the pregnant uterus. Tissues were enzymatically digested into cell suspensions. Cells were enriched using Lympholyte-M (Cedarlane) and CD45-positive, IL-18R-positive cells were sorted using a FACS Aria II (BD) for sample preparation. Total RNA extraction was all performed using the SMART-Seq HT PLUS Kit (Takara Bio USA, CA, USA) following to the manufacturer's instructions.
cDNA synthesis and library construction were all performed using the SMART-Seq HT PLUS Kit following to the manufacturer's instructions.

tag: tissue

value: Uterine myometrium

value: CD45-positive, IL-18R-positive cells

tag: Sex

value: Female

tag: developmental stage

value: 8 - 12 weeks

tag: time

value: Embryonic day 13.5


title: Uterine immune cells, E13.5, SMC-specific Il18 cKO_1

description:
Library name: Sample4
Column name in raw_counts.csv: cko_1


title: Uterine immune cells, E13.5, Control_3

description:
Library name: Sample3
Column name in raw_counts.csv: control_3

value: Il18-floxed (C57BL/6 background)


title: Uterine immune cells, E13.5, SMC-specific Il18 cKO_3

description:
Library name: Sample6
Column name in raw_counts.csv: cko_3


title: Uterine immune cells, E13.5, Control_1

description:
Library name: Sample1
Column name in raw_counts.csv: control_1


title: Uterine immune cells, E13.5, Control_2

description:
Library name: Sample2
Column name in raw_counts.csv: control_2


title: 2426I

city: Salt Lake City

first: Li

last: Li

state: Utah

address: 201 PRESIDENTS CIRCLE

country: USA

institute: University of Utah

description: Library name: 23792X26

data_processing:
NovaSeq X Series 10B Reagent Kit_150x150 bp Sequencing (1250 M read-pairs/lane). Reads were aligned to mm10 mouse genome version using Novoalign (Version 3.00) for paired-end reads. Peaks were called from each of the aligned bam files against input reads using MACS2 , (version 2.2.9) with the parameters: callpeak -B --SPMR --qvalue = 1e-3 --mfold 15 100. ChIP input was used as the background for MACS2. MACS was used to produce normalized bedgraphs, which were subsequently converted to bigWig files. Peaks were filtered to remove peaks that are in blacklist, including ENCODE blacklisted regions. Duplicate reads were removed using samtools rmdup for all downstream analyses . Merged bigWig enrichment files for each condition with multiple replicas were generated in an average manner followed by normalization of read depth.
Assembly: mm39
Supplementary files format and content: bigWig

source_name: Tumor

extract_protocol:
Nuclei were isolated and sonicated using a Covaris ultrasonicator (Active motif). Sheared chromatin was incubated with 5µg antibody per sample overnight at 4°C on a rotator, followed by immunoprecipitation using magnetic beads. After washing, DNA was purified using a DNA Clean & Concentrator Kit (Zymo).
ChIP-Seq with NEBNext Ultra II DNA Library Prep Kit

value: Tumor

tag: strain

value: Rosa26hSS2 and Myf5Cre mouse

value: SS18-SSX fusion

tag: treatment

value: Decitabine

tag: chip antibody

value: none (Input)


title: COLO320DM ATMi WGS

value: DM

value: ATM inhibitor


title: 1388I

description: Library name: 23792X19

value: Vehicle


title: 2802K

description: Library name: 23792X15

value: AZA


title: 2426F

description: Library name: 23792X8


title: 2802F

description: Library name: 23792X6


title: 2426K

description: Library name: 23792X17


title: 1388K

description: Library name: 23792X10


title: 2426

description: Library name: 21411X8

data_processing:
NovaSeq X Series 10B Reagent Kit_150x150 bp Sequencing (1250 M read-pairs/lane). The quality of raw paired-end sequence reads was assessed using FastQC. Low-quality (< 20) bases and adapter sequences were trimmed using Trimmomatic software (version 0.38) with the following parameters ILLUMINACLIP: path/to/adapter.fa:2:30:10 LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36. The trimmed reads were aligned to the reference genome (mouse genome version mm10 and human genome version hg38) using the HISAT2 RNA-seq aligner (version 2.1.0).
Assembly: hg38, mm10
Supplementary files format and content: txt, raw counts

extract_protocol:
RNA was extracted from samples using TRIzol (Ambion, Inc., Life Technologies, Carlsbad, CA, USA; 15596018), followed by chloroform to 16.67% by volume. RNA was then purified from the suspended lysate and eluted in water using a kit (Zymo Research, Irvine, CA, USA; RNA Clean & Concentrator R1018).
NEBNext Ultra II Directional RNA Library Prep with rRNA Depletion Kit (human,mouse,rat)


title: 1388F

description: Library name: 23792X1


title: 1467

description: Library name: 21411X7


title: 1388

description: Library name: 23793X7


title: 2434

description: Library name: 21411X5


title: 2800

description: Library name: 23793X2


title: 2482

description: Library name: 23793X6


title: 2481

description: Library name: 23793X5


title: 2803

description: Library name: 23793X4


title: Control CRISPRi mRNA

city: Geneva

first: Denis

last: Jabaudon

address: Rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

description:
Library name: E12_epor_P1_TrackerSeq_Ctl_mRNA
CRIPSRi

library_source: transcriptomic single cell

data_processing:
For mRNA libraries:Read were mapped and counted with cellranger 6.1.1
For mRNA libraries: Count matrix were processed with Seurat package using SCTransform
For barcodes: reads were processed with TrackerSeq pipeline, code available at:  https://github.com/mayer-lab/Bandler-et-al_lineage/tree/main/TrackerSeq
Assembly: mm10
Supplementary files format and content: For mRNA library: RDS file contains Seurat object with expression matrices and metadata
Supplementary files format and content: For barcodes: csv table with detected clones

molecule: polyA RNA

source_name: neocortex FACS cell

extract_protocol:
Three electroporated cortices with Ef1a-Pbase+ITR-CAG-TurboRFP-NLS-Index1 with either pX458-CAG-dCas9-KRAB-MECP2-H2B-GFP-NogRNA or pX458-CAG-dCas9-KRAB-MECP2-H2B-GFP-Fam210b-gRNA1+2 at E12 were collected at P1. Dissociations were performed using the Neural Dissociation kit (Miltenyi, 130-092-628) as detailed above for progenitor cultures, with the exception of adding tissue for 7mins in Enzyme mix 1 and 3min in Enzyme mix 2. Only RFP+ cells were sorted into a tube containing sorting buffer. Before loading on the 10x Chip G, cell suspension was centrifuged for 5min at 4C with 300g and all but around 43.2 μL was removed.
Library construction was performed according to 10X Genomics Chromium Single Cell 3’ v3 .1 reagents and protocol.

value: neocortex FACS cell


title: 2802

description: Library name: 23793X3


title: 2467

description: Library name: 23793X1


title: DN.mTEClo.FBC for B6 rep1 (HT1), B6 rep2 (HT2), BALBC rep1 (HT3), BALBC rep2 (HT5), NOD rep1 (HT6), NOD rep1 (HT8)

city: Boston

first: Liang

last: Yang

state: MA

address: 77 Avenue Louis Pasteur

department: Pathology

institute: Harvard Medical School

description: Library name: Pdpn-CD104-mTEClo.FBC

library_source: other

data_processing:
The demultiplexing, barcode process and gene/ hash counts were generated using Cellranger software v7.0.0.
Assembly: mm10
Supplementary files format and content: Processed data files: barcodes.tsv, genes.tsv, matrix.mtx - Barcodes, features and counts for RNA & HTO for DNs in our samples (includes all samples listed in title).

molecule: protein

extract_protocol:
Tissue was minced with scissors and lymphocyte-rich supernatant removed. Thymic fragments were digested with collagenase and dispase. CD45+ cells were magnetically depleted. Cells were stained with fluorescent antibodies and hashtag-oligo antibodies and flow sorted. Single cells were encapsulated following 10X Genomics protocols.
Libraries were prepared according to the 10x Genomics 3' v3.1 protocol for GEX and FBC.
scRNA-seq, CITE-seq

tag: organ

value: Thymus

tag: age

value: 6 weeks


title: Fam210b CRISPRi mRNA

description: Library name: E12_epor_P1_TrackerSeq_Fam210b_CRISPRi_mRNA


title: 2802I

description: Library name: 23792X24


title: Control CRISPRi TrackerSeq barcode

description: Library name: E12_epor_P1_TrackerSeq_Ctl_barcodes

molecule: other


title: Y6_T

city: Yangling, CN

first: Wen Chuan

last: Peng

address: No.22, Xinong Road, Yangling District, Xianyang City, Shaanxi Province

institute: Northwest A&F University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/, version:cutadapt-1.9).The raw data were filtered using the Fast QC program (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/,0.11.9). Then the clean reads were aligned against the pig reference genome Sus scrofa 11.1 (http://www.ensembl.org/info/data/ftp/index.html) using HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1).The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/, version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software (http://ccb.jhu.edu/software/stringtie/gffcompare.shtml, version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.he gene expression level was quantified by fragments per kilobase of transcript per million mapped reads (FPKM) which could normalize the number of reads and the length of transcripts. Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples).
Assembly: Longissimus dorsi muscle of pig
Supplementary files format and content: Tab-delimited text files include FPKM values for each Sample

organism: Sus scrofa

source_name: longissimus dorsi muscle

extract_protocol:
Total RNA was extracted from frozen longissimus dorsi muscle samples using Trizol reagent (thermofisher, 15596018). The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511), high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp.

value: longissimus dorsi muscle

tag: breed

value: Yorkshire pig


title: Y5_T


title: Fam210b CRISPRi

description: Library name: E14_epor_24h_Fam210b_CRISPRi

data_processing:
Read were mapped and counted with cellranger 6.1.1
Count matrix were processed with Seurat package using SCTransform
Assembly: mm10
Supplementary files format and content: RDS file contains Seurat object with expression matrices and metadata

source_name: neocortex FANS nuclei

extract_protocol:
Two electroporated cortices with either CAG-CRISPRi-Fam210b-gRNA1+2 or CAG-CRISPRi-NogRNA at E14 were collected 24 hours later in 1X HBSS. Electoporated regions were then microdissected and frozen. Nuclei were isolated by first thawing the frozen tissue on ice and centrifuging at 4C with 500g for 5min . Supernatant was removed and 100μl of Lysis buffer (10mM Tris-HCL pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% NP-40, 1% BSA, 1mM DTT) was added for 3min on ice.  900μl of washing buffer (10mM Tris-HCL pH7.4, 10mM NaCl, 3mM MgCl2, 1% BSA, 1mM DTT, 0.5U/μl SUPERase-In RNase inhibitor (ThermoFisher Scientific, AM2694)) was added and samples were pipetted 10 times using the P1000. The samples were then centrifuged for 5min at 4C with 500g. After washing one more time, the nuclei pellet was resuspended in sorting buffer (1XPBS, 1%BSA and 0.5U/μl SUPERase-In RNase inhibitor (ThermoFisher Scientific, AM2694)) using the P200 pipette and passed through a 30μm filter. Hoechst was added to label nuclei for FANS gating. Hoechst+GFP+ nuclei were sorted directly into empty 1.5ml Eppendorf.
Library construction was performed according to 10X Genomics Chromium Single Cell 3’ v3 .1 reagents and protocol.

value: neocortex FANS nuclei


title: Y4_T


title: Control CRISPRi

description: Library name: E14_epor_24h_Ctl


title: 1929

description: Library name: 21411X6


title: Y2_T


title: WT

city: Changsha

last: Cai

address: Renmin middle road 139

institute: Second xiangya hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Islet

extract_protocol:
Briefly, mice were anesthetized with intraperitoneal Avertin injection (1 mL/40 g body weight) and the pancreas was infused with 3 mL of a collagenase P solution (Sigma Chemical, St. Louis, MO; 0.5 mg/mL in HBSS). The pancreases were subsequently removed and incubated at 37°C for approximately 12 minutes until complete digestion was achieved. Digestion was stopped by adding 30 mL of HBSS, followed by three washes of 20 mL HBSS. The isolated islets were carefully selected under a stereoscopic microscope using a pipette and then cultured in RPMI-1640 supplemented with 10% FBS and 100 U/mL penicillin-streptomycin.
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Islet

value: WT


title: L6_T

value: Laiwu pig


title: Y1_T


title: KO

value: KO


title: L5_T


title: DN.mTEClo.GEX for B6 rep1-2, BALBC rep1-2, NOD rep1-2

description: Library name: Pdpn-CD104-mTEClo.GEX

value: Female


title: WI-38, replicative senescence, MeRIP, Rep2

value: Human fetal lung fibroblast cells


title: LFRA19

city: New York

first: Genomics-core-facility

last: WCM

state: New York

address: 1300 York Ave

institute: Weill Cornell Medicine

data_processing:
The samples were sequenced using Illumina NovaSeq6000 sequencer with paired-end 100 bps reads. The raw sequencing reads in BCL format were processed through bcl2fastq 2.20 (Illumina) for FASTQ conversion and demultiplexing.
The RNA reads were aligned and mapped to the GRCm39 human reference genome by STAR (Version2.5.2).
The transcriptome reconstruction was performed by Cufflinks (Version 2.1.1). The abundance of transcripts was measured with Cufflinks in Fragments Per Kilobase of exon model per Million mapped reads (FPKM).
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file include normalized abundance measurements(FPKM) at gene level for each samples

source_name: Lung

growth_protocol: Mice were placed on 10% fat diet or 60% fat diet (Research diets D12450B and D12492) for 12 weeks.

extract_protocol:
RNA was extracted from isolated alveolar epithelial type 2 cells using the RNeasy Mini Kit (QIAGEN GmbH, Hilden, Germany)
cDNA libraries were generated using the Illumina Stranded mRNA Library Preparation Kit

treatment_protocol: Mice were treated with >95% O2 or Room Air for 48 hrs

value: Lung

value: Alveolar Epithelial Type 2

value: Wild Type

value: 10percent fat diet room air


title: L1_T


title: LFRA17


title: Fam210b CRISPRi TrackerSeq barcode

description: Library name: E12_epor_P1_TrackerSeq_Fam210b_CRISPRi_barcodes


title: PAM_6h_H3K27ac_HiChIP_rep1

city: wuhan

first: zhe

last: jin

state: hubei

address: Lion Rock Street

department: College of Animal Science and Technology

institute: Huazhong Agricultural University

description:
H3K27ac HiChIP of porcine alveolar macrophages infected by African swine fever virus for 6h
real_FDR.merged.6h.bedpe

data_processing:
Sequencing reads were aligned to the susScr11 reference genome
eaks for all cells were identified with MACS2 (version 2.2.7.1)
Assembly: Sscrofa11.1
Supplementary files format and content: bam,bigwig and peak
Library strategy: HiChIP-Seq

source_name: H3K27ac HiChIP of Sus scrofa : alveolar macrophages infected by African swine fever virus for 6h of 1-month-old male

extract_protocol: Total RNA from PAM cells at 0 and 6 hpi was extracted with TRIzol reagent (Invitrogen 15596026) according to the manufacturer’s instructions, and the RNA-seq libraries construction and sequencing were completed by BioMarker Company. cDNA was obtained via reverse transcription of 1 μg of RNA using a High-Capacity cDNA Reverse Transcription kit (Thermo Fisher 4374967). THUNDERBIRD SYBR qPCR Mix (Toyobo) was used with a CFX384 real-time PCR system (Bio-Rad). All primer sequences in this study are listed in Supplementary Table 1.    Chromosome features capture was performed as previously described46. ConA beads were equilibrated to room temperature, and washed twice with Binding buffer (20 Mm HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2 and 1 mM MnCl2). 100,000 cells were washed once with wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5mM spermidine and 1× Protease Inhibitor), gently mixed with ConA beads at room temperature for 10 min and bead-cell complex collected after passing through a magnetic stand. Beads were then resuspended in 100μL Antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 12.5 μL 0.5mM spermidine, 0.05% Digitonin, 2mM EDTA and 0.1% BSA) containing 2μg primary antibody (H3K4me3 mc315, H3K27ac ab4729, POL-II BioLegend 664906, H3K27me3 C15410069，IgG AC005) and incubated at room temperature for 2 hours. bead-cell complex and resuspend beads were collected in 100μL Dig-wash buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 12.5 μL 0.5mM spermidine, 0.05% Digitonin) with 2 μg secondary antibody (H&L IgG ab6702) and incubated at room temperature for 1 hour. Beads were washed twice with Dig-wash buffer and resuspended in 100ul Dig-300 buffer (20 mM HEPES pH 7.5, 300 mM NaCl, 12.5μM spermidine, 0.01% Digitonin) containing 0.04 μM pnG-Tn5 and incubated at room temperature for 1 hour. Beads were washed twice again with Dig-300 buffer, resuspended in 300ul Tagmentation Buffer (Dig-300 buffer with 10 mM MgCl2), and incubated at 37℃ for 1 hour. Added 10 μL 0.5 M EDTA, 3 μL 10% SDS and 5 μL 20mg/mL Proteinase K to the reaction mixture and incubated at 55℃ for 1 hour to stop the Tagmentation and digest the protein. DNA fragments were extracted with saturated phenol and amplified in 50 μL PCR reaction (24 μL DNA, 10 μL 5×TAB, 5 μL P5 Primer, 5 μL P7 Primer, 5 μL PPM, 1 μL TAE). The PCR amplification was carried out at the following conditions: 72℃ 3min, 98℃ 30s, 98 ℃ 10s, 63℃ 30s, 72℃ 30s (13-15 cycles), 72℃ 5min, 4℃ ∞.      ATAC-seq was conducted primarily following previous studies47. About 50,000 PAM cells were lysed in 50 μL cold ATAC-seq Resuspension buffer (10 mmol/L Tris-HCl, pH 7.4, 10 mmol/L NaCl, 3 mmol/L MgCl2) containing 0.1% NP40, 0.1% Tween-20, and 0.01% digitonin and incubated on ice for 10 minutes. 1 mL cold ATAC-seq Resuspension buffer was added to stop the lysis. Cells were then pelleted at 500 RCF for 10 minutes at 4°C to remove the supernatant. The following transposition reaction mix (25 µL Illumina Tagment DNA buffer Cat#: 15027866, 16.5 µL 1 × PBS, 0.5 µL 1% digitonin, 0.5 μL 10% Tween-20, 2.5 μL ddH2O and 2.5 μL Illumina Tagment DNA enzyme (Cat#: 15027916) was added to the cell pellet and incubated at 37°C for 1 hour on thermocycler. ZYMO RESEARCH DNA Clean & Concentrator-5 Kit (Cat#: D4013) was used to purify the DNA fragments. The Transposed DNA quality control and library preparation was performed according to a previous study47. Finally, library was electrophoresed in a 2% high-resolution agarose gel and 100-1000 bp fragments were cut out and sequenced by using Illumina Novaseq 6000 platform.     10 million cells were used in the BL-HiChIP experiments. Cultured cells were collected and washed once with 1×PBS. The cells were then resuspended in 1% formaldehyde solution and incubated at room temperature for 10 minutes with rotation. Glycine was added to a final concentration of 0.125M and incubated for 5 minutes at room temperature to stop the cross-linking reaction. Crosslinked cells were resuspended in 1mL cold Hi-C lysis buffer (10mM Tris-HCl pH8.0、10Mm NaCl、0.2% v/v Igepal CA630、1× protease inhibitors) and incubated on ice for 30min. After spinning down at 2500g for 5 minutes at 4℃, the pellet was washed with cold Hi-C lysis buffer and CutSmart wash buffer (1×CutSmart and 0.1% Tween-20). Resuspended the pellet in 1mL SDS buffer (1×CutSmart and 0.3% SDS), incubated at 62℃ for 10 minutes, and then immediately added 200μL 10% TritionX-100 and incubated at room temperature for another10 minutes to neutralize the SDS. Samples were centrifuge at 2500g for 5min at 4 ℃ to remove the supernatant. Pellet was then washed twice with CutSmart wash buffer, and again resuspended in 500 µL restriction digest mix (1×CutSmart, 1% TritonX-100, 1× protease inhibitors and 0.6 U/µL Alu1) and incubated at 37℃ for 7 hours in Thermomixer (1200rpm 15s/pause 2 minutes). After pelleting and washing once with 1×NEB buffer 2, the nuclei were resuspended in 500 µL A tailing solution (1×NEB buffer 2, 1% TritonX-100, 0.2 mM dATP and 10 µL Klenow 3’-5’ exo-) and incubated at 37℃ for 1 hours. Pelleting again, the nuclei was washed twice with 1×T4 DNA ligase buffer containing 1% TritonX-100,  and then, pelleted, resuspend in 996µL ligation mix (1×T4 DNA ligase buffer, 1% TritonX-100, 0.1mg/mL BSA and 6 µL T4 DNA liagse) with 4µL (200 ng/µL) Phosphorthioate & Biotin Linker (F:CG*CG*AT*AT*C/iBiotin-dT/TA*TC*TG*ACT, R:GT*CA*GA*TA*AG*AT*AT*CG*CGT) and incubate at 16℃ overnight. After in situ ligation, the nuclei were pelleted at 2500g for 5min and resuspended in 1mL Nuclear lysis buffer (50Mm Tris-HCl pH7.5, 350mM NaCl, 1mM EDTA, 1% TritonX-100, 0.1% Sodium Deoxycholate, 0.1%SDS and 1× protease inhibitors). The entire suspension was transferred into a new falcon tub and sonicated in ice bath for 4 minutes (pulse on for 30 seconds, pulse off for 30 seconds at an amplitude of 37%). After spin down at 6000rpm, 4℃ for 10min, the supernatant was incubated with prepared antibody-coupled beads at 4°C overnight. Preformed three washes with each buffer: PRPA wash buffer (50 Mm HEPES pH 8.0, 1% NP-40, 0.7% DOC, 0.5 M LiCl, 1 Mm EDTA and 1×Protease inhibitor); High salt wash buffer (20 Mm Tris-HCl pH 8.0, 2 Mm EDTA, 500 mM NaCl, 1% TritionX-100 and 0.1% SDS); Low salt wash buffer（50Mm HEPES pH7.5, 150Mm NaCl, 1mM EDTA, 1% TritonX-100, 0.1% Sodium Deoxycholate, 0.1%SDS and 1×Protease inhibitor); TE buffer (10 mM Tris-HCl pH8.0 and 1mM EDTA). Resuspended the beads into 500 µL Elution buffer (10 mM Tris-HCl pH8.0, 1mM EDTA and 1% SDS) and incubated at 65℃ for 30 minutes with 1300rpm to release captured chromatin. Placed the tube on a magnet stand and transferred the liquid to a new tube, added 30 µL 20mg/ml Proteinase K and incubated at 55℃ for more than 4 hours with 600 RPM mixing. After proteinase K has cleared all the proteins, added an equal volume of Phenol: Chloroform: Isoamyl (25:24:1) alcohol and shake the tube vigorously, centrifuged at 1500 rpm for 10 minutes and extracted the supernatant. Added 50μL 3M NaAc, 2μL 20mg/ml glycogen and 550μL isopropanol to the supernatant, mixed gently and incubated at -20℃ for 2 hours. Spined at 1500rpm for 30 minutes at 4℃ and washed the pellet with cold 75% ethanol, removed all the liquid and added 30μL ddH2O to dissolve the ChIP-DNA. Qubit 3.0 was used to estimate the ChIP-DNA concentration. For H3K27ac BL-HiChIP with 1×107 cells, the expected ChIP-DNA output was between 50ng to 150ng. Next used the TruePrep DNA Library Preparation Kit (Vazyme TD501) for library construction following the manufacturer’s recommendations, and put all the sample into Streptavidin C1 beads (Thermo 65001) for biotin pull-down. The enriched DNA quality control and library preparation was preformed following the Hi-ChIP process.    About 50,000 Culturing PAM cells were collected and washed twice with PBS. Added cold lysis buffer (10mM Tris-HCL pH 7.5，10mM NaCl，3mM MgCl2，0.1% Tween-20，0.1% IGEPAL-CA630) to resuspend the cells and incubated on ice for 3min. The lysed cells were collected by centrifugation at 500×g for 5 min at 4°C. After washing with PBS, the nuclei were then resuspended with 1 mL of high salt tagmentation buffer (36.3 mM Tris-HCl, 72.6 mM KCl, 11 mM MgCl2, 17.6% DMF). Adjusted nucleus concentration to 2000 / 9 μL and dispensed nucleus suspension into 96-well plates at 9 µl per well. Added 1µl of Barcoded-Tn5 to each well, mixed thoroughly and incubated in PCR at 37°C for 1h. After incubation, added 10 μL of 40 mM EDTA and incubated for 10 min at 37°C to terminate the transposition reaction. Collected nuclei and resuspended in PBS(5 nuclei / μL). Redispersed 20 nuclei per well into new 96-well plates and then 1 μL of 0.2% SDS was added to each well and incubated at 72°C for 10 min in PCR to break up the nuclei. Subsequently, 5 μL PCR Primer Mix (10 pmol index i5 + 10 pmol index i7) and PCR Enzyme Mix (4 μL 5× TAB + 0.4 μL TAE + 7.6 μL H2O) were added to each well and PCR amplification was carried out at the following conditions ：72°C for 5 min, 98°C for 30 s, (98°C for 15 s, 60°C for 30 s, 72°C for 60 s) × 12 cycles, hold at 12°C. The amplified product was purified using DNA Clean & Concentrator-500 (zymo) and fragment selection was performed with KAPA Pure Beads. The final libraries were quantified with Qubit and the fragment distribution of the libraries were detected with Agilent 2100. Libraries were sequenced in Novaseq 6000 (illumina).

tag: antibody

value: H3K27ac HiChIP

value: alveolar macrophages

tag: agent

value: African swine fever virus

tag: time point

value: male

value: PAM


title: LFHO19

value: 10percent fat diet hyperoxia


title: PAM_0h_H3K27ac_HiChIP_rep2

description:
H3K27ac HiChIP of porcine alveolar macrophages
real_FDR.merged.0h.bedpe

source_name: H3K27ac HiChIP of Sus scrofa : alveolar macrophages of 1-month-old male


title: Dere.H3K9me3.2 [CUT&RUN]

city: Cambridge

first: Susanne

last: Bornelöv

address: Robinson Way

department: Cancer Research UK - Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Assembly: GCF_003286155
Sequencing adapters were removed using Trim Galore! (v0.6.4, ‑‑paired ‑‑stringency 6 ‑a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
The resulting reads were mapped to their respective reference genome using Bowtie (v1.2.3, ‑S ‑y ‑M 1 ‑‑best ‑‑strata ‑‑fr ‑‑minins 10 ‑‑maxins 600 ‑‑chunkmbs 2000 ‑‑nomaqround), reporting at most one hit for each read and considering insert sizes between 10 and 600nt.
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, ‑‑binSize 1 ‑‑ignoreForNormalization chrM ‑‑normalizeUsing CPM  ‑‑exactScaling ‑‑scaleFactor s ‑‑skipNonCoveredRegions ‑‑minMappingQuality 50 --extendReads --centerReads), where the scale factor, s, was set to the number of uniquely mapped reads divided by all mapped reads.
Supplementary files format and content: BigWig with read coverage per position across the genome.
Library strategy: CUT&RUN

organism: Drosophila erecta

source_name: ovary

growth_protocol: All flies were kept at 18 C or 25 C on standard cornmeal or propionic food.

extract_protocol:
10-20 fly ovaries were dissected in ice cold PBS per sample.  Ovaries were digested in 250 µl of dissociation buffer (0.5% Trypsin and 2.5 mg/ml Collagenase A in PBS) for an hour with shaking at 800 rpm at 30 °C.  The digestion was stopped with 250 µl of Schneider medium containing 10% FBS.  Cell suspensions were filtered through 40 µm strainers, pelleted and washed three times with Wash buffer and resuspended in 1 ml of Wash buffer. Following sample preparation, CUT&RUN was performed according to instructions in CUT&RUN protocol V.3 with some modifications ).  10 µl of activated Concanavalin A-coated magnetic beads (Bangs Laboratories) were added to each sample and rotated for 10 min at RT.  Bead-bound cells were incubated with 5 µl of antibody (Table S3) and 95 µl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin) overnight at 4 °C.  Bead-bound cells were washed twice with Dig-wash buffer (0.05% digitonin in Wash buffer).  Bead-bound cells were resuspended in Dig-wash buffer containing 1x CUTANA™ pAG-MNase (Epicypher) and rotated for 1 hr at RT.  Following pAG-MNase binding, bead-bound cells were washed twice with Dig-wash buffer and resuspended in 100 µl Dig-wash buffer.  Chromatin digestion was performed on ice for 30 min by adding 2 μL 100  CaCl2 mM.  Digestion was stopped by the addition of 2x STOP Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 µg/ml RNase A (Thermo Fisher Scientific), 50 µg/ml glycogen) and samples were incubated at 37 °C for 30 min to release DNA fragments into the solution.  After centrifugation, 0.1% SDS and 0.2 μg/μl Proteinase K were added to the supernatant and samples were incubated for 1 hour at 50 °C.  DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Sigma) according to the manufacturer’s instructions.
Libraries were prepared following the manufacturer’s instructions with NEBNext Ultra II DNA Library Prep Kit for Illumina.

value: ovary

value: H3K9me3 (active motif 39161)


title: Dere.IgG.1 [CUT&RUN]

value: WT

value: Rabbit Anti-mouse (Abcam ab6709)

tag: qc fail

value: TRUE


title: Dere.IgG.2 [CUT&RUN]


title: Dere.H3K9me3.1 [CUT&RUN]


title: PAM_6h_H3K27ac_HiChIP_rep2

tag: cell line


title: Dere.H3K27me3.2 [CUT&RUN]

value: H3K27me3 (cell signalling 9733S)


title: L3_T

value: longissimus dorsi muscle

value: Laiwu pig


title: LFHO20

value: Lung

tag: cell type

value: Alveolar Epithelial Type 2


title: LFHO18

tag: genotype

value: Wild Type


title: PAM_0h_H3K27ac_HiChIP_rep1

value: H3K27ac HiChIP


title: Dere.H3K27me3.1 [CUT&RUN]

tag: tissue


title: LFRA16

value: 10percent fat diet room air


title: Y3_T

value: Yorkshire pig


title: Dana.IgG.2 [CUT&RUN]

data_processing:
Assembly: GCF_003285975
Sequencing adapters were removed using Trim Galore! (v0.6.4, ‑‑paired ‑‑stringency 6 ‑a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
The resulting reads were mapped to their respective reference genome using Bowtie (v1.2.3, ‑S ‑y ‑M 1 ‑‑best ‑‑strata ‑‑fr ‑‑minins 10 ‑‑maxins 600 ‑‑chunkmbs 2000 ‑‑nomaqround), reporting at most one hit for each read and considering insert sizes between 10 and 600nt.
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, ‑‑binSize 1 ‑‑ignoreForNormalization chrM ‑‑normalizeUsing CPM  ‑‑exactScaling ‑‑scaleFactor s ‑‑skipNonCoveredRegions ‑‑minMappingQuality 50 --extendReads --centerReads), where the scale factor, s, was set to the number of uniquely mapped reads divided by all mapped reads.
Supplementary files format and content: BigWig with read coverage per position across the genome.
Library strategy: CUT&RUN

organism: Drosophila ananassae


title: L2_T


title: PAM_0h_scATAC

description: scATAC-seq of porcine alveolar macrophages

library_source: genomic single cell

data_processing:
Sequencing reads were aligned to the susScr11 reference genome
eaks for all cells were identified with MACS2 (version 2.2.7.1)
Assembly: Sscrofa11.1
Supplementary files format and content: bam,bigwig and peak

source_name: Single cell ATAC-seq of Sus scrofa : alveolar macrophages infected by African swine fever virus for 0h and 6h of 1-month-old male

value: alveolar macrophages

value: African swine fever virus

value: 0h and 6h

tag: Sex

value: male


title: LFRA18


title: LFHO16

value: 10percent fat diet hyperoxia


title: PAM_6h_ATAC_rep1

description:
ATAC-seq of porcine alveolar macrophages infected by African swine fever virus for 6h
6h_PAM_ATAC_rep.pooled.pval.signal.bigwig

source_name: ATAC-seq of Sus scrofa : alveolar macrophages infected by African swine fever virus for 6h of 1-month-old male

value: PAM


title: Dana.IgG.1 [CUT&RUN]

value: ovary

value: WT

value: Rabbit Anti-mouse (Abcam ab6709)


title: HFRA19

value: 60percent fat diet room air


title: LFHO17


title: L4_T

value: longissimus dorsi muscle

value: Laiwu pig


title: Dana.H3K9me3.2 [CUT&RUN]

value: H3K9me3 (active motif 39161)


title: PAM_0h_ATAC_rep2

description:
ATAC-seq of porcine alveolar macrophages
0h_PAM_ATAC_rep.pooled.pval.signal.bigwig

source_name: ATAC-seq of Sus scrofa : alveolar macrophages of 1-month-old male


title: HFRA18

value: Lung

value: Alveolar Epithelial Type 2

value: Wild Type


title: Dana.H3K9me3.1 [CUT&RUN]


title: PAM_0h_ATAC_rep1


title: Dana.H3K27me3.1 [CUT&RUN]

value: H3K27me3 (cell signalling 9733S)


title: HFRA16


title: PAM_6h_IgG_rep2

description: IgG CUT&Tag of porcine alveolar macrophages infected by African swine fever virus for 6h

data_processing:
Sequencing reads were aligned to the susScr11 reference genome
eaks for all cells were identified with MACS2 (version 2.2.7.1)
Assembly: Sscrofa11.1
Supplementary files format and content: bam,bigwig and peak
Library strategy: Cut & Tag

source_name: IgG CUT&Tag of Sus scrofa : alveolar macrophages infected by African swine fever virus for 6h of 1-month-old male

value: IgG CUT&Tag

value: alveolar macrophages


title: Dana.H3K27me3.2 [CUT&RUN]


title: PAM_6h_IgG_rep1

value: African swine fever virus


title: HFRA17


title: HFHO20

value: 60percent fat diet hyperoxia


title: D21 Embryoid Bodies

city: Ann Arbor

first: Joshua

last: Welch

state: MI

address: 100 Washtenaw Ave

institute: University of Michigan

description:
Library name: D21_EBs
Fresh frozen spatial transcriptome sequencing

data_processing:
Raw data were processed using BclConvert software (Illumina) was used to generate de-multiplexed FASTQ files
The CurioSeeker Pipeline (Curio Biosciences) was used to align reads and generate feature-spot matrices
Assembly: hg38
Supplementary files format and content: EB_barcodes.tsv: list of spatial barcodes
Supplementary files format and content: EB_genes.tsv: list of gene list
Supplementary files format and content: EB_MatchedBeadLocation.csv: spatial coordinates
Supplementary files format and content: EB_mMoleculesPerMatchedBead: cell by gene count matrix
Library strategy: Spatial Transcriptomics

source_name: Embryoid Body

extract_protocol:
Fresh frozen EBs were OCT embedded, and 10 um frozen sections were cut with cryostat
Spatial transcriptome sequence libraries were prepared with Curio Seeker protocol according to the manufactor's contruction protocol.

value: Embryoid Body

value: iPSCs


title: PAM_6h_pol2_rep2

description:
Pol2 CUT&Tag of porcine alveolar macrophages infected by African swine fever virus for 6h
6h_pol2_rep.pooled_x_ctl.pooled.pval.signal.bigwig

source_name: Pol2 CUT&Tag of Sus scrofa : alveolar macrophages infected by African swine fever virus for 6h of 1-month-old male

value: Pol2 CUT&Tag

value: male

value: PAM


title: PAM_6h_RNA_rep3_library

description: RNA-seq of porcine alveolar macrophages infected by African swine fever virus for 6h

source_name: RNA-seq of Sus scrofa : alveolar macrophages infected by African swine fever virus for 6h of 1-month-old male


title: PAM_6h_ATAC_rep2


title: HFHO18


title: PAM_6h_RNA_rep2_library


title: HFHO19


title: HFHO17


title: PAM_6h_H3K27me3_rep2

description:
H3K27me3 CUT&Tag of porcine alveolar macrophages infected by African swine fever virus for 6h
6h_H3K27me3_rep.pooled_x_ctl.pooled_no_chrMT.bw

source_name: H3K27me3 CUT&Tag of Sus scrofa : alveolar macrophages infected by African swine fever virus for 6h of 1-month-old male

value: H3K27me3 CUT&Tag


title: HFHO16


title: PAM_6h_RNA_rep1_library


title: PAM_6h_H3K27me3_rep1


title: MEF, nomal, MeRIP, Rep2

data_processing:
After obtaining raw data, paired-end reads were harvested and trimmed by fastp (version 0.20.1) to remove adaptor sequences and low-quality nucleotides.
High-quality reads were then aligned to ENSEMBL GRCh38 or GRCm39 reference genome using HISAT2 (version 2.2.1) with default parameters
For RNA-seq, featureCounts (version 2.0.1) software was used to count reads mapped to RefSeq genes, and differential gene expression analysis was conducted using DESeq2 R package (version 1.38.3).
m6A peaks on RefSeq transcripts and differentially m6A peaks were analyzed using exomePeak2 R package (version 1.10.0).
Assembly: GRCh38 and GRCm39
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 diffpeaks of Senescence vs nomal cells
Library strategy: MeRIP-seq

source_name: MEF

value: MEF

value: Mouse Embryonic Fibroblast


title: PAM_6h_H3K27ac_rep2

description:
H3K27ac CUT&Tag of porcine alveolar macrophages infected by African swine fever virus for 6h
6h_PAM_H3K27ac_rep.pooled_x_ctl.pooled.pval.signal.bigwig

source_name: H3K27ac CUT&Tag of Sus scrofa : alveolar macrophages infected by African swine fever virus for 6h of 1-month-old male

value: H3K27ac CUT&Tag


title: PAM_0h_RNA_rep3_library

description: RNA-seq of porcine alveolar macrophages

source_name: RNA-seq of Sus scrofa : alveolar macrophages of 1-month-old male


title: MEF, nomal, MeRIP, Rep1


title: PAM_0h_RNA_rep2_library

description: RNA-seq of porcine alveolar macrophages


title: PAM_6h_H3K27ac_rep1


title: MEF, replicative senescence, MeRIP,Rep2


title: PAM_6h_H3K4me3_rep2

description:
H3K4me3 CUT&Tag of porcine alveolar macrophages infected by African swine fever virus for 6h
6h_PAM_H3K4me3_rep.pooled_x_ctl.pooled.pval.signal.bigwig

source_name: H3K4me3 CUT&Tag of Sus scrofa : alveolar macrophages infected by African swine fever virus for 6h of 1-month-old male

value: H3K4me3 CUT&Tag


title: PAM_0h_RNA_rep1_library

description: RNA-seq of porcine alveolar macrophages


title: pTOsk-rhi-KD.2 [sRNA]

data_processing:
Adapters were removed using Trim Galore! (v0.6.4, ‑‑stringency 6 ‑‑length 18 ‑‑max_length 29 ‑q 0)
The resulting reads were mapped to dm6 using Bowtie (v2.3.1, -S -n 2 -M 1 ‑‑best ‑‑strata ‑‑nomaqround ‑‑chunkmbs 1024 ‑‑no-unal)
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, ‑‑binSize 1 ‑‑ignoreForNormalization chrM ‑‑normalizeUsing CPM  ‑‑exactScaling ‑‑scaleFactor s ‑‑skipNonCoveredRegions ‑‑minMappingQuality 255), where the scale factor, s, was set to the to the number of uniquely mapped reads divided by all mapped reads.
Additionally, ‘‑‑filterRNAstrand’ and ‘‑‑minFragmentLength 23 ‑‑maxFragmentLength 30’ was used to select piRNAs for each strand, separately.
Assembly: dm6
Supplementary files format and content: BigWig with read coverage per position across the genome for each strand.

organism: Drosophila melanogaster

growth_protocol:
Flies were kept at standard conditon at 25°C
All flies were kept at 18 C or 25 C on standard cornmeal or propionic food.

extract_protocol:
Regulatory small RNA extraction was performed as described in (Grentzinger et al. 2020).  Argonaute-small RNA complexes were isolated from 10 to 30 pairs of ovaries from 3-5-day-old flies using TraPR ion exchange spin columns (Lexogen, Catalog Nr.128.08).
gel-free protocol without size selection - Library preparation using QIAseq-miRNA kit

value: ovary

value: 3-6 day old

value: female

value: Nanos Gal4 VP16-expressed dsRNA-white BDSC_35573


title: PAM_6h_H3K4me3_rep1

value: alveolar macrophages


title: PAM_0h_IgG_rep2

description: IgG CUT&Tag of porcine alveolar macrophages

source_name: IgG CUT&Tag of Sus scrofa : alveolar macrophages of 1-month-old male

value: IgG CUT&Tag


title: pTOsk-rhi-KD.1 [sRNA]


title: PAM_6h_pol2_rep1

value: African swine fever virus


title: Sample_WTA_EV_RNA_WTB_EV_RNA_WTC_EV_RNA

city: Rochester

first: Iker

last: Martinez-Zalbidea

address: 1 Lomb Memorial Dr

department: Department of Biomedical Engineering

institute: Rochester Institute of Technology

description: Library name: WTA_EV_RNA_WTB_EV_RNA_WTC_EV_RNA

data_processing:
The raw reads generated from the Illumina basecalls were demultiplexed using bcl-convert version 4.1.7.
miRge2.0 (2.0.3) was used to align reads with bowtie (1.2.1.1) and identify miRs with the following project-specific parameters: miRge2.0 annotate -s fileList -d miRBase  -sp human -ad TGGAATTCTCGGGTGCCAAGG.
The differential expression analysis was performed using DESeq2-1.34.0 with a P-value threshold of 0.05 within R version 4.0.2 (https://www.R-project.org/).
PCA plot was generated within R using pcaExplorer c2.14.2 to measure sample expression variance. Heatmaps were generated using the pheatmap 1.0.12 package was given the rLog transformed expression values. Volcano plots and dot plots were created using ggplot2.
Assembly: GRCh38
Supplementary files format and content: Counts Table

source_name: Mesenchymal stem cell-derived extracellular vesicles

extract_protocol:
MSC-EV RNA was extracted with the Cell Culture Media Exosome Purification and RNA Isolation Mini Kit (Norgen Biotek, 60700) following the manufacturer’s instructions. RNA concentration was determined using the Nanophotometer N50 instrument (Implen). Prior to sequencing, RNA concentration and quality were assessed using the NanopDrop 1000 spectrophotometer and Agilent Bioanalyzer 2100.
500ng of Total RNA was utilized as input for sequencing library construction with the Illumina TruSeq Small RNA Library Prep kit (Illumina), following the manufacturer’s manual. Initially, 3’ and 5’ adaptors were diluted 2-fold for ligation, following 3’ adaptor ligation, RT primer incubation, and 5’ adaptor ligation. cDNA was synthesized, and library amplification was performed with 12 cycles of PCR. Library quantity and quality were determined with a Qubit fluorometer (ThermoFisher) and Tapestation 4200/Bioanalyzer/Fragment Analyzer (Agilent). Sample libraries were proportionally pooled and isolated from the PCR reaction mix using the Qiagen MinElute PCR Reaction Cleanup kit. Library fragments between 125 – 160bp were size-selected using a 3% cassette on a PippinHT (Sage Science). The size-selected library pool was then sequenced on an Illumina NextSeq 2000, generating single-end reads of 50nt.

value: WT-EV


title: MEF, nomal, RNA-seq, Rep2

description:
MEF_RNAseq_counts.txt
MEF_Y_2_RNAseq

data_processing:
After obtaining raw data, paired-end reads were harvested and trimmed by fastp (version 0.20.1) to remove adaptor sequences and low-quality nucleotides.
High-quality reads were then aligned to ENSEMBL GRCh38 or GRCm39 reference genome using HISAT2 (version 2.2.1) with default parameters
For RNA-seq, featureCounts (version 2.0.1) software was used to count reads mapped to RefSeq genes, and differential gene expression analysis was conducted using DESeq2 R package (version 1.38.3).
m6A peaks on RefSeq transcripts and differentially m6A peaks were analyzed using exomePeak2 R package (version 1.10.0).
Assembly: GRCh38 and GRCm39
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 diffpeaks of Senescence vs nomal cells


title: Sample_WB1_WB2_WB3

description: Library name: WB1_WB2_WB3

value: Mesenchymal stem cell-derived extracellular vesicles


title: Sample_WA1_WA2_WA3

description: Library name: WA1_WA2_WA3


title: pTOsk-Ez-KD.2 [sRNA]


title: PAM_0h_IgG_rep1


title: MEF, nomal, RNA-seq, Rep1

description:
MEF_RNAseq_counts.txt
MEF_Y_1_RNAseq


title: PAM_0h_pol2_rep2

description:
Pol2 CUT&Tag of porcine alveolar macrophages
0h_pol2_rep.pooled_x_ctl.pooled.pval.signal.bigwig

source_name: Pol2 CUT&Tag of Sus scrofa : alveolar macrophages of 1-month-old male

value: Pol2 CUT&Tag


title: pTOsk-Ez-KD.1 [sRNA]


title: Sample_TSGA_EV_RNA_TSGB_EV_RNA_TSGC_EV_RNA

description: Library name: TSGA_EV_RNA_TSGB_EV_RNA_TSGC_EV_RNA

value: TSG6 -EV


title: MEF, replicative senescence, RNA-seq,Rep2

description:
MEF_RNAseq_counts.txt
MEF_S_2_RNAseq


title: Sample_TB1_TB2_TB3

description: Library name: TB1_TB2_TB3


title: MEF, replicative senescence, RNA-seq, Rep1

description:
MEF_RNAseq_counts.txt
MEF_S_1_RNAseq


title: Sample_TA1_TA2_TA3

description: Library name: TA1_TA2_TA3


title: PAM_0h_pol2_rep1

value: male

value: PAM


title: PAM_0h_H3K27me3_rep2

description:
H3K27me3 CUT&Tag of porcine alveolar macrophages
0h_H3K27me3_rep.pooled_x_ctl.pooled_no_chrMT.bw

source_name: H3K27me3 CUT&Tag of Sus scrofa : alveolar macrophages of 1-month-old male

value: H3K27me3 CUT&Tag


title: Sample_NTA_EV_RNA_NTB_EV_RNA_NTC_EV_RNA

description: Library name: NTA_EV_RNA_NTB_EV_RNA_NTC_EV_RNA

value: NT-EV


title: WD_CCl4 _Dbi-/- -S27

city: PARIS

first: Guido

last: Kroemer

address: 15 rue de L'école de médecine

country: France

institute: Centre de Recherche des Cordeliers

data_processing:
FastQC V0.12.1
HISAT2 V2.2.1
Htseq-count V2.0.3
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw-count for each samples

source_name: Liver

extract_protocol:
Murine liver tissue samples were homogenized in QIAzol lysis reagent (Cat. 79306, QIAGEN, Hilden, Germany). Total RNA was extracted and purified by means of the miRNeasy Mini Kit (Cat. 217084, Qiagen), following the manufacturer's protocol.
Total RNA was subjected to RNA sequencing on a NovaSeq 6000 PE150 instrument by Novogene (London, UK). The RNA sequencing data were obtained in Fasta file format.

value: Liver

value: Dbi knockout

value: Western Diet with CCL4


title: MEF, replicative senescence, MeRIP, Rep1

extract_protocol:
RNA was extracted using Dynabeads® mRNA DIRECT (Thermo Fisher) to deplete ribosomal RNA and avoid DNA contamination. The purified product was divided into two parts, one for RNA-seq and the other for MeRIP-seq.
The fragmented mRNA underwent m6A IP using the EpiMark® N6-Methyladenosine Enrichment Kit (NEB) following the manufacturer's protocol. RNA libraries were prepared for both input RNA and m6A-enriched mRNA after IP using the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) according to the manufacturer's instructions.

value: MEF

value: Mouse Embryonic Fibroblast


title: PAM_0h_H3K27me3_rep1


title: WD_CCl4 _Dbi-/- -S26


title: Sample_NB1_NB2_NB3

description: Library name: NB1_NB2_NB3


title: MCF7; HD; ER-Y537S; Imlunestrant; 6hr; biol rep 1

first: Rinath

last: Jeselsohn

address: 450 Brookline Ave.

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: Library name: MDL62

data_processing:
The VIPER pipeline was used for alignment and quality control of samples using STAR v2.7.0f for alignment, cufflinks v2.2.1 for transcript assembly, and RSeQC v2.6.2 for quality control metrics.
Downstream analysis was done on raw STAR gene counts with DESeq2 v1.44.0 and ashr v2.2-63. cameraPR from the limma v3.60.6 R package was used for gene set testing with genes preranked by their Wald statistic from DESeq2 testing.
Assembly: hg19, GTF annotation taken from the Broad Institute's Trinity Cancer Transcriptome Analysis Toolkit (CTAT). See https://github.com/TrinityCTAT/Trinity_CTAT/wiki and https://github.com/STAR-Fusion/STAR-Fusion/wiki
Supplementary files format and content: STAR raw gene counts in csv text file raw-counts-cellline.csv, with column (sample) names corresponding to the library name metadata field.

source_name: Breast cancer

growth_protocol: MCF7 and T47D cells were grown according to ATCC.

extract_protocol:
Cell lines were snap frozen followed by RNA extraction using Trizol and the Qiagen Rneasy kit.
Novagene protocol for polyA capture, RNA fragmentation, cDNA reverse transcription, RNA library preparation and quality control.

value: Breast cancer

value: ER+ breast cancer

tag: media

value: HD

tag: esr1 status

value: Imlunestrant

tag: timepoint


title: MCF7; HD; ER-Y537S; Imlunestrant; 6hr; biol rep 2

description: Library name: MDL63

tag: treatment


title: MCF7; HD; ER-Y537S; Imlunestrant; 12hr; biol rep 2

description: Library name: MDL123


title: MCF7; HD; ER-Y537S; Imlunestrant; 12hr; biol rep 1

description: Library name: MDL122


title: WD_CCl4 _Dbi-/- -S25


title: Sample_NA1_NA2_NA3

description: Library name: NA1_NA2_NA3


title: PAM_0h_H3K27ac_rep2

description:
H3K27ac CUT&Tag of porcine alveolar macrophages
0h_PAM_H3K27ac_rep.pooled_x_ctl.pooled.pval.signal.bigwig

source_name: H3K27ac CUT&Tag of Sus scrofa : alveolar macrophages of 1-month-old male

value: H3K27ac CUT&Tag

value: alveolar macrophages


title: MCF7; HD; ER-Y537S; Fulvestrant; 12hr; biol rep 2

description: Library name: MDF123

value: Fulvestrant


title: WD_CCl4 _Dbi-/- -S24


title: PAM_0h_H3K27ac_rep1


title: MCF7; HD; ER-Y537S; Fulvestrant; 12hr; biol rep 1

description: Library name: MDF122


title: WD_CCl4 _Dbi+/+ -S23

value: WT


title: S2-siRL.Pc-CBX1.FLAG.3 [CUT&RUN]

description: Library name: S2-siRL.Pc-CBX1.FLAG.3

data_processing:
*library strategy: CUT&RUN
Sequencing adapters were removed using Trim Galore! (v0.6.4, ‑‑paired ‑‑stringency 6 ‑a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
The resulting reads were mapped to their respective reference genome using Bowtie (v1.2.3, ‑S ‑y ‑M 1 ‑‑best ‑‑strata ‑‑fr ‑‑minins 10 ‑‑maxins 600 ‑‑chunkmbs 2000 ‑‑nomaqround), reporting at most one hit for each read and considering insert sizes between 10 and 600nt.
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, ‑‑binSize 1 ‑‑ignoreForNormalization chrM ‑‑normalizeUsing CPM  ‑‑exactScaling ‑‑scaleFactor s ‑‑skipNonCoveredRegions ‑‑minMappingQuality 50 --extendReads --centerReads), where the scale factor, s, was set to the number of uniquely mapped reads divided by all mapped reads.
Assembly: dm6
Supplementary files format and content: BigWig with read coverage per position across the genome.
Supplementary files format and content: BED-like files with differentially bound peaks, fields include: chromosome, start, end, log2(mean), log2(mean siRen), log2(mean siEz), log2FC, p, padj.
Supplementary files format and content: BroadPeak files from MACS2.
Supplementary files format and content: NarrowPeak files from MACS2.

growth_protocol: Drosophila Schneider 2 (S2) cells were purchased from Thermo Fisher Scientific (R69007) and were grown at 26 °C in Schneider media (Gibco) supplemented with 10% Heat-Inactivated FBS (Sigma).

extract_protocol:
1 million cells per sample were harvested and washed three times with Wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM spermidine supplemented with protease inhibitors) and resuspended in 1 ml of Wash buffer. Following sample preparation, CUT&RUN was performed according to instructions in CUT&RUN protocol V.3 with some modifications ).  10 µl of activated Concanavalin A-coated magnetic beads (Bangs Laboratories) were added to each sample and rotated for 10 min at RT.  Bead-bound cells were incubated with 5 µl of antibody (Table S3) and 95 µl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin) overnight at 4 °C.  Bead-bound cells were washed twice with Dig-wash buffer (0.05% digitonin in Wash buffer).  Bead-bound cells were resuspended in Dig-wash buffer containing 1x CUTANA™ pAG-MNase (Epicypher) and rotated for 1 hr at RT.  Following pAG-MNase binding, bead-bound cells were washed twice with Dig-wash buffer and resuspended in 100 µl Dig-wash buffer.  Chromatin digestion was performed on ice for 30 min by adding 2 μL 100  CaCl2 mM.  Digestion was stopped by the addition of 2x STOP Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 µg/ml RNase A (Thermo Fisher Scientific), 50 µg/ml glycogen) and samples were incubated at 37 °C for 30 min to release DNA fragments into the solution.  After centrifugation, 0.1% SDS and 0.2 μg/μl Proteinase K were added to the supernatant and samples were incubated for 1 hour at 50 °C.  DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Sigma) according to the manufacturer’s instructions.
Libraries were prepared following the manufacturer’s instructions with NEBNext Ultra II DNA Library Prep Kit for Illumina.

treatment_protocol: For knockdown experiments, two rounds of electroporation (48hrs apart) were performed using the Cell Line Nucleofector kit V (Amaxa Biosystems) and the program G-030, as described (Batki et al. 2019).  Chromodomain constructs were co-transfected with 200 pmol of siRNA duplexes during the second nucleofection round or transfected using the TransIT®-Insect Transfection Reagent 24hrs after the second nucleofection round.  Cells were collected 5 days after the first nucleofection round.

value: siRen

value: ANTI-FLAG(R) M2 (Sigma Aldrich F1804)


title: PAM_0h_H3K4me3_rep1

description:
H3K4me3 CUT&Tag of porcine alveolar macrophages
0h_PAM_H3K4me3_rep.pooled_x_ctl.pooled.pval.signal.bigwig

source_name: H3K4me3 CUT&Tag of Sus scrofa : alveolar macrophages of 1-month-old male

value: H3K4me3 CUT&Tag

value: male

value: PAM


title: MCF7; HD; ER-Y537S; Fulvestrant; 6hr; biol rep 2

description: Library name: MDF62


title: WD_CCl4 _Dbi+/+ -S22

value: Liver


title: PBMC_RNA_rep3_library

description: RNA-seq of PBMC

source_name: RNA-seq of Sus scrofa : PBMC of 1-month-old male

value: PBMC


title: S2-siRL.Pc-CBX1.FLAG.1 [CUT&RUN]

description: Library name: S2-siRL.Pc-CBX1.FLAG.1


title: WD_CCl4 _Dbi+/+ -S21

value: Western Diet with CCL4


title: PAM_0h_H3K4me3_rep2


title: MCF7; HD; ER-Y537S; Vehicle (DMSO); 12hr; biol rep 1

description: Library name: MDD122

value: Vehicle (DMSO)


title: WD_CCl4 _Dbi+/+ -S20


title: S2-siRL.2xRhi.FLAG.1 [CUT&RUN]

description: Library name: S2-siRL.2xRhi.FLAG.1


title: HFD_DEN_KLH-DBI-S19

value: High Fat Diet with DEN

value: KLH-ACBP


title: PBMC_RNA_rep1_library

description: RNA-seq of PBMC


title: MCF7; HD; ER-Y537S; Vehicle (DMSO); 12hr; biol rep 2

description: Library name: MDD123

value: Breast cancer

value: ER+ breast cancer

value: HD


title: MCF7; HD; ER-Y537S; Fulvestrant; 6hr; biol rep 1

description: Library name: MDF61


title: S2-siRL.Pc-CBX1.FLAG.2 [CUT&RUN]

description: Library name: S2-siRL.Pc-CBX1.FLAG.2


title: HFD_DEN_KLH-DBI-S18


title: MCF7; HD; ER-Y537S; Vehicle (DMSO); 6hr; biol rep 1

description: Library name: MDD62


title: MCF7; HD; ER-Y537S; Vehicle (DMSO); 6hr; biol rep 2

description: Library name: MDD63


title: HFD_DEN_KLH-DBI-S17


title: S2-siRL.2xPc.FLAG.2 [CUT&RUN]

description: Library name: S2-siRL.2xPc.FLAG.2


title: Lymphocyte_RNA_rep1_library

description: RNA-seq of lymphocyte

source_name: RNA-seq of Sus scrofa : lymphocyte of 1-month-old male

value: lymphocyte

value: Lymphocyte


title: S2-siRL.2xRhi-F48A.FLAG.1 [CUT&RUN]

description: Library name: S2-siRL.2xRhi-F48A.FLAG.1


title: MCF7; HD; ER-WT; Imlunestrant + E2; 12hr; biol rep 1

description: Library name: MEL121

value: ER-WT

value: Imlunestrant + E2


title: 3D4_RNA_rep3_library

description: RNA-seq of 3D4 cell

source_name: RNA-seq of Sus scrofa : 3D4 cell

value: 3D4 cell


title: S2-siRL.2xRhi.FLAG.2 [CUT&RUN]

description: Library name: S2-siRL.2xRhi.FLAG.2

value: siRen

value: ANTI-FLAG(R) M2 (Sigma Aldrich F1804)


title: PBMC_RNA_rep2_library

description: RNA-seq of PBMC

value: male


title: HFD_DEN_KLH-DBI-S16

value: Liver

value: WT


title: MCF7; HD; ER-WT; Imlunestrant + E2; 6hr; biol rep 2

description: Library name: MEL63


title: S2-siRL.2xCBX1.FLAG.2 [CUT&RUN]

description: Library name: S2-siRL.2xCBX1.FLAG.2


title: S2-siRL.2xPc.FLAG.1 [CUT&RUN]

description: Library name: S2-siRL.2xPc.FLAG.1


title: 3D4_RNA_rep2_library

description: RNA-seq of 3D4 cell


title: HFD_DEN_KLH-S14

value: KLH


title: S2-siRL.2xRhi-F48A.FLAG.2 [CUT&RUN]

description: Library name: S2-siRL.2xRhi-F48A.FLAG.2


title: HFD_DEN_KLH-S13


title: 3D4_RNA_rep1_library

description: RNA-seq of 3D4 cell


title: S2-siRL.2xCBX1.FLAG.1 [CUT&RUN]

description: Library name: S2-siRL.2xCBX1.FLAG.1


title: MCF7; HD; ER-WT; Fulvestrant + E2; 12hr; biol rep 2

description: Library name: MEF62

value: Fulvestrant + E2


title: Lymphocyte_RNA_rep2_library

description: RNA-seq of lymphocyte


title: Lymphocyte_RNA_rep3_library

description: RNA-seq of lymphocyte


title: S2-siRL.1xRhi.FLAG.2 [CUT&RUN]

description: Library name: S2-siRL.1xRhi.FLAG.2


title: S2-siRL.1xRhi.FLAG.1 [CUT&RUN]

description: Library name: S2-siRL.1xRhi.FLAG.1


title: MCF7; HD; ER-WT; Imlunestrant + E2; 12hr; biol rep 2

description: Library name: MEL123


title: HFD_DEN_KLH-S12

value: High Fat Diet with DEN


title: MCF7; HD; ER-WT; Fulvestrant + E2; 6hr; biol rep 2

description: Library name: MEF63


title: HFD_DEN_KLH-S11


title: WD_CCl4_KLH-ACBP-S10

value: Western Diet with CCL4

value: KLH-ACBP


title: S2-siKipf.Pc-CBX1.FLAG.3 [CUT&RUN]

description: Library name: S2-siKipf.Pc-CBX1.FLAG.3

value: siKipf


title: HFD_DEN_KLH-S15


title: MCF7; HD; ER-WT; Fulvestrant + E2; 6hr; biol rep 1

description: Library name: MEF123

value: Breast cancer

value: ER+ breast cancer

value: HD


title: MCF7; HD; ER-WT; Fulvestrant + E2; 12hr; biol rep 1

description: Library name: MEF121

value: ER-WT


title: S2-siKipf.Pc-CBX1.FLAG.2 [CUT&RUN]

description: Library name: S2-siKipf.Pc-CBX1.FLAG.2


title: MCF7; HD; ER-WT; E2; 12hr; biol rep 2

description: Library name: MED123


title: S2-siKipf.Pc-CBX1.FLAG.1 [CUT&RUN]

description: Library name: S2-siKipf.Pc-CBX1.FLAG.1


title: MCF7; HD; ER-WT; E2; 12hr; biol rep 1

description: Library name: MED121


title: WD_CCl4_KLH-ACBP-S9


title: WD_CCl4_KLH-ACBP-S8


title: WD_CCl4_KLH-ACBP-S7


title: S2-siKipf.2xRhi.FLAG.2 [CUT&RUN]

description:
Library name: S2-siKipf.2xRhi.FLAG.2
2xRhi.siKipf_2xRhi.siRen.down.broad.bed
2xRhi.siKipf_2xRhi.siRen.down.narrow.bed


title: S2-siKipf.2xRhi.FLAG.1 [CUT&RUN]

description:
Library name: S2-siKipf.2xRhi.FLAG.1
2xRhi.siKipf_2xRhi.siRen.down.broad.bed
2xRhi.siKipf_2xRhi.siRen.down.narrow.bed


title: MCF7; HD; ER-WT; Imlunestrant + E2; 6hr; biol rep 1

description: Library name: MEL62

value: Imlunestrant + E2


title: WD_CCl4_KLH-ACBP-S6


title: MCF7; HD; ER-WT; E2; 6hr; biol rep 2

description: Library name: MED63


title: WD_CCl4_KLH-S5


title: S2-siKipf.2xPc.FLAG.2 [CUT&RUN]

description: Library name: S2-siKipf.2xPc.FLAG.2


title: MCF7; HD; ER-WT; Imlunestrant; 12hr; biol rep 1

description: Library name: MNL121

value: Imlunestrant


title: MCF7; HD; ER-WT; Imlunestrant; 12hr; biol rep 2

description: Library name: MNL123


title: WD_CCl4_KLH-S3


title: S2-siKipf.2xPc.FLAG.1 [CUT&RUN]

description: Library name: S2-siKipf.2xPc.FLAG.1


title: MCF7; HD; ER-WT; Imlunestrant; 6hr; biol rep 2

description: Library name: MNL63


title: S2-siEz.Pc-CBX1.FLAG.3 [CUT&RUN]

description:
Library name: S2-siEz.Pc-CBX1.FLAG.3
Pc_CBX1.siEz_Pc_CBX1.siRen.down.broad.bed
Pc_CBX1.siEz_Pc_CBX1.siRen.up.broad.bed
Pc_CBX1.siEz_Pc_CBX1.siRen.down.narrow.bed
Pc_CBX1.siEz_Pc_CBX1.siRen.up.narrow.bed

value: siEz


title: S2-siKipf.2xCBX1.FLAG.2 [CUT&RUN]

description:
Library name: S2-siKipf.2xCBX1.FLAG.2
2xCBX1.siKipf_2xCBX1.siRen.up.broad.bed
2xCBX1.siKipf_2xCBX1.siRen.up.narrow.bed

value: ANTI-FLAG(R) M2 (Sigma Aldrich F1804)


title: MCF7; HD; ER-WT; Fulvestrant; 12hr; biol rep 2

description: Library name: MNF123

value: Fulvestrant


title: WD_CCl4_KLH-S4

value: Liver


title: T43

city: HangZhou

first: Xiaoqin

last: Liu

state: ZheJiang

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

institute: Westlake University

data_processing:
Raw reads were trimmed by TrimGalore with paired end mode and default parameter. Quality control was done with fastqc . Then UMI-tools was used to get the count matrix. Briefly, top 100 barcode list were retained using whitelist tool in UMI-tools . Then barcode and UMI information which were extracted from read2 using extract tool in UMI-tools was added to read1. After that, read1 were aligned to the mm10 genome using STAR with default parameter except that the outFilterMultimapNmax was set to 1. Finally, we got the count matrix file, in which the number of UMIs represents transcript number of each gene within each individual cell, using featurecounts and count tools in UMI-tools.
Assembly: mm10
Supplementary files format and content: count expression profile

source_name: mammary gland

extract_protocol:
FACS sorted single cells were directly sorted into 96-well plate containing lysis buffer using FACS. Single cell was immediately lysed at 70 degree for 3min in the PCR system.
Single cell RNA libraries were prepared for sequencing using 3’ UTR Smartseq protocols. The sample was reverse transcribed to cDNA using SuperScriptIIreverse transcriptase (invitrogen, 18064-071) with a template switch oligo (TSO) primer and a sample-specific 25 nt oligo dT reverse transcription primer. Then the cDNA was amplified by 16 cycles of PCR with 3’P2 primer and IS primer using KAPA HiFi HotStart Ready Mix (Kapa Biosystem, KK2602). The barcoded DNAs were amplified using biotinylated pre-index primers. After purified by AMpure XP beads, cDNA was sonicated to approximately 300 bp fragments using Covaris ME220. 3’ terminal of the cDNA was enriched using Dynabeads® MyOne Streptavidin C1 beads (Invitrogen, 65001). The RNA-seq libraries were constructed using the Kapa Hyper Prep Kit (Kapa Biosystem, KK8504) according to the manufacturer’s instructions.; ChIP DNA library was performed by VAHTS Universal DNA Library Prep Kit for Illumina V2 (Vazyme, ND606). Briefly, after end preparation and adapter ligation, ChIP DNA was amplified 12 cycles and purified using AMpure XP beads (Beckman, A63881) twice and then were submitted to 150 bp paired-end sequencing on an Illumina novaseq 6000 platform (Novogene).

tag: strain

value: mammary gland

tag: tissue source

value: TEB


title: MCF7; HD; ER-WT; Imlunestrant; 6hr; biol rep 1

description: Library name: MNL61


title: WD_CCl4_KLH-S2

value: WT

value: KLH


title: S2-siEz.Pc-CBX1.FLAG.2 [CUT&RUN]

description:
Library name: S2-siEz.Pc-CBX1.FLAG.2
Pc_CBX1.siEz_Pc_CBX1.siRen.down.broad.bed
Pc_CBX1.siEz_Pc_CBX1.siRen.up.broad.bed
Pc_CBX1.siEz_Pc_CBX1.siRen.down.narrow.bed
Pc_CBX1.siEz_Pc_CBX1.siRen.up.narrow.bed


title: WD_CCl4_KLH-S1

value: Western Diet with CCL4


title: MCF7; HD; ER-WT; Fulvestrant; 12hr; biol rep 1

description: Library name: MNF122


title: S2-siEz.Pc-CBX1.FLAG.1 [CUT&RUN]

description:
Library name: S2-siEz.Pc-CBX1.FLAG.1
Pc_CBX1.siEz_Pc_CBX1.siRen.down.broad.bed
Pc_CBX1.siEz_Pc_CBX1.siRen.up.broad.bed
Pc_CBX1.siEz_Pc_CBX1.siRen.down.narrow.bed
Pc_CBX1.siEz_Pc_CBX1.siRen.up.narrow.bed


title: T42


title: S2-siEz.2xRhi.FLAG.2 [CUT&RUN]

description:
Library name: S2-siEz.2xRhi.FLAG.2
2xRhi.siEz_2xRhi.siRen.down.broad.bed
2xRhi.siEz_2xRhi.siRen.up.broad.bed
2xRhi.siEz_2xRhi.siRen.down.narrow.bed
2xRhi.siEz_2xRhi.siRen.up.narrow.bed


title: T33


title: S2-siEz.2xPc.FLAG.2 [CUT&RUN]

description:
Library name: S2-siEz.2xPc.FLAG.2
2xPc.siEz_2xPc.siRen.down.broad.bed
2xPc.siEz_2xPc.siRen.up.broad.bed
2xPc.siEz_2xPc.siRen.down.narrow.bed
2xPc.siEz_2xPc.siRen.up.narrow.bed


title: T34


title: S2-siEz.2xPc.FLAG.1 [CUT&RUN]

description:
Library name: S2-siEz.2xPc.FLAG.1
2xPc.siEz_2xPc.siRen.down.broad.bed
2xPc.siEz_2xPc.siRen.up.broad.bed
2xPc.siEz_2xPc.siRen.down.narrow.bed
2xPc.siEz_2xPc.siRen.up.narrow.bed


title: S2-siEz.2xCBX1.FLAG.2 [CUT&RUN]

description:
Library name: S2-siEz.2xCBX1.FLAG.2
2xCBX1.siEz_2xCBX1.siRen.down.broad.bed
2xCBX1.siEz_2xCBX1.siRen.up.broad.bed
2xCBX1.siEz_2xCBX1.siRen.down.narrow.bed
2xCBX1.siEz_2xCBX1.siRen.up.narrow.bed


title: MCF7; HD; ER-WT; E2; 6hr; biol rep 1

description: Library name: MED62


title: MCF7; HD; ER-WT; Fulvestrant; 6hr; biol rep 1

description: Library name: MNF61


title: S2-siEz.2xCBX1.FLAG.1 [CUT&RUN]

description:
Library name: S2-siEz.2xCBX1.FLAG.1
2xCBX1.siEz_2xCBX1.siRen.down.broad.bed
2xCBX1.siEz_2xCBX1.siRen.up.broad.bed
2xCBX1.siEz_2xCBX1.siRen.down.narrow.bed
2xCBX1.siEz_2xCBX1.siRen.up.narrow.bed


title: MCF7; HD; ER-WT; Vehicle (DMSO); 12hr; biol rep 1

description: Library name: MND122

value: Vehicle (DMSO)


title: MCF7; HD; ER-WT; Fulvestrant; 6hr; biol rep 2

description: Library name: MNF63


title: MCF7; HD; ER-WT; Vehicle (DMSO); 6hr; biol rep 2

description: Library name: MND63


title: N24

value: nipple


title: T32


title: Nos-kipf-KD.3 [sRNA]

data_processing:
Adapters were removed using Trim Galore! (v0.6.4, --stringency 6 --length 18 --max_length 29 -q 0)
The resulting reads were mapped to dm6 using Bowtie (v2.3.1, -S -n 2 -M 1 --best --strata --nomaqround --chunkmbs 1024 --no-unal)
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, --binSize 1 --ignoreForNormalization chrM --normalizeUsing CPM  --exactScaling --scaleFactor s --skipNonCoveredRegions --minMappingQuality 255), where the scale factor, s, was set to the to the number of uniquely mapped reads divided by all mapped reads.
Additionally, '--filterRNAstrand' and '--minFragmentLength 23 --maxFragmentLength 30' was used to select piRNAs for each strand, separately.
Assembly: dm6
Supplementary files format and content: BigWig with read coverage per position across the genome for each strand.

source_name: ovary

growth_protocol: Flies were kept at standard conditon at 25°C

extract_protocol:
Regulatory small RNA extraction was performed as described in (Grentzinger et al. 2020).  Argonaute-small RNA complexes were isolated from 10 to 30 pairs of ovaries from 3-5-day-old flies using TraPR ion exchange spin columns (Lexogen, Catalog Nr.128.08).
Small RNA-Seq Library Prep Kit from Lexogen

value: ovary

tag: age

value: 3-6 day old

value: female

value: Nanos Gal4 VP16-expressed shRNA-Kipferl  VDRC_314048


title: T31


title: MCF7; HD; ER-WT; Vehicle (DMSO); 6hr; biol rep 1

description: Library name: MND62

value: Breast cancer

value: ER+ breast cancer

value: HD

value: ER-WT


title: N23


title: T47D; HD; ER-Y537S; Imlunestrant; 12hr; biol rep 2

description: Library name: TDL122

value: Imlunestrant


title: N22


title: T47D; HD; ER-Y537S; Imlunestrant; 12hr; biol rep 1

description: Library name: TDL121


title: Nos-Ez-w-dKD.2 [sRNA]

value: Nanos Gal4 VP16-expressed dsRNA-white BDSC_35573 and dsRNA-E(z) BDSC_36068


title: T47D; HD; ER-Y537S; Imlunestrant; 6hr; biol rep 2

description: Library name: TDL63


title: Nos-kipf-KD.1 [sRNA]


title: D62

value: mammary gland

value: duct


title: Nos-Ez-kipf-dKD.2 [sRNA]

value: Nanos Gal4 VP16-expressed shRNA-Kipferl VDRC_314048 and dsRNA-E(z) BDSC_36068


title: D61


title: Nos-Ez-w-dKD.1 [sRNA]


title: MCF7; HD; ER-WT; Vehicle (DMSO); 12hr; biol rep 2

description: Library name: MND123


title: T47D; HD; ER-Y537S; Fulvestrant; 12hr; biol rep 2

description: Library name: TDF123

value: Fulvestrant


title: Nos-Ez-kipf-dKD.1 [sRNA]


title: T47D; HD; ER-Y537S; Fulvestrant; 12hr; biol rep 1

description: Library name: TDF121


title: D52


title: nos-white-KD.2 [sRNA]

growth_protocol:
Grown at 25C
All flies were kept at 18 C or 25 C on standard cornmeal or propionic food.

extract_protocol:
Regulatory small RNA extraction was performed as described in (Grentzinger et al. 2020).  Argonaute-small RNA complexes were isolated from 10 to 30 pairs of ovaries from 3-5-day-old flies using TraPR ion exchange spin columns (Lexogen, Catalog Nr.128.08).
Small RNA-SeqLibrary Prep Kit fromLexogen

value: pTOSK (Brennecke)xBL35573


title: T47D; HD; ER-Y537S; Fulvestrant; 6hr; biol rep 2

description: Library name: TDF62


title: nos-white-KD.1 [sRNA]


title: D32


title: Nos-kipf-KD.2 [sRNA]


title: nos-Ez-KD.2 [sRNA]

value: pTOSK (Brennecke)xBL35171


title: D31


title: IgM_UT_3

city: Chicago

first: Vipul

last: Shukla

state: Illinois

address: 303 E. Superior Street

department: Department of Cell and Developmental Biology

institute: Northwestern University

data_processing:
Paired-end (50bp) reads were mapped to the mouse genome mm10/GRCm38 using STAR(A)(2.7.10a) (--genomeLoad LoadAndRemove --outFilterMismatchNmax 4 --outFilterMultimapNmax 100 --winAnchorMultimapNmax 100).
Counts were obtained with featureCounts (-g gene_name -s 0 ) (-g gene_name -s 2 -S rf).
Differentially expressed genes were calculated with DESeq2(C)71, filtering out genes that did not have any count in any condition; cut off to define DEGs was an adjusted pvalue 0.05 and a log2 fold change >= +/−1
Assembly: mm10
Supplementary files format and content: tab delimited file with the raw counts
Supplementary files format and content: tab delimited file with TPM normalized counts

source_name: Hematopoietic

growth_protocol: Naive B cells were isolated from wild-type C57BL/6J mice spleen and cultured using the in vitro iGB culture system and stimulated (or not) with 1ug/mL anti-kappa antibody for 12 hours

extract_protocol:
Total RNA was isolated using the RNeasy® Plus Kit (74134, Qiagen) according to the manufacturer’s instructions. Quality of RNA was assessed using Agilent Bioanalyzer® RNA 6000 Pico Chip Bioanalyzer.
The RNA sequencing libraries were prepared using purified RNA (40ng) with NEBNext® UltraTM II RNA Library Prep Kit (E7770, New England Biolabs) according to the manufacturer’s instructions.

treatment_protocol: After stimulation, B cells were FACS sorted from live cells, CD19+ and CD138- into IgG1+ and IgM+ using BD FACSAria™ 5L Sorter at the Northwestern University RHLCCC Flow Cytometry Facility.

value: Hematopoietic

value: naive B cells

value: wild-type

tag: cell subtype

value: IgM+


title: T47D; HD; ER-Y537S; Fulvestrant; 6hr; biol rep 1

description: Library name: TDF61


title: nos-Ez-KD.1 [sRNA]

value: ovary

value: 3-6 day old

value: female


title: T47D; HD; ER-Y537S; Vehicle (DMSO); 12hr; biol rep 1

description: Library name: TDD121

value: Breast cancer

value: ER+ breast cancer

value: HD

value: Vehicle (DMSO)


title: IgG1_UT_3


title: T47D; HD; ER-Y537S; Vehicle (DMSO); 12hr; biol rep 2

description: Library name: TDD123


title: N21

value: mammary gland

value: nipple


title: T47D; HD; ER-Y537S; Imlunestrant; 6hr; biol rep 1

description: Library name: TDL61

value: Imlunestrant


title: pTOsk-white-KD.1 [sRNA]

value: pTOSK (Brennecke)xBL36068


title: T47D; HD; ER-Y537S; Vehicle (DMSO); 6hr; biol rep 2

description: Library name: TDD62


title: IgM_UT_2


title: pTOsk-white-KD.2 [sRNA]


title: IgG1_UT_2


title: T47D; HD; ER-WT; Imlunestrant + E2; 12hr; biol rep 2

description: Library name: TEL123

value: ER-WT

value: Imlunestrant + E2


title: IgM_UT_1

value: Hematopoietic


title: T47D; HD; ER-Y537S; Vehicle (DMSO); 6hr; biol rep 1

description: Library name: TDD61


title: D51

value: duct


title: pTOsk-white-KD.2 [total RNA]

extract_protocol:
Total RNA was extracted from 10 to 20 ovaries from 3-6 day-old flies using TRizol (Thermo Fisher Scientific). Ribosomal RNA was depleted using RiboPOOL (siTOOLs, Biotech) following the manufacturer provided protocol.
RNA-seq libraries were produced using NEBNext Ultra Directional Library Prep Kit for Illumina, following the manufacturer’s instructions for rRNA depleted RNA.

value: pTOSK (Brennecke)xBL35573


title: Dam only male

city: London

first: Tony

middle: David

last: Southall

address: South Kensington Campus

department: Life Sciences

institute: Imperial College London

data_processing:
The forward sequencing reads were mapped to release 6 of the Drosophila genome using Bowtie2 (see PMID: 26112292 for details of the damidseq_pipeline)
Reads were extended to adjacent GATC sites and binned for each GATC fragment
GATC fragments without any reads were excluded, followed by quantile normalisation and pseudocount addition.
Ratio files (log2) were then generated from the experimental and Dam-only control data.
Assembly: BDGP6
Supplementary files format and content: log2 normalised fold changes between the experimental and Dam-only control as a gff file produced by the damidseq_pipeline

source_name: Larval CNS

growth_protocol: Flies were maintained on standard fly media.

extract_protocol:
Genomic DNA was isolated,RNAseA treated and DpnI digested. DamID adaptors were ligated to DpnI digested DNA followed by DpnII digestion PCR amplification, sonication and removal of DamID adaptors (Marshall et al., 2016).
Libraries were generated using the Illumina Truseq Library Kit
DamID-seq

treatment_protocol: Animals were raised at 18 degrees, then shifted to 29 degrees 24 h before DNA extraction

value: Larval CNS

value: neurons

value: DamID material


title: T47D; HD; ER-WT; Imlunestrant + E2; 12hr; biol rep 1

description: Library name: TEL122


title: IgG1_UT_1

value: naive B cells

value: wild-type


title: T47D; HD; ER-WT; Imlunestrant + E2; 6hr; biol rep 2

description: Library name: TEL63

value: Breast cancer

value: ER+ breast cancer


title: pTOsk-white-KD.1 [total RNA]

value: ovary

value: 3-6 day old

value: female


title: Dam only female


title: IgM_1ug_3

value: 1ug/mL anti-kappa antibody

value: IgM+


title: pTOsk-rhi-KD.4 [total RNA]

value: pTOSK (Brennecke)xBL35171


title: T47D; HD; ER-WT; Imlunestrant + E2; 6hr; biol rep 1

description: Library name: TEL61

value: HD

value: ER-WT

value: Imlunestrant + E2


title: IgG1_1ug_3

value: Hematopoietic


title: T47D; HD; ER-WT; Fulvestrant + E2; 12hr; biol rep 2

description: Library name: TEF123

value: Fulvestrant + E2


title: pTOsk-rhi-KD.3 [total RNA]


title: Dam only binding 1

description: RPM normalised

value: Larval CNS

value: neurons


title: pTOsk-rhi-KD.2 [total RNA]


title: T47D; HD; ER-WT; Fulvestrant + E2; 12hr; biol rep 1

description: Library name: TEF121


title: IgG1_1ug_2

value: naive B cells


title: pTOsk-white-KD.3 [total RNA]

value: pTOSK (Brennecke)xBL35573


title: pTOsk-white-KD.4 [total RNA]


title: T47D; HD; ER-WT; Fulvestrant + E2; 6hr; biol rep 2

description: Library name: TEF63

value: Breast cancer


title: IgM_1ug_1

value: wild-type


title: IgM_1ug_2


title: Dam only binding in Polr3A RNAi 2

description: RPM normalised

value: DamID material


title: Dam only binding in Polr3A RNAi 1

description: RPM normalised


title: T47D; HD; ER-WT; Fulvestrant + E2; 6hr; biol rep 1

description: Library name: TEF62

value: ER+ breast cancer


title: Dam only binding in Polr3E RNAi 3


title: pTOsk-Ez-KD.4 [total RNA]

value: ovary

value: 3-6 day old

value: female

value: pTOSK (Brennecke)xBL36068


title: pTOsk-Ez-KD.3 [total RNA]


title: T47D; HD; ER-WT; E2; 12hr; biol rep 2

description: Library name: TED122

value: HD


title: P56_KO_YL13

city: Dallas

first: Genevieve

last: Konopka

state: Texas

address: 5323 Harry Hines Blvd.

department: Neuroscience

institute: University of Texas Southwestern Medical Center

description: transcriptome

data_processing:
10X Genomics CellRanger v3.0.2
Seurat v3 and v4
Supplementary files format and content: raw counts matrix for filtered cells/nuclei in H5AD format

source_name: frontal cortex

extract_protocol:
Nuclei isolation protocol was modified from our previous work (Ayhan et al., 2021). Since homogenization of mouse cortex generated much fewer debris, we just did twice fltering through 40-μm Flowmi Cell Strainer (#H13680-0040, Bel-Art) without doing sucrose-gradient centrifugation
The single-nuclei RNA-seq libraries were prepared using Chromium Single Cell 3ʹ Reagent Kits v3 (CG000185 Rev B) from 10x Genomics

value: KO

tag: gender

value: M

tag: rna preparation batch

tag: library preparation batch

tag: sequencing batch


title: Dam only binding in Polr3E RNAi 2

description: RPM normalised


title: IgG1_1ug_1

value: Hematopoietic

value: 1ug/mL anti-kappa antibody


title: Dam only binding 2

description: RPM normalised

value: Larval CNS


title: pTOsk-Ez-KD.2 [total RNA]


title: T47D; HD; ER-WT; E2; 12hr; biol rep 1

description: Library name: TED121

tag: cell line

value: ER-WT


title: Dam only binding in Polr3E RNAi 1

description: RPM normalised

tag: cell type

value: neurons


title: T47D; HD; ER-WT; E2; 6hr; biol rep 2

description: Library name: TED63


title: P56_KO_YL07

description: transcriptome

tag: genotype

value: F


title: pTOsk-Ez-KD.1 [total RNA]

tag: tissue


title: Sxl binidng in Polr3E RNAi 3


title: pTOsk-rhi-KD.1 [total RNA]

tag: Sex

value: pTOSK (Brennecke)xBL35171


title: Sxl binidng in Polr3E RNAi 2


title: P56_KO_YL03

description: transcriptome


title: Sxl binidng in Polr3E RNAi 1


title: T47D; HD; ER-WT; Imlunestrant; 12hr; biol rep 2

description: Library name: TNL122

value: Breast cancer

tag: media

value: Imlunestrant


title: T47D; HD; ER-WT; E2; 6hr; biol rep 1

description: Library name: TED62

value: ER+ breast cancer

tag: esr1 status


title: nos-white-KD.2 [polyA RNA]

extract_protocol:
Total RNA was extracted from 30 ovaries from 3-6 day-old flies using TRIzol (Thermo Fisher Scientific).
illumina stranded mRNA prep

value: ovary

value: Nanos Gal4 VP16-expressed dsRNA-white BDSC_35573


title: T47D; HD; ER-WT; Imlunestrant; 12hr; biol rep 1

description: Library name: TNL121

tag: timepoint


title: P56_HU_YL11

description: transcriptome

value: HU


title: P56_HU_YL09

description: transcriptome


title: T47D; HD; ER-WT; Imlunestrant; 6hr; biol rep 2

description: Library name: TNL63

tag: treatment


title: nos-Ez-KD.3 [polyA RNA]

value: 3-6 day old

value: female

value: Nanos Gal4 VP16-expressed dsRNA-E(z) BDSC_33659


title: Polr3E binding in larval neurons 2

value: DamID material


title: Polr3E binding in larval neurons 1


title: P56_HU_YL05

description: transcriptome

tag: strain

value: M


title: nos-Ez-KD.2 [polyA RNA]


title: T47D; HD; ER-WT; Imlunestrant; 6hr; biol rep 1

description: Library name: TNL61

value: HD


title: Sxl_GS binding in neurons

value: Larval CNS


title: P56_HU_YL02

description: transcriptome


title: nos-Ez-KD.1 [polyA RNA]


title: P07_KO_YL18

description: transcriptome

value: KO


title: T47D; HD; ER-WT; Fulvestrant; 12hr; biol rep 2

description: Library name: TNF122

value: ER-WT

value: Fulvestrant


title: Dmel.IgG.2 [CUT&RUN]

data_processing:
Assembly: dm6
Sequencing adapters were removed using Trim Galore! (v0.6.4, ‑‑paired ‑‑stringency 6 ‑a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
The resulting reads were mapped to their respective reference genome using Bowtie (v1.2.3, ‑S ‑y ‑M 1 ‑‑best ‑‑strata ‑‑fr ‑‑minins 10 ‑‑maxins 600 ‑‑chunkmbs 2000 ‑‑nomaqround), reporting at most one hit for each read and considering insert sizes between 10 and 600nt.
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, ‑‑binSize 1 ‑‑ignoreForNormalization chrM ‑‑normalizeUsing CPM  ‑‑exactScaling ‑‑scaleFactor s ‑‑skipNonCoveredRegions ‑‑minMappingQuality 50 --extendReads --centerReads), where the scale factor, s, was set to the number of uniquely mapped reads divided by all mapped reads.
Supplementary files format and content: BigWig with read coverage per position across the genome.
Library strategy: CUT&RUN

value: w; AID_3xFLAG_V5_Precission_GFP_rhino/(CyO); ;  VDRC 313998

tag: antibody

value: Rabbit Anti-mouse (Abcam ab6709)


title: nos-white-KD.3 [polyA RNA]

tag: age


title: Sxl_RNA binding in neurons 2

value: neurons


title: T47D; HD; ER-WT; Fulvestrant; 12hr; biol rep 1

description: Library name: TNF121

value: Breast cancer

value: ER+ breast cancer


title: Sxl_RNA binding in neurons 1


title: P56_KO_YL04

description: transcriptome

value: F


title: nos-white-KD.1 [polyA RNA]

value: ovary

value: Nanos Gal4 VP16-expressed dsRNA-white BDSC_35573


title: P07_KO_YL06

description: transcriptome


title: P07_KO_YL09

description: transcriptome


title: Dmel.IgG.1 [CUT&RUN]

value: w; AID_3xFLAG_V5_Precission_GFP_rhino/(CyO); ;  VDRC 313997


title: x16 binding in larval neurons 1


title: x16 binding in larval neurons 2


title: T47D; HD; ER-WT; Fulvestrant; 6hr; biol rep 1

description: Library name: TNF61


title: Dmel.H3K9me3.2 [CUT&RUN]

value: w; AID_3xFLAG_V5_Precission_GFP_rhino/(CyO); ;  VDRC 313996

value: H3K9me3 (active motif 39161)


title: Dmel.H3K9me3.1 [CUT&RUN]

value: w; AID_3xFLAG_V5_Precission_GFP_rhino/(CyO); ;  VDRC 313995


title: U2af50 binding in larval neurons

value: DamID material


title: P07_HU_YL17

description: transcriptome

value: HU


title: T47D; HD; ER-WT; Vehicle (DMSO); 12hr; biol rep 2

description: Library name: TND123

value: HD

value: Vehicle (DMSO)


title: T47D; HD; ER-WT; Vehicle (DMSO); 12hr; biol rep 1

description: Library name: TND122

value: ER-WT


title: U1 binding in larval neurons 2

value: Larval CNS


title: P07_HU_YL12

description: transcriptome


title: Dmel.H3K27me3.2 [CUT&RUN]

value: w; AID_3xFLAG_V5_Precission_GFP_rhino/(CyO); ;  VDRC 313994

value: H3K27me3 (cell signalling 9733S)


title: U1 binding in larval neurons 1

value: neurons


title: P07_HU_YL05

description: transcriptome

value: M


title: S2-siRen.H3K9me3.5 [CUT&RUN]

data_processing:
Sequencing adapters were removed using Trim Galore! (v0.6.4, ‑‑paired ‑‑stringency 6 ‑a GATCGGAAGAGCACACGTCTGAACTCCAGTCAC).
The resulting reads were mapped to their respective reference genome using Bowtie (v1.2.3, ‑S ‑y ‑M 1 ‑‑best ‑‑strata ‑‑fr ‑‑minins 10 ‑‑maxins 600 ‑‑chunkmbs 2000 ‑‑nomaqround), reporting at most one hit for each read and considering insert sizes between 10 and 600nt.
Uniquely mapped reads were converted into BigWig files using the deepTools bamCoverage module (v3.3.2, ‑‑binSize 1 ‑‑ignoreForNormalization chrM ‑‑normalizeUsing CPM  ‑‑exactScaling ‑‑scaleFactor s ‑‑skipNonCoveredRegions ‑‑minMappingQuality 50 --extendReads --centerReads), where the scale factor, s, was set to the number of uniquely mapped reads divided by all mapped reads.
Peaks were called using MACS2 to capture either narrow (callpeak -f BAMPE -g dm -q 0.01) or broad (callpeak -f BAMPE -g dm -q 0.05 --broad --broad-cutoff 0.1) peaks. Only uniquely mapped reads were used for the peak calling.  As controls we used the corresponding IgG libraries.
Differential binding affinity analysis was performed using DiffBind (v2.14.0) applied on the MACS2 narrow or broad peaks siRen and siEz samples, using the corresponding IgG libraries as controls and without specifying any blacklist regions. For the analysis, we used the dba, dba.count, dba.normalize, dba.contrast, and dba.analyze modules with default options.
Assembly: dm6
Supplementary files format and content: BigWig with read coverage per position across the genome.
Supplementary files format and content: BED-like files with differentially bound peaks, fields include: chromosome, start, end, log2(mean), log2(mean siRen), log2(mean siEz), log2FC, p, padj.
Supplementary files format and content: BroadPeak files from MACS2.
Supplementary files format and content: NarrowPeak files from MACS2.
Library strategy: CUT&RUN

extract_protocol:
1 million cells per sample were harvested and washed three times with Wash buffer (20 mM HEPES, pH7.5, 150 mM NaCl, 0.5 mM spermidine supplemented with protease inhibitors) and resuspended in 1 ml of Wash buffer.   Following sample preparation, CUT&RUN was performed according to instructions in CUT&RUN protocol V.3 with some modifications ).  10 µl of activated Concanavalin A-coated magnetic beads (Bangs Laboratories) were added to each sample and rotated for 10 min at RT.  Bead-bound cells were incubated with 5 µl of antibody (Table S3) and 95 µl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin) overnight at 4 °C.  Bead-bound cells were washed twice with Dig-wash buffer (0.05% digitonin in Wash buffer).  Bead-bound cells were resuspended in Dig-wash buffer containing 1x CUTANA™ pAG-MNase (Epicypher) and rotated for 1 hr at RT.  Following pAG-MNase binding, bead-bound cells were washed twice with Dig-wash buffer and resuspended in 100 µl Dig-wash buffer.  Chromatin digestion was performed on ice for 30 min by adding 2 μL 100  CaCl2 mM.  Digestion was stopped by the addition of 2x STOP Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 µg/ml RNase A (Thermo Fisher Scientific), 50 µg/ml glycogen) and samples were incubated at 37 °C for 30 min to release DNA fragments into the solution.  After centrifugation, 0.1% SDS and 0.2 μg/μl Proteinase K were added to the supernatant and samples were incubated for 1 hour at 50 °C.  DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Sigma) according to the manufacturer’s instructions.
Libraries were prepared following the manufacturer’s instructions with NEBNext Ultra II DNA Library Prep Kit for Illumina.

value: siRen


title: Tra binding in larval neurons 2


title: T47D; HD; ER-WT; Vehicle (DMSO); 6hr; biol rep 1

description: Library name: TND61

value: Breast cancer

value: ER+ breast cancer


title: P07_HU_YL03

description: transcriptome


title: S2-siRen.H3K9me3.4 [CUT&RUN]


title: Tra binding in larval neurons 1


title: P07_WT_YL16

description: transcriptome

value: WT


title: T47D; HD; ER-WT; Fulvestrant; 6hr; biol rep 2

description: Library name: TNF63

value: Fulvestrant


title: S2-siRen.H3K9me3.3 [CUT&RUN]

value: H3K9me3 (active motif 39161)


title: P07_KO_YL01

description: transcriptome

value: KO


title: Healthy control-derived i3LMNs, ND CSF-treated, rep 3

city: Worcester

first: Alberto

last: Brusati

address: N Lake Ave 55

department: Neurology

institute: UMass Chan Medical School

description: Library name: ND biol rep 3

data_processing:
Reads were realigned on the reference genome (GRCh38) with the STAR tool using Genecode.v45 as gene annotation file. Post-alignment quality control was performed using Qualimap.
Quantification was performed using Salmon.
Assembly: GRCh38
Supplementary files format and content: Quant file provided by salmon for each sample.

source_name: i3 LMNs

extract_protocol:
RNA was extracted using TRIzol™ reagent
RNA libraries for RNA -seq were prepared in service (N/A)

treatment_protocol: For CSF treatment: 10% CSF for 24 h; for ARS treatment: 10 uM ARS for 24 h

value: i3 LMNs

value: ND CSF

tag: batch

value: C


title: C-term truncated Sxl binding in larval neurons 2

value: DamID material


title: P07_WT_YL11

description: transcriptome

tag: gender


title: S2-siRen.H3K9me3.2 [CUT&RUN]


title: Healthy control-derived i3LMNs, ND CSF-treated, rep 2

description: Library name: ND biol rep 2

value: B


title: C-term truncated Sxl binding in larval neurons 1

value: Larval CNS


title: S2-siRen.H3K27me3.5 [CUT&RUN]


title: Healthy control-derived i3LMNs, ND CSF-treated, rep 1

description: Library name: ND biol rep 1

value: A


title: N-term truncated Sxl binding in larval neurons 2


title: P07_WT_YL02

description: transcriptome

value: F

tag: rna preparation batch


title: P07_WT_YL04

description: transcriptome

tag: library preparation batch


title: Healthy control-derived i3LMNs, C9 CSF-treated, rep 5

description: Library name: C9 biol rep 5

value: C9 CSF

value: E


title: N-term truncated Sxl binding in larval neurons 1

value: neurons


title: T47D; HD; ER-WT; Vehicle (DMSO); 6hr; biol rep 2

description: Library name: TND63

value: Breast cancer

value: HD

value: ER-WT

value: Vehicle (DMSO)


title: Dmel.H3K27me3.1 [CUT&RUN]

extract_protocol:
10-20 fly ovaries were dissected in ice cold PBS per sample.  Ovaries were digested in 250 µl of dissociation buffer (0.5% Trypsin and 2.5 mg/ml Collagenase A in PBS) for an hour with shaking at 800 rpm at 30 °C.  The digestion was stopped with 250 µl of Schneider medium containing 10% FBS.  Cell suspensions were filtered through 40 µm strainers, pelleted and washed three times with Wash buffer and resuspended in 1 ml of Wash buffer. Following sample preparation, CUT&RUN was performed according to instructions in CUT&RUN protocol V.3 with some modifications ).  10 µl of activated Concanavalin A-coated magnetic beads (Bangs Laboratories) were added to each sample and rotated for 10 min at RT.  Bead-bound cells were incubated with 5 µl of antibody (Table S3) and 95 µl of antibody buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM spermidine, 0.05% digitonin) overnight at 4 °C.  Bead-bound cells were washed twice with Dig-wash buffer (0.05% digitonin in Wash buffer).  Bead-bound cells were resuspended in Dig-wash buffer containing 1x CUTANA™ pAG-MNase (Epicypher) and rotated for 1 hr at RT.  Following pAG-MNase binding, bead-bound cells were washed twice with Dig-wash buffer and resuspended in 100 µl Dig-wash buffer.  Chromatin digestion was performed on ice for 30 min by adding 2 μL 100  CaCl2 mM.  Digestion was stopped by the addition of 2x STOP Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 µg/ml RNase A (Thermo Fisher Scientific), 50 µg/ml glycogen) and samples were incubated at 37 °C for 30 min to release DNA fragments into the solution.  After centrifugation, 0.1% SDS and 0.2 μg/μl Proteinase K were added to the supernatant and samples were incubated for 1 hour at 50 °C.  DNA was extracted using Phenol:Chloroform:Isoamyl Alcohol 25:24:1 (Sigma) according to the manufacturer’s instructions.
Libraries were prepared following the manufacturer’s instructions with NEBNext Ultra II DNA Library Prep Kit for Illumina.

value: ovary

value: w; AID_3xFLAG_V5_Precission_GFP_rhino/(CyO); ;  VDRC 313993

value: H3K27me3 (cell signalling 9733S)