title: Passage 4 Basal cell isolates in PEX media -Repliate 1

city: Duarte

first: Crystal

middle: N

last: Marconett

email: cmarcone@usc.edu, cmarconett@coh.org

address: 1500 E Duarte Rd

department: Integrative Translational Sciences

institute: City of Hope

data_processing:
Paired end FASTQ read files were assessed for quality using FastQC [Andrews, S. (2010) FastQC: A Quality Control Tool for High Throughput Sequence Data]. Reads were cleaned by filtering out those with less than 90% of the read having a quality score of < Q30 and were subsequently aligned to the Homo.Sapiens.GRCh38.96 transcriptome using Kallisto (version 0.46.0) [N. L. Bray, H. Pimentel, and P. M. &. L. Pachter. 2016. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. 34(5): 525-527.].
To account for the wide range of raw sequencing depth between samples (35M to 135M), total read numbers were adjusted to ~42M per sample [aligned read range: ~31 - 45M] prior to calculation of read count per transcript (Supplemental Table 1). Kallisto count tables were filtered to include transcripts with counts per million > 50 (Supplemental Table 2) and were subsequently input into R (v 4.0.2 GUI 1.72 Catalina build 7847) and EdgeR [Robinson MD, McCarthy DJ, Smyth GK (2010). “edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.” Bioinformatics, 26(1), 139-140. doi:10.1093/bioinformatics/btp616.] was used to calculate differential expression and FDR correction of significance.
Assembly: Homo.Sapiens.GRCh38.96 transcriptome
Supplementary files format and content: Bigwig density files showing read alignment in human hg38 genome
Supplementary files format and content: Kallisto-aligned pseudocount tables were filtered to include transcripts with counts per million > 50

source_name: Lung proximal basal cells

growth_protocol: Basal cells were isolated from donors using established protocols ().

extract_protocol:
Total bulk RNA (2ug/sample) was sent to Azenta (formerly Genewiz) for poly-A tail library construction and sequencing.
Libraries were constructed with unique adapters that allowed for all samples to be run on one Illunima HiSeq 2500 run.

treatment_protocol: Basal cells were grown in 2D culture using the indicated media.

value: Lung proximal basal cells

tag: passages

value: Purified Basal Cells in Culture

value: Pneumacult EX (PEX) media


title: iCell-RPE, Ctrl, experiment 1

status: Public on Jun 20 2025

type: SRA

city: Aachen

first: Teodora

last: Piskova

address: Wendlingweg 2

country: Germany

institute: RWTH Aachen University

description:
Library name: iRPE 1
Sample name in salmon.merged.gene_counts.csv: DE61NGSUKBR144381

library_source: transcriptomic

data_processing:
The raw data was processed using the nf-core/rnaseq v3.12.0 (https://doi.org/10.5281/zenodo.1400710)
Sequence reads were quality checked using FastQC before and after adapter trimming.
Adapter sequences and low-quality bases were trimmed using Cutadapt (3' adapter: AAAAAAAA).
Trimmed reads were aligned to the GENCODE GRCh38 v44 genome using STAR (key parameters: max intron size 1,000,000; max mismatches 10%; max multimaps 20).
Alignment quality was assessed using Samtools, RSeQC, and QualiMap.
Gene-level quantification was performed using featureCounts (grouped by gene_type).
Assembly: GRCh38 (GENCODE v44)
Supplementary files format and content: .csv file contains raw gene counts for all samples

molecule: total RNA

organism: Homo sapiens

source_name: iCell-RPE (Fujifilm 01279)

growth_protocol: HiPSCs-derived RPE cells (Fujifilm Cellular Dynamics, R1102) were seeded on 4 kPa polyacrylamide hydrogels with a basement membrane-like coating and were grown for 10 days in a medium recommended by the manufacturer.

extract_protocol:
RNA isolation was performed using the RNeasy Micro RNA isolation kit (Qiagen, 74004) with DNase treatment. 100 ng RNA was used for the library preparation.
RNA libraries for RNAseq were prepared using the QuantSeq 3’-mRNA Library Prep/ Lexogen enrichment.

treatment_protocol: On day 10 after seeding, AAV5 were used at 7x106 infectious units per cell for 24 h to transduce the cells with FKBP-casp8 containing plasmid (VectorBuilder, VB230127-1043eaq) in addition to a non-transduced control. On day 15, FKBP-casp8 was dimerised by addition of 100 nM AP20187 in medium (Sigma Aldrich, SML2838) for 24 h. Paired non-transduced cells  were also subjected to the AP20187 treatment. The RNA isolation was performed on day 20, or four days after apoptosis treatment finalisation.

tag: cell line

value: iCell-RPE (Fujifilm 01279)

tag: cell type

value: retinal pigment epithelial cells

tag: genotype

value: WT

tag: treatment


title: 5B-2517

city: Barcelona

first: Júlia

last: Perera-Bel

address: Doctor Aiguader, 88

department: MARData-BU

country: Spain

institute: Hospital del Mar Research Institute

data_processing:
Reads were mapped with STAR software (v.2.7.1a) against the moouse reference genome mm10.
The table of counts was obtained with featureCounts function in the package subread (v.1.6.4).
Counts were normalized with log2 counts per million (CPM) with the edgeR package with a prior.count=3. Genes with more than 10 counts in at least 2 samples were kept.
Assembly: mm10
Supplementary files format and content: counts

molecule: polyA RNA

organism: Mus musculus

growth_protocol: Mouse SCLC cells (KP1 and 5B) (1 million) were collected, resuspended in sterile PBS with Matrigel (354234, Corning, 1:1) and injected into the right flank of 6 to 12-week old B6129SF1/J mice.

extract_protocol:
Mouse tumor fragments were immediately frozen in liquid nitrogen after isolation. RNA was isolated using the RNeasy Mini Kit (Qiagen), and RNA integrity (RIN) was determined by Bioanalyzer (Agilent). All samples exhibited acceptable quality (RIN > 7) for RNAseq with polyA capture.
NGS libraries, prepared according to the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolab) (version 4.0, 4/21) manual by MARGenomics Core Facility at Hospital del Mar Research Institute, yielded a final library size of ~40M counts per sample. Sequencing was conducted on the Illumina Nextseq 500 High-output platform with 2x75bp read length at the UPF Genomics Core Facility.

treatment_protocol: Group allocation was randomized using RandoMice software (https://doi.org/10.1371/journal.pone.0237096) three days after tumor cell inoculation. Mice were distributed into three treatment arms: cisplatin (Cis), cisplatin plus anti-PD-L1 (Cis+D-D), or cisplatin plus anti-PD-L1 and savolitinib (Cis+S+D-S+D).  Schedule administration was the following a) cisplatin: 4 mg/kg i.p. on days 0 and 7 of treatment; b) anti-mouse PD-L1 [clone 80] or NIP228 mIgG1 D265A isotype: 10 mg/kg i.p. twice a week; c) savolitinib: 30 mg/kg orally daily.

value: Cis

tag: batch

tag: mouse model

tag: strain


title: Anterior hindlimb, wild-type-hZRS404G>A, ATAC, rep1

city: Irvine

first: Evgeny

last: Kvon

state: CA

address: 836 Health Sciences Road

country: USA

institute: University of California, Irvine

description: Library name: Sample1

library_source: genomic

data_processing:
Paired-end reads were first trimmed using Fastp, version 0.23.2 and then mapped using Bowtie2, version 2.5.1 with the following parameters: --local --very-sensitive --no-mixed --no-discordant -I 25 -X 700.
Bam files were sorted and indexed using samtools, version 1.15.1, and converted to bigwig files for genome visualization using deeptools, version 3.5.1
Assembly: Wild-type + reporter samples = A custom mm10 genome (mm10 reference and an extra chromosome for the hZRS transgene reporter). Knock-in + reporter samples = A custom mm10 genome (mm10 with variant mouse ZRS allele replacing the wild type ZRS at chromosome 5 and an extra chrosome for the hZRS transgene reporter)
Supplementary files format and content: bigwig

molecule: genomic DNA

source_name: FVB

extract_protocol:
Hindlimb cells were dissected, dissociated, sorted, and then lysed into nuclei. Nuclei were then incubated with Tn5 for the transposition reaction.
Transposased DNA was extracted and then indexed before being sequenced for 50M reads.

tag: tissue

value: FVB

value: wild-type

tag: reporter


title: iCell-RPE, AgeD, experiment 2

description:
Library name: AgeD-iRPE 2
Sample name in salmon.merged.gene_counts.csv: DE23NGSUKBR144386

value: apoptosis via 100 nM AP20187


title: YG_MG1655_24hr_rep1

city: La Jolla

first: Heera

last: Bajpe

address: 9500 Gilman Dr.

institute: UC San Diego

description: Library name: YG_MG1655_24hr_1

data_processing:
Raw sequencing reads were mapped to the reference genome using bowtie v1.1.2 with parameters -X 1000 -3 3 -n 2 -S
Read counts were generated using featureCounts
Assembly: NC_000913.2
Supplementary files format and content: Comma-delimited text files containing TPM values for each sample

organism: Escherichia coli str. K-12 substr. MG1655

source_name: K-12 substr. MG1655

growth_protocol: Glycerol stocks of E. coli strains were inoculated into M9 minimal media with the glucose M9 minimal medium for each candidate TF. The concentration of carbon sources was 0.2% (w/v). M9 minimal media was also supplemented with 1 ml trace element solution (100X). The culture was incubated at 37 ℃ overnight with agitation, and then was used to inoculate the fresh media (initial OD600 = 0.05). The fresh culture was incubated at 37 ℃ with agitation for additional 24 hrs.

extract_protocol:
Three milliliters of cells from mid-log phase culture were mixed with 6 ml RNAprotect Bacteria Reagent (Qiagen), mixed immediately by vortexing for 5 seconds, incubated for 5 minutes at room temperature, and then centrifuged at 5000g for 10 minutes. The supernatant was decanted and any residual supernatant was removed, then samples were frozen at -80℃. Next, RNA was harvested using RNeasy Plus Mini kit (Qiagen) in accordance with the manufacturer’s instruction. Illumina Ribo-Zero rRNA removal kit (bacteria) (MRZMB126) was used with 1 ug of total RNA for the removal of rRNA procedure. Then KAPA RNA HyperPrep kits(Cat.No.08098107702) was used with rRNA-depleted RNA samples for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: 24 hours incubation for the strains

value: K-12 substr. MG1655

value: 24 hours incubation


title: YG_yfeCKO_24hr_rep1

description: Library name: YG_yfeCKO_24hr_1

value: yfeC deletion


title: human, siAEBP1-1, replicate3

city: Nagakute

first: Kenji

last: Kasai

state: Aichi

address: 1-1 Yazakokarimata

department: Pathology

country: Japan

institute: Aichi Medical University School of Medicine

description: Library name: siAEBP3/5637

data_processing:
Quality check for sequence reads were performed using FastQC version 0.11.7
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic version 0.38 with LEADING:20 TRAILING:20 SLIDINGWINDOW:4:15 MINLEN:36 as command option
Trimmed sequence reads were mapped to hg38 using HISAT2 version 2.1.0
Raw read counts were determined using featureCounts version 1.6.3
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: bladder cancer

growth_protocol: Human bladder cell line 5637 cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
72 hours after siRNA transfection, cells were harvested for RNA extraction using Qiagen RNeasy Mini Kit.
RNA libraries for RNA-seq were prepared using NEBNext Poly(A) mRNA Magnetic Isolation Module for PolyA selection and NEB NEXT Directional Ultra RNA Library Prep Kit for Illumina for strand specific library follwing manufacturer's protocols.

treatment_protocol: Cells were transfected with either siAEBP1-1 or its control siControl using Thermo-Fisher's Lipofectamine RNAiMAX transfection reagent.The experiments were repeated to obtain three biological replicates, named siAEBP1-3_5637 and soControl1-3_5637.

value: bladder cancer

value: cell line

value: AEBP1 knockdown

value: siRNA transfection


title: Passage 4 Basal cell isolates in PEX media -Repliate 2

value: Lung proximal basal cells


title: 5B-2513


title: Passage 4 Basal cell isolates in DSI media -Repliate 2

value: Purified Basal Cells in Culture

value: Dual Smad Inhibitor (DSI) media


title: BDH6804 Het female

city: Memphis

first: Stanislav

last: Zakharenko

state: Tennessee

address: 262 Danny Thomas Pl, M2426

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description: Library name: 2697133_mhp007

library_source: transcriptomic single cell

data_processing:
Processed files were generated using cellranger-7.0.0 with force-cells set to 8000.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files from CellRanger, filtered_feature_bc_matrix outputs.

molecule: nuclear RNA

source_name: dorsal striatum

extract_protocol:
Nuclei were isolated from frozen tissue as previously described (PMID 30371670)
Libraries were prepared using the 10× Genomics Chromium Next GEM Single Cell Kit (v3.1).

tag: sample id

value: dorsal striatum

tag: Sex

value: female

value: Het


title: 5B-2518

value: Cis+D-D


title: human, siControl, replicate3

description: Library name: siCont3/5637

value: control


title: 5B-2516

value: Cis+S+D-S+D


title: iCell-RPE, Ctrl, experiment 3

description:
Library name: iRPE 3
Sample name in salmon.merged.gene_counts.csv: DE93NGSUKBR144387

value: iCell-RPE (Fujifilm 01279)

value: retinal pigment epithelial cells

value: WT


title: Passage 4 Basal cell isolates in AECGM media -Repliate 2

value: AECGM media


title: iCell-RPE, Ctrl, experiment 2

description:
Library name: iRPE 2
Sample name in salmon.merged.gene_counts.csv: DE77NGSUKBR144384


title: Passage 4 Basal cell isolates in AECGM media -Repliate 1


title: BDH6800 Het female

description: Library name: 2697131_mhp005


title: human, siAEBP1-1, replicate2

description: Library name: siAEBP2/5637

value: bladder cancer


title: human, siControl, replicate2

description: Library name: siCont2/5637

value: cell line


title: BDH6817 Het male

description: Library name: 2697130_mhp004

value: male


title: Passage 1 Basal cell isolates in PEX media -Repliate 2

value: Pneumacult EX (PEX) media


title: human, siAEBP1-1,replicate1

description: Library name: siAEBP1/5637

value: AEBP1 knockdown

value: siRNA transfection


title: BDH6815 WT male

description: Library name: 2697132_mhp006


title: human, siControl, replicate1

description: Library name: siCont1/5637


title: CD34_2

city: Fort Collins

first: Robert

middle: Adam

last: Harris

state: CO

address: 1601 Campus Delivery

department: MIP

institute: Colorado State University

description:
Library name: C34165634
10x Genomics

data_processing:
The demultiplexing, barcode processing, and gene counting was completed using Cell Ranger software v7.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: canFam3.1
Supplementary files format and content: Tab-separated values files and matrix files

organism: Canis lupus familiaris

source_name: Bone Marrow

extract_protocol:
Bone marrow cells were collected from femurs that were stored on ice prior to processing. Single cell suspensions were collected by flushing the bone marrow cavity with sterile Hank's balanced salt solution and washed with phosphate-buffered saline (PBS). Red blood cells were then lysed using ammonium-chloride-potassium lysis buffer for 5-10 minutes at room temperature. The cell suspensions were again washed with PBS  and aliquoted for CD34+ cell enrichment and immunophenotyping. Viable (propidium iodide-negative) CD34+ cells were enriched from 2 of the 3 bone marrow samples (BM2 and BM3) using a Sony SH800 cell sorter, and post-sort purity was evaluated prior to GEM generation. For all three whole bone marrow samples prepared for GEM generation, viability was assessed using propidium iodide, and neutrophil proportions (CD4+CD3-CD5-CD18+ cells) were determined. Only samples with >70% viability and <25% neutrophils were used for sequencing. Sorted (CD34+ cells) and unsorted (whole bone marrow) were subject to a final 15-minute centrifugation (100 rcf at 8C), then cells were resuspended in 0.04% molecular grade bovine serum albumin (Sigma-Aldrich; St. Louis, MO) in PBS. Cell suspensions were adjusted to a concentration between 700-1200 cells/uL and were processed on a Chromium iX instrument (10x Genomics; Pleasanton, CA) within 30 minutes of preparation.  The instumnet was loaded to target 5,000 cells per sample.
Library construction was performed according to the manufacturer’s instructions (Chromium Next GEM Single Cell 3ʹ Kit v3.1 protocol, 10x Genomics). Briefly, a Chromium iX instrument was used to pass cells and oligonucleotide coated gel beads at a limiting dilution to obtain a coupling of cells and beads in a 1:1 ratio. The cell-bead pair was then passed from an aqueous phase to an oil phase to form an emulsion. Within the emulsions, cells were lysed, and the oligonucleotide sequences on the gel beads pull down message RNA and other RNA molecules that have long adenosine stretches with an oligo-d(T) pull down. After hybridization, reverse transcription is completed to generate a cDNA library with each transcript now associated with a unique cell barcode and an Illumina R1 primer sequence.  Once cells were barcoded and unique molecular identifiers (UMIs) added, a standard Illumina library preparation kit was completed with SPRIselect used for fragment size selection. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Bone Marrow

value: Primary

value: Wt


title: BDH6813 Het male

description: Library name: 2697128_mhp002

value: dorsal striatum

value: Het


title: Passage 4 Basal cell isolates in DSI media -Repliate 1

value: Lung proximal basal cells

value: Purified Basal Cells in Culture

value: Dual Smad Inhibitor (DSI) media


title: Passage 1 Basal cell isolates in DSI media -Repliate 2


title: Passage 1 Basal cell isolates in DSI media -Repliate 1


title: BeWo cells, OE-RNF126-3

city: Guangzhou

first: Jing

last: Li

state: Guangdong

address: Jingxi Street

department: Department of Obstetrics and Gynecology

country: China

institute: Southern Medical University Nanfang Hospital

description:
Library name: SAMPLES6
Column name in FPKM_allsamples.txt and counts_allsamples.txt: OE-RNF126-3

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples.
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample.
Supplementary files format and content: Tab-delimited text files include raw counts for each sample.

source_name: placenta

growth_protocol: BeWo cells were maintained in Ham's F-12 supplemented with 15% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37°C

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA).
RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: placenta

value: BeWo

value: trophoblast cells

value: RNF126 overexpression


title: CD34_1

description:
Library name: C34157855
10x Genomics


title: OE, Sup

type: RNA

city: Nanchang

first: yunfei

last: Luo

address: No. 1 Min De Road

institute: nanchang university

description: Biological sample 1 of 1. overexpressed METTL3 plasmid transfected human amniotic epithelial stem cells, harvested after differentiation into insulin-producing cells.

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled RNAs were mixed. The RNA mixture was fragmented by adding 5 μL 10x Blocking Agent and 1 μL of 25x Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2x Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-RNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using an Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities. After Spike-in normalization, the probe signals having Present (P) or Marginal (M) QC flags in at least 3 out of 6 samples were retained for further “m6A quantity” analyses. “m6A quantity” was calculated for the m6A methylation amount based on the IP (Cy5-labelled) normalized intensities.

label_protocol: The enriched “IP” RNAs and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labeling Kit.

growth_protocol: human amniotic epithelial stem cells were supplemented with knockout-DMEM containing the main components, 2% knockout-serum, 1 mM β-mercaptoethanol, 1% GlutaMax, 1% B-27, 1% N-2, 1% non-essential amino acids, 20 ng/ml bFGF, 20 ng/ml EGF, and treated with 100ng/ml activin A, 3μM CHIR99021 for 24  hours, then 100ng/ml activin A for another 48 hours, 1μM dorsomorphin, 2μM retinoic acid plus 10μM SB431542 for 7 days, and 10μM forskolin, 10μM Dexamethasone, 5μM Alk5 inhibitor II plus 10mM nicotinamide for 11 days.

extract_protocol: total RNA extracted using Trizol following manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Transfection of human amniotic epithelial stem cells was performed according to the manufacturer’s protocols of TransIntro EL Transfection Reagent . The overexpressed METTL3 plasmid originated from Genechem, and normal induction commenced post-overnight transfection.

value: epithelial stem cells

tag: age

value: day 21

value: amniotic membranes

tag: fraction

value: supernatant unmodified RNAs


title: OE, IP

value: IP enriched m6A methylated RNAs


title: BeWo cells, OE-RNF126-2

description:
Library name: SAMPLES5
Column name in FPKM_allsamples.txt and counts_allsamples.txt: OE-RNF126-2


title: BDH6809 WT male

description: Library name: 2697127_mhp001

value: male

value: WT


title: BeWo cells, OE-RNF126-1

description:
Library name: SAMPLES4
Column name in FPKM_allsamples.txt and counts_allsamples.txt: OE-RNF126-1


title: Passage 1 Basal cell isolates in AECGM media -Repliate 2

value: AECGM media


title: E13 placenta,Male,Stress,Replicate 6

city: Iowa City

first: Benjamin

last: Hing

state: IA

address: 51 Newton Road, BSB 6-509

institute: University of Iowa

description:
Library name: R9_12
Sample data is present in column with sample name for all processed files

data_processing:
Illumina adapter sequence was removed using Trim Galore (v0.5.0)
Alignment using Salmon (v1.10.1) to mm10 transcriptome
Read counts and TPM was extracted from Salmon output
Normalized data and gene expression was analyzed using DESeq2 (v1.34.0)
Assembly: mm10
Supplementary files format and content: csv file for raw counts for each sample
Supplementary files format and content: csv file for TPM for each sample

source_name: Placenta

extract_protocol:
RNA Mini Kit (Qiagen)
NEBNext® Ultra™ II RNA Library Prep Kit

treatment_protocol: Pregnant mice were placed in plexiglass restraints under bright lights three times daily for 45 min per session. Restraint stress continued daily through pregnancy until collection at E13.

value: Placenta

value: Male

value: Stress


title: BeWo cells, OE-NC-3

description:
Library name: SAMPLES3
Column name in FPKM_allsamples.txt and counts_allsamples.txt: OE-NC-3

value: empty vector


title: BM_1

description:
Library name: BM154801
10x Genomics

value: Bone Marrow

value: Primary

value: Unsorted

value: Wt


title: BeWo cells, OE-NC-2

description:
Library name: SAMPLES2
Column name in FPKM_allsamples.txt and counts_allsamples.txt: OE-NC-2

value: placenta

value: BeWo

value: trophoblast cells


title: scRNAs Keloid10

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

data_processing:
For the expression profiling among lymph edema and keloids, the following procedures were performed. Raw read counts were created using samtools (ver. 1.6) 12. Using the information of GeneID, read counts for each transcript were summarized into those for each gene. Normalization of Gene Expression: Normalization of Gene Expression was performed with the following procedure 13,14. （１）Total count normalization was performed, based on the following calculation. （２）A Trimmed Mean of M-values (TMM) normalization was performed using the edgeR (ver. 3.16.5) package. Differential expression analysis was performed using the edgeR (ver. 3.16.5) package. Gene annotations were added to the results, using our in-house script.
Assembly: mm10
Supplementary files format and content: Tab-separated values files

source_name: Skin

extract_protocol:
According to the supplier's manual, total RNA purification was performed using an RNeasy Plus Kit (QIAGEN) with an RNase-free DNase Set (QIAGEN) described in our previous study. In brief, twenty 4um-thick thin sections were cut from cryopreserved skin tissue using a cryostat, dissolved in Lysis Buffers in the RNAeasy Kit to extract total RNA.  The quality and amount of the RNA in each sample were evaluated using Experion (Bio-Rad, Hercules, CA, USA) and NanoDrop (Thermo Fisher Scientific), respectively.
For RNA-seq analysis using a next-generation sequencer (NGS), library construction and sequencing for the Illumina HiSeq 4000 was provided as a custom service of Eurofins Genomics K. K. (Tokyo, Japan).
The polyA fraction (mRNA) was isolated from total RNA, followed by its fragmentation. Then double-stranded (ds) cDNA was reverse transcribed from fragmented mRNA. The ds cDNA fragments were processed for adaptor ligation, size selection (for 200 bp inserts) and amplification to generate strand-specific cDNA libraries. Prepared libraries were subjected to paired-end 2 x 101 bp sequencing on the HiSeq 4000 platform using HiSeq 3000/4000 SBS Kit (Illumina, San Diego, U.S.)

value: Skin

tag: assay

value: scRNA-seq

value: Epithelial, stromal cell

tag: status

value: Keloid Case Group


title: Passage 1 Basal cell isolates in PEX media -Repliate 1

value: Lung proximal basal cells

value: Purified Basal Cells in Culture

value: Pneumacult EX (PEX) media


title: WT, IP

description: Biological sample 1 of 1. human amniotic epithelial stem cells Wild type, harvested after differentiation into insulin-producing cells.

source_name: Wild type

value: epithelial stem cells

value: day 21

value: amniotic membranes

value: IP enriched m6A methylated RNAs


title: E13 placenta,Male,Stress,Replicate 5

description:
Library name: R8_3
Sample data is present in column with sample name for all processed files

value: Placenta

value: Male

value: Stress


title: BDH6802 WT female

description: Library name: 2697134_mhp008

value: dorsal striatum

value: female

value: WT


title: Bovine mammary epithelial cells transfected with miR-199a-3p mimic 3

city: Yinchuan

first: Xing-Ping

last: Wang

state: Ningxia

address: No. 489, Helan Shanxi Road, Xixia District

department: College of animal science and technology

institute: Ningxia University

data_processing:
Illumina Novaseq 6000 used for basecalling.
Clean reads were obtained by removing the connector sequences and filtering out low-quality reads (the number of bases with a base mass value ≤ 25 accounted for over 60% of the total reads). The proportion of N (undetermined bases) was < 5%.
The obtained clean data was mapped to the bovine reference genome UMD 3.1 (http://oct2018.archive..ensembl.org/Bos_taurus/Info/Index) using HiSAT2 software (http://daehwankimlab.github.io/hisat2/).
Differential expression analysis of genes in miR-199a-3p mimic group comparing to mimic NC group was performed using DESeq2 (http://bioconductor.org/packages/release/bioc/html/DESeq2.html). The default filter thresholds for DEGs are |log2Foldchange| > 1 and padj < 0.05.
Assembly: UMD3.1
Supplementary files format and content: Matrix table with information of gene and gene count for each sample.

organism: Bos taurus

source_name: Bovine mammary epithelial cells

growth_protocol: Bovine mammary epithelial cells were thawed and cultured in DFEM/F12 medium supplemented with 10% fetal bovine serum at 37℃ under 5% CO2 and 100% humidity. MAC-T cells were seeded and cultured in 6-well plates. When the cells reached 60-70% confluence, they were transfected with miR-199a-3p mimic or negative control (NC) mimic (final concentration 50nM). The experiment was performed in triplicate.

extract_protocol:
Total RNA was extracted from the transfected bovine mammary epithelial cells using the TriZol kit protocol.
The sequencing library was constructed using the ABclonal mRNA-seq Lib Prep Kit (ABclonal, Wuhan, China), following the manufacturer's protocol.

treatment_protocol: Bovine mammary epithelial cells were transfected with NC mimic (50 nM) or miR-199a-3p mimic (50 nM). The experiment was performed in triplicate. Cells were collected after 48 hours of transfection.

value: Bovine mammary epithelial cells

value: miR-199a-3p mimic


title: BM_3

description:
Library name: BM165596
10x Genomics

value: Bone Marrow

value: Primary

value: Unsorted

value: Wt


title: BeWo cells, OE-NC-1

description:
Library name: SAMPLES1
Column name in FPKM_allsamples.txt and counts_allsamples.txt: OE-NC-1

value: placenta

value: BeWo

value: trophoblast cells

value: empty vector


title: WT, Sup

value: epithelial stem cells

value: day 21

value: amniotic membranes

value: supernatant unmodified RNAs


title: scRNAs Keloid9

value: Skin

value: scRNA-seq

value: Epithelial, stromal cell

value: Keloid Case Group


title: BDH6811 WT male

description: Library name: 2697129_mhp003

value: dorsal striatum

value: male

value: WT


title: scRNAs Keloid8


title: E13 placenta,Male,Stress,Replicate 3

description:
Library name: R6_4
Sample data is present in column with sample name for all processed files

value: Placenta

value: Male

value: Stress


title: Bovine mammary epithelial cells transfected with miR-199a-3p mimic 1

value: Bovine mammary epithelial cells

value: miR-199a-3p mimic


title: OMRD_6B

city: Houston

first: Sanghoon

last: Lee

state: TX

address: 1881 East Road

institute: The University of Texas MD Anderson Cancer Center

description:
Library name: OMRD_6B
Surgical MRD sample

library_source: other

data_processing:
The raw sequencing files (FASTQ files) first underwent pre-processing using the 10× Genomics Space Ranger pipeline (version 2.0.0).
Assembly: GRCh38
Supplementary files format and content: Gene expression matrix.
Library strategy: Spatial Transcriptomics

molecule: other

source_name: ovarian cancer

extract_protocol:
Library preparation of Visium spatial transcriptomics was conducted in accordance with the 10× Genomics Visium CytAssist Spatial Gene Expression protocol. The Human Whole Transcriptome Probe V2 (PN: 2000657/2000658, 10× Genomics) was used for probe hybridization.
Library preparation of Visium spatial transcriptomics was conducted in accordance with the 10× Genomics Visium CytAssist Spatial Gene Expression protocol.

value: ovarian cancer

value: chemotherapy


title: E13 placenta,Male,Stress,Replicate 2

description:
Library name: R3_12
Sample data is present in column with sample name for all processed files


title: scRNAs Keloid7


title: OMRD_4B

description:
Library name: OMRD_4B
Surgical MRD sample


title: Bovine mammary epithelial cells transfected with NC mimic 3

value: NC mimic


title: E13 placenta,Male,Stress,Replicate 1

description:
Library name: R1_9
Sample data is present in column with sample name for all processed files


title: Passage 1 Basal cell isolates in AECGM media -Repliate 1

value: Lung proximal basal cells

value: Purified Basal Cells in Culture

value: AECGM media


title: scRNAs Keloid6

value: Skin

value: scRNA-seq


title: Bovine mammary epithelial cells transfected with NC mimic 2


title: OMRD_3A

description:
Library name: OMRD_3A
Surgical MRD sample


title: E13 placenta,Male,Stress,Replicate 4

description:
Library name: R7_3
Sample data is present in column with sample name for all processed files


title: OMRD_1B

description:
Library name: OMRD_1B
Surgical MRD sample


title: Bovine mammary epithelial cells transfected with NC mimic 1


title: E13 placenta,Female,Stress,Replicate 5

description:
Library name: R8_2
Sample data is present in column with sample name for all processed files

value: Female


title: scRNAs Keloid4

value: Epithelial, stromal cell

value: Keloid Case Group


title: scRNA-seq of Homo sapiens treated with anti-CD40 and Flt3L: adult female PDAC tumor_HT692

city: St. Louis

first: David

middle: G

last: DeNardo

state: Missouri

address: 425 S Euclid Ave

institute: Washington University

description:
Library name: HT692
10X Genomics

data_processing:
The cellranger mkfastq pipeline (10X Genomics) was used to demultiplex Illumina base call files to FASTQ files. Raw FASTQ files were aligned to a human genome reference (GRCh38 v2020-A) with CellRanger v6 (10X Genomics) using the ‘count’ function.
Unfiltered feature-barcode matrices from each sample were loaded into Seurat as Seurat objects after removing any cells that expressed fewer than 300 total transcript counts (Seurat v5). For each object, the following quality control thresholds were then applied: cells were prefiltered if they expressed fewer than 200 genes or greater than 10,000 genes; if they expressed fewer than 1000 UMI or greater than 80,000 UMI; and if they expressed greater than 10% mitochondrial genes. All objects were then merged with a previously published dataset of human PDAC samples that received standard of care therapy generated through the Washington University Human Tumor Atlas Network (83).
Assembly: GRCh38 v2020-A
Supplementary files format and content: Tab-separated values and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Pancreatic tumor

extract_protocol: Approximately 17,500 to 25,000 cells were partitioned into nanoliter droplets Utilizing the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v.3.1 on a Chromium instrument (10X Genomics), to achieve single-cell resolution for a target of at least 10,000 cells/sample. GEMs then underwent a reverse transcriptase (RT) reaction in which cDNA was tagged with a Unique Molecular Identifier (UMI). Full-length cDNA was enzymatically fragmented and size-selected for library construction (10X Genomics). cDNA concentration was standardized by qPCR (Kapa Biosystems) and libraries were sequenced on a NovaSeq 6000 system (Illumina) with a minimum target of 50,000 mean reads per cell.

treatment_protocol: Human PDAC samples were obtained from clinical trial (NCT04536077), in which 16 consenting patients diagnosed with resectable PDAC at Washington University and Siteman Cancer Center underwent neoadjuvant treatment with CDX-1140 +/- CDX-301. Both drugs were provided by Celldex Therapeutics. Patients received either an i.v. injection of CDX1140 (1.5mg/kg) 7-12 days prior to surgery, or 5-subcutaneous doses of CDX-301 (75 mcg/kg/day) followed by CDX1140 on day 8 +/- 1-day, with surgery 7-12 days thereafter. Blood was drawn at enrollment, at time of CDX1140 infusion, and at time of surgery. At time of surgery, tumor-containing tissue was identified and sampled by an attending pathologist. Per routine clinical care, gross tissue sections were fixed in formalin and embedded in paraffin for pathologic analysis. When possible, an additional 0.5 × 1.5 × 0.5-cm3 portion of the pancreatic tumor or liver metastasis was taken for scRNAseq processing and sequencing. All patients were treated after informed consent, and tissues were taken under this informed consent. Washington University Institutional Review Board committee approved the clinical trial study under IRB protocol #202011125. All other archival pathology tissue blocks for these cases were accessed under IRB protocol #201908148.

value: Pancreatic tumor

tag: disease

value: PDAC

value: Adult

value: anti-CD40 and Flt3L


title: HUVECs, OS_3

city: Tianjin

first: Bochuan

address: Qixiangtai

department: Department of Physiology and Pathophysiology

institute: Tianjin Medical University

description: Library name: OS_3_1

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic (v0.38).
Trimmed sequence reads were mapped to the reference genome (GENCODE v38 GRCh38) using hisat2 (v2.2.1).
Read count extraction were performed using the featureCounts function included in the Rsubread (v2.4.3).
Differentially expressed genes between ST and OS treatments were identified using DEGseq
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files includes m6A peaks in OS
Supplementary files format and content: tab-delimited text files include fold changes of genes enriched in OS

source_name: HUVECs

growth_protocol: HUVECs were cultured in M199

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) and the concentration and integrity of total RNA were measured by Qubit RNA HS Assay and Agilent 2100 Bioanalyzer (Agilent Technology), respectively.
MeRIP-seq libraries were  directly constructed using the KAPA RNA HyperPrep kit (KAPA Biosystems, KK8541) following the manufacturer’s instructions.

treatment_protocol: HUVECs were treated by OS or ST

value: HUVECs

value: Human umbilical vein endothelial cells

value: WT

value: Treated by oscillatory shear stress for 6 hours


title: Bovine mammary epithelial cells transfected with miR-199a-3p mimic 2

value: Bovine mammary epithelial cells

value: miR-199a-3p mimic


title: scRNAs Keloid3


title: E13 placenta,Female,Stress,Replicate 3

description:
Library name: R6_1
Sample data is present in column with sample name for all processed files

value: Placenta

value: Stress


title: scRNAs Keloid2

value: Skin


title: E13 placenta,Female,Stress,Replicate 4

description:
Library name: R7_1
Sample data is present in column with sample name for all processed files


title: HUVECs, OS_2

description: Library name: OS_2_1


title: scRNA-seq of Homo sapiens treated with anti-CD40: adult male PDAC tumor_HT561

description:
Library name: HT561
10X Genomics

value: Male


title: scRNA-seq of Homo sapiens treated with anti-CD40: adult male PDAC tumor_HT555

description:
Library name: HT555
10X Genomics


title: HUVECs, OS_1

description: Library name: OS_1_1


title: E13 placenta,Female,Stress,Replicate 2

description:
Library name: R3_3
Sample data is present in column with sample name for all processed files

value: Female


title: scRNA-seq of Homo sapiens treated with anti-CD40 and Flt3L: adult female PDAC liver metastasis_HT544

description:
Library name: HT544
10X Genomics

source_name: Liver metastasis

value: Liver metastasis


title: HUVECs, ST_3

description: Library name: st_3_1

value: Static for 6 hours


title: scRNA_sl10

value: scRNA-seq

value: Epithelial, stromal cell

value: Control cases group2


title: E13 placenta,Female,Stress,Replicate 6

description:
Library name: R9_10
Sample data is present in column with sample name for all processed files


title: E13 placenta,Female,Stress,Replicate 1

description:
Library name: R1_6
Sample data is present in column with sample name for all processed files


title: HUVECs, ST_2

description: Library name: st_2_1


title: scRNAs Keloid5

value: Keloid Case Group


title: E13 placenta,Male,Ctrl,Replicate 6

description:
Library name: N8_4
Sample data is present in column with sample name for all processed files

value: Ctrl


title: scRNA_sl9


title: HUVECs, ST_1

description: Library name: st_1_1

value: HUVECs

value: Human umbilical vein endothelial cells


title: E13 placenta,Male,Ctrl,Replicate 5

description:
Library name: N7_9
Sample data is present in column with sample name for all processed files


title: scRNA_sl8


title: scRNA-seq of Homo sapiens treated with anti-CD40: adult male PDAC tumor_HT442

description:
Library name: HT442
10X Genomics

value: Pancreatic tumor

value: PDAC

value: Adult


title: HUVECs, OS_3, IP

description: Library name: OS_3_IP

value: WT

value: Treated by oscillatory shear stress for 6 hours


title: scRNA-seq of Homo sapiens treated with anti-CD40 and Flt3L: adult female PDAC tumor_HT434

description:
Library name: HT434
10X Genomics

value: anti-CD40 and Flt3L


title: E13 placenta,Male,Ctrl,Replicate 4

description:
Library name: N5_1
Sample data is present in column with sample name for all processed files

value: Placenta

value: Male


title: scRNA_sl7

value: Skin


title: HUVECs, OS_2, IP

description: Library name: OS_2_IP


title: scRNA-seq of Homo sapiens treated with anti-CD40: adult male PDAC tumor_HT400

description:
Library name: HT400
10X Genomics


title: E13 placenta,Male,Ctrl,Replicate 3

description:
Library name: N4_9
Sample data is present in column with sample name for all processed files


title: HUVECs, ST_3, IP

description: Library name: ST_3_IP

value: Static for 6 hours


title: scRNA_sl6

value: scRNA-seq


title: E13 placenta,Male,Ctrl,Replicate 2

description:
Library name: N2_2
Sample data is present in column with sample name for all processed files


title: scRNA_sl5

value: Epithelial, stromal cell


title: E13 placenta,Male,Ctrl,Replicate 1

description:
Library name: N1_4
Sample data is present in column with sample name for all processed files


title: Caco-2, NoTreat, 3

city: Boston

first: Bjoern

last: Reinhard

address: 590 Commonwealth Ave

institute: Boston University

data_processing:
BCL2FASTQ
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the genemodel annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts 1.5.0-p3 was utilized for quantification
Assembly: Homo Sapiens(GRCh38/hg38)
Supplementary files format and content: tab delimited text file contains raw counts for each sample (gene_count.txt)
Supplementary files format and content: tab delimited text file contains fpkm values for each sample (gene_fpkm.txt)

source_name: Cell Line

extract_protocol:
RNeasy Micro Kit (Qiagen, catalog no. 74004) was utilized for RNA extraction. NanoDrop 2000 Spectrophotometer (Thermo Scientific, catalog no. ND-2000) was utilized to determine purity and concentration.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using randomhexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library ordTTP for non-directional library.

value: Cell Line

value: epithelial cell

value: M cell differentiation, No Treatment

tag: time

value: Day 1


title: scRNA_sl4

value: Control cases group2


title: Caco-2, NoTreat, 2

tag: cell line


title: scRNAs Keloid1

tag: cell type

value: Keloid Case Group


title: scRNA_sl3


title: HUVECs, ST_2, IP

description: Library name: ST_2_IP

value: HUVECs

value: Human umbilical vein endothelial cells

tag: genotype


title: E13 placenta,Female,Ctrl,Replicate 6

description:
Library name: N7_7
Sample data is present in column with sample name for all processed files

value: Female

tag: treatment

value: Ctrl


title: scRNA-seq of Homo sapiens treated with anti-CD40 and Flt3L: adult female PDAC liver metastasis_HT543

description:
Library name: HT543
10X Genomics

value: Liver metastasis

value: PDAC

value: Adult

value: anti-CD40 and Flt3L


title: Caco-2, NoTreat, 1

value: WT


title: HUVECs, OS_2, Input

description: Library name: OS_2_Input

value: Treated by oscillatory shear stress for 6 hours


title: HUVECs, OS_3, Input

description: Library name: OS_3_Input


title: scRNA_sl2

value: Skin

value: scRNA-seq

value: Epithelial, stromal cell


title: Caco-2, Water PAH , 3

value: Cell Line

value: epithelial cell

value: WT + Water PAH  3

value: M cell differentiation, PAH aq solubility limit exposure


title: E13 placenta,Female,Ctrl,Replicate 4

description:
Library name: N4_1
Sample data is present in column with sample name for all processed files

value: Placenta


title: scRNA_sl1

value: Control cases group2


title: E13 placenta,Female,Ctrl,Replicate 5

description:
Library name: N5_11
Sample data is present in column with sample name for all processed files

value: Female


title: HUVECs, ST_2, Input

description: Library name: ST_2_Input

value: HUVECs

value: Human umbilical vein endothelial cells

value: Static for 6 hours


title: Caco-2, Water PAH , 2

value: WT + Water PAH  2

value: Day 1


title: E13 placenta,Female,Ctrl,Replicate 3

description:
Library name: N3_16
Sample data is present in column with sample name for all processed files

value: Ctrl


title: Caco-2, Water PAH, 1

value: WT + Water PAH 1


title: Caco-2, NoTreat, 4

value: WT

value: M cell differentiation, No Treatment


title: scRNA_ml10

value: Skin

value: scRNA-seq

value: Epithelial, stromal cell

value: Control cases group1


title: E13 placenta,Female,Ctrl,Replicate 2

description:
Library name: N2_4
Sample data is present in column with sample name for all processed files


title: Caco-2, HDPE W4 PAH, 1

value: Cell Line

value: epithelial cell

value: WT + HDPE W4 PAH 1

value: M cell differentiation, nanoplastic + PAH exposure


title: scRNA_ml9


title: Input ChIP-seq

city: Hong Kong

first: Chengmin

last: Qian

address: L3-68, Laboratory Block, 21 Sassoon Road

department: School of Biomedical Sciences

country: Hong Kong

institute: The University of Hong Kong

description: ChIP-seq of Input in U2OS

data_processing:
ChIP-seq reads were mapped to UCSC hg19 genome by Bowtie 1.2.2. Only the uniquely mapped reads were kept for the subsequent analyses.
Binding peaks (q < 0.01) for Spindlin1, C11orf84 were identified using MACS software (version 2.1.0).
Genome_build: hg19
Supplementary_files_format_and_content: narrowpeak txt files

source_name: Homo sapiens bone osteosarcoma cell line

growth_protocol: U2OS cells were cultured in McCoy's 5A media, supplemented with 10% FBS at 37°C with 5% CO2

extract_protocol:
U2OS cells were fixed for 10 min with 1% formaldehyde and quenched crosslinking with 0.125 M glycine for 5 min. Nuclei was isolated using cell lysis buffer (20 mM Tris-HCl pH8.0, 85 mM KCl, 0.5% NP40).
ChIP libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: No treatment of cells

tag: chip antibody


title: C11orf84 ChIP-seq

description: ChIP-seq of C11orf84 in U2OS


title: BM_2

description:
Library name: BM157848
10x Genomics

value: Bone Marrow

value: Primary

value: Unsorted

value: Wt


title: Spindlin1 ChIP-seq

description: ChIP-seq of Spindlin1 in U2OS


title: scRNA_ml8


title: PCV2

city: xianyang

first: Tengfei

last: Shi

address: No.22 Xinong Road. Yangling

institute: Northwest A&F University

description: Library name: Sample2

data_processing:
Sequencing results were demultiplexed and converted to FASTQ format using Illumina bcl2fastq software (version2.20). Sample demultiplexing, barcode processing and single-cell 3’gene counting by using the Cell Ranger pipeline (https://support.10xgenomics.com/single-cell-geneexpression/ software/pipelines/latest/what-is-cell-ranger, version 3.1.0) and scRNA-seq data were aligned to Ensembl genome GRCm38 reference genome.
Assembly: Ensembl_v105_mus_musculus
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
On the 28th day post infection, one mouse was randomly selected from the control group and the PCV2 group, and their spleens were prepared for preparation of single-cell suspension. Place a sterile RNase-free culture dish containing an appropriate amount of calcium-free and magnesium-free PBS on ice, the spleen tissue was transferred into the culture dish and cut it into 0.5 mm2 pieces, the tissues were washed with PBS, and remove as many non-purpose tissues as possible such as blood stains and fatty layers. Tissues were dissociated into single cells in dissociation solution (0.35% collagenase IV5, 2 mg/ml papain, 120 Units/ml DNase I) in 37 ℃ water bath with shaking for 20 min at 100 rpm. Digestion was terminated with 1× PBS containing 10% fetal bovine serum（FBS, V/V）, then pipetting 5-10 times. The resulting cell suspension was filtered by passing through 70-30 um stacked cell strainer and centrifuged at 300 g for 5 min at 4 °C. The cell pellet was resuspended in 100 ul PBS (0.04% BSA) and added with 1 ml 1× red blood cell lysis buffer（MACS 130-094-183, 10×）and incubated at room temperature or on ice for 2-10 min to lyse remaining red blood cells. After incubation, the suspension was centrifuged at 300 g for 5 min at room temperature. The suspension was resuspended in 100 μl Dead Cell Removal MicroBeads (MACS 130-090-101) and remove dead cells using Miltenyi ® Dead Cell Removal Kit (MACS 130-090-101). Then the suspension was resuspended in PBS (0.04% BSA) and centrifuged at 300 g for 3 min at 4 °C（repeat twice）. The cell pellet was resuspended in 50 μl of PBS (0.04% BSA). The overall cell viability was confirmed by trypan blue exclusion, which needed to be above 85%, single cell suspensions were counted using Countess II Automated Cell Counter and concentration adjusted to 700-1200 cells/μl.
Single-cell suspensions were loaded to 10x Chromium to capture 5000 single cell according to the manufacturer’s instructions of 10X Genomics Chromium Single-Cell 3’ kit (V3). The following cDNA amplification and library construction steps were performed according to the standard protocol. Libraries were sequenced on an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150 bp) by LC-Bio Technology co.ltd., (Hangzhou, China) at a minimum depth of 20,000 reads per cell.

value: spleen


title: scRNA_ml7


title: Control_Group

description: Library name: Sample1


title: scRNA_ml6


title: HUVECs, ST_3, Input

description: Library name: ST_3_Input

value: HUVECs

value: Human umbilical vein endothelial cells

value: Static for 6 hours


title: Caco-2, HDPE W10, 1

value: WT + HDPE W10 1

value: M cell differentiation, nanoplastic exposure

value: Day 1


title: FLT3L 2

description:
Library name: F2
F2
10X Genomics

data_processing:
Raw FASTQ files were processed with CellRanger v6 (10X Genomics) using the cellranger count function for alignment to the mouse reference genome (mm10 v2020-A).
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files (barcodes.tsv, features.tsv, matrix.mtx).

source_name: Pancreas

extract_protocol:
Mice were anesthetized with isoflurane and euthanized by intra-cardiac PBS/heparin perfusion. Tissues were harvested, minced, and digested in HBSS (Gibco) supplemented with 2mg/mL collagenase-A (Roche), and 50μg/mL DNase-I (Sigma), for 30min at 37°C with constant agitation. Tissue digestion was neutralized with 10% FBS (R&D) and digests were filtered through 40μm cell strainers, then cells were counted with a Countessa-II automated cell counter (Life technologies). Samples were then stained with fluorescently conjugated anti-CD45 antibody, washed, and resuspended in FACs buffer containing 7-AAD (BD Biosciences) to distinguish live cells. Cell suspensions were then sorted for viable immune cells (7-AAD-/CD45+) using an Aria-II cell sorter (BD Biosciences). Cell sorting was done through an 85um nozzle into ice-cold PBS supplemented with 20% FBS. Sorted cells were washed and resuspended in PBS with 0.04% BSA. Cell concentration and post-sort viability were measured with a BD Rhapsody single cell system (BD Biosciences).
Libraries were sequenced on a NovaSeq 6000 sequencing system (Illumina) with a minimum target of 50,000 mean reads per cell. The cellranger mkfastq pipeline (10X Genomics) was used to demultiplex Illumina base call files to FASTQ files.

value: Pancreas

value: CD45 sort

value: FLT3L 12 days


title: scRNA_ml5

value: Skin

value: scRNA-seq

value: Epithelial, stromal cell

value: Control cases group1


title: Caco-2, HDPE Native PAH, 1

value: Cell Line

value: epithelial cell

value: WT + HDPE Native PAH 1

value: M cell differentiation, nanoplastic + PAH exposure


title: FLT3L 1

description:
Library name: F1
F1
10X Genomics


title: Caco-2, HDPE Native, 1

value: WT + HDPE Native 1


title: CD40 4

description:
Library name: C4
C4
10X Genomics

value: CD40 12 days


title: Caco-2, PS W4 PAH, 1

value: WT + PS W4 PAH 1


title: scRNA_ml2


title: E13 placenta,Female,Ctrl,Replicate 1

description:
Library name: N1_12
Sample data is present in column with sample name for all processed files

value: Placenta

value: Female

value: Ctrl


title: CD40 3

description:
Library name: C3
C3
10X Genomics

value: Pancreas


title: Caco-2, HDPE W4, 1

value: WT + HDPE W4 1

value: M cell differentiation, nanoplastic exposure

value: Day 1


title: shHSP27-shTGFβ1 dual knockdown at SNU-449 SR

city: Seoul

first: Song

last: Jae Jin

address: Room 330, Ludlow Faculty Building, 50-1 Yonsei-ro, Seodaemun-gu

department: Biomedical science

country: South Korea

institute: Yonsei University College of medicine

description: Dual knockdown of shHSP27 and shTGFβ1

hyb_protocol: Approximately 5.5 μg of labeled DNA target was hybridized to the Affymetrix GeneChip Array at 45°C for 16hour

scan_protocol: Hybridized arrays were washed and stained on a GeneChip Fluidics Station 450 and scanned on a GCS3000 Scanner (Affymetrix).

data_processing: The probe cell intensity data computation and a CEL file generation was performed using Affymetrix® GeneChip Command Console® Software (AGCC). Affymetrix Power Tools (affymetrix-power-tools.html)  R 3.3.3 (https://www.r-project.org/)

label: total RNA

source_name: SNU449 SR with shHSP27 shTGFβ1 KD

label_protocol: The sense cDNA was then fragmented and biotin-labeled with TdT (terminal deoxynucleotidyl transferase) using the GeneChip WT Terminal labeling kit

growth_protocol: SNU449 and derivative cell lines were cultured in RPMI media (Gibco) with 10% FBS under standard conditions.

extract_protocol: TRIzol (invitrogen) extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Sorafenib resistance was induced in SNU449 cells; additional treatments included Ad-shHSP27, Ad-shTGFβ1, Ad-shGRP78, and Ad-shHSP27-shTGFβ1, and Ad-shTGFβ1-shGRP78 virus knockdowns.

value: Hepatocellular carcinoma


title: scRNA_ml3

value: Skin

value: scRNA-seq

value: Epithelial, stromal cell


title: shTGFβ1-shGRP78 dual knockdown at SNU-449 SR

description: Dual knockdown of shTGFβ1 and shGRP78

source_name: SNU449 SR with shTGFβ1 shGRP78 KD


title: scRNA_ml1

value: Control cases group1


title: Caco-2, HDPE W10 PAH, 1

value: Cell Line

value: epithelial cell

value: WT + HDPE W10 PAH 1


title: Caco-2, PS W10 PAH, 1

value: WT + PS W10 PAH 1

value: M cell differentiation, nanoplastic + PAH exposure


title: shGRP78 knockdown at SNU-449 SR

description: shGRP78 knockdown

source_name: SNU449 SR with shGRP78


title: CD40 1

description:
Library name: C1
C1
10X Genomics

value: CD45 sort

value: CD40 12 days


title: CD40 + FLT3L 2

description:
Library name: CF2
CF2
10X Genomics

value: CD40 + FLT3L 12 days


title: shTGFβ1 knockdown at SNU-449 SR

description: shTGFβ1 knockdown in sorafenib-resistant SNU449

source_name: SNU449 SR with shTGFβ1


title: shHSP27 knockdown at SNU449-SR

description: GRP78-related shHSP27 knockdown

source_name: SNU449 SR with shHSP27


title: Il6p_rep2

city: seattle

first: xueqiu

last: lin

state: wa

address: 1100 Fairview Ave N

institute: FRED HUTCHINSON CANCER CENTER

data_processing:
We calculated the gRNA count matrix by exact match for each read. Counts between replicates of the same condition were highly correlated (Pearson correlation coefficient was 0.835 for the RSS day 30 sample, and 0.894 for the ISS D30 screening sample), indicating the high reproducibility of the RSS and ISS CRISPRi screening.
The gRNA count table was loaded into MaGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) to use the maximum likelihood estimation (MLE) approach to estimate the essentiality of genes in cell senescence by comparing the experimental in replicative arrest and inflammation (IL6 stimulation) condition. The beta score was calculated to call gene essentialities: a positive beta score means a gene is positively selected (the gene expression positively functions in cell senescence), and a negative beta score means a gene is negatively selected (the gene expression negatively functions in cell senescence).
Assembly: hg19
Supplementary files format and content: CountMatrix.xlsx file: sequenced  sgRNA counts mapped to the sgRNA library at different conditions (d0, without and with  IL-6)  for two biological replicates
Library strategy: CRISPR screen

source_name: human primary mesenchymal stem cells (MSC) derived from adipose tissues

growth_protocol: Primary adipose derived cell (Lifeline) were maintained on gelatin-coated tissue culture plates with medium specific for MSC growing (StemLife MSC Medium Complete Kit, Lifeline) .Human embryonic kidney (HEK293T) cells (ATCC) were cultured in 10% fetal bovine serum (Thermo Fisher Scientific) in DMEM (Thermo Fisher Scientific). Cells were maintained at 37℃ in a cell incubator containing 5% CO2.

extract_protocol:
About 7-8weeks later, cells were harvested and genomic DNA was extracted from all samples
The sgRNA-encoding regions were then amplified by PCR using HiSeq forward and reverse primers and then sequenced on an Illumina HiSeq-4000 using HiSeq custom primer with previously described protocols at high coverage. Primers used are summarized in TableS3.

treatment_protocol: The senescence screens were performed in two independent replicates. 1. On day −3, 125M MSC cells were seeded at 2.5M cells/15cm gelatin-coated dishes; 2. On day −1, cells were transduced with pooled lentiviral sgRNA library with a MOI of 0.3; 3. On day 0, cells were switched to basal medium with and puromycin at 2μg/mL; 4. 7days after puromycin selection, 25 million cells were harvested as the initial population of the screen. 5. Fresh medium with puromycin at 1μg/mL was changed every day starting day 7; 6. On day 14，cells intergrated lentiviral sgRNA libray were transduced with a lentiviral constructs pSLQ6604 that express dCas9-KRAB from SFFVpromoter 7. On day 17, cells were harvested and divided into 2 parts: one part is for growing naturally until their growing limitation, other part is for growing in the presence of 10ng/ml recombinant human IL-6 protein(Abcam, ab259381) until their growing limitation. Fresh medium was changed every 2 days.

value: mesenchymal stem cells

value: Add the low concentration of 10 ng/ml IL-6


title: Caco-2, PS W10, 1

value: WT + PS W10 1

value: M cell differentiation, nanoplastic exposure


title: SNU449 sorafenib resistant cell line

description: Gene expression from SNU449-SR cells

source_name: SNU449 SR

value: Hepatocellular carcinoma


title: Il6p_rep1

value: human primary mesenchymal stem cells (MSC) derived from adipose tissues


title: scRNA_ml4

source_name: Skin

value: Skin

value: scRNA-seq


title: shTGFβ1-shGRP78 dual knockdown

description: Dual knockdown of shTGFβ1 and shGRP78

source_name: SNU449 with shTGFβ1 shGRP78 KD


title: CD40 + FLT3L 1

description:
Library name: CF1
CF1
10X Genomics

value: Pancreas


title: Caco-2, PS W4, 1

value: Cell Line

value: WT + PS W4 1

value: Day 1


title: Caco-2, PS Native, 1

value: epithelial cell

value: WT + PS Native 1


title: CD40 2

description:
Library name: C2
C2
10X Genomics

value: CD45 sort


title: Il6m_rep2

value: Without  IL-6


title: Il6m_rep1


title: shHSP27-shTGFβ1 dual knockdown

description: Dual knockdown of shHSP27 and shTGFβ1

source_name: SNU449 with shHSP27 shTGFβ1 KD


title: Vehicle 5

description:
Library name: V5
V5
10X Genomics

value: Vehicle 12 days


title: Caco-2, PET W4 PAH, 1

value: WT + PET W4 PAH 1

value: M cell differentiation, nanoplastic + PAH exposure


title: Vehicle 3

description:
Library name: V3
V3
10X Genomics


title: d0_rep2

value: mesenchymal stem cells


title: Caco-2, PET W4, 1

value: WT + PET W4 1

value: M cell differentiation, nanoplastic exposure


title: d0_rep1

value: human primary mesenchymal stem cells (MSC) derived from adipose tissues


title: Caco-2, PS Native PAH, 1

value: WT + PS Native PAH 1


title: Vehicle 4

description:
Library name: V4
V4
10X Genomics


title: HMLE-TWIST1_KD-D4_3

first: Gracia

middle: M.

last: Bonilla

state: MA

address: 185 Cambridge St

department: Molecular Biology

institute: Massachusetts General Hospital

data_processing:
Illumina software used for basecalling.
Reads were mapped using the STAR aligner (Dobin, Davis et al. 2013) and the hg19 assembly of the human genome.
Read counts for individual transcripts were obtained using HTSeq (Anders, Pyl et al. 2014) and the Ensembl GRCh37 release 75 gene annotation.
Analysis of differential expression was performed using only genes with normalized counts (CPM) >=1 in at least one sample
Assembly: hg19
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with RPKM normalized counts for every gene and every sample

growth_protocol: HMLE cells and HMLE-TWIST cells were cultured in 10 cm dish with mammary epithelial growth (MEGM) medium plus DMEM/F12 medium with 10% FCS and penicillin/streptomycin (P/S) (3:7).

extract_protocol:
Total RNA was extracted using Trizol (Invitrogen) following the manufacturer’s protocol and concentrated by ethanol precipitation. Column purification of 50µg of extracted RNA was performed using RNeasy Mini kits (Qiagen, 74106), with minor modifications to the manufacturer’s protocol, including an extension of on-column DNase treatment from 15 to 30 minutes. For each sample, 1µg of RNA was used to generate libraries using SMARTer Stranded Total RNA Sample Prep kits (Takara, 634876), with integrated RiboGone enzymatic rRNA depletion.
RNA libraries were prepared for sequencing using SMARTer Stranded Total RNA Sample Prep kits (Takara, 634876) protocols

treatment_protocol: HMLE and HMLE-TWIST cells were treated in 3 ways; 1) Three replicates were treated with different doses of chaetocin (0, 100, 150, 200, 500nM) for 48h; 2) Three replicates were treated with 80 nM of chaetocin for 15 h and washed out, and then cells were incubated with fresh medium for additional 48h; 3) Three replicates were transfected with DsiRNA against SUV39H1/H2 genes for 48h, and then cells were incubated with fresh medium for additional 48h.

value: Mammary gland epithelial cells

value: Breast

value: overexpressing TWIST1

value: SUV39H1/H2 DsiRNA for two days and washed and incubated in fresh media for an additional two days


title: shTGFβ1 knockdown

source_name: SNU449 with shTGFβ1

value: Hepatocellular carcinoma


title: Caco-2, PET W10 PAH, 1

value: Cell Line

value: epithelial cell

value: WT + PET W10 PAH 1

value: Day 1


title: Vehicle 2

description:
Library name: V2
V2
10X Genomics

value: Pancreas

value: CD45 sort

value: Vehicle 12 days


title: HMLE-TWIST1_KD-D4_2


title: Caco-2, PET W10, 1

value: WT + PET W10 1


title: Vehicle 1

description:
Library name: V1
V1
10X Genomics


title: shHSP27 knockdown

description: GRP78-related shHSP27 knockdown

source_name: SNU449 with shHSP27


title: SNU449 parental cell

description: Gene expression from parental SNU449 cells

source_name: SNU449 control


title: Caco-2, PET Native PAH, 1

source_name: Cell Line

value: WT + PET Native PAH 1

value: M cell differentiation, nanoplastic + PAH exposure


title: Roots of six day old seedlings, Rep2

city: Tuebingen

first: Marja

last: Timmermans

address: Morgenstelle 32

institute: University of Tuebingen

description: Library name: Rep2

library_source: genomic single cell

data_processing:
Read pairs were processed with Cell Ranger ATAC (v2.1.0, 10X Genomics)
Assembly: TAIR10.55
Supplementary files format and content: Cell Ranger output files: filtered_peak_bc_matrix.h5, fragments.tsv.gz, fragments.tsv.gz.tbi, and singlecell.csv

organism: Arabidopsis thaliana

source_name: Root tip

growth_protocol: Plants were grown at 22 °C on 1 % agar plates containing 0.5 x Murashige and Skoog (MS) medium (Duchefa Biochem.) in long day conditions (16 hours light, 8 hours dark) following stratification for three days at 4 °C.

extract_protocol:
Roots of six day old seedlings or A. thaliana Col-0 were cut 0.5 - 0.7 cm from their tip and a total of 180 mg of root tissue was collected.
Single cell ATAC-seq libraries were produced from freshly isolated nuclei in accordance with the 10X Genomics Chromium Single Cell ATAC-seq kit protocol (v 1.1 protocol, Rev D), targeting ~14-15,000 nuclei per reaction. The adapter-ligated libraries were amplified using nine PCR cycles.

value: Root tip


title: Roots of six day old seedlings, Rep1

description: Library name: Rep1


title: shGRP78 knockdown

description: shGRP78 knockdown

source_name: SNU449 with shGRP78


title: Wounding-SlOS-24h-rep4

city: Lausanne

first: Philippe

last: Reymond

address: Biophore building

department: Department of Plant Molecular Biology

country: Switzerland

institute: University of Lausanne

description: Library name: Wounding-SlOS-24h-rep4

data_processing:
Adapter-free purity-filtered reads were generated with Cutadapt (v. 2.5) (Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065) (Davis et al. 2013).  The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1) (Anders et al. 2014) using gene annotation. Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7) (Wang et al. 2012). The htseq-generated counts data was used for the analysis.
Assembly: Reads were aligned against Arabidopsis thaliana TAIR10.39 genome using STAR (v. 2.5.3a) (Dobin et al. 2013).
Supplementary files format and content: tab-delimited text file, normalized counts
Supplementary files format and content: tab-delimited text file, fold change

source_name: leaf

growth_protocol: Arabidopsis thaliana ecotype Col-0 plants were vernalized for 2 days at 4°C and cultivated in pots containing moist compost. Plants were grown in a controlled environmental chamber with a 10 h day / 14 h night cycle (22°C, 100 mmol m-2 sec-1, RH 65%). Experiments were conducted with five-week-old plants.

extract_protocol:
Leaf discs were ground in a Qiagen tissue lyser and RNA was extracted using a ReliaPrepTM RNA Tissue Miniprep System (Promega).
Individual libraries made from the 150 ng of RNA of each sample were processed by the Genomic Technologies Facility (GTF) at the University of Lausanne. Samples were paired-end (SE) sequenced on a Illumina NovaSeq6000 generating reads with a length of 150 bp.

treatment_protocol: Leaves were wounded by piercing four holes of 1 mm each. Two μl of either H2O, Pieris brassicae oral secretions(OS) or Spodoptera littoralis OS were applied to each hole. Samples were collected either 3h after wounding or 24h after wounding. Unwounded controls were collected 3h after wounding. Leaf discs of 1 cm diameter around the wound site were collected, frozen in liquid nitrogen and stored at -80°C

value: leaf

value: five weeks


title: Caco-2, PET Native, 1

value: WT + PET Native 1

value: M cell differentiation, nanoplastic exposure


title: P301S_neg_CD8_WT_30weeks

city: Bethesda

first: Kory

middle: R

last: Johnson

state: MD

address: 10/3B01, 9000 Rockville Pike

department: DIR IT & Bioinformatics

institute: NINDS/NIH

description: 10x Genomics

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

source_name: spinal cord

extract_protocol:
Two mice per experimental group were collected and perfused with chilled normal saline. Spinal cords from each animal were dissected and two spinal cords were combined per tube for processing. Tissues were then processed using the Miltenyi Tumor Dissociation Kit (#130-096-730, Miltenyi Biotec) and the gentleMACS™ Octo Dissociator with Heaters on the soft/medium program (37C_m_TDK_1). Following dissociation, myelin was removed using Myelin Removal Beads II (#130-096-731, Mitenyi Biotec) according to the manufacturer’s.  protocol. single cell suspension quality, number and viability were assessed with the dual fluorescence cell counter Luna-FX7 (Logos Bio). Gel Bead-in-Emulsions were prepared by loading up to 10,000 cells per sample onto the 10X Genomics Chromium Next GEM Chip G (cat#1000127).
Barcoded single cell cDNAs and DNA libraries were generated with Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics; cat#1000269) following the manufacturer’s standard protocol

value: spinal cord

value: leukocytes & spinal cord cells

value: P301S negative


title: HMLE_KD-D4_3

source_name: HMLE

value: HMLE

value: Mammary gland epithelial cells

value: Breast

value: Wild type

value: SUV39H1/H2 DsiRNA for two days and washed and incubated in fresh media for an additional two days


title: HMLE-TWIST1_KD-D4_1

value: overexpressing TWIST1


title: Wounding-SlOS-24h-rep3

description: Library name: Wounding-SlOS-24h-rep3


title: HMLE_KD-D4_2


title: P301S_hom_CD8_WT_33weeks

description: 10x Genomics

value: P301S homozygous


title: Caco-2, PVC W4 PAH, 1

value: Cell Line

value: epithelial cell

value: WT + PVC W4 PAH 1

value: Day 1


title: P301S_hom_CD8_WT_30weeks

description: 10x Genomics


title: Caco-2, PVC W4, 1

value: WT + PVC W4 1


title: Wounding-SlOS-24h-rep2

description: Library name: Wounding-SlOS-24h-rep2

value: leaf

value: five weeks


title: HMLE_KD-D4_1


title: P301S_hom_CD8_KO_30weeks

description: 10x Genomics

value: spinal cord


title: HMLE-TWIST1_scr-D4_3

value: scramble siRNA for 2 days and washed and incubated in fresh media for an additional two days.


title: SC_CD8 VDJ

description: 10x Genomics

extract_protocol:
Six homozygous P301S mice (28-30 weeks) were harvested and perfused with chilled normal saline. Spinal cords from each animal were dissected and two spinal cords were combined per tube for processing. All three mediastinal lymph nodes were also collected per mouse and combined into one tube for processing. Tissues for both experiments were then processed using the Miltenyi Tumor Dissociation Kit (#130-096-730, Miltenyi Biotec) and the gentleMACS™ Octo Dissociator with Heaters on the soft/medium program (37C_m_TDK_1). Following  spinal cord dissociation, myelin was removed using Myelin Removal Beads II (#130-096-731, Mitenyi Biotec) according to the manufacturer’s protocol. The spinal cord and lymph node derived cell suspensions were stained the following antibodies obtained from Biolegend (BL) or BD Biosciences (BD): CD11b BV570 (1:200, #101233, BL), CD45 BUV395 (1:200, #564279, BD), CD4 FITC (1:200, #100510, BL), CD44 BUV737 (1:200, #612799, BD), CD8 BUV805 (1:200, #612898, BD) as well as LiveDead fixable Blue Cell Staining kit (1:500 in PBS, #L34962, ThermoFisher).  CD8+ and CD4+ T cells were then sorted using a BD S6 Symphony Cell Sorter into X-vivo 15 Serum-free Hematopoietic Cell Medium (Lonza cat#02-053Q). For both experiments, single cell suspension quality, number and viability were assessed with the dual fluorescence cell counter Luna-FX7 (Logos Bio). Gel Bead-in-Emulsions were prepared by loading up to 10,000 cells per sample onto the 10X Genomics and Chromium Next GEM Chip K (cat#1000287) and run using the Chromium Controller (10x Genomics version 5.0).
Barcoded single cell cDNAs and DNA libraries were generated with the 10X Genomics Chromium Next GEM Single Cell 5' Kit v2 (cat#1000265) and the Chromium Single Cell Mouse TCR Amplification Kit (cat#1000254) following the manufacturer’s standard protocol.

value: CD4 T cells


title: Wounding-PbOS-24h-rep3

description: Library name: Wounding-PbOS-24h-rep3


title: HMLE-TWIST1_scr-D4_2


title: SC_CD8 GEX

description: 10x Genomics


title: Wounding-SlOS-24h-rep1

description: Library name: Wounding-SlOS-24h-rep1


title: Caco-2, PVC W10, 1

value: WT + PVC W10 1

value: M cell differentiation, nanoplastic exposure


title: Wounding-PbOS-24h-rep4

description: Library name: Wounding-PbOS-24h-rep4


title: Wounding-PbOS-24h-rep2

description: Library name: Wounding-PbOS-24h-rep2


title: Caco-2, PVC Native, 1

value: WT + PVC Native 1


title: Caco-2, PVC Native PAH, 1

value: WT + PVC Native PAH 1

value: M cell differentiation, nanoplastic + PAH exposure


title: SC_CD4 VDJ

description: 10x Genomics


title: Caco-2, PVC W10 PAH, 1

value: WT + PVC W10 PAH 1


title: HMLE-TWIST1_scr-D4_1

value: Mammary gland epithelial cells

value: Breast

value: overexpressing TWIST1


title: SC_CD4 GEX

description: 10x Genomics

value: P301S homozygous


title: huvec_nSi_3

city: College Station

first: Akhilesh

last: Gaharwar

address: 101 Bizzell St

department: BME

institute: Texas A&M University

description: Nanosilicate-treated endothelial cells

data_processing:
Sequence cluster identification, quality prefiltering, base calling and uncertainty assessment were done in real time using Illumina's NCS 1.0.2 and RFV 1.0.2 software with default parameter settings. Sequencer .cbcl basecall files were demultiplexed and formatted into .fastq files using bcl2fastq 2 2.19.0 script configureBclToFastq.pl.
Sequenced reads were trimmed for adaptor sequence and aligned by STAR aligner
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons (excluding 5UTR and 3UTR) of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library (only reads mapping to annotated regions of the genome were used for the total libraray size).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for all samples

source_name: Endothelial cells derived from human umbilical vein

growth_protocol: HUVECs  were cultured under aseptic conditions at 37°C under 5% carbon dioxide with endothelial cell medium 2 (PromoCell, Catalog # C22011) and 1% penicillin/streptomycin (100U/100 µg/mL; Gibco, Catalog # 15140163). After every 2-3 days, culture media was exchanged for fresh media. Cells were passaged with 0.5% trypsin-EDTA upon reaching 90% confluency and seeded at approximately 7,500 cells per cm2. All experiments were completed with cell populations under P5.

extract_protocol:
At the end of 7 days of culture, total RNA was extracted (Zymogen, High Purity RNA Isolation kit), and then converted into cDNA (>1 μg).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: HUVECs were cultured and treated with/without nSi (10µg/mL). Excess nanoparticles were washed after 48 hours, and the cells were allowed to grow for another five days.

value: Nanosilicate-treated


title: Wounding-PbOS-24h-rep1

description: Library name: Wounding-PbOS-24h-rep1


title: HMLE_scr-D4_3

value: HMLE

value: Wild type


title: HMLE_scr-D4_2


title: LN_CD8 VDJ

description: 10x Genomics

source_name: mediastinal lymph node

value: mediastinal lymph node


title: Wounding-H2O-24h-rep4

description: Library name: Wounding-H2O-24h-rep4

value: leaf

value: five weeks


title: huvec_nSi_2

description: Nanosilicate-treated endothelial cells

value: Endothelial cells derived from human umbilical vein


title: Wounding-H2O-24h-rep3

description: Library name: Wounding-H2O-24h-rep3


title: HMLE_scr-D4_1

value: scramble siRNA for 2 days and washed and incubated in fresh media for an additional two days.


title: huvec_nSi_1

description: Nanosilicate-treated endothelial cells


title: HMLE-TWIST1_KD-D2_3

value: SUV39H1/H2 DsiRNA for 2 days


title: LN_CD4 VDJ

description: 10x Genomics

value: CD4 T cells


title: LN_CD8 GEX

description: 10x Genomics


title: huvec_cntrl_3

description: Untreated endothelial cells

value: Untreated control


title: Wounding-H2O-24h-rep2

description: Library name: Wounding-H2O-24h-rep2


title: HMLE-TWIST1_KD-D2_2


title: LN_CD4 GEX

description: 10x Genomics


title: HMLE-TWIST1_KD-D2_1


title: Wounding-H2O-24h-rep1

description: Library name: Wounding-H2O-24h-rep1


title: huvec_cntrl_2

description: Untreated endothelial cells


title: Wounding-SlOS-3h-rep4

description: Library name: Wounding-SlOS-3h-rep4


title: HMLE_KD-D2_3


title: mouse, 5×FAD, ST, M

city: Hangzhou

first: Tianhao

state: Zhejiang

address: Yuhangtang Road, 866

institute: Zhejiang University

description: 10× Visium

data_processing:
Raw gene expression matrices were generated for samples by the Cell Ranger (v.6.0.1) Pipeline & Space Ranger (v.6.0.1) Pipeline aligned to mm10 genome
Assembly: mm10
Supplementary files format and content: tsv.gz, mtx.gz, spatial and single-cell transcriptomic data matrix
Supplementary files format and content: csv, spatial locations of spots in spatial transcriptomic data

source_name: 5×FAD mouse brain

growth_protocol: Mice are housed under a 12-h light/dark cycle in a controlled environment with food and water provided ad libitum

extract_protocol:
For samples embedded in paraffin, they are immersed in 4% paraformaldehyde (PFA) overnight, followed by transfer to 0.9% NaCl. For samples used for snRNA-seq, they are snap-frozen in a bath of isopentane and liquid nitrogen.
RNA libraries are prepared for sequencing using standard Illumina protocols
Spatial Transcriptomics

treatment_protocol: Mice are perfused with PBS transcardially. Remove mice brains and divide them into two hemispheres.

value: 5×FAD mouse brain

value: male

value: 6 months


title: mouse, 5×FAD, ST, L

description: 10× Visium


title: huvec_cntrl_1

description: Untreated endothelial cells


title: scRNAseq from normal skin

city: Yachiyo-City

first: Kota

last: Kokubo

state: Chiba

address: Yachiyodai-minami 1-10-12

department: Department of Immunology

institute: Chiba University

description: 10x Genomics

data_processing:
We used Cell Ranger (10X Genomics) to process and aggregate sample sequence reads.
Assembly: GRCh38
Supplementary files format and content: Matrix, features, and barcodes files

extract_protocol:
Keroid tissues were dissociated in a gentleMACS C-tube (Miltenyi Biotec) with digestion buffer composed of DMEM (Gibco) and Multi Tissue Dissociation Kit 1 using a gentle MACS Octo dissociator (Miltenyi Biotec). After running the program “37°C_multi_H”, cell suspensions were passed through a 70-μm nylon mesh sheet.
Libraries were prepared using Chromium Single Cell 3’ Reagent Kits v3.1 following the manufacturer’s protocol (10X Genomics, CA, USA). The generated scRNA-seq libraries were sequenced using a total of 127 cycles (paired-end reads) with a NovaSeq 6000 (Illumina, Inc., CA, USA).

value: Skin

value: whole cell


title: HMLE_KD-D2_2

value: Mammary gland epithelial cells

value: Breast


title: Wounding-SlOS-3h-rep3

description: Library name: Wounding-SlOS-3h-rep3


title: mouse, 5×FAD, ST, S

description: 10× Visium


title: Wounding-SlOS-3h-rep1

description: Library name: Wounding-SlOS-3h-rep1


title: HMLE_KD-D2_1

value: HMLE


title: Wounding-SlOS-3h-rep2

description: Library name: Wounding-SlOS-3h-rep2


title: mouse, WT, ST, L

description: 10× Visium

source_name: wild type mouse brain

value: wild type mouse brain


title: HMLE-TWIST1_scr-D2_3

value: overexpressing TWIST1

value: scramble siRNA for 2 days


title: mouse, WT, ST, M

description: 10× Visium


title: scRNAseq from keloid patient No.1

description: 10x Genomics


title: scRNAseq from keloid patient No.3

description: 10x Genomics


title: scRNAseq from keloid patient No.2

description: 10x Genomics


title: Wounding-PbOS-3h-rep4

description: Library name: Wounding-PbOS-3h-rep4

value: leaf

value: five weeks


title: Wounding-PbOS-3h-rep3

description: Library name: Wounding-PbOS-3h-rep3


title: HMLE-TWIST1_scr-D2_2


title: RNAseq_NT2_shBrat1_Day28_Dox_rep2

city: Miami

first: Ramin

last: Shiekhattar

state: Florida

address: 1501 NW 10th Avenue

department: Department of Human Genetics

institute: University of Miami - Sylvester Comprehensive Cancer Center

data_processing:
Adapter trimming:  Total RNA-seq: FASTQ data were processed with Trimmomatic v0.38 to remove adapters and low-quality reads.
RNA-seq: reads were aligned to the hg19 human genome using STAR aligner v2.5.3a with default parameters and RSEM v1.2.28 to obtain expected gene counts against the human Ensembl reference (release 87).
Assembly: hg19
Supplementary files format and content: The processed data files are in bigWig format normalized by Count Per Million (CPM) produced by bamCoverage from DeepTools (v. 3.1.2). Raw and normalized counts per gene were produced by RSEM v1.2.28 and provided in tab-delimited format. Differential gene expression was quantified using Deseq2 (v. 1.22.2).

source_name: NTERA-2 cl.D1

growth_protocol: NT2/D1 (NTERA-2cl.D1) cells containing stable BRAT1 shRNA were maintained at 37°C with 5% CO2 and passaged every 2-3 days at a 1:3 split ratio, according to ATCC recommendations.

extract_protocol:
500ng of the Total RNA was extracted using Trizol reagent (Thermo Fisher Scientific, #15596026) according to the manufacturer’s instructions. Genomic DNA was removed by Turbo DNAse treatment (Invitrogen, #AM1907). The quality of total RNA was assessed by running it on 1% agarose gel and visualized by ethidium bromide staining.
Total RNA-seq libraries were depleted from ribosomal RNA and produced using Stranded Total RNA library prep kit (Illumina, #20020596). RNA samples were treated by Turbo DNase RNase free Kit (Invitrogen, #AM1907) to remove genomic DNA.

treatment_protocol: Neural differentiation of NT2 cells was performed as published previously by Peter W. Andrews with some modifications. One day after cell seeding, cells were treated with 10-5 M of all trans retinoic acid (ATRA) for 28 days. Media supplemented with fresh ATRA was exchanged every other day. Cells were harvested at days 0 and 28 and used for RNA extractions. For depletion of BRAT1, the cells were treated with 1ug/ml Dox along with ATRA treatment at the same time.

value: pluripotent embryonal carcinoma

tag: cell source

tag: modification

value: Tet-pLKO_shBRAT1 stable cells

tag: time point

tag: agent

value: Dox


title: mouse, WT, ST, S

description: 10× Visium

tag: tissue


title: mouse, 5×FAD, snRNA-seq, rep3

description: 10× Genomics

tag: Sex


title: Wounding-PbOS-3h-rep2

description: Library name: Wounding-PbOS-3h-rep2

tag: age


title: Wounding-PbOS-3h-rep1

description: Library name: Wounding-PbOS-3h-rep1


title: HMLE_scr-D2_3

value: Wild type


title: RNAseq_NT2_shBrat1_Day28_Dox_rep1


title: HMLE_scr-D2_2


title: Wounding-H2O-3h-rep3

description: Library name: Wounding-H2O-3h-rep3


title: mouse, 5×FAD, snRNA-seq, rep1

description: 10× Genomics

value: 5×FAD mouse brain


title: RNAseq_NT2_shBrat1_Day28_noDox_rep1


title: mouse, WT, snRNA-seq, rep3

description: 10× Genomics

value: male


title: Wounding-H2O-3h-rep2

description: Library name: Wounding-H2O-3h-rep2


title: mouse, WT, snRNA-seq, rep2

description: 10× Genomics

value: 6 months


title: HMLE-TWIST1_80nm-D4_3

value: 80 nm of chaetocin for 15 hours, then the cells were washed and placed in chaetocin-free media for an additional 2 days


title: RNAseq_NT2_shBrat1_Day0_rep2


title: HMLE-TWIST1_80nm-D4_2


title: RNAseq_NT2_shBrat1_Day0_rep1


title: Wounding-H2O-3h-rep1

description: Library name: Wounding-H2O-3h-rep1


title: mouse, WT, snRNA-seq, rep1

description: 10× Genomics


title: Control-rep4

description: Library name: Control-rep4

value: Control


title: HMLE-TWIST1_80nm-D4_1

value: Mammary gland epithelial cells


title: Input_HMLE-TWIST_KD_3

description: genomic DNA (INPUT)

data_processing:
ChIP-seq reads were aligned to the hg19 genome using BWA version 0.7.15
bigWig files were generated using the deepTools bamCompare command by comparing ChIP with Input, normalizing using CPM, and with bin size of 100, and smooth length of 300
Supplementary files format and content: bigWig

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Sequencing libraries were made from 5ng of ChIP DNA using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) or 1ng of ChIP DNA using Nextera XT DNA Library Prep kit (Illumina).

treatment_protocol: H3K9me3 ChIP-seq of HMLE and HMLE-TWIST1 cells  treated DMSO or 80nM chaetocin for two days, after which the cells were washed and incubated in chaetocin-free media for an additional two days (n=3). Also, H3K9me3 ChIP-seq of HMLE and HMLE-TWIST1 cells in which SUV39H1/H2 were knocked down using DsiRNAs for two after which the cells were incubated for an additional two days (n=3). Next generation high throughput sequencing libraries were then generated.

value: Breast

value: Input DNA before adding antibody

value: SUV39H1/H2 DsiRNA for 2 days


title: Embryo LSK/PreproB/ProB HTO

city: Lund

first: Charlotta

last: Böiers

state: Lund

address: BMC B12

country: Sweden

institute: Lund University,

data_processing:
Post sequencing the BCL files were processed using Cell Ranger mkfastq to produce FASTQ files, which were then processed using Cell Ranger count(v7.0.0)
Assembly: mm10
Supplementary files format and content: mtx/gene/cell files containing raw count data
Library strategy: CITE-seq

source_name: Blood cells

extract_protocol:
Samples (adult prepared in 2 batches) were loaded onto the 10x genomics 3’ version 2 platform (10x Genomics) and single-cell RNA-seq was performed according to the manufacturer’s instruction with minor changes to allow for CITE-seq
The CITE-seq and hashtag protocol described by Stoeckius et al was used to generate an antibody-derived tag (ADT) sequencing library, a hashtag oligo (HTO) library and a 3´gene expression library (Stoeckius et al, 2017).

value: Blood cells

value: LSK/PreproB/ProB

value: Control (Cre-) and KMT2A::AFF1+


title: Input_HMLE-TWIST_KD_2

description: genomic DNA (INPUT)

value: overexpressing TWIST1


title: HMLE-TWIST1_DMSO-D4_3

value: DMSO for 15 hours, then the cells were washed and placed in DMSO-free media for an additional 2 days


title: Embryo LSK/PreproB/ProB


title: Input_HMLE-TWIST_KD_1

description: genomic DNA (INPUT)


title: Control-rep2

description: Library name: Control-rep2

value: leaf

value: five weeks


title: Control-rep1

description: Library name: Control-rep1


title: Adult LSK/PreproB/ProB Batch2 HTO


title: HMLE_scr-D2_1

value: HMLE

value: Wild type

value: scramble siRNA for 2 days


title: Input_HMLE_KD_3

description: genomic DNA (INPUT)


title: HMLE-TWIST1_DMSO-D4_1


title: Adult LSK/PreproB/ProB Batch1 HTO


title: HMLE-TWIST1_scr-D2_1


title: CowO8

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

description: Bulk RNA-seq

data_processing:
Bulk RNA-seq reads were aligned with STAR 2.7.1a to the reference sequence (mm10 from UCSC). Rat reference was used for gene annotation and counting (mRatBN7.2). Uniquely mapped reads were quantified using featureCounts using protein coding genes by gene.
Assembly: mRatBN7.2
Supplementary files format and content: Input tables are included as tab separated files.

organism: Rattus norvegicus

source_name: Sprague Dawley

extract_protocol:
Tissue was processed for RNA extraction using a modified manufacturer’s procedure (miRNA Easy Kit, Qiagen)
Tissue was processed for RNA extraction using a modified manufacturer’s procedure (miRNA Easy Kit, Qiagen). Frozen samples were sent to BGI Americas Cooperation (Cambridge, MA) and sequencing was performed using polyA mRNA directional RNA-seq library preparation using a DNBSEQTM platform.

tag: strain

value: Sprague Dawley

value: Cocaine

value: eGFP

value: 13-15 weeks


title: mouse, 5×FAD, snRNA-seq, rep2

last: Wang

description: 10× Genomics

value: 5×FAD mouse brain

value: male

value: 6 months


title: HMLE_DMSO-D4_3

value: Mammary gland epithelial cells

value: Breast


title: Input_HMLE_KD_2

description: genomic DNA (INPUT)

value: Input DNA before adding antibody

value: SUV39H1/H2 DsiRNA for 2 days


title: RNAseq_NT2_shBrat1_Day28_noDox_rep2

value: pluripotent embryonal carcinoma

value: Tet-pLKO_shBRAT1 stable cells


title: CowO7

description: Bulk RNA-seq


title: HMLE_DMSO-D4_2

value: DMSO for 15 hours, then the cells were washed and placed in DMSO-free media for an additional 2 days


title: Control-rep3

description: Library name: Control-rep3

value: leaf

value: Control

value: five weeks


title: Input_HMLE_KD_1

description: genomic DNA (INPUT)

value: HMLE

value: Wild type


title: Input_HMLE-TWIST_scr_3

description: genomic DNA (INPUT)

value: overexpressing TWIST1

value: scramble siRNA for 2 days


title: CowO6

description: Bulk RNA-seq

value: Sprague Dawley

value: Cocaine

value: eGFP

value: 13-15 weeks


title: Cd4creGlut10fl/fl-3

city: Beijing

first: Ying

last: Liu

address: Tiantan street, Tiantan Xili 2rd

department: Institute of Medicinal Biotechnology

institute: Chinese Academy of Medical Sciences

data_processing:
In order to guarantee the data quality which was used to analysis, the useful Perl script was used to filter the original data (Raw Data)
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.
The IGV (Integrative Genomics Viewer) was used to view the mapping result by the Heatmap, histogram, scatter plot or other stytle.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
DEGseq v1.18.0 was used for differential gene expression analysis between two samples with non biological replicates.
Assembly: mm8
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...

source_name: spleen

extract_protocol:
CD8+ T cells were collected from spleen of Cd4cre or Cd4creGlut10fl/fl mice, flash frozen on dry ice, and RNA was harvested using Trizol reagent. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA)
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spleen

value: primary

value: CD8 + T cell


title: CowO3

description: Bulk RNA-seq


title: HMLE_DMSO-D4_1

value: Mammary gland epithelial cells

value: Breast


title: HMLE-TWIST1_500nm-D2_3

value: 500 nm Chaetocin for 2 days


title: Input_HMLE-TWIST_scr_2

description: genomic DNA (INPUT)

value: Input DNA before adding antibody


title: Cd4creGlut10fl/fl-2


title: CowO2

description: Bulk RNA-seq


title: Input_HMLE-TWIST_scr_1

description: genomic DNA (INPUT)


title: HMLE-TWIST1_DMSO-D4_2

value: DMSO for 15 hours, then the cells were washed and placed in DMSO-free media for an additional 2 days


title: HMLE-TWIST1_500nm-D2_2


title: Cd4creGlut10fl/fl-1


title: CowO21

description: Bulk RNA-seq


title: Input_HMLE_scr_3

description: genomic DNA (INPUT)


title: HMLE-TWIST1_500nm-D2_1


title: Input_HMLE_scr_2

description: genomic DNA (INPUT)


title: CowO15

description: Bulk RNA-seq

value: Saline


title: Adult LSK/PreproB/ProB Batch2

value: Blood cells

value: LSK/PreproB/ProB

value: Control (Cre-) and KMT2A::AFF1+


title: Adult LSK/PreproB/ProB Batch1


title: CowO14

description: Bulk RNA-seq


title: Input_HMLE_scr_1

description: genomic DNA (INPUT)

value: HMLE

value: Wild type

value: scramble siRNA for 2 days


title: Cd4cre-1


title: CowO13

description: Bulk RNA-seq

value: Sprague Dawley


title: HMLE-TWIST1_200nm-D2_1

value: overexpressing TWIST1

value: 200 nm Chaetocin for 2 days


title: HMLE-TWIST1_150nm-D2_3

value: 150 nm Chaetocin for 2 days


title: H3K9me3_HMLE-TWIST_KD_2

description: Immunoprecipitated (IP) DNA

value: H3K9me3 antibody (ab8898)

value: SUV39H1/H2 DsiRNA for 2 days


title: DMS-MaPseq of HEK293 total RNA, replicate 1

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

description:
Library name: DMS-MaP_HEK293_totalRNA_rep1
Instrument: Illumina NextSeq 1000

data_processing:
Following sequencing, reads were clipped of sequencing adapters using Cutadapt (parameters: -a AGATCGGAAG -m 75 -O 1). Clipped reads were then mapped to a reference composed of 18S and 28S rRNA sequences, using the rf-map tool of the RNA Framework and Bowtie2, after clipping terminal bases with Phred quality < 20, and discarding reads containing internal Ns (parameters: -b2 -cq5 20 -ctn -cmn 0 -mp "--very-sensitive-local" -bnr). Alignments in SAM format were sorted and converted to BAM format using Samtools. BAM alignments were then processed using RNA Framework’s rf-count to generate both RC files (containing per-base mutations and coverage). Aligned reads spanning less than 100 nt, as well as reads having more than 10% mutated bases, or less than 2 mutations, were discarded. Insertions and ambiguously aligned deletions, as well as deletions longer than 1 nt, were ignored. Mutations were considered only if both the mutated base and the two surrounding bases had Phred quality > 20, and consecutive mutations falling within 3 nt from each other were ignored (parameters: -m -mm -ds 100 -es -na -ni -md 1 -dc 3 -me 0.1).
Supplementary files format and content: Wiggle files of bulk normalized DMS-MaPseq mutation frequencies

growth_protocol: Human HEK293 cells were cultured in high glucose DMEM medium (cat. L0104, Biowest), supplemented with 10% fetal bovine serum (FBS) (cat. H1138, Merck), 25 U/mL penicillin and 25 μg/mL streptomycin, at 37°C and 5% CO2.

extract_protocol:
Cell pellets were immediately lysed by direct addition of 1 mL ice-cold TRIzol™ Reagent (cat. 15596018, ThermoFisher Scientific). RNA was extracted as per manufacturer instructions. Residual gDNA was removed by digestion with TURBO DNase I (cat. AM2239, ThermoFisher Scientific) at 37°C for 30 min.
To mimic the same conditions used for the 5′UTR-MaP library preparation, 100 ng total RNA per sample were fragmented in 4 mM MgCl2, for 5.5 min at 94°C, and then cleaned up on Monarch® Spin RNA Cleanup columns, as per manufacturer instructions. 2′-3′-cyclic phosphates generated by chemical fragmentation were removed by treatment with 1 U rSAP, in a final volume of 20 μl, at 37°C for 30 min, followed by heat inactivation of the enzyme at 70°C for 5 min. Reactions were then supplemented with 20 U T4 Polynucleotide Kinase (cat. M0201L, New England Biolabs), 1 mM ATP, 5 mM DTT, in a final volume of 50 μl, and incubated at 37°C for 1 h. 5′-phosphorylated RNA fragments were then cleaned up on Monarch® Spin RNA Cleanup columns, and then subjected to adapter ligation, reverse transcription and PCR as for 5UTR-MaP libraries.

treatment_protocol: Dimethyl sulfate (DMS; cat. D186309, Merck) from a fresh 1:4 dilution in ethanol (~2.64 M) was directly added to the cells at a final concentration of 150 mM. Probing was conducted for 2 min at 37°C. Reactions were then quenched by addition of 1 volume 1 M DTT, after which cells were collected by centrifugation at 5,000g for 1 min.


title: Cd4cre-2

value: spleen

value: primary

value: CD8 + T cell


title: H3K9me3_HMLE-TWIST_KD_3

description: Immunoprecipitated (IP) DNA

value: Mammary gland epithelial cells

value: Breast


title: HMLE-TWIST1_200nm-D2_2


title: CowO12

description: Bulk RNA-seq

value: Saline

value: eGFP

value: 13-15 weeks


title: HMLE-TWIST1_150nm-D2_2


title: H3K9me3_HMLE-TWIST_KD_1

description: Immunoprecipitated (IP) DNA