title: RA_1st

city: Seoul

first: Bong-Ki

last: Hong

address: 222 Banpo-daero, Seocho-gu

department: School of Medicine

country: South Korea

institute: Catholic University of Korea

data_processing:
All resulting sequence libraries were preprocessed on an Illumina platform (Roket Genomics, Seoul, South Korea).
Assembly: GRCh38-1.2.0
Supplementary files format and content: tab-delimited file includes raw counts for each sample.

source_name: Blood

extract_protocol: Single-cell 3’ gene expression libraries were prepared by strictly following the protocols of a Chromium Single Cell 3’v2 Library kit (10× Genomics). All resulting libraries were sequenced on an Illumina platform (Roket Genomics, Seoul, South Korea).

value: Blood


title: DQGD123

status: Public on Jan 13 2025

type: SRA

city: Strasbourg

first: Dominique

last: Gagliardi

address: 12, rue du General Zimmer

department: IBMP

country: France

institute: CNRS

description:
Library name: Sample18
total RNA-seq

library_source: transcriptomic

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq None.
Reads have been mapped against the TAIR10 genome using hisat2 (v.2.2.1), with the following options: -p 4 -k 20 --max-intronlen 2000 --rna-strandness R.
Read counts were then extracted for each representative transcript using FeatureCounts (v.2.0.6) and the Araport11 annotation (“Araport11_GTF_genes_transposons.Jul2023.gtf”) by specifying “gene” as feature type (-t option) and “gene_id” as attribute type (-g option).
Differential expression analysis was performed in R (v.4.2.2) using the DESeq2 package (Love et al. 2014) (v1.38.3).
Assembly: TAIR10
Supplementary files format and content: Gene count matrices from FeatureCount are given (1 file for seeds, 1 file for flowers)

molecule: total RNA

organism: Arabidopsis thaliana

source_name: Flower

growth_protocol: Arabidopsis plants were grown on soil in long-day conditions with a 16 h light/8 h darkness photoperiod in a greenhouse (at 21/18 °C). The Arabidopsis thaliana plants used in this work are of Columbia accession (Col-0). Arabidopsis mutants analyzed in this study are T-DNA insertion lines described previously: urt1-1 (SALK_087647C) (Sement et al. 2013) and heso1-4 (GK-369H06-017072) (Joly et al. 2023; Vigh et al. 2024). Flowers (unopened flower buds) and dry mature seeds were harvested from a minimum of five plants each for three biological replicates. Samples were harvested two weeks after the onset of flowering for flowers and eight weeks after the onset of flowering for dry mature seeds, when all siliques of the plants were dry.

extract_protocol:
Total RNA from seeds was extracted according to the protocol (Meng and Feldman 2010) except for the last precipitation performed at -80 °C for 1 hour. RNA from flowers was extracted with TRI Reagent (EUROMEDEX, TR118-100) following the manufacturer's protocol. Total RNA was then purified using the RNeasy MinElute Cleanup kit (Qiagen, 74204).
Total RNA was treated with DNase I (Thermo Fisher Scientific, EN0521) and purified using the RNeasy MinElute Clean-up (Qiagen, 74204). RNA-seq libraries were then produced from 500 ng of DNase-treated RNAs using the TruSeq Stranded Total RNA Library Prep Plant (Illumina, 20020610) according to manufacturer’s instructions. Sequencing was performed on an Illumina NextSeq 2000 system by the GenomEast platform (paired-end sequencing, 2 × 50 bases).

tag: tissue

value: Flower

tag: replicate

value: Biological replicate 2

tag: genotype


title: Hi-C_rsc2d

city: Paris

first: Axel

last: Cournac

address: 28 rue du docteur Roux

institute: Institut Pasteur

library_source: genomic

data_processing:
Reads were aligned and contact maps generated and processed using Hicstuff (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 (Langmead and Salzberg, 2012) in its most sensitive mode against their reference genome. Each uniquely mapped read was assigned to a restriction fragment.
Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in (Cournac et al., 2012)).
PCR duplicates (defined as multiple pairs of reads positioned at the exact same position) were discarded.
Contacts were binned at 1kb resolution and multiple-resolution balanced contact maps (in mcool format) were generated using cooler (Abdennur and Mirny, 2020).
Assembly: GCF_000146045.2 for S.cerevisiae , J01347.1 for the 2µ plasmid , GCA_000011445 for mycoides /    GCF_000004695.1 for D.discoideum / GCA_900074765.1 for L.fermentati / GCA_030580015.1 for L.waltii
Supplementary files format and content: Contact matrices are provided in multiple resolution mcool files.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. (2020). Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with a Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions. Briefly, Cells were resuspended in 500ul water and transferred in VK05-0.5ml (ozyme, P000934-LYSK0-A.0) tubes containing glass beads before mechanical cells lysis. 8ul of samples were permeabilized by sequentially adding lysis buffer (15min at 4C), conditioning solution (10min at 62C) and stop solution 2 (15min at 37C) to the samples. DNA was digested using a mix of buffer A, DpnII, and Hinf1 (45min at 37C followed by 20min at 65C).
DNA was repaired and biotin was added by adding a mix of buffer B and enzyme B for 45min at room temperature. DNA was re-ligated by adding a mix of buffer C and enzyme C during 15min at room temperature. Samples were then digested by protease and de-crosslinked by adding a mix of buffer D, enzyme D and buffer E during 30 min à 55°C followed by 90 min at 68°C. Samples were purified using AMPure XP beads (Beckman A63882), recovered in 120ul H2O and sonicated using Covaris (DNA 300bp) in Covaris microTUBE (Covaris, 520045). Biotinylated DNA was loaded on Dynabeads™ Streptavidin C1 (FISHER SCIENTIFIC, 10202333). Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.

tag: background

tag: strain


title: DQGD122

description:
Library name: Sample17
total RNA-seq

value: WT (Col-0)


title: Hi-C_pARS


title: 20201207-NMK52FU1

city: Saint Louis

first: Li

last: Ding

state: MO

address: 660 S Euclid Ave

country: USA

institute: Washington University in St Louis

description:
Library name: 20201207-NMK52-F-Fc1U1Z1Bs1
20201207-NMK52FU1 (W52.Female.Single specimen)

data_processing:
For Visium: After cDNA library construction and sequencing, the read alignment algorithm ‘count’ method in Space Ranger (v1.3.0) from the 10X Genomics was used to align reads to the mouse reference genome (mm10, 2020A). The resulting count matrix and associated H&E physiological images were then used by the R package Seurat (v.4.0.4) for subsequent analysis. The filtered gene-count matrices of all samples were normalized using SCTransform before being merged into one object for joint processing and analysis using the FindNeighbors and FindClusters function in Seurat using standard processing parameters (30 PCs, original Louvain algorithm).
Assembly: mm10
Supplementary files format and content: for Visium data, for each library, a Seurat object in rds format was provided.
Library strategy: Spatial Transcriptomics

organism: Mus musculus

source_name: kidney

growth_protocol: To get E16.5 kidneys, 4 female mice and 1 male mouse were grouped for mating on day 1 at 5 pm. Then the male was removed from the females on day 2 at 10 am. Day 2 was designated as E0.5 for any pregnant females. For kidneys collected from other ages, mice were purchased from the Jackson Laboratory.

extract_protocol:
Mice at E16.5 and P0 were euthanized by decapitation. Older mice were euthanized by carbon dioxide asphyxiation. For each mouse, one kidney was embedded in optimal cutting temperature compound (OCT) and the other one was fixed in 10% neutral buffered formalin (Epredia, 5725) and then embedded in paraffin.
For Visium: Fresh mouse kidneys were embedded with OCT on dry ice. OCT-embedded tissues sectioned at 10 μm thickness were then placed on Visium Spatial Gene Expression Slide following Visium Spatial Protocols-Tissue Preparation Guide (10X Genomics, CG000240 Rev A). Visium ST libraries were constructed following Visium Spatial Gene Expression Reagent Kits User Guide CG000239 Rev A (10X Genomics).

value: kidney

tag: age

tag: Sex

value: Female

value: WT


title: 20201207-NMK52MU1

description:
Library name: 20201207-NMK52-M-Fc1U1Z1Bs1
20201207-NMK52MU1 (W52.Male.Single specimen)

value: Male


title: Hi-C_5toA


title: Hi-C_hst2d


title: 20201201-NMK3MU4

description:
Library name: 20201201-NMK-M-Fc1U4Z1B1
20201201-NMK3MU4 (W3.Male.Single specimen)


title: Hi-C_Heatshock_5min


title: Hi-C_Heatshock_2min


title: Hi-C_dot1d


title: DQGD119

description:
Library name: Sample14
total RNA-seq

value: Biological replicate 1


title: Hi-C_Heatshock_1min


title: Hi-C_Heatshock_before


title: 20201201-NMK3MU3

description:
Library name: 20201201-NMK-M-Fc1U3Z1B1
20201201-NMK3MU3 (W3.Male.Single specimen)


title: 20201201-NMK3MU2

description:
Library name: 20201201-NMK-M-Fc1U2Z1B1
20201201-NMK3MU2 (W3.Male.Single specimen)


title: 20201201-NMK3MU1

description:
Library name: 20201201-NMK-M-Fc1U1Z1B1
20201201-NMK3MU1 (W3.Male.Single specimen)


title: Hi-C_pKAN-STBd


title: DQGD117

description:
Library name: Sample12
total RNA-seq

source_name: Seed

value: Seed

value: Biological replicate 3

value: heso1-4 urt1-1


title: 20201201-NMK3FU4

description:
Library name: 20201201-NMK-F-Fc1U4Z1B1
20201201-NMK3FU4 (W3.Female.Single specimen)


title: Hi-C_rsc1d


title: Hi-C_pKAN-rep1d


title: DQGD116

description:
Library name: Sample11
total RNA-seq


title: DQGD121

description:
Library name: Sample16
total RNA-seq


title: 20201201-NMK3FU2

description:
Library name: 20201201-NMK-F-Fc1U2Z1B1
20201201-NMK3FU2 (W3.Female.Single specimen)


title: Hi-C_BHB

value: BHB


title: Hi-C_jhd2d


title: 20201201-NMK3FU3

description:
Library name: 20201201-NMK-F-Fc1U3Z1B1
20201201-NMK3FU3 (W3.Female.Single specimen)


title: Hi-C_set2d


title: DQGD115

description:
Library name: Sample10
total RNA-seq


title: DQGD120

description:
Library name: Sample15
total RNA-seq


title: NSC treated with ultrasound, sample1 of C grup, Day5

city: Jinan

first: Keyi

last: Li

state: Shandong Province

address: 27 Shanda Nanlu

country: China

institute: Shandong University

description: Library name: C1

data_processing:
BGI Dr.TOM
Assembly: NCBI-GCF_000001895.5_Rnor_6.0
Supplementary files format and content: csv files include FPKM values for each sample
Supplementary files format and content: All_samples.CorrelationHeatmap.xls

organism: Rattus

source_name: neural stem cells

extract_protocol: The BGI Optimal series dual module mRNA library construction kit (BGI Shenzhen, China) was used for library preparation. Take a certain amount of RNA sample, perform temperature denaturation to open the secondary structure, and use oligo (dT) magnetic beads to enrich mRNA. At an appropriate temperature, add a disruption reagent to the mRNA obtained in the previous step, and perform a temperature appropriate reaction to fragment it.                                                                                Then, the first strand cDNA was generated by reverse transcription using random hexamer primers, followed by the synthesis of the second strand cDNA. Afterwards, prepare the reaction system, repair the double stranded cDNA end, and add A base at the 3 'end. Prepare a linker connection reaction system, connect the linker to cDNA, and finally amplify and quality control the product.                                                      After denaturing the PCR product into a single strand, a cyclization reaction system is prepared and a reaction program is set up to obtain a single stranded circular product. The linear DNA molecules that have not been cyclized are digested to obtain the final library. The final library was amplified by phi29 to produce DNA nanospheres (DNBs). The obtained DNBs were added to the mesh like pores on the chip using high-density DNA nanochip technology, and PE100/PE150 sequencing was performed on a G400/T7/T10 sequencer (BGI Shenzhen, China) using co probe anchoring polymerization technology (cPAS).

tag: cell type

value: neural stem cells


title: NSC treated with ultrasound, sample2 of C grup, Day5

description: Library name: C2


title: Hi-C_Mmyco


title: NSC cultured with piezoelectric nanostickers, sample2 of D group, Day5

description: Library name: D2


title: control replicate 4

type: RNA

city: Atanta

first: Tim

last: Gershon

state: GA

address: Emory University School of Medicine

department: Pediatrics

institute: Emory University

description: RMA expression values derived from Partek software using gene expression workflow

hyb_protocol: Samples were hybridized with Affymetrix Mouse Gene 2.1 ST arrays and scanned at the UNC-Chapel Hill Microarray Core Facility.

scan_protocol: Array scanning was performed according to the manufacturer's instruction (Affymetrix)

data_processing: Data was processed using Partek Genomics Suite

label: biotin

source_name: transgenic, medulloblastoma-prone mouse

label_protocol: Affymetrix® HT WT Terminal Labeling and Controls Kit (#901647)

growth_protocol: tumors were freshly harvested from P15 mice of the indicated genotype

extract_protocol: total RNA was isolated using the RNeasy Mini Kit, #74104, QIAGEN

treatment_protocol: mice were maintained with their dams until tissue harvest and were not treated with any exogenous agent.

tag: bcl2l1 status

value: Bcl2l1 deleted


title: Hi-C_pKAN


title: DQGD114

description:
Library name: Sample9
total RNA-seq


title: PD21 tKO, pooled, scRNAseq

first: Yan

last: Yin

address: 660 S. Euclid Ave

department: Medicine

description: paired-end

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software
Assembly: mm10
Supplementary files format and content: h5 Cell Ranger Feature Barcode Matrices

source_name: Uterine cells

extract_protocol:
Uterine horns were longitudinally incised and segmented into 2-3 mm pieces following dissection. These tissue fragments were then enzymatically digested in 15-ml conical tubes containing 1% trypsin in Ca2+- and Mg2+-free Hank's Balanced Salt Solution (CM-HBSS) at room temperature for one hour with agitation. To terminate the digestion, an equal volume of fetal bovine serum (FBS) was added, and the tubes were vigorously shaken to dislodge uterine cells. The supernatant, which contained the dissociated cells, was carefully pipetted out and passed through 70 µm nylon filters to remove debris. The filtered cells were washed twice, collected by low-speed centrifugation, and subsequently resuspended in 0.04% bovine serum albumin (BSA) in 1x PBS at a concentration of 1000 cells/µl, with cell viability exceeding 85%. The cell suspension was then sent to the McDonnell Genome Institute (MGI) at Washington University School of Medicine for single-cell RNA sequencing.
cDNA was prepared after the GEM generation and barcoding, followed by the GEM-RT reaction and bead cleanup steps.  Purified cDNA was amplified for 11-16 cycles before being cleaned up using SPRIselect beads.  Samples were then run on a Bioanalyzer to determine the cDNA concentration.  Gene Expression libraries were prepared as recommended by the 10x Genomics Chromium Chromium Single Cell 5' Reagent Kits User Guide (v2 Chemistry Dual Index user guide, with appropriate modifications to the PCR cycles based on the calculated cDNA concentration.  For sample preparation on the 10x Genomics platform, the Chromium Next GEM Single Cell 5’ Kit v2, 16 rxns (PN-1000263), Chromium Next GEM Chip K Single Cell Kit, 48 rxns (PN-1000286), Dual Index Kit TT Set A, 96 rxns (PN-1000215) were used.  The concentration of each library was accurately determined through qPCR utilizing the KAPA library Quantification Kit according to the manufacturer’s protocol (KAPA Biosystems/Roche) to produce cluster counts appropriate for the Illumina NovaSeq6000 instrument.  Normalized libraries were sequenced on a NovaSeq6000 S4 Flow Cell using the XP workflow and a 151x10x10x151 sequencing recipe according to the manufacturer protocol.  A median sequencing depth of 50,000 reads/cell was targeted for each Gene Expression library.

value: Uterine cells

value: Rara fl/fl; Rarb fl/fl; Rarg fl/fl; PgrCre


title: DQGD110

description:
Library name: Sample5
total RNA-seq


title: NSC cultured with piezoelectric, sample 1 of B group, Day5

description: Library name: B1


title: control replicate 2


title: PD21 CTRL, pooled, scRNAseq

institute: Washington University School of Medicine

description: paired-end

value: Rara fl/fl; Rarb fl/fl; Rarg fl/fl


title: DQGD109

description:
Library name: Sample4
total RNA-seq


title: NSC treated without anything, sample 2 of A group, Day5

description: Library name: A2


title: 20201201-NMK3FU1

description:
Library name: 20201201-NMK-F-Fc1U1Z1B1
20201201-NMK3FU1 (W3.Female.Single specimen)


title: DQGD118

description:
Library name: Sample13
total RNA-seq

value: Flower


title: Hi-C_Y9


title: DQGD113

description:
Library name: Sample8
total RNA-seq

value: Biological replicate 2


title: Bcl2l1-deleted replicate 4

value: Math1-Cre/SmoM2/Bcl2l1 f/f


title: Bcl2l1-deleted replicate 3


title: PD54 tKO, pooled, scRNAseq

description: paired-end


title: DQGD106

description:
Library name: Sample1
total RNA-seq

value: WT (Col-0)


title: PD54 CTRL, pooled, scRNAseq

description: paired-end


title: Bcl2l1-deleted replicate 2


title: RAW264.7,Control_3

city: hangzhou

first: Zhaoming

last: Ye

address: 88 jiefang road

institute: The Second Affiliated Hospital, Zhejiang University School of Medicine

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: not provided
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

tag: cell line

tag: treatment

value: control


title: DQGD111

description:
Library name: Sample6
total RNA-seq


title: RNA-seq_Lfermentati

data_processing:
Reads were aligned against reference genome using bowtie2. bam files were then filtered to remove duplicates , low mapping quality(>10) reads and unpaired reads. The CPM tracks were generated using bamcoverage
Assembly: GCA_900074765.1 for L.fermentati / GCA_030580015.1 for L.waltii
Supplementary files format and content: unstranded CPM tracks are provided in .bw format

molecule: polyA RNA

organism: Lachancea fermentati

growth_protocol: Cells were grown in YPD at 30C° overnight then fresh YPD was ensemenced by diluting the overnight culture 1:100 until OD600 0,7

extract_protocol:
2mL of culture were peleted at 6000g for 5 min. Total RNA were extracted using the Machenery-Nagel RNA Nucleospin kit
The total RNA extract was sent to Novogene for further processing

value: WT


title: control replicate 3


title: NSC cultured with piezoelectric, sample 2 of B group, Day5

description: Library name: B2


title: Thap1C54Y/C54Y_mouse_embryo_rep1

city: Bunkyo-ku

first: Hiroki

last: Sugishita

state: Tokyo

country: Japan

institute: The University of Tokyo

description:
Library name: Sample4
JH_JH-5

data_processing:
Sequencing reads were aligned to the UCSC-hg38 provided from Illumina iGenome using STAR (2.7.10) with some options [--outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --alignIntronMin 20 --alignIntronMax 10000 --alignMatesGapMax 1000000].
Row read counts of each gene was calculated using featureCounts (v2.0.1) and wes quantified as TPM.
Assembly: mm10
Supplementary files format and content: tsv file of raw count in each sample

source_name: e10.5 whole embryo

extract_protocol:
For RNA-seq analysis for mouse embryo, total RNA was extracted using NucleoSpin RNA kit (TAKARA).
RNA libraries for RNA-Seq were prepared using bulk FLASH-Seq protocol (Siwicki et al. protocols.io(2023) and Pavlinic et al. Nat Biotech(2022))

value: e10.5 whole embryo


title: Sample 6, Location 3

city: Houston

first: Briana

middle: Amicarella

last: Burns

state: TX

address: 1 Baylor Plaza

institute: Baylor College of Medicine

description: Library name: 64963_S6_L003

data_processing:
Raw sequencing reads were processed using 10x Genomics Space Ranger v2.1.0. Reads were demultiplexed to assign read pairs to the corresponding libraries. Quality control metrics included barcode correction to match the whitelist, UMI filtering to remove sequences containing Ns or homopolymers, and calculation of sequencing saturation to assess library complexity.
Reads were aligned to the GRCh38-2020-A reference transcriptome using the Visium Human Transcriptome Probe Set v2.0. Only reads with valid barcodes, valid UMIs, and a mapping quality (MAPQ) of 255 were used for UMI counting. The pipeline reported the fraction of reads confidently mapped to the probe set, as well as Q30 scores for barcodes, UMIs, and probe reads. Filtered reads were counted based on unique probe mappings with MAPQ of 255.
Assembly: GRCh38-2020-A
Supplementary files format and content: Loupe Browser file (.cloupe) contains spatial transcriptomics data processed using 10x Genomics Space Ranger v2.1.0. It includes gene expression matrices, spatial coordinates, clustering results, dimensionality reduction (e.g., t-SNE/UMAP), and metadata for individual spots.
Supplementary files format and content: This file can be viewed using the 10x Genomics Loupe Browser software, available at https://www.10xgenomics.com.
Library strategy: Spatial Transcriptomics

organism: Homo sapiens

source_name: FFPE brain tumor tissue

growth_protocol: FFPE tissue blocks

extract_protocol:
Tissue sections were mounted onto poly-L-lysine coated slides, deparaffinized, H&E stained, and imaged. One library per section was generated using the Visium CytAssist Spatial Gene Expression for FFPE kit according to the manufacturer’s instructions (10X Genomics, Pleasanton, CA). Briefly, sections were destained and decrosslinked prior to probe hybridization overnight. Following hybridization, probe pairs were ligated and tissues restained with H&E and imaged on the CytAssist instrument. Sections were treated with RNase prior to tissue permeabilization. Slides were loaded onto the CytAssist where probe release and transfer to the capture area (6.5 x 6.5 mm) of the 10X Visium GEX slide were performed. Capture probes were extended, pre-amplified, and the resulting PCR product purified. Probe libraries were indexed in a final PCR reaction with 12-15 cycles, as determined by the qPCR, prior to cleanup.
Spatial transcriptomics libraries were prepared using Visium V4 Slide - FFPE v2 chemistry following 10x Genomics protocols.

value: FFPE brain tumor tissue


title: NSC cultured with piezoelectric nanostickers, sample1 of D group, Day5

description: Library name: D1


title: RAW264.7,MMP_3

value: cultured with Mn2+@Man-phage for 24 h


title: DQGD112

description:
Library name: Sample7
total RNA-seq

value: Seed


title: control replicate 1


title: NSC treated without anything, sample 1 of A group, Day5

description: Library name: A1


title: DQGD107

description:
Library name: Sample2
total RNA-seq

value: Biological replicate 1


title: Sample 6, Location 1

description: Library name: 64963_S6_L001


title: RAW264.7,MMP_2


title: Thap1C54Y/C54Y_mouse_embryo_rep2

description:
Library name: Sample5
JH_JH-6


title: PHF6-KO_Input (TF-2)

city: NEW YORK

first: Mayukh

last: Biswas

state: NY

address: 1130 Saint Nicholas Ave, Room 401B

department: Irving Cancer Research Center

institute: Columbia University Medical Center

description: Crosslinking: Disuccinimidyl glutarate and Formaldehyde

data_processing:
ChIP-seq reads were aligned to the Human hg19 genome assembly using Bowtie2 and further processed using SAMtools.
SICER pipeline was used to identify spatial clusters of ChIP-enriched regions (1000 bp window, 3000 bp gap size).
Peaks were called using MACS2 v2.1.1  with the following setting: FC>1.5 and FDR< 10EXP-20 compairing PHF6-WT and PHF6-KO samples.
Bigwigs were generated and analyzed using Deeptools 3.3.0. Bigwigs were RPKM normalized.
Genome_build: hg19
Supplementary_files_format_and_content: bw and bed files

source_name: Acute T cell leukemia

growth_protocol: Jurkat T-ALL cells were purchased, grown and maintained as suspension culture as per ATCC's recommendations. Cells were cultured in RPMI media supplemented with 10% FBS and 1% Pen-Strep.

extract_protocol:
Cells were double-crosslinked with disuccinimidyl glutarate and formaldehyde followed by lysis and nuclei isolation. Nuclei were sonicated in a Bioruptor Pico (Diagenode) and clarified chromatin was immunoprecipitated by antibodies against either histone marks or chromatin remodeling factors.
Libraries were prepared according to manufacturer's instructions accompanying the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645S/L). Briefly, DNA was end-repaired followed by 5´ phosphorylation and dA-tailing. Next, adaptor ligation was carried out using NEBNext Adaptor followed by U excision using USER enzyme. Adaptor-ligated DNA was cleaned up using AMPure XP beads (Beckman Coulter, A63881), PCR amplified with NEBNext Multiplex Oligos for Illumina (Set 1, NEB #E7335; Set 2, NEB #E7500) for 8-10 cycles and PCR amplified library was cleaned up using AMPure XP beads. Purified libraries were quantified based on the average fragment size according to Bioanalyzer and Qubit results, pooled at equimolar concentrations, and sequenced as a pool to a total read-depth target of approximately 4 × 107, paired-end, 150-nucleotide-long reads per sample on an Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: Jurkat cells were electroporated with RNP complex to generate PHF6-KO lines. Post electroporation, single clones were selected followed by generation of stable lines and ChIP experiments were carried out.

tag: cell type/genotype

value: Jurkat cells_PHF6-KO

value: Peripheral blood

tag: chip antibody

value: Input DNA (for Samples 19,20)

tag: drosophila spike-in

value: No


title: WT_mouse_embryo_rep2

description:
Library name: Sample2
JH_JH-2


title: Thap1C54Y/C54Y_mouse_embryo_rep3

description:
Library name: Sample6
JH_JH-7


title: DQGD108

description:
Library name: Sample3
total RNA-seq


title: RAW264.7,MMP_1


title: WT_mouse_embryo_rep1

description:
Library name: Sample1
JH_JH-1


title: Sample 5, Location 3

description: Library name: 64962_S5_L003


title: RAW264.7,Control_2


title: Colon epi, Cdiff, M579

city: Nashville

first: Nicholas

last: Markham

state: TN

address: 2213 Garland Ave

institute: VUMC

description: inDrop single-cell encapsulation, TruDrop structure library prep

data_processing:
Raw reads were processed into counts matrices with an open-source pipeline published by Petukhov V, Guo J, Baryawno N, et al. dropEst: pipeline for accurate estimation of molecular counts in droplet-based single-cell RNA-seq experiments. Genome Biol 2018; 19: 78.
Counts matrices were filtered and converted into AnnData files using the Dropkick package, published by Heiser CN, Wang VM, Chen B, et al. Automated quality control and cell identification of droplet-based single-cell data using dropkick. Genome Res 2021; 31: gr.271908.120
Assembly: mouse genome GRCm38.85
Supplementary files format and content: barcodes and features in text files, counts are in matrix files

source_name: colon

extract_protocol:
For each mouse, the colon was harvested and washed with sterile, cold PBS. The colon then underwent chelation at 4°C, followed by mechanical and enzymatic dissociation using a cold-activated protease-DNase approach into single-cell suspensions, which were then encapsulated into droplets using the inDrop platform following the protocol of Banerjee A, Herring CA, Chen B, et al. Succinate Produced by Intestinal Microbes Promotes Specification of Tuft Cells to Suppress Ileal Inflammation. Gastroenterology 2020.
Libraries were prepared using the TruDrop structure as described by Southard-Smith AN, Simmons AJ, Chen B, et al. Dual indexed library design enables compatibility of in-Drop single-cell RNA-sequencing with exAMP chemistry sequencing platforms. BMC Genom 2020; 21: 456.

treatment_protocol: GF ApcMin/+ mice were housed in the Germ-Free Mouse Core in the Johns Hopkins University School of Public Health in sterile bubble isolators (Controlled Environment Products #041-4205-0888) with an unlimited sterile diet (LabDiet JL rat and mouse/Auto 6F 5k67) and double-autoclaved tap water. Fecal pellets from GF mice were screened monthly by culture and qPCR to ensure maintenance of their GF status. For experiments, 6- to 8-week-old mice were transferred into sterile isocages (Allentown, Sentry SPP) with both rack and intracage HEPA filters (#HF884-H14 and #228535). GF ApcMin/+ mice 6 to 8 weeks of age were gavaged with 100 μL of  the 3728T bacterial isolates with or without 10,000 spores of the human colorectal cancer–derived C. difficile strain.

value: colon

value: ApcMin

value: Cdiff


title: PHF6-KO_SMARCA5

value: SMARCA5 (Abcam, ab72499)


title: WT_mouse_embryo_rep3

description:
Library name: Sample3
JH_JH-3


title: RAW264.7,Control_1


title: PHF6-KO_CHD4_L64

value: CHD4 (Abcam, ab72418)


title: Bcl2l1-deleted replicate 1

value: Math1-Cre/SmoM2/Bcl2l1 f/f

value: Bcl2l1 deleted


title: Sample 4, Location 3

description: Library name: 64961_S4_L003


title: Sample 6, Location 2

description: Library name: 64963_S6_L002


title: Colon epi, control, M577

value: control


title: Sample 4, Location 1

description: Library name: 64961_S4_L001


title: PHF6-KO_Input (TF-1)

value: Input DNA (for Samples 13,14)


title: ARM-seq Day 70 AlkB Positive c305 Organoid 1

city: Santa Cruz

first: Todd

middle: Michael

last: Lowe

state: CA

address: 1156 High Street / MS: SOE-2

department: Biomolecular Engineering

institute: University of California, Santa Cruz

description: ARM-seq

data_processing:
Adapters were removed and reads were merged with SeqPrep [John st. John unpub] using a minimum read length of 15 and adapters AGATCGGAAGAGCACACGTC and GATCGTCGGACTGTAGAACTC.  Reads that could not be merged were discarded before mapping.
Data were analyzed with tRAX (https://github.com/UCSC-LoweLab/tRAX), tRAX maps reads using bowtie2 to a custom database containing mature tRNA transcripts and the genome sequence.
tRNAs were converted into genome space with tRAX and coverage tracks were created with bedGraphToBigWig and genomeCoverageBed from UCSC Genome Browser tools and BEDtools.
Assembly: hg38
Supplementary files format and content: BigWig files of the sequencing results aligned to hg38 tRNAs

growth_protocol: Samples were obtained from 3 c305-derived brain organoids at 0, 2, 5, and 10 weeks old timepoints. They were grown in conditions as described in Kadoshima, et al., 2013

extract_protocol:
Isolation of total RNA from cerebral cortical organoids and stem cells was performed using Direct-Zol RNA MiniPrep Kit (Zymo Research) with TRI Reagent (Molecular Research Center, Inc.). Since a single organoid would yield far less total RNA, approximately 3-8 organoids would be pooled in trizol depending on organoid size for each sample replicate. Manufacturer’s recommended volume of TRI Reagent was added to each sample (~1 mL). For RNA purification of stem cells Trizol was directly added to cell culture plates on ice, scraped, and homogenized via pipetting. Organoids in Trizol were broken down via pipetting inside a 1mL eppendorf tube on ice via a syringe. All total RNA was processed using a MirVana miRNA Isolation Kit (Life Technologies), according to the manufacturer's instructions, to select for RNA <200 nt. This was followed by a RNA Clean and Concentrate-25 (Zymo Research). Samples were divided into plus-AlkB experimental treatment and minus-AlkB control as previously described in ARM-seq methods (Cozen, et al., 2015). This was followed by a phenol chloroform cleanup treatment. RNA samples were then used for library preparations.
For ARM-seq, libraries were constructed as previously described (Hrabeta-Robinson, et al. Methods Mol Biol. 2017) which utilizes the NEBNext Multiplex Small RNA Library Prep Set (NEB). PCR-amplified libraries were purified using DNA Clean and Concentrate-5 (Zymo Research) and then size-selected (140-250 nts) on a 6% non-denaturing TBE-acrylamide gel. Libraries were eluted from gel pieces using Gel Elution Buffer (NEB) and precipitated using .3 M NaOAc, 80% Ethanol, and 1 uL of Linear Acrylamide (supplied in NEBNext Kit) at final concentration.  Samples were left in -80C freezer overnight to precipitate. Precipitated libraries were then pelleted, washed twice in 80% Ethanol, and resuspended in Pure H2O. Libraries were then quantified using NanoDrop and Agilent DNA High Sensitivity kit. For DM-tRNA-seq, libraries were constructed as using the TGIRT™ Improved Modular Template-Switching RNA-seq Kit (InGex, LLC), which utilizes Illumina-compatible adapters for amplification and sequencing purposes. Libraries were amplified using PCR primers supplied with the NEBNext Small RNA library Prep Set (NEB) and  purified using Agencourt AMPure XP beads (Beckman). Resulting purified sequencing libraries were quantified using NanoDrop and Agilent DNA High Sensitivity kit. Libraries were then pooled equimolarly, and concentrated using a DNA Clean and Concentrate-5 (Zymo Research).  Pooled PCR-amplified libraries were size-selected (140-250 nts) on a 6% non-denaturing TBE-acrylamide gel to remove unwanted primer dimer products. Libraries were eluted from gel pieces using Gel Elution Buffer (NEB) and precipitated using .3 M NaOAc, 80% Ethanol, and 1 uL of Linear Acrylamide (supplied in NEBNext Kit) at final concentration.  Samples were left in -80C freezer overnight to precipitate. Precipitated libraries wer then pelleted, washed twice in 80% Ethanol, and resuspended in Pure H2O.

treatment_protocol: Samples were divided into plus-AlkB experimental treatment and minus-AlkB control as described in ARM-seq methods in Cozen et al. 2015

value: iPSC

tag: timepoint

value: day 70

tag: library type

value: total small RNA (≤ 250 nts)

value: plus AlkB


title: Colon epi, Cdiff, M582


title: PHF6-WT_SMARCA5

value: Jurkat cells_WT


title: Sample 5, Location 2

description: Library name: 64962_S5_L002

value: FFPE brain tumor tissue


title: Colon epi, Cdiff, M455

description: FFPE spatial transcriptomics with GeoMx DSP

library_source: other

data_processing:
Raw sequencing files for each segment were compiled with bcl2fastq conversion software (Illumina), demultiplexed, and converted to Digital Count Conversion (DCC) files by NanoString Technologies (GeoMx DnD pipeline v2.3.4)
For each "no template PCR control" (NTC), a minimum of 1,000 raw reads was required to pass filtering, and each probe was required to pass the global Grubbs outlier test in at least 20% of segments (α = 0.01), which left 16,471 targets. We removed 1 segment that contained less than 5% of targets above these thresholds, which left 172 segments. Expression values were normalised using the 3rd quartile method. Differential expression analysis was performed with linear mixed-effect models, accounting for inter-mouse heterogeneity.
Assembly: n/a
Supplementary files format and content: non-normalized raw counts for all probes/segments and Q3 normalized counts for quality controlled probes/segments
Library strategy: Spatial Transcriptomics

molecule: other

growth_protocol: GF ApcMin/+ mice were housed in the Germ-Free Mouse Core in the Johns Hopkins University School of Public Health in sterile bubble isolators (Controlled Environment Products #041-4205-0888) with an unlimited sterile diet (LabDiet JL rat and mouse/Auto 6F 5k67) and double-autoclaved tap water. Fecal pellets from GF mice were screened monthly by culture and qPCR to ensure maintenance of their GF status.

extract_protocol:
For each mouse, the colon was harvested and washed with sterile, cold PBS. Colon tissue was fixed in 4% paraformaldehyde and embedded in paraffin. Sections of colon tissue (5 um) were cut onto microscopy slides.
Libraries of the UV-cleaved barcodes were prepared following the NanoString GeoMx DSP user manual instructions for NGS readout.

treatment_protocol: 6- to 8-week-old mice were transferred into sterile isocages (Allentown, Sentry SPP) with both rack and intracage HEPA filters (#HF884-H14 and #228535). GF ApcMin/+ mice 6 to 8 weeks of age were gavaged with 100 μL of  the 3728T bacterial isolates with or without 10,000 spores of the human colorectal cancer–derived C. difficile strain.


title: Colon epi, Control, M454


title: PHF6-KO_SMARCC1

value: Jurkat cells_PHF6-KO

value: Peripheral blood

value: SMARCC1 (Cell Signaling, 11956S)


title: PHF6-KO_CHD4_L59

value: CHD4 (Abcam, ab70469)

value: No


title: Sample 3, Location 2

description: Library name: 64960_S3_L002


title: INPUT_Mimic

city: Lincoln

first: Ivan

middle: J

last: Vechetti

state: NE

address: 1700 N. 35th Street

institute: University of Nebraska-Lincoln

data_processing:
UMIs were removed from sequencing reads and appended to read names for PCR deduplication further downstream using umi_tools v1.1.1.
Sequencing adapters were trimmed from reads using cutadapt v3.2.
Reads were mapped to Eclipsebio's proprietary repetitive element database using STAR v2.7.7a, and reads that aligned to the repetitive element database were removed.
The remaining reads were mapped to the mouse genome (mm10) using STAR v2.7.7a requiring end to end alignment and unique mapping
PCR duplicates were removed using umi_tools v1.1.1
bigWig files were generated using a proprietary Eclipsebio script
Clusters of nonchimeric reads in IP samples were identified using CLIPper v2.1.0, and each cluster was normalized against the corresponding input sample using a proprietary Eclipsebio script
miRNA sequences from miRBase v22.1 were mapped to all unmapped reads using bowtie v1.2.3
For each candidate chimeric read, the best miRNA alignment was selected and trimmed from the read using a proprietary Eclipsebio script
The remaining portion of each read was mapped to the mouse genome (mm10) using STAR v2.7.7a requiring end to end alignment and unique mapping. PCR duplicates were removed using umi_tools v1.1.1.
Clusters of chimeric reads in IP samples were identified using CLIPper v2.1.0, and each cluster was annotated with the miRNA(s) that target it
Significantly enriched peaks were annotated using transcript information from GENCODE Release M25
Motif enrichment analysis of peaks was run using HOMER v4.11. GO term and KEGG pathway enrichment analysis of genes containing peaks were run using clusterProfiler v3.8.1
Assembly: mm10
Supplementary files format and content: BED file containing locations of chimeric read clusters (“peaks”)
Supplementary files format and content: For INPUT: RPM-normalized genomic non-chimeric read coverage Bigwig files

source_name: Plantaris muscle

extract_protocol:
Mouse plantaris muscle was homogenized by cryogenic pulverization, then samples were then UV (254 nm) cross-linked twice. mmiRNA-mRNA complexes were ligated together on-bead after Ago2 immunoprecipitation.
Ligating a barcoded RNA adapter to the complexes. Ligation occurs on-bead with PEG8000 to enhance efficiency. Post ligation, samples undergo gel electrophoresis and transfer to isolate RNA, which is then reverse transcribed. Excess oligos are removed, and a second DNA adapter is added. Cleanup precedes qPCR for cycle optimization, followed by PCR amplification and size selection through agarose gel electrophoresis.
eCLIP-seq

value: Plantaris muscle

tag: antibody

value: Eclipse Ago2 Antibody

value: INPUT


title: Colon epi, control, M578

tag: tissue

value: colon

value: ApcMin


title: PHF6-WT_Input (TF-1)

value: Input DNA (for Samples 10,11)


title: ARM-seq Day 35 AlkB Positive c305 Organoid 1

description: ARM-seq

value: iPSC

value: day 35


title: PHF6-WT_CHD4_L61

value: CHD4 (Abcam, ab72418)


title: PHF6-WT_Input (TF-2)

value: Input DNA (for Samples 16,17)


title: INPUT_Control


title: PHF6-KO_H3K9me3

value: H3K9me3 (Abcam, ab8898)

value: Yes


title: Sample 5, Location 1

description: Library name: 64962_S5_L001

value: FFPE brain tumor tissue


title: Colon epi, Cdiff, M580

value: Cdiff


title: MOV_Mimic


title: Colon epi, control, M576

value: control


title: Sample 2, Locaiton 2

description: Library name: 64959_S2_L002


title: Sample 4, Location 2

description: Library name: 64961_S4_L002


title: MOV_Control


title: PHF6-WT_SMARCC1

value: Jurkat cells_WT

value: Peripheral blood

value: SMARCC1 (Cell Signaling, 11956S)


title: Sample 3, Location 3

description: Library name: 64960_S3_L003


title: Colon epi, Cdiff, M383


title: ARM-seq Day 35 AlkB Positive c305 Organoid 5

description: ARM-seq

value: total small RNA (≤ 250 nts)

value: plus AlkB


title: PHF6-WT_CHD4_L58

value: CHD4 (Abcam, ab70469)

value: No


title: Colon epi, Control, M453

value: colon

value: ApcMin


title: Sample 2, Locaiton 1

description: Library name: 64959_S2_L001


title: cKO1_cortex

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

data_processing:
Raw FASTQ files were aligned to the genome using Cell Ranger pipeline (10x Genomics Cell Ranger 6.0.1)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Brain

extract_protocol:
Cell suspensions are handed off to the Broad Clinical Labs Single Cell processing team. Appropriate volume adjustments are made to ensure thetarget cell recoveryis met prior to the addition of reverse transcription mastermix. The cells in mastermix are then added to the 10x chip G along with 10x gel beads and partitioning oil. The chip is run on the 10x Chromium Controller to create an emulsion of single cells, RT mastermix and a barcoded gel bead. After emulsions are created, samples are immediately put on reverse transcription thermalcycler protocol set at 53OC for 45 minutes, 85OC for 5 minutes before holding at 4OC. The emulsion is then broken, and debris is removed via a Silane bead cleanup. The purified cDNA is then amplified with the following PCR conditions: Initial denaturation at 98°C for 3 minutes, followed by12 cyclesof denaturation at 98°C for 15 seconds, annealing at 63°C for 20 seconds, and extension at 72°C for 1 minute. A 0.6X SPRI cleanup is performed before being quanted on a Qubit.
cDNA library construction is run on an entirely automated workflow. The cDNA is fragmented and repaired with the addition of an A-tail at 32OC for 5 minutes then 65OC for 30 minutes. A 0.8X double sided SPRI cleanup then removes undesired fragments. Adapters are ligated onto the DNA at 20OC for 15 minutes followed by a 0.8X SPRI. 10x dual indexed barcodes are added before a PCR reaction with the following conditions: An initial denaturation at 98°C for 45 seconds, followed by 12 cycles of denaturation at 98°C for 20 seconds, annealing at 54°C for 30 seconds, and extension at 72°C for 20 seconds. These libraries undergo a final 0.8X double sided SPRI cleanup for size selection. Following PCR Cleanup, quality is confirmed using Quant-iT PicoGreen and an Agilent TapeStation to confirm library size. Samples are pooled together to accommodate the desired reads per cell.

value: Brain

value: Female

value: Microglia


title: ARM-seq Day 70 AlkB Positive c305 Organoid 2

description: ARM-seq

value: iPSC

value: day 70


title: ARM-seq Day 35 AlkB Positive c305 Organoid 3

description: ARM-seq

value: day 35


title: Sample 1, Location 3

description: Library name: 64958_S1_L003

value: FFPE brain tumor tissue


title: Sample 3, Location 1

description: Library name: 64960_S3_L001


title: Sample 1, Location 2

description: Library name: 64958_S1_L002


title: Colon epi, Control, M452

value: control


title: ARM-seq Day 70 AlkB Negative c305 Organoid 1

description: ARM-seq

value: minus AlkB


title: Colon epi, Cdiff, M384

value: Cdiff


title: ARM-seq Day 0 AlkB Positive c305 Organoid 6

description: ARM-seq

value: day 0


title: Sample 2, Locaiton 3

description: Library name: 64959_S2_L003


title: PHF6-KO_H3K27me3

value: Jurkat cells_PHF6-KO

value: Peripheral blood

value: H3K27me3 (Active Motif, 39155)

value: Yes


title: con1_cortex


title: PHF6-KO_H3K27ac

value: H3K27ac (Abcam, ab4729)


title: cKO2_cortex


title: PHF6-WT_H3K27ac

value: Jurkat cells_WT


title: ARM-seq Day 0 AlkB Positive c305 Organoid 1

description: ARM-seq

value: total small RNA (≤ 250 nts)

value: plus AlkB


title: Sample 1, Location 1

description: Library name: 64958_S1_L001


title: ARM-seq Day 35 AlkB Negative c305 Organoid 5

description: ARM-seq


title: OV_mimic_D5

data_processing:
Quality control preprocessing was performed with FastQC v0.11.9, followed by adapter and low-quality base removal using Cutadapt 4.4 and Trim Galore 0.6.10, respectively
The reads were aligned to the GRCm38reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the number of reads mapped to each gene.
DESeq2 (Version 1.34.0) was used for normalization and differential analyses of RNA-seq data to identify differentially expressed genes (DEGs) between groups.
Then Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package
Assembly: GRCm38reference
Supplementary files format and content: tab-delimited text files include count values for each Sample

extract_protocol:
RNA extraction was performed using TRI reagent (Sigma-Aldrich, St. Louis, MO, USA) coupled with further columns-based processing using the Direct-zol Kit (Zymo Research, Irvine, CA, USA).
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit, and the resulting cDNA was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection.

value: Plantaris muscle

value: MOV surgery, miR-1 mimicl virus, replicate 5


title: OV_mimic_D4

value: MOV surgery, miR-1 mimicl virus, replicate 4


title: OPTN Axon_4

city: Portland

first: Chi

last: Zhang

state: Oregon

address: 3303 S.W. Bond Avenue

department: Biomedical Engineering

institute: Oregon Health & Science University

description: Library name: Sample 12

data_processing:
Data is mapping to genome GRCH38 using STAR software
Assembly: GRCH38
Supplementary files format and content: txt; counts

source_name: OPTN RGC axon

extract_protocol:
At 4 weeks after plating, RNA was collected from soma and axon compartments of microfluidic devices using the PicoPureTM RNA Isolation Kit (KIT0204, Applied Biosystems), following manufacturer’s instructions. Due to the low RNA concentration obtained from the axon compartment, samples were then pre-amplified using the SuperScript™ IV Single Cell/Low Input cDNA PreAmp Kit (Invitrogen, 11752048), following manufacturer’s instructions. After pre-amplification, cDNA samples were purified using the Agencourt AMPure XP beads (Beckman Coulter, A63880) and the DynaMag-2 Magnet (Invitrogen, 12321D). The cDNA products were next checked on Agilent Bioanalyzer.
The Nextera XT DNA Library Preparation Kit (Illumina) was used for subsequent library preparation. The resulting libraries were quantified, and quality accessed by Qubit and Agilent TapeStation. The libraries were pooled in equal molarity and sequenced with 2×150bp paired-end configuration on an Illumina NovaSeq 6000 sequencer.

value: OPTN RGC axon

value: hPSC-derived Retinal Ganglion Cells


title: PHF6-WT_Input (Histone)

value: Input DNA (for Samples 2,3,4)


title: OPTN Axon_3

description: Library name: Sample 11


title: OPTN Axon_2

description: Library name: Sample 10


title: OV_mimic_D2

value: MOV surgery, miR-1 mimicl virus, replicate 2


title: OV_mimic_D1

value: MOV surgery, miR-1 mimicl virus, replicate 1


title: Mac, DENV+IgG, scRNAseq

city: Syracuse

first: Adam

middle: Tully

last: Waickman

state: New York

address: 766 Irving Avenue

institute: SUNY Upstate Medical University

description: 10x Genomics

data_processing:
Raw sequencing data (BCL files) were demultiplexed and coverted to fastq files using the CellRanger v7.1.0 mkfastq pipline (10x Genomics) and bcl2fastq2 v 2.20.0 (Illumina). Data qualty control, data filtering, cell barcode processing, UMI compression, 5' transcript alignment, and single-cell gene counting was performed using the CellRanger v7.1.0 count pipeline (10x Genomics).
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: healthy human donor

extract_protocol:
Single-cell RNAseq libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) and the Chromium Single Cell Analyzer (10x Genomics). Indexed sequencing libraries were generated using the Chromium Single Cell 5' v2 Reagents Kit (10x Genomics) according to the manufacture's protocol (User guide RevC). according to the manufacture's protocol (User guide RevC)
Library construction was performed according to the manufacturer's instructions (single cell 5' v2 protocol, 10x Genomics). In short, sequencing libraries were generated by 1) transcript fragmentation and end-repair, 2) post-fragmentation size-selection using SPRIselect beads, 3) Adaptor ligation and 4) sample index PCR and SPRIselect cleanup

treatment_protocol: Peripheral blood mononuclear cells (PBMC) was isolated and cryopreserved form whole blood of healthy human donors. The Mojosort monocyte isolation kit was used to isolate monocytes by negative selection according to the manufacture’s protocol (Biolegend, #480059) and cells were resuspended in RPMI supplemented to with 100ng/mL M-CSF (Peprotech, # 300-25), 10% (v/v) FBS (Gibco), 1% penicillin/streptomycin, 1% L-glutamine. Cells were plated on tissue culture treated 24 well plates at a cell density of 1.25-1.5x106 cells per mL and 2mL/well plated in tissue culture-treated 24 well plates. In order to ensure monocyte adhesion, plates were briefly centrifuged for 2 minutes at 500 g. Day 1 was defined as the day of isolation and plating. Cells were subsequently incubated at 37oC/5% CO2 with culture media repletion on day 5 by adding 1 mL of differentiation media per well. Inocula were prepared by incubating DENV-2 with VDB33 monoclonal IgG (ADE condition), DENV-2 alone with media (conventional infection condition), or media alone (uninfected control) at 37 oC/5% CO2 for 60 minutes. An antibody concentration of 1 ug/mL, previously demonstrated to induce enhancing conditions in primary human macrophages, was used43,44. On day 6 of culture, supernatants were aspirated from monocyte-derived macrophage cultures and 200 uL of inoculum was added to each well according to desired infection conditions. Cells were incubated with inoculum for 2 hours at 37oC/5% CO2 , inoculum was removed, and cells were washed twice with 2mL of RPMI medium. 500 mL of differentiation media was added to each well and plates incubated for 48 hours at 37C/5% CO2. Macrophages were then detached from plates by adding 600 mL of Accutase (Stemcell technologies, 07920) per well and incubated at 37oC for 20 minutes. Cells were dissociated by pipetting and transferred to15 mL conical tubes. Cells were resuspended at a concentration of 500 cells/uL in PBS.

value: peripheral blood

value: Macrophage

value: inoculated with DENV2 and monoclonal IgG


title: OV_control_C5

value: MOV surgery, control virus, replicate 5


title: Mac, DENV, scRNAseq

description: 10x Genomics

value: inoculated with DENV2 alone


title: KC_Fgfr2HO_6_D5

city: Cold Spring Harbor

first: David

middle: A

last: Tuveson

address: 1 Bungtown Road

department: Cancer Center

institute: Cold Spring Harbor Laboratory

data_processing:
The quality of the RNA-seq reads was first confirmed using FastQC version 0.11.9 (Babraham Bioinformatics).
Reads were trimmed using Trim Galore software verion 0.6.7.
Reads were then mapped to transcripts from GENCODE release M35 on mus musculus GRCm39 genome using STAR alignment software version 2.7.9a.
RSEM version 1.3.3 was used to calculate expression estimates per gene and per isoform.
DESeq2 version 1.44.0 was used to perform count normalization. A pre-filtering step was performed to remove genes that have reads in less than two samples. The normalization was done using only protein coding genes as  identifed by GENCODE M35 annotation.
Assembly: mus musculus NCBI genome build 39
Supplementary files format and content: The gene.results files are tab-delimited text files that include expected counts, TPM and FKPM values per gene for each sample as generated by RSEM.
Supplementary files format and content: The isoforms.results files are tab-delimited text files that include expected counts, TPM and FKPM values per isoform for each sample as generated by RSEM.
Supplementary files format and content: The Fgfr2_ADM_ALL_Samples_TPM_M35.txt  file is a tab-separated text file that includes the transcript per million (TPM) per transcript for all samples as extracted from the files generated by RSEM.
Supplementary files format and content: The Fgfr2_ADM_ALL_Samples_expected_counts_M35.txt file is a tab-separated text file that includes the expected count per transcript for all samples as extracted from the files generated by RSEM.
Supplementary files format and content: The Fgfr2_ADM_ALL_Samples_normalized_expected_counts_Protein_Coding_Only.csv  file is a comma-separated text file that includes the normalized counts per protein-coding transcript for all samples as obtained by DESeq2 after pre-filtering for genes expressed in less than two samples and not identified as protein-coding in M35 GENCODE annotation.

source_name: acinar-enriched explants

growth_protocol: Acinar-enriched epithelial explants were cultured in rat tail collagen I and RPMI1640 medium.

extract_protocol:
Total RNA was extracted using the TRIzol Plus RNA Purification Kit (ThermoFisher) per manufacturer’s instructions. RNA samples were treated on column with PureLink DNase (ThermoFisher). The quality of purified RNA samples was determined using a Bioanalyzer 2100 (Agilent) with an RNA 6000 Nano Kit.
Libraries for RNA-Seq were prepared with the KAPA mRNA HyperPrep Kit (Roche) following manufacturer instructions.

value: acinar-enriched explants

value: KrasLSLG12D/+; Pdx1-Cre; Fgfr2 fl/fl

tag: time

value: HO


title: KC_Fgfr2WT_4_D5

tag: genotype

value: KrasLSLG12D/+; Pdx1-Cre

value: WT


title: ARM-seq Day 70 AlkB Negative c305 Organoid 3

description: ARM-seq

value: iPSC

value: day 70

value: total small RNA (≤ 250 nts)

value: minus AlkB


title: PHF6-KO_Input (Histone)

value: Jurkat cells_PHF6-KO

value: Peripheral blood

value: Input DNA (for Samples 6,7,8)

value: Yes


title: OVCAR8 IgG CUT&RUN control

city: Bloomington

first: Richard

middle: L

last: Carpenter

state: IN

department: Biochemistry and Molecular Biology

institute: Indiana University

data_processing:
*library strategy: CUT&RUN
The demultiplexing of the reads was performed using bcl2fastq, version 2.20.0. Raw data was trimmed and aligned to the human (GRCh38/hg38) reference genome using Bowtie2. CUT&RUN peaks were called using MACS2. with peak stringency set to 10^-4 for HSF1 peaks and 10^-10 for MYC peaks.
Cut&Run reads aligned to UCSC hg38 using Bowtie2.
Samples were then converted from .sam to .bam files and sorted with samtools. Duplicate reads and blacklist regions were removed using bedtools.
Prior to peak calling, samtools was used to index .bam files to output a corresponding .bam.bai file.
Peak calling carried out using MACS2 with IgG as the control. Peaks in HSF1 samples were called with a p-value of 0.0001 (1E-04). Peaks in MYC samples were called with a p-value of 0.0000000001 (1E-10)
Assembly: hg38
Supplementary files format and content: .bam and .bam.bai files contain information about aligned reads prior to peak calling. Duplicate reads and blacklist regions have been removed from this data.
Supplementary files format and content: .xls contains information about called peaks. This file is a direct output from MACS2.

source_name: Ovarian tumor

growth_protocol: growth: 21% O2, 5% CO2 in DMEM + 10% FBS + 1% P/S

extract_protocol:
CUTANA CUT&RUN kit (EpiCypher) was used on proliferating OVCAR8 cells that were crosslinked with 1% formaldehyde in PBS for 1 minute on culture plates followed by glycine quenching. Cells were then scraped and counted with 5e5 cells and then incubated with CUT&RUN antibodies. Cross-link reversal was performed using 0.8 μL of 10% SDS and 1 μL of 10 μg/μL Proteinase K and overnight incubation at 55°C. DNA was then purified using the EpiCypher kit.
Libraries were prepared by NEBNext Ultra II DNA Library Preparation Kit protocol (NEB #E7645L) and analyzed by Agilent 4200 TapeStation. The libraries were pooled and loaded on a NextSeq 1000/2000 P2 Reagents (100 cycles) v3 flow cell (#20046811) configured to generated paired end reads.

treatment_protocol: No treatment

value: Ovarian tumor

value: epithelial cells

value: IgG CUT&RUN Antibody


title: ARM-seq Day 70 AlkB Negative c305 Organoid 2

description: ARM-seq


title: con2_cortex

value: Brain

value: Female

value: Microglia


title: PHF6-WT_H3K9me3

value: Jurkat cells_WT

value: H3K9me3 (Abcam, ab8898)


title: OV_control_C3

value: Plantaris muscle

value: MOV surgery, control virus, replicate 3


title: Control Axon_1

description: Library name: Sample 5

source_name: Control RGC axon

value: Control RGC axon

value: hPSC-derived Retinal Ganglion Cells

value: Isogenic control


title: KC_Fgfr2WT_3_D5

value: acinar-enriched explants

value: KrasLSLG12D/+; Pdx1-Cre

value: WT


title: PHF6-WT_H3K27me3

value: Peripheral blood

value: H3K27me3 (Active Motif, 39155)

value: Yes


title: Control Axon_3

description: Library name: Sample 7


title: OV_control_C2

value: MOV surgery, control virus, replicate 2


title: ARM-seq Day 35 AlkB Negative c305 Organoid 3

description: ARM-seq

value: iPSC

value: day 35

value: total small RNA (≤ 250 nts)

value: minus AlkB


title: OV_mimic_D3

value: MOV surgery, miR-1 mimicl virus, replicate 3


title: ARM-seq Day 35 AlkB Negative c305 Organoid 1

description: ARM-seq


title: KC_Fgfr2HO_9_D5

value: KrasLSLG12D/+; Pdx1-Cre; Fgfr2 fl/fl

value: HO


title: ARM-seq Day 0 AlkB Negative c305 Organoid 2

description: ARM-seq

value: day 0


title: KC_Fgfr2HO_8_D5


title: OPTN Axon_1

description: Library name: Sample 9

value: OPTN RGC axon

value: hPSC-derived Retinal Ganglion Cells


title: KC_Fgfr2HO_9_D2

value: acinar-enriched explants


title: Soma_RGC_3

description: Library name: Sample 3

source_name: Control RGC soma

value: Control RGC soma

value: Isogenic control


title: OVCAR8 MYC CUT&RUN Rep1

value: Ovarian tumor

value: epithelial cells

value: MYC CUT&RUN Antibody


title: Sham_mimic_B4

value: Plantaris muscle

value: sham surgery, miR-1 mimic virus, replicate 4


title: KC_Fgfr2HO_7_D5


title: Control Axon_4

description: Library name: Sample 8

value: Control RGC axon


title: Mac, Control, scRNAseq

description: 10x Genomics

value: peripheral blood

value: Macrophage

value: control


title: OV_control_C4

value: MOV surgery, control virus, replicate 4


title: Control Axon_2

description: Library name: Sample 6


title: CD4+ Tcells, WT-d2-3

first: SI

last: SUN

address: 8055 Cambridge Street Apt 16, 16

department: Transplant

institute: Transplant

data_processing:
For RNA preparation, 2 million resting and 48-h activated CD4+ T cells were used for RNA extraction using the miRNeasy Mini Kit (QIAGEN). PolyA+ RNA was isolated and RNA sequencing libraries were prepared and sequenced at BGI Genomics  Cooperation. After removing low-quality bases RNAs, the clean data were mapped to mouse genome (mm10) by using HISAT2 (v2.0.5). The mapped reads of each sample were assembled by StringTie (v1.3.3b). FeatureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. A 1.5-fold variance in expression levels, and an adjusted P value less than 0.05 were used as cutoffs to define differentially expressed genes (DEGs).
Assembly: mm10
Supplementary files format and content: processed data.xlsx

source_name: Lymph nodes, spleen

extract_protocol:
RNA was harvested using miRNeasy Mini Kit (QIAGEN). 1.5 ug of total RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seg were prepared using SMARTER mRNA-Seg LibraryPrep Kit following manufacturer's protocols.

value: Lymph nodes, spleen

value: CD4+ Tcells

value: T-lymphocyte

value: WT D2


title: KYSE450-Cortisol_L2_Q0058W0149

city: Zhengzhou

first: Ting

last: Wang

address: No. 100 Keke Avenue, Zhengzhou City, Henan Province

institute: Zhengzhou University

description: Library name: samples 15

data_processing:
Reads containing junction sequences need to be filtered out
Assembly: hg38
Supplementary files format and content: bedgraph, narrowPeak
Library strategy: CUT&Tag

source_name: cell

extract_protocol:
The Hyperactive Universal CUT&TAG Assay Kit for Illumina Pro was employed to prepare DNA libraries for Illumina high-throughput sequencing platforms. A total of 1 × 10^5 input cells were harvested as input material
Initially, cells were fixed using the cross-linking reagent, followed by the binding of 2 μg of specific antibodies (HMGB2, SREBF1, H3K27ac, H3K4me, H3K27me, GCR, and IgG antibody), respectively. Subsequently, the transposase enzyme was activated, leading to the cleavage of DNA at the targeted sites. The Tn5 transposase was then utilized to tag the DNA, introducing adapters for downstream analysis. After a series of washing steps to remove unbound fragments, the eluted material was subjected to PCR amplification to enrich the targeted DNA fragments. The amplified DNA was finally sequenced to obtain high-throughput data for further analysis.

value: cell

value: ESCC

value: cortisol


title: OVCAR8 MYC CUT&RUN Rep2

value: Ovarian tumor


title: KC_Fgfr2WT_2_D5

value: acinar-enriched explants

value: KrasLSLG12D/+; Pdx1-Cre

value: WT


title: Soma_RGCs_4

description: Library name: Sample 4

value: Control RGC soma

value: hPSC-derived Retinal Ganglion Cells

value: Isogenic control


title: KC_Fgfr2HO_6_D2

value: KrasLSLG12D/+; Pdx1-Cre; Fgfr2 fl/fl

value: HO


title: KYSE450-DMSO_L2_Q0057W0149

description: Library name: samples 13

value: DMSO


title: CD4+ Tcells, WT-d2-1

value: Lymph nodes, spleen


title: OV_control_C1

value: Plantaris muscle

value: MOV surgery, control virus, replicate 1


title: Soma_RGCs_2

description: Library name: Sample 2


title: Sham_mimic_B5

value: sham surgery, miR-1 mimic virus, replicate 5


title: Sham_mimic_B1

value: sham surgery, miR-1 mimic virus, replicate 1


title: OVCAR8 HSF1 CUT&RUN Rep2

value: epithelial cells

value: HSF1 CUT&RUN Antibody


title: KC_Fgfr2WT_4_D2


title: KC_Fgfr2HO_8_D2


title: KC_Fgfr2WT_1_D5


title: CD4+ Tcells, WT-d0-3

value: CD4+ Tcells

value: T-lymphocyte

value: WT D0

value: primary culture cell


title: Sham_control_A5

value: sham surgery, control virus, replicate 5


title: OVCAR8 HSF1 CUT&RUN Rep1

value: Ovarian tumor


title: CD4+ Tcells, WT-d0-2


title: Soma_RGCs_1

description: Library name: Sample 1

value: Control RGC soma

value: hPSC-derived Retinal Ganglion Cells

value: Isogenic control


title: KYSE450-H3K4me antibody

description: Library name: samples 7

value: cell

value: ESCC


title: Sham_mimic_B2

value: Plantaris muscle

value: sham surgery, miR-1 mimic virus, replicate 2


title: Sham_mimic_B3

value: sham surgery, miR-1 mimic virus, replicate 3


title: KC_Fgfr2HO_7_D2

value: acinar-enriched explants

value: KrasLSLG12D/+; Pdx1-Cre; Fgfr2 fl/fl

value: HO


title: KYSE450-H3K27me antibody_L1_Q0061W0150

description: Library name: samples 11


title: Sham_control_A2

value: sham surgery, control virus, replicate 2


title: Karpas422-delSBD-EZH2-GOF-rescue-H3K27me3-CR

city: New York City

first: Agata

middle: Lemiesz

last: Patriotis

address: 1230 York ave

institute: Rockefeller University

description:
Library name: Karpas422-delSBD-EZH2-GOF-rescue-H3K27me3
Cut&Run

data_processing:
Cut&Run reads were aligned using the Rsubread R Bioconductor package (v1.30.6) and predicted fragment lengths calculated by the ChIPQC R Bioconductor package (v1.16.2). Normalized, fragment-extended signal bigWigs were created using the rtracklayer R Bioconductor package (v1.40.6), and peaks called using MACS2 (v2.1.1)
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: CUT&Run

growth_protocol: Karpas-422 (Sigma) were cultured in suspension in RPMI-1640 (Invitrogen) supplemented with 20% FBS (Sigma).

extract_protocol:
CUT&RUN was performed with minor modifications of the CUTANA (EpiCypher) protocol. Briefly, cells were fixed with 0.1% formaldehyde in PBS for 1 minute, followed by quenching with 125 mM glycine. Cells were washed with cold Wash Buffer (20 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 0.5 mM Spermidine, protease inhibitor cocktail) and then bound to concavalin A beads for 10 minutes at room temperature. Supernatant was removed and beads were resuspended in Antibody Buffer (20 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, 2 mM EDTA, protease inhibitor cocktail) along with primary antibody. Samples were incubated overnight in the cold room, rotating. Beads were then resuspended in cold Digitonin Buffer 20 mM HEPES-KOH, pH 7.9, 150 mM NaCl, 0.5 mM Spermidine, 0.01% Digitonin, protease inhibitor cocktail), washed twice, then incubated with CUTANA pAG-MNase (Epicypher) for 10 minutes at RT. Beads were then washed twice with cold Digitonin buffer, resuspended in Digitonin Buffer with 50 mM CaCl2, and samples incubated for two hours with rotation at 4 °C. MNase was quenched by addition of STOP Buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 50 mg/ml RNase, 50 mg/ml Glycogen) and incubation for 10 mins at 37 °C. 0.1% SDS and Proteinase K was added to the supernatant and incubated for one hour at 55 °C followed by two hours at 65 °C. DNA was purified using Phenol-Chloroform Isoamyl Alcohol mix (Millipore) and PhaseLock tubes (5PRIME), and quantified using a Qubit 4 Fluorometer (Thermo) prior to proceeding with library preparation.
ChIP and CUT&RUN libraries were prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. All libraries were analyzed by TapeStation prior to sequencing. Single-end sequencing was performed on the Illumina NextSeq 500 sequencer.

value: Diffuse large B cell lymphoma

value: EZH2 KD + delSBD-EZH2-Y641N

tag: batch


title: KC_Fgfr2HO_9_D0

tag: strain


title: KC_Fgfr2WT_3_D2

value: KrasLSLG12D/+; Pdx1-Cre

value: WT


title: KYSE450-H3K27ac antibody_L1_Q0059W0150

description: Library name: samples 9


title: Karpas422-delSBD-EZH2-GOF-rescue-IgG-CR

description:
Library name: Karpas422-delSBD-EZH2-GOF-rescue-IgG
Cut&Run


title: KC_Fgfr2HO_8_D0


title: KC_Fgfr2WT_2_D2


title: KC_Fgfr2HO_7_D0


title: CD4+ Tcells, WT-d0-1

value: Lymph nodes, spleen

value: CD4+ Tcells

value: T-lymphocyte

value: WT D0

value: primary culture cell


title: CD4+ Tcells, WT-d2-2

value: WT D2


title: KYSE450-SREBF1 antibody

description: Library name: samples 3

value: cell

value: ESCC


title: KYSE450-GCR antibody_L3_Q0056W0149

description: Library name: samples 5


title: Sham_control_A1

value: Plantaris muscle

value: sham surgery, control virus, replicate 1


title: Sham_control_A3

value: sham surgery, control virus, replicate 3


title: KC_Fgfr2WT_1_D2

value: acinar-enriched explants


title: KYSE450-HMGB2 antibody

description: Library name: samples 1


title: KC_Fgfr2WT_4_D0


title: MDAMB468 cells, shNT, biol rep 1

city: Saint Louis

first: Che-Pei

last: Kung

state: Missouri

address: 1 Brookings Dr.

institute: Washington University in St. Louis

description: Library name: MDAMB468_ADAR1-Intact_1

data_processing:
Base calls and demultiplexing were performed with Illumina’s bcl2fastq software and a custom python demultiplexing program with a maximum of one mismatch in the indexing read.  RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.5.1a1.
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 1.4.6-p52. Sequencing performance was assessed for the total number of aligned reads, total number of uniquely aligned reads, and features detected.
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.
Assembly: Ensembl release 76 primary assembly
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: cell line

growth_protocol: All cancer cell lines were maintained in Dulbecco’s Modification of Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum (FBS), Sodium Pyruvate, Non-Essential Amino Acids, and L-glutamine in humidified atmosphere in 5% CO2 at 37°C.

extract_protocol:
Total RNA was isolated from cells using miRNeasy Mini Kit (Qiagen) including on-column DNase digestion following the manufacturer’s protocol. 1µg of total RNA was used to construct the libraries for sequencing.
RNA libraries for RNA-seq was prepared using KAPA Riboerase kit (Roche) according to manufacturer's instructions.

treatment_protocol: For transduction, one million cells were infected with lentivirus containing shRNA for 24hr in the presence of 10 µg/ml protamine sulfate to facilitate viral entry. Cells transduced with viruses were selected with puromycin (2 µg/ml) for at 72hr.

value: cell line

value: breast cancer cell

value: shNT

value: lentiviral shRNA


title: Karpas422-shEZH2-IgG-CR

description:
Library name: Karpas422-shEZH2-IgG
Cut&Run

value: Diffuse large B cell lymphoma

value: EZH2 KD


title: Atf3CreER_F7dpi

city: Bethesda

first: Claire

middle: E

last: LE PICHON

state: MD

address: 35A Convent Drive, 2D933

department: NICHD

institute: National Institutes of Health

description: 10X Genomics

data_processing:
Reads were aligned and assigned to Ensembl GRm38 transcript definitions using the CellRanger v3.1.0 pipeline (10X Genomics)
Outlier identification and removal based on number of expressed genes and mitochondrial proportions (Seurat)
Data normalization and scaling (Seurat)
Batch correction by data integration (Seurat)
PCA, clustering, and UMAP projection (Seurat)
Differential expression analysis (Seurat, DESeq2)
Assembly: mm10
Supplementary files format and content: CellRanger output filtered feature
Supplementary files format and content: RDS object containing processed data
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: 4 male

extract_protocol:
Brains were rapidly dissected and the ipsilateral cortex was subdissected and immediately frozen.  Tissue was homogenized and nuclei were isolated (see protocol) prior to FACS sorting for GFP+ nuclei. Samples were processed on a Sony SH800 Cell Sorter with a 100 mm sorting chip and GFP+/DRAQ5+ nuclei were collected.
Libraries were constructed according to the manufacturer’s instructions (10X Genomics).

value: Cerebral cortex

value: Atf3-CreER:+/wt; SUN-SfGFP:+/wt

value: male

tag: age

value: > 7 weeks old

value: mTBI


title: MDAMB468 cells, shADAR1, biol rep 3

description: Library name: MDAMB468_ADAR1-Deficient_3


title: MDAMB468 cells, shNT, biol rep 3

description: Library name: MDAMB468_ADAR1-Intact_3


title: Sham_control_A4

value: sham surgery, control virus, replicate 4


title: KC_Fgfr2HO_6_D0

value: KrasLSLG12D/+; Pdx1-Cre; Fgfr2 fl/fl

value: HO


title: Karpas422-EZH2-GOF-rescue-H3K27me3-CR

description:
Library name: Karpas422-EZH2-GOF-rescue-H3K27me3
Cut&Run

value: EZH2 KD + EZH2-Y641N


title: MDAMB468 cells, shNT, biol rep 2

description: Library name: MDAMB468_ADAR1-Intact_2


title: Brain, cTBS, biol rep 3

city: Perth

first: Alexander

last: Tang

state: Western Australia

address: 35 Stirling Highway, University of Western Australia

department: School of Biomedical Science

country: Australia

institute: University of Western Australia

description: Fresh frozen spatial transcriptome sequencing

data_processing:
Raw sequencing bcl files were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were then aligned to the mm10 genome to obtain gene expression counts using the Space Ranger count pipeline
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of all detected spatial barcodes (from raw_feature_bc_matrix/ spaceranger output folder)
Supplementary files format and content: features.tsv.gz: list of all detected gene IDs (from raw_feature_bc_matrix/ spaceranger output folder)
Supplementary files format and content: matrix.mtx.gz: gene expression count data in the Matrix Market Exchange format (from raw_feature_bc_matrix/ spaceranger output folder)
Supplementary files format and content: filtered_feature_bc_matrix.h5:
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: high resolution image of brain hemisphere tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image of brain hemisphere tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

extract_protocol:
Freshly dissected right mouse brain hemisphere was flash frozen in OCT using a set-up of isopentane and liquid nitrogen (as per 10xGenomics Visium Spatial Gene Expression protocols). Fresh frozen tissue was directly sectioned onto Visium Spatial Gene Expression Slides at 10μm using a cryostat.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's instructions

value: Brain

value: cTBS


title: Brain, cTBS biol rep 4


title: Karpas422-EZH2-GOF-rescue-IgG-CR

description:
Library name: Karpas422-EZH2-GOF-rescue-IgG
Cut&Run


title: MDAMB468 cells, shADAR1, biol rep 1

description: Library name: MDAMB468_ADAR1-Deficient_1

value: cell line


title: Karpas422-delSBD-EZH2-GOF-rescue-3

description:
Library name: delSBD-EZH2-GOF-rescue-3
RNA-seq

data_processing:
Transcript abundance was determined from FASTQ files using Salmon (v0.8.1) and the GENCODE reference transcript sequences. Transcript counts were imported into R with the tximport R Bioconductor package (v1.8.0), and differential gene expression performed with the DESeq2 R Bioconductor package (v1.20.0). Normalized counts were retrieved from the DESeq2 results and z-scores for the indicated gene sets visualized with heatmaps generated using the ComplexHeatmap R Biconductor package (v 2.8.0). Genes in heatmaps were annotated with ChIPseq signal by quantifying signal in regions starting at the transcription start site (TSS) and extending 5 kb downstream. Signal was quantified and then summarized as the mean signal in 50bp bins across these regions using the profileplyr R Bioconductor package (v1.8.1)
Assembly: hg38
Supplementary files format and content: feature counts

extract_protocol:
Total RNA was isolated from cultured cells using RNeasy Mini Kit (Qiagen) with on-column DNA digestion. RNA samples were analyzed on the Bioanalyzer RNA 6000 Pico (Agilent) prior to library preparation.
RNA libraries were converted to cDNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB) and NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB) according to the manufacturer’s instructions. All libraries were analyzed by TapeStation prior to sequencing. Single-end sequencing was performed on the Illumina NextSeq 500 sequencer.

value: EZH2 KD + delSBD-EZH2-Y641N


title: KC_Fgfr2WT_3_D0

value: acinar-enriched explants

value: KrasLSLG12D/+; Pdx1-Cre

value: WT


title: Karpas422-shEZH2-H3K27me3-CR

description:
Library name: Karpas422-shEZH2-H3K27me3
Cut&Run

value: Diffuse large B cell lymphoma

value: EZH2 KD


title: Karpas422-H3K27me3-CR

description:
Library name: Karpas422-H3K27me3
Cut&Run


title: MDAMB468 cells, shADAR1, biol rep 2

description: Library name: MDAMB468_ADAR1-Deficient_2

value: breast cancer cell

value: lentiviral shRNA


title: Brain, cTBS, biol rep 2


title: KC_Fgfr2WT_2_D0


title: Brain, cTBS, biol rep 1


title: Atf3CreER_M7dpi

description: 10X Genomics

value: Cerebral cortex

value: Atf3-CreER:+/wt; SUN-SfGFP:+/wt

tag: Sex

value: male

value: > 7 weeks old


title: KC_Fgfr2WT_1_D0


title: RNA-seq_Lwaltii

city: Paris

first: Axel

last: Cournac

address: 28 rue du docteur Roux

institute: Institut Pasteur

data_processing:
Reads were aligned against reference genome using bowtie2. bam files were then filtered to remove duplicates , low mapping quality(>10) reads and unpaired reads. The CPM tracks were generated using bamcoverage
Assembly: GCA_900074765.1 for L.fermentati / GCA_030580015.1 for L.waltii
Supplementary files format and content: unstranded CPM tracks are provided in .bw format

organism: Lachancea waltii

extract_protocol:
2mL of culture were peleted at 6000g for 5 min. Total RNA were extracted using the Machenery-Nagel RNA Nucleospin kit
The total RNA extract was sent to Novogene for further processing


title: Brain, iTBS, biol rep 4

value: iTBS


title: Hi-C_Lfermentati

data_processing:
Reads were aligned and contact maps generated and processed using Hicstuff (https://github.com/koszullab/hicstuff). Briefly, pairs of reads were aligned iteratively and independently using Bowtie2 (Langmead and Salzberg, 2012) in its most sensitive mode against their reference genome. Each uniquely mapped read was assigned to a restriction fragment.
Quantification of pairwise contacts between restriction fragments was performed with default parameters: uncuts, loops and circularization events were filtered as described in (Cournac et al., 2012)).
PCR duplicates (defined as multiple pairs of reads positioned at the exact same position) were discarded.
Contacts were binned at 1kb resolution and multiple-resolution balanced contact maps (in mcool format) were generated using cooler (Abdennur and Mirny, 2020).
Assembly: GCA_900074765.1 for L.fermentati / GCA_030580015.1 for L.waltii
Supplementary files format and content: Contact matrices are provided in multiple resolution mcool files.

extract_protocol:
Cell fixation with 3% formaldehyde (Sigma-Aldrich, Cat. F8775) was performed as described in Dauban et al. (2020). Quenching of formaldehyde with 300 mM glycine was performed at 4°C for 20 min. Hi-C experiments were performed with a Hi-C kit (Arima Genomics) with a double DpnII + HinfI restriction digestion following manufacturer instructions. Briefly, Cells were resuspended in 500ul water and transferred in VK05-0.5ml (ozyme, P000934-LYSK0-A.0) tubes containing glass beads before mechanical cells lysis. 8ul of samples were permeabilized by sequentially adding lysis buffer (15min at 4C), conditioning solution (10min at 62C) and stop solution 2 (15min at 37C) to the samples. DNA was digested using a mix of buffer A, DpnII, and Hinf1 (45min at 37C followed by 20min at 65C).
DNA was repaired and biotin was added by adding a mix of buffer B and enzyme B for 45min at room temperature. DNA was re-ligated by adding a mix of buffer C and enzyme C during 15min at room temperature. Samples were then digested by protease and de-crosslinked by adding a mix of buffer D, enzyme D and buffer E during 30 min à 55°C followed by 90 min at 68°C. Samples were purified using AMPure XP beads (Beckman A63882), recovered in 120ul H2O and sonicated using Covaris (DNA 300bp) in Covaris microTUBE (Covaris, 520045). Biotinylated DNA was loaded on Dynabeads™ Streptavidin C1 (FISHER SCIENTIFIC, 10202333). Preparation of the samples for paired-end sequencing on an Illumina NextSeq500 (2x35 bp) was performed using Invitrogen TM Collibri TM PS DNA Library Prep Kit for Illumina and following manufacturer instructions.


title: 20240208-NMK12F2

first: Li

last: Ding

address: 660 S Euclid Ave

institute: Washington University in St Louis

description: 20240208-NMK12F2 (W12.Female.Single specimen)

hyb_protocol: Overnight in situ probe hybridization was performed utilizing 379 probes from the Xenium Mouse Tissue Atlassing Panel (10x Genomics, 1000627) plus an additional 100 custom probes. Probe ligation, rolling circle amplification, background quenching, nuclei staining were done following the protocol (10x Genomics, CG000582, Rev D).

scan_protocol: Samples, buffers and decoding consumables were loaded into the Xenium analyzer (10x Genomics, 1000481). The run was initialized utilizing the guidance provided (10x Genomics, CG000584, Rev C). These fluorescent reporters hybridized to targeted complementary regions of the barcoded circularized cDNA were imaged.

data_processing:
H&E images were integrated with Xenium data using manual Image Alignment workflow from Xenium Explorer 1.3.0 (See “Image Alignment in Xenium Explorer” from the 10x Genomics Xenium Tutorial Page). Cell types were assigned by reviewing the top DEGs of each unsupervised cluster, confirming their anatomical locations, and/or reviewing morphological structure with the aligned H&E image.
Xenium Onboard Analysis (XOA) on-instrument software pipeline version 1.9.2.0 were used to collect and process Xenium In Situ Gene Expression data on the Xenium Analyzer (XA).

label: Xenium Mouse Probe Set

source_name: kidneys

label_protocol: Xenium Mouse Probe Set

growth_protocol: W12 and W92 mice were purchased from the Jackson Laboratory.

extract_protocol: Freshly procured mouse kidneys were fixed and embedded into paraffin blocks (FFPE blocks). Kidneys were processed following the FFPE Tissue Preparation Guide (10x Genomics, CG000578, Rev B).

treatment_protocol: Before kidney extraction, mice were euthanized by carbon dioxide asphyxiation. No additional prior treatment were performed.

value: kidneys

value: 12 weeks

value: female


title: Karpas422-IgG-CR

description:
Library name: Karpas422-IgG
Cut&Run

tag: cell type


title: Brain, iTBS, biol rep 1

value: Brain


title: MDAMB231 cells, shNT, biol rep 3

description: Library name: MDAMB231_ADAR1-Intact_3

value: cell line

value: shNT


title: Karpas422-delSBD-EZH2-GOF-rescue-2

description:
Library name: delSBD-EZH2-GOF-rescue-2
RNA-seq

value: EZH2 KD + delSBD-EZH2-Y641N


title: Brain, iTBS, biol rep 3


title: MDAMB231 cells, shADAR1, biol rep 2

description: Library name: MDAMB231_ADAR1-Deficient_2


title: MDAMB231 cells, shNT, biol rep 2

description: Library name: MDAMB231_ADAR1-Intact_2


title: Karpas422-delSBD-EZH2-GOF-rescue-1

description:
Library name: delSBD-EZH2-GOF-rescue-1
RNA-seq


title: Brain, sham, biol rep 3

value: sham


title: MDAMB231 cells, shADAR1, biol rep 1

description: Library name: MDAMB231_ADAR1-Deficient_1


title: 20240208-NMK12M2

description: 20240208-NMK12M2 (W12.Male.Single specimen)


title: Brain, iTBS, biol rep 2


title: Brain, sham, biol rep 2


title: MDAMB231 cells, shNT, biol rep 1

description: Library name: MDAMB231_ADAR1-Intact_1


title: HCC1806 cells, shNT, biol rep 3

description: Library name: HCC1806_ADAR1-Intact_3


title: Micro-C of Fbn2 cell line, replicate 1

city: Cambridge

first: James

middle: Martin

last: Jusuf

address: Building 56 Room 787B, 32 Vassar Street

department: Biological Engineering

institute: Massachusetts Institute of Technology

description:
Library name: Fbn2_rep1
Cell line containing TetO and Anchor3 arrays for fluorescent labeling of the Fbn2 loop on chr18

data_processing:
Base calls for NovaSeq output were obtained using bcl2fastq (v2.20.0.422).
Paired-end reads were aligned to the mm39 reference genome or modified versions of mm39 using bwa-mem2 (v2.2.1). The modified genomes contained the synthetic DNA sequences inserted at the anchors of the Fbn2 or Npr3 loops.
Aligned paired-end reads were then parsed with pairtools (v1.0.3) parse with --add-columns mapq --walks-policy all --min-mapq 30.
When aligning to the modified genomes only, a custom pipeline was implemented to recover multiply mapping reads in the synthetic regions by randomly assigining them to unique positions.
Parsed reads were filtered for PCR duplicates and unmapped/mutiply mapping reads with pairtools dedup with --max-mismatch 1.
For all samples, trans reads were downsampled in order to ensure that trans reads constituted a fixed 5% of total reads.
These filtered reads were subsequently converted to .cool format with cooler (v.0.9.3) cload pairs and subsequently to .mcool format with cooler zoomify with --balance --balance-args '--ignore-dist 20000'
Assembly: mm39
Supplementary files format and content: mcool files contain all valid Micro-C pairs stored in HDF5 format with multiple resolutions
Supplementary files format and content: mESC_merged_15.6B_mm39.mcool contains all valid Micro-C pairs of untreated mESC cells from this study, Hansen et al. 2019, Hsieh et al. 2020, Hsieh et al. 2022, and Narducci & Hansen 2024.

growth_protocol: Fbn2 cell line: Cells were cultured on plates pre-coated with 0.1% gelatin solution (Sigma-Aldrich, G1890) in KnockOut Dulbecco's Modified Eagle Medium (Thermo Fisher, 10829018) supplemented with 15% fetal bovine serum (HyClone, SH30396.03),  2 mM GlutaMAX (Thermo Fisher, 35050061), 1% MEM Non-Essential Amino Acid Solution (Thermo Fisher, 11140050), 0.1 mM 2-mercaptoethanol (Sigma-Aldrich, M3148), 1000 U/mL leukemia inhibitory factor (home-made [Hansen et al 2017]), 10 μM MEK inhibitor (Tocris, PD0325901), 3 μM GSK3 inhibitor (Sigma-Aldrich, SML1046), and 100 μg/ml Penicillin-Streptomycin (Thermo Fisher, 15140122) in 5% CO2 at 37 °C. Npr3 cell line: Cells were cultured on plates pre-coated with 0.1% gelatin solution (Sigma-Aldrich, G2500) in Glasgow Minimum Essential Medium (Sigma-Aldrich, G5154) supplemented with 15% fetal calf serum (Eurobio Abcys), 1% L-Glutamine (Thermo Fisher, 25030024), 1% Sodium Pyruvate MEM (Thermo Fisher, 11360039), 1% MEM Non-Essential Amino Acids (Thermo Fisher, 11140035), 0.1 mM 2-mercaptoethanol (Thermo Fisher, 31350010), 20 U/mL leukemia inhibitory factor (Miltenyi Biotec, premium grade), 1 µM MEK inhibitor (Axon, 1408), and 3 µM GSK3 inhibitor (Axon, 1386) in 8% CO2 at 37 °C.

extract_protocol:
Cells were fixed with 3 mM DSG for 35 minutes, followed by an additional 10 minutes with 1% formaldehyde. Following quenching, nuclei were prepared from fixed cells. Chromatin was digested in situ using MNase, DNA 3' ends were chewed back and biotinylated, and then free DNA ends were proximity ligated. Unligated ends were digested, and chromatin crosslinks were reversed. DNA was purified by the DNA Clean and Concentrator kit (Zymo), and size selected for dinucleosomal fragments on an agarose gel. Following end polishing of DNA fragments, a streptavidin pulldown was used to enrich for ligated dinucleosomal fragments.
Size selected DNA fragments bound to streptavidin coated beads were used to prepare Micro-C libraries using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB), using NEBNext Multiplex Oligos for Illumina for indexing samples. Libraries were amplified with 7 PCR cycles on the thermocycler using KAPA HiFi HotStart ReadyMix (Roche) and purified using AMPure XP beads (Beckman Coulter). Purified libraries were quantified using qPCR and pooled in a 1:1 ratio. Following qPCR quantification, the library pool was submitted for sequencing.

treatment_protocol: Micro-C was performed on cells in untreated condition.

value: Embryonic stem cells


title: MDAMB231 cells, shADAR1, biol rep 3

description: Library name: MDAMB231_ADAR1-Deficient_3


title: Karpas422-EZH2-KD-2

description:
Library name: EZH2-KD-2
RNA-seq

value: Diffuse large B cell lymphoma

value: EZH2 KD


title: Karpas422-EZH2-GOF-rescue-3

description:
Library name: EZH2-GOF-rescue-3
RNA-seq

value: EZH2 KD + EZH2-Y641N


title: Karpas422-EZH2-GOF-rescue-2

description:
Library name: EZH2-GOF-rescue-2
RNA-seq


title: 20210908-NMK92F

description: 20210908-NMK92F (W92.Female.Single specimen)

value: 92 weeks


title: Micro-C of Npr3 cell line, replicate 2

description:
Library name: Npr3_rep2
Cell line containing 3xCTCF sites forming synthetic Npr3 loop on chr15 and flanking TetO and LacO arrays for fluorescent labeling


title: Brain, sham, biol rep 4

description: Fresh frozen spatial transcriptome sequencing


title: Karpas422-EZH2-GOF-rescue-1

description:
Library name: EZH2-GOF-rescue-1
RNA-seq


title: 20210907-NMK92M

description: 20210907-NMK92M (W92.Male.Single specimen)


title: Somatosensory cortex cells, sham, replicate 4

data_processing:
First 15 base pairs of sequencerd reads were trimmed to remove low-quality sequences using fastp.
Trimmed sequence reads were mapped to GRCm39/mm39 using the STAR RNA-seq aligner. STAR-aligned SAM files were converted into BAM files.
Read counts were generated using GenomicAlignments.
Normalisation of counts was performed using the DESeq2 R package, using a variance stabilising transformation (VST) function.
Assembly: mm39
Supplementary files format and content: Comma-separated values files containing the raw read counts for each sample
Supplementary files format and content: Comma-separated values files containing the read counts that have been normalised using the variance stabilising transformation (VST) for each sample

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen). A minimum of 50ng total RNA was sent to the Australian Genome Research Facility (Melbourne, Australia) for the construction of sequencing-ready libraries.
RNA libraries for whole transcriptome RNA-seq were prepared using the Illumina Stranded Total RNA Library Preparation Kit with Ribo-Zero Plus, by the technical staff at the Australian Genome Research Facility (Melbourne, Australia).


title: HCC1806 cells, shNT, biol rep 2

description: Library name: HCC1806_ADAR1-Intact_2

value: breast cancer cell

value: lentiviral shRNA


title: Karpas422-EZH2-KD-3

description:
Library name: EZH2-KD-3
RNA-seq


title: HCC1806 cells, shADAR1, biol rep 2

description: Library name: HCC1806_ADAR1-Deficient_2


title: Micro-C of Fbn2 cell line, replicate 2

description:
Library name: Fbn2_rep2
Cell line containing TetO and Anchor3 arrays for fluorescent labeling of the Fbn2 loop on chr18


title: Karpas422-EZH2-KD-1

description:
Library name: EZH2-KD-1
RNA-seq


title: HCC1806 cells, shNT, biol rep 1

description: Library name: HCC1806_ADAR1-Intact_1


title: APAP+SIRP-EV, replicate3

city: Seonbuk-gu

first: Yoon Kyoung

last: Kim

state: Seoul

address: Hwarang-ro 76, Unit102

institute: SHIFTBIO

data_processing:
Trimmed reads were mapped using HISAT2 (version 2.1.0) to genomic reference (mm10) and aligned reads were generated.
The aligned reads were assembled using SrtingTie (version 2.1.3b).
Assembly: StringTie
Supplementary files format and content: Tab-separted values files for each sample

source_name: Liver

extract_protocol:
The freshly harvested mouse livers were dissociated into single cells, and CD11b+ cells were isolated. RNA from CD11b+ single cells was extracted using Trizol (Sigma). DNA contamination was removed with DNase.
RNA libraries for bulk RNA-seq were prepared using TruSeq Stranded mRNA Library Prep Kit following manufacturer's intruction.

value: Liver

value: CD11b+ cell

tag: condition

value: APAP induction

value: MSC derived SIRP-EV


title: Somatosensory cortex cells, sham, replicate 5


title: DMD-004 Batch 2_ Urinary Extracellular Vesicles

first: Preeti

last: Kumari

address: 13 street

department: Neurology

institute: Massachusetts General Hospital

description:
Library name: DMD-004 Batch 2
Column name in TPM_All Samples.txt. DMD-004 Batch 2

data_processing:
Sequencing was performed in two separate batches using an Illumina NextSeq 500 platform at the George Washington University Genomics Core (https://www.gwgenomics.org) and a high output 150-cycle kit to generate more than 83 million paired end reads per sample.
Sequences were trimmed for adaptor sequence/low quality sequence using bbmap with parameters ktrim=r, k=21, mink=11, tbo, tpe, hdist=2, minlen=31, qtrim=r, trimq=10, maq=10, entropy=0.3, entropywindow=50, and entropyk=5.
The trimmed sequence reads were mapped to the human GRCh38 genome using Salmon (v. 1.10.2). The specific mapping procedure involves aligning the reads using the salmon quant function with flags for sequence and GC bias corrections (--seqBias --gcBias), library type specification (-l A), and enhanced statistical modeling (--numBootstraps=20).
Read count extraction and normalization were also performed using Salmon (v. 1.10.2)
Assembly: hg38
Supplementary files format and content: Tab-delimited text files include TPM values for each Sample

source_name: Urinary Extracellular Vesicles

extract_protocol:
We extracted RNA using 1ml TRIzol Reagent according to the manufacturer's instructions
RNA libraries for RNA-seq were prepared using Takara SMARTer Stranded Total RNA Sequencing kit V2 - pico input mammalian (Takara product number 634412).

value: Urinary Extracellular Vesicles

value: DMD


title: Micro-C of Npr3 cell line, replicate 1

description:
Library name: Npr3_rep1
Cell line containing 3xCTCF sites forming synthetic Npr3 loop on chr15 and flanking TetO and LacO arrays for fluorescent labeling

tag: cell line


title: DMD-001 Batch 1_ Urinary Extracellular Vesicles

description:
Library name: DMD-001 Batch 1
Column name in TPM_All Samples.txt. DMD-001 Batch 1


title: HCC1806 cells, shADAR1, biol rep 3

description: Library name: HCC1806_ADAR1-Deficient_3

value: cell line

tag: treatment


title: HCC1806 cells, shADAR1, biol rep 1

description: Library name: HCC1806_ADAR1-Deficient_1


title: DMD-003 Batch 2_ Urinary Extracellular Vesicles

description:
Library name: DMD-003 Batch 2
Column name in TPM_All Samples.txt. DMD-003 Batch 2


title: Somatosensory cortex cells, cTBS, replicate 5

value: Brain

value: cTBS


title: DMD-002 Batch 2_ Urinary Extracellular Vesicles

description:
Library name: DMD-002 Batch 2
Column name in TPM_All Samples.txt. DMD-002 Batch 2


title: Somatosensory cortex cells, cTBS, replicate 4


title: DM1-003_Batch 2_ Urinary Extracellular Vesicles

description:
Library name: DM1-003 Batch 2
Column name in TPM_All Samples.txt. DM1-003 Batch 2


title: APAP+SIRP-EV, replicate2


title: Somatosensory cortex cells, iTBS, replicate 5

value: iTBS


title: Brain, sham, biol rep 1

value: sham


title: BT549 cells, shNT, biol rep 3

description: Library name: BT549_ADAR1-Intact_3

value: shNT


title: APAP+SIRP-EV, replicate1


title: Somatosensory cortex cells, iTBS, replicate 4


title: APAP+HEKSIRP-EV, replicate1

value: HEK cell derived SIRP-EV