title: Hair cells, 1 day post sham lesion, rep 3

first: Rohan

middle: Saleem

last: Roy

address: 1230 York Avenue

institute: The Rockefeller University

description: Library name: Sample 6

data_processing:
Fastq read quality was assessed using the Rfastp package and filtered based on number of unassigned bases (N<5), read length (minimum read length 15), and phred score (minimum 15). Filtered reads were aligned to the reference genomes using the Rsubread package (v 2.8.2) and reads assigned to genes using the featurecounts function. Transcript abundance was calculated using Salmon (v1.8.0). Normalized counts for each sample were generated using the DESeq2 (v.1.34.0) package utilizing the median of ratios methods on transcript quantifications derived from Salmon.
Assembly: GRCz11
Supplementary files format and content: tab-delimited text file includes normalized read counts generated by DESeq2 for each sample.

organism: Danio rerio

source_name: Posterior lateral line hair cells

extract_protocol:
Hair cells were isolated by fluoresence-activated cell sorting directly into lysis buffer, and total RNA was extracted using the RNeasy Plus Micro Kit (QIAGEN). 1 ng of total RNA from each sample was used for library preparation.
Full length cDNA was generated using the Clontech Smart-Seq v4 Ultrat Low Input RNA kit. 1 ng of cDNA was then used to prepare libraries using the Illumina Nextera XT DNA sample preparation kit.

value: Posterior lateral line hair cells

value: Uncut


title: Zea mays B73, primary and seminal root tip (0-1mm), Nuclear EU nascent RNA-seq, biorep1

status: Public on Jul 23 2025

type: SRA

city: Raleigh

first: Linda

last: Hanley-Bowdoin

state: NC

address: 851 Main Campus Drive, Partners III Suite 360

department: Plant and Microbial Biology

country: USA

institute: North Carolina State University

description: EU-nuclear RNA from biotin-streptavidin pulldown

library_source: transcriptomic

data_processing:
Adapter trimming (trimmomatic-0.36 PE -phred33 -validatePairs ILLUMINACLIP:/Trimmomatic-0.39/adapters/TruSeq3-PE-2.fa:2:30:10:2:True LEADING:5 TRAILING:5 MINLEN:20)
Contaminants filtration (sortmerna -ref contaminants.fasta -reads $SAMPLE.input.fw.fastq -reads $SAMPLE.input.rv.fastq --out2 True --kvdb $SAMPLE.kvdb --readb $SAMPLE.readb --idx-dir sortmerna.idx-dir --zip-out Yes --fastx true --blast '1 cigar qcov qstrand' --paired_in true --other $SAMPLE.processed)
Read mapping (STAR --genomeDir STAR_2.7.10b.GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0 --outSAMtype BAM SortedByCoordinate --outMultimapperOrder Random --outFilterMultimapNmax 1 --readFilesIn $SAMPLE.fw.fastq $SAMPLE.rv.fastq --outFileNamePrefix $SAMPLE.mapped)
Alignments filtering (samtools view -bh -f 0x2 $SAMPLE.bam)
Alignments deduplication (umi_tools dedup -I $SAMPLE.bam -S $SAMPLE.deduplicated.bam --umi-separator=":" --paired )
Genomic coverage (bamCoverage --binSize 50 --normalizeUsing RPGC --effectiveGenomeSize 2209328549 --outFileFormat bigwig --filterRNAstrand forward --bam $SAMPLE.deduplicated.bam --outFileName $SAMPLE.deduplicated.fw.bw )
Read count (htseq-count -f bam --order=pos --stranded=reverse -a 0 -t exon -i gene --nonunique=fraction --mode=union --counts_output=$SAMPLE.counts.tsv $SAMPLE.deduplicated.bam Zm-B73-REFERENCE-NAM-5.0_genomic.with_scaffolds.GENE.coding+non_coding+pseudo.EXONS.gff)
Assembly: GCF_902167145.1_Zm-B73-REFERENCE-NAM-5.0_genomic.fasta
Supplementary files format and content: bigwig files with read density coverage
Supplementary files format and content: tables with raw read counts

molecule: nuclear RNA

organism: Zea mays

source_name: Terminal 1 mm of primary and seminal roots

growth_protocol: B73 seeds were imbibed overnight with stirring and aeration, and the next day surface sterilized with 10% commercial bleach; 0.05% Tween 20 solution for 15 min at room temperature, rinsed 4X with sterile water and germinated in sterilized magenta boxes with paper towels dampened with sterile water. Seedlings were grown in a growth chamber at 28 C for 3 days under continuous dim fluorescent light (~500 lux).

extract_protocol:
Nuclear RNA was isolated using the Qiagen RNeasy FFPE Kit (ref # 73504). The kit is designed to purify RNA from fixed, paraffin-embedded tissue sections. We skipped the deparaffinization steps and began the protocol at step six of the handbook. Nuclear RNAs were DNAase treated with the Invitrogen Turbo DNA-free kit and ribosomal RNAs were removed with the Vazyme Ribo-off rRNA depletion kit for plants.
NEBNext Ultra II Directional RNA Library kit for Illumina with NEBNext Multiplex Oligos for Illumina, Unique Dual Index UMI Adaptors RNA set 1.

treatment_protocol: Conditioned for 1 hr in water then labeled for 1 hr in 175 uM 5-ethynyl uridine.

tag: tissue

tag: developmental stage

value: seedling primary and seminal root meristem region

tag: cultivar

tag: age

value: 3-days after germination

tag: treatment

value: conditioned for 1 hr in water then labeled for 1 hr in 175 uM 5-ethynyl uridine


title: Hair cells, 1 day post sham lesion, rep 1

city: New York

state: NY

description: Library name: Sample 4

molecule: total RNA

tag: cell type

tag: genotype

value: WT


title: Hair cells, 1 day post nerve lesion, rep 3

description: Library name: Sample 3

value: Cut


title: kidney biopsy N510

type: RNA

city: Edmonton

first: Jessica

last: Chang

address: 250 Heritage Medical Research Centre

department: Medicine

country: Canada

institute: University of Alberta

hyb_protocol: (Affymetrix, Santa Clara, CA).  Amplified RNA (10ug) was hybridized for 16 hr at 45C on  GeneChip® PrimeView™ Human Gene Expression Array . GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Gene Array Scanner 3000 7G (Affymetrix) and processed with GeneChip® Command Console® Software (AGCC)(Affymetrix).

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

label: biotin

organism: Homo sapiens

source_name: kidney biopsy

label_protocol: Total RNA (0.5µg) was labeled using GeneChip 3` IVT Express Labeling kit. Quality of labeled aRNA was assessed on an Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA) before hybridization to GeneChip® PrimeView™ Human Gene Expression Array

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

treatment_protocol: All human kidney biopsies taken for clinical indication during the period specified above were included. Tissue was immediately placed in RNA later.

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)

value: ABMR


title: kidney biopsy N507

value: NR


title: CX3CR1V249IHom_S12

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 14

data_processing:
The sequencing data was next assessed using FastQC (Babraham Bioinfomatics, Cambridge, UK) and then mapped to the Human genome (GRCH38) using STAR RNA-seq aligner (Dobin et al., 2013) with the parameter: “— outSAMmapqUNIQUE 60”. Uniquely mapped sequencing reads were assigned to GRCH38 reference genome using featureCounts.
Assembly: GRCH38
Supplementary files format and content: txt; counts

growth_protocol: Human induced pluripotent stem cells were differentiated first into hematopoeitic progenitor cells using the Stem Cell Technologies kit and further differentiated for 25 days into human microglia-like cells using previously described methods.

extract_protocol:
Total RNA was collected from hMGLs on day 25 of differentiation across all genotypes using the Pcipure RNA extraction kit (Life Technologies)
mRNAseq was then performed upon these samples to identify transcriptional changes across all conditions using a NovaSeq 6000 sequencer at the Indiana University Center for Medical Genomics. RNA quality was determined with an Agilent Bioanalyzer 2011, with a RIN number of 7 or higher. cDNA library preparation included mRNA purification/enrichment, RNA fragmentation, cDNA synthesis, ligation of index adaptors, and amplification, following the KAPA mRNA Hyper Prep Kit Technical Data Sheet, KR1352 – v4.17 (Roche Corporation). Approximately 30M reads per library were generated.

treatment_protocol: Differences were based on genotype, not treatment

tag: cell line

value: iPSC-derived human microglia-like cells

value: In vitro differentiation

tag: batch


title: Hair cells, 1 day post nerve lesion, rep 1

description: Library name: Sample 1


title: CX3CR1V249IHom_S9

description: Library name: Sample 13


title: CX3CR1V249IHom_S15

description: Library name: Sample 15


title: CX3CR1V249IHom_S6

description: Library name: Sample 12


title: kidney biopsy N508


title: kidney biopsy N509


title: kidney biopsy N505


title: WT_4_5h_rep1

city: Berkeley

first: Olesia

last: Ignatenko

state: CA

address: Morgan Hall

institute: UC Berkeley

description:
Library name: S10
RNAseq_MAPLKO_BMDM

data_processing:
Trimmomatic
HISAT2
featureCounts
DeSeq2
Assembly: mm10
Supplementary files format and content: xlsx, raw counts, normalised counts, differential expression analysis

organism: Mus musculus

source_name: primary BMDM

extract_protocol:
Nucleospin columns
PolyA selection, KAPA RNA HyperPrep protocol with xGene Dual Index UMI Adapter (IDT)

tag: Sex

value: Male

value: primary BMDM

value: MAPL control

value: LPS+IFNy 4.5h


title: WT_4_5h_rep2

description:
Library name: S4
RNAseq_MAPLKO_BMDM


title: WT_4_5h_rep3

description:
Library name: S16
RNAseq_MAPLKO_BMDM


title: kidney biopsy N506

value: Mixed


title: kidney biopsy N511


title: kidney biopsy N504

value: pABMR


title: WT_24h_rep3

description:
Library name: S17
RNAseq_MAPLKO_BMDM

value: LPS+IFNy 24h


title: WT_24h_rep2

description:
Library name: S5
RNAseq_MAPLKO_BMDM


title: CX3CR1V249IHom_S3

description: Library name: Sample 11


title: Hair cells, 1 day post sham lesion, rep 2

description: Library name: Sample 5

value: Posterior lateral line hair cells

value: Uncut


title: WT_0h_rep3

description:
Library name: S15
RNAseq_MAPLKO_BMDM

value: untreated


title: kidney biopsy N503


title: Hair cells, 1 day post nerve lesion, rep 2

description: Library name: Sample 2


title: WT_0h_rep2

description:
Library name: S3
RNAseq_MAPLKO_BMDM


title: CX3CR1V249IHet_S11

description: Library name: Sample 9


title: kidney biopsy N376


title: WT_0h_rep1

description:
Library name: S9
RNAseq_MAPLKO_BMDM


title: CX3CR1V249IHet_S8

description: Library name: Sample 8


title: KO_4_5h_rep2

description:
Library name: S13
RNAseq_MAPLKO_BMDM

value: MAPL KO


title: WT_24h_rep1

description:
Library name: S11
RNAseq_MAPLKO_BMDM


title: CX3CR1V249IHet_S14

description: Library name: Sample 10


title: KO_4_5h_rep3

description:
Library name: S7
RNAseq_MAPLKO_BMDM


title: KO_24h_rep1

description:
Library name: S20
RNAseq_MAPLKO_BMDM


title: KO_4_5h_rep1

description:
Library name: S19
RNAseq_MAPLKO_BMDM


title: KO_24h_rep2

description:
Library name: S14
RNAseq_MAPLKO_BMDM


title: CX3CR1V249IHet_S5

description: Library name: Sample 7


title: KO_0h_rep3

description:
Library name: S6
RNAseq_MAPLKO_BMDM


title: CX3CR1V249I_Het_S2

description: Library name: Sample 6


title: kidney biopsy N374


title: kidney biopsy N373


title: WTC11_Iso Control_S13

description: Library name: Sample 5

value: control


title: KO_0h_rep2

description:
Library name: S12
RNAseq_MAPLKO_BMDM


title: kidney biopsy N501


title: WTC11_Iso Control_S10

description: Library name: Sample 4


title: KO_0h_rep1

description:
Library name: S18
RNAseq_MAPLKO_BMDM


title: cNFs_P365_all_18h

city: Créteil

first: Pernelle

last: Pulh

address: 8 rue du général Sarrail

country: France

institute: INSERM - IMRB

description: Library name: 2023_12

library_source: transcriptomic single cell

data_processing:
BCL files from Illumina were processed using 10x Genomics Cell Ranger 7.0.1, using cellranger mkfastq and cellranger count commands. Reads were mapped on GRCm39 release 108 transcriptome. The 12 fastq files correspond to the output for cellranger mkfastq command while the 3 matrices files correspond to the output of cellranger count command. The count matrix is the unfiltered (raw) one, as used in the publication. Each raw count matrix was load using Seurat.  Empty droplets were removed using the emptyDrops function from the package DropletsUtils version 1.6.1. A false discovery rate (FDR) of 1E-3 was set to define empty droplets. Cells having less than 6 log number of unique molecular identifiers (UMI) or less than 600 genes were filtered out. Doublet cells were removed using scDblFinder package (version 1.1.8) and scds package (1.2.0) in hybrid mode. For scDblFinder eponymous function, the size.factors.norm parameter value was defined using DESeq2::sizeFactors function, DESeq2 version 1.26.0. For the cxds_bcds_hybrid function from the scds package, default setting was used and a hybrid_score greater than 1 was used to define double cells.  Then, cells having more than 20 % of UMI related to mitochondrial genes or more than 40 % related to ribosomal genes were filtered out. UMI count matrix for remaining cells was normalized using LogNormalize method implemented in Seurat::NormalizeData function. Single cells were annotated for cell type using Seurat::AddModuleScore. For the 2D projection, 3000 highly variable features (HVFs) were identified using Seurat::FindVariableFeatures. Then, a PCA with 100 components was generared from these 3000 HVFs, using Seurat::RunPCA. A UMAP was generated using 20 components from the PCA, using the Seurat::RunUMAP function.
Assembly: GRCm39 release 108 transcriptome
Supplementary files format and content: Raw count matrix provided by Cell Ranger

molecule: polyA RNA

source_name: cNFs from back skin

growth_protocol: Data are directly obtained from mouse skin cells.

extract_protocol:
3-hour dissociation protocol Animals were anesthetized, shaved, depilated, and transcardially perfused with 50 mL PBS to remove any blood. Their skin was carefully dissected, and adipose tissue was removed with scalpels, supplemented by three successive washes in 30 mL RPMI. Each piece of skin was then carefully placed in a petri dish, epidermis side down, and treated with 15 mL of 0.15% trypsin-EDTA at 37°C for 30 minutes. After this incubation, the skins were removed from the trypsin-EDTA solution and placed in a PBS/5%FBS solution at 4°C, where the detached epidermis was gently scraped off with scalpels. The skins were then washed three times in 30 mL of RPMI before being exposed to the trypsin-EDTA medium at 37°C for another 30 minutes. After this second incubation, the same procedure was used to scrape off the enzymatically dissociated epidermis. After a final rinse with RPMI, the skins were carefully dissected under a Leica epi-fluorescence microscope to isolate cNFs and HLS regions, which were then finely minced on a -20°C metal block using scissors and scalpels. The minced tissue (0.5 g per tube) was then immersed in 10 mL of prewarmed RPMI medium containing Liberase DH (0.25 mg/mL) and placed in a 37°C water bath for 3 hours. To achieve complete dissociation, the skin tissue was mechanically dissociated every 30 minutes with a 1 ml pipette. After 40 minutes of dissociation, DNAseI was added to the medium. After the 3-hour incubation period, the dissociation tubes were immediately placed on ice. Any remaining skin pieces were then mechanically dissociated using an up-and-down motion, first with a 1 ml pipette and then with a glass Pasteur pipette pre-coated with FBS. To stop the action of the enzymes, 30 ml of RPMI containing 10% FBS was added to each tube. The tubes were then centrifuged at 300g for 10 minutes. After discarding the supernatant, the pellet was gently resuspended in 5 ml of RPMI and filtered through a 100 μm filter, followed by a 70 μm filter, and finally a 30 μm filter to remove any remaining tissue fragments or cellular debris. The cells were then centrifuged again at 300g for 10 min before being resuspended in a solution of PBS/1% BSA. To assess cell viability, we added DAPI viability dye at a concentration of 5 μg/ml. The prepared cells were then sorted using Fluorescence-Activated Cell Sorting (FACS) at the IMRB FACS facility. The sorting process was based on the cells' DAPI labeling and Tomato fluorescence to ensure the selection of viable and relevant cell populations. 18-hour dissociation protocol Animals were anesthetized, shaved, depilated, and transcardially perfused with 50 mL PBS to remove any blood. Their skin was carefully dissected, and adipose tissue was removed with scalpels, supplemented by three successive washes in 30 mL RPMI. Each piece of skin was then carefully placed in a petri dish, epidermis side down, and treated with 15 mL of 0.15% trypsin-EDTA at 37°C for 30 minutes. After this incubation, the skins were removed from the trypsin-EDTA solution and placed in a PBS/5%FBS solution at 4°C, where the detached epidermis was gently scraped off with scalpels. The skins were then washed three times in 30 mL of RPMI before being exposed to the trypsin-EDTA medium at 37°C for another 30 minutes. After this second incubation, the same procedure was used to scrape off the enzymatically dissociated epidermis. After a final rinse with RPMI, the skins were carefully dissected under a Leica epi-fluorescence microscope to isolate cNFs and HLS regions. Small pieces (2x2 mm) of each sample type were cut and then immersed (6 pieces per well) in 2 ml of DMEM medium containing 10% FBS, 10% penicillin/streptomycin, and Liberase DH (0.25 mg/mL). The filled 6-well plate was then placed into an incubator (37°C, 5% CO2) overnight for 18 hours without agitation. The following day, to stop the action of the enzymes, 8 ml of DMEM medium containing 10% FBS were added to each well, followed by gentle mechanical dissociation with a 1 ml pipette. The tubes were then centrifuged at 300g for 10 minutes. After discarding the supernatant, the pellet was gently resuspended in 5 ml of DMEM and filtered through a 100 μm filter, followed by a 70 μm filter, and finally a 30 μm filter to remove any remaining tissue fragments or cellular debris. The cells were then centrifuged again at 300g for 10 min before being resuspended in a solution of PBS/1% BSA. To assess cell viability, we added DAPI viability dye at a concentration of 5 μg/ml. The prepared cells were then sorted using Fluorescence-Activated Cell Sorting (FACS) at the IMRB FACS facility. The sorting process was based on the cells' DAPI labeling to ensure the selection of viable cell populations.
All or Tom+ skin cells were sorted (BD InfluxTM Cell Sorter) using a DAPI nuclear labeling viability dye and the Tomato endogenous fluorescence. Cells were collected in 0.04% BSA-PBS solution. Around 25,000 cells were loaded into one channel of the Chromium system using the V3.1 single-cell reagent kit (10X Genomics) to generate single-cell GEMs. Following capture and lysis, cDNAs were synthesized, and then amplified by PCR for 12 cycles as per the manufacturer’s protocol (10X Genomics). The amplified cDNAs were used to generate Illumina sequencing libraries that were each sequenced on one flow cell Nextseq500 Illumina.

treatment_protocol: No treatment was applied prior to extract preparation.

value: cNFs from back skin

value: all skin cells

value: Prss56Cre/+, R26tdTom/+, Nf1fl/fl

tag: dissociation protocol


title: WTC11_Iso Control_S7

description: Library name: Sample 3

value: iPSC-derived human microglia-like cells


title: kidney biopsy N371

value: ABMR


title: kidney biopsy N500


title: cNFs_P365_Tom_1

description: Library name: 2023_18

value: Male

value: Tomato+ skin cells (melanocytes and Schwann cells)


title: HLS_P365_all_18h

description: Library name: 2023_11

source_name: NF1 healthy-looking back skin

value: NF1 healthy-looking back skin


title: kidney biopsy N316


title: HLS_P365_Tom_2

description: Library name: 2023_40


title: kidney biopsy N335

value: NR


title: WTC11_Iso Control_S4

description: Library name: Sample 2

value: In vitro differentiation


title: KO_24h_rep3

description:
Library name: S8
RNAseq_MAPLKO_BMDM

value: primary BMDM


title: HLS_P365_Tom_1

description: Library name: 2023_17


title: HS_P365_Tom_2

description: Library name: 2023_27

source_name: healthy back skin

value: healthy back skin

value: Prss56Cre/+, R26tdTom/+


title: HS_P365_Tom_1

description: Library name: 2023_21


title: kidney biopsy N315

value: Mixed


title: kidney biopsy N372


title: cNFs_P90_Tom_2

description: Library name: 2023_44


title: DLD1_PP24

city: shenzhen

first: Yibo

last: Hou

state: State...

address: Guangdong province

country: China

institute: TsingHua university

description: Library name: Sample 8

data_processing:
Agilent 2100 bioanalyzer
Assembly: Reference  genome and gene model annotation files were  downloaded from genome website directly. Index of the reference  genome was built using Hisat2 (v2.0.5) and paired-end clean  reads  were  aligned  to  the  reference  genome using Hisat2  (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a  database of splice junctions based on the gene model annotation file and thus  a better mapping result than other non-splice mapping tools
Supplementary files format and content: featureCounts (v1.5.0-p3) was used to count the reads numbers mapped  to each gene. And then FPKM of each gene was calculated based on the  length of the geneand reads count mapped to this gene. FPKM,  expected number of Fragments PerKilobase of transcript sequence  per Millions base pairs sequenced, considers theeffect of  sequencingdepthandgenelengthfor thereadscountat thesametime, andis  currently themost commonly usedmethod for estimating gene expression  levels.

source_name: Cell line

extract_protocol:
RNA was extracted by using Trizol
Total RNA was used as input material for the RNA sample preparations.  Briefly, mRNA was purified from total RNA by using poly-T oligo-attached  magnetic beads. Fragmentation was carried out using divalent cations under  elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand  cDNA was synthesized using random hexamer primer and M- MuLV Reverse  Transcriptase, then use RNaseH to degrade the RNA. Second strand cDNA  synthesis was subsequently performed using DNA Polymerase I and dNTP.  Remaining  overhangs  exonuclease/polymerase  were  activities.  converted  After  into  blunt  adenylation  ends  via  of 3’ ends  of DNA fragments, Adaptor with hairpin loop structure were  ligated  to  prepare  for hybridization. In  order to select cDNA  fragments of preferentially 370~420 bp in length, the library fragments  were purified with AMPure XP system (BeckmanCoulter,Beverly, USA).  Then PCR amplification, the PCR product was purified by AMPure XP beads, and  the library was finally obtained

value: Cell line

value: Colorectal cancer cell

value: WT


title: DLD1_PP10

description: Library name: Sample 7


title: cNFs_P90_Tom_1

description: Library name: 2023_34

value: cNFs from back skin


title: HS_P90_Tom_2

description: Library name: 2023_48


title: HLS_P90_Tom_2

description: Library name: 2023_46


title: HLS_P90_Tom_1

description: Library name: 2023_36


title: DLD1_CON2

description: Library name: Sample 6

value: Control


title: HLS_P365_all_2

description: Library name: 2023_39

value: all skin cells

value: Prss56Cre/+, R26tdTom/+, Nf1fl/fl


title: cNFs_P365_all_2

description: Library name: 2023_41


title: DLD1_CON1

description: Library name: Sample 5


title: HCT116_PP24

description: Library name: Sample 4


title: HLS_P365_all_1

description: Library name: 2023_10


title: WTC11_Iso Control_S1

description: Library name: Sample 1

value: iPSC-derived human microglia-like cells

value: control


title: cNFs_P365_all_1

description: Library name: 2023_09

value: Male


title: kidney biopsy N344


title: kidney biopsy N327


title: kidney biopsy N389


title: HS_P365_all_2

description: Library name: 2023_26


title: kidney biopsy N328


title: kidney biopsy N370

value: pABMR


title: HCT116_PP10

description: Library name: Sample 3


title: cNFs_P90_all_2

description: Library name: 2023_43


title: HCT116_CON2

description: Library name: Sample 2


title: cNFs_P90_all_1

description: Library name: 2023_33


title: SW1990, rep2

city: shanghai

first: shengnan

last: luo

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: SW1990-2

data_processing:
Sequence reads were trimmed for adaptor sequence sequence using porechop
Trimmed sequence reads were mapped to GRCh38 using minimap2
Transcript extraction and normalization were performed using FLAIR
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample
Supplementary files format and content: all_samples_collapsed.isoforms: transcripts collapsed with FLAIR v2.0.0., representing the non-redundant isoform set across all 20 samples.

source_name: Pancreatic cancer cell

extract_protocol:
Total RNA was extracted from the samples using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England BioLabs), following the manufacturer's protocol to selectively enrich for poly(A) RNA.
For long-read RNA sequencing, cDNA synthesis was performed using the strand-switching protocol provided by Oxford Nanopore Technologies (ONT). In this protocol, the first-strand synthesis incorporates a unique sequence at the 3' end of the cDNA to enable strand-specific information. Full-length cDNA libraries were then prepared from the poly(A)-selected mRNA using the ONT cDNA-PCR Sequencing Kit (SQK-PCS109). The cDNA was amplified through PCR for 13-14 cycles, using specific barcoded adapters from the Oxford Nanopore PCR Barcoding Kit (SQKPBK004) to facilitate sample multiplexing. After PCR amplification, a 1D sequencing adapter was ligated to the cDNA to prepare the samples for sequencing.

value: Pancreatic cancer cell

value: epithelial cell


title: kidney biopsy N313

value: ABMR


title: HCT116_CON1

description: Library name: Sample 1


title: BMH-21 exp3

city: Rome

first: Marco

last: Cippitelli

state: Italy

address: Viale Regina Elena, 291

department: Molecular Medicine

country: Italy

institute: Univ. of Rome - Sapienza

description: Library name: sample9

data_processing:
Post-sequencing Quality Control was performed by FastQC v.0.12.1.
Adapter sequences were trimmed, and low-quality reads were removed using Trimmomatic v.039.
Mapping of RNA and generation of gene counts was done using HISAT2 aligner v.2.2.1 against human reference (GRCh38 build hg38) and FeatureCounts 2.0.8 using locally cached gene annotation. Differential Expression Analysis (DEGs) was performed by DESeq2 v.2.11.40.8.
Mapping of RNA and generation of TPMs were calculated using Salmon quant v.1.10.1 (GRCh38.cdna.all.release_2024).
Assembly: GRCh38
Supplementary files format and content: TPMs.txt (Matrix)

extract_protocol:
Total RNA was extracted using “Total RNA Mini kit” (Geneaid Biotech, New Taipei City, Taiwan), using Ambion™ DNase I (RNase-free), according to manufacturer’s instructions. The concentration and quality of the extracted total RNA were determined by measuring light absorbance at 260 nm (A260) and the ratio of A260/A280 (Qbit System - ThermoFisher).
Sequencing libraries were generated using Nextflex Rapid Directional RNA-Seq kit 2.0 Kit with Poly(A) Beads 2.0 (PerkinElmer). Libraries were sequenced on Illumina NovaSeq with 2x150 bp paired-end run. Average seq throughput for the project ≥ 30M PE read per sample; Q30 ≥ 85%.

treatment_protocol: Cells were treated with RNA Pol I inhibitors for 24h.

value: Human MM cells

value: wt


title: SW1990, rep1

description: Library name: SW1990-1


title: HLS_P90_all_2

description: Library name: 2023_45

value: NF1 healthy-looking back skin


title: HLS_P90_all_1

description: Library name: 2023_35


title: HS_P90_Tom_1

description: Library name: 2023_32

value: healthy back skin

value: Tomato+ skin cells (melanocytes and Schwann cells)

value: Prss56Cre/+, R26tdTom/+


title: PANC1005, rep2

description: Library name: PANC1005-2


title: BMH-21 exp2

description: Library name: sample8


title: kidney biopsy N312


title: HS_P365_all_1

description: Library name: 2023_20


title: PANC1005, rep1

description: Library name: PANC1005-1


title: HS_P90_all_1

description: Library name: 2023_31


title: BMH-21 exp1

description: Library name: sample7


title: Panc0327, rep2

description: Library name: Panc0327-2


title: kidney biopsy N311


title: Serum Deprivation - Nprl3 KO - 6

city: Melbourne

last: Herold

state: VIC

address: 145 Studley Rd

department: School of Cancer Medicine, La Trobe University

country: Australia

institute: Olivia Newton-John Cancer Research Institute

description:
Library name: Nprl3-270_S19_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

data_processing:
FastQ files were trimmed using Cutadapt (v1.16) and mapped to the mouse reference genome (mm10 GRCm38) using HISAT2 (v2.1.0). Samtools (v1.4.1) was used to convert SAM files to BAM format and to sort BAM files. Counts were generated using featureCounts (v1.6.0). Filtering and normalization of data were carried out using edgeR (v3.16) and differential gene expression analysis was carried out using limma-voom (v3.4.6) . Heatmaps were generated using pheatmap (v1.0.12).
Assembly: mm10
Supplementary files format and content: Tab-separated file containing raw RNA-seq counts for all samples together with Entrez Geneid.

source_name: 270 Nprl3 knockout  Cas9  EM  Myc lymphoma cell line

growth_protocol: Lymphoma cell lines were cultured in FMA medium containing full serum (10% FCS) or under starvation conditions (FMA medium containing only 1% FCS) for 24 h prior to harvesting.

extract_protocol:
RNA was isolated from Eµ-Myc lymphoma cells using a NucleoSpin RNA kit (Macherey-Nagel) following the manufacturer’s instructions.
The 3’ libraries were sequenced with an Illumina NextSeq 500, with single-end 75 bp reads to a depth of 15 M reads per sample.

value: Nprl3 KO, serum deprivation (1% FCS, 24 h)


title: Panc0327, rep1

description: Library name: Panc0327-1


title: kidney biopsy N499


title: CX-5461 exp2

description: Library name: sample5


title: kidney biopsy N314


title: CX-5461 exp3

description: Library name: sample6


title: Serum Deprivation - Nprl3 KO - 5

description:
Library name: Nprl3-268_S18_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 268 Nprl3 knockout  Cas9  EM  Myc lymphoma cell line


title: kidney biopsy N498

value: NR


title: kidney biopsy N492


title: kidney biopsy N369


title: HS_P90_all_2

description: Library name: 2023_47

value: all skin cells


title: CX-5461 exp1

description: Library name: sample4


title: DMSO exp3

description: Library name: sample3

value: DMSO


title: Serum Deprivation - Nprl3 KO - 4

description:
Library name: Nprl3-267_S17_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 267 Nprl3 knockout  Cas9  EM  Myc lymphoma cell line


title: PANC0203, rep1

description: Library name: PANC0203-1


title: Serum Deprivation - Nprl3 KO - 3

description:
Library name: Nprl3-265_S16_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 265 Nprl3 knockout  Cas9  EM  Myc lymphoma cell line


title: Mia-Paca-2, rep2

description: Library name: Mia-Paca-2-2


title: DMSO exp2

description: Library name: sample2


title: Mia-Paca-2, rep1

description: Library name: Mia-Paca-2-1


title: DMSO exp1

description: Library name: sample1


title: Serum Deprivation - Nprl3 KO - 1

description:
Library name: Nprl3-262_S14_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 262 Nprl3 knockout  Cas9  EM  Myc lymphoma cell line


title: HuP-T4, rep2

description: Library name: HuP-T4-2


title: Serum Deprivation - Nprl3 KO - 2

description:
Library name: Nprl3-263_S15_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 263 Nprl3 knockout  Cas9  EM  Myc lymphoma cell line


title: Oo-85_THC2_MII

city: Toronto

first: Brandon

last: Wyse

state: ON

address: 790 Bay St

institute: CReATe Fertility Centre

description: Library name: Oo-85_THC2_MII

data_processing:
Raw sequencing reads were trimmed based on read quality (Phred > 28) and aligned and quantified to hg38 using STAR (Spliced Transcripts Alignment to a Reference; v2.7.8a). Low abundant transcripts were excluded (maximum <20) and normalized using the default normalization method built into DESeq2 (v3.5). We conducted differential expression (DE) using DESeq2 comparing THC1 vs. Ctrl and THC2 vs. Ctrl. Significantly differentially expressed genes were defined as p-value < 0.05 and |log2fold change (FC)| of >1. The complete list of DE genes is available in the Supplementary data 4 (THC1 vs Ctrl) and the Supplementary data 4 (THC2 vs Ctrl)). This analysis was conducted in Partek Flow (version 11.0.23.1004). Gene Set Enrichment Analysis (GSEA)104,105 was conducted to determine what gene sets were impacted by exposure to THC.
Assembly: hg38
Supplementary files format and content: noramlized read counts with features on rows

source_name: Oocyte

growth_protocol: GV oocytes were cultured for 24h using standard clinical IVM media (SAGE One-step (CooperSurgical, Canada) + 7.5 IU/mL of Menopur (Ferring, Canada)

extract_protocol:
Cells were directly lysed and cDNA conversion done using SmartSeq-v4 (Takara)
cDNA from single oocytes were synthesized using the SMART-seq v4 Ultra Low Input RNA Kit (Takara Bio Inc., Japan). The amplified cDNA was purified using Agencourt AMPure XP beads (Beckman Coulter, USA) and eluted. The purified cDNA was quantified using the Qubit dsDNA high sensitivity assay (ThermoFisher, Canada) and length and molarity were assessed using the DNF-474 HS NGS Fragment Kit (1-6000 bp) with the Fragment Analyzer 5200 (Agilent Technologies, USA).  The amplified cDNA (0.2 ng) was used to construct sequencing libraries using a modified and miniaturized Nextera XT library preparation protocol (Illumina, Canada) developed for the use with the Mosquito HV liquid handling robot (SPT labtech, Boston, USA). The quality of the libraries was assessed using the same Fragment Analyzer kit DNF-474 HS NGS Fragment Kit (1-6000 bp), quantified using Qubit dsDNA high sensitivity assay (ThermoFisher), normalized and pooled. Sequencing was performed on a NovaSeq 6000 S2 flow cell (Illumina, Canada) at Princess Margaret Genomics Centre (2 x 150 bp) (Toronto, Canada).

treatment_protocol: Ctrl (only IVM media), THC1 (23: 25 ng/mL Δ9-THC (Sigma-Aldrich, Canada), 5 ng/mL 11-OH-THC (Sigma-Aldrich, Canada), 50 ng/mL 11-COOH-THC (Sigma-Aldrich, Canada)) and THC2 (100 ng/mL Δ9-THC, 50 ng/mL 11-OH-THC, 200 ng/mL 11-COOH-THC).

value: Oocyte

tag: binomial treatment

value: Treated

tag: final stage

value: MII

tag: participant number

tag: age (years)

tag: bmi (kg/m2)

tag: amh (pmol/l)

tag: lh (iu)

tag: fsh (iu)

tag: e2 (pmol/l)

tag: total gt_(iu)


title: Serum Deprivation - Control - 6

description:
Library name: hBim-82_S9_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 82 Control Cas9  EM  Myc lymphoma cell line

value: Control KO, serum deprivation (1% FCS, 24 h)


title: Oo-84_THC1_MII

description: Library name: Oo-84_THC1_MII

tag: cell type

tag: treatment


title: Serum Deprivation - Control - 5

description:
Library name: hBim-384_S13_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 384 Control Cas9  EM  Myc lymphoma cell line

tag: genotype


title: Capan-2, rep2

description: Library name: Capan-2-2

tag: cell line

value: Pancreatic cancer cell


title: Oo-82_Ctrl_MII

description: Library name: Oo-82_Ctrl_MII

value: Ctrl

value: Untreated

tag: batch


title: Serum Deprivation - Control - 4

description:
Library name: hBim-383_S12_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 383 Control Cas9  EM  Myc lymphoma cell line


title: Capan-2, rep1

description: Library name: Capan-2-1

value: epithelial cell


title: Oo-67_THC2_MII

description: Library name: Oo-67_THC2_MII


title: Capan-1, rep2

description: Library name: Capan-1-2


title: Oo-65_THC2_MII

description: Library name: Oo-65_THC2_MII


title: Serum Deprivation - Control - 3

description:
Library name: hBim-2_S8_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 2 Control Cas9  EM  Myc lymphoma cell line


title: Serum Deprivation - Control - 2

description:
Library name: hBim-282_S11_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 282 Control Cas9  EM  Myc lymphoma cell line


title: Capan-1, rep1

description: Library name: Capan-1-1


title: Oo-60_Ctrl_MII

description: Library name: Oo-60_Ctrl_MII


title: BXPC3, rep2

description: Library name: BXPC3-2


title: HuP-T4, rep1

description: Library name: HuP-T4-1


title: Serum Deprivation - Depdc5 KO - 6

description:
Library name: Depdc5-396_S25_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 396 Depdc5 knockout  Cas9  EM  Myc lymphoma cell line

value: Depdc5 KO, serum deprivation (1% FCS, 24 h)


title: Oo-57_THC2_MII

description: Library name: Oo-57_THC2_MII


title: BXPC3, rep1

description: Library name: BXPC3-1


title: Serum Deprivation - Depdc5 KO - 5

description:
Library name: Depdc5-394_S24_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 394 Depdc5 knockout  Cas9  EM  Myc lymphoma cell line


title: APSC-1, rep2

description: Library name: APSC-1-2


title: Oo-56_THC2_MII

description: Library name: Oo-56_THC2_MII


title: Serum Deprivation - Control - 1

description:
Library name: hBim-132_S10_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 132 Control Cas9  EM  Myc lymphoma cell line


title: Serum Deprivation - Depdc5 KO - 4

description:
Library name: Depdc5-392_S23_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 392 Depdc5 knockout  Cas9  EM  Myc lymphoma cell line


title: APSC-1, rep1

description: Library name: APSC-1-1

source_name: Pancreatic cancer cell


title: Oo-54_THC1_MII

description: Library name: Oo-54_THC1_MII


title: Serum Deprivation - Depdc5 KO - 3

description:
Library name: Depdc5-389_S22_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 389 Depdc5 knockout  Cas9  EM  Myc lymphoma cell line


title: miR-seq of 100K-EVs isolated from BV-2 cells traited with WT-GAGs - rep 3

city: Toulouse

first: Chloe

last: Dias

address: CHU Purpan

institute: Infinity

description: Library name: 100K-WT-3_S12

library_source: other

data_processing:
Three independent replicates were analyzed using QIAGEN RNA-seq Analysis Portal 4.1 (QIAGEN, Aarhus, Denmark) and the analysis workflow (v1.2) and using the Legacy Analysis Pipeline on the QIAGEN GeneGlobe portal. The sequences were aligned against the reference miRBase_v22 and the Mus musculus genome (GRCm38.101). Gene expression–level differences were accepted as statistically significant when the p-value in an ANOVA was < 0.05 and when the fold change was between 1 and − 1 after an intergroup comparison.
Assembly: miRBase_v22 and Mus musculus genome (GRCm38.101)
Supplementary files format and content: Raw counts and CPM for each samples in .txt format (tabulation separation)

molecule: other

source_name: Brain

extract_protocol:
Total RNAs from EV preparations and 0.5 × 106 cells were extracted using the miRNeasy Tissue/Cells Advanced Micro Kit (QIAGEN), according to the manufacturer’s instructions. The purified RNAs were eluted into 20 μl nuclease-free water, and stored at − 80 °C until analysis. RNA was quantified using the Qubit RNA HS Assay Kit on the Qubit Fluorometer (Invitrogen). The quality was evaluated on an Agilent 4150 TapeStation with the High Sensibility RNA ScreenTape kit (Agilent).
Each sample’s libraries were built with the QIAseq miRNA UDI Library Kit (QIAGEN), according to the manufacturer’s instructions and quantified using the Qubit 1X dsDNA HS kit on the Qubit Fluorometer (Invitrogen). All libraries were sequenced using a single-read strategy (10 million reads per sample) on an NextSeq550 platform, with 150 cycles of the MidOutput flowcell (Illumina), a read length of 72 bp, and dual indices of 10 bp. Raw data were converted to FASTQ files using bcl2fastq (v2.20).

tag: tissue

value: Brain

value: Microglia

value: WT-GAGs


title: Oo-51_Ctrl_MII

description: Library name: Oo-51_Ctrl_MII


title: Serum Deprivation - Depdc5 KO - 2

description:
Library name: Depdc5-388_S21_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 388 Depdc5 knockout  Cas9  EM  Myc lymphoma cell line


title: miR-seq of 100K-EVs isolated from BV-2 cells traited with MPS-GAGs - rep 3

description: Library name: 100K-MPS-3_S11

value: MPS-GAGs


title: Oo-50_Ctrl_MII

description: Library name: Oo-50_Ctrl_MII


title: Serum Deprivation - Depdc5 KO - 1

description:
Library name: Depdc5-386_S20_R1_001.fastq.gz
Serum Deprivation (1% FCS), 24 hours

source_name: 386 Depdc5 knockout  Cas9  EM  Myc lymphoma cell line


title: miR-seq of 12K-EVs isolated from BV-2 cells traited with WT-GAGs - rep 3

description: Library name: 12K-WT-3_S10


title: Oo-61_Ctrl_MII

description: Library name: Oo-61_Ctrl_MII


title: Oo-49_Ctrl_MII

description: Library name: Oo-49_Ctrl_MII


title: Full Serum - Nprl3 KO - 6

description:
Library name: Nprl3-270_S92_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 270 Nprl3 knockout  Cas9  EM  Myc lymphoma cell line

value: Nprl3 KO, full serum (10%)


title: miR-seq of 12K-EVs isolated from BV-2 cells traited with MPS-GAGs - rep 3

description: Library name: 12K-MPS-3_S9


title: Oo-39_THC2_MII

description: Library name: Oo-39_THC2_MII


title: Full Serum - Nprl3 KO - 5

description:
Library name: Nprl3-268_S91_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 268 Nprl3 knockout  Cas9  EM  Myc lymphoma cell line


title: Oo-9_THC1_MII

description: Library name: Oo-9_THC1_MII

source_name: Oocyte


title: miR-seq of 100K-EVs isolated from BV-2 cells traited with WT-GAGs - rep 2

description: Library name: 100K-WT-2_S8


title: Full Serum - Nprl3 KO - 3

description:
Library name: Nprl3-265_S89_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 265 Nprl3 knockout  Cas9  EM  Myc lymphoma cell line


title: Full Serum - Nprl3 KO - 4

description:
Library name: Nprl3-267_S90_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 267 Nprl3 knockout  Cas9  EM  Myc lymphoma cell line


title: miR-seq of 100K-EVs isolated from BV-2 cells traited with MPS-GAGs - rep 2

description: Library name: 100K-MPS-2_S7


title: miR-seq of 12K-EVs isolated from BV-2 cells traited with WT-GAGs - rep 2

description: Library name: 12K-WT-2_S6


title: Oo-377_THC1_MII

description: Library name: Oo-377_THC1_MII


title: Oo-378_THC2_MII

description: Library name: Oo-378_THC2_MII


title: Full Serum - Nprl3 KO - 2

description:
Library name: Nprl3-263_S88_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 263 Nprl3 knockout  Cas9  EM  Myc lymphoma cell line


title: Full Serum - Nprl3 KO - 1

description:
Library name: Nprl3-262_S87_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 262 Nprl3 knockout  Cas9  EM  Myc lymphoma cell line


title: Oo-373_CTRL_MII

description: Library name: Oo-373_CTRL_MII


title: miR-seq of 100K-EVs isolated from BV-2 cells traited with WT-GAGs - rep 1

description: Library name: 100K-WT-1_S4


title: PANC0203, rep2

description: Library name: PANC0203-2


title: Oo-374_CTRL_MII

description: Library name: Oo-374_CTRL_MII


title: miR-seq of 12K-EVs isolated from BV-2 cells traited with MPS-GAGs - rep 2

description: Library name: 12K-MPS-2_S5


title: Oo-372_CTRL_MII

description: Library name: Oo-372_CTRL_MII


title: miR-seq of 100K-EVs isolated from BV-2 cells traited with MPS-GAGs - rep 1

description: Library name: 100K-MPS-1_S3


title: Full Serum - Control - 4

description:
Library name: hBim-384_S86_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 384 Control Cas9  EM  Myc lymphoma cell line

value: Control, full serum (10% FCS)


title: Full Serum - Control - 5

description:
Library name: hBim-82_S82_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 82 Control Cas9  EM  Myc lymphoma cell line


title: Oo-371_THC2_MII

description: Library name: Oo-371_THC2_MII


title: miR-seq of 12K-EVs isolated from BV-2 cells traited with WT-GAGs - rep 1

description: Library name: 12K-WT-1_S2


title: Full Serum - Control - 3

description:
Library name: hBim-383_S85_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 383 Control Cas9  EM  Myc lymphoma cell line


title: Oo-370_THC1_MII

description: Library name: Oo-370_THC1_MII


title: Full Serum - Control - 2

description:
Library name: hBim-282_S84_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 282 Control Cas9  EM  Myc lymphoma cell line


title: miR-seq of 12K-EVs isolated from BV-2 cells traited with MPS-GAGs - rep 1

description: Library name: 12K-MPS-1_S1


title: kidney biopsy N340

source_name: kidney biopsy

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)

value: NR


title: kidney biopsy N480


title: Oo-369_CTRL_MII

description: Library name: Oo-369_CTRL_MII

tag: binomial treatment


title: kidney biopsy N476


title: kidney biopsy N397

value: TCMR


title: kidney biopsy N310


title: Full Serum - Control - 1

description:
Library name: hBim-132_S83_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 132 Control Cas9  EM  Myc lymphoma cell line


title: Oo-359_THC2_MII

description: Library name: Oo-359_THC2_MII

value: Oocyte

tag: final stage


title: Full Serum - Depdc5 KO - 6

description:
Library name: Depdc5-396_S98_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 396 Depdc5 knockout  Cas9  EM  Myc lymphoma cell line

value: Depdc5 KO, full serum (10% FCS)


title: kidney biopsy N309

value: ABMR


title: kidney biopsy N359


title: kidney biopsy N483


title: kidney biopsy N353

value: pTCMR


title: kidney biopsy N482


title: kidney biopsy N351


title: kidney biopsy N388


title: kidney biopsy N396

value: Mixed


title: kidney biopsy N481


title: kidney biopsy N387


title: Oo-357_THC2_MII

description: Library name: Oo-357_THC2_MII

value: Treated

value: MII

tag: participant number


title: kidney biopsy N469


title: kidney biopsy N463

value: pABMR


title: kidney biopsy N478


title: kidney biopsy N326


title: kidney biopsy N334


title: kidney biopsy N402


title: Full Serum - Depdc5 KO - 5

description:
Library name: Depdc5-394_S97_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 394 Depdc5 knockout  Cas9  EM  Myc lymphoma cell line


title: kidney biopsy N350


title: kidney biopsy N475


title: kidney biopsy N368


title: kidney biopsy N479


title: kidney biopsy N472


title: Oo-354_THC1_MII

description: Library name: Oo-354_THC1_MII

tag: age (years)


title: kidney biopsy N462


title: kidney biopsy N352


title: Oo-351_CTRL_MII

description: Library name: Oo-351_CTRL_MII

value: Ctrl

value: Untreated

tag: bmi (kg/m2)


title: kidney biopsy N307


title: Oo-326_THC1_MII

description: Library name: Oo-326_THC1_MII


title: JHGBM651 shYAP Biological Replicate 3

city: Jackonsville

first: Alfredo

last: Quinones-Hinojosa

state: FL

address: 4500 San Pablo Rd

institute: Mayo Clinic

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Raw data files were processed in aroma.affymetrix (http://statistics.berkeley.edu/sites/default/files/tech-reports/745.pdf)  Differential expression analysis was performed using the sam function of the siggenes package (version 1.28.0) in R.

source_name: JHGBM651 shYAP 3

label_protocol: Microarray experiment performed at: The Single Cell & Transcriptomics Core, Johns Hopkins School of Medicine, Baltimore, MD, USA.

growth_protocol: Cells were cultured in DMEM/F12 was supplemented with B27 supplement, antibiotic/antimycotic, human EGF, and FGF and cultured on laminin-coated (1μg/cm2) plates.

extract_protocol: RNeasy

treatment_protocol: Cells were transduced with equal titers of concentrated virus in complete growth media supplemented with 1 μg/ml polybrene for 24 hours. Following transduction, cells were given 24 hours to recover before selection in 0.25 μg/ml (JHGBM651) or 0.5 μg/ml (JHGBM612) puromycin for a minimum of 6 days before RNA extraction.

value: Patient-derived primary GBM cells


title: Oo-352_CTRL_MII

description: Library name: Oo-352_CTRL_MII

tag: amh (pmol/l)


title: Full Serum - Depdc5 KO - 2

description:
Library name: Depdc5-388_S94_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 388 Depdc5 knockout  Cas9  EM  Myc lymphoma cell line


title: kidney biopsy N308


title: JHGBM651 shYAP Biological Replicate 1

source_name: JHGBM651 shYAP 1


title: Full Serum - Depdc5 KO - 1

description:
Library name: Depdc5-386_S93_R1_001.fastq.gz
Full Serum (10% fetal calf serum; FCS)

source_name: 386 Depdc5 knockout  Cas9  EM  Myc lymphoma cell line


title: JHGBM651 shYAP Biological Replicate 2

source_name: JHGBM651 shYAP 2


title: Oo-324_CTRL_MII

description: Library name: Oo-324_CTRL_MII

source_name: Oocyte


title: Oo-323_THC2_MII

description: Library name: Oo-323_THC2_MII

tag: lh (iu)


title: PLACseq_Scid.ahd.2C2, H3K4me3, rep2

city: Linköping

first: Mikael

last: Sigvardsson

address: Lab1, Level 13

department: Department of Biomedical and Clinical Sciences

country: Sweden

institute: Linköping University

library_source: genomic

data_processing:
FASTQ files from two replicates were merged and trimmed with Trim Galore (v0.6.7) using the following options: (--paired --fastqc --clip_R1 10 --clip_R2 10 --three_prime_clip_R1 3 --three_prime_clip_R2 3. Trimmed reads were processed through the HiC-Pro pipeline (v2.11.4) (Servant et al. 2015) for the generation of valid interaction pairs. The HiC-pro processing included alignment to the mm10 reference genome (GRCm38) using Bowtie2 (v2.4.2) (Langmead et al. 2009; Langmead and Salzberg 2012) and the assignment of mapped reads to an mm10 MboI restriction map. interaction calling was performed with FitHiChIP (v9.1) (Bhattacharyya et al. 2019) using the merged validParirs output from the HiC-Pro pipeline with the following parameters: IntType=3, BINSIZE=5000, LowDistThr=10000, UppDistThr=3000000, UseP2PBackgrnd=0, BiasType=1, MergeInt=1, QVALUE=0.05. H3K4me3 ChIPseq peaks (this study) was provided as PeakFile references.  Merged close PEAK-to-ALL/ALL-to-ALL interactions, passing the significance threshold (q<0.05) were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: Valid pairs from HiC-Pro: H3K4me3_PLAC_P2C2_trimmed.allValidPairs.txt.gz
Supplementary files format and content: 2D-bed file with interaction anchor points (PEAK2ALL): P2C2_H3K4me3_FitHiChIP.interactions_FitHiC_Q0.05_MergeNearContacts.bed
Supplementary files format and content: 2D-bed file with interaction anchor points (ALL2ALL): P2C2_H3K4me3_FitHiChIP_ALL2ALL.interactions_FitHiC_Q0.05_MergeNearContacts.bed
Supplementary files format and content: Longrange file for genome browser visualization: P2C2_H3K4me3_FitHiChIP.interactions_FitHiC_Q0.05_MergeNearContacts_WashU.bed.gz, P2C2_H3K4me3_FitHiChIP.interactions_FitHiC_Q0.05_MergeNearContacts_WashU.bed.gz.tbi
Library strategy: PLAC-seq

molecule: genomic DNA

growth_protocol: Scid.adh.2C2 cells were cultured in RPMI1640 with 10% fetal bovine serum, sodium pyruvate, non-essential amino acids, gentamicine and 50 μM β-mercaptoethanol.

extract_protocol:
PLAC-seq was carried out similar to previously reported (Okuyama et al, 2019) with minor modifications. Cells that had been cross-linked with 1% formaldehyde for 5 min (Covaris sonication) or 10 min (Bioruptor sonication) were thawed on ice for 5 min, re-suspended in ice cold lysis buffer (10 mM Tris-HCl pH 7.5, 10 mM NaCl, 0.2% NP-40, 1x Roche protease inhibitors – 11697498001 (PIC), and subsequently processed for PLAC-seq.
PLAC-seq was carried out similar to previously reported (Okuyama et al, 2019) with minor modifications. NEXTflex DNA barcode ligation (BIOO scientific) was performed using the Fast-link ligation kit (Epicenter, LK0750H). PLAC-seq libraries were subject to 2X38 cycles of paired-end sequencing on a NextSeq500.

value: T-cell progenitor

tag: cell line_background

value: Pro-T tumor derived cell line from CB17-Prkdc<scid> mice

tag: chip antibody

value: H3K4me3 (Millipore, #07-473)


title: PLACseq_Scid.ahd.2C2, H3K4me3, rep1


title: Full Serum - Depdc5 KO - 3

description:
Library name: Depdc5-389_S95_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 389 Depdc5 knockout  Cas9  EM  Myc lymphoma cell line


title: Full Serum - Depdc5 KO - 4

description:
Library name: Depdc5-392_S96_R1_001.fastq.gz
Full Serum (10% FCS)

source_name: 392 Depdc5 knockout  Cas9  EM  Myc lymphoma cell line


title: 230-238, H3K4me3, input

data_processing:
Reads were trimmed with Trim Galore (v.0.6.7) using the following options: -fastqc --clip_R1 5 --three_prime_clip_R1 3. Trimmed reads were mapped to the mm10 reference genome (GRCm38) using Bowtie (v.2.4.4). Bigwig files for genome browser visualization were generated with bamCoverage (--normalizeUsing RPGC --centerReads) from deepTools (v1.9). Peak calling was performed with a custom pipeline (https://github.com/Tingvall/macs2_idr), which included peak calling with MACS2 (v2.2.7.1) followed by IDR (v.2.0.4.2). The pipeline was run in narrow mode and the following options were used: --macs_q 0.05 --idr_threshold 0.05. The IDR optional peak set was used for the downstream analysis.
Assembly: mm10
Supplementary files format and content: IDR peaks: H3K4me3_P2C2_optimal_set.IDR0.05.narrowPeak.gz, H3K4me3_239238_optimal_set.IDR0.05.narrowPeak.gz
Supplementary files format and content: Bigwig of pooled replicates: H3K4me3_P2C2_pooled.bw, H3K4me3_230238_pooled.bw

growth_protocol: Scid.adh.2C2 cells were cultured in RPMI1640 with 10% fetal bovine serum, sodium pyruvate, non-essential amino acids, gentamicine and 50 μM β-mercaptoethanol. 230-238 cells were maintained in RPMI1640 supplimented with 10% heat-inactivated fetal calf serum, 25mM HEPES, 50μg/ml Gentamicin, and 50μM β-mercaptoethanol

extract_protocol:
Cells for histone modification ChIP were fixed in 1% formaldehyde for 10 min at RT. The reactions were quenched by addition of 1/10 volume of 0.125M glycine and the cells were washed in PBS. Nuclei were isolated by 10 min incubation in Nuclei Isolation buffer (50 mM Tris-pH 8.0, 60 mM KCl, 0.5% NP40) + protease inhibitor cocktail (PIC) (Roche) on ice. Pelleted nuclei were dissolved in Lysis buffer (0.5% SDS, 10 mM EDTA, 0.5 mM EGTA, 50 mM Tris-HCl (pH 8)) + PIC and sonicated on a Bioruptor (Diagenode). Sonication was followed by pelleting of debris and the supernatant was transferred to new tube and chromatin was diluted in HBSS (Lonza, Verviersa, Belgium) +PIC and 2X RIPA buffer (20 mM Tris–HCl, pH 7.5, 2 mM EDTA, 2% Triton X-100, 0.1% SDS, 0.2% Sodiumdeoxycholate, 200 mM NaCl + PIC). 1% of samples was used for input.
Libraries were constructed using Illumina Truseq Nano DNA library preparation kit or by addition of Bioo-scientiffic Nextflex barcodes following standard procedures.

value: B-cell progenitor

value: Abelson transformed Progenitor B cell-line


title: Oo-321_THC2_MII

description: Library name: Oo-321_THC2_MII

tag: fsh (iu)

tag: e2 (pmol/l)

tag: total gt_(iu)


title: kidney biopsy N461

value: NR


title: 230-238, H3K4me3, rep2

tag: cell type


title: Oo-317_THC1_MII

description: Library name: Oo-317_THC1_MII

value: Oocyte

tag: treatment


title: kidney biopsy N333


title: kidney biopsy N458


title: kidney biopsy N386


title: kidney biopsy N357


title: 230-238, H3K4me3, rep1

tag: cell line


title: Scid.ahd.2C2, H3K4me3, input


title: JHGBM651 shCtrl Biological Replicate 2

source_name: JHGBM651 shCtrl 2


title: kidney biopsy N367


title: Oo-316_THC1_MII

description: Library name: Oo-316_THC1_MII

tag: batch


title: Oo-322_THC2_MII

description: Library name: Oo-322_THC2_MII


title: JHGBM612 shYAP Biological Replicate 2

source_name: JHGBM612 shYAP 2


title: JHGBM651 shCtrl Biological Replicate 3

source_name: JHGBM651 shCtrl 3


title: JHGBM612 shYAP Biological Replicate 3

source_name: JHGBM612 shYAP 3


title: Control lung paracancer tissue [ANT Sup for anti-m5C]

city: Nanning

first: Aruo

address: No.22 Shuangyong Road, Qingxiu District

institute: Guangxi Medical University

hyb_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed. The cRNA mixture was fragmented by adding 5 μL 10 Blocking Agent and 1 μL of 25 Fragmentation Buffer, heated at 60°C for 30 min, and combined with 25 μL 2 Hybridization buffer. 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m5C-circRNA Epitranscriptomic Microarray slide. The slides were incubated at 65°C for 17 hours in an Agilent Hybridization Oven.

scan_protocol: Scanned on Agilent Scanner G2505C.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

source_name: lung cancer  para-tissue

label_protocol: The “IP” RNAs and “Sup” RNAs digested with RNase R (Epicentre, Inc.) to remove linear RNAs and enrich circular RNAs. The enriched “IP” RNAs and “Sup” RNAs were then added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labeling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit.

extract_protocol: Total RNA extracted using Trizol following manufacturer's instructions.3-5 μg total RNA and m5C spike-in control mixture were added to 300 μL 1IP buffer (50mM Tris-HCl, pH7.4, 150mM NaCl, 0.1% NP40, 40U/μL RNase Inhibitor) containing 2 μg anti-m5C mouse monoclonal antibody (Diagenode). The reaction was incubated with head-over-tail rotation at 4°C for 2 hours. 20 uL Dynabeads™ M-280 Sheep Anti-Mouse IgG suspension per sample was blocked with freshly prepared 0.5% BSA at 4°C for 2 hours, washed three times with 300 μL 1IP buffer, and resuspended in the total RNA-antibody mixture prepared above. The RNA binding to the m5C-antibody beads was carried out with head-over-tail rotation at 4°C for 2 hours. The beads were then washed three times with 500 μL 1IP buffer and twice with 500 μL Wash buffer (50 mM Tris-HCl, pH7.4, 50 mM NaCl, 0.1% NP40, 40 U/μL RNase Inhibitor). The enriched RNA was eluted with 200 μL Elution buffer (10 mM Tris-HCl, pH7.4, 1 mM EDTA, 0.05% SDS, 40U Proteinase K, 1 μL RNase inhibitor) at 50°C for 1 hour. The RNA was extracted by acid phenol-chloroform and ethanol precipitated.

tag: tissue

value: lung cancer  para-tissue

tag: molecule subtype

value: circRNA


title: kidney biopsy N454

source_name: kidney biopsy

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)


title: JHGBM612 shYAP Biological Replicate 1

source_name: JHGBM612 shYAP 1


title: kidney biopsy N325


title: Scid.ahd.2C2, H3K4me3, rep2


title: Oo-314_CTRL_MII

description: Library name: Oo-314_CTRL_MII

tag: binomial treatment

tag: final stage

tag: participant number


title: JHGBM651 shCtrl Biological Replicate 1

source_name: JHGBM651 shCtrl 1


title: Scid.ahd.2C2, H3K4me3, rep1


title: Lung cancer tissue [LCA Sup for anti-m5C]

source_name: lung cancer tissue

value: lung cancer tissue


title: Oo-315_CTRL_MII

description: Library name: Oo-315_CTRL_MII

tag: age (years)


title: JHGBM612 shCtrl Biological Replicate 2

source_name: JHGBM612 shCtrl 2


title: JHGBM612 shCtrl Biological Replicate 1

source_name: JHGBM612 shCtrl 1


title: kidney biopsy N343

value: ABMR


title: RNA, lG1, rep2

city: Lausanne

first: David

middle: Michael

last: Suter

address: Station 19

department: SV-IBI

country: Switzerland

institute: EPFL

data_processing:
Sequencing libraries were aligned to the Mus musculus mm10 genome (GRCm38 release M25) using STAR 2.7.0e (Dobin et al., 2013). Duplicated reads were removed with Picard (Broad Institute), and indexed using SAMTools 1.10 (Li et al., 2009). RNA-seq samples were scaled to the same number of reads in each file using SAMTools. For replicates, bam files were merged using SAMTools, and BigWig files were computed using the deepTools 3.5.1 (Ramírez et al., 2016) function bamCoverage with the setting “--normalizeUsing RPKM”.
Assembly: mm10
Supplementary files format and content: bigWig file includes RPKM normalized reads

growth_protocol: Cdt-MD cells were cultured in neurobasal Medium and DMEM/F-12, supplemented with B-27, N-2, 2 mM L-glutamine, 1% penicillin and streptomycin, 100µM 2-mercaptoethanol, 3 µM CHIR99021, 1 µM PD184352, and leukemia inhibitory factor. All cell lines were cultured on 0.1% gelatin-coated Petri dishes at 37°C and 5% CO2.

extract_protocol:
50'000 nuclei were isolated following the low cell input nuclei isolation protocol of the 10x protocol for cell lines and PBMCs. Briefly, cells were resuspended in 500 µl lysis buffer composed of 10 mM Tris pH 7.4, 10 mM NaCl, 3 mM MgCl2, 1% BSA, 0.1% Tween, 1 mM DTT, 0.5U/µl Rnase inhibitor, 0.1% NP-40, and 0.01% Digitonin. After incubation for 5 min on ice, 500 µl wash buffer was added (same as lysis buffer but without NP-40 and digitonin) and nuclei were spun down. The washing step was repeated for a total of three times. RNA extraction was done using the Rneasy Plus Micro Kit (Qiagen, 74034) with the following adjustments. Nuclei were resuspended in 350 µl lysis buffer comprising 40 mM DTT. Upon gDNA elimination, the samples were washed with ethanol and transferred to the RNeasy MinElute column. Next, 350 µl of RW1 buffer was added, and samples were spun down. The flow-through was discarded and a mix of 70 µl buffer RDD with 10 µl DNAse was added to the columns. 15 minutes later, 350 µl buffer RW1 was added to the columns and the manufacturer’s protocol was followed. Sequencing libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760S), and sequenced on a NextSeq 500 using 75-nucleotide read length paired-end sequencing.
Libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB, E7760S)

treatment_protocol: no treatment

value: mouse embryonic stem cells

tag: genotype

value: WT


title: Lung cancer tissue [LCA anti-m5C IP]

source_name: Cancerous tissue

value: Cancerous tissue

tag: antibody

value: anti-m5C mouse monoclonal antibody (Diagenode)


title: JHGBM612 shCtrl Biological Replicate 3

source_name: JHGBM612 shCtrl 3


title: kidney biopsy N322


title: kidney biopsy N305


title: RNA, lG1, rep1


title: Oo-311_THC2_MII

description: Library name: Oo-311_THC2_MII

value: Treated

value: MII

tag: bmi (kg/m2)

tag: amh (pmol/l)

tag: lh (iu)


title: Oo-308_THC2_MII

description: Library name: Oo-308_THC2_MII

tag: fsh (iu)

tag: e2 (pmol/l)

tag: total gt_(iu)


title: PBMC - NS3

city: Miryang

first: SungYong

last: Joo

address: 1268-50, Samnangjin-ro, Samnangjin-eup

country: South Korea

institute: Pusan National University

description:
Library name: PBNS3
10XGenomics, 5000 cells

data_processing:
Sequencing reads were processed with the Cell Ranger version 7.0.1 (10X Genomics, CA) using the Rat reference transcriptome mRatBN7.2 from ensembl.
Assembly: mRatBN7.2
Supplementary files format and content: 1. Features (Genes): This file lists the genes that were measured in the experiment. Essentially, it provides the names or identifiers of all the genes for which expression levels were quantified. 2. Barcodes (Cells): This file contains the "barcodes" associated with each individual cell that was captured and sequenced. In scRNA-seq, barcodes are short DNA sequences that uniquely identify each cell. This allows researchers to trace each RNA molecule back to its cell of origin. 3. Matrix (Expression Matrix): This file contains the core expression data. It's a matrix where: Rows represent genes (from the "Features" file). Columns represent cells (from the "Barcodes" file). The values within the matrix represent the expression level of each gene in each cell (e.g., the number of RNA molecules detected).

organism: Rattus norvegicus

source_name: Blood

extract_protocol:
Isolated small intestinal lamina propria cell and PBMCs were washed and resuspended in 0.04% BSA in PBS. Cells were counted automatically with Countess II (Thermo Fisher, Waltham, MA) to determine their concentration.
Single-cell RNA-sequencing libraries were the prepared using the Chromium Next GEM Single Cell 3’ reagent kit v3.1 (10X Genomics, Pleasanton, CA) in accordance with the manufacturer’s protocol. Briefly, the cells were diluted into the Chromium Next GEM Chip G as to yield a recovery of ~ 5,000 single-cell. Following the library preparation, the libraries were sequenced in multiplex on the Novaseq 6000 sequencer (Illumina, San Diego, CA) to produce on average a minimum of 60,000 reads per single cell.

value: Blood

tag: cell type

value: PBMCs


title: PBMC - NS2

description:
Library name: PBNS2
10XGenomics, 5000 cells


title: RNA, AS, rep2

tag: cell line


title: Oo-305_THC1_MII

description: Library name: Oo-305_THC1_MII

source_name: Oocyte

tag: treatment

tag: batch


title: Oo-309_THC2_MII

description: Library name: Oo-309_THC2_MII


title: PBMC - NS1

description:
Library name: PBNS1
10XGenomics, 5000 cells

tag: tissue


title: RNA, AT, rep1


title: PBMC - HS3

description:
Library name: PBHS3
10XGenomics, 5000 cells


title: Control lung paracancer tissue [ANT anti-m5C IP]

source_name: Paracancer tissue

value: Paracancer tissue

tag: molecule subtype


title: PBMC - HS2

description:
Library name: PBHS2
10XGenomics, 5000 cells


title: Oo-304_THC1_MII

description: Library name: Oo-304_THC1_MII

tag: binomial treatment

tag: final stage


title: Oo-303_THC1_MII

description: Library name: Oo-303_THC1_MII

tag: participant number

tag: age (years)


title: ChIP, Nanog, SOX2ON, MDON, rep2

data_processing:
Sequencing libraries were aligned to the Mus musculus mm10 genome (GRCm38 release M25) and to the Drosophila Melanogaster genome (BDGP6 release 28) using STAR 2.7.0e (Dobin et al., 2013). Duplicated reads were removed with Picard (Broad Institute), and indexed using SAMTools 1.10 (Li et al., 2009). ChIP-seq samples were spike-in-normalized based on the sample with the lowest abundance of Drosophila reads (Bonhoure et al., 2014; Orlando et al., 2014) using SAMTools. For replicates, bam files were merged using SAMTools, and BigWig files were computed using the deepTools 3.5.1 (Ramírez et al., 2016) function bamCoverage with the setting “--normalizeUsing RPKM”. Peaks were called using MACS 2.2.4 (Zhang et al., 2008) with settings “-f BAMPE -g mm”, and merged using awk. Blacklisted peaks (Dunham et al., 2012) were removed with BEDTools (Quinlan and Hall, 2010) using the setting “-v”.
Assembly: mm10
Supplementary files format and content: bigWig file includes RPKM normalized reads; bigWig file includes TMM normalized reads (except for input)
Supplementary files format and content: bed file containing peaks (except for input)

growth_protocol: CGR8 WT, 2TS22C, ZHBTc4, and 44iN cells in GMEM supplemented with 10% inactivated ESC qualified fetal bovine serum, 1% nonessential amino acids, 2 mM L-glutamine, 2 mM sodium pyruvate, 100µM 2-mercaptoethanol, 1% penicillin and streptomycin, leukemia inhibitory factor (made in-house), 3 µM CHIR99021 and 0.8 µM PD184352. Cdt-MD cells were neurobasal Medium and DMEM/F-12, supplemented with B-27, N-2, 2 mM L-glutamine, 1% penicillin and streptomycin, 100µM 2-mercaptoethanol, 3 µM CHIR99021, 1 µM PD184352, and leukemia inhibitory factor. All cell lines were cultured on 0.1% gelatin-coated Petri dishes at 37°C and 5% CO2.

extract_protocol:
Briefly, cells were collected after trypsinization and fixed with 2 mM DSG in PBS for 50 min at room temperature on a rotating platform. Subsequently, cells were pelleted, and fixed for 10 min with 1 % formaldehyde on a rotating platform. The reaction was stopped using 200 mM Tris-HCl pH 8.0 for 10 min on a rotating platform. Tubes were filled with 1 % FBS in PBS and cells were spun down. Nuclei were extracted by resuspending the cell pellet twice in LB1 (50 mM HEPES-KOH pH 7.4, 140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 10% Glycerol, 0.5% NP-40, 0.25% Triton X-100), incubated for 10 min at 4°C and with gentle shaking at 100 rpm, and pelleted. The nuclei were then resuspended in LB2 (10 mM Tris-HCl pH 8.0, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA), incubated for 10 min at 4°C and with gentle shaking at 100 rpm, and spun down. To wash nuclei, SDS shearing buffer (10 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.15% SDS) was added twice without disturbing the pellet, the tube was rolled to rinse the walls and spun down. All buffers were supplemented with a 1:100 dilution of protease inhibitor cocktail. Chromatin was sheared for 20 min at 5% duty, 140 W, 200 cycles, or for samples with 50,000 cells for 10 min, 10% duty, 75 W, 200 cycles in a Covaris E220 focused ultrasonicator. To remove the insoluble material, chromatin was spun down and the supernatant was transferred to a new tube. As total input control and to evaluate the sonication efficiency, a few microliters of chromatin were incubated with 1X TE buffer pH 8.0 and 10 ng/µl RNAse A at 37°C for 30 min. Proteinase K was added at 400 ng/µl and the reaction was incubated for another 30 min at 55°C and shaking at 1100 rpm. Finally, 200 mM NaCl was added to reverse the crosslinks at 65°C for 16 h and shaking at 1100 rpm. The chromatin was purified using a MinElute PCR purification kit (Qiagen, 28004) and quality-checked on a 1 % agarose gel. Next steps were performed using the ChIP-IT High Sensitivity kit (Active motif, 53040) with a few modifications highlighted below. For immunoprecipitation of samples made from at least 1 million cells, 3.5 µg chromatin were used unless stated otherwise, and for samples made from 50,000 cells, all extracted chromatin was used. The following antibodies were used: anti-OCT4A (Cell Signaling Technology, 5677S) at 3.1 µl per 3.5 µg chromatin, anti-SOX2 (Cell Signaling Technology, 23064) at 3.1 µl per 3.5 µg chromatin, and anti-NANOG (Cell Signaling Technology, 8822) at 1.55 µl per 3.5 µg chromatin. To obtain quantitative ChIP-seq results, drosophila spike-in chromatin and spike-in antibody (Active motif, 61686) were used according to the manufacturer’s recommendations. Before binding the immunoprecipitated chromatin to the beads, the beads were washed once with ChIP buffer. For cross-link reversal, 2 µl proteinase K was added, the reaction was incubated at 55°C for 30 min and the temperature increased to 65°C and shaking at 1100 rpm for 16 h. Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L), and sequenced on a NextSeq 500 using 75-nucleotide read length paired-end sequencing.
Libraries were prepared using NEBNext Ultra II DNA Library Prep Kit (NEB, E7645L)

treatment_protocol: 44iN cells were maintained in culture with 1 µg/ml doxycycline or left untreated for 24h, 2TS22C and ZHBTc4 were treated with 1 µg/ml doxycycline or left untreated for 26h (2TS22C) or 24h (ZHBTc4), Cdt-MD cells untreated


title: ChIP, Nanog, SOX2ON, MDON, rep1


title: PBMC - HS1

description:
Library name: PBHS1
10XGenomics, 5000 cells


title: kidney biopsy N450

data_processing: Microarray data files were preprocessed using robust multi-chip averaging (RMA) implemented in Bioconductor.

extract_protocol: Tissue was homogenization in 0.5ml of Trizol reagent (Invitrogen, Carlsbad, CA) and total RNA was extracted and purified using the Rneasy Micro Kit (Quiagen, Ontario, Canada) (average yield 8µg/core, (RNA integrity number >7).

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)


title: kidney biopsy N342


title: kidney biopsy N385


title: Oo-299_CTRL_MII

description: Library name: Oo-299_CTRL_MII

value: Ctrl

value: Untreated

tag: bmi (kg/m2)


title: Small intestine laminaproria - NS4

description:
Library name: SINS4
10XGenomics, 5000 cells

source_name: Small intestine

value: Small intestine

value: Small intestinal lamina propria cell


title: kidney biopsy N448

value: NR


title: Oo-306_THC2_MII

description: Library name: Oo-306_THC2_MII

value: Oocyte

tag: amh (pmol/l)


title: ChIP, Nanog, OCT4ON, MDON, rep2


title: kidney biopsy N449


title: RNA, AS, rep1

tag: genotype


title: Oo-296_CTRL_MII

description: Library name: Oo-296_CTRL_MII

tag: lh (iu)

tag: fsh (iu)


title: ChIP, Nanog, OCT4ON, MDON, rep1


title: Small intestine laminaproria - NS3

description:
Library name: SINS3
10XGenomics, 5000 cells


title: kidney biopsy N441

value: TCMR


title: Oo-290_THC2_MII

description: Library name: Oo-290_THC2_MII

tag: e2 (pmol/l)

tag: total gt_(iu)


title: kidney biopsy N442

value: pABMR


title: kidney biopsy N436


title: Small intestine laminaproria - NS2

description:
Library name: SINS2
10XGenomics, 5000 cells

tag: cell type


title: kidney biopsy N438


title: Oo-289_THC2_MII

description: Library name: Oo-289_THC2_MII

tag: treatment


title: ChIP, Nanog, OCT4ON, MDOFF, rep2

tag: cell line

value: mouse embryonic stem cells


title: ChIP, Nanog, OCT4ON, MDOFF, rep1


title: Small intestine laminaproria - NS1

description:
Library name: SINS1
10XGenomics, 5000 cells

tag: tissue


title: Small intestine laminaproria - HS4

description:
Library name: SIHS4
10XGenomics, 5000 cells


title: Oo-287_THC1_MII

description: Library name: Oo-287_THC1_MII

tag: batch


title: kidney biopsy N435


title: ChIP, Input, SOX2OFF, MDON, rep2


title: Oo-283_THC1_MII

description: Library name: Oo-283_THC1_MII

tag: binomial treatment


title: kidney biopsy N434


title: ChIP, Input, SOX2OFF, MDON, rep1


title: Oo-280_CTRL_MII

description: Library name: Oo-280_CTRL_MII

tag: final stage


title: Small intestine laminaproria - HS3

description:
Library name: SIHS3
10XGenomics, 5000 cells


title: Small intestine laminaproria - HS2

description:
Library name: SIHS2
10XGenomics, 5000 cells


title: ChIP, Input, SOX2OFF, MDOFF, rep2


title: Small intestine laminaproria - HS1

description:
Library name: SIHS1
10XGenomics, 5000 cells


title: kidney biopsy N432

value: ABMR


title: kidney biopsy N431


title: Oo-270_CTRL_MII

description: Library name: Oo-270_CTRL_MII

tag: participant number


title: Oo-272_THC1_MII

description: Library name: Oo-272_THC1_MII

tag: age (years)


title: Oo-257_THC1_MII

description: Library name: Oo-257_THC1_MII


title: cardiac fibroblasts，Ang II+ vericiguat _3

city: Taizhou

first: Xiaolin

last: Sun

state: Jiangsu Province

address: 366 Taihu Road, Taizhou Pharmaceutical High-tech Zone, Jiangsu Province

department: Department of Cardiology

institute: The Affiliated Taizhou People's Hospital of Nanjing Medical University

data_processing:
Raw reads were quality-checked using FastQC v0.11.9
Adapter sequences and low-quality bases were trimmed using Trimmomatic v0.39
Clean reads were aligned to the reference genome using HISAT2 v2.2.1
Gene expression was quantified using featureCounts v2.0.1
Assembly: Oryctolagus cuniculus genome assembly OryCun2.0 (GCA_000003625.1)
Supplementary files format and content: Gene expression counts are provided in tab-delimited text files (.txt).
Supplementary files format and content: tab-delimited text files include gene ID and FPKM for each sample

source_name: Heart

growth_protocol: The cell pellets were resuspended in Dulbecco’s modified Eagle’s medium with 10% fetal bovine serum (FBS; Gibco), and 1% penicillin/streptomycin, plated onto a T25 flask, and incubated 37 °C for 2 h. CFs were collected after differential adherence. Following the incubation period, the media was replaced with complete media, and the cells were maintained at 37°C in a humidified atmosphere containing 5% CO₂ for the duration of the experiment. CFs of the second or third passage were used in our experiments.

extract_protocol:
Total RNA was extracted from cell samples using TRIzol reagent following the manufacturer's instructions
RNA-seq libraries were prepared using the Illumina TruseqTM RNA sample prep Kit according to the manufacturer's protocol.

treatment_protocol:
For CFs in the AngII group, AngII (0.1 μM; MedChem Express) was applied for 72 h.
For CFs in the AngII+vericiguat group, after 24h of incubation with vericiguat (1.0 μM), AngII was applied for 72 h.

value: Heart

value: cardiac fibroblasts

value: 0.1μM Ang II+ vericiguat (1.0 μM)


title: ChIP, Input, SOX2OFF, MDOFF, rep1


title: cardiac fibroblasts，Ang II+ vericiguat _2


title: ChIP, Input, OCT4OFF, MDON, rep2


title: ChIP, Input, OCT4OFF, MDON, rep1


title: Oo-253_CTRL_MII

description: Library name: Oo-253_CTRL_MII

value: MII


title: cardiac fibroblasts，Ang II+ vericiguat _1


title: cardiac fibroblasts，Ang II_3

value: 0.1  μM Ang II


title: ChIP, Input, OCT4OFF, MDOFF, rep2


title: ChIP, Input, OCT4OFF, MDOFF, rep1


title: Oo-251_THC2_MII

description: Library name: Oo-251_THC2_MII

value: Treated


title: cardiac fibroblasts，Ang II_2


title: ChIP, Nanog, SOX2OFF, MDON, rep1


title: kidney biopsy N427

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)


title: kidney biopsy N429


title: cardiac fibroblasts，Ang II_1


title: Oo-250_THC2_MII

description: Library name: Oo-250_THC2_MII

tag: bmi (kg/m2)


title: kidney biopsy N426


title: kidney biopsy N384


title: kidney biopsy N332


title: cardiac fibroblasts，CF_3


title: ATAC, 10K, LM, N2B27, rep1

data_processing:
Sequencing libraries were aligned to the Mus musculus mm10 genome (GRCm38 release M25) using STAR 2.7.0e (Dobin et al., 2013). Duplicated reads were removed with Picard (Broad Institute), and indexed using SAMTools 1.10 (Li et al., 2009). ATAC-seq samples were scaled to the same number of reads in each file using SAMTools. For replicates, bam files were merged using SAMTools, and BigWig files were computed using the deepTools 3.5.1 (Ramírez et al., 2016) function bamCoverage with the setting “--normalizeUsing RPKM”. Peaks were called using MACS 2.2.4 (Zhang et al., 2008) with settings “-f BAMPE -g mm”, and merged using awk. Blacklisted peaks (Dunham et al., 2012) were removed with BEDTools (Quinlan and Hall, 2010) using the setting “-v”.
Assembly: mm10
Supplementary files format and content: bigWig file includes RPKM normalized reads
Supplementary files format and content: bed file containing peaks

growth_protocol: 44iN cells were cultured in GMEM supplemented with 10% inactivated ESC qualified fetal bovine serum, 1% nonessential amino acids, 2 mM L-glutamine, 2 mM sodium pyruvate, 100µM 2-mercaptoethanol, 1% penicillin and streptomycin, leukemia inhibitory factor (made in-house), 3 µM CHIR99021 and 0.8 µM PD184352. Cdt-MD cells were cultured in neurobasal Medium and DMEM/F-12, supplemented with B-27, N-2, 2 mM L-glutamine, 1% penicillin and streptomycin, 100µM 2-mercaptoethanol, 3 µM CHIR99021, 1 µM PD184352, and leukemia inhibitory factor. All cell lines were cultured on 0.1% gelatin-coated Petri dishes at 37°C and 5% CO2.

extract_protocol:
Briefly, 50,000 cells were sorted or collected after trypsinization. Cells were then pelleted, washed once with cold PBS, and kept on ice. Subsequently, cells were resuspended in 50 µl cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40), and centrifuged. For the transposition reaction, pelleted nuclei were resuspended in 50 µl of 0.5 µM Tn5 (in-house produced according to (Chen et al., 2017)) in TAPS-DMF buffer (10  mM TAPS-NaOH, 5 mM Mgcl2, 10% DMF) and incubated at 37°C for 30 min. During the reaction, the tubes were flicked gently several times, and DNA was immediately purified using the DNA Clean & Concentrator kit (Zymo Research, D4003) with a binding buffer to sample ratio of  5:1. Transposed DNA was diluted in 10 µl DNA elution buffer, and amplified in a solution containing 0.5 mM Ad1.1 universal primer, 0.5 mM of Ad2.X indexing primer, 0.6X SYBR Green I and 1X NEBNext High-Fidelity 2X PCR Master Mix at 72°C for 5 min, 98°C for 30 s, and 5 cycles of 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min. The PCR reaction was monitored to stop the amplification before saturation by sampling 10 µl of amplified DNA and analyzing it by qPCR. The number of cycles to add was determined by the time at which the fluorescence was still in the rising phase. The remaining DNA was further amplified at 98°C for 30 s, and 4-7 cycles of 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min. Next, the library was purified using the DNA Clean & Concentrator kit with a binding buffer-to-sample ratio of 5:1. The purified library was further size-selected using a 0.55X and 1.2X ratio of AMPure XP beads. Library concentrations were determined by Qubit, analyzed on a fragment analyzer, and sequenced on an Illumina NextSeq 500 using 75 nucleotide read-length paired-end sequencing.
Libraries were prepared using NEBNext High-Fidelity 2X PCR Master Mix

treatment_protocol: 44iN cells were maintained in culture with 1 µg/ml doxycycline or left untreated for 24h, Cdt-MD cells are untreated


title: kidney biopsy N304


title: kidney biopsy N349


title: Oo-249_THC2_MII

description: Library name: Oo-249_THC2_MII

tag: amh (pmol/l)


title: Oo-246_THC1_MII

description: Library name: Oo-246_THC1_MII


title: Oo-252_THC2_MII

description: Library name: Oo-252_THC2_MII


title: ATAC, 10K, mito, N2B27, rep2


title: kidney biopsy N358


title: cardiac fibroblasts，CF_1


title: kidney biopsy N331


title: ATAC, 10K, mito, N2B27, rep1


title: ATAC, 10K, eG1-1, N2B27, rep2


title: Oo-244_CTRL_MII

description: Library name: Oo-244_CTRL_MII


title: ChIP, Nanog, SOX2OFF, MDON, rep2


title: kidney biopsy N341


title: Oo-245_THC1_MII

description: Library name: Oo-245_THC1_MII


title: ATAC, 10K, eG1-1, N2B27, rep1


title: cardiac fibroblasts，CF_2


title: ATAC, 10K, LM, N2B27, rep2


title: Oo-243_CTRL_MII

description: Library name: Oo-243_CTRL_MII


title: Oo-242_CTRL_MII

description: Library name: Oo-242_CTRL_MII


title: Oo-248_THC1_MII

description: Library name: Oo-248_THC1_MII


title: KO_rep2

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

description: Cells were FACS sorted based on ID4-GFP fluorescence to enrich for SSCs

data_processing:
Aligned using STAR
Counts generated with featureCounts and GENCODE vM18
Assembly: mm10
Supplementary files format and content: tab-delimited text: column 1 = gene, column 2 = counts

source_name: Neonatal testis (P8)

extract_protocol:
RNA was extracted with BioRad Aurum Total RNA Mini Kit
RNA-seq library was constructed using the Illumina TruSeq  Stranded Total RNA kit.

value: Neonatal testis (P8)

value: Tissue

value: Testis cell suspension

tag: genotype

value: Cnot3 KO

value: 4OHT injection from P1-P3


title: Oo-168_CTRL_MII

description: Library name: Oo-168_CTRL_MII

value: Ctrl

value: Untreated

tag: lh (iu)


title: WT_rep1

value: wild-type


title: Oo-165_CTRL_MII

description: Library name: Oo-165_CTRL_MII

value: Oocyte

tag: fsh (iu)


title: KO_rep1


title: WT_rep2


title: Oo-157_THC1_MII

description: Library name: Oo-157_THC1_MII

tag: e2 (pmol/l)


title: NS_WT-P8

description: Cells were FACS sorted based on CD9 and THY1 to enchrich for SSCs and germ cells

data_processing:
Processed with Cell Ranger v3.0.1 and GENCODE vM17
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
CD9+/THY1+ testis cells were collected by FACS sorting (see experimental design for details)
scRNA-seq libraries were prepared with 10xGenomics Chromium Single Cell 3' Kit v3.1.

value: 4OHT injection from P1-P1


title: Oo-156_THC1_MII

description: Library name: Oo-156_THC1_MII

tag: total gt_(iu)


title: NS_Cre-P8

tag: cell type


title: Oo-154_CTRL_MII

description: Library name: Oo-154_CTRL_MII

tag: treatment


title: RNA, eG1-4, rep2

tag: cell line

value: mouse embryonic stem cells

value: WT


title: Oo-151_CTRL_MII

description: Library name: Oo-151_CTRL_MII


title: Oo-172_THC1_MII

description: Library name: Oo-172_THC1_MII


title: kidney biopsy N366

city: Edmonton

address: 250 Heritage Medical Research Centre

institute: University of Alberta

value: NR


title: Oo-149_THC1_MII

description: Library name: Oo-149_THC1_MII


title: kidney biopsy N329


title: kidney biopsy N424


title: kidney biopsy N395

value: Mixed


title: Oo-142_THC1_MII

description: Library name: Oo-142_THC1_MII

value: MII


title: kidney biopsy N330


title: kidney biopsy N383


title: RNA, eG1-2, rep2


title: kidney biopsy N394


title: RNA, eG1-3, rep1


title: RNA, eG1-3, rep2


title: kidney biopsy N365


title: kidney biopsy N423

value: ABMR


title: kidney biopsy N393


title: kidney biopsy N422


title: kidney biopsy N425


title: RNA, eG1-2, rep1


title: kidney biopsy N391


title: Oo-108_THC2_MII

description: Library name: Oo-108_THC2_MII

value: Treated


title: Oo-110_THC2_MII

description: Library name: Oo-110_THC2_MII


title: RNA, eG1-4, rep1


title: kidney biopsy N392


title: RNA, eG1-1, rep1


title: Oo-141_THC1_MII

description: Library name: Oo-141_THC1_MII


title: ChIP, Sox2, 50K, telo, rep1

data_processing:
Sequencing libraries were aligned to the Mus musculus mm10 genome (GRCm38 release M25) and to the Drosophila Melanogaster genome (BDGP6 release 28) using STAR 2.7.0e (Dobin et al., 2013). Duplicated reads were removed with Picard (Broad Institute), and indexed using SAMTools 1.10 (Li et al., 2009). ChIP-seq samples were spike-in-normalized based on the sample with the lowest abundance of Drosophila reads (Bonhoure et al., 2014; Orlando et al., 2014) using SAMTools. For replicates, bam files were merged using SAMTools, and BigWig files were computed using the deepTools 3.5.1 (Ramírez et al., 2016) function bamCoverage with the setting “--normalizeUsing RPKM”. Peaks were called using MACS 2.2.4 (Zhang et al., 2008) with settings “-f BAMPE -g mm”, and merged using awk. Blacklisted peaks (Dunham et al., 2012) were removed with BEDTools (Quinlan and Hall, 2010) using the setting “-v”.
Assembly: mm10
Supplementary files format and content: bigWig file includes RPKM normalized reads
Supplementary files format and content: bed file containing peaks (except for input)
Supplementary files format and content: bigWig file includes TMM normalized reads (except for input)

tag: chip antibody


title: RNA, eG1-1, rep2


title: Oo-86_THC2_MII

description: Library name: Oo-86_THC2_MII

tag: batch


title: kidney biopsy N421


title: ChIP, Sox2, 50K, mito, rep1


title: ChIP, Sox2, eG1-4, rep3


title: kidney biopsy N347


title: Oo-23_THC1_MII

description: Library name: Oo-23_THC1_MII

tag: binomial treatment


title: kidney biopsy N364


title: kidney biopsy N348


title: kidney biopsy N418


title: ChIP, Sox2, eG1-4, rep2


title: Oo-18_THC2_MII

description: Library name: Oo-18_THC2_MII

tag: final stage


title: Oo-97_THC2_MII

description: Library name: Oo-97_THC2_MII

tag: participant number


title: kidney biopsy N420

value: pABMR


title: Oo-17_THC1_MII

description: Library name: Oo-17_THC1_MII

tag: age (years)


title: ChIP, Sox2, eG1-3, rep3


title: ChIP, Sox2, eG1-3, rep2


title: Oo-90_CTRL_MII

description: Library name: Oo-90_CTRL_MII


title: Oo-15_THC2_MII

description: Library name: Oo-15_THC2_MII


title: kidney biopsy N415

tag: mmdx (abmr, mixed, nr[no rejection], pabmr, ptcmr, tcmr)


title: Oo-4_THC2_MII

description: Library name: Oo-4_THC2_MII


title: ChIP, Sox2, eG1-3, rep1


title: Valid_hESC_ChIP-H9_WT_input-D14K4-1

city: Shanghai

first: Jincan

last: He

address: siping road 1239

institute: Tongji university

description: Library name: Valid_hESC_ChIP-H9_WT_input-D14K4-1

data_processing:
Sequencing reads for RNA were initially processed to remove adapters, followed by alignment to the annotated human transcriptome (UCSC hg38) using Hisat2 (v2.2.1) with the parameters -k 1 --dta --dta-cufflinks --no-unal. The aligned reads were subsequently assembled into transcripts with reference to the UCSC refGene GTF annotation files utilizing Stringtie (v2.2.1). Gene expression levels were quantified in TPM (Transcripts Per Million).
Sequencing reads for ChIP-seq were first processed to remove adapters and aligned to the human genome (UCSC hg38) using Bowtie2 (v2.4.4) with the parameters: -t --no-mixed --no-discordant --no-unal. High-confidence mapped reads were retained using sambamba (v1.0.1) with the parameters: -F "mapping_quality >= 20 and not (unmapped or mate_is_unmapped)". Duplicated reads were removed with picard (v3.1.0) MarkDuplicates function. Genome-wide signals were calculated using ‘bamCoverage’ from deepTools (v3.5.4).
Assembly: hg38
Supplementary files format and content: Gene expression quantification in TPM
Supplementary files format and content: ChIP signal bigwig file

growth_protocol: hESCs (H9, passages 25-45, Wicell agreement No. 14.W0377) were cultured on feeders in hESCM composed of DMEM/F12, 20% Knockout serum replacer, minimal essential medium (MEM) non-essential amino acids solution, L-glutamine solution, 0.1 mM β-mercaptoethanol, and 4ng/mL fibroblast growth factor 2. Cells were passaged every 5 days through Dispase digestion and the medium was changed every day.

extract_protocol:
The Smart-seq2 method followed previously published studies. Briefly, approximately 10 -100 cells/sample were lysed, and cDNA was synthesized directly from cytoplasmic lysate. This full-length was amplified for 17 cycles, and libraries were prepared using the KAPA Hyper Prep kit. 3 biological replicates were perfomed. Sequenced on Illumina NovaSeq.
ULI-NChIP-seq was performed using 200-500 cells/ sample, with two or three biological replicates per group. Isolated cells were washed with PBS/BSA, and the ULI-NChIP procedure was performed as previously described using 1μg of a histone H3K27me3 or H3K4me3 antibody per immunoprecipitation reaction77. Libraries were prepared using the KAPA Hyper Prep Kit. Sequenced on Illumina Novaseq.

value: wild type


title: Oo-40_THC2_MII

description: Library name: Oo-40_THC2_MII

tag: bmi (kg/m2)


title: ChIP, Sox2, eG1-2, rep2


title: Valid_hESC_ChIP-H9_WT_input-D14K27-1

description: Library name: Valid_hESC_ChIP-H9_WT_input-D14K27-1


title: ChIP, Sox2, eG1-1, rep2


title: ChIP, Sox2, eG1-2, rep3


title: Valid_hESC_ChIP-H9_WT_H3K4me3-D14K4-2

description: Library name: Valid_hESC_ChIP-H9_WT_H3K4me3-D14K4-2


title: Valid_hESC_ChIP-H9_WT_H3K4me3-D14K4-1

description: Library name: Valid_hESC_ChIP-H9_WT_H3K4me3-D14K4-1


title: ChIP, Sox2, eG1-1, rep1


title: Valid_hESC_ChIP-H9_WT_H3K27me3-D14K27-2

description: Library name: Valid_hESC_ChIP-H9_WT_H3K27me3-D14K27-2


title: Valid_hESC_ChIP-H9_WT_H3K27me3-D14K27-1

description: Library name: Valid_hESC_ChIP-H9_WT_H3K27me3-D14K27-1


title: Valid_hESC_ChIP-H9_KO_input-D14K4-1

description: Library name: Valid_hESC_ChIP-H9_KO_input-D14K4-1

value: ZBTB17 KO


title: ChIP, Oct4, 51K, telo, rep1


title: ChIP, Oct4, mito, rep1


title: kidney biopsy N419

first: Jessica

last: Chang


title: kidney biopsy N414


title: kidney biopsy N416


title: ChIP, Oct4, eG1-4, rep3


title: Valid_hESC_ChIP-H9_KO_input-D14K27-1

description: Library name: Valid_hESC_ChIP-H9_KO_input-D14K27-1


title: kidney biopsy N411


title: kidney biopsy N412


title: kidney biopsy N413


title: ChIP, Oct4, eG1-4, rep2


title: kidney biopsy N303


title: kidney biopsy N363


title: ChIP, Sox2, 50K, rep1


title: kidney biopsy N301


title: Valid_hESC_ChIP-H9_KO_H3K4me3-D14K4-1

description: Library name: Valid_hESC_ChIP-H9_KO_H3K4me3-D14K4-1


title: ChIP, Oct4, eG1-4, rep1


title: ChIP, Sox2, 50K, eG1-1, rep1


title: Valid_hESC_ChIP-H9_KO_H3K27me3-D14K27-2

description: Library name: Valid_hESC_ChIP-H9_KO_H3K27me3-D14K27-2


title: kidney biopsy N362


title: Valid_hESC_ChIP-H9_KO_H3K27me3-D14K27-1

description: Library name: Valid_hESC_ChIP-H9_KO_H3K27me3-D14K27-1


title: ChIP, Oct4, eG1-3, rep2


title: kidney biopsy N302


title: kidney biopsy N410


title: Valid_hESC_ChIP-H9_KO_H3K4me3-D14K4-2

description: Library name: Valid_hESC_ChIP-H9_KO_H3K4me3-D14K4-2


title: Valid_hESC_RNA-H9_WT-D14-3

description:
Library name: Valid_hESC_RNA-H9_WT-D14-3
hESC_samples_TPM_matrix.csv


title: ChIP, Oct4, eG1-3, rep1


title: Valid_hESC_RNA-H9_WT-D14-2

description:
Library name: Valid_hESC_RNA-H9_WT-D14-2
hESC_samples_TPM_matrix.csv


title: kidney biopsy N361


title: kidney biopsy N409


title: ChIP, Oct4, eG1-2, rep3


title: Valid_hESC_RNA-H9_WT-D14-1

description:
Library name: Valid_hESC_RNA-H9_WT-D14-1
hESC_samples_TPM_matrix.csv


title: kidney biopsy N45


title: Valid_hESC_RNA-H9_KO-D14-3

description:
Library name: Valid_hESC_RNA-H9_KO-D14-3
hESC_samples_TPM_matrix.csv


title: kidney biopsy N34


title: ChIP, Oct4, eG1-1, rep3


title: ChIP, Oct4, eG1-2, rep2


title: ChIP, Oct4, eG1-1, rep2


title: ChIP, Oct4, eG1-3, rep3


title: Valid_hESC_RNA-H9_KO-D14-1

description:
Library name: Valid_hESC_RNA-H9_KO-D14-1
hESC_samples_TPM_matrix.csv


title: ChIP, Oct4, eG1-1, rep1


title: kidney biopsy N35


title: Valid_hESC_RNA-H9_KO-D14-2

description:
Library name: Valid_hESC_RNA-H9_KO-D14-2
hESC_samples_TPM_matrix.csv


title: MDAMB468, Ctr, Sample3

city: Oslo

first: Eivind Valen

last: Egeland

address: Ullernchausseen 70

department: Department of Tumor Biology, Institute for Cancer Research

country: Norway

institute: Oslo University Hospital

description:
Library name: S52
col S52 in raw_data_mdamb468.txt

data_processing:
Fastq files were cropped to longest common read length, 75 bp, with Trimmomatic (v0.38).
Trimmed samples were aligned to grch38 with STAR (v2.7.8a), and transcript reference (UCSC KnownGene downloaded March 7th 2022) using default parameters.
Gene counts were retrieved with featureCounts from Subread.
Assembly: hg38
Supplementary files format and content: tab-delimited txt-file containes raw-counts from all Samples

source_name: TNBC

growth_protocol: The human TNBC cell line MDA-MB-468 (RRID:CVCL_0419) was obtained from the American Type Culture Collection (ATCC) (Manassas, VA, USA). Cells were cultured in high glucose DMEM containing GlutaMAX (Gibco, Life Technologies, Carlsbad, CA, USA) and supplemented with 10% heat-inactivated fetal bovine serum (FBS) (Sigma-Aldrich, St. Louis, MO, USA).

extract_protocol:
RNA was extracted with AllPrep DNA/RNA/miRNA Unviersal kit (Qiagen).
Libraries were prepared with Kapa RNA HyperPrep with dual index to generate cDNA, followed by Twist Human Comprehensive Exome for the mRNA capturing according to manufacturer's protocol. Amount of starting material 100 ng total RNA.

tag: tissue

value: TNBC


title: kidney biopsy N32

value: TCMR


title: MDAMB468, Ctr, Sample2

description:
Library name: S50
col S50 in raw_data_mdamb468.txt


title: MDAMB468, Resistant, Sample3

description:
Library name: S49
col S49 in raw_data_mdamb468.txt


title: ChIP, Oct4, 51K, rep1


title: MDAMB468, Resistant, Sample2

description:
Library name: S47
col S47 in raw_data_mdamb468.txt


title: ChIP, Oct4, 51K, eG1-1, rep1


title: ChIP, Oct4, 51K, mito, rep1


title: DHA3

city: KUNMING City

first: Weixing

last: Zeng

state: Yunnan

address: GuiZhou

institute: Kunming Medical University

description:
Library name: Sample6
DHA3

data_processing:
The library was sequenced using the DNBSEQ-T7/G400 sequencing platform, generating 150 bp paired-end reads. The raw reads in fastq format were processed using fastp software to remove low-quality reads, resulting in clean reads for subsequent data analysis. HISAT2 software was used for reference genome alignment, and gene expression levels (FPKM) were calculated. The reads count for each gene was obtained using HTSeq-count. PCA analysis and plotting of gene (counts) data were performed using R (v 3.2.0) to assess biological replicates of the samples.
Assembly: The human reference genome GRCh38 (Genome Reference Consortium Human Build 38) was used for alignment and quantification.
Supplementary files format and content: Processed data files are in CSV format, containing gene expression counts for each sample. The files include gene IDs, gene names, and raw read counts.

source_name: tongue

extract_protocol:
Total RNA was extracted from cells using the TRIzol reagent (Invitrogen) following the manufacturer's instructions. RNA quality was assessed using an Agilent Bioanalyzer, and only samples with an RNA Integrity Number (RIN) > 8 were used for library construction.
The transcriptome library was constructed using the VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the instructions provided in the manual.

value: tongue

value: oral squamous cell carcinoma (keratinocyte)

tag: genotype

value: DHA treatment of Cal-27 cells

value: DHA


title: ChIP, Nanog, 54K, telo, rep1

value: Nanog (CST, #8822)


title: ChIP, Nanog, 54K, mito, rep1

value: mouse embryonic stem cells


title: kidney biopsy N299


title: kidney biopsy N276


title: DHA1

description:
Library name: Sample4
DHA1


title: ChIP, Nanog, eG1-4, rep3


title: ChIP, Oct4, asyn, rep1


title: kidney biopsy N4


title: DMSO3

description:
Library name: Sample3
CG3

value: DMSO treatment of Cal-27 cells

value: DMSO


title: ChIP, Nanog, eG1-4, rep1


title: DMSO2

description:
Library name: Sample2
CG2


title: kidney biopsy N277


title: kidney biopsy N172

value: NR


title: DMSO1

description:
Library name: Sample1
CG1


title: ChIP, Nanog, eG1-3, rep4


title: DHA2

description:
Library name: Sample5
DHA2


title: ChIP, Nanog, eG1-3, rep3


title: kidney biopsy N279


title: ChIP, Nanog, eG1-2, rep3