title: UVAL5

first: Peter

last: Sykora

address: 1121 5th Street NW

institute: Amelia Technologies

description: Library name: Uval_5

data_processing:
Raw FASTQ files were quality checked prior to downstream analysis.
Sequencing reads were processed and aligned or quantified against a human reference genome/transcriptome.
Downstream expression analysis was performed to compare baseline transcriptional profiles among HaCaT, HPV E6/E7-transduced keratinocytes, and normal human keratinocyte/UVAL control samples.
Assembly: Homo sapiens GRCh38/hg38 reference genome assembly. Verify against the original RNA-seq analysis pipeline before final GEO submission.
Supplementary files format and content: gene_counts.txt: Tab-delimited text file containing gene-level raw read counts generated from RNA-seq data. Rows correspond to genes/features and columns correspond to individual RNA-seq samples. Values represent raw counts used for downstream gene-expression analysis and comparison among untreated HaCaT, HPV E6/E7 keratinocyte, HEKa, and UVAL-derived keratinocyte samples.

source_name: Uval

growth_protocol: Human keratinocyte models were cultured under standard mammalian cell-culture conditions prior to RNA extraction. Cell models included HaCaT keratinocytes, HPV E6/E7-transduced keratinocytes, and normal human epidermal keratinocyte/UVAL-derived keratinocyte control cultures. Cultures were maintained as untreated baseline samples before harvest for RNA sequencing.

extract_protocol:
Total RNA was isolated from untreated human keratinocyte cultures for RNA-seq library preparation. RNA quantity and integrity were assessed prior to sequencing-library construction.
RNA-seq libraries were prepared from total RNA for transcriptome profiling and sequenced using an Illumina HiSeq 4000 platform.

value: Uval

value: Keratinocyte


title: UVAL4

status: Public on Jun 30 2026

type: SRA

city: Washington

state: DC

country: USA

description: Library name: Uval_4

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: cell line

tag: cell type

tag: genotype

value: WT


title: WT under well-watered condition replicate3

city: Saskatoon

first: Peng

last: Gao

state: Saskatchewan

address: 107 Science Place

country: Canada

institute: Agriculture and Agri-Food Canada

description:
Library name: WT_CK_3
RNA-seq of WT under well-watered condition replicate 3

data_processing:
Illumina Casava software used for basecalling.
Trimming the adaptor sequences, filtering low-quality reads  and eliminating short reads using Trimmomatic.
Filtered reads were mapped toIWGSC Version 2.1 genome assembly reference genome using STAR.
Reads quantification was performed by Salmon.
Normalized counts were obtained from R tximport and DESeq2 package.
Assembly: IWGSC Version 2.1 genome assembly reference genome
Supplementary files format and content: Matrix table files include normalized counts for each sample

organism: Triticum aestivum

source_name: Leaf

growth_protocol: Spring wheat (T. aestivum) line Fielder regarded as wild-type was used in genetic transformation for generation of TOR expression lines UBQ/TOR, DREM/TOR and DEH2/TOR. Depending on the experiment, plants were grown either in soil or hydroponic solution. Uniform seeds of different wheat lines were surface sterilized with 20% bleach containing 0.1% Tween 20 (v/v) for 10 min, rinsed 4 times with deionized H2O and soaked in deionized water overnight at 4℃, seeds were then germinated in petri dish with wet filter paper. After 7 days, uniform seedlings were selected and transferred to soil or hydroponic solution. All the plants were grown in a growth chamber with light intensity of 300μmol photons m-2 s-1 and a relative humidity of 60%, the photoperiod cycle and temperature were set as 24 ℃, 16-h-light /18 ℃, 8-h-dark.

extract_protocol:
RNA was extracted from 0.1 g of each sample using a Qiagen RNeasy Mini Kit, and checked for quality using a Thermo Scientific NanoDrop™ One/OneC Microvolume UV-Vis Spectrophotometer.
RNA-seq libraries were prepared using the Illumina TruSeq UD V1.5 Kit. Libraries were prepared by using RNA according to manufacturer's instruction and then loaded on an Illumina NovaSeq 6000 platform for pair-end sequencing with 150 cycles.

treatment_protocol: For the drought tolerance assessment, wheat lines were initially grown under well-watered condition (80% field capacity) until they reached 4-week-old. Subsequently, water was withheld for a period of 12 days to induce drought stress, after which the plants were re-watered, the plant survival rates were assessed 7 days later.

tag: tissue

value: Leaf

tag: treatment

value: Well watered

tag: batch


title: Western diet, brown adipose, wild-type repicate 3

city: Richmond

first: Christopher

last: Green

state: Virginia

address: 1101 E. Marshall St.

institute: Virginia Commonwealth University

description: Library name: RB21

data_processing:
Fastq files were subsequently generated with Illumina BaseSpace. Raw fastq files were checked for quality using FastQC and collated using MultiQC.
Adapters were trimmed using CutAdapt and reads were aligned using STAR (Aligner) version 2.7.9a to the mouse GRCm39/mm39 mouse primary assembly genome (https://ftp.ensembl.org/pub/release-108/fasta/mus_musculus/dna/) using default parameters
Raw counts were generated using the FeatureCounts tool from the SourceForge Subread package and subsequently counted genes using the ensembl gtf file for Mus musculus, GRCm39 assembly, version release 108. Raw counts were then analysed using the EdgeR package.
Assembly: mm39vM30
Supplementary files format and content: comma separated text file includes raw counts for each Sample

molecule: polyA RNA

organism: Mus musculus

source_name: brown adipose

extract_protocol:
RNA was extracted from equal weights of frozen tissue using TRIzol (#15596026, Fisher). 1ug of total RNA was used for construction of sequencing libraries.
RNA libraries for RNA-seq were constructed from poly(A) isolated RNA using NEBNext Poly(A) mRNA Magnetic Isolation Module (#E7490S/L, New England BioLabs) and enriched with a SMARTer Apollo Library Prep System (#640078, Takara). The library was prepared using a dUTP-based stranded NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (#E7760S, New England BioLabs), indexed and amplified with 8 PCR cycles. Uniquely barcoded libraries were then analyzed and sequenced with the paired end read 2x61 base pair setting.

treatment_protocol: Mice were fed chow diet or Western diet for 18 weeks.

value: brown adipose

value: wild-type


title: E15.5 cortex, 12DIV, NCM, rep4

city: Syracuse

first: Jessica

middle: L.

last: MacDonald

state: NY

address: 107 College Place

department: Biology

institute: Syracuse University

description:
Library name: Sample 8
Column Name in "ACM_Raw_Counts": NCM.5

data_processing:
Sequence reads were trimmed using Trimmomatic v.0.36
Trimmed reads were mapped to the reference genome available on ENSEMBL using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using featurecounts from the Subread package v.1.5.2.
Sequence reads underwent batch correction R using RUVseq and differentially expressed genes were calculated using edgeR
Assembly: mm10
Supplementary files format and content: .csv file includes mapped raw counts
Supplementary files format and content: .xlsx files include fold change comparisons between treatments

source_name: Neocortex

growth_protocol: E15.5 primary cortical cultures were maintained in neurobasal media supplemented with N2, B27, Glutamax and containing PenStrep in a humidified chamber at 37C with 5% C02

extract_protocol:
Neurons were harvested in TRIzol at 12DIV and total RNA extracted with RNeasy Mini kit (Qiagen)
RNA libraries were prepared by Azenta Life Sciences using the NEBNext Ultra RNA Library Prep Kit for Illumina

treatment_protocol:
Cultures were treated with AraC at 3DIV to deplete astrocytes
Astrocyte Cultured Media (ACM) from either Mecp2 +/y or Mecp2 -/y or NonConditioned Media (NCM) was added to cultures at 6DIV

value: Neocortex

value: E15.5 primary cortical culture

tag: in vitro_stage

value: NCM


title: UVAL3

description: Library name: Uval_3


title: E15.5 cortex, 12DIV, NCM, rep3

description:
Library name: Sample 7
Column Name in "ACM_Raw_Counts": NCM.4


title: WT under well-watered condition replicate2

description:
Library name: WT_CK_2
RNA-seq of WT under well-watered condition replicate 2


title: Western diet, brown adipose, wild-type repicate 2

description: Library name: RB20


title: UVAL2

description: Library name: Uval_2


title: E15.5 cortex, 12DIV, NCM, rep2

description:
Library name: Sample 6
Column Name in "ACM_Raw_Counts": NCM.3


title: WT under well-watered condition replicate1

description:
Library name: WT_CK_1
RNA-seq of WT under well-watered condition replicate 1


title: Chow diet, subcutaneous white adipose, Sphk2 deleted repicate 3

description: Library name: RB18

source_name: subcutaneous white adipose

value: subcutaneous white adipose

value: Sphk2 deleted


title: E15.5 cortex, 12DIV, NCM, rep1

description:
Library name: Sample 5
Column Name in "ACM_Raw_Counts": NCM.1


title: Western diet, brown adipose, wild-type repicate 1

description: Library name: RB19


title: PDAC_24, Untreated

city: Rozzano

first: Anna Rita

last: Putignano

state: Milano

address: Via Alessandro Manzoni, 56

country: Italy

institute: IRCCS Humanitas Research Hospital

description:
Library name: PDAC_24
FFPE pancreatic tumor RNA-seq, patient PDAC_24, condition: Untreated, run: run_3

data_processing:
BCL demultiplexed with bcl2fastq v2.20.0; adapter trimming with Cutadapt; alignment to GRCh38 with STAR via CogentAP v3.1; rRNA filtering with SortMeRNA; deduplication with UMI-tools; quantification with Salmon;
Gene-level summarization with tximport v1.30 (R v4.3.3); normalization with TMM (edgeR v4.0.16
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw gene-level read counts for each sample, generated with Salmon and summarized with tximport
Supplementary files format and content: tab-delimited text file containing sample annotations including library name, treatment, patient ID, run and barcode

source_name: pancreas

extract_protocol:
3-4 consecutive FFPE slides per patient; tumor area scraped and RNA extracted using NucleoSpin totalRNA FFPE XS kit followed by NucleoSpin RNA Clean-up XS kit (Macherey-Nagel).
SMARTer Stranded Total RNA-seq Kit v3 Pico Input Mammalian (Takara Bio)

value: pancreas

value: Untreated


title: E6/E7

description: Library name: E6E7_2

value: P53 Null


title: UVAL1

description: Library name: Uval_1


title: E15.5 cortex, 12DIV, KO ACM, rep4

description:
Library name: Sample 4
Column Name in "ACM_Raw_Counts": KO.ACM.5

value: KO ACM


title: PDAC_23, Untreated

description:
Library name: PDAC_23
FFPE pancreatic tumor RNA-seq, patient PDAC_23, condition: Untreated, run: run_3


title: Chow diet, subcutaneous white adipose, Sphk2 deleted repicate 2

description: Library name: RB17


title: NHEK

description: Library name: NHEK

source_name: NHEK

value: NHEK


title: E15.5 cortex, 12DIV, KO ACM, rep3

description:
Library name: Sample 3
Column Name in "ACM_Raw_Counts": KO.ACM.4


title: PDAC_22, Untreated

description:
Library name: PDAC_22
FFPE pancreatic tumor RNA-seq, patient PDAC_22, condition: Untreated, run: run_3


title: HaCaT

description: Library name: HaCaT

source_name: HaCaT

value: HaCaT

value: P53 Mutant


title: Chow diet, subcutaneous white adipose, Sphk2 deleted repicate 1

description: Library name: RB16


title: E15.5 cortex, 12DIV, KO ACM, rep2

description:
Library name: Sample 2
Column Name in "ACM_Raw_Counts": KO.ACM.3

value: WT


title: PDAC_21, Untreated

description:
Library name: PDAC_21
FFPE pancreatic tumor RNA-seq, patient PDAC_21, condition: Untreated, run: run_3


title: normal liver tissue 05.fastq.gz

city: Shanghai

first: Gong

middle: Ke

last: Tao

address: Jimo Road 150#

country: China

institute: easthospital

description:
Library name: Sample 10
tissues were obtained from patients undergoing surgery

data_processing:
Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
Library sequencing was performed on an illumina Hiseq instrument with 150bp paired end reads.
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
circRNA: The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis. GO and KEGG analysis were performed for the differentially expressed circRNA-associated genes.
LncRNA & mRNA: The high quality reads were aligned to the human reference genome (UCSC hg19) with hisat2 software (v2.0.4). Then, guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified. LncRNA target genes were predicted by the locations to nearby genes. And GO and Pathway analysis were performed on these target genes. GO and Pathway enrichment analysis were also performed based on the differentially expressed mRNAs.
Assembly: hg19
Supplementary files format and content: The file,  RNA Expression Profiling, includes transcript_id, gene_id,  FPKM values and raw counts of all samples of the transcript.

source_name: liver fibrosis tissue

growth_protocol: Liver fibrosis and normal tissues were collected from patients undergoing hepatectomy for HCC or cirrhosis requiring transplantation.

extract_protocol:
Briefly, total RNA was used for removing the rRNAs with NEBNext rRNA Depletion Kit (New England Biolabs, Inc., Massachusetts, USA) following the manufacturer's instructions.
RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions.

treatment_protocol: Total RNA were extracted from tissue using Trizol reagent (Life Technologies Corporation, Carlsbad, CA, USA).

value: liver fibrosis tissue


title: E15.5 cortex, 12DIV, KO ACM, rep1

description:
Library name: Sample 1
Column Name in "ACM_Raw_Counts": KO.ACM.1


title: Chow diet, subcutaneous white adipose, wild-type repicate 3

description: Library name: RB15


title: PDAC_20, Untreated

description:
Library name: PDAC_20
FFPE pancreatic tumor RNA-seq, patient PDAC_20, condition: Untreated, run: run_3


title: Chow diet, subcutaneous white adipose, wild-type repicate 2

description: Library name: RB14


title: normal liver tissue 04.fastq.gz

description:
Library name: Sample 09
tissues were obtained from patients undergoing surgery


title: Neuronal Nuclei, WT+ASO, plate8

city: Cambridge

middle: Peter

last: Pukszta

state: MA

address: 455 Main St

institute: Massachusetts Institute of Technology

description:
Library name: Plate 8
Metadata for plate included in p008-Meta.csv

data_processing:
Reads were alligned using Kalisto with an index built from the GRCm39 mouse reference genome.
Nuclei were filtered using a custom python script on several metrics: abnrmally low or high read counts, low ERCC reads, High Precentage ERCC reads, and high mitochondrial percentage.
Filtered nuclei were clustered and each cluster was evalutated on the prevelance of neuron specific genes and other cell type specific genes to remove contamination.
Clusters were labeled with their cell type using Sctype and gene lists compiled from Drokhlyansky et al. 2020.
Assembly: GRCm39
Supplementary files format and content: H5AD files containing each step of data filtering and associated metadata of each sequenced well.

source_name: Colon

extract_protocol:
Nuclei were extracted following the chopping extraction with the “RAISIN” (Ribosomes And Intact Single Nucleus) method described in Drokhlyansky et al. 2020 with the addition of 0.132M trehalose added to each buffer28,46. Whole mouse large intestine was cleaned of fat and fecal matter before being segmented into ~2-3 cm long pieces (3-4 segments) and flash frozen. Tissues were disaggregated in 1 mL of CST buffer + trehalose by mild chopping for 10 minutes on ice using Tungsten Carbide Straight 11.5 cm Fine Scissors (Fine Science Tools 14558-11). Each sample was then recombined with others from the same 2-3 cm segment and filtered through a 40-um strainer (Falcon). The filters were washed with 1 additional mL of CST buffer + trehalose. 3 mL of ST (Salts and Tris) + trehalose was added to extracted nuclei before pelleting at 500 xg for 5 minutes at 4 ºC. The supernatant was discarded, and the pellet was resuspended in 100-500 µL of ST + trehalose buffer. DNA was dyed with 5 μM Vybrant DyeCycle Ruby stain (ThermoFisher V-10273) at 37 ºC for 15-30 minutes protected from light. The samples were then kept on ice in the dark until sorting.
RNA Libraries were prepared by Single Cell Discoveries as following the SMART-Seq2 protocol.

value: Colon


title: PDAC_19, Untreated

description:
Library name: PDAC_19
FFPE pancreatic tumor RNA-seq, patient PDAC_19, condition: Untreated, run: run_3


title: Chow diet, subcutaneous white adipose, wild-type repicate 1

description: Library name: RB13


title: Neuronal Nuclei, WT+ASO, plate7

description:
Library name: Plate 7
Metadata for plate included in p007-Meta.csv


title: normal liver tissue 03.fastq.gz

description:
Library name: Sample 08
tissues were obtained from patients undergoing surgery


title: PDAC_18, Untreated

description:
Library name: PDAC_18
FFPE pancreatic tumor RNA-seq, patient PDAC_18, condition: Untreated, run: run_3


title: normal liver tissue 02.fastq.gz

description:
Library name: Sample 07
tissues were obtained from patients undergoing surgery


title: Chow diet, gonadal white adipose, Sphk2 deleted repicate 3

description: Library name: RB12

source_name: gonadal white adipose

value: gonadal white adipose


title: Neuronal Nuclei, WT+ASO, plate6

description:
Library name: Plate 6
Metadata for plate included in p006-Meta.csv


title: PDAC_17, Untreated

description:
Library name: PDAC_17
FFPE pancreatic tumor RNA-seq, patient PDAC_17, condition: Untreated, run: run_3


title: Neuronal Nuclei, WT+ASO, plate5

description:
Library name: Plate 5
Metadata for plate included in p005-Meta.csv


title: normal liver tissue 01.fastq.gz

description:
Library name: Sample 06
tissues were obtained from patients undergoing surgery


title: Chow diet, gonadal white adipose, Sphk2 deleted repicate 2

description: Library name: RB11


title: Chow diet, gonadal white adipose, Sphk2 deleted repicate 1

description: Library name: RB10


title: PDAC_13, Treated

description:
Library name: PDAC_13
FFPE pancreatic tumor RNA-seq, patient PDAC_13, condition: Treated, run: run_2

value: Treated


title: Hepatic fibrosis tissue 05.fastq.gz

description:
Library name: Sample 05
tissues were obtained from patients undergoing surgery


title: Neuronal Nuclei, WT+ASO, plate4

description:
Library name: Plate 4
Metadata for plate included in p004-Meta.csv


title: PDAC_12, Treated

description:
Library name: PDAC_12
FFPE pancreatic tumor RNA-seq, patient PDAC_12, condition: Treated, run: run_2


title: Chow diet, gonadal white adipose, wild-type repicate 3

description: Library name: RB09

value: wild-type


title: Neuronal Nuclei, WT+ASO, plate3

description:
Library name: Plate 3
Metadata for plate included in p003-Meta.csv


title: PDAC_11, Treated

description:
Library name: PDAC_11
FFPE pancreatic tumor RNA-seq, patient PDAC_11, condition: Treated, run: run_2


title: Hepatic fibrosis tissue 04.fastq.gz

description:
Library name: Sample 04
tissues were obtained from patients undergoing surgery


title: Hepatic fibrosis tissue 03.fastq.gz

description:
Library name: Sample 03
tissues were obtained from patients undergoing surgery


title: Neuronal Nuclei, WT+ASO, plate2

description:
Library name: Plate 2
Metadata for plate included in p002-Meta.csv


title: PDAC_09, Treated

description:
Library name: PDAC_09
FFPE pancreatic tumor RNA-seq, patient PDAC_09, condition: Treated, run: run_2


title: Chow diet, gonadal white adipose, wild-type repicate 1

description: Library name: RB07


title: Hepatic fibrosis tissue 02.fastq.gz

description:
Library name: Sample 02
tissues were obtained from patients undergoing surgery


title: Chow diet, brown adipose, Sphk2 deleted repicate 3

description: Library name: RB06

value: brown adipose


title: Hepatic fibrosis tissue 01.fastq.gz

description:
Library name: Sample 01
tissues were obtained from patients undergoing surgery


title: KrasG12D+Trp53R172H,rep6

city: Baltimore

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

description:
Library name: KPC_6
Column name in raw_count_all.txt:KPC_6

data_processing:
reads passed QC  are aligned to humann  reference hg38 using aligner HiSat (HISAT2-2.1.0)
read counts were estimated using htseq (2.1.0)
ERCC normalization and batch effect correction is done using RUVseq(1.38.0)
Differential expression analysis is conducted using DESeq2(1.44.0)
Assembly: hg38
Supplementary files format and content: tab-delimited files included the raw counts for each sample.

source_name: Pancreas

growth_protocol: The mice were housed in controlled temperature, humidity, and scheduled light and dark cycles, in groups of no more than five per cage. Food and water were freely available to animals. Cohort age-(>3-5 weeks) and sex-matched mice with the genotypes: (i) Pdx1-Cre (P)/ROSA26-LSL-rtTA-IRES-GFP (G)/LSL-KrasG12D (R) (or PGR) mice; and (ii) Pdx1-Cre/ROSA26-LSL-rtTA-IRESGFP/Twist1-tetO-Luc (T) (or PGT) mice; and (iii) Pdx1-Cre/ROSA26-LSL-rtTA-IRES-GFP/LSL-KrasG12D/Twist1-tetO-Luc (or PGRT) were used in this study. Gene expression in the mouse pancreas was induced using the Pdx1 (Pancreatic and duodenal homeobox 1) promoter-Cre (P) allele to specifically express the Cre recombinase in pancreatic ductal epithelium leading to the stable expression of the KrasG12D oncogene (R) and rtTA-IRES-GFP (G) alleles. Twist1 expression used a reverse tetracycline-controlled transactivator (rtTA), which is knocked in within Rosa26 locus. Doxycycline (DOX) (2 mg/mL in drinking water to 3.4-5 weeks old mice) was added for the temporal gene expression of Twist1. The animals were followed for the  pancreatic cancer symptoms and necropsy was performed to collect the tissues for further analysis. Mice age was indicated in the figure legends for the progression of cancer in genotypes (PGR and PGRT).

extract_protocol:
Total RNA from each sample was extracted using TRIzol Reagent and qc was done through a NanoDrop (Thermo Fisher Scientific Inc.) and agarose gel (1%).
To prepare the library, 1µg of total RNA was used. The libraries of cDNA were prepared using TruSeq sample preparation kit and enriched for mRNA with rRNA depletion and with ERCC spike-in

value: Pancreas


title: Chow diet, brown adipose, Sphk2 deleted repicate 2

description: Library name: RB05


title: PDAC_06, Treated

description:
Library name: PDAC_06
FFPE pancreatic tumor RNA-seq, patient PDAC_06, condition: Treated, run: run_1


title: KrasG12D+Trp53R172H,rep5

description:
Library name: KPC_5
Column name in raw_count_all.txt:KPC_5


title: 22Rv1 cells, rs11067228 WT#2

city: Tianjin Shi

first: Yuan

last: Jiang

state: Tianjin Shi

address: No. 94 Weijin Road, Nankai District, Tianjin

institute: Nankai University

data_processing:
Clean reads were mapped to the Ensemble hg19 human genome using Hisat2 with default parameters.
Gene reads were counted by Htseq. Fold changes (FC) were computed as a log2 ratio of normalized reads per gene using the DEseq2 R package.
Assembly: hg19
Supplementary files format and content: Tab-delimited includes raw counts for each sample.

growth_protocol: 22Rv1 cell lines were obtained from ATCC. Cells were incubated at 37 ℃ in 5% CO2 and cultured in complete RPMI1640 (Gibco) supplemented with 10% FBS (Bio-logical Industries) and 1% Penicillin/Streptomycin (Gibco).

extract_protocol:
Total RNA was isolated from cultured cells using TRIzol reagent (ThermoFisher Scientific, 15596018) based on the manufacturer’s protocol. 2 μg RNA was reverse transcribed to cDNA using the PrimeScript RT reagent with a gDNA eraser Kit (Takara, no. RRO47B).RNA libraries were prepared for sequencing using standard Illumina protocols
RNA libraries were prepared for sequencing using standard Illumina protocols


title: Chow diet, brown adipose, Sphk2 deleted repicate 1

description: Library name: RB04


title: KrasG12D+Trp53R172H,rep4

description:
Library name: KPC_4
Column name in raw_count_all.txt:KPC_4


title: Chow diet, brown adipose, wild-type repicate 3

description: Library name: RB03


title: KrasG12D+Trp53R172H,rep3

description:
Library name: KPC_3
Column name in raw_count_all.txt:KPC_3


title: PDAC_03, Treated

description:
Library name: PDAC_03
FFPE pancreatic tumor RNA-seq, patient PDAC_03, condition: Treated, run: run_1


title: PDAC_01, Treated

description:
Library name: PDAC_01
FFPE pancreatic tumor RNA-seq, patient PDAC_01, condition: Treated, run: run_1


title: Chow diet, brown adipose, wild-type repicate 2

description: Library name: RB02


title: 22Rv1 cells, rs11067228 MUT#1

value: rs11067228 mutation (MUT)


title: Chow diet, brown adipose, wild-type repicate 1

description: Library name: RB01


title: 22Rv1 cells, rs11067228 KO#3

value: rs11067228 knockout (KO)


title: KrasG12D+Trp53R172H,rep1

description:
Library name: KPC_1
Column name in raw_count_all.txt:KPC_1


title: tumor tissue derived from FFPE synovial sarcoma sample AYA13

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

institute: IRCCS Istituto Nazionale dei Tumori

description: Library name: AYA13

data_processing:
Raw sequencing data underwent quality assessment using FastQC. High-quality reads were aligned to the human reference genome (hg38) using the STAR aligner (v2.7.10a). Gene-level quantification was performed with featureCounts (v1.6.4) to obtain raw read counts. For gene expression analysis, we applied the voom/limma pipeline. Genes with fewer than 10 reads in more than 95% of samples were excluded to reduce background noise. Normalization was conducted using the trimmed mean of M-values (TMM) method to account for differences in library size and reduce technical variability. The data were then transformed using voom, which converts raw counts into log2 counts per million (log2-CPM) and assigns precision weights to each observation. Differential expression analysis was performed using these transformed values, and P values were adjusted for multiple comparisons using the Benjamini-Hochberg false discovery rate (FDR) method. Differential expressed protein coding genes were selected at 0.05 adjusted p-value and 1.5 fold change cut off values.
Assembly: hg18
Supplementary files format and content: compressed FASTQ file obtained from each strand sequencing for all the samples

source_name: cancer tissue

extract_protocol:
Total RNA was extracted after the manually microdissection of neoplastic cells from tumor-representative FFPE  8–10 µm thick sections using the Maxwell® RSC RNA FFPE Kit (Cat: AS1440, Promega Corporation, Madultison, WI, USA) on a semi-automated Maxwell® RSC extractor (Promega) and following the manufacturer’s instructions
Libraries for RNAseq were performed using Illumina Stranded Total RNA Prep with Ribo-ZeroTM Plus (Cat: 20040525, Illumina, San Diego, CA, USA) according to the manufacturer's protocol. Final libraries with optimal quality and quantity criteria, assessed by D1000 Screen tape kit (Agilent Technologies) and Qubit® dsDNA High Sensitivity Assay Kit (Thermofisher) were run on NextSeq550 sequencer (Illumina)

value: soft tissue

value: synovial sarcoma


title: 22Rv1 cells, rs11067228 KO#2


title: KrasG12D+Twist1 overexpression Late,rep9

description:
Library name: PGRT_4-6M_PDAC9
Column name in raw_count_all.txt:PGRT_4-6M_PDAC9

value: KrasG12D+Twist1 overexpression Late


title: 22Rv1 cells, rs11067228 KO#1


title: KrasG12D+Twist1 overexpression Late,rep8

description:
Library name: PGRT_4-6M_PDAC8
Column name in raw_count_all.txt:PGRT_4-6M_PDAC8


title: 22Rv1 cells, WT rep3

description: 22Rv1_WT_hm_rep 3


title: MLL-AF9+ WT fetal liver cells, sample 2

city: Chicago

first: Yan

last: Liu

state: IL

address: 303 E. Superior Street, Lurie 5-107, Northwestern University

department: Department of Medicine

institute: Northwestern University

description:
Library name: MLL-AF9_WT_2
WT3

data_processing:
Raw reads were aligned to the mm10 mouse genome using STAR RNA-seq aligner
Uniquely mapped reads and mapping statistics were generated using STAR and bamutils
Reads mapped to genes were quantified using featureCounts, and reads mapped to rRNA were quantified using bowtie2
Gene-level expression values were calculated and reported as raw read counts, logCPM (log Counts Per Million), and logRPKM (log Reads Per Kilobase of transcript per Million mapped reads) for each sample
Differential expression analysis between KO and WT samples was performed, including log2 fold change, average expression (logCPM), p-values, and false discovery rate (FDR); Values lower than 1e-299 were rounded to 0 due to Excel limitations
Assembly: mm10
Supplementary files format and content: Excel file includes raw counts for each sample

source_name: Fetal liver

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Plus Kit
Libraries were prepared using the standard RNA-Seq library preparation protocol

value: Fetal liver

value: Leukemia-initiating cells

value: Wildtype


title: KrasG12D+Twist1 overexpression Late,rep7

description:
Library name: PGRT_4-6M_PDAC7
Column name in raw_count_all.txt:PGRT_4-6M_PDAC7


title: tumor tissue derived from FFPE synovial sarcoma sample AYA10

description: Library name: AYA10


title: MLL-AF9+ WT fetal liver cells, sample 1

description:
Library name: MLL-AF9_WT_1
WT2


title: aorta, angiotensinII, KO, male, rep03

city: Halle

first: Alexander

last: Nolze

address: Magdeburger Strasse 6

country: Germany

institute: MLU Halle-Wittenberg

data_processing:
adaptor removal: cutadapt 1.8.1
alignment: Tophat 2.0.14 with bowtie2 2.2.5
counting: featureCounts 1.4.6
Assembly: mm10
Supplementary files format and content: txt file containing raw counts obtained after Counting with featureCounts

source_name: aorta

growth_protocol: see experimental design

extract_protocol:
Total RNA was isolated with TriZol Reagent, following the manufacturer's instructions. Eventual gDNA contaminations were removed using Turbo DNAse (ambion, Life Technologies).
rRNA were removed using RiboMinus (Life Technologies) according to the manufacturer's instructions. RNA was fragmented (w/ Tris-acetate, Potassium acetate and Magnesium acetate) and precipitated (w/ 100% Ethanol, Ammonium acetate and glycogen). Resulting RNAs were used to generate cDNA libraries using Illumina index adapters.  10nM of pools of up to 10 libraries were used for cluster generation (Illumina cBot).

treatment_protocol: see experimental design

value: aorta

value: Ppp3cb KO

value: angiotensinII


title: 22Rv1 cells, WT rep1

description: 22Rv1_WT_hm_rep 1

value: WT


title: KrasG12D+Twist1 overexpression Late,rep5

description:
Library name: PGRT_4-6M_PDAC5
Column name in raw_count_all.txt:PGRT_4-6M_PDAC5


title: tumor tissue derived from FFPE synovial sarcoma sample AYA8

description: Library name: AYA8


title: aorta, angiotensinII, KO, male, rep02


title: RWPE1_H3K27ac_ChIP

library_source: genomic

data_processing:
Reads were mapped to the GRCh37/hg19 reference genome using HISAT2 and further analyzed with the HOMER (Hypergeometric Optimization of Motif Enrichment) package.
Assembly: hg19
Supplementary files format and content: bigwig

molecule: genomic DNA

extract_protocol:
1 × 10^7 cells were cross-linked with 1% formaldehyde and quenched in 0.125 M glycine. Cell pellets were harvested in Farnham lysis buffer [50 mM Tris-HCl (pH 7.5), 150 mM NaCl, 0.5% NP-40, 5 mM EDTA, 1% Triton X-100] supplemented with 1 mM phenylmethylsulfonyl fluoride (PMSF) and 1× protease inhibitor cocktail and incubated 30 min on ice to isolate nuclei. Nuclei were suspended in SDS lysis buffer [1% SDS, 50 mM Tris-HCl, 10 mM EDTA and 1× protease inhibitor cocktail] and sonicated to shear chromatin to DNA fragment sizes of 100-500 base pairs (bp). Supernatants were collected by centrifuging at 12,000 rcf for 10 mins at 4°C and precleared 1 h with 50 μl protein G agarose beads (Invitrogen). 2% of the precleared sample served as input, and the remainder was immunoprecipitated with 5 μg H3K27ac antibody (ab4729, Abcam) bound to 50 μl protein G agarose beads at 4°C overnight. Beads were washed 5 times with LiCl IP washing buffer [100 mM Tris-HCl (pH7.5), 500 mM LiCl, 1% NP-40 and 1% sodium deoxycholate] and cross-links were reversed in buffer containing Proteinase K overnight at 65°C. Finally, DNA was purified using a PCR Purification Kit (Qiagen) and eluted in 30 μl H2O. Precipitated and input DNA were sequenced using an Illumina HiSeq4000 sequencer platform.
Library was constructed using TruePrep® DNA Library Prep Kit V2 for Illumina and sequenced.

tag: antibody

value: H3K27ac antibody (ab4729, Abcam)


title: KrasG12D+Twist1 overexpression Late,rep4

description:
Library name: PGRT_4-6M_PDAC4
Column name in raw_count_all.txt:PGRT_4-6M_PDAC4


title: tumor tissue derived from FFPE synovial sarcoma sample AYA7

description: Library name: AYA7


title: aorta, angiotensinII, KO, male, rep01


title: RWPE1_ChIP_Input


title: Chow diet, gonadal white adipose, wild-type repicate 2

description: Library name: RB08

value: gonadal white adipose


title: Tau5, eCLIP, AD Low 1

city: Gainesville

first: John

last: Koren

state: FL

address: 1275 Center Dr

institute: University of Florida

description:
Library name: 20-031-IP
Tau5-eCLIP

data_processing:
Eclipse's proprietary analysis pipeline (v1). UMIs were pruned from read sequences using umi_tools (v1.1.1). Next, 3' adapters were trimmed from reads using cutadapt (v3.2). Reads were then mapped to a custom database of repetitive elements and rRNA sequences. All non-repeat mapped reads were mapped to the hg38 genome using STAR (v2.7.7a). PCR duplicates were removed using umi_tools (v1.1.1). For each peak, IP versus input fold enrichments and p-values were calculated. Peaks were annotated using transcript information from GENCODE v41 with the following priority hierarchy to define the final annotation of overlapping features: protein coding transcript (CDS, UTRs, intron), followed by non-coding transcripts (exon, intron).
Assembly: Human (hg38)
Supplementary files format and content: excel filss with gene ID, ensemble ID, -log10(P-value), Log2 Fold Change, and feature
Library strategy: iCLIP

source_name: hippocampus

extract_protocol:
Frozen human hippocampal samples tissue was disrupted by cryogrinder and UV crosslinked at 400 mJoules/cm2 with 254 nm radiation
Van Nostrand, E.L., et al., Robust, Cost-Effective Profiling of RNA Binding Protein Targets with Single-end Enhanced Crosslinking and Immunoprecipitation (seCLIP). Methods Mol Biol, 2017. 1648: p. 177-200.

value: hippocampus

value: ApoE 3/3


title: Neuronal Nuclei, WT+ASO, plate1

description:
Library name: Plate 1
Metadata for plate included in p001-Meta.csv

value: Colon


title: genomic DNA from maternal peripheral blood [0464-V3]

type: genomic

city: Kalyani

first: Arindam

last: Maitra

state: West Bengal

address: PO: NSS

country: India

institute: National institute of Biomedical Genomics

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium EPIC BeadChip using standard Illumina protocol.

scan_protocol: Arrays were imaged using GenomeStudio using standard recommended Illumina scanner setting.

data_processing: GenomeStudio software (Illumina) version 2011.1.

label: Cy5 and Cy3

source_name: peripheral blood

label_protocol: Standard Illumina Protocol.

extract_protocol: Genomic DNA was extracted and purified from peripheral blood samples using QIAamp blood midi kit (Qiagen) according to manufacturer’s protocol.

tag: Sex

value: Female

value: Peripheral blood

tag: status

value: Pregnant

tag: time point

value: Sampled during 26-28 weeks of gestation

tag: delivery

value: Preterm

tag: individual


title: P2 cerebellar cells, Wildtype1, KDM1A CUTRUN

city: Memphis

first: Xinwei

last: Cao

state: TN

address: 62 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description:
Library name: Wildtype1_CUTRUN, KDM1A
KDM1A CUTRUN of Wildtype1

data_processing:
TrimGalore v0.6.3 was used to trim bulk RNA-seq reads prior to alignment against GRCm38.p6 with STAR v2.7.9a (Gencode M22) and quantification with RSEM v1.3.3. Differential expression was tested with limma-voom (limma v3.42.2, R v4.1.0) on TMM-normalized counts from genes with CPM > 0.1 in at least one condition. For scRNA-seq (Parse Evercode WT), FASTQs were processed with Parse Trailmaker (mm10), and cells passing QC (≥800 UMIs, <5% mitochondrial reads) were retained after doublet removal. Seurat v4.4.0 was used for log-normalization, variable feature selection (2,000 VST features), PCA, and Leiden clustering on 20 PCs without batch correction. ATAC-seq reads were trimmed with Trim-Galore v0.4.4/cutadapt (Q20, first 15 bp removed), aligned with BWA-MEM v0.7.17, and deduplicated with fq2bam v3.0.0.6. Only fragments <2 kb were used; bigWigs were built from 80 bp fragment centers normalized to 20M fragments (UCSC tools v4). Per-sample peaks from MACS2 v2.1.1 were merged across replicates, and differential accessibility was tested with ComBat-seq + edgeR TMM + limma-voom. CUT&RUN reads were trimmed with Trim-Galore v0.4.4/cutadapt (Q20), aligned with bwa aln/samse v0.7.12, and duplicate-marked with biobambam2 v2.0.87. Fragments <2 kb were retained for bigWig generation (80 bp fragment centers, 10M fragment normalization, UCSC tools v4). Narrow peaks for TFs were called with MACS2 v2.1.1 and broad peaks for histone marks with SICER v1.1.
Assembly: Mouse mm10
Supplementary files format and content: Tab separated values files, bigwig files, comma separated values files and matrix files
Library strategy: CUT&Run

source_name: Cerebelleum

extract_protocol:
For Bulk RNA-seq, P2 mouse cerebella were dissected from individual pups in cold PBS and immediately processed for total RNA extraction. For scRNA-seq, P7 cerebella were dissected from individual pups (one cerebellum per sample, no pooling) and dissociated into a single-cell suspension with a papain-based kit (Miltenyi Biotec 130-094-802); 1 × 10⁶ cells per animal were fixed with the Parse Biosciences Evercode Fixation v3 kit (ECWT3300), slow-frozen in a Mr. Frosty container, and stored at −80 °C until library preparation. For ATAC-seq, P2 cerebella were dissected in cold PBS and nuclei isolated by brief lysis in cold ATAC lysis buffer prior to Tn5 tagmentation. For CUT&RUN, P2 cerebella were dissected in cold PBS, dissociated into a single-cell/nuclei suspension, immobilized on Concanavalin A–coated magnetic beads, and processed for antibody incubation and pAG-MNase digestion.
For Bulk RNA-seq, total RNA was isolated from P2 cerebella using the Direct-zol RNA MiniPrep kit (Zymo Research #R2052), and sequencing libraries were prepared with the Illumina Stranded Total RNA Prep library kit (Illumina #20040529) according to the manufacturer's instructions. For scRNA-seq, fixed cells were thawed and loaded onto the Parse Biosciences Evercode WT v3 kit, then processed through split-pool combinatorial barcoding per the manufacturer's protocol with a target recovery of ~100,000 cells. For ATAC-seq, nuclei isolated from P2 cerebella were tagmented with the Tn5 transposase using the ATAC-seq kit (Active Motif 53150) and libraries were prepared according to the manufacturer's instructions. For CUT&RUN, cells/nuclei from P2 cerebella were bound to Concanavalin A–coated magnetic beads and incubated at room temperature for 4 h with antibodies against TEAD1, HA (for INSM1 in Insm1^HA/HA^ tissue), KDM1A, H3K4me3, H3K27me3, or H3K27ac, or rabbit IgG as a negative control; chromatin was digested by Ca²⁺-activated pAG-MNase, released fragments purified, and libraries prepared. CUT&RUN libraries were prepared using the NEBNext Ultra II kit (NEB #E7103) with modifications as in https://dx.doi.org/10.17504/protocols.io.bagaibse. Library size and quality for all assays were assessed on an Agilent TapeStation/ Bioanalyzer prior to sequencing.

value: Cerebelleum


title: P2 cerebellar cells, Wildtype1, IgG Control

description:
Library name: Wildtype1_CUTRUN, IgG
IgG Control CUTRUN of Wildtype1


title: PDAC_07, Treated

description:
Library name: PDAC_07
FFPE pancreatic tumor RNA-seq, patient PDAC_07, condition: Treated, run: run_1

value: pancreas

value: Treated


title: Tau5, eCLIP, AD Low 2

description:
Library name: 110-0337-IP
Tau5-eCLIP


title: P2 cerebellar cells, Tead1/2 mutant3, ATACSeq

description:
Library name: Tead_Mutant3_ATACSeq
Genome-wide chromatin accessibility of TEAD Mutant3

data_processing:
TrimGalore v0.6.3 was used to trim bulk RNA-seq reads prior to alignment against GRCm38.p6 with STAR v2.7.9a (Gencode M22) and quantification with RSEM v1.3.3. Differential expression was tested with limma-voom (limma v3.42.2, R v4.1.0) on TMM-normalized counts from genes with CPM > 0.1 in at least one condition. For scRNA-seq (Parse Evercode WT), FASTQs were processed with Parse Trailmaker (mm10), and cells passing QC (≥800 UMIs, <5% mitochondrial reads) were retained after doublet removal. Seurat v4.4.0 was used for log-normalization, variable feature selection (2,000 VST features), PCA, and Leiden clustering on 20 PCs without batch correction. ATAC-seq reads were trimmed with Trim-Galore v0.4.4/cutadapt (Q20, first 15 bp removed), aligned with BWA-MEM v0.7.17, and deduplicated with fq2bam v3.0.0.6. Only fragments <2 kb were used; bigWigs were built from 80 bp fragment centers normalized to 20M fragments (UCSC tools v4). Per-sample peaks from MACS2 v2.1.1 were merged across replicates, and differential accessibility was tested with ComBat-seq + edgeR TMM + limma-voom. CUT&RUN reads were trimmed with Trim-Galore v0.4.4/cutadapt (Q20), aligned with bwa aln/samse v0.7.12, and duplicate-marked with biobambam2 v2.0.87. Fragments <2 kb were retained for bigWig generation (80 bp fragment centers, 10M fragment normalization, UCSC tools v4). Narrow peaks for TFs were called with MACS2 v2.1.1 and broad peaks for histone marks with SICER v1.1.
Assembly: Mouse mm10
Supplementary files format and content: Tab separated values files, bigwig files, comma separated values files and matrix files

value: Atoh1Cre;Tead1fl/fl; ;Tead2fl/fl


title: PDAC_05, Treated

description:
Library name: PDAC_05
FFPE pancreatic tumor RNA-seq, patient PDAC_05, condition: Treated, run: run_1


title: KrasG12D+Twist1 overexpression Late,rep3

description:
Library name: PGRT_4-6M_PDAC3
Column name in raw_count_all.txt:PGRT_4-6M_PDAC3

value: Pancreas

value: KrasG12D+Twist1 overexpression Late


title: tumor tissue derived from FFPE synovial sarcoma sample AYA6

description: Library name: AYA6

value: soft tissue

value: synovial sarcoma


title: 22Rv1 cells, rs11067228 WT#1


title: LNCaP_H3K27ac_ChIP

source_name: LNCaP

value: LNCaP

value: H3K27ac antibody (ab4729, Abcam)


title: KrasG12D+Twist1 overexpression Late,rep2

description:
Library name: PGRT_4-6M_PDAC2
Column name in raw_count_all.txt:PGRT_4-6M_PDAC2


title: LNCaP_ChIP_Input


title: aorta, control, KO, male, rep02

value: aorta

value: Ppp3cb KO

value: control


title: aorta, control, KO, male, rep03


title: KrasG12D+Twist1 overexpression Late,rep1

description:
Library name: PGRT_4-6M_PDAC1
Column name in raw_count_all.txt:PGRT_4-6M_PDAC1


title: tumor tissue derived from FFPE synovial sarcoma sample AYA5

description: Library name: AYA5


title: tumor tissue derived from FFPE synovial sarcoma sample AYA4

description: Library name: AYA4


title: 22Rv1 cells, rs11067228 MUT#2

value: rs11067228 mutation (MUT)


title: KrasG12D+Trp53R172H,rep2

description:
Library name: KPC_2
Column name in raw_count_all.txt:KPC_2


title: tumor tissue derived from FFPE synovial sarcoma sample AYA14

description: Library name: AYA14


title: aorta, control, KO, male, rep01


title: KrasG12D+Twist1 overexpression Early,rep3

description:
Library name: PGRT_2-4M_3
Column name in raw_count_all.txt:PGRT_2-4M_3

value: KrasG12D+Twist1 overexpression Early


title: C4-2B_H3K27ac_ChIP


title: tumor tissue derived from FFPE synovial sarcoma sample AYA3

description: Library name: AYA3


title: aorta, angiotensinII, WT, male, rep03

value: wildtype

value: angiotensinII


title: C4-2B_ChIP_Input


title: KrasG12D+Twist1 overexpression Early,rep2

description:
Library name: PGRT_2-4M_2
Column name in raw_count_all.txt:PGRT_2-4M_2


title: aorta, angiotensinII, WT, male, rep02


title: KrasG12D+Twist1 overexpression Early,rep1

description:
Library name: PGRT_2-4M_1
Column name in raw_count_all.txt:PGRT_2-4M_1


title: MLL-AF9+ Prl2KO fetal liver cells, sample 2

description:
Library name: MLL-AF9_Prl2KO_2
KO3

value: Fetal liver

value: Leukemia-initiating cells

value: Prl2 knockout


title: 22Rv1_H3K27ac_ChIP


title: tumor tissue derived from FFPE synovial sarcoma sample AYA12

description: Library name: AYA12


title: tumor tissue derived from FFPE synovial sarcoma sample AYA2

description: Library name: AYA2


title: tumor tissue derived from FFPE synovial sarcoma sample AYA1

description: Library name: AYA1


title: aorta, angiotensinII, WT, male, rep01


title: 22Rv1_ChIP_Input


title: KrasG12D,rep3

description:
Library name: PGR_4-6M_3
Column name in raw_count_all.txt:PGR_4-6M_3


title: tumor tissue derived from FFPE synovial sarcoma sample adult 8

description: Library name: adult 8


title: aorta, control, WT, male, rep03


title: MLL-AF9+ Prl2KO fetal liver cells, sample 1

description:
Library name: MLL-AF9_Prl2KO_1
KO2


title: 4C-7228en_rep 2

description: 22Rv1_7228en_4C_rep 2

library_source: other

data_processing:
*library strategy: 4C-seq
Raw fastq files (paired-end data) were first trimmed to remove adaptor sequences using Trim Galore and then processed through the HiC-Pro pipeline to create valid interacting pairs and raw contact count matrices.
Assembly: hg19
Supplementary files format and content: bedgraph, read count of restriction fragments

molecule: other

extract_protocol:
1 × 10^7 cells were cross-linked in 1% formaldehyde at room temperature for 10 min, and then quenched by 0.125 M glycine. Nuclei were resuspended in 5 ml cold lysis buffer (10 mM Tris- HCl pH 7.5, 10 mM NaCl, 5 mM MgCl2, 10 mM EGTA, 0.2% NP-40 and 1 mM PMSF), incubated on ice for 10 min, and then digested with 400 U DpnII enzyme at 37°C with rotation, followed by addition of 4000 U T4 DNA ligase for in-situ ligation overnight at 16°C. Ligated DNA was de-crosslinked overnight using 30 μl of buffer containing Proteinase K (10 mg/ml) at 65°C overnight. Remaining RNA was removed by treatment with 30 μl RNase A (10 mg/ml) and incubation at 37 °C for 45 min. DNA was extracted with an equivalent volume of phenol/chloroform/isoamyl alcohol, and pellets were dissolved in 150 μl 10 mM Tris-HCl (pH 7.5). Purified DNA was digested with 100 U CviQI enzyme, which was then inactivated at 65 °C for 20 min and DNA was circularized by incubation 4 h with 4000 U T4 DNA ligase at room temperature. DNA was purified using phenol/chloroform and further purified using a QIAquick PCR purification kit. DNA concentration was determined using Qubit (Thermo Fisher). Circularized DNA was amplified with SNP-specific inverse primers (Table S6). Each 4C library was sequenced as 150 bp paired-end reads using the Illumina Hiseq 4000 system.
The 4C-seq library was constructed by amplification of template using the TruePrep® DNA Library Prep Kit V2 with locus- specific primers containing Illumina sequences.


title: tumor tissue derived from FFPE synovial sarcoma sample adult 7

description: Library name: adult 7


title: aorta, control, WT, male, rep02


title: KrasG12D,rep2

description:
Library name: PGR_4-6M_2
Column name in raw_count_all.txt:PGR_4-6M_2


title: KrasG12D,rep1

description:
Library name: PGR_4-6M_1
Column name in raw_count_all.txt:PGR_4-6M_1


title: tumor tissue derived from FFPE synovial sarcoma sample AYA11

description: Library name: AYA11


title: 4C-7228en_rep 1

description: 22Rv1_7228en_4C_rep 1


title: tumor tissue derived from FFPE synovial sarcoma sample adult 6

description: Library name: adult 6


title: aorta, control, WT, male, rep01


title: Twist1 Overexpression,rep 4

description:
Library name: PGT_4
Column name in raw_count_all.txt:PGT_4

value: Twist1 Overexpression


title: aorta, angiotensinII, KO, female, rep03


title: Sample 1_oldbdd 2 a

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

institute: University Clinic Bonn

data_processing:
Fastqc was used for quality analysis of the sequences. Cutadapt was used to remove the illumina universal adapter sequence in the reads. miARma-seq pipeline was used for further analysis. Tophat2 with bowtie algorithm was used as a mapper whereas gtf file of genome build HG38 from ensemble was used as annotation file. Read counts were generated from miARma-seq and Qlucore omics explorer 3.6 was used to convert read counts into expression value. Trimmed mean of M-values (TMM) normalization was performed using Qlucore Omics explorer 3.5, where the same gtf file was used to annotate genes. Gene with less than five read counts per sample were removed.
Assembly: hg38
Supplementary files format and content: tab delimited text file included TMM normalized values for each sample with ensemble gene id with chromosome and external gene names

source_name: Embryonic Kidney

growth_protocol: HEK28 specialized cell line with B-Domain Deleted Factor VIII and Full length Factor VIII were cultured until about 70% confluency in six well plates

extract_protocol:
RNA was purified using the PureLink™ RNA mini kit according to manufacturer’s instructions (Invitrogen 12183018A) from the collected cell pellets.
The concentration of the RNA was determined by measuring absorbance at 260 nm using NanoDrop One (ThermoFisher Scientific).
RNA samples of different cell clones were then sequenced on ILLUMINA sequencer. Raw reads files of different cell clones were generated using Illumina Hi-Seq 4000 as fastq files

treatment_protocol: No treatment

value: Embryonic Kidney

value: human embryonic kidney 293 cells

value: B-domain deleted FVIII


title: 958-pop2, Blasts

city: Roma

first: Serena

last: Travaglini

address: Via Montpellier 1

institute: Università di Roma Tor Vergata

data_processing:
Paired reads were aligned to the human reference genome (GRCh38/hg38) using the splice-aware aligner STAR v 2.5.0c
Per-gene read counts were generated using the STAR quantMode geneCounts option.
Raw per-gene read counts were then processed using the Bioconductor package DESeq2 package v. 1.30 in order to perform the differential expression analysis.
Assembly: hg38
Supplementary files format and content: excel with normalised counts

source_name: primary Acute myeloid leukemia cells

extract_protocol:
Trizol extraction
SMARTer Stranded Total RNA-Seq Kit v2- Pico Input Mammalian protocol.

value: primary Acute myeloid leukemia cells

tag: sorted cells

value: Blasts

tag: pair id


title: tumor tissue derived from FFPE synovial sarcoma sample adult 5

description: Library name: adult 5

value: soft tissue

value: synovial sarcoma


title: Twist1 Overexpression,rep 3

description:
Library name: PGT_3
Column name in raw_count_all.txt:PGT_3

value: Pancreas


title: tumor tissue derived from FFPE synovial sarcoma sample adult 4

description: Library name: adult 4


title: 804-pop1, Blasts


title: aorta, angiotensinII, KO, female, rep02

value: aorta

value: Ppp3cb KO


title: Twist1 Overexpression,rep 2

description:
Library name: PGT_2
Column name in raw_count_all.txt:PGT_2


title: tumor tissue derived from FFPE synovial sarcoma sample adult 3

description: Library name: adult 3


title: 552-pop5, Blasts


title: aorta, angiotensinII, KO, female, rep01


title: Twist1 Overexpression,rep 1

description:
Library name: PGT_1
Column name in raw_count_all.txt:PGT_1


title: aorta, control, KO, female, rep03

value: control


title: tumor tissue derived from FFPE synovial sarcoma sample adult 2

description: Library name: adult 2


title: tumor tissue derived from FFPE synovial sarcoma sample adult 1

description: Library name: adult 1


title: Renal tiusse_B31_uIR14d_hep

city: Changsha

first: Lijun

last: Yin

address: No. 139 Renmin Middle Road

institute: The Second Xiangya Hospital of Central South University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mm9
Supplementary files format and content: FPKM values for each Sample

source_name: kidney

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The unilateral renal ischemia-reperfusion (uIR) model was established as recently described. Briefly, mice were anesthetized with pentobarbital (50 mg/kg, i.p.). During surgery, a Homeothermic Blanket Control Unit (Harvard Apparatus Ltd., U.K.) was used to monitor and maintain the body temperature at 36.5±0.3 °C. A flank incision was made to expose the left renal pedicle, which was clamped for 30 min to induce ischemia before reperfusion, while the right kidney kept intact. with pentobarbital (50 mg/kg) for anesthesia, and their body temperature was maintained at 36.5±0.3°C with a Homeothermic Blanket Control Unit (Harvard Apparatus Ltd, U.K.). Bilateral renal pedicles were exposed through flank incisions and clamped for 30 minutes to induce ischemia. The clamps were removed to restore renal blood supply, and the mice were sacrificed 24 hours after reperfusion. The mice in sham group underwent the similar procedures without clamping the renal pedicles. The uIR mice received subcutaneous injections of Heparin (Hep, 5 units/mouse)  2 hours after the uIR procedure. Subsequent doses of Heparin with 5 units/mouse or NAH with 200ug/mouse were administered once daily until the day preceding sacrifice.

value: kidney

tag: strain

value: Mus

value: male


title: 49-pop3, Blasts


title: 37-pop7, Blasts


title: aorta, control, KO, female, rep02


title: Renal tiusse_B30_uIR14d_hep


title: 22Rv1 cells, WT rep2

description: 22Rv1_WT_hm_rep 2

value: WT


title: CNI patient 3

city: Cincinnati

first: Stella

last: Davies

state: OH

address: 3333 Burnet Ave

department: Cancer & Blood Disease Institute

institute: Cincinnati Children's Hospital

description: Library name: SDAI12

data_processing:
General bioinformatic analysis was performed via SEQUECNCE HUB app RNA-Seq Alignment v2.0.2 followed by RNA-Seq Differential Expression version 1.0.1. The analysis used STAR for alignment and Salmon for quantification (Transcripts Per Million, TPM), followed by DESeq2 to identify differentially expressed genes.
Assembly: Homo sapiens (PAR-masked)/GRCh38Decoy (RefSeq)
Supplementary files format and content: genes.tpm

source_name: Peripheral Blood

extract_protocol:
Cyropreserved neutrophils were rapidly thawed and RNA was isolated using using the MagMAX mirVana Total RNA Isolation Kit (ThermoFisher, A27828) according to the manufacturer’s instructions.
NEBNext Ultra II Directional RNA Library Prep kit was used for RNA-seq library preparation.

value: Peripheral Blood

value: Neutrophils


title: aorta, control, KO, female, rep01


title: 1388-pop6, Blasts


title: Renal tiusse_B24_uIR14d_hep


title: aorta, angiotensinII, WT, female, rep03

value: wildtype

value: angiotensinII


title: CNI patient 2

description: Library name: SDAI04


title: aorta, angiotensinII, WT, female, rep02


title: 804-pop3, LPCs

value: LPCs


title: aorta, angiotensinII, WT, female, rep01


title: Renal tiusse_B18_uIR14d


title: 552-pop3, LPCs

value: primary Acute myeloid leukemia cells


title: 49-pop2, LPCs


title: Abatacept + CNI, patient 2

description: Library name: SDAI09


title: aorta, control, WT, female, rep03


title: 37-pop3, LPCs


title: aorta, control, WT, female, rep01


title: 1388-pop3, LPCs


title: Renal tiusse_B11_sham

value: sham


title: Sham_HGG_P80

status: Public on Jun 29 2026

city: Houston

first: Qi

last: Te

address: 1250 Moursund st

institute: Baylor College of Medicine

description:
Library name: sample 3
10x genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (v3.0, 10x Genomics)
Assembly: mm10 mouse genome
Supplementary files format and content: matrix files and csv

source_name: brain

extract_protocol:
For scRNA seq, tumor-bearing mice were anesthetized under isoflurane inhalation. Tumors were dissected on ice based on the presence of GFP (Leica M80 stereomicroscope). Tumors were dissociated by incubation with papain (Worthington, no. LK003178) and DNaseI (Worthington, no. LK003172). Following the manufacturer’s instruction, red blood cells (RBC) were removed using an RBC removal kit (Miltenyi, 130-094-183). Debris was removed using a debris removal kit (Miltenyi, 130-109-398), followed by dead cell removal with the dead cell removal Kit (Miltenyi,130-090-101).
For scRNA seq, a single-cell gene expression library was prepared using the Chromium Single Cell Gene Expression 3v3.1 kit (10x Genomics, PN-1000268). In brief, single cells, reverse transcription reagents, gel beads containing barcoded oligonucleotides, and oil were loaded on a Chromium controller to generate single-cell Gel Beads-In-Emulsions (GEMs) where full-length cDNA was synthesized and barcoded for each single cell. Subsequently, the GEMs were broken, and cDNA from each single cell was pooled. Following cleanup using Dynabeads MyOne Silane Beads, cDNA was amplified by PCR. The amplified product is fragmented to optimal size before end-repair, A-tailing, and adaptor ligation. The final library was generated by amplification.

value: brain

value: tumor and tumor microenviroment cells

tag: surgery


title: PTS_HGG_P60

description:
Library name: sample 2
10x genomics

value: PTS


title: s6_t4w_Neo_Rep3_N5

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

institute: University of Turin

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_Blast ctrl) selection in mouse keratinocytes, replicate 3, 5 PCR upstream nt

data_processing:
Following quality controls (performed with FastQC), sequencing reads were trimmed of the common portion of the vector and upstream PCR nucleotides using Cutadapt v2.6 (options: -e 0.2 -a TGCCTACTGCCTCGGACTTCAAGGGGCTAGAATTC -g TAGTGAAGCCACAGATGTA -m 22 -M 22 -n 2 --discard-untrimmed). The extracted hairpin seed sequences (22 nt) were aligned to the reference shRNA library using Bowtie v1.2.3 (options: -a --best --strata -v 2 -m 1 -S -q). Counts per hairpin were retrieved running Samtools (v1.9) idxstats utility on BAM files.
Assembly: mm10/GRCm38.p6
Supplementary files format and content: Tab-delimited text files of raw read counts per hairpin / per sample.
Library strategy: ReGenT-seq

source_name: Keratinocytes

growth_protocol: Mouse keratinocytes were grownin low-calcium Dulbecco’s modified Eagle medium supplemented with 10% FBS, 100 U ml−1 penicillin–streptomycin, HCE cocktail consisting of hydrocortisone 0.5 μg ml−1, insulin 5 μg ml−1 (Thermo Fisher), cholera enterotoxin 10−10 M (Sigma-Aldrich) and EGF 10 ng ml−1 (PeproTech) and cultured at 37 °C in a humidifiedatmosphere, with 8% CO2.

extract_protocol:
30 millions of mouse keratinocytes expressing cell-activation reporter systems (with Krt6b promoter-Blasticidin resistance gene or Krt6b promoter-DTR gene) were transduced with 5% efficiency in triplicate. 48 h after infection cells were treated with G418 antibiotic (30 mg ml−1) for 10 days. At t=0 (day 11 after infection), replicates of G418-selected cells were subsequently split to generate the Treated group, treated with Blasticidin (30 μg ml−1) or Cholera Toxin (DT) (0.05 ng ml−1), and the Untreated group. t=3w (time 3 weeks) and t=4w (time 4 weeks) were collected in triplicate and stored for genomic DNA extraction (gDNA). Specifically, gDNA was isolated by two rounds of Phenol-Chloroform extraction.
DNA-sequencing libraries were generated by performing two consecutive PCR. For each sample, gDNA from 5-10 × 106 cells were used as template in three parallel PCR-1 reactions to amplify shRNA cassette. The three PCR-1 products were mixed and purified using AMPure XP beads (Beckman Coulter). For PCR-2, the purified PCR-1 product of each replicate was used as a template in two parallel PCR reactions to be tagged with standard Illumina adapter (p7, p5). The two PCR-2 were combined, checked on 2% agarose gel and then quantified. 100 ng DNA of each sampled were pooled together and purified on 0.6% agarose gel (Minielute gel extraction kit, Qiagen). The final library was quantified on a Bioanalyzer (Agilent). DNA libraries were sequenced on an Illumina NextSeq 500 platform, according to manufacturer's guideline (Illumina).

value: Keratinocytes

tag: replicate

tag: pcr upstream_nt

tag: time

tag: selection

value: Neo

tag: reporter


title: s6_t4w_Neo_Rep3_N0

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_Blast ctrl) selection in mouse keratinocytes, replicate 3, 0 PCR upstream nt

tag: cell type


title: Sham_HGG_P60

description:
Library name: sample 1
10x genomics

tag: tissue


title: s6_t4w_Neo_Rep2_N0

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_Blast ctrl) selection in mouse keratinocytes, replicate 2, 0 PCR upstream nt


title: s6_t4w_NeoBlast_Rep3_N5

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 4 weeks of NeoBlast selection, replicate 3, 5 PCR upstream nt

value: NeoBlast


title: s6_t4w_NeoBlast_Rep3_N0

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 4 weeks of NeoBlast selection, replicate 3, 0 PCR upstream nt


title: s6_t4w_NeoBlast_Rep2_N5

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 4 weeks of NeoBlast selection, replicate 2, 5 PCR upstream nt


title: s6_t3w_Neo_Rep3_N5

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_Blast ctrl) selection in mouse keratinocytes, replicate 3, 5 PCR upstream nt


title: s6_t3w_Neo_Rep3_N0

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_Blast ctrl) selection in mouse keratinocytes, replicate 3, 0 PCR upstream nt


title: s6_t3w_Neo_Rep2_N5

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_Blast ctrl) selection in mouse keratinocytes, replicate 2, 5 PCR upstream nt


title: s6_t3w_Neo_Rep2_N0

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_Blast ctrl) selection in mouse keratinocytes, replicate 2, 0 PCR upstream nt


title: s6_t3w_Neo_Rep1_N0

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_Blast ctrl) selection in mouse keratinocytes, replicate 1, 0 PCR upstream nt


title: 958-pop3, LPCs

tag: genotype


title: Renal tiusse_B29_uIR14d

value: kidney

tag: Sex

tag: treatment


title: (KT10434) BW3446UK5099 50uM +pep-7

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Library name: FIX10434-022
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

data_processing:
Multiplexed sequencing data were prepared using a preprocessing pipeline based on 10x Genomics CellRanger software using the Fixed RNA Profiling capability (version 9.0.1), with the 10x Genomics GRCh38/hg38 Human Transcriptome Reference (refdata-cellranger-GRCh38-3.0.0; based on the GRCh38 genome reference and Ensembl v93 transcriptome annotations; Released Nov. 19, 2018) to generate cell x UMI count matrices for each sample
Data from individual samples assembled across all wells were given a first pass of cell type labels using Seurat label transfer with reference to the PBMC dataset provided by the Satija Lab (Stuart and Butler, et al. (2019); DOI: 10.1016/j.cell.2019.05.031) and provided online with the Seurat PBMC scATAC-seq vignette (v 3.0; Compiled June 6, 2019).
scRNA counts matrices were normalized and scaled using Seurat. Cell populations were manually re-labelled via clustering using a combination of selected reference markers for each cell type. Doublets were identified and removed using Scrublet.
Assembly: Ensembl GRCh38-3.0.0
Supplementary files format and content: h5 files, gene expression matrix

source_name: Blood

growth_protocol: VST culture and fixation: Culture was performed using GREX-10, 6 well plates (Wilson Wolf), largely following a previously published rapid expansion protocol (Lazarski 2021). Briefly, PBMC were thawed, pelleted at 400 xg and resuspended in 2% BSA/PBS for counting. Cells were pelleted once again and resuspended at 1.5x107 cells per mL in CTL culture media including 300ng/mL each of CMV derived pp65 and IE-1 peptide pools (Peptivator, Milltenyi) or vehicle control (water). CTL culture media contained 44% RPMI, 44% Clicks, 10% FBS, 1% PenStrep, 1x Glutamax. Cells were incubated/pulsed for 1h at 37C. Following peptide pulse, cells were distributed into GREX-10 6 well plates containing 30mL total volume CTL media. Media was supplemented with IL4 (400U/mL), IL7, and/or IL15 (10ng/mL) as indicated. On day 7 of culture, the upper 15mL of media was carefully removed from each well without disturbing cells and replaced with 15mL fresh CTL media including 2x cytokine addition. If applicable, treatment with metabolic inhibitors UK5099 (Sigma), TWS-119 (Selleck Chem.) or vehicle/DMSO, was initiated on day 1 of culture. Further addition of inhibitors was done at 1x concentration and occurred only during day 7 media exchange. Individual wells were harvested at indicated timepoints during VST culture. Upon harvest, cells were washed 1x with cold 0.4% BSA/PBS followed by 1x with cold PBS alone prior to pelleting and resuspension in cold 10x fixation buffer per the standard FLEX protocol. Cells were counted and fixed at a maximum of 1x107 per mL fixation buffer. Fixation occurred for 20-26 hours at 4C. After fixation, cells were pelleted at 850 xg and resuspended in 1mL ice cold quenching buffer per 10x FLEX guideline. 10x Enhancer and 50% glycerol were added, prior to storage at -80°C, per 10x FLEX guidelines.

extract_protocol:
Single cells were encapsulated in Gel-Beads-in emulsion (GEMs) using the 10X Controller with a Chromium Single Cell FLEX GEM Library and Gel Bead kit.
REFLEX (Library prep, pre-amp): Following GEM incubation, 125 μL of Recovery Agent was added to break the GEM emulsion. Mixtures were inverted 10x and incubated for 2 minutes at room temperature. 125 μL of recovery agent was then carefully removed from the bottom of each well. The remaining approximately 65 μL of recovered GEM sample was combined with a master mix containing 27 μL of Amp Mix (10X PN-2000047), 10 μL of Pre-Amp Primers B (10XPN-20000529), 1.5 μL of TruSeq1 [1 μM], and 3 μL of a pre-mixed TCR Variable Primer Pool (See Supplemental Note [REF]) [0.66 μM] for a total volume of 106.5 μL of master mix plus recovered GEM. Samples were inverted 10x to mix and placed in a thermal cycler with the following cycling conditions: 98C for 3 minutes; 8 cycles of 98C/20 seconds, 60C for 30 seconds, 72C for 2 minutes; 72C for 5 minutes, 4C infinite hold. Upon completion of the PCR, tubes were pulsed briefly on a minifuge to collect liquid. 90 μL was then transferred into a new 1.5 mL Eppendorf tube. A 1.8X SPRI bead cleanup was performed and sample was eluted into 100 μL of elution solution in accordance with 10X User Guide CG000673 Rev B.
REFLEX (library prep, re-amplification): Pre-amplified library eluates were split into two or three pools for preparation of gene expression libraries,TCR libraries, and ADT libraries (when applicable). Gene expression and ADT libraries were prepared using 20uL pre-amp product and following 10x guidelines for Multiplexed samples with Feature Barcode technology for Protein using Barcode Oligo Capture (CG000673, Rev B). Linear PCR master mix for TCR libraries consisted of 20 μL 1X KAPA HiFi HotStart (Roche, KK260), 10 uL molecular biology grade water (Fisher, BP2819100), and 0.5 μL TruSeq2 primer at 123.4 nM per reaction. TCR libraries utilized 40 μL of pre-amp product total, divided into 4, 10 μL aliquots. Each 10 μL aliquot was combined with 30.5 μL master mix in a PCR strip tube and incubated with the following PCR program: 95C/3min activation, [98C/20s denaturation, 62C/30s annealing, 72C/90s extension] repeat x4 for 5 total cycles, 72C/5min final extension, hold 4C. After the 5 cycle linear PCR was completed, 0.5 μL TruSeq1, at 123.4 nM per reaction, was spiked into each reaction and an exponential PCR was performed with the following conditions: 95C/3 min activation, [98C/20s denaturation, 62C/30s annealing, 72C/90s extension] repeated x7 for 8 total cycles, 72C/5min final extension, hold 4C. Following exponential PCR, each of the four 41 μL reactions per library condition were repooled for a total volume of 164 μL. Samples were SPRI cleaned at 0.8X ratio, eluted in 50 μL aforementioned “elution solution ”.
REFLEX (Indexing TCR Libraries): PCR indexing master mix was prepared with 50 μL 1X Kapa HiFi HotStart and 10 μL molecular biology grade water per reaction. Indexing reactions combined 20 μL cleaned re-amplified product, 60 μL master mix, and 20 μL Dual Index TT Set A (10X Genomics, PN-1000215). Each library used a unique TT index well enabling later identification via sequencing. Samples were inverted to mix and briefly spun down. Thermocycler conditions used were as follows: 98C/45s activation [98C/20s denaturation, 54C/30s annealing, 72C/90s] repeated x12-15 for 13-16 total cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. A final SPRIselect bead clean up was performed at a 0.7X ratio with cleaned product eluted into 40 μL Buffer EB (Qiagen, Cat No. 19086).
REFLEX (Indexing GEX libraries): GEX library preparation was performed separately per 10x User Guide CG000673 Rev B, Sample Index PCR guidelines, Section 4.1, using 20 μL pre-amplification product with 60 μL Sample Index PCR Mix (Amp Mix PN-2000103, Water) and 20 μL of a unique well of Dual Index TS Set A primers (PN-3000511). The combined solution was gently mixed and spun down. PCR performed per the following guidelines: 98C/45s activate, [98C/20s denature, 54C/30s anneal, 72C/20s elongate] repeat 7-14x for a total 8 to 15 cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. Indexed products were cleaned using a 1.0X SPRIselect bead cleanup and eluted in 40 μL Buffer EB.
REFLEX (Indexing ADT libraries): ADT library preparation was performed separately per 10x User Guide CG000673 Rev B, Sample Index PCR guidelines, Section 5.1, using 20 μL pre-amplification product with 60 μL Sample Index PCR Mix (Amp Mix PN-2000103, Water) and 20 μL of a unique well of Dual Index TN Set A primers for the ADT libraries (10X, PN 1000250). The combined solution was gently mixed and spun down. PCR performed per the following guidelines: 98C/45s activate, [98C/20s denature, 54C/30s anneal, 72C/20s elongate] repeat 7-14x for a total 8 to 15 cycles, 72C/60s final extension, hold 4C. Cycle number was adjusted to account for cell input during GEM generation. Indexed products were cleaned using a 1.0X SPRIselect bead cleanup and eluted in 40 μL Buffer EB.
Sequencing: Final scRNAseq libraries were sequenced using a NovaSeq X 25B PE300 or NextSeq2000 P4 300 cycle flow cell, Read1:80 Read2:200. A read depth of 5000 reads per cell for TCR libraries or 10,000 reads per cell for GEX libraries was targeted. ADT or CITEseq libraries were targeted at 5000 reads per cell.

treatment_protocol: Cell Lines: Parental Jurkat T cells were originally purchased from ATCC and were transduced with pMW39 lentivirus (CXCR4 sgRNA) + pMW5 lentivirus (dCas9 ) by our group for use in other studies. No modifications were made to the native Jurkat TCR. The Raji CCL-86 cell line was purchased from ATCC.

value: Blood

value: PBMC

tag: subject id

tag: age at_blood_drawn

value: Male

tag: ethnicity/race

value: Asian/Non-Hispanic Origin

tag: cmv stats

value: CMV+

tag: treatment time

tag: batch id

tag: pool id

value: PA

tag: batch pool

tag: probe barcode_id


title: CNI patient 1

description: Library name: SDAI03

value: Peripheral Blood

value: Neutrophils


title: Abatacept + CNI, patient 3

description: Library name: SDAI10


title: s6_t3w_NeoBlast_Rep3_N5

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 3 weeks of NeoBlast selection, replicate 3, 5 PCR upstream nt

tag: replicate

tag: pcr upstream_nt

tag: time


title: Abatacept + CNI, patient 1

description: Library name: SDAI05

tag: cell type


title: Renal tiusse_B13_uIR14d

tag: tissue

tag: strain

value: Mus

value: male


title: s6_t3w_NeoBlast_Rep3_N0

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 3 weeks of NeoBlast selection, replicate 3, 0 PCR upstream nt

tag: selection

tag: reporter


title: Renal tiusse_B15_sham

tag: Sex

tag: genotype

tag: treatment

value: sham


title: aorta, control, WT, female, rep02

value: aorta

value: wildtype

value: control


title: Renal tiusse_B12_sham


title: miALI_scRNA

city: Montpellier

first: Said

last: Assou

state: Languedoc-Roussillon

address: 80 av Augustin fliche, IRMB

country: France

institute: IRMB, Hôpital Saint Eloi

description: 10x Genomics

data_processing:
Image analyses and base calling were performed using the NextSeq Control Software (Illumina, v4.2.0).
Demultiplexing was performed using cellranger mkfastq v6.1.2. The quality of the raw data was assessed using FastQC from the Babraham Institute and the Illumina software SAV (Sequencing Analysis Viewer).
cellranger count v6.1.2 was used to align reads to the reference genome (refdata-gex-GRCh38-2020-A) and generate the raw and filtered gene-barcodes matrices.
cellranger aggr v6.1.2 was used to combine the results of the two samples.
Assembly: GRCh38
Supplementary files format and content: MEX file format: the matrix.mtx file contains the filtered gene-barcode matrix (total UMI count per cell and gene combination); the .tsv files contain all annotated genes and cell barcodes represented in the mtx file.

source_name: Lung

growth_protocol: Bronchial epithelial cells were generated from induced pluripotent stem cell (hiPSC) as previously described (Ahmed et al 2022). HiPSCs (80,000 cells/cm2) were seeded on 35 mm Geltrex™-coated dishes in E8 medium. After 15 hours, to promote differentiation into the anterior primitive streak. Then, from day 3 to 7, cells were differentiated to ventral anterior foregut endoderm. At day 7, cells were passaged into large clumps and placed on top of the Collagen Chitosan matrix colonized by fibroblasts (after 42 days of culture), and expanded in PneumaCultTM-Ex Plus Medium for few days. At day 12, cells were polarized and maintained in ALI culture for 40 days by placing the matrix on a silicone support with PneumaCultTM-ALI Medium on the basolateral side

extract_protocol:
At day 82 of culture, the matrix-shaped iALI (miALI) structure was dissociated with Versene (37°C for 10 minutes) and cells were gently detached from the fibroblast-rich Collagen Chitosan matrix by pipetting to recover the apical side with epithelial cells. To ensure that only single cells were used, cells were dissociated again with Trypsin-EDTA, filtered through a 40 μm filter with PneumaCult-ALI medium complemented with 5% fetal calf serum, and centrifuged (1200 rpm for 5 minutes). The concentration of freshly dissociated cells was adjusted to 1000 cells/μL in HBSS with 0.05% BSA. The single-cell RNA sequencing (scRNA-seq) experiments were done using a 10x Chromium Controller instrument and the Chromium Single Cell 3′ Reagent Kit V3.1 (10X Genomics). Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell 3' v3.1 Reagent Kits and a Chromium instrument.
Libraries were constructed according to the manufacturer’s instructions using Chromium™ Single Cell 3' v3.1 Reagent Kits and a Chromium instrument.

value: Lung

tag: cell line

value: iPS-derived bronchial mesenchymal cells


title: s6_t3w_NeoBlast_Rep2_N0

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 3 weeks of NeoBlast selection, replicate 2, 0 PCR upstream nt

value: Keratinocytes

value: NeoBlast


title: s6_t3w_NeoBlast_Rep2_N5

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 3 weeks of NeoBlast selection, replicate 2, 5 PCR upstream nt


title: s6_t3w_NeoBlast_Rep1_N5

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 3 weeks of NeoBlast selection, replicate 1, 5 PCR upstream nt


title: s5_t4w_Neo_Rep3_N5

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 3, 5 PCR upstream nt

value: Neo


title: s6_t3w_NeoBlast_Rep1_N0

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 3 weeks of NeoBlast selection, replicate 1, 0 PCR upstream nt


title: s5_t4w_Neo_Rep3_N0

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 3, 0 PCR upstream nt


title: PTS_HGG_P80

description:
Library name: sample 4
10x genomics

value: brain

value: tumor and tumor microenviroment cells

tag: surgery

value: PTS


title: s5_t4w_Neo_Rep2_N25

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 2, 25 PCR upstream nt


title: s5_t4w_Neo_Rep2_N5

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 2, 5 PCR upstream nt


title: s5_t4w_Neo_Rep2_N0

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 2, 0 PCR upstream nt


title: s5_t4w_Neo_Rep1_N5

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 1, 5 PCR upstream nt


title: s6_t4w_Neo_Rep2_N5

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_Blast ctrl) selection in mouse keratinocytes, replicate 2, 5 PCR upstream nt


title: s5_t4w_Neo_Rep1_N0

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 1, 0 PCR upstream nt


title: s5_t4w_Neo_Rep1_N25

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 1, 25 PCR upstream nt


title: s5_t4w_NeoDT_Rep3_N5

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of NeoDT selection, replicate 3, 5 PCR upstream nt

value: NeoDT


title: s6_t4w_Neo_Rep1_N5

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_Blast ctrl) selection in mouse keratinocytes, replicate 1, 5 PCR upstream nt


title: s5_t4w_NeoDT_Rep3_N25

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of NeoDT selection, replicate 3, 25 PCR upstream nt


title: s5_t4w_NeoDT_Rep3_N0

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of NeoDT selection, replicate 3, 0 PCR upstream nt


title: s5_t4w_NeoDT_Rep2_N25

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of NeoDT selection, replicate 2, 25 PCR upstream nt


title: s5_t4w_NeoDT_Rep2_N0

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of NeoDT selection, replicate 2, 0 PCR upstream nt


title: s5_t4w_NeoDT_Rep2_N5

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of NeoDT selection, replicate 2, 5 PCR upstream nt


title: s5_t4w_NeoDT_Rep1_N5

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of NeoDT selection, replicate 1, 5 PCR upstream nt


title: s5_t4w_NeoDT_Rep1_N25

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of NeoDT selection, replicate 1, 25 PCR upstream nt


title: s5_t4w_NeoDT_Rep1_N0

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 4 weeks of NeoDT selection, replicate 1, 0 PCR upstream nt


title: s6_t4w_Neo_Rep1_N0

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 4 weeks of Neo (Krt6b_Blast ctrl) selection in mouse keratinocytes, replicate 1, 0 PCR upstream nt


title: s5_t3w_Neo_Rep3_N5

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 3, 5 PCR upstream nt


title: s5_t3w_Neo_Rep3_N25

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 3, 25 PCR upstream nt


title: s5_t3w_Neo_Rep3_N0

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 3, 0 PCR upstream nt


title: s6_t4w_NeoBlast_Rep2_N0

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 4 weeks of NeoBlast selection, replicate 2, 0 PCR upstream nt


title: s5_t3w_Neo_Rep2_N5

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 2, 5 PCR upstream nt


title: s6_t4w_NeoBlast_Rep1_N5

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 4 weeks of NeoBlast selection, replicate 1, 5 PCR upstream nt


title: s5_t3w_Neo_Rep2_N25

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 2, 25 PCR upstream nt


title: s5_t3w_Neo_Rep2_N0

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 2, 0 PCR upstream nt


title: s6_t4w_NeoBlast_Rep1_N0

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 4 weeks of NeoBlast selection, replicate 1, 0 PCR upstream nt


title: s5_t3w_Neo_Rep1_N5

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 1, 5 PCR upstream nt


title: Decidualized MC1 cells, siTSPYL2 replicate 3

city: Nagoya

first: Jiali

last: Ruan

state: Aichi

address: 65 Tsurumai-cho

country: Japan

institute: Nagoya University

description:
Library name: Sample 6
Column name in gene_raw_counts_STAR_featureCounts.csv: siTSPYL2_3

data_processing:
Reads were aligned to the human GRCh38 reference genome using STAR v2.7.10a.
Gene-level read counts were generated using featureCounts v2.0.3.
Differential expression analysis was performed using DESeq2 with siNC as the reference group and siTSPYL2 as the comparison group.
Assembly: GRCh38
Supplementary files format and content: gene_raw_counts_STAR_featureCounts.csv: CSV file containing gene-level raw read counts generated by featureCounts for all samples. The first column contains gene IDs, and the remaining columns correspond to siNC_1, siNC_2, siNC_3, siTSPYL2_1, siTSPYL2_2, and siTSPYL2_3.

source_name: endometrium

growth_protocol: MC1 cells, a human endometrial stromal cell line, were maintained in DMEM/F12 supplemented with 10% fetal bovine serum and antibiotics in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
RNA was harvested using RNeasy mini kit (Qiagen) and submitted to Macrogen Japan.
cDNA library preparation and RNA sequencing were performed by Macrogen Japan (Tokyo, Japan) using a stranded mRNA-seq workflow. Paired-end sequencing was performed on an Illumina NovaSeq X platform.

treatment_protocol: MC1 cells were cultured in phenol red-free DMEM/F12 containing 0.5 mM 8-Br-cAMP, 1 μM MPA, and 2% charcoal-stripped fetal bovine serum for 4 days to induce decidualization. The medium was changed every other day. Decidualized MC1 cells were then transfected with 50 nM siTSPYL2 or siNC for 48 h using RNAiMAX.

value: endometrium

value: human endometrial stromal cells

value: wild type

value: cAMP + MPA 4 days; siTSPYL2

tag: batch


title: Decidualized MC1 cells, siTSPYL2 replicate 2

description:
Library name: Sample 5
Column name in gene_raw_counts_STAR_featureCounts.csv: siTSPYL2_2


title: s5_t3w_Neo_Rep1_N25

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 1, 25 PCR upstream nt


title: s5_t3w_NeoDT_Rep3_N25

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of NeoDT selection, replicate 3, 25 PCR upstream nt


title: s5_t3w_NeoDT_Rep3_N5

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of NeoDT selection, replicate 3, 5 PCR upstream nt


title: Decidualized MC1 cells, siTSPYL2 replicate 1

description:
Library name: Sample 4
Column name in gene_raw_counts_STAR_featureCounts.csv: siTSPYL2_1


title: s5_t3w_NeoDT_Rep3_N0

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of NeoDT selection, replicate 3, 0 PCR upstream nt


title: Decidualized MC1 cells, siNC replicate 3

description:
Library name: Sample 3
Column name in gene_raw_counts_STAR_featureCounts.csv: siNC_3

value: cAMP + MPA 4 days; siNC


title: s5_t3w_Neo_Rep1_N0

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_DT ctrl) selection in mouse keratinocytes, replicate 1, 0 PCR upstream nt


title: Decidualized MC1 cells, siNC replicate 2

description:
Library name: Sample 2
Column name in gene_raw_counts_STAR_featureCounts.csv: siNC_2


title: s5_t3w_NeoDT_Rep2_N25

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of NeoDT selection, replicate 2, 25 PCR upstream nt


title: Decidualized MC1 cells, siNC replicate 1

description:
Library name: Sample 1
Column name in gene_raw_counts_STAR_featureCounts.csv: siNC_1


title: s5_t3w_NeoDT_Rep2_N5

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of NeoDT selection, replicate 2, 5 PCR upstream nt


title: s5_t3w_NeoDT_Rep2_N0

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of NeoDT selection, replicate 2, 0 PCR upstream nt


title: s5_t3w_NeoDT_Rep1_N5

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of NeoDT selection, replicate 1, 5 PCR upstream nt


title: Si30 cells at P0, replicate 1

city: Guangzhou

first: Jiangfan

address: Xiaoguwei Street

institute: South China University of Technology

description:
Library name: Si30-P0-1
cryosilicification with Si30

data_processing:
Raw FASTQ data were quality controlled using FastQC and filtered using Cutadapt to remove adapters and low-quality reads (Q<20, length <75 bp).
Clean reads were aligned to the human reference genome (GRCh38) using HISAT2.
Gene expression was quantified using Cufflinks/Cuffdiff to obtain read counts and FPKM values.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Gene count matrices are provided in CSV format for P0 and P1-P3 samples
Supplementary files format and content: FPKM expression matrices are also provided in CSV format for the same samples, with identical structure

source_name: cervical cancer

growth_protocol: HeLa cells were cultured in standard DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA quality was assessed by agarose gel electrophoresis and RNA integrity number (RIN).
RNA sequencing libraries were prepared using standard Illumina TruSeq RNA library preparation kits following the manufacturer's protocol, including mRNA enrichment, fragmentation, cDNA synthesis, end repair, adaptor ligation, and PCR amplification.

treatment_protocol: Cells were subjected to cryosilicification treatment using Si20 or Si30 conditions. Native cells without cryosilicification treatment were used as controls. Samples were collected at early response stage (P0, 0 h and 6 h) and after passaging (P1–P3).

value: cervical cancer

value: Hela

value: epithelial-like cervical cancer cell

value: cryosilicification with Si30

tag: passage


title: Si30 cells at P0, replicate 2

description:
Library name: Si30-P0-2
cryosilicification with Si30


title: s5_t3w_NeoDT_Rep1_N25

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of NeoDT selection, replicate 1, 25 PCR upstream nt


title: Si20 cells at P0, replicate 2

description:
Library name: Si20-P0-2
cryosilicification with Si20

value: cryosilicification with Si20


title: s5_t3w_NeoDT_Rep1_N0

description: ReGenT-seq (Krt6b_DT reporter) in mouse keratinocytes, 3 weeks of NeoDT selection, replicate 1, 0 PCR upstream nt

value: Keratinocytes


title: Si20 cells at P0, replicate 1

description:
Library name: Si20-P0-1
cryosilicification with Si20


title: Native cells at P0, 6 h, replicate 2

description:
Library name: Native II-2
Native, without cryosilicification treatment,cluture 6h

value: No cryosilicification, culture 6h


title: Suv420h2_sh34_8

description: Mini-bulk RNA-seq of Suv420h2-silenced mouse keratinocytes, infected with sh-Suv420h2 (KD sh #2), replicate 5

data_processing:
Following quality controls, raw sequencing reads were processed with Trim Galore! v0.5.0 (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore) to perform quality and adapter trimming (parameters: --stringency 3). Trimmed reads were next aligned to the mouse reference genome (mm10/GRCm38.p6) using STAR v2.7.1a with options: --outFilterMultimapNmax 10 --outFilterMultimapScoreRange 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.04. Gene expression levels were quantified with featureCounts v1.6.1 (options: -t exon -g gene_name) using the GENCODE Release M23 annotation. Multi-mapped reads were excluded from quantification.
Assembly: mm10/GRCm38.p6
Supplementary files format and content: Tab-delimited text file of raw read counts per gene/samples.

extract_protocol:
Mini bulk RNA-seq were performed as described before (Levra Levron C. et al., 2023) with some modifications. GFP+ mouse keratinocytes (expressing the shRNAs for Cbx3, Ehmt2, Kmt5c or a scramble shRNA) were sorted in 100 μl of lysis buffer (0.5% Triton X-100), in presence of RNase inhibitor. Then, a biotinylated Oligo(dT) was bound to Dynabeads MyOne Streptavidin T1 beads (ThermoFisher Scientific) and used to isolate mRNA from the cell lysate. Reverse transcription was perform on total RNA with SuperScript II Reverse Transcriptase (ThermoFisher Scientific) at 42°C x 50', for 10 cycles of [ 50°C x 2' 42°C x 2'], at 50° x 15 minutes  and at 70°C x 15'. The resulting cDNA was amplified with 25 cycles of PCR and libraries were prepared for sequencing with Illumina NexteraXT Illumina protocol (Illumina).
For extracted RNA, indexed cDNA libraries were obtained following the NexteraXT Illumina protocol. Libraries were sequenced on Illumina NextSeq 500 and 1000 System.
Mini-bulk RNA-seq

tag: condition

value: Suv420h2 KD

tag: shRNA

tag: shRNA type


title: Suv420h2_sh34_6

description: Mini-bulk RNA-seq of Suv420h2-silenced mouse keratinocytes, infected with sh-Suv420h2 (KD sh #2), replicate 4

tag: replicate


title: Native cells at P0, 6 h, replicate 1

description:
Library name: Native II-1
Native, without cryosilicification treatment,cluture 6h


title: Suv420h2_sh34_5

description: Mini-bulk RNA-seq of Suv420h2-silenced mouse keratinocytes, infected with sh-Suv420h2 (KD sh #2), replicate 3


title: Native cells at P0, 0 h, replicate 2

description:
Library name: Native I-2
Native, without cryosilicification

value: No cryosilicification


title: Suv420h2_sh34_2

description: Mini-bulk RNA-seq of Suv420h2-silenced mouse keratinocytes, infected with sh-Suv420h2 (KD sh #2), replicate 2


title: s6_t3w_Neo_Rep1_N5

description: ReGenT-seq (Krt6b_Blast reporter) in mouse keratinocytes, 3 weeks of Neo (Krt6b_Blast ctrl) selection in mouse keratinocytes, replicate 1, 5 PCR upstream nt

tag: pcr upstream_nt

tag: time

value: Neo


title: Suv420h2_sh34_1

description: Mini-bulk RNA-seq of Suv420h2-silenced mouse keratinocytes, infected with sh-Suv420h2 (KD sh #2), replicate 1

tag: cell type


title: Suv420h2_sh24_8

description: Mini-bulk RNA-seq of Suv420h2-silenced mouse keratinocytes, infected with sh-Suv420h2 (KD sh #1), replicate 5


title: MCF7, Day15, FulvPalbo, RNA

city: New York

first: Viviana

middle: I.

last: Risca

address: 1230 York Ave, Box 176

department: Laboratory of Genome Architecture and Dynamics

institute: The Rockefeller University

description:
Library name: MCF7_Day15_FulvPalbo
Column name in MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt: 022Day15FP_8_Aligned.sortedByName.out.bam

data_processing:
For RNA samples sent to Novogene for sequencing, reads containing adapters, N > 10% (N represents the base cannot be determined) and low quality (Qscore<= 5) base were filtered out.  For RNA samples sent to Plasmidsaurus for sequencing, quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3.
Pseudoalignment and quantification of transcripts were performed with kallisto for LS8817 cells. Alignment and quantification of transcripts were performed with STAR v2.7.10a for MCF7 cells.
for LS8817 cells, kallisto counts were imported into R using tximport v1.14.2, and counts matrix normalized by sequencing depth was generated using was DESeq2 v1.26.0  for MCF7 cells, STAR counts were imported into R and counts matrix normalized by sequencing depth was generated using was DESeq2 v1.26.0
Assembly: hg38
Supplementary files format and content: files ending in kallisto_abundance.tsv is the abundance estimates of transcripts by kallisto
Supplementary files format and content: Files ending in ReadsPerGene.out.tab is the abundance counts of transcripts by STAR.
Supplementary files format and content: MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt is the counts of transcripts by STAR for all samples from the 21 day 100 nM palbociclib + 10 nM fulvestrant timecourse experiment

source_name: mammary gland

growth_protocol: LS8817 Cells were cultured in DMEM high glucose no glutamine (11960044, Gibco™), supplemented with 9% FBS (10082147, Gibco™), 1% of 100x GlutaMAX™ Supplement (35050061, Gibco™) and 1% of 10,000U/mL penicillin/streptomycin (15140122, Gibco™) and maintained at 37°C and 5% CO2.  Human MCF-7 cells (RRID:CVCL_0031) were cultured in in 75 cm2 flasks DMEM/F-12 (#Cat 10565018, Thermo Fisher Scientific) supplemented with GlutaMAX, 10% Fetal Bovine Serum (Cat# F4135, Sigma-Aldrich) and 1% Penicillin-Streptomycin at 37 °C and 5% CO2.

extract_protocol:
RNA extraction was done using the Quick-RNA Microprep Kit (Zymo Research, cat# R1050).
Total RNA from at least 2 biological replicates per condition was sent to Novogene for stranded library preparation and sequencing. cDNA libraries were made with NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina (NEB cat# E7765). For MCF7 samples treated with  MCF7 cells were treated with 100 nM doxorubicin, 1 uM palbociclib or 100 nM palbociclib + 10 nM fulvestrant, samples were sent to PlasmidSaurus for forward-stranded library preparation. Plasmidsaurus'  RNA-seq service sequences polyadenylated (poly-A) eukaryotic transcripts using a 3′ end-counting approach to provide gene-level counts only, where a short stretch of RNA (~90nt) located within the last 300-400nt of the transcript is sequenced.

treatment_protocol: Cells were passaged at a 1:3 ratio one day before drug treatment and treated with drugs at the specified concentrations, with media changes every 2–3 days until harvest.

tag: tissue

value: mammary gland

value: epithelial

value: WT

value: day15 100nM palbociclib+10nM fulvestrant


title: Suv420h2_sh24_7

description: Mini-bulk RNA-seq of Suv420h2-silenced mouse keratinocytes, infected with sh-Suv420h2 (KD sh #1), replicate 4


title: MCF7, Day10, FulvPalbo, RNA

description:
Library name: MCF7_Day10_FulvPalbo
Column name in MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt: 011Day10FP_2_Aligned.sortedByName.out.bam

value: day10 100nM palbociclib+10nM fulvestrant


title: MCF7, Day5, FulvPalbo, RNA

description:
Library name: MCF7_Day5_FulvPalbo
Column name in MCF7_RNA_counts_Cycling.vs.FulvPalbo.clean.txt: 007Day5FP_14_Aligned.sortedByName.out.bam

value: day5 100nM palbociclib+10nM fulvestrant