title: XSB_03

city: Cambridge

first: Nir

last: Hacohen

address: 415 Main St

institute: Broad Institute of MIT and Harvard

description:
Library name: XSB_03
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10_v1.2.0
Supplementary files format and content: H5 formattted tab separated values, genes x cells raw counts

extract_protocol:
Murine kidney dissociation and single cell suspension: Under terminal anesthesia, mice were perfused by gentle intracardiac injection of 10 ml prewarmed (37°C) PBS 1x and kidneys were harvested. To obtain single cell suspensions, kidneys were then incubated for 12 minutes in DMEM containing 1 mg/ml Collagenase D (Roche), 100U/ml DNAse I (Sigma), 0.25mg/ml Liberase (Invitrogen) at 37°C. Tissues were gently dissociated using a pipette and then passed through a 70 μm cell strainer (BD). This single cell suspension was finally enriched for myeloid cells or total CD45+ cells using Mouse anti-CD11b and anti-CD11c or anti-CD45 MicroBeads (Miltenyi) and LS magnetic Columns (Miltenyi) for flow cytometry or FACS sorting.
Up to 10,000 live cells were loaded into separate 10x channels for single cell RNAseq on the Chromium platform (10x Genomics). DNA amplification and library construction were carried out according to the manufacturer’s instructions.

value: kidney

value: myeloid

tag: library type

value: mRNA


title: Mv4;11 12hrs PMR 1uM n1

status: Public on Jul 08 2025

type: SRA

city: Canberra

first: Zaka

last: Yuen

address: Australian National University, Canberra ACT 2601

country: Australia

institute: Australian National University

description:
Library name: Sample_44_S44_R1_001
counts_pol1.txt
info_pol1.txt

library_source: transcriptomic

data_processing:
Transcript abundance was quantified using Salmon (v1.5.2) in quasi-mapping mode against the GENCODE v37 human transcriptome (GRCh38.p13).
Transcript-level quantification estimates were summarized to the gene level using tximport in R.
Gene-level counts were normalized using the “lengthScaledTPM” method and used for downstream differential expression analysis in DESeq2.
Assembly: GRCh38.p13 (GENCODE v37)
Supplementary files format and content: Two TSV files contain gene-level count matrices generated by tximport. For KG-1 samples, counts_pol1_batch2_trimmed.txt includes 32 high-quality samples from batch 2 (n=4 per condition), with sample details provided in info_pol1_batch2.txt. For Mv4;11 samples, counts_pol1.txt includes all 48 samples from batch 1 (n=3 per condition), from which 24 Mv4;11 samples were used, as detailed in info_pol1.txt. In both files, column names match the sample IDs (with _R1_001 removed).

molecule: total RNA

organism: Homo sapiens

source_name: Cell line

growth_protocol: KG-1 and Mv4;11 AML cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, 1% penicillin/streptomycin, and maintained at 37 °C in 5% CO₂.

extract_protocol:
Total RNA was extracted using the Nucleospin RNA kit (Macherey-Nagel, 740955.250) according to the manufacturer’s instructions.
RNA-seq libraries were prepared using the Illumina Stranded mRNA Prep Kit. Libraries were pooled and sequenced by the Biomolecular Resource Facility (BRF) at the Australian National University.

treatment_protocol: Cells were treated with 1 µM PMR-116, 1 µM CX-5461, or vehicle control (50 mM citric acid, 50 mM NaH₂PO₄) for 3 or 12 hours.

tag: tissue

value: Cell line

tag: cell line

tag: cell type

value: AML cells

tag: treatment

tag: batch


title: XSB_02

state: MA

country: USA

description:
Library name: XSB_02
10x Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus

source_name: kidney


title: Mv4;11 12hrs CX 1uM n2

description:
Library name: Sample_40_S40_R1_001
counts_pol1.txt
info_pol1.txt


title: XSB_04

description:
Library name: XSB_04
10x Genomics


title: Mut_BAP_T4007

city: Houston

first: Mitchell

last: Frederick

state: Texas

address: One Baylor Plaza

department: Otolaryngology

institute: Baylor College of Medicine

description: Library name: Mut_BAP_T4007

data_processing:
Raw RNA transcript counts mapped to the C57BL/6J genome (CRCm39) were summed to generate gene-level counts, filtered for protein-coding genes, normalized by gene size, and upper quartile (UQ) normalized FPKM values calculated with in-house software in Python. Following normalization, FPKM-UQ values were log-transformed as log2 (X + 0.01), and then gene expression values were globally centered so that every sample had a global median gene expression of 7. Negative log2 expression values were replaced by zero for consistency and to avoid data distortion of small values. A cut-off of 2 in log2 space was chosen to identify low-expression genes. Principal component analysis (PCA) to identify outliers was performed with the top 1000 most variable genes using JMP statistical software (JMP version 17.2), excluding genes with a maximum cohort value of <2.
Assembly: CRCm39
Supplementary files format and content: Xlsx file with matrix of genes and normalized log2 values

source_name: primary tumor

extract_protocol:
Tumors were wrapped in aluminum foil and submerged in liquid nitrogen for 15 seconds, then pulverized using a hammer. A Quick-RNA Miniprep kit from Zymo Research (Cat # R1057) was utilized to extract RNA and sent to Novogene Corporation Inc. for RNA sequencing. All samples were tested for RNA purity using Nanodrop. Potential contamination was evaluated via agarose gel electrophoresis, and sample integrity was further assessed using the Agilent 2100.
The cDNA library was constructed from RNA samples, and its quality was assessed prior to Illumina paired-end sequencing. The library preparations were then sequenced using the Illumina platform, generating paired-end reads (2×150 bp, 20M reads/sample).

value: primary tumor

value: Squamous carcinoma

tag: genotype

value: Krt5CreER-T2/+; Trp53fl/fl; Rosa26LSL-PIK3CA(H1047R)/LSL-PIK3CA(H1047R); Keap1fl/fl

value: BAP


title: Mv4;11 3hrs PMR 1uM n2

description:
Library name: Sample_34_S34_R1_001
counts_pol1.txt
info_pol1.txt


title: Mv4;11 12hrs CX 1uM n1

description:
Library name: Sample_38_S38_R1_001
counts_pol1.txt
info_pol1.txt


title: Mut_BAP_T3706R

description: Library name: Mut_BAP_T3706R


title: Mv4;11 12hrs CX Veh n3

description:
Library name: Sample_41_S41_R1_001
counts_pol1.txt
info_pol1.txt

value: vehicle (CX-5461)


title: MRL_05

description:
Library name: MRL_05
10x Genomics


title: Mv4;11 3hrs PMR Veh n3

description:
Library name: Sample_35_S35_R1_001
counts_pol1.txt
info_pol1.txt

value: vehicle (PMR-116)


title: Mut_T4484

description: Library name: Mut_T4484


title: Mut_BAP_T3832R

description: Library name: Mut_BAP_T3832R


title: Mut_BAP_T3581

description: Library name: Mut_BAP_T3581


title: Mv4;11 3hrs PMR 1uM n3

description:
Library name: Sample_36_S36_R1_001
counts_pol1.txt
info_pol1.txt


title: Mv4;11 3hrs PMR Veh n2

description:
Library name: Sample_33_S33_R1_001
counts_pol1.txt
info_pol1.txt


title: Mut_BAP_T4006

description: Library name: Mut_BAP_T4006


title: Mut_T4509R

description: Library name: Mut_T4509R


title: MRL_06

description:
Library name: MRL_06
10x Genomics


title: Mut_T3181

description: Library name: Mut_T3181


title: Mv4;11 12hrs CX Veh n1

description:
Library name: Sample_37_S37_R1_001
counts_pol1.txt
info_pol1.txt


title: Mut_T3299

description: Library name: Mut_T3299


title: Mv4;11 12hrs CX 1uM n3

description:
Library name: Sample_42_S42_R1_001
counts_pol1.txt
info_pol1.txt


title: Mv4;11 3hrs PMR 1uM n1

description:
Library name: Sample_32_S32_R1_001
counts_pol1.txt
info_pol1.txt


title: Mut_T3090

description: Library name: Mut_T3090


title: Mv4;11 3hrs PMR Veh n1

description:
Library name: Sample_31_S31_R1_001
counts_pol1.txt
info_pol1.txt


title: Mv4;11 3hrs CX 1uM n3

description:
Library name: Sample_30_S30_R1_001
counts_pol1.txt
info_pol1.txt


title: Mv4;11 3hrs CX Veh n3

description:
Library name: Sample_29_S29_R1_001
counts_pol1.txt
info_pol1.txt


title: Mv4;11 3hrs CX Veh n2

description:
Library name: Sample_27_S27_R1_001
counts_pol1.txt
info_pol1.txt


title: KG-1 12hrs PMR Veh n4

description:
Library name: Batch2_Sample_31_S31_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: Wt_T3146R

description: Library name: Wt_T3146R


title: KG-1 3hrs PMR 1uM n4

description:
Library name: Batch2_Sample_28_S28_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: Wt_BAP_T3383R

description: Library name: Wt_BAP_T3383R


title: Wt_BAP_T3511

description: Library name: Wt_BAP_T3511


title: Mv4;11 3hrs CX Veh n1

description:
Library name: Sample_25_S25_R1_001
counts_pol1.txt
info_pol1.txt


title: KG-1 3hrs CX 1uM n4

description:
Library name: Batch2_Sample_26_S26_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: Wt_T2680R

description: Library name: Wt_T2680R


title: Wt_BAP_T3416

description: Library name: Wt_BAP_T3416


title: Wt_BAP_T3519

description: Library name: Wt_BAP_T3519


title: WT_T3086R

description: Library name: WT_T3086R


title: Mv4;11 3hrs CX 1uM n2

description:
Library name: Sample_28_S28_R1_001
counts_pol1.txt
info_pol1.txt


title: KG-1 12hrs CX Veh n4

description:
Library name: Batch2_Sample_29_S29_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: Wt_BAP_T3421

description: Library name: Wt_BAP_T3421


title: WT_T3342

description: Library name: WT_T3342


title: Wt_BAP_T3518

description: Library name: Wt_BAP_T3518


title: KG-1 12hrs CX 1uM n4

description:
Library name: Batch2_Sample_30_S30_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: Mv4;11 3hrs CX 1uM n1

description:
Library name: Sample_26_S26_R1_001
counts_pol1.txt
info_pol1.txt


title: KG-1 12hrs PMR 1uM n4

description:
Library name: Batch2_Sample_32_S32_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: Wt_T3195

description: Library name: Wt_T3195


title: KG-1 3hrs PMR Veh n4

description:
Library name: Batch2_Sample_27_S27_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: P53-NoCre_mTEChi_Rep3

city: Chicago

first: Noah

last: Gamble

state: IL

department: Pathology

institute: University of Chicago

description: Library name: P53-NoCre_mTEChi_Rep3

data_processing:
RNA-seq reads were mapped to the mm10 mouse genome assembly using TopHat (v2.1.1) with setting --microexon-search. Unmapped, unpaired and low quality reads (MAPQ < 5) were removed using samtools (v1.9) view with settings -q 5 -f 2. Paired reads were counted for each gene using featureCounts from Subread (v2.0.1). Transcripts-per-million (TPM) values were calculated for each gene to quantify the relative abundance of transcripts for clustering analysis.
Assembly: mm10
Supplementary files format and content: Count table text file
Supplementary files format and content: Count matrix csv file

source_name: Thymus

extract_protocol:
Thymic epithelial cells were isolated using a previously published protocol (Kim & Serwold, Methods in Molecular Biology, 2019) with minor modifications. Briefly, thymi from 4-5 week-old mice were harvested and connective tissue was removed. Stromal tissue was perforated using scissors and incubated with rotation in DMEM-F12 (Sigma D6421) at room temperature for for 10min to liberate thymocytes. Remaining stromal tissue was enzymatically digested (0.5mg/mL Collagenase D (Sigma 11088858001), 0.2mg/mL DNaseI (Sigma 10104159001), 0.5mg/mL Papain (Worthington Biochemical LS003126)). Cells were stained with anti-EpCAM antibodies conjugated to APC-Cy7 and EpCAM+ cells were enriched via positive selection using magnetic anti-Cy7 beads (Miltenyi 130-091-652). Enriched fraction was stained with fluorescently conjugated antibodies for FACS or analysis. 75,000 primary mTECs were FACS-sorted directly into RULT lysis buffer (Qiagen RNEasy Kit) and total RNA was extracted using manufacturer’s instructions.
mRNA was enriched and RNA-seq libraries were constructed using the Illumina TruSeq Stranded mRNA Kit. Paired-end, dual-index sequencing was performed on the Illumina NovaSeq 6000 platform.

value: Thymus

value: mTEChi


title: P53-cKO_mTEChi_Rep3

description: Library name: P53-cKO_mTEChi_Rep3


title: KG-1 3hrs CX veh n4

description:
Library name: Batch2_Sample_25_S25_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: Wt_T3144R

description: Library name: Wt_T3144R


title: P53-cKO_mTEChi_Rep2

description: Library name: P53-cKO_mTEChi_Rep2


title: KG-1 12hrs PMR 1uM n3

description:
Library name: Batch2_Sample_24_S24_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: KG-1 12hrs PMR Veh n3

description:
Library name: Batch2_Sample_23_S23_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: P53-NoCre_mTEChi_Rep2

description: Library name: P53-NoCre_mTEChi_Rep2


title: P53-cKO_mTEChi_Rep1

description: Library name: P53-cKO_mTEChi_Rep1


title: P53-NoCre_mTEChi_Rep1

description: Library name: P53-NoCre_mTEChi_Rep1


title: KG-1 3hrs PMR Veh n3

description:
Library name: Batch2_Sample_19_S19_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: CD8Tcells, CX3CR1CreNeg, CervialLN, rep2

city: Hannover

first: Ulrich

last: Kalinke

state: Lower Saxony

address: Feodor-Lynen-Str. 7

department: Institute for Experimental Infection Research

country: Germany

institute: Twincore, Centre for Experimental and Clinical Infection Research

description: Library name: APS50

data_processing:
Illumina Casava1.7 software used for basecalling.
Quality control of the sequenced raw FASTQ-files was performed with FastQC software (version 0.11.9) and mapped to Ensembl mouse genome reference version GRCm38 (mm10) using STAR (version 2.5.4b). Gene abundance was also determined by STAR. Differential expression analysis was performed using DESeq2 package in R environment (version 1.26.0).
Assembly: mm10
Supplementary files format and content: Matrix table with raw counts for every gene and there corresponding Ensembl ID

source_name: Cervical lymph nodes

extract_protocol:
The RNA from sorted CD8 T cells was isolated using NucleoSpin® RNA Kit following manufactures instruction. RNA quality and concentrations were accessed using Bioanalyzer RNA kit and samples with RIN value >8.0 were selected for further processing.
RNA libraries for RNA-seq were prepared using NEBNext Low input RNA library Prep Kit for Illumina (NEB, E6420) following manufacturer's protocols.

value: Cervical lymph nodes

value: Infected


title: KG-1 12hrs PMR 1uM n2

description:
Library name: Batch2_Sample_16_S16_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: CD8Tcells, CX3CR1CreNeg, CervialLN, rep1

description: Library name: APS49


title: CD8Tcells, CX3CR1CrePos, CervialLN, rep2

description: Library name: APS53


title: KG-1 12hrs CX Veh n2

description:
Library name: Batch2_Sample_13_S13_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: CD8Tcells, WT, CervialLN, rep1

description: Library name: APS46

value: Wild Type


title: CD8Tcells, CX3CR1CrePos, CervialLN, rep3

description: Library name: APS54


title: KG-1 12hrs CX 1uM n3

description:
Library name: Batch2_Sample_22_S22_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: CD8Tcells, CX3CR1CrePos, Brain, rep2

description: Library name: APS20

source_name: Brain

value: Brain


title: KG-1 12hrs CX Veh n3

description:
Library name: Batch2_Sample_21_S21_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: CD8Tcells, CX3CR1CrePos, CervialLN, rep1

description: Library name: APS52


title: KG-1 12hrs PMR Veh n2

description:
Library name: Batch2_Sample_15_S15_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: CD8Tcells, CX3CR1CreNeg, CervialLN, rep3

description: Library name: APS51


title: KG-1 3hrs PMR Veh n2

description:
Library name: Batch2_Sample_11_S11_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: CD8Tcells, WT, CervialLN, rep2

description: Library name: APS47


title: KG-1 3hrs CX 1uM n2

description:
Library name: Batch2_Sample_10_S10_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: KG-1 3hrs CX 1uM n3

description:
Library name: Batch2_Sample_18_S18_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: KG-1 3hrs CX Veh n3

description:
Library name: Batch2_Sample_17_S17_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: KG-1 3hrs PMR 1uM n2

description:
Library name: Batch2_Sample_12_S12_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: CD8Tcells, CX3CR1CrePos, Brain, rep3

description: Library name: APS21


title: CD8Tcells, CX3CR1CrePos, Brain, rep1

description: Library name: APS19


title: KG-1 3hrs PMR 1uM n3

description:
Library name: Batch2_Sample_20_S20_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: KG-1 3hrs CX Veh n2

description:
Library name: Batch2_Sample_9_S9_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: KG-1 12hrs CX 1uM n2

description:
Library name: Batch2_Sample_14_S14_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: CD8Tcells, WT, CervialLN, rep3

description: Library name: APS48


title: CD8Tcells, CX3CR1CreNeg, Brain, rep2

description: Library name: APS12


title: KG-1 12hrs PMR 1uM n1

description:
Library name: Batch2_Sample_8_S8_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: CD8Tcells, CX3CR1CreNeg, Brain, rep1

description: Library name: APS8


title: KG-1 12hrs PMR Veh n1

description:
Library name: Batch2_Sample_7_S7_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: KG-1 3hrs PMR 1uM n1

description:
Library name: Batch2_Sample_4_S4_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: CD8Tcells, WT, Brain, rep2

description: Library name: APS4


title: CD8Tcells, WT, Brain, rep1

description: Library name: APS2


title: KG-1 12hrs CX 1uM n1

description:
Library name: Batch2_Sample_6_S6_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: KG-1 3hrs CX Veh n1

description:
Library name: Batch2_Sample_1_S1_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: KG-1 3hrs PMR Veh n1

description:
Library name: Batch2_Sample_3_S3_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: KG-1 3hrs CX 1uM n1

description:
Library name: Batch2_Sample_2_S2_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt


title: E43 Pol 10uM CX n=3

description: Library name: 45

library_source: genomic

data_processing:
Sequencing reads were aligned to a custom reference genome based on GRCh38.p13, with rDNA-like regions masked and one copy of the rDNA repeat (GenBank KY962518.1) added as an extra chromosome. Alignment was performed using Bowtie2 v2.3.5.1 with default parameters.
Normalized coverage tracks were generated using bamCompare from deepTools v3.4.3 to compute log₂-transformed ChIP/Input signal.
Visualisation of ChIP-seq signal was performed in Integrative Genomics Viewer (IGV). Peak calling was not performed as the focus was on rDNA occupancy profiles.
Assembly: Custom GRCh38.p13 with rDNA-like regions masked and GenBank KY962518.1 rDNA repeat appended as an extra chromosome.
Supplementary files format and content: bigWig signal tracks representing log₂-transformed ChIP/Input signal across the genome and rDNA pseudochromosome.

molecule: genomic DNA

growth_protocol: Mv4;11 and KG-1 cells were cultured in RPMI-1640 medium supplemented with 20% heat-inactivated fetal bovine serum and GlutaMAX (Thermo), following DSMZ and ATCC recommendations.

extract_protocol:
Cells were crosslinked with 0.8% formaldehyde for 10 minutes. Chromatin was sheared by sonication and immunoprecipitation was performed using antibodies against RPA194 (Pol I) or UBF. DNA was purified using the Zymo ChIP DNA Clean and Concentrator Kit according to the manufacturer’s instructions.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England BioLabs) and sequenced on an Illumina NovaSeq 6000 (S1 flow cell, 2×50 bp paired-end reads).

treatment_protocol: Cells were treated with PMR-116 at 1 µM (3xTIC50) or vehicle (50 mM citric acid and 50 mM NaH₂PO₄) for 30 minutes prior to crosslinking

value: acute myeloid leukemia


title: E43 Pol 10uM PMR n=3

description: Library name: 43


title: E43 Pol 1uM PMR n=3

description: Library name: 42

value: 1uM PMR-116


title: E43 Pol 1uM CX n=3

description: Library name: 44


title: BV-2 cells, RGS10 knockout, IFNγ 10ng/mL, 48 hours, biol rep 2

city: Irvine

first: Benita

last: Sjogren

state: California

address: 847 Health Sciences Quad

department: Pharmaceutical Sciences

institute: University of California, Irvine

description:
Library name: RKOIFN2
Column name in rawcounts.txt: RKOIFN2

data_processing:
Raw reads were checked for quality using FastQC and low quality RNA was trimmed using TrimGalore.
Reads were aligned to GRCm39 mouse genome using STAR aligner and gene counts were determined from the corresponding annotation file using STAR's Gene Count feature
Genes with count per million < 0.5 were filtered out. The resulting genes were normalized using DESeq2 and differentially expressed genes were determined.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for all samples

growth_protocol: BV-2 cells were maintained in DMEM containing 10% fetal bovine serum and 1% antibiotic-antimycotic in an incubator maintained at 37C, 5% CO2 and humidity.

extract_protocol:
Total RNA was extracted using Qiagen Rneasy Mini Kit
Poly(A) enrichment and further library construction was done using in-house standardized protocol by Novogene Corporation Inc.

treatment_protocol: BV-2 wild-type and RGS10 knockout cells were treated with media (vehicle) or IFNγ at 10ng/mL for 48 hours

value: immortalized murine microglial cells

value: RGS10 knockout

value: IFNγ


title: BV-2 cells, RGS10 knockout, IFNγ 10ng/mL, 48 hours, biol rep 4

description:
Library name: RKOIFN4
Column name in rawcounts.txt: RKOIFN4


title: BV-2 cells, RGS10 knockout, Vehicle, 48 hours, biol rep 5

description:
Library name: RKOC5
Column name in rawcounts.txt: RKOC5

value: Vehicle


title: BV-2 cells, RGS10 knockout, IFNγ 10ng/mL, 48 hours, biol rep 3

description:
Library name: RKOIFN3
Column name in rawcounts.txt: RKOIFN3


title: BV-2 cells, RGS10 knockout, IFNγ 10ng/mL, 48 hours, biol rep 1

description:
Library name: RKOIFN1
Column name in rawcounts.txt: RKOIFN1


title: BV-2 cells, RGS10 knockout, Vehicle, 48 hours, biol rep 4

description:
Library name: RKOC4
Column name in rawcounts.txt: RKOC4


title: BV-2 cells, RGS10 knockout, Vehicle, 48 hours, biol rep 3

description:
Library name: RKOC3
Column name in rawcounts.txt: RKOC3


title: BV-2 cells, RGS10 knockout, IFNγ 10ng/mL, 48 hours, biol rep 5

description:
Library name: RKOIFN5
Column name in rawcounts.txt: RKOIFN5


title: E43 Pol vehicle n=3

description: Library name: 41

value: AML cells

value: vehicle


title: E43 Pol 10uM CX n=2

description: Library name: 40


title: BV-2 cells, RGS10 knockout, Vehicle, 48 hours, biol rep 2

description:
Library name: RKOC2
Column name in rawcounts.txt: RKOC2


title: E43 Pol 1uM CX n=2

description: Library name: 39


title: BV-2 cells, RGS10 knockout, Vehicle, 48 hours, biol rep 1

description:
Library name: RKOC1
Column name in rawcounts.txt: RKOC1


title: BV-2 cells, wild-type, IFNγ 10ng/mL, 48 hours, biol rep 5

description:
Library name: BIFN5
Column name in rawcounts.txt: BIFN5

value: Wild-type


title: KG-1 12hrs CX Veh n1

description:
Library name: Batch2_Sample_5_S5_R1_001
counts_pol1_batch2_trimmed.txt
info_pol1_batch2.txt

value: Cell line

value: vehicle (CX-5461)


title: CD8Tcells, WT, Brain, rep3

description: Library name: APS6


title: E43 Pol 10uM PMR n=2

description: Library name: 38


title: E43 Pol 1uM PMR n=2

description: Library name: 37


title: BV-2 cells, wild-type, IFNγ 10ng/mL, 48 hours, biol rep 4

description:
Library name: BIFN4
Column name in rawcounts.txt: BIFN4


title: BV-2 cells, wild-type, IFNγ 10ng/mL, 48 hours, biol rep 2

description:
Library name: BIFN2
Column name in rawcounts.txt: BIFN2


title: E43 Pol vehicle n=2

description: Library name: 36


title: E43 Pol 10uM CX n=1

description: Library name: 35


title: BV-2 cells, wild-type, IFNγ 10ng/mL, 48 hours, biol rep 1

description:
Library name: BIFN1
Column name in rawcounts.txt: BIFN1


title: E43 Pol 1uM CX n=1

description: Library name: 34


title: E43 Pol 10uM PMR n=1

description: Library name: 33


title: BV-2 cells, wild-type, vehicle, 48 hours, biol rep 4

description:
Library name: BC4
Column name in rawcounts.txt: BC4


title: E43 Pol 1uM PMR n=1

description: Library name: 32


title: BV-2 cells, wild-type, vehicle, 48 hours, biol rep 1

description:
Library name: BC1
Column name in rawcounts.txt: BC1


title: BV-2 cells, wild-type, vehicle, 48 hours, biol rep 3

description:
Library name: BC3
Column name in rawcounts.txt: BC3


title: E43 Pol vehicle n=1

description: Library name: 31


title: UBF 10uM CX  n=3

description: Library name: 30


title: UBF 10uM PMR n=3

description: Library name: 28


title: BV-2 cells, wild-type, vehicle, 48 hours, biol rep 2

description:
Library name: BC2
Column name in rawcounts.txt: BC2


title: UBF 1uM PMR n=3

description: Library name: 27


title: UBF 1uM CX n=3

description: Library name: 29


title: UBF vehicle n=3

description: Library name: 26


title: lung, post-inoculation Day28-2

city: Guang Zhou

first: Zhou

last: Yan

state: Please select -

address: 135 Xingang West Road Guangzhou, Guangdong China

country: China

institute: Sun Yat-Sen University

description: Library name: library 4

data_processing:
10X Genomics Cell Ranger software (version 3.1.0) was used to convert raw BCL files to FASTQ files, alignment and counts quantification. After data quality control and genome alignment, the gene expression was determined to obtain unique molecular identifiers (UMIs) matrices using CellRanger.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

source_name: lung

extract_protocol:
For CD45+ immune cells isolation, the Miltenyi MACS bead sorting system (Miltenyi Biotec,130-052-301) was used according to the manufacturer’s guidelines. After isolation, cell number and viability were determined with Trypan blue using a Countess II Automated Cell Counter (Thermo Fisher). The collected cells were then resuspended at 1×105 cells/mL with a final viability of > 90%, assessed by the Countess Cellular suspension was loaded on a 10X Genomics instrument for Gel Bead-In-EMlusion (GEMs) generation and barcoding according to the manufacturer’s protocol. The GEMs were then mixed with enzymes to produce full-length, barcoded cDNAs that were then amplified by PCR to generate sufficient mass for library construction.
To prepare the library construction, amplified cDNA was enzymatically fragmented into 200bp~300bp fragments, which were then end-repaired, polyA-tagged and amplified by PCR for final libraries. Samples were sequenced on an Illumina NovaSeq platform.

value: lung


title: Submandibular_sublingual, IL-14, 12 month

city: Columbia

first: Gary

last: Weisman

state: MO

address: 547 Life Sciences Center, 1201 Rollins Rd

department: Biochemistry

institute: University of Missouri

description:
Library name: sectionD_IL1412MO
fresh frozen spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed to FASTQ files using the spaceranger 2.0.0 pipeline from 10X Genomics.
Assembly: GRCm39
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of detected tissue and spots
Supplementary files format and content: filtered_feature_bc_matrix.h5: Includes spatial barcodes, gene IDs and gene expression count data from spaceranger output
Supplementary files format and content: scalefactors_json.json: scale factors in json format
Supplementary files format and content: spatial_enrichment.csv: file in CSV format that contains table of Moran's I values for each feature
Supplementary files format and content: tissue_hires_image.png: High resolution tissue image
Supplementary files format and content: tissue_lowres_image.png: Low resolution tissue image
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specfying spots
Library strategy: Spatial Transcriptomics

source_name: Submandibular and sublingual gland

growth_protocol: Mice were housed in vented cages with 12 h light/dark cycles and received food and water ad libitum.

extract_protocol:
Submandibular and sublingual glands were remove, embedded in OCT media, snap frozen in 2-methylbutane cooled with liquid nitrogen, and 10 µm cryosections were adhered to a Visium v1 spatial gene expression slide.
Spatial transcriptome libraries were prepared using Visium Spatial Gene Expression Reagent Kit protocol CG000239 for Visium  V1 3' slide from 10X Genomics

value: Submandibular and sublingual gland

value: IL-14a transgenic


title: Submandibular_sublingual, C57BL6, 12 month

description:
Library name: sectionC_C5712MO
fresh frozen spatial transcriptome sequencing


title: lung, post-inoculation Day28-1

description: Library name: library 3


title: UBF 10uM CX  n=2

description: Library name: 25


title: lung, PBS-2

description: Library name: library 2

value: PBS


title: UBF 1uM CX n=2

description: Library name: 24


title: lung, PBS-1

description: Library name: library 1


title: BV-2 cells, wild-type, IFNγ 10ng/mL, 48 hours, biol rep 3

description:
Library name: BIFN3
Column name in rawcounts.txt: BIFN3


title: EasySci, mouse brain [snRNA-seq]

city: New York

first: Zehao

last: Zhang

state: NY

address: 1230 York Ave, The Rockefeller University

institute: The Rockefeller University

data_processing:
Demultiplex - bcl2fastq/v2.19.0.316 tolerating one mismatched base in barcodes (edit distance (ED) < 2)
Trim - trim_galore/v0.4.1 with default settings
Alignment - STAR/v2.5.2b with default settings
SAM spilt and gene count generation - customized scripts (https://github.com/JunyueCaoLab/EasySci)
Assembly: mm39
Supplementary files format and content: genecount.mtx - gene count sparse matrix file for each organ
Supplementary files format and content: df_cell.csv - cell annotation csv file for each organ
Supplementary files format and content: df_gene.csv - gene annotation csv file for each organ

molecule: nuclear RNA

source_name: brain

extract_protocol:
Prior to nuclei extraction, nuclei buffer (NB) was prepared by combining 10 mM Tris-HCl pH 7.5, 10 mM NaCl,, 3 mM MgCl2 in RNase-free water. The solution was stored at 4°C for one week before beginning the experiment. To extract the nuclei, lysis buffer solution was freshly prepared with EZ Lysis Buffer containing 1% diethyl pyrocarbonate. Brain tissues were removed from -80C, and added to a 6cm cell culture dish containing 3mL of lysis buffer solution. Brains were homogenized with a razor blade until the solution could be aspirated with 1000uL tips to pass through a 40μM filter above a 50mL tube containing 6 mL of lysis buffer solution. Using the plunger from a 10mL syringe, the solution was homogenized further until the sample had passed through completely. The filters were washed with 1 mL of additional lysis solution. The nuclei were concentrated by centrifugation at 500g for 5 minutes at 4°C. The lysis buffer solution supernatant was removed and the nuclei were washed 3 times in nuclei wash buffer (NWB), containing NB supplemented by 1% of 10% Tween-20 diluted in RNase-free water, 1% recombinant albumin (NEB, #B9200S), and 0.1% SUPERase•In™ RNase Inhibitor. After the washes, nuclei were aliquoted into 2 cryovials containing 500μL of nuclei resuspended in NWB containing 10% dimethyl sulfoxide and stored in slow freezers, cooling 1°C per minute, in the -80C overnight.
The sequencing library generation for the sorted nuclei was conducted in accordance with the EasySci protocol [doi: https://doi.org/10.1101/2022.09.28.509825]. Briefly, the sorted nuclei were first distributed into 96-well plates for reverse transcription, where indexed oligo-dT primers and indexed random hexamers were used to add the first index. After this, the nuclei were then pooled, washed, and redistributed into fresh 96-well plates for the attachment of a second index by ligation. Following another pooling and washing step, the nuclei were redistributed into the final plates for second-strand synthesis, purification, tagmentation with Tn5 transposase and finally PCR to add the final indexes. Final PCR product is pooled and purified with 0.8X AMPure XP SPRI Reagent (Beckman coulter, #A63882). Each library's quality was assessed using an Agilent TapeStation and sequencing was performed on an Illumina NovaSeq 6000 System with an S4 Flow Cell. For the current study, in addition to the previously reported mouse brain data, a total of 25 NovaSeq S4 runs were executed to generate the new data.

value: brain

tag: strain

value: multiplexed sample:Caloric restriction and Ad libitum


title: UBF vehicle n=2

description: Library name: 21

value: acute myeloid leukemia


title: BV-2 cells, wild-type, vehicle, 48 hours, biol rep 5

description:
Library name: BC5
Column name in rawcounts.txt: BC5


title: CD11b_bulk_11

first: Veronica

last: Locher

data_processing:
Reads were pseudoaligned to the Mus musculus genome reference transcriptome (GRCm39) using the quantification function in kallisto (v.0.50.0). Gene-level expression estimates were calculated using the R (v4.3.0) package tximport (v1.30.0)
Assembly: GRCm39
Supplementary files format and content: processed data file (Deepika_CD11b_bulkRNASeq_kallisto_GRCm39_geneName_counts.rds) contains gene expression level estimates for all samples

source_name: Colon

extract_protocol:
RNA was extracted from CD11b+ MACS-enriched single cell suspension from colons of Tet2f/f and Tet2DLysM mice
libraries prepared using Illumina library preparation

value: Colon

value: Tet2 fl/fl


title: CD11b_bulk_10

value: Tet2 delta-LysM


title: CD11b_bulk_9


title: UBF 10uM CX  n=1

description: Library name: 20


title: CD11b_bulk_8


title: UBF 1uM CX n=1

description: Library name: 19


title: UBF 10uM PMR n=1

description: Library name: 18


title: CD11b_bulk_6


title: CD11b_bulk_7


title: input 14 n3

description: Library name: 14


title: CD11b_bulk_5


title: UBF vehicle n=1

description: Library name: 16


title: CD11b_bulk_4


title: input 15 n3

description: Library name: 15


title: UBF 1uM PMR n=1

description: Library name: 17

value: 1uM PMR-116


title: input 12 n3

description: Library name: 12


title: UBF 10uM PMR n=2

description: Library name: 23


title: CD11b_bulk_3


title: input 13 n3

description: Library name: 13


title: input 11 n3

description: Library name: 11


title: input 10 n2

description: Library name: 10


title: CD11b_bulk_1


title: KPY2-02

city: Stanford

first: Julien

last: Couthouis

state: CA

address: 279 Campus Dr

department: Genetics

institute: Stanford University

data_processing:
illumina basecalling
STAR alignment
RSEM counts
DESeq2 normalization and analyzis
Full pipeline with settings used available on https://github.com/emc2cube/Bioinformatics/blob/master/sh_RNAseq.sh
Assembly: mm10
Supplementary files format and content: comma separated value text files with normalized abundance measurements (output from DESeq2)

source_name: hippocampus

extract_protocol:
RNA extracted using Qiagen Rneasy extraction
polyA enriched mRNA libraries (SureSelect Automated Strand-Specific RNA Library Prep, mRNA Library Prep for Illumina Paired-End Multiplexed Sequencing)

value: hippocampus

tag: Sex

value: male

tag: age

value: Young

value: wt


title: UBF 1uM PMR n=2

description: Library name: 22

value: AML cells


title: KPY3-03


title: input 9 n2

description: Library name: 9


title: input 8 n2

description: Library name: 8


title: KPO3-06

value: Old


title: input 7 n2

description: Library name: 7


title: input 6 n2

description: Library name: 6

value: vehicle


title: 9932


title: KPY1-01


title: input 5 n1

description: Library name: 5


title: 9926

value: Control


title: CD11b_bulk_2


title: 9925


title: 9915


title: input 2 n1

description: Library name: 2


title: 9918


title: 9923


title: 9914


title: 9910


title: Patient 4, HUVEC, Pregnancy-induced Hypertension (PIH)

city: Cheras

first: Adila A

last: Hamid

state: Kuala Lumpur

address: Jalan Yaacob Latif, Bandar Tun Razak

department: Physiology

country: Malaysia

institute: National University of Malaysia

description: Library name: PIH4

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. Clean data (clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’ adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw data were calculated. Then, chose a certain range of length from clean reads to do all the downstream analyses.
The small RNA tags were mapped to reference sequence by Bowtie without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria: Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Assembly: miRBase 20.0
Supplementary files format and content: raw counts,Q20, Q30 and GC-content for each sample.
Supplementary files format and content: readcount and TPM value for each sample.

source_name: Endothelial cells

growth_protocol: Endothelial cell medium (ECM), 5% fetal bovine serum (FBS), 1% endothelial cell growth medium (ECGS), 1% penicillin-streptomycin. Cells were cultured at 37oC with 5% CO2.

extract_protocol:
RNA was extracted by using miRNeasy kit (Qiagen). 3µg of total RNA was used for the construction of sequencing libraries.
Sequencing libraries were generated using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

tag: subject status

value: Pregnancy-induced Hypertension (PIH)

value: Endothelial cells


title: Patient 5, HUVEC, Pregnancy-induced Hypertension (PIH)

description: Library name: PIH5


title: 9905


title: MHCC97H_AZD,MYC CUT-ATG

city: Wuhan

first: chen

last: su

address: No. 1095, Jiefang Avenue

institute: Huazhong University of Science and Technology

description: Library name: MHCC97H_AZD

data_processing:
Sequenced reads were trimmed for adaptor sequence and low-quality bases, then mapped to hg38 whole genome using Bowtie with standard alignment parameters. PCR duplicates were marked with the Picard “Mark Duplicates” utility and removed from further analysis. Bam files were converted to BigWig files using deepTools. Peaks were identified using the MACS2 peak caller with the following parameters: –f BAMPE –keep-dup all –g hs –q 0.01 Assembly: hg38 Supplementary files format and content: wig files were generated using deepTools.
Assembly: hg38
Supplementary files format and content: BigWig files
Library strategy: CUT&Tag

source_name: liver

growth_protocol: cells was cultured in DMEM (Invitrogen, CA, USA) supplemented with 10% fetal bovine serum (FBS) (Gibco, CA, USA) and antibiotics in an incubator at 37°C with 5% CO2.

extract_protocol:
CUT&Tag was performed according to the manufacturer’s protocol (Vazyme, TD-904, China).
The library was constructed by Hyperactive Universal CUT&Tag Assay Kit(TD-904) for Illumina  and PCR amplification

value: liver

value: human hepatocellular carcinoma

value: WT

value: using AZD7762 to treat MHCC97H cells  for 24 hours


title: 9904


title: 9901


title: 9895


title: MHCC97H_CON,MYC CUT-ATG

description: Library name: MHCC97H_CON


title: KPO2-05


title: MHCC97H_IgG,IgG CUT-ATG

description: Library name: MHCC97H_IgG


title: Patient 5, HUVEC, normal pregnancy

description: Library name: NH5

value: normal pregnancy


title: shFtl5


title: shFtl4


title: input 4 n1

description: Library name: 4

value: acute myeloid leukemia


title: TSBEv1_3 plus Pol_eta, Day5

city: Xihu District, Hangzhou

first: Xing

last: Chang

state: Zhejiang

address: No.18 Shilongshan Road Cloud Town

department: School of Life Sciences

institute: Westlake University

description:
Library name: sample 9
TP_rep3

data_processing:
Adapter sequences were removed from reads using Trim Galore (v.0.6.10).
Reads were aligned to hg38 by STAR (v.2.7.11b).
Aligned BAMs were tag added and sorted by SAMtools (v.1.22). Duplication was removed by the Picard MarkDuplicates module (v.3.11) and unmapped reads were filtered with SAMtools. BAMs were converted to mpileup format using SAM- tools.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: HeLa

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
TRIzol
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: Base editor and sgRNA plasmids transfection

value: HeLa


title: shFtl3

value: hippocampus


title: Pre treatment

city: Miramar

first: Varghese

last: George

state: FL

address: 2929 N Commerce Pkwy

institute: HCW Biologics

description: Library name: SAMPLE1

data_processing:
The sequencing reads were analyzed with human reference genome GRCh38 using Cell Ranger v7.0.1. Introns were included in the analysis.
Assembly: GRCh38
Supplementary files format and content: tab separated values files and matrix file

source_name: LN tumor biopsy

extract_protocol:
isolated nuclei from frozen human lymph node biopsy tissue samples (singulomics corporation)
constructed 3’ single cell gene expression libraries (Next GEM v3.1) using the 10x Genomics Chromium system. The libraries were sequenced with ~200 million PE150 reads per sample on Illumina NovaSeq 6000.

value: LN tumor biopsy


title: Post treatment, HCW9218

description: Library name: SAMPLE2


title: shFtl1

value: male


title: input 3 n1

description: Library name: 3


title: TSBEv1_2 plus Pol_eta, Day5

description:
Library name: sample 8
TP_rep2


title: input 1 n1

description: Library name: 1


title: Patient 8, HUVEC, normal pregnancy

description: Library name: NH8


title: ctrl3


title: TSBEv1_2, Day5

description:
Library name: sample 5
T_rep2


title: TSBEv1_3, Day5

description:
Library name: sample 6
T_rep3


title: ctrl2


title: ctrl1


title: TSBEv1_1, Day5

description:
Library name: sample 4
T_rep1


title: IL17a-mAb rat skin: DHT+  FeCl₃, replicate 2

city: Los Angeles

first: Bo

last: Tao

address: 675 Charles E Young Drive

department: Cardiology

institute: University of California Los Angeles

description: Library name: IL17a-2

data_processing:
Bulk RNA-seq data were processed using STAR (v2.7.10a) for alignment to the Rattus norvegicus reference genome (Rnor_6.0).  ScRNA-seq data were processed using Cell Ranger (v7.1.0) for demultiplexing and counting.
Gene counts were generated using featureCounts v2.0.3.
Assembly: Rattus norvegicus Rnor_6.0 (Ensembl release 107).
Supplementary files format and content: Bulk RNA-seq: Gene-level expression matrices in CSV format. Rows represent Ensembl gene IDs for Rattus norvegicus; columns represent individual samples. Values represent log2-transformed normalized expression from DESeq2 (using rlog transformation). File names: PBS_CPA_expression.csv, WT_SRG_expression.csv, main_groups_expression.csv, WT_SRG_expression.csv, LPS_DHT_LPS_expression.csv. ScRNA-seq:HDF5 (.h5) format expression matrix file. The file contains gene-by-cell expression count matrix for Rattus norvegicus skin tissue, generated using Cell Ranger (or Seurat/Scanpy). Rows are genes, columns are cell barcodes. Values are raw or normalized counts depending on processing step.

organism: Rattus norvegicus

source_name: IL17a-mAb treated rat,  DHT + FeCl₃

growth_protocol: Sprague-Dawley rats were housed in a temperature- and humidity-controlled facility with a 12 h light/dark cycle and ad libitum access to food and water.

extract_protocol:
For bulk RNA-seq: Total RNA was extracted from skin tissue using the RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. For scRNA-seq: Cell pellets were obtained from dissociated skin tissue using enzymatic digestion, followed by centrifugation. Cell pellets were directly used for RNA extraction or single-cell library preparation.
For bulk RNA-seq, RNA-seq libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB), following polyA enrichment or rRNA depletion. For scRNA-seq, chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics) were used.

treatment_protocol: (1)Sprague-Dawley(SD) Rats were given vehicle (p.o.) + FeCl₃ (s.c.), DHT (p.o.) + FeCl₃ (s.c.), DHT (p.o.) + LPS (s.c.). (2) SD Rats and SRG rats were given DHT (p.o.) + FeCl₃ (s.c.). (3) SD Rats were given DHT (p.o.) + FeCl₃ (s.c.) with PBS/CPA/IgG/IL-17a treatments, as described in the Methods section.

value: skin

value: wiid type

value: IL17a (i.p.) treated DHT (p.o.) + FeCl₃ (s.c.)


title: Mock3, Day5

description:
Library name: sample 3
WT_rep3


title: IL17a-mAb rat skin: DHT+  FeCl₃, replicate 1

description: Library name: IL17a-1


title: MNase_E16.5_M_soma_MNase_rep1

city: Beijing

first: Jiansen

last: Lu

address: No. 5 Yiheyuan Road, Haidian District

department: Biomedical Pioneering Innovation Center (BIOPIC)

institute: Peking University

data_processing:
For scATAC-seq, demultiplexed raw fastq files were trimmed by cutadapt (v3.3) to remove adapter sequences and short reads. ‘Clean reads’ were then mapped to mm10 using bowtie2 (v2.4.5) with parameters ‘--mm --no-unal --very-sensitive’, duplicated and low quality (MAPQ < 30) alignments were further removed with samtools (v1.11). Cell identifiers were attached to ‘CB’ tag of bam files manually, then fragment files of each cell were generated using sinto (v0.7.6) with default parameters. We followed the ArchR (v1.0.2) pipeline to perform downstream analysis of scATAC-seq data.
For ULI-NChIP-seq and low-input MNase-seq, raw data files were firstly trimmed by TrimGalore (v0.6.4) to remove sequencing adapters and low-quality reads. Bowtie2 were used to align reads to mm10 reference, duplicate alignments were identified and removed by ‘MarkDuplicates’ (v2.23.6) function of picard. Alignments with MAPQ < 30 were filtered. Aligned bam files were normalized to RPKM and converted to bigwig format for visualization by ‘bamCoverage’ function of deeptools (v3.4.3).
Assembly: mm10
Supplementary files format and content: .bed.gz: compressed bed files containing the scATAC-seq fragments for single cells
Supplementary files format and content: .bed.gz.tbi: index files related to compressed bed format fragment files
Supplementary files format and content: .bw: bigwig files containing RPKM normalized ChIP-seq signal

source_name: gonad

extract_protocol:
Male mice homozygous for the Oct4-EGFP transgene in the C57BL/6J background were crossed with wild-type C57BL/6J females. When a copulatory plug was evident around noon, that time was counted as E0.5. Gonads were isolated from E13.5, E14.5, E15.5 and E16.5 embryos, female and male samples were collected separately.Gonads were treated with 0.25% trypsin-EDTA for 10 min at 37 °C, and then, trypsin was inactivated by addition of 15% fetal bovine serum (FBS)/DMEM. Cells were ﬁltered through 40 µ m cell strainers to obtain a single-cell suspension for FACS (FACSAria II SORP, BD Bioscience).
The sequence libraries were generated using the KAPA Hyper Prep Kit according to the manufacturer’s instructions.
scATAC-seq, ulltra-low-input native ChIP-seq (ULI-NChIP-seq) and low-input MNase-seq

value: gonad

value: somatic cell

tag: developmental stage


title: IgG rat skin: DHT+  FeCl₃, replicate 3

description: Library name: IgG-3

source_name: IgG treated rat,  DHT + FeCl₃

value: IgG (i.p.) treated DHT (p.o.) + FeCl₃ (s.c.)


title: Mock2, Day5

description:
Library name: sample 2
WT_rep2


title: MNase_E13.5_M_soma_MNase_rep1


title: IgG rat skin: DHT+  FeCl₃, replicate 1

description: Library name: IgG-1


title: MNase_E16.5_F_soma_MNase_rep1

value: female


title: IgG rat skin: DHT+  FeCl₃, replicate 2

description: Library name: IgG-2


title: Mock1, Day5

description:
Library name: sample 1
WT_rep1


title: MNase_E13.5_F_soma_MNase_rep1


title: ctrl5

value: Control


title: TSBEv1_1 plus Pol_eta, Day5

description:
Library name: sample 7
TP_rep1


title: GBA3_B8

city: Belval

first: Matthieu

last: Gobin

address: 6, avenue du Swing

country: Luxembourg

institute: LCSB

description: Library name: R48

data_processing:
Reads were mapped to the human reference genome hg38 using the HISAT2 tool
Assembly: hg38
Supplementary files format and content: count_matrix.csv

source_name: Midbrain organoids

growth_protocol: Nickels et al, 2020

extract_protocol:
RNA isolation was done using the RNeasy Mini Kit (Qiagen, cat.no. 74106) following the manufacturer’s protocol.
In-home kit - Novogene NGS  RNA Library Prep Set

value: Midbrain organoids

value: human induced pluripotent stem cells


title: ChIP_E16.5_M_soma_H4ac_rep2

tag: chip antibody


title: GBA2_B8

description: Library name: R47


title: ChIP_E16.5_M_soma_H4ac_rep1


title: IL17a-mAb rat skin: DHT+  FeCl₃, replicate 3

description: Library name: IL17a-3


title: GBA1_B8

description: Library name: R46


title: Patient 10 control - urine

type: RNA

city: Barretos

first: Stéphanie

last: Calfa

state: São Paulo

address: Antenor Duarte Viléla, 1331 - Dr. Paulo Prata

country: Brazil

institute: Barretos Cancer Hospital

description: URINE sample from Patient 10 control (matched with LBC and plasma), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

hyb_protocol: Hybridization was performed using the NanoString nCounter Human v3 miRNA Panel, following the manufacturer's instructions. A total of 100 ng of total RNA was hybridized at 65°C for 24 hours.

scan_protocol: Post-hybridization processing and scanning were performed using the NanoString nCounter Prep Station and Digital Analyzer. All samples were scanned at a depth of 555 Fields of View (FOVs).

data_processing: Raw data were deposited as RCC files generated by the NanoString nCounter system. Quality control was performed in nSolver Analysis Software (NanoString Technologies). All downstream analyses and normalization (based on low-CV reference miRNAs) were performed in R and are described in the associated publication.

source_name: urine

label_protocol: Not applicable

extract_protocol: LBC, plasma, and urine total RNA isolation were performed using the miRNeasy Mini Kit (Qiagen, Hilden, GER - cat. nº 217004), miRNeasy Serum/Plasma Kit (Qiagen, Hilden, GER - cat. nº 217184), and Urine Cell-Free Circulating RNA Purification Mini Kit (Norgen Biotek Corp. - cat. nº 56900), respectively, according to the manufacturer's protocol. The total RNA extracted was stored at -80◦C until use. Each sample's total RNA concentration and purity were measured using the NanoDrop™ 2000/2000c Spectrophotometers (Thermo Fisher Scientific, Waltham, MA, USA).

tag: histology

value: 27 years

value: Female

tag: Stage


title: Patient 8 control - urine

description: URINE sample from Patient 8 control (matched with LBC and plasma), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 43 years


title: Patient 11 control - urine

description: URINE sample from Patient 11 control (matched with LBC and plasma), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 41 years


title: Patient 12 control - urine

description: URINE sample from Patient 12 control (matched with LBC and plasma), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 28 years


title: Patient 7 control - urine

description: URINE sample from Patient 7 control (matched with LBC and plasma), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 35 years


title: WT3_B8

description: Library name: R45

value: wt/wt


title: Patient 9 control - urine

description: URINE sample from Patient 9 control (matched with LBC and plasma), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 6 control - urine

description: URINE sample from Patient 6 control (matched with LBC and plasma), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 31 years


title: ChIP_E16.5_M_soma_H3K9me3_rep3

value: male


title: ChIP_E16.5_M_soma_H3K9me3_rep2


title: Patient 5 control - urine

description: URINE sample from Patient 5 control (matched with LBC and plasma), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 40 years


title: ChIP_E16.5_M_soma_H3K9me3_rep1

value: gonad


title: Patient 4 control - urine

description: URINE sample from Patient 4 control (matched with LBC and plasma), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 3 control - urine

description: URINE sample from Patient 3 control (matched with LBC and plasma), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 32 years


title: WT1_B8

description: Library name: R43


title: WT2_B8

description: Library name: R44


title: Patient 2 control - urine

description: URINE sample from Patient 2 control (matched with LBC and plasma), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 25 years


title: Patient 12 case - urine

description: URINE sample from Patient 12 case (matched with LBC and plasma), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 1 control - urine

description: URINE sample from Patient 1 control (matched with LBC and plasma), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 48 years


title: Patient 11 case - urine

description: URINE sample from Patient 11 case (matched with LBC and plasma), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 30 years


title: GBA2_B7

description: Library name: R41

value: Midbrain organoids


title: ChIP_E16.5_M_soma_H3K9me2_rep1

value: somatic cell


title: Patient 9 case - urine

description: URINE sample from Patient 9 case (matched with LBC and plasma), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_M_soma_H3K4me3_rep2


title: Patient 10 case - urine

description: URINE sample from Patient 10 case (matched with LBC and plasma), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 27 years


title: Patient 8 case - urine

description: URINE sample from Patient 8 case (matched with LBC and plasma), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: Female


title: Patient 7 case - urine

description: URINE sample from Patient 7 case (matched with LBC and plasma), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_M_soma_H3K4me1_rep2


title: WT3_B7

description: Library name: R39

value: human induced pluripotent stem cells


title: ChIP_E16.5_M_soma_H3K4me3_rep1


title: WT2_B7

description: Library name: R38


title: ChIP_E16.5_M_soma_H3K9me2_rep2


title: Patient 5 case - urine

description: URINE sample from Patient 5 case (matched with LBC and plasma), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient  case - urine

description: URINE sample from Patient 4 case (matched with LBC and plasma), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 3 case - urine

description: URINE sample from Patient 3 case (matched with LBC and plasma), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_M_soma_H3K4me1_rep1


title: WT1_B7

description: Library name: R37


title: ChIP_E16.5_M_soma_H3K36me3_rep2


title: GBA3_B6

description: Library name: R36


title: Patient 2 case - urine

description: URINE sample from Patient 2 case (matched with LBC and plasma), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 12 control - plasma

description: PLASMA sample from Patient 12 control (matched with LBC and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

source_name: plasma


title: ChIP_E16.5_M_soma_H3K36me3_rep1


title: Patient 1 case - urine

description: URINE sample from Patient 1 case (matched with LBC and plasma), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_M_soma_H3K27ac_rep2


title: Patient 9 control - plasma

description: PLASMA sample from Patient 9 control (matched with LBC and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: GBA3_B7

description: Library name: R42


title: Patient 11 control - plasma

description: PLASMA sample from Patient 11 control (matched with LBC and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 41 years


title: Patient 8 control - plasma

description: PLASMA sample from Patient 8 control (matched with LBC and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 43 years


title: GBA1_B7

description: Library name: R40


title: GBA1_B6

description: Library name: R34


title: Patient 6 case - urine

description: URINE sample from Patient 6 case (matched with LBC and plasma), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_M_soma_H3K27ac_rep1


title: WT3_B6

description: Library name: R33


title: Patient 7 control - plasma

description: PLASMA sample from Patient 7 control (matched with LBC and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 35 years


title: Patient 6 control - plasma

description: PLASMA sample from Patient 6 control (matched with LBC and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_M_H4ac_rep2

value: fetal germ cell


title: Patient 5 control - plasma

description: PLASMA sample from Patient 5 control (matched with LBC and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: WT2_B6

description: Library name: R32

value: wt/wt


title: ChIP_E16.5_M_H4ac_rep1

value: male


title: Patient 4 control - plasma

description: PLASMA sample from Patient 4 control (matched with LBC and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 28 years


title: WT1_B6

description: Library name: R31


title: GBA2_B6

description: Library name: R35


title: Patient 3 control - plasma

description: PLASMA sample from Patient 3 control (matched with LBC and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 10 control - plasma

description: PLASMA sample from Patient 10 control (matched with LBC and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_M_H3K9me3_rep3

value: gonad


title: GBA3_B5

description: Library name: R30


title: ChIP_E16.5_M_H3K9me2_rep2


title: Patient 1 control - plasma

description: PLASMA sample from Patient 1 control (matched with LBC and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 12 case - plasma

description: PLASMA sample from Patient 12 case (matched with LBC and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 11 case - plasma

description: PLASMA sample from Patient 11 case (matched with LBC and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 10 case - plasma

description: PLASMA sample from Patient 10 case (matched with LBC and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: GBA2_B5

description: Library name: R29


title: GBA1_B5

description: Library name: R28


title: ChIP_E16.5_M_H3K9me2_rep1


title: Patient 9 case - plasma

description: PLASMA sample from Patient 9 case (matched with LBC and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_F_soma_H4ac_rep2

value: female


title: Patient 8 case - plasma

description: PLASMA sample from Patient 8 case (matched with LBC and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 7 case - plasma

description: PLASMA sample from Patient 7 case (matched with LBC and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 6 case - plasma

description: PLASMA sample from Patient 6 case (matched with LBC and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 31 years


title: WT3_B5

description: Library name: R27


title: WT2_B5

description: Library name: R26


title: Patient 5 case - plasma

description: PLASMA sample from Patient 5 case (matched with LBC and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 40 years


title: Patient 2 control - plasma

description: PLASMA sample from Patient 2 control (matched with LBC and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 25 years


title: Patient  case - plasma

description: PLASMA sample from Patient 4 case (matched with LBC and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: WT1_B5

description: Library name: R25

value: Midbrain organoids


title: ChIP_E16.5_F_soma_H3K9me3_rep3

value: somatic cell


title: ChIP_E16.5_F_soma_H3K9me3_rep2


title: Patient 2 case - plasma

description: PLASMA sample from Patient 2 case (matched with LBC and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 3 case - plasma

description: PLASMA sample from Patient 3 case (matched with LBC and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 32 years


title: GBA3_B4

description: Library name: R24


title: Patient 12 control - LBC

description: LBC sample from Patient 12 control (matched with plasma and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

source_name: cervical liquid-based cytology

value: Female


title: Patient 11 control - LBC

description: LBC sample from Patient 11 control (matched with plasma and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: GBA2_B4

description: Library name: R23

value: human induced pluripotent stem cells


title: Patient 10 control - LBC

description: LBC sample from Patient 10 control (matched with plasma and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 27 years


title: GBA1_B4

description: Library name: R22


title: Patient 9 control - LBC

description: LBC sample from Patient 9 control (matched with plasma and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 8 control - LBC

description: LBC sample from Patient 8 control (matched with plasma and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 43 years


title: ChIP_E16.5_F_soma_H3K9me2_rep1


title: ChIP_E16.5_F_soma_H3K9me2_rep2


title: Patient 7 control - LBC

description: LBC sample from Patient 7 control (matched with plasma and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 35 years


title: WT3_B4

description: Library name: R21


title: Patient 5 control - LBC

description: LBC sample from Patient 5 control (matched with plasma and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: WT2_B4

description: Library name: R20


title: ChIP_E16.5_F_soma_H4ac_rep1


title: ChIP_E16.5_F_soma_H3K4me3_rep2


title: Patient 3 control - LBC

description: LBC sample from Patient 3 control (matched with plasma and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 4 control - LBC

description: LBC sample from Patient 4 control (matched with plasma and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_F_soma_H3K4me3_rep1


title: Patient 2 control - LBC

description: LBC sample from Patient 2 control (matched with plasma and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_F_soma_H3K9me3_rep1


title: Patient 1 case - plasma

description: PLASMA sample from Patient 1 case (matched with LBC and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 48 years


title: ChIP_E16.5_F_soma_H3K4me1_rep2


title: WT1_B4

description: Library name: R19

value: wt/wt


title: GBA3_B3

description: Library name: R18


title: ChIP_E16.5_F_soma_H3K4me1_rep1


title: Patient 1 control - LBC

description: LBC sample from Patient 1 control (matched with plasma and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: GBA1_B3

description: Library name: R16


title: Patient 6 control - LBC

description: LBC sample from Patient 6 control (matched with plasma and urine), classified as CO, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_F_soma_H3K36me3_rep1


title: ChIP_E16.5_F_soma_H3K27ac_rep2


title: Patient 11 case - LBC

description: LBC sample from Patient 11 case (matched with plasma and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 30 years


title: WT3_B3

description: Library name: R15


title: WT2_B3

description: Library name: R14


title: Fas Indel Input

city: Heidelberg

first: Pablo

last: Baeza Centurion

address: Im Neuenheimer Feld 580

institute: DKFZ

library_source: other

data_processing:
FastQ files from paired-end sequencing were processed with DiMSum v1.2.7 using default settings with minor adjustments (https://github.com/lehner-lab/DiMSum). First, DiMSum was run in default paired-end mode to demultiplex reads into input and replicate output samples (Stage 0 only). Second, DiMSum Stages 1-5 were run in single-end mode ('--paired' = F) using only demultiplexed forward reads that have full coverage of the exon sequence. Reverse reads, originally intended to cover a unique molecular identifier (UMI) and a 3' portion of the exon sequence, were discarded. The final stage estimates an enrichment score (ES) and associated error for each mutant variant based on its frequency in the input and output libraries, and relative to the wild type sequence in both libraries. Experimental design files and command-line options required for running DiMSum on this dataset are available on GitHub (https://github.com/lehner-lab/fas-indel-library).
The PSI of the wild type FAS exon 6 sequence has been previously experimentally shown to be 49.1%5. Therefore, the PSI of a variant of interest is estimated as follows: 49.1 * (ES_variant/ES_WT)
Assembly: GRCh38
Supplementary files format and content: Supplementary_Table_1.tsv: a TSV file containing information about exon sequence and associated PSI values.

molecule: other

extract_protocol:
A sequence library was designed to include: 63-nucleotide-long wild-type sequence of FAS exon 6, all possible 189 single-nucleotide substitutions, all 2010 possible deletions ranging in length from 1 to 60 nts, all 5208 possible 1-, 2-, and 3-nucleotide-long insertions as well as 400 randomly-selected 4-nucleotide insertions (full library design along with measured PSI values available in Supplementary Table 1). The library was synthesized and purified by Twist Bioscience.
Oligo libraries were resuspended in 10 mM Tris buffer, pH 8.0 to a concentration of 20 ng/ul. 20 ng of template ssDNA Twist  library were amplified with Pfx Accuprime polymerase (Thermo scientific, 12344024) in a 50 ul reaction total volume in quadruplicate, for 12 cycles (as recommended by Twist Bioscience for a 100-150 nt oligo pool) using the following flanking intronic primers: FAS_i5_GC_F (5’-tgtccaatgttccaacctacag-3’) and FAS_i6_GC_R (5’-ctacttcccaagttatttcaatctg-3’). PCR reactions were combined and cleaned-up with the Quiaquick PCR purification kit, eluted with 50 ul EB buffer and dsDNA measured with a NanoDrop spectrophotometer. The amplified library was recombined with pCMV FAS wt minigene exon 5-6-7 46. We used a vector:insert ratio of 1:8, using 150 ng of vector backbone and 20 ng of dsDNA amplified libraries and incubated at 50ºC for two hours for DNA assembly, using a mix developed at our CRG proteomic facility, which contains a mix of three enzymes an exonuclease, a polymerase and a DNA ligase. After transformation into Stellar competent cells (Clontech, 636766) combining five replicates in order to maximise the number of individual transformants amplified by growing for 18 hours in LB medium containing ampicillin. We obtained approximately 4.29 million clones. After bacterial transformation, the final plasmid library was purified using the Quiagen plasmid maxi kit (50912163, Quiagen) and quantified with a NanoDrop spectrophotometer. 750,000 Hek293 cells were plated on 100x20 mm petri dishes and transfected with 80 ng cloned libraries in 8 ml OPTIMEM Reduced Serum Medium with no phenol Red (Life technologies, 11058021) using Lipofectamine 2000 (Life technologies, 11668019) in nine biological replicates. 48h post transfection, cells were collected and RNA was prepared using Maxwell simplyRNA Tissue Kit (Promega, AS1280). cDNA was prepared with 400 ng total RNA using specific vector backbone PT2 primer (5’- AAGCTTGCATCGAATCAGTAG -3’) and Superscript III reverse transcriptase (Thermo Fisher, 18080085). PCR amplification of cDNA samples was performed with GoTaq flexi (PROMEGA, M7806) using a distinct 8-mer barcoded oligos to distinguish the nine experimental replicates. PCR products were run on a 2% agarose gel and the smear corresponding in sizes to the amplification product of exon inclusion was excised, purified using the Quiaquick Gel extraction kit (Quiagen, 50928704) and quantified with a NanoDrop spectrophotometer.
OTHER: DNA seq of PCR amplicon


title: Patient 9 case - LBC

description: LBC sample from Patient 9 case (matched with plasma and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 28 years


title: Patient 10 case - LBC

description: LBC sample from Patient 10 case (matched with plasma and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: Patient 8 case - LBC

description: LBC sample from Patient 8 case (matched with plasma and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_F_soma_H3K36me3_rep2

value: gonad


title: Patient 12 case - LBC

description: LBC sample from Patient 12 case (matched with plasma and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: ChIP_E16.5_F_soma_H3K27ac_rep1

value: female


title: ChIP_E16.5_F_H4ac_rep2

value: fetal germ cell


title: WT1_B3

description: Library name: R13


title: Patient 7 case - LBC

description: LBC sample from Patient 7 case (matched with plasma and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: GBA3_B2

description: Library name: R12


title: Fas Indel Output


title: GBA2_B3

description: Library name: R17


title: ChIP_E16.5_F_H4ac_rep1


title: GBA2_B2

description: Library name: R11


title: Patient 6 case - LBC

description: LBC sample from Patient 6 case (matched with plasma and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 31 years


title: 04 HIKO HT at 42°C for 90 min

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

country: Japan

institute: University of Toyama

description: HSC-3 HIKO cells were treated with HT at 42°C for 90 min, followed by incubation at 37°C for 3 h.

hyb_protocol: After fragmentation, biotin-labeled cRNA was hybridized to microarrays at 45°C for 16 h.

scan_protocol: Arrays were washed, stained with streptavidin-phycoerythrin, and scanned using a probe array scanner (Thermo Fisher Scientific).

data_processing: Data were processed using the GeneChip® Analysis Suite.

label: biotin

source_name: human oral squamous cell carcinoma HSC-3 cells

label_protocol: Five hundred nanograms of total RNA were used to synthesize complementary RNA (cRNA) using the GeneChip® 3' IVT Express Kit (Thermo Fisher Scientific).

growth_protocol: Human oral squamous cell carcinoma HSC-3 cells and HSC-3 HIKESHI-knockout (HIKO) cells were cultured in E-MEM medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol: Total RNA was extracted using the NucleoSpin® RNA isolation kit (MACHEREY-NAGEL GmbH) with on-column DNase I treatment. RNA quality was assessed using a 4150 TapeStation system (Agilent Technologies), and samples with RNA integrity number (RIN) values greater than 9.5 were considered suitable for further analysis.

treatment_protocol: Hyperthermia (HT) treatment was performed by immersing plastic culture dishes in a 42°C water bath for 90 min, followed by incubation at 37°C in a CO₂ incubator for 3 h.

value: HSC-3 cells

tag: gender

value: male

value: tongue

tag: life span

value: infinite

tag: morphology

value: epithelial-like


title: 02 HSC-3 HT at 42°C for 90 min

description: HSC-3 cells were treated with HT at 42°C for 90 min, followed by incubation at 37°C for 3 h.

tag: tissue


title: 01 HSC-3 control

description: HSC-3 cells were cultured at 37°C for 90 min, followed by incubation at 37°C for 3 h.

tag: cell line


title: PANC1 CTR 8

city: Segrate

first: Marcella

last: Bonanomi

state: Milan

address: Via Fratelli Cervi 93

department: IBSBC

country: Italy

institute: CNR

description: Gene expression after 72 hours of multi-stage treatment

hyb_protocol: Labeled cRNA was hybridized to a SurePrint G3 Human Gene Expression v3 8x60K Microarray Gene Chip (Agilent Technologies) for 16h at 68°C

scan_protocol: Scanned using a SureScan Microarray Scanner (Agilent Technologies) using the Agilent G3_GX_1color default scan settings.

data_processing: Expression values were calculated by the software package Feature Extraction 12.2.0.7 (Agilent Technologies). Statistical analysis of the expression data was performed using the Gene Spring GX Software (Agilent Technologies).

source_name: whole cell homogenate

label_protocol: 100ng of total RNA were applied for Cy3-labelling reaction using the one-color Quick Amp Labeling protocol (Agilent Technologies).

growth_protocol: PANC-1 were grown in Roswell Park Memorial Institute (RPMI) 1640 supplemented with 10% FBS and 2 mM L-glutamine. All media were supplemented with 100 U/mL penicillin and 100 μg/mL streptomycin. Cells were grown at 37 °C in a 5% CO2 incubator.

extract_protocol: Total RNA for microarray analysis was extracted using the RNeasy mini kit (Qiagen, Hilden, Germany), and its concentration, purity, and RNA integrity, measured as RNA integrity number (RIN), were assessed using a TapeStation 4150 (Agilent Technologies).

treatment_protocol: PANC-1 were plated in 6-well plates and treated with 0.6 uM erastin and 0.5 uM methothrexate for 72 h, then the medium was replaced with fresh medium without drugs for another 72 h. After that, the cells were placed in the presence or absence of the drugs for the next 72 hours and then harvested for analysis.

tag: treated

value: no


title: 03 HIKO control

description: HSC-3 HIKO cells were cultured at 37°C for 90 min, followed by incubation at 37°C for 3 h.


title: PANC1 CTR 7


title: Patient 5 case - LBC

description: LBC sample from Patient 5 case (matched with plasma and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 40 years

value: Female


title: ChIP_E16.5_F_H3K9me3_rep3

tag: cell type


title: WT3_B2

description: Library name: R9

value: Midbrain organoids

value: human induced pluripotent stem cells


title: WT2_B2

description: Library name: R8

value: wt/wt


title: PANC1 CTR 6


title: ChIP_E16.5_F_H3K9me2_rep1


title: Patient  case - LBC

description: LBC sample from Patient 4 case (matched with plasma and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC


title: WT1_B2

description: Library name: R7


title: Patient 3 case - LBC

description: LBC sample from Patient 3 case (matched with plasma and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 32 years


title: Patient 2 case - LBC

description: LBC sample from Patient 2 case (matched with plasma and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 25 years


title: ChIP_E13.5_M_soma_H4ac_rep2

value: gonad

value: somatic cell


title: ChIP_E16.5_F_H3K9me2_rep2

value: fetal germ cell

value: female


title: ChIP_E13.5_M_soma_H4ac_rep1


title: Patient 1 case - LBC

description: LBC sample from Patient 1 case (matched with plasma and urine), classified as CA, profiled using NanoString miRNA v3 panel (555 FOVs), passed QC

value: 48 years


title: GBA3_B1

description: Library name: R6


title: ChIP_E13.5_M_soma_H3K9me3_rep3

value: male


title: mid-blastula embryos, derived from sperm_14day-post stripping, rep3

city: Vodnany

first: Yu

last: Cheng

state: South Bohemia

address: Zátiší 728/II

department: Faculty of Fisheries and Protection of Waters

country: Czech Republic

institute: University of South Bohemia in Ceske Budejovice

description: Library name: Sample 18

data_processing:
Clean reads were obtained after filtering the raw data and mapped to the reference genome (GCF_018340385.1) for further bioinformatics analysis. Clean reads mapping to the reference genome was conducted using HISAT2 software (Kim et al., 2015), and followed by StringTie (Pertea et al., 2015). The assembled results of all samples were combined with Cuffmerge. Bowtie2 software was used to align clean reads to the reference sequence (Langmead and Salzberg, 2012). The differentially expressed genes (DEGs) were identified using the DEseq2 method (Wang et al., 2010) with the fold change ≥2, and the corrected P-value (Q-value) ≤ 0.001. GO and KEGG pathway enrichment analyses were performed by the Phyper function in R Project to obtain the annotation of these genes for analysing gene function. The Q-value ≤0.05 was considered significant.
Assembly: GCF_018340385.1
Supplementary files format and content: csv

organism: Cyprinus carpio

source_name: Embryos

extract_protocol:
Total RNA was extracted from embryos using RNA isolation kits (Invitrogen, USA) in accordance with the instructions provided in the manual. The quality and integrity of the total RNA were ascertained using a Nanodrop spectrophotometer and an Aglient 2100 Bioanalyzer (Thermo Fisher Scientific, USA).
The mRNA was enriched using oligo (dT) magnetic beads and fragmented to synthesize cDNA for PCR amplification. Then, the PCR products were denatured into single strand to develop the single-stranded circular DNA library and sequenced using DNBSEQ (BGI, China).

value: Embryos


title: PANC1 CTR 5


title: GBA2_B1

description: Library name: R5


title: PANC1 CTR 4


title: GBA1_B2

description: Library name: R10


title: PANC1 CTR 2


title: ChIP_E13.5_M_soma_H3K9me3_rep2


title: GBA1_B1

description: Library name: R4


title: ChIP_E13.5_M_soma_H3K9me3_rep1


title: mid-blastula embryos, derived from sperm_14day-post stripping, rep1

description: Library name: Sample 16


title: PANC1 TREAT 7

value: yes


title: WT3_B1

description: Library name: R3


title: mid-blastula embryos, derived from sperm_0day-post stripping, rep3

description: Library name: Sample 15


title: ChIP_E13.5_M_soma_H3K9me2_rep2


title: mid-blastula embryos, derived from sperm_0day-post stripping, rep2

description: Library name: Sample 14


title: WT2_B1

description: Library name: R2


title: ChIP_E13.5_M_soma_H3K9me2_rep1


title: WT1_B1

description: Library name: R1


title: PANC1 TREAT 6


title: ChIP_E13.5_M_soma_H3K4me3_rep2


title: mid-blastula embryos, derived from sperm_14day-post stripping, rep2

description: Library name: Sample 17


title: PANC1 TREAT 4


title: PANC1 CTR 1


title: C008T4 Visium

city: Singapore

first: Pierce

middle: Kah Hoe

last: Chow

address: 11 Hospital Cres

country: Singapore

institute: National Cancer Center Singapore

description:
C008T4
Fresh frozen spatial transcriptomics sequencing

data_processing:
Raw sequencing data were processed using 10x Genomics Space Ranger to generate processed files
Sequences were aligned to hg38 reference genome using Space Ranger with default setting and generated gene expression counts
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Liver

extract_protocol:
Fresh frozen tissues were OCT embedded and 10 microns frozen sections were cut using cryostat
Spatial transcriptome sequencing libraries were prepared with 10Xgenomics Visium Gene Expression Slides & Reagent kit according to manufacturer's protocol

value: Liver

value: Male

tag: tumour stage

value: TNM Stage IIIA


title: Patient derived organoid treated with 1:1000 DMSO for 24 hours

city: Worcester

first: Emmet

middle: Rue

last: Karner

address: 364 Plantation St

department: MCCB

institute: University of Massachusetts Chan

description:
Library name: 9657T-DMSO-24hrs
10X Genomics Chromium 3'

data_processing:
Barcode processing, genome allignment,  gene counting, and aggregation were performed using CellRanger v6.1.1
Assembly: Human GRC38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Left Breast, Lumpectomy

growth_protocol: The organoid used in this study was generated from a PDX established from a de-identified breast tumor specimen obtained the University of Massachusetts Chan Tumor Bank and maintained as previously in  described in N. Sachs, et al., A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity. Cell 172, 373-386.e10 (2018).

extract_protocol:
Organoid culture medium was aspirated and Matrigel was digested with trypsin at 37ºC for 10 minutes. The samples were then washed 3X with cold PBS and dissociated for 45 minutes with Accumax (StemCell cat. 07921) at room temperature to generate a single cell suspension, which was passed through a 0.45μm filter to prevent cell clumping. Samples were frozen at -80ºC in cryopreservation medium (30% organoid media with 10% DMSO and 60% FBS). Samples were then processed by GeneWiz where they underwent MACS dead cell removal and quality control
Library was constructed using the 10x Genomics Chromium 3' v3 single cell RNA sequencing protocol

treatment_protocol: Organoids were subject to treatment with either 10 μM IKE for 3hrs, 10 μM IKE for 12hrs, or DMSO control for 24hours

value: INVASIVE DUCTAL CARCINOMA, GRADE 3

value: Left Breast, Lumpectomy

value: Female

tag: er/pr status

value: Negative

tag: her2 status


title: Patient derived organoid treated with 10µM IKE for 3 hours

description:
Library name: 9657T-10uM-IKE-3hrs
10X Genomics Chromium 3'

tag: Sex


title: ChIP_E13.5_M_soma_H3K4me3_rep1

tag: strain


title: C008T3 Visium

description:
C008T3
Fresh frozen spatial transcriptomics sequencing


title: ChIP_E13.5_M_soma_H3K4me1_rep2


title: Patient derived organoid treated with 10µM IKE for 12 hours

description:
Library name: 9657T-10uM-IKE-12hrs
10X Genomics Chromium 3'

tag: age


title: C008T2 Visium

description:
C008T2
Fresh frozen spatial transcriptomics sequencing


title: PANC1 TREAT 5


title: PANC1 TREAT 3


title: PANC1 TREAT 1


title: ChIP_E13.5_M_soma_H3K36me3_rep2

tag: developmental stage


title: A2780 Cells, shJAM3

city: Guiyang City

first: Haiyan

last: Wang

state: Guizhou

address: No. 9, Beijing Road, Yunyan District,

institute: Guizhou Meidical University

description:
Library name: Sample 2
shA2780 in gene_fpkm.txt

data_processing:
Quality control  Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis (For DESeq2 with biological replicates) Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . Genes with an adjusted P-value <=0.05 found by DESeq2 were assigned as differentially expressed. (For edgeR without biological replicates) Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two conditions was performed using the edgeR R package (3.22.5). The P values were adjusted using the Benjamini & Hochberg method. Corrected P-value of 0.05 and absolute foldchange of 2 were set as the threshold for significantly differential expression.
GO and KEGG enrichment analysis of differentially expressed genes Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected. GO terms with corrected Pvalue less than 0.05 were considered significantly enriched by differential expressed genes. KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-through put experimental technologies (http://www.genome.jp/kegg/). We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.Gene Set Enrichment Analysis (GSEA) is a computational approach to determine if a predefined Gene Set can show a significant consistent difference between two biological states. The genes were ranked according to the degree of differential expression in the two samples, and then the predefined Gene Set were tested to see if they were enriched at the top or bottom of the list. Gene set enrichment analysis can include subtle expression changes. We use the local version of the GSEA analysis tool http://www.broadinstitute.org/gsea/index.jsp, GO, KEGG data set were used for GSEA independently.
AS analysis Alternative Splicing is an important mechanism for regulate the expression of genes and the variable of protein. rMATS(4.1.0) software was used to analysis the AS event.
SNP analysis GATK (v4.1.1.0) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 ; FS > 30.0; DP < 10.
Fusion Analysis Fusion gene refers to the chimeric gene formed by the fusion of all or part of the sequences of two genes, which is generally caused by chromosome translocation, deletion and other reasons. We used SATR-fusion software (1.9.0) to detect genes that are fused. SATR-fusion is a software package uses fusion output results of STAR alignment to detect fusion transcripts, including SATR alignment, SATR fusion.predict, SATR-fusion.filter was used to correct the predicted results of Star-fusion to ensure the accuracy of the results.
Assembly: human NCBI genome build 36
Supplementary files format and content: gene_fpkm.txt

growth_protocol: Cells are cultured under standard conditions (37°C, 5% CO₂) to the logarithmic growth phase.

extract_protocol:
Remove culture medium and wash cells once with PBS. Add 1 mL TRIzol reagent per 10 cm² culture dish, incubate for 5 minutes at room temperature, and homogenize by pipetting. Add 0.2 mL chloroform per 1 mL TRIzol, vortex vigorously for 15 seconds, and incubate for 2-3 minutes at room temperature. Centrifuge at 12,000 × g for 15 minutes at 4°C, then carefully transfer the colorless upper aqueous phase to a new tube. Add 0.5 mL isopropanol per 1 mL initial TRIzol, mix gently, and incubate for 10 minutes at room temperature. Centrifuge at 12,000 × g for 10 minutes at 4°C to pellet RNA, discard the supernatant, and wash the pellet with 1 mL 75% ethanol. Centrifuge at 7,500 × g for 5 minutes at 4°C, discard ethanol, and air-dry the RNA pellet for 5-10 minutes. Dissolve RNA in 20-50 µL DEPC-treated water, briefly incubating at 55-60°C if necessary. Quantify RNA using absorbance (A260/A280) and store at -80°C. Maintain strict RNase-free conditions throughout the procedure.
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Human ovarian cancer cell line

tag: genotype

value: JAM3 knockdown


title: HPAF CTR 8

growth_protocol: HPAF-2 were grown in Roswell Park Memorial Institute (RPMI) 1640 supplemented with 10% FBS and 2 mM L-glutamine. All media were supplemented with 100 U/mL penicillin and 100 μg/mL streptomycin. Cells were grown at 37 °C in a 5% CO2 incubator.

treatment_protocol: HPAF-2 were plated in 6-well plates and treated with 3 uM erastin and 15 uM alpelisib for 72 h, then the medium was replaced with fresh medium without drugs for another 72 h. After that, the cells were placed in the presence or absence of the drugs for the next 72 hours and then harvested for analysis.

value: no


title: PANC1 TREAT 2


title: mid-blastula embryos, derived from sperm_0day-post stripping, rep1

description: Library name: Sample 13


title: A2780 Cells, shControl

description:
Library name: Sample 1
ctrlA2780 in gene_fpkm.txt

value: WT


title: C008T1 Visium

description:
C008T1
Fresh frozen spatial transcriptomics sequencing


title: ChIP_E13.5_M_soma_H3K36me3_rep1

value: gonad

value: somatic cell

tag: chip antibody


title: HPAF CTR 7


title: C004T1R Visium

description:
C004T1R
Fresh frozen spatial transcriptomics sequencing

value: TNM Stage IB


title: Neuron-KI, Rep4

city: Edinburgh

first: Graeme

last: Grimes

address: MRC Institute of Genetics & Molecular Medicine, Crewe Road,

country: United Kingdom

institute: University of Edinburgh

data_processing:
The QuantSeq protocol generates one fragment per transcript, resulting in extremely accurate gene expression values, and the sequences obtained were close to the 3’ end of the transcripts. Library generation was initiated by oligo-dT priming (already containing Illumina- compatible linker sequences). After first strand synthesis the RNA was removed, and second strand synthesis initiated by random priming and a DNA polymerase. With the QuantSeq FWD kit the Read 1 linker sequence is contained in the second strand synthesis primer, so that NGS reads are generated towards the poly (A) tail and directly correspond to the mRNA sequence. Second strand synthesis was followed by a magnetic bead-based purification step before cDNA libraries were amplified for 18 cycles, introducing the sequences required for cluster generation and index sequences to allow multiplexing of sequencing libraries. After amplification, a final bead-purification removed any excess primers or adapter-dimers that may interfere with sequencing. Libraries were quantified by fluorometry using the Qubit dsDNA High Sensitivity assay and assessed for quality and fragment size using the Agilent Bioanalyser with the DNA High Sensitivity kit. Fragment size and quantity measurements were used to calculate molarity for each library pool. Single read (1x75bp) sequencing was performed on the NextSeq 550 platform (Illumina Inc, SY-415-1002) using the NextSeq 500/550 High-Output v2.5 kit (20024906). Libraries were combined in a single equimolar sample based on Qubit and Bioanalyser assay results, and run across a High Output v2.5 Flow Cell.
Reads alignment and differential data analyses were performed following pipeline integration onto the Bluebee genomics analysis platform (www.bluebee.com/quantseq).
Assembly: hg38
Supplementary files format and content: bam files aligned using the bluebee platform provided by Lexogen.
Supplementary files format and content: tab delimited text file with normalized counts generated from  Bluebee genomics analysis platform (www.bluebee.com/quantseq).

source_name: ATRX KI-clone2

growth_protocol: iPSCs were maintained on vitronectin (Stem Cell Technologies, 7180), with a complete media change every day in Essential 8 media (Life Technologies, A1517001); 0.5mM EDTA was used for passaging; Accutase (Stem cell Technologies 07920) and 10 μM Rho-associated kinase (ROCK) inhibitor (Sigma-Aldrich Y0503) were used for single-cell dissociation purposes. Neural progenitor cells (NPCs) were established following the STEMdiff Neural System based on STEMdiff SMADi Neural Induction kit (Stem cell Technologies, 08581). NPCs were used at passage 2, 3 or 5 to generate forebrain neurons following the instructions of STEMdiff Forebrain Neuron Differentiation Kit (Stem cell Technologies, 08600) and STEMdiff Forebrain Neuron Maturation Kit (Stem cell Technologies, 08605). Differentiating neurons were fed twice a week, and cultured for 3 to 4 weeks.

extract_protocol:
total RNA was extracted using RNeasy Micro Kit (Qiagen, 74004)
Individual libraries were generated from 100ng of each total RNA sample using the QuantSeq 3’mRNA-Seq Library Prep kit (FWD) protocol for Illumina (Lexogen Inc, #015), where enough material was available, 50ng was inputted otherwise.
QuantSeq 3’ mRNA-Seq

tag: time

value: 29 days of culture

value: forebrain neuron

value: ATRX KI


title: HPAF CTR 6

description: Gene expression after 72 hours of multi-stage treatment


title: ChIP_E13.5_M_soma_H3K27ac_rep2

value: male


title: HPAF CTR 5


title: B013T5 Visium

description:
B013T5
Fresh frozen spatial transcriptomics sequencing

value: Liver

value: Male


title: ChIP_E13.5_M_soma_H3K27ac_rep1


title: Neuron-KI, Rep2

value: 21 days of culture


title: Neuron-KI, Rep3

source_name: ATRX KI-clone3


title: ChIP_E13.5_M_H4ac_rep2


title: ChIP_E13.5_M_soma_H3K4me1_rep1


title: B0013T4 Visium

description:
B0013T4
Fresh frozen spatial transcriptomics sequencing

value: TNM Stage IIIA


title: ChIP_E13.5_M_H4ac_rep1


title: HPAF CTR 3


title: Neuron-KI, Rep1

source_name: ATRX KI-clone1