title: LRJZ29, lower incisors, VDR-null

city: ILLKIRCH

first: Yann

last: HERAULT

address: 1 rue Laurent Fries

institute: IGBMC/PHENOMIN-ICS

data_processing:
Image analysis and base calling were performed using RTA 2.7.7 and bcl2fastq 2.20.0.422.
Alignment was performed with STAR version 2.5.3a on mm10 mus musculus genome
Quantification step was performed with htseq-count version 0.6.1p1 with annotations coming from Ensembl version 102
Assembly: mm10
Supplementary files format and content: tab-delimited text file provides raw read counts for each gene together with gene annotations. This file contains only genes with at least one read count in one sample.

source_name: lower incisors

extract_protocol:
Lower incisors of  5 control, 3 VDRgem and 5 VDR-null postnatal 5 days males were pulled and frozen in dry ice.  RNA extraction was performed using RNeasy Plus Micro Kit (Qiagen).
P2685 : RNA-Seq libraries were generated from 300 ng of total RNA using TruSeq Stranded mRNA Library Prep Kit and IDT for Illumina - TruSeq RNA UD Indexes (96 Indexes, 96 Samples) (Illumina, San Diego, USA), according to manufacturer's instructions. Briefly, following purification with poly-T oligo attached magnetic beads, the mRNA was fragmented using divalent cations at 94oC for 8 minutes. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity was achieved by replacing dTTP with dUTP during second strand cDNA synthesis using DNA Polymerase I and RNase H. Following addition of a single 'A' base and subsequent ligation of the adapter on double stranded cDNA fragments, the products were purified and enriched with PCR (30 sec at 98oC; [10 sec at 98oC, 30 sec at 60oC, 30 sec at 72oC] x 12 cycles; 5 min at 72oC) to create the cDNA library. Surplus PCR primers were further removed by purification using SPRI select beads (Beckman-Coulter, Villepinte, France) and the final cDNA libraries were checked for quality and quantified using capillary electrophoresis.

value: lower incisors

value: male

tag: age

value: VDR-null


title: 207492240028_R12C02

status: Public on Jun 30 2026

type: genomic

city: RALEIGH

first: Dereje

last: Jima

state: NC

address: 850 Main Campus Drive

department: CHHE

country: USA

institute: NCSU

description: Sample name: 11003

hyb_protocol: Illumina protocol

scan_protocol: Illumina protocol

data_processing:
The raw IDAT file produced from the array were processed using the openSesame function in the Sesame R package. We processed the arrays with the Sesame preprocessing code “0CDB” that applies a non-linear dye bias correction and background subtraction using the noob method (Norm-Exp out of band signal), which deconvolves out-of-band fluorescent signal from true signal. The beta values are calculated by the ratio of the methylated signal to unmethylated signal for each probe. These processing steps produced a beta measurement for each probe and patient, along with a corresponding Sesame signal detection p-value that is used as a quality score. Signal detection p-values were assigned using the pOOBAH method (P-value with out-of-band (OOB) array hybridization.) Probes that did not map to a CpG site in the Imprintome were discarded, and any remaining probes were also discarded if their signal detection p-value exceeded 0.2 for more than 10% of samples measured. For cases where multiple probes targeted the same CpG site, we averaged the beta values to produce beta measurements for each CpG site and participant. Finally, we averaged the beta values across CpG sites that correspond to the same ICR, which produced beta measurements for each ICR site and participant.   A series of student t-tests were performed to compare cases and controls (null hypothesis of µ = 0, two-tailed, α = 0.05, unpaired, unequal variance assumed) between methylation fractions, beta values. Beta values represent a number between 0 and 1 and are calculated by comparing the intensity of methylated beads to the total intensity of the locus. CpG sites were selected based on the statistical significance of differential methylation between cases and controls examined in this analysis. P-values from the t-test were corrected based on false discovery rate for the number of ICR sites tested. CpG sites were reported as significant based on an adjusted p-value < 0.05.
matrix processed value definition: Raw beta values (see supplementary linked to the Series record)

label: Cy3, Cy5

molecule: genomic DNA

organism: Homo sapiens

source_name: leukocytes from whole blood

label_protocol: Illumina protocol

extract_protocol: For the preparation of samples, 200 ng of DNA were bisulfite converted using the EZ DNA Methylation kit (Zymo Research, Irvine, CA) according to the manufacturer’s instructions. Bisulfite-converted DNA samples were randomly assigned to a chip well on the Human Imprintome array BeadChip (Illumina, Inc., San Diego, CA), amplified, hybridized onto the array, stained, washed, and imaged with the Illumina iScan SQ instrument (Illumina, Inc., San Diego, CA) to obtain raw image intensities.

tag: cell type

value: leukocytes

tag: disease state

value: HCC case


title: CD68+, TB3, MGC WO-002

type: SRA

city: Rozzano

first: Anna Rita

last: Putignano

state: Milano

address: Via Alessandro Manzoni, 56

country: Italy

institute: IRCCS Humanitas Research Hospital

description:
Library name: DSP-1001660036826-A-B01
CD68+ AOI from tuberculosis patient TB3, slide: CD68_Slide1, ROI: TB3-MGC_WO-002, area: 16121.2 um2, nuclei: 24

library_source: transcriptomic

data_processing:
For each AOI, digital count conversion (.dcc) files were generated from fastqs using the GeoMx NGS Pipeline (version 3.1.1).
From each tissue under investigation DCC files were read into a NanoStringGeoMxSet object using the readNanoStringGeoMxSet function from GeomxTools R package (version 3.5, R version 4.3.3), and segments were assessed for sequence quality.
After generating gene-level counts, segments with high fraction of genes detected below the limit of quantification (LOQ) were removed. Count matrix, sample annotations, and feature annotations were read into a SpatialExperiment object and analyzed with standR package (version 1.6) workflow.
Genes with low expression levels were removed. Counts were normalized using the upper-quartile method from the edgeR package (version 4.0.16).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files containing raw expression values for each AOI/sample
Supplementary files format and content: DCC files containing raw probe read counts for each AOI/sample; RTS_IDs are interpretable using the accompanying PKC file

molecule: total RNA

source_name: lung

extract_protocol:
After deparaffinization and target retrieval, slides were incubated with 0.1 μg/mL proteinase K for 15 minutes at 37°C and then post fixed for 5 minutes in 10% neutral buffered formalin followed by two washes in NBF stop buffer (24.5 g Tris base and 15 g Glycine in 2 L DEPC water). Slides were incubated with the Whole Transcriptome Atlas (WTA) RNA Probe set (121401102, NanoString), according to the manufacturer’s protocol.
Following probe incubation, slides were washed and incubated with the morphology marker solution: AlexaFluor™ 647 anti-human CD68 (BL13756, 375606 BioLegend, 1:400, RRID:AB_3097193) plus SYTO 13 (provided in GeoMx Nuclear Stain Morphology Kit, 121300303, NanoString) for 1 hour at RT and processed through the GeoMx® Digital Spatial Profiler instrument. Regions of interest (ROIs) with a circular shape and a diameter of 600 μm were selected, with an average of 3 ROIs without MGCs and 5 ROIs with MGCs per patient. For each ROI, the CD68+ area of interest (AOI) was selected to collect barcodes in a 96-well plate. Barcoded oligonucleotides were prepared for Illumina-based sequencing to generate target probe-specific count files, which were then saved in a digital count conversion format.

tag: tissue

value: lung

value: macrophages


title: IP_P4_VDJ

city: Philadelphia

first: Nelson

last: Freeburg

state: PA

address: 421 Curie Blvd

department: Cancer Biology

institute: University of Pennsylvania

description: Library name: IP_P4_VDJ

data_processing:
FASTQ files aligned and preprocessed using 10x Genomics CellRanger Multi v8.0.1 pipeline
For Single-cell, single-nucleus gene expression: Ambient RNA contamination removed using CellBender Remove-Background (CellBender v0.3.0).
For single-cell, single-nucleus gene expression, cellbender-adjusted counts imported intor seurat. Genes and cells were filtered for quality and expression thresholds, and data were lognormalized. Cells were annotated manually based on marker gene expression.
For bulk RNA sequencing, Fastq files were trimmed with umi_tools (v1.1.6) to extract UMIs. Cutadapt (v5.2) was used to trim nonbiological sequences from reads. Reads were aligned using the STAR aligner (v2.7.9a). Reads were deduplicated based on UMI identity using umi_tools (v1.1.6) and counted using FeatureCounts (v2.1.1). Normalized counts are in transcripts per milliion (TPM). Raw counts are also provided.
genome build/assembly: GRCh38
processed data files format and content: Processed gene expression data is in .h5 format and contains CellBender-processed gene expression counts.
processed data files format and content: Processed V(D)J data is the output of CellRanger and in .csv format. It contains cell barcode and TCR A a B chain sequence as DNA and protein.
processed data files format and content: Supplementary .rds files contain Seurat objects for single-cell CSF, single-cell Infusion product, and single-nucleus tumor samples

molecule: polyA RNA

source_name: CAR T cells

extract_protocol:
Tumors (single-nucleus): Single cell supsensions produced by tumor sample dissociation with gentleMACS Octo Dissociator and filtered through 75 uM strainer before single nucleus prep with CHAPS; Cerebrospinal and infusion product: Cells or nucei input directly into 10x genomics single cell library preparation protocol. Tumors (Bulk RNAseq from FFPE). Malignant cell-enriched regions were extracted from slides using laser-capture microdissection. RNA was extracted using a Qiagen RNA FFPE kit.
Chromium GEM-X Single Cell 5' Kit v3 with Chromium Single Cell Human TCR Amplification kit (single-cell, single-nucleus). SMART-Seq® Total RNA Pico Input with UMIs (ZapR™ Mammalian) (Bulk RNA sequencing)

treatment_protocol: 5e6, 1e7 or 2.5e7 bivalent CAR T cells targeting EGFR and IL13RA2 administered intracerebroventricularly

value: CAR T cells

tag: cell line

value: Primary cells

tag: genotype

value: Normal

tag: treatment

value: Pre-treatment

tag: batch


title: LRJZ28, lower incisors, VDR-null

country: France

organism: Mus musculus

tag: Sex


title: 207492240028_R10C02

description: Sample name: 11001


title: CD68+, TB3, MGC WO-001

description:
Library name: DSP-1001660036826-A-A12
CD68+ AOI from tuberculosis patient TB3, slide: CD68_Slide1, ROI: TB3-MGC_WO-001, area: 18617.57 um2, nuclei: 32


title: CD68+, TB3, MGC WO-003

description:
Library name: DSP-1001660036826-A-B02
CD68+ AOI from tuberculosis patient TB3, slide: CD68_Slide1, ROI: TB3-MGC_WO-003, area: 23557.67 um2, nuclei: 30


title: IP_P3_VDJ

description: Library name: IP_P3_VDJ


title: LRJZ26, lower incisors, VDR-null


title: 207448290029_R05C02

description: Sample name: 21040


title: CD68+, TB4, MGC W-005

description:
Library name: DSP-1001660036826-A-A11
CD68+ AOI from tuberculosis patient TB4, slide: CD68_Slide1, ROI: TB4-MGC_W-005, area: 27747.18 um2, nuclei: 31


title: 207448290029_R01C02

description: Sample name: 21036


title: LRJZ25, lower incisors, VDR-null


title: IP_P6_GEX

description: Library name: IP_P6_GEX

library_source: transcriptomic single cell


title: CD68+, TB4, MGC W-004

description:
Library name: DSP-1001660036826-A-A10
CD68+ AOI from tuberculosis patient TB4, slide: CD68_Slide1, ROI: TB4-MGC_W-004, area: 34206.56 um2, nuclei: 46


title: IP_P4_GEX

description: Library name: IP_P4_GEX


title: LRJZ24, lower incisors, VDRgem

value: VDRgem


title: 207448290029_R12C01

description: Sample name: 21034


title: Tumor_P7_Pre_infusion_VDJ

description: Library name: Tumor_P7_Pre_infusion_VDJ

value: EGFR Potential copy number gain


title: CD68+, TB4, MGC W-003

description:
Library name: DSP-1001660036826-A-A09
CD68+ AOI from tuberculosis patient TB4, slide: CD68_Slide1, ROI: TB4-MGC_W-003, area: 19171.33 um2, nuclei: 9


title: Tumor_P4_Pre_infusion_VDJ

description: Library name: Tumor_P4_Pre_infusion_VDJ

value: EGFR Copy number gain


title: IP_P3_GEX

description: Library name: IP_P3_GEX


title: LRJZ22, lower incisors, VDRgem


title: 207448290029_R10C01

description: Sample name: 21033


title: CD68+, TB4, MGC W-002

description:
Library name: DSP-1001660036826-A-A08
CD68+ AOI from tuberculosis patient TB4, slide: CD68_Slide1, ROI: TB4-MGC_W-002, area: 31592.28 um2, nuclei: 146


title: AC16, human cultured under normal conditions

city: Aachen

first: Ralf

last: Weiskirchen

address: Pauwelsstr. 30

department: IFMPEGKC

country: Germany

institute: RWTH University Hospital Aachen

description: Library name: mRNA expression in AC16 cells, cultured under standard conditions

data_processing:
FASTQ files were generated using bcl2fastq (Illumina) prior to downstream analyses. Samples were processed using the nf-core/RNA-seq pipeline version 3.12 in Nextflow 23.10.0. Lane-level reads were trimmed with Trim Galore 0.6.7, aligned to the human genome (GRCh39) via STAR 2.7.9a, and quantified at both gene and transcript levels with Salmon v1.10.1, yielding length-normalized Transcripts Per Million (TPM) values.
Assembly: GRCh39
Supplementary files format and content: AC16.txt

source_name: cell line

growth_protocol: The human cardiomyocyte cell line AC16 was obtained from Merck (#SC109, Darmstadt, Germany) and expanded in DMEM/F12 containing 12.5% fetal bovine serum (FBS, #F7524, Sigma-Aldrich, Merck), 2 mM L-Glutamine (#G7513, Sigma-Aldrich), and 1x Penicillin-Steptomycin solution (DE17-602E, Lonza, Cologne, Germany). The culture medium was refreshed every 2-3 days, and the cells were passaged using Accutase® solution (A6964-100ML, Sigma-Aldrich) at a ratio of 1:3 once they reached confluence. All experiments were conducted at passages 5-7 after receiving the cells from Merck. The cells were cultured in an atmosphere of 95% air and 5% CO2 at 37°C.

extract_protocol:
Total cellular RNA was isolated from five 100 mm² plates of AC16 cells that were cultured to 80% confluence using CsCl2 density gradient centrifugation. The concentration, purity, and quality of the RNA were evaluated through UV spectroscopy and the Agilent 4200 TapeStation platform.
Following ribosomal RNA depletion, mRNA was converted into a sequencing library utilizing the NEBNext Multiplex Oligos for Illumina Index Primers Set 1 kit. Sequencing was carried out on the Illumina platform with pre-filled cartridges (MiSeq Reagent kit V2, 300-cycles), and the results were transformed into fastq data files.

treatment_protocol: No special treatment

value: cell line

value: cardiomyocyte

value: no treatment


title: LRJZ21, lower incisors, VDRgem

value: lower incisors


title: 207448290029_R08C01

description: Sample name: 21032


title: CD68+, TB4, MGC W-001

description:
Library name: DSP-1001660036826-A-A07
CD68+ AOI from tuberculosis patient TB4, slide: CD68_Slide1, ROI: TB4-MGC_W-001, area: 24403.37 um2, nuclei: 100


title: Tumor_P1_Pre_infusion_VDJ

description: Library name: Tumor_P1_Pre_infusion_VDJ

value: Copy number gain, p.R108K


title: ST-FF07794205

city: Miami

first: Glaucia Maria

middle: de

last: Mendonça Fernandes

state: FL

address: 4060 SW 97th PL

department: HWCOM Cellular and Molecular Medicine

institute: Florida International University

description:
Library name: Sample 29
FF07794057

data_processing:
Raw reads were quality-filtered using FastQC and trimmed with Trimmomatic. Clean reads were aligned to the human genome (hg38) using STAR. circRNAs were annotated and quantified with CIRCexplorer2. TPM values were calculated by normalizing read counts by transcript length and scaling per million mapped reads.
Assembly: Homo sapiens genome build GRCh38 (hg38).
Supplementary files format and content: Processed data files include circRNA raw count matrices (.txt) and TPM count data (.cvs)

source_name: Meningioma

growth_protocol: Not applicable – samples were obtained from human meningioma surgical resections.

extract_protocol:
Tissue samples were extracted either by conventional methods or using the NICO Myriad system, which preserves RNA integrity through in situ collection in a refrigerated chamber with Ringer’s Lactate. Total RNA was isolated using the Trizol based protocol following the manufacturer's protocol.
circRNA libraries were constructed following ribosomal RNA depletion and enrichment for circular RNAs, using a strand-specific protocol compatible with Illumina sequencing platforms.

treatment_protocol: Patients underwent standardized surgical resection of meningiomas without preoperative adjuvant therapy.

value: Meningioma

tag: protocol

value: Standard

tag: who grade

value: I

tag: gender

value: Male

tag: anatomical location

value: Frontal lobe


title: LRJZ18, lower incisors, control

value: male

value: control


title: 207448290029_R06C01

description: Sample name: 21030

value: leukocytes

value: HCC case


title: CD68+, TB4, MGC WO-005

description:
Library name: DSP-1001660036826-A-A06
CD68+ AOI from tuberculosis patient TB4, slide: CD68_Slide1, ROI: TB4-MGC_WO-005, area: 21836.8 um2, nuclei: 59

value: lung

value: macrophages


title: LRJZ17, lower incisors, control


title: ST-FF07794178

description:
Library name: Sample 28
FF07794427

value: II

value: Female


title: 207448290029_R04C01

description: Sample name: 21029


title: CD68+, TB4, MGC WO-004

description:
Library name: DSP-1001660036826-A-A05
CD68+ AOI from tuberculosis patient TB4, slide: CD68_Slide1, ROI: TB4-MGC_WO-004, area: 17736.68 um2, nuclei: 62


title: ST-FF07794164

description:
Library name: Sample 27
FF07793989

value: Frontal and temporal lobe


title: LRJZ16, lower incisors, control


title: Tumor_P7_Pre_infusion_GEX

description: Library name: Tumor_P7_Pre_infusion_GEX

value: CAR T cells

value: Primary cells

value: EGFR Potential copy number gain

value: Pre-treatment


title: 207448290029_R02C01

description: Sample name: 21028

value: no HCC/control


title: Control mouse with high potassium diet, replicate 3

city: Baltimore

first: Hyun Jun

last: Jung

state: MD

address: 720 Rutland Ave, Ross Research Building 1165B

department: Medicine (Nephrology)

institute: Johns Hopkins University School of Medicine

data_processing:
Two technical repliates of each biological replicate were concatenated into one replicate for further downstream data processing.
Counts and abundance of transcripts were generated by quantifying sequence reads on transcripts from Gencode GRCm38.p6 (M22) using salmon (0.14.10).
Assembly: Gencode vM21 (GRCm38.p6; primary assembly)
Supplementary files format and content: tab-delimited text files include TPM values for each sample
Supplementary files format and content: tab-delimited text files include raw gene counts for each gene

source_name: Pax8-rtTA, TRE-LC-1, MRflox/flox

growth_protocol: For induction of Nr3c2 knockout, mice were freely accessed to 2mg/ml doxycycline in 5% Sucrose water for 2 weeks and then washout with rescue diet for 2 weeks. Control mice (non-induction) were supplied with 5% Sucrose water not containing doxycycline.

extract_protocol:
The microdissected tubules were washed in PBS three times and lyzed in Trizon solution. Total RNA was extracted using Direct-zol RNA Microprep kit (ZYMO RESEARCH).
For library preparation, cDNA was synthesized using SMART-Seq HT Kit (Clontech) and Nextera XT DNA Library Preparation Kit (Illumina).

treatment_protocol: After doxycycline treatment, four groups were prepared to distinguish between K+ diet and MR knockout effects for 4 days: 1) control mice on normal K+ diet (CT-NK) or 2) high K+ diet (CT-HK) and 3) MR knockout mice on normal K+ diet (KO-NK) or 4) low K+ diet (KO-LK).

value: Kidney

value: Connecting tubule and collecting duct cell

value: High potassium diet


title: CD68+, TB4, MGC WO-003

description:
Library name: DSP-1001660036826-A-A04
CD68+ AOI from tuberculosis patient TB4, slide: CD68_Slide1, ROI: TB4-MGC_WO-003, area: 57657.1 um2, nuclei: 123


title: 207448290029_R11C01

description: Sample name: 21027


title: ST-FF07794133

description:
Library name: Sample 26
FF07794260

value: Meningioma

value: Standard

value: I

value: Skull base


title: LRJZ15, lower incisors, control

value: lower incisors

value: male

value: control


title: CD68+, TB4, MGC WO-002

description:
Library name: DSP-1001660036826-A-A03
CD68+ AOI from tuberculosis patient TB4, slide: CD68_Slide1, ROI: TB4-MGC_WO-002, area: 30542.45 um2, nuclei: 197

value: lung

value: macrophages


title: LRJZ14, lower incisors, control


title: ST-FF07794121

description:
Library name: Sample 25
FF07794015

value: Female


title: 207448290029_R09C01

description: Sample name: 21026

value: leukocytes

value: HCC case


title: CD68+, TB4, MGC WO-001

description:
Library name: DSP-1001660036826-A-A02
CD68+ AOI from tuberculosis patient TB4, slide: CD68_Slide1, ROI: TB4-MGC_WO-001, area: 42544.84 um2, nuclei: 237


title: ST-FF07794048

description:
Library name: Sample 24
FF07794443

value: Male


title: 207448290029_R07C01

description: Sample name: 21025


title: Tumor_P1_Post_infusion_GEX

description: Library name: Tumor_P1_Post_infusion_GEX

value: CAR T cells

value: Primary cells

value: Copy number gain, p.R108K

value: 1e7 bivalent CAR T cells (EGFR, IL13RA2)


title: ST-FF07794019

description:
Library name: Sample 23
FF07794214

value: Meningioma

value: II


title: 207448290029_R05C01

description: Sample name: 21024


title: No Template Control, run_1

description:
Library name: DSP-1001660036826-A-A01
No Template Control (NTC), run: run_1

source_name: No Template Control

value: No Template Control


title: LRJZ30, lower incisors, VDR-null

value: VDR-null


title: 207448290029_R03C01

description: Sample name: 21023

value: no HCC/control


title: ST-FF07794000

description:
Library name: Sample 22
FF07794056

value: Standard

value: Frontal lobe


title: Human ileal enteroid, NEC, sample 3

city: Oklahoma City

first: Adam

last: Wilson

state: Oklahoma

address: 800 Research Parkway

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

description:
Library name: NEC_-HA
10X Genomics Chromium

data_processing:
FASTQ files were processed using Cell Ranger (v. 9.0.1) and high-performance computing.
Reads were alligned to the GRCh38-2024-A reference transcriptome.
Downstream scRNA-seq analyses, including QC, filtering, normalization, annotation, and visualization, were performed in R.
The processed data files submitted to GEO include the per-sample Cell Ranger filtered feature barcode matrix in HDF5 format.
Assembly: GRCh38-2024-A
Supplementary files format and content: filtered_feature_barcode_matrix.h5 files containg the barcodes, features, and matrices

source_name: ileal organoid

extract_protocol:
Enteroids were removed from ECM domes using Organoid Recovery Solution and dissociated into a single-cell suspension using TryplE. Dead cells were removed from the suspension using a Dead Cell Removal (Annexin V) kit.
Libraries were generated using the 10x Genomics Chromium GEM-X Single Cell 3' Gene Expression kit. Libraries were sequenced on an Illumina NextSeq 2000 instrument.

treatment_protocol: Human ileal enteroids were differentiated for 72 h in differentiation medium. In the last 48 h, enteroids were treated with 150 µg/mL hyaluronan 35 kDa.

value: ileal organoid

value: NEC


title: Human ileal enteroid, HA-treated NEC, sample 3

description:
Library name: NEC_posHA
10X Genomics Chromium

value: HA


title: ST-FF07789213

description:
Library name: Sample 21
FF07788695

value: I

value: Female

value: Skull base


title: 207448290029_R01C01

description: Sample name: 21022

value: leukocytes

value: HCC case


title: Human ileal enteroid, HA-treated NEC, sample 2

description:
Library name: 158_posHA
10X Genomics Chromium


title: 207448290038_R12C02

description: Sample name: 21021


title: ST-FF07789103

description:
Library name: Sample 20
FF07789016


title: Human ileal enteroid, NEC, sample 2

description:
Library name: 158_-HA
10X Genomics Chromium


title: ST-FF07173266

description:
Library name: Sample 19
FF07788835

value: Male


title: Human ileal enteroid, HA-treated NEC, sample 1

description:
Library name: NEC_HA
10X Genomics Chromium


title: 207448290038_R10C02

description: Sample name: 21020


title: ST-FF07172307

description:
Library name: Sample 18
FF07171890


title: 207448290038_R08C02

description: Sample name: 21018


title: ST-FF07172290

description:
Library name: Sample 17
FF07171839


title: 207448290038_R06C02

description: Sample name: 21016


title: Human ileal enteroid, NEC, sample 1

description:
Library name: NEC
10X Genomics Chromium


title: WT-C-Untreated

city: CAMBRIDGE

first: Jacques

last: Deguine

state: Massachusetts

address: 415 Main Street, 415M-7175 - Xavier lab

department: Immunology Program

institute: Broad Institute

description: Library name: WT-C-Untreated

data_processing:
The flow cell data was demultiplexed with bcl-convert (Illumina, version 4.2.7) and quality control was performed using FastQC (Babraham Bioinformatics, version 0.11.5). Paired FASTQs were pseudoaligned and counted using kallisto version 0.46.1 and a 31-mer index built from the reference human transcriptome GRCh38.
Assembly: GRCh38
Supplementary files format and content: Processed data is provided as h5 files containing isoform level count data and the results of kallisto bootstrapping analyses to estimate technical variation.

source_name: HEK 293T

growth_protocol: Fresh HEK293T (noted as genotype = WT) and α-syn-GFP-mCherry (noted as genotype = CG8) stocks were thawed and grown to confluence. Cells were harvested and seeded into 12-well plates at 4 x 105 cells per well and incubated overnight to reach a confluency of 80-90%.

extract_protocol:
RNA was extracted with TRIzol reagent as per manufacturer’s instructions (Invitrogen 15596062). The quality of isolated RNA samples was assessed using Agilent HS RNA ScreenTape (Agilent, 5067-5579) on the Agilent 4200 TapeStation.
To obtain full-length transcriptomic data from cultured cells we performed SmartSeq2-based bulk RNA sequencing. In brief, RNA lysate clean-up was performed with Agencourt RNAClean XP Beads (Beckman Coulter, A639867). Next, Maxima H minus reverse Transcriptase (Thermo Fisher Scientific, EP0753) was used for reverse transcription and KAPA HotStart HIFI PCR ReadyMix (KAPA Biosystems, KK2602) was used for whole-transcription amplification (WTA). WTA products were purified with Ampure XP DNA SPRI beads (Beckman Coulter, A63881) and quantified using Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, Q32851). Quality was assessed with D5000 HS ScreenTape (Agilent, 5067-5588) on an Agilent 2200 TapeStation. WTA products were diluted for tagmention and indexing with the Nextera XT DNA Library Preparation Kit (Illumina, FC-131-1096) and two subsequent clean-ups with Ampure XP DNA SPRI beads. For quality control, Qubit dsDNA HS Assay Kit and Agilent D1000 ScreenTape (Agilent, 5067-5584) were used to determine concentration and size.  Samples were pooled together and sequenced on a NextSeq 2000 (Illumina) using a P2 flow cell and the following read configuration: R1, R2 = 38bp, I1, I2 = 8bp.

treatment_protocol: Prior to transfection, Lipofectamine 3000 was added to Opti-MEM medium at a 5% (v/v) concentration and incubated at room temperature for 5 minutes. PFFs (StressMarq, SPR-322) were thawed on ice for 15 minutes. Thawed PFFs were diluted in Opti-MEM medium and sonicated in Covaris milliTUBEs (Covaris, 520128) at room temperature using a Covaris LE220Rsc focused ultrasonicator (2 bursts, 65 seconds / burst, 1000 cycles / burst, 75W peak power, 15W average power, 20% duty factor). Sonicated PFFs were diluted to 40 µg/mL in Opti-MEM medium, then mixed with Lipofectamine 3000/Opti-MEM solution and incubated at room temperature for 20 minutes. For transfection, 200 µL of this PFF-Lipofectamine mixture was added to each well, resulting in a final well volume of 1mL and a final PFF concentration of 4 µg/mL. Negative control wells received 2.5% Lipofectamine 3000 in Opti-MEM without PFFs. 8ul of harman (Med Chem Express, HY-101392, 10 mM stock  in DMSO) was added after transfection for a final  at a concentration of 80uM. Negative control wells received 0.8% DMSO only. Altogether, 4 different treatment conditions were examined: no harman and no PFF (Untreated), no harman and PFF (PFFonly), harman and no PFF (Harmanonly) and harman+PFF (PFFharman).

value: HEK 293T

value: Epithelial

value: WT

value: Untreated

value: C


title: 207448290038_R04C02

description: Sample name: 21015

value: no HCC/control


title: WT-C-PFFonly

description: Library name: WT-C-PFFonly

value: PFFonly


title: ST-FF07172093

description:
Library name: Sample 15
FF07172300

value: Meningioma

value: Standard

value: Frontal and parietal lobe


title: ST-FF07172226

description:
Library name: Sample 16
FF07172261


title: WT-C-PFFHarman

description: Library name: WT-C-PFFHarman

value: PFFHarman


title: ST-FF07171997

description:
Library name: Sample 14
FF07788864

value: I


title: 207448290038_R11C02

description: Sample name: 21013


title: 207448290038_R02C02

description: Sample name: 21014


title: WT-C-Harmanonly

description: Library name: WT-C-Harmanonly

value: Harmanonly


title: NICO-FF07794443

description:
Library name: Sample 13
FF07794443

value: NICO

value: Skull base


title: 207448290038_R09C02

description: Sample name: 21011

value: leukocytes


title: WT-B-Untreated

description: Library name: WT-B-Untreated

value: B


title: NICO-FF07794260

description:
Library name: Sample 12
FF07794260

value: Female


title: 207448290038_R07C02

description: Sample name: 21010

value: HCC case


title: WT-B-PFFonly

description: Library name: WT-B-PFFonly

value: HEK 293T

value: Epithelial

value: WT


title: NICO-FF07794057

description:
Library name: Sample 11
FF07794057

value: Male

value: Frontal lobe


title: WT-B-PFFHarman

description: Library name: WT-B-PFFHarman


title: 207448290038_R05C02

description: Sample name: 21009


title: NICO-FF07794056

description:
Library name: Sample 10
FF07794056

value: Meningioma

value: II


title: WT-B-Harmanonly

description: Library name: WT-B-Harmanonly


title: 207448290038_R01C02

description: Sample name: 21007


title: NICO-FF07794023

description:
Library name: Sample 9
FF07794023


title: WT-A-Untreated

description: Library name: WT-A-Untreated

value: Untreated

value: A


title: 207448290038_R12C01

description: Sample name: 21006


title: WT-A-PFFonly

description: Library name: WT-A-PFFonly

value: PFFonly


title: NICO-FF07789077

description:
Library name: Sample 7
FF07789077


title: 207448290038_R08C01

description: Sample name: 21004


title: WT-A-PFFHarman

description: Library name: WT-A-PFFHarman

value: PFFHarman


title: NICO-FF07789016

description:
Library name: Sample 6
FF07789016

value: NICO

value: I


title: WT-A-Harmanonly

description: Library name: WT-A-Harmanonly

value: Harmanonly


title: NICO-FF07788864

description:
Library name: Sample 5
FF07788864

value: Skull base


title: Stage 17 gonad, female, rep1

city: Dos Hermanas

first: Iván

last: Barberá Aura

address: Avenida Rectora Rosario Valpuesta 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo (CABD)

description:
Library name: female_17_rep1
10x genomics

data_processing:
The demultiplexing, barcoded processing, alignment to genome and transcriptome, gene counting and aggregation was performed using the Cell Ranger software (v7.0.2)
Assembly: UM_NZW_1.0 (GCA_009806435.2)
Supplementary files format and content: Barcode, feature tsv files and matrix files from filtered CellRanger output.

organism: Oryctolagus cuniculus

source_name: Embryonic gonad

growth_protocol: Pregnant New Zealand White rabbits at the stages 13-21 dpc were obtained from Charles River (France branch). For 24 and 28 dpc, fetal ovaries were obtained from New Zealand rabbits bred at the SAJ rabbit facility (Jouy-en-Josas, France).

extract_protocol:
Pregnant New Zealand White rabbits at the stages 13-21 dpc were obtained from Charles River (France branch). Dissected gonads were dissociated into single-cells by incubating them with 0.05% Trypsin-EDTA (Gibco cat#25300-054) in addition to 1/10 portion of 5% BSA (Sigma-Aldrich cat#A7030-50G) /DPBS for 7-10 minutes at 37ºC. Dissociation was facilitated by pipetting gently every 2-3 minutes. Residual connective tissue, which appeared as whitish clumps at the end of the dissociation process, was discarded. Trypsin activity was halted by adding 2 portions of 5% BSA/DPBS. Cell suspension was passed through a 40 µm FlowMi cell strainer (Fisher Scientific cat#15342931) to remove cell clumps and debris. Filtrated cells were collected by centrifugation at 250-300g for 5 minutes at 4°C. The cell pellet was resuspended in DPBS for counting and viability check using 50% v/v trypan blue staining (Sigma Aldrich cat#T8154-20ML) under a light microscope. Only samples with ≥ 80% were used for downstream single-cell library preparation. Finally cells were fixed with 98% methanol added drop by drop and stored in -80°C freezer. For ovaries collected at 24 and 28 dpc, gonads were obtained from New Zealand rabbits bred at the SAJ rabbit facility (Jouy-en-Josas, France). The two gonads from the same fetus were pooled per stage in 500 µl of Trypsin-EDTA 0.05% at 37°C for 30 min. Dissociation was facilitated by gently pipetting every 5 minutes. Tryspin activity was stopped by adding SVF for a final 2% concentration. The cell suspension was passed through a 70 µm filter, then a 40 µm FlowMi Cell Strainer (Sigma-Aldrich cat #BAH136800040) to remove cell clumps and debris. The filtrated cells were collected by centrifugation at 300g for 10 minutes. The cell pellet was resuspended in 500 µL (24 dpc) or 1 mL (28 dpc) of DMEM/F12-SVF 2%. To determine whether the obtained cells were suitable for downstream analysis (cell viability > 80%), cell viability was evaluated using trypan blue staining with a haemocytometer r (TC20, Bio-Rad cat#1450102). The cell concentration was then adjusted to around 1000 cells/μl before loading onto the single-cell chip.
For the data from gonads at the stages 13-21 dpc, fixed cells were equilibrated to 4ºC on ice for at least 5 minutes. Subsequently, the cells were pelleted at 1,000g for 5 minutes at 4℃. The cells were rehydrated and gently washed with rehydration buffer (0.04% BSA, 1mM DTT (Life Technologies cat#707265ML), 0.4U/µl RNaseIn (Life Technologies cat#AM2682), 0.2U/µl SuperaseIn (Life Technologies cat#AM2696), in DPBS), using wide-bore tips (Corning Axygen Cat#T- 205-WB-C-R-S). Cell number and quality after rehydration were assessed using 50% v/v trypan blue staining. Cell suspensions were adjusted to a final concentration of 700-1,200 cells/µl. Single-cell libraries were generated using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics), according to manufacturer’s instructions, targeting 10,000 cells per reaction. Two libraries were prepared for each developmental stage and sex, except for female gonads at stage 15, for which only one library was prepared. Libraries were sequenced to a minimum depth of 200 million reads per library using the paired-end sequencing format: Read 1, 28 cycles; I7 index, 10 cycles; I5 index, 10 cycles; Read 2, 90 cycles.  For the data from ovaries at 24 and 28 dpc, Gel-Bead in Emulsions (GEMs) were generated using a Chromium 10X Single Cell System (10X Genomics) and cDNA libraries were prepared using the Chromium Next GEM Single Cell 5' Reagent v2 (10X Genomics). Two libraries were prepared for each developmental stage. The I2BC High-throughput Sequencing Platform (https://www.i2bc.paris-saclay.fr/sequencing/ng-sequencing/; Université Paris-Saclay, Gif-sur-Yvette, France) provided the facilities and expertise for library preparation and sequencing (Paired-end 28-64 bp, Illumina NextSeq500).

value: Embryonic gonad

value: female

value: Stage 17


title: 207448290038_R04C01

description: Sample name: 21002

value: leukocytes

value: HCC case


title: CG8-C-Untreated

description: Library name: CG8-C-Untreated

value: HEK 293T

value: Epithelial

value: C


title: NICO-FF07788835

description:
Library name: Sample 4
FF07788835

value: Meningioma

value: Male


title: 207448290038_R02C01

description: Sample name: 21001

value: no HCC/control


title: CG8-C-PFFonly

description: Library name: CG8-C-PFFonly

value: PFFonly


title: 207448290038_R11C01

description: Sample name: 21000


title: CG8-C-PFFHarman

description: Library name: CG8-C-PFFHarman

value: PFFHarman


title: NICO-FF07172300

description:
Library name: Sample 2
FF07172300

value: NICO

value: Frontal and parietal lobe


title: NICO-FF07171890

description:
Library name: Sample 1
FF07171890

value: I

value: Female


title: 207344530005_R12C01

description: Sample name: AD-137


title: 207344530005_R11C02

description: Sample name: AD-145


title: STRIDE reponse

city: FUKUI

first: Yosuke

last: Murata

address: 23-3 Matsuoka Shimoaizuki, Eiheiji-cho, Yoshida-gun

department: second Department of Internal Medicine

country: Japan

institute: University of Fukui

description: Library name: STRIDE reponse

data_processing:
Local Run Manager RNA Amplicon Analysis Module (Illumina)
Normalization of read count information and identification of differentially expressed genes (DEGs) between baseline and treatment effect assessment was performed using the edgeR package,
Functional annotation was performed on the samples using the gene set enrichment analysis (GSEA) method
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes differential expression for each sample

source_name: tumor cell

extract_protocol:
Total RNA was extracted with the RNeasy Mini Kit (Qiagen, Germany). Library construction commenced with 1–3 ng of RNA input.
AmpliSeq cDNA Synthesis for Illumina (Illumina, San Diego, CA, USA) was utilized for cDNA synthesis. For RNA library preparation, the AmpliSeq for Illumina custom RNA panel (Illumina), AmpliSeq library PLUS for Illumina (Illumina), and AmpliSeq CD indexes Set A for Illumina (Illumina) were employed, with the custom panel comprising 373 genes associated with cancer progression.

value: tumor cell

value: STRIDE


title: 207344530005_R04C01

description: Sample name: AD-133


title: CG8-B-PFFHarman

description: Library name: CG8-B-PFFHarman

value: B


title: lenvatinib reponse

description: Library name: LEN reponse

value: lenvatinib


title: 207344530005_R08C02

description: Sample name: AD-149

value: leukocytes


title: CG8-B-Harmanonly

description: Library name: CG8-B-Harmanonly

value: HEK 293T

value: Harmanonly


title: 207344530010_R08C01

description: Sample name: AD-163


title: lenvatinib preteatment

description: Library name: LEN pre


title: Atezo reponse

description: Library name: Atezo reponse

value: Atezo+Bev


title: 207344530010_R03C02

description: Sample name: AD-167


title: Atezo pretreatent

description: Library name: Atezo pre


title: CG8-A-PFFonly

description: Library name: CG8-A-PFFonly

value: Epithelial

value: A


title: 207344530010_R04C02

description: Sample name: AD-173

value: no HCC/control


title: CG8-A-PFFHarman

description: Library name: CG8-A-PFFHarman


title: genomic DNA from maternal peripheral blood [1845-V5]

city: Kalyani

first: Arindam

last: Maitra

state: West Bengal

address: PO: NSS

country: India

institute: National institute of Biomedical Genomics

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

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

data_processing: GenomeStudio software (Illumina) version 2011.1.

label: Cy5 and Cy3

source_name: peripheral blood

label_protocol: Standard Illumina Protocol.

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

value: Peripheral blood

tag: status

value: Pregnant

tag: time point

value: Sampled at delivery

tag: delivery

value: Preterm

tag: individual


title: 207344530010_R12C02

description: Sample name: AD-177


title: CG8-A-Harmanonly

description: Library name: CG8-A-Harmanonly


title: genomic DNA from maternal peripheral blood [1845-V3]

value: Sampled during 26-28 weeks of gestation


title: Bcell_hs-08

city: kisarazu

first: Keiko

last: Nakano

state: chiba

address: kazusa-kamatari 2-6-7

institute: Kazusa DNA Research institute

description:
Library name: Bcell_hs-08
Column name in CPM_count2.tsv: Bcell_hs-08

data_processing:
For 3' mRNA sequencing (QuantSeq), single-end reads (101 bp) were processed using fastp (version 0.23.4) to remove adapter sequences and poly(A) tails.
Clean reads were aligned using STAR (version 2.7.10a) to the following reference genomes: - Mus musculus: GRCm39 (mm39; GCA_000001635.9) - Homo sapiens: GRCh38 (hg38; GCA_000001405.15)
Gene-level read counts were generated using Subread featureCounts (version 2.0.6) at the meta-feature (exon) level using Ensembl annotations: - Mus musculus: Ensembl release 113 (Mus_musculus.GRCm39.113.gtf) - Homo sapiens: Ensembl release 115 (Homo_sapiens.GRCh38.115.gtf)
Counting was performed with strand-specific settings (forward), assigning reads to gene_id.
CPM values were calculated for each sample using a scaling factor (1,000,000 divided by the total assigned reads).
Assembly: Mus musculus: GRCm39 (Ensembl release 113 / GCA_000001635.9) Homo sapiens: GRCh38 (Ensembl release 115 / GCA_000001405.15)
Supplementary files format and content: Excel files include CPM values for each Sample

source_name: B cell

extract_protocol:
See method in article
Quant-Seq 3' mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen)

value: B cell


title: 207344530005_R07C02

description: Sample name: AD-141


title: genomic DNA from maternal peripheral blood [1845-V2]

value: Female

value: Sampled during 18-20 weeks of gestation


title: 207344530005_R03C02

description: Sample name: AD-139


title: genomic DNA from maternal peripheral blood [1845-V1]

value: Sampled during 11-14 weeks of gestation


title: Bcell_hs-07

description:
Library name: Bcell_hs-07
Column name in CPM_count2.tsv: Bcell_hs-07


title: 207344530005_R07C01

description: Sample name: AD-129


title: Bcell_hs-06

description:
Library name: Bcell_hs-06
Column name in CPM_count2.tsv: Bcell_hs-06


title: genomic DNA from maternal peripheral blood [1769-V5]

value: Term


title: 207448290038_R03C02

description: Sample name: 21008

value: leukocytes


title: NICO-FF07793989

description:
Library name: Sample 8
FF07793989

value: Meningioma

value: NICO

value: I

tag: age

value: Frontal and temporal lobe


title: 207344530005_R05C01

description: Sample name: AD-127

tag: cell type


title: Bcell_hs-05

description:
Library name: Bcell_hs-05
Column name in CPM_count2.tsv: Bcell_hs-05


title: 207344530005_R11C01

description: Sample name: AD-131

tag: disease state


title: genomic DNA from maternal peripheral blood [1769-V3]

tag: tissue


title: Bcell_hs-04

description:
Library name: Bcell_hs-04
Column name in CPM_count2.tsv: Bcell_hs-04


title: 207448290038_R06C01

description: Sample name: 21003


title: genomic DNA from maternal peripheral blood [1769-V2]


title: 207344530005_R01C01

description: Sample name: AD-125


title: genomic DNA from maternal peripheral blood [1769-V1]


title: Bcell_hs-03

description:
Library name: Bcell_hs-03
Column name in CPM_count2.tsv: Bcell_hs-03


title: 207344530002_R10C02

description: Sample name: AD-123


title: genomic DNA from maternal peripheral blood [1656-V5]


title: Bcell_hs-02

description:
Library name: Bcell_hs-02
Column name in CPM_count2.tsv: Bcell_hs-02


title: NICO-FF07788695

description:
Library name: Sample 3
FF07788695

value: Skull base


title: 207344530002_R06C02

description: Sample name: AD-121

value: no HCC/control


title: genomic DNA from maternal peripheral blood [1656-V3]

value: Peripheral blood


title: Bcell_hs-01

description:
Library name: Bcell_hs-01
Column name in CPM_count2.tsv: Bcell_hs-01


title: 207344530010_R01C01

description: Sample name: AD-153


title: CG8-B-Untreated

description: Library name: CG8-B-Untreated

tag: cell line

value: HEK 293T

value: Epithelial

value: Untreated

value: B


title: CG8-C-Harmanonly

description: Library name: CG8-C-Harmanonly

tag: genotype

value: Harmanonly

value: C


title: Tcell_hs-08

description:
Library name: Tcell_hs-08
Column name in CPM_count2.tsv: Tcell_hs-08

source_name: T cell

value: T cell


title: genomic DNA from maternal peripheral blood [1656-V2]

value: Female

value: Pregnant

value: Sampled during 18-20 weeks of gestation

value: Preterm


title: 207344530002_R02C02

description: Sample name: AD-119

value: leukocytes


title: STRIDE pretreatment

description: Library name: STRIDE pre

value: tumor cell

tag: treatment

value: STRIDE


title: CG8-B-PFFonly

description: Library name: CG8-B-PFFonly

value: PFFonly

tag: batch


title: 207344530002_R09C02

description: Sample name: AD-117

value: no HCC/control


title: genomic DNA from maternal peripheral blood [1656-V1]

tag: Sex

value: Peripheral blood

value: Sampled during 11-14 weeks of gestation


title: Tcell_hs-07

description:
Library name: Tcell_hs-07
Column name in CPM_count2.tsv: Tcell_hs-07


title: Tcell_hs-06

description:
Library name: Tcell_hs-06
Column name in CPM_count2.tsv: Tcell_hs-06


title: 207344530002_R05C02

description: Sample name: AD-115


title: genomic DNA from maternal peripheral blood [1563-V5]

value: Sampled at delivery

value: Term


title: Tcell_hs-05

description:
Library name: Tcell_hs-05
Column name in CPM_count2.tsv: Tcell_hs-05


title: genomic DNA from maternal peripheral blood [1563-V3]

value: Sampled during 26-28 weeks of gestation


title: 207344530002_R10C01

description: Sample name: AD-111


title: genomic DNA from maternal peripheral blood [1563-V2]


title: Tcell_hs-04

description:
Library name: Tcell_hs-04
Column name in CPM_count2.tsv: Tcell_hs-04


title: 207344530002_R01C02

description: Sample name: AD-113


title: CG8-A-Untreated

description: Library name: CG8-A-Untreated

value: HEK 293T

value: Epithelial

value: Untreated

value: A


title: 207344530002_R06C01

description: Sample name: AD-109


title: genomic DNA from maternal peripheral blood [1563-V1]

value: Female

value: Pregnant


title: Tcell_hs-02

description:
Library name: Tcell_hs-02
Column name in CPM_count2.tsv: Tcell_hs-02

value: T cell


title: 207344530002_R02C01

description: Sample name: AD-107

value: leukocytes


title: Tcell_hs-03

description:
Library name: Tcell_hs-03
Column name in CPM_count2.tsv: Tcell_hs-03


title: genomic DNA from maternal peripheral blood [0328-V5]

value: Preterm


title: 207344530002_R09C01

description: Sample name: AD-105


title: Tcell_hs-01

description:
Library name: Tcell_hs-01
Column name in CPM_count2.tsv: Tcell_hs-01


title: genomic DNA from maternal peripheral blood [0328-V3]


title: 207344530002_R03C01

description: Sample name: AD-101


title: genomic DNA from maternal peripheral blood [0328-V2]

value: Sampled during 18-20 weeks of gestation


title: m6A, input, AD Low 4

city: Gainesville

first: John

last: Koren

address: 1275 Center Dr

institute: University of Florida

description:
Library name: 110337-m6AINPUT
m6A-eCLIP

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

source_name: hippocampus

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

value: hippocampus

value: ApoE 3/3


title: m6A, input, AD Low 3

description:
Library name: 110002-m6AINPUT
m6A-eCLIP


title: genomic DNA from maternal peripheral blood [0328-V1]

value: Peripheral blood


title: m6A, input, AD Low 2

description:
Library name: 110001-m6AINPUT
m6A-eCLIP


title: Uninjected mouse brain rep 3

city: Coralville

first: Ahmad

last: Al Saneh

state: IA

address: 1708 5th Street Apartment 404

department: Molecular Physiology and Biophysics

institute: University of Iowa

description: Library name: Uninjected-806

data_processing:
Paired-end reads were split by barcode sequence using Je demultiplex with the options “BPOS = BOTH BM = READ_1 LEN = 4:6 FORCE = true C = false”.
FASTQ files from individual samples were then mapped against a reference genome of mouse mature nuclear-encoded tRNAs, with Arg-TCA-1-1 added, and intron-containing variants of Arg-TCA-1-1 and native Arg-TCT-1-1.
Alignments were performed using read 2 only with Bowtie2 in local alignment mode.
Mapped reads were then filtered using a custom script (sam_anticodon.py) to include only reads where one end is 5’ of position 32 and the other end is 3’ of position 37, thus ensuring coverage across the ArgUCU/ArgUCA anticodon and eliminating ambiguous reads.
tRNA abundance measurements were derived using a custom script (sam_counter.py) by counting the number of filtered reads mapping to each reference gene.
For modification analysis, SAM files were converted to WIG files using IGV-2.19.6 count command with the options “-z 5 -w 1 -e 250 –bases”.
WIG files were then reformatted using a custom script (wig_to_tsv_low_mem.py) adapted from the original MSR-seq pipeline.
Assembly: Custom build: mouse mature nuclear-encoded tRNAs, with Arg-TCA-1-1 added, and intron-containing variants of Arg-TCA-1-1 and native Arg-TCT-1-1
Supplementary files format and content: Abundance TSV files contain total read counts generated via custom python script.
Supplementary files format and content: Basewise TSV files contain per-base read coverage generated by igvtools and converted via custom python scripts.

source_name: Brain

extract_protocol:
Total RNA, including small RNAs and tRNAs, was extracted from mouse brain tissue using TRIzol reagent. Tissues were homogenized in TRIzol followed by chloroform phase separation. The aqueous phase was precipitated overnight using sodium acetate (0.3M final concentration) and ethanol (70-75% final concentration) to maximize small-RNA recovery. The resulting RNA pellet was washed with 75% ethanol and resuspended in a 10 mM NaOAc, 1 mM EDTA (pH 4.8) buffer.
Small RNA sequencing libraries were constructed by MesoRNA (Chicago, IL, USA) utilizing MSR-seq (PMID: 35513407) Multiplexed NGS library preparation workflow to simultaneously capture tRNA abundance, processing, aminoacylation, and modification signatures from a single assay.

value: Brain

value: LumA heterozygous reporter


title: Uninjected mouse brain rep 2

description: Library name: Uninjected-800


title: genomic DNA from maternal peripheral blood [0251-V5]

value: Sampled at delivery

value: Term


title: Uninjected mouse brain rep 1

description: Library name: Uninjected-584


title: genomic DNA from maternal peripheral blood [0251-V3]

value: Sampled during 26-28 weeks of gestation


title: Injected mouse brain rep 3

description: Library name: Injected-979


title: m6A, eCLIP, AD Low 4

description:
Library name: 110337-m6AIP
m6A-eCLIP


title: genomic DNA from maternal peripheral blood [0251-V2]


title: m6A, input, AD Low 1

description:
Library name: A20-031-m6AINPUT
m6A-eCLIP


title: Injected mouse brain rep 2

description: Library name: Injected-976


title: genomic DNA from maternal peripheral blood [0251-V1]

value: Sampled during 11-14 weeks of gestation


title: m6A, eCLIP, AD Low 3

description:
Library name: 110002-m6AIP
m6A-eCLIP


title: Injected mouse brain rep 1

description: Library name: Injected-974


title: m6A, eCLIP, AD Low 2

description:
Library name: 110001-m6AIP
m6A-eCLIP


title: genomic DNA from maternal peripheral blood [0876-V5]


title: P2 cerebellar cells, Tead mutant2, H3K27ac CUTRUN

city: Memphis

first: Xinwei

last: Cao

state: TN

address: 62 Danny Thomas Pl

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description:
Library name: Tead_Mutant2_CUTRUN, H3K27ac
H3K27ac CUTRUN of Tead_Mutant2

library_source: genomic

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

source_name: Cerebelleum

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

value: Cerebelleum

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


title: m6A, eCLIP, AD Low 1

description:
Library name: A20-031-m6AIP
m6A-eCLIP


title: genomic DNA from maternal peripheral blood [0876-V3]

value: Female


title: m6A, input, Ctrl 4

description:
Library name: 110003-m6AINPUT
m6A-eCLIP


title: P2 cerebellar cells, Tead mutant1, H3K27ac CUTRUN

description:
Library name: Tead_Mutant1_CUTRUN, H3K27ac
H3K27ac CUTRUN of Tead_Mutant1


title: P2 cerebellar cells, Tead control2, H3K27ac CUTRUN

description:
Library name: Tead_Control2_CUTRUN, H3K27ac
H3K27ac CUTRUN of Tead_Control2

value: Tead1fl/fl; ;Tead2fl/fl


title: genomic DNA from maternal peripheral blood [0876-V2]

value: Pregnant


title: genomic DNA from maternal peripheral blood [0876-V1]


title: m6A, input, Ctrl 3

description:
Library name: HBT474-m6AINPUT
m6A-eCLIP


title: P2 cerebellar cells, Tead control1, H3K27ac CUTRUN

description:
Library name: Tead_Control1_CUTRUN, H3K27ac
H3K27ac CUTRUN of Tead_Control1


title: genomic DNA from maternal peripheral blood [0682-V5]


title: m6A, input, Ctrl 2

description:
Library name: A21-053-m6AINPUT
m6A-eCLIP


title: m6A, input, Ctrl 1

description:
Library name: 110408-m6AINPUT
m6A-eCLIP


title: P2 cerebellar cells, Insm1 mutant3, H3K27ac CUTRUN

description:
Library name: Insm1_Mutant3_CUTRUN, H3K27ac
H3K27ac CUTRUN of Insm1_Mutant3

value: Atoh1Cre; Insm1fl/fl


title: P2 cerebellar cells, Insm1 mutant2, H3K27ac CUTRUN

description:
Library name: Insm1_Mutant2_CUTRUN, H3K27ac
H3K27ac CUTRUN of Insm1_Mutant2


title: genomic DNA from maternal peripheral blood [0682-V2]


title: m6A, eCLIP, Ctrl 3

description:
Library name: HBT474-m6AIP
m6A-eCLIP


title: genomic DNA from maternal peripheral blood [0682-V1]


title: P2 cerebellar cells, Insm1 control3, H3K27ac CUTRUN

description:
Library name: Insm1_Control3_CUTRUN, H3K27ac
H3K27ac CUTRUN of Insm1_Control3


title: m6A, eCLIP, Ctrl 2

description:
Library name: A21-053-m6AIP
m6A-eCLIP


title: P2 cerebellar cells, Insm1 control2, H3K27ac CUTRUN

description:
Library name: Insm1_Control2_CUTRUN, H3K27ac
H3K27ac CUTRUN of Insm1_Control2


title: P2 cerebellar cells, Insm1 mutant1, H3K27ac CUTRUN

description:
Library name: Insm1_Mutant1_CUTRUN, H3K27ac
H3K27ac CUTRUN of Insm1_Mutant1


title: genomic DNA from maternal peripheral blood [1441-V3]

value: Preterm


title: P2 cerebellar cells, Insm1 control1, H3K27ac CUTRUN

description:
Library name: Insm1_Control1_CUTRUN, H3K27ac
H3K27ac CUTRUN of Insm1_Control1


title: genomic DNA from maternal peripheral blood [1441-V2]

value: Sampled during 18-20 weeks of gestation


title: m6A, eCLIP, Ctrl 4

description:
Library name: 110003-m6AIP
m6A-eCLIP

value: hippocampus


title: 7F2, input, AD Low 4

description:
Library name: 110337-INPUT7F2
7F2-eCLIP

value: ApoE 3/3


title: 7F2, input, AD Low 3

description:
Library name: A20-031-INPUT7F2
7F2-eCLIP


title: genomic DNA from maternal peripheral blood [1441-V1]

value: Peripheral blood


title: P2 cerebellar cells, Wildtype1, H3K27me3 CUTRUN

description:
Library name: Wildtype1_CUTRUN, H3K27me3
H3K27me3 CUTRUN of Wildtype1

value: Wildtype


title: 7F2, input, AD Low 2

description:
Library name: 110002-INPUT7F2
7F2-eCLIP


title: genomic DNA from maternal peripheral blood [1213-V5]


title: 7F2, input, AD Low 1

description:
Library name: 110001-INPUT7F2
7F2-eCLIP


title: genomic DNA from maternal peripheral blood [1213-V3]


title: P2 cerebellar cells, Wildtype2, TEAD1 CUTRUN

description:
Library name: Wildtype2_CUTRUN, TEAD1
TEAD1 CUTRUN of Wildtype2


title: 7F2, eCLIP, AD Low 4

description:
Library name: 110337-IP7F2
7F2-eCLIP


title: 7F2, eCLIP, AD Low 3

description:
Library name: A20-031-IP7F2
7F2-eCLIP


title: P2 cerebellar cells, Wildtype1, TEAD1 CUTRUN

description:
Library name: Wildtype1_CUTRUN, TEAD1
TEAD1 CUTRUN of Wildtype1


title: genomic DNA from maternal peripheral blood [1213-V1]


title: P2 cerebellar cells, Wildtype3, KDM1A CUTRUN

description:
Library name: Wildtype3_CUTRUN, KDM1A
KDM1A CUTRUN of Wildtype3


title: 7F2, eCLIP, AD Low 2

description:
Library name: 110002-IP7F2
7F2-eCLIP


title: P2 cerebellar cells, Wildtype2, KDM1A CUTRUN

description:
Library name: Wildtype2_CUTRUN, KDM1A
KDM1A CUTRUN of Wildtype2


title: genomic DNA from maternal peripheral blood [0978-V3]


title: 7F2, eCLIP, AD Low 1

description:
Library name: 110001-IP7F2
7F2-eCLIP


title: Tau5, input, AD Low 4

description:
Library name: 110-002-INPUT
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0978-V2]


title: Tau5, input, AD Low 3

description:
Library name: 110-001-INPUT
Tau5-eCLIP


title: P2 cerebellar cells, Wildtype2, INSM1-HA CUTRUN

description:
Library name: Wildtype2_CUTRUN, INSM1-HA
INSM1-HA CUTRUN of Wildtype2


title: genomic DNA from maternal peripheral blood [0978-V1]


title: P2 cerebellar cells, Wildtype1, INSM1-HA CUTRUN

description:
Library name: Wildtype1_CUTRUN, INSM1-HA
INSM1-HA CUTRUN of Wildtype1


title: Tau5, input, AD Low 2

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


title: P2 cerebellar cells, Wildtype2, H3K4me3 CUTRUN

description:
Library name: Wildtype2_CUTRUN, H3K4me3
H3K4me3 CUTRUN of Wildtype2


title: genomic DNA from maternal peripheral blood [0828-V5]


title: Tau5, input, AD Low 1

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


title: genomic DNA from maternal peripheral blood [0828-V3]


title: P2 cerebellar cells, Wildtype1, H3K4me3 CUTRUN

description:
Library name: Wildtype1_CUTRUN, H3K4me3
H3K4me3 CUTRUN of Wildtype1


title: genomic DNA from maternal peripheral blood [0828-V2]


title: Tau5, eCLIP, AD Low 4

description:
Library name: 110-002-IP
Tau5-eCLIP


title: P2 cerebellar cells, Wildtype2,  IgG Control

description:
Library name: Wildtype2_CUTRUN, IgG
IgG Control CUTRUN of Wildtype2


title: HTR15/SVneo cells, pAKK+H/R

city: Beijing

first: Di

last: Liu

address: No. 45 West Street, Beijing

country: China

institute: Xuanwu Hospital, Capital Medical University

description: Library name: Sample 8

data_processing:
Fastqc was used to assess the quality of the reads. Fastp was used to trim low-quality bases and remove adapters.
Bowtie2 was used to map the reads to the hg19 reference genome.
SAMTools was used to convert, sort, and index the BAM files.
HTSeq was used to count the number of reads mapping to each gene.
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Trophoblast

growth_protocol: HTR-8/SVneo cells were cultured in RPMI 1640 medium (Procell, Wuhan, China), enriched with 10% FBS and antibiotics. The cultures were maintained in a humidified incubator at 37°C, 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qjagen),. 1.3 ug of total RNA w as used for the construction of sequencing libraries
RNA libraries for RNA-seg w ere prepared using SMARTER mRNA-Seg Library Prep Kifollow ing manufacturer's protocols

treatment_protocol: For the induction of a trophoblast cell model of PE, HTR-8/SVneo cells were subjected to hypoxic conditions (2% O2) at 37°C for 8 h, followed by a 16 h reoxygenation period with 5% CO2/air (H/R). To test the impact of pAKK, cells were pretreated with 1 × 108 CFU/mL pAKK in a fresh culture medium for 24 h, and then co-treat with 1 × 108 CFU/mL pAKK and H/R for 24 h.

value: Trophoblast

value: Human Villous Trophoblasts

value: WT

value: pAKK+H/R


title: genomic DNA from maternal peripheral blood [0828-V1]

value: Sampled during 11-14 weeks of gestation

value: Term


title: genomic DNA from maternal peripheral blood [0464-V5]

value: Sampled at delivery


title: Tau5, input, Ctrl 4

description:
Library name: 21-053-INPUT
Tau5-eCLIP


title: P2 cerebellar cells, Tead1/2 mutant4, ATACSeq

description:
Library name: Tead_Mutant4_ATACSeq
Genome-wide chromatin accessibility of TEAD Mutant4

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

value: Cerebelleum

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


title: genomic DNA from maternal peripheral blood [0464-V2]

value: Female

value: Pregnant


title: P2 cerebellar cells, Tead1/2 mutant2, ATACSeq

description:
Library name: Tead_Mutant2_ATACSeq
Genome-wide chromatin accessibility of TEAD Mutant2


title: Tau5, input, Ctrl 3

description:
Library name: 110-408-INPUT
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0464-V1]

value: Preterm


title: Tau5, input, Ctrl 2

description:
Library name: 110-003-INPUT
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0375-V5]


title: P2 cerebellar cells, Tead1/2 control3, ATACSeq

description:
Library name: Tead_Control3_ATACSeq
Genome-wide chromatin accessibility of TEAD Control3

value: Tead1fl/fl; ;Tead2fl/fl


title: Tau5, input, Ctrl 1

description:
Library name: HBT474-INPUT
Tau5-eCLIP

value: hippocampus


title: genomic DNA from maternal peripheral blood [0375-V3]

value: Sampled during 26-28 weeks of gestation


title: P2 cerebellar cells, Tead1/2 control2, ATACSeq

description:
Library name: Tead_Control2_ATACSeq
Genome-wide chromatin accessibility of TEAD Control2


title: Tau5, eCLIP, Ctrl 4

description:
Library name: 21-053-IP
Tau5-eCLIP

value: ApoE 3/3


title: genomic DNA from maternal peripheral blood [0375-V2]

value: Peripheral blood

value: Sampled during 18-20 weeks of gestation


title: P2 cerebellar cells, Tead1/2 control1, ATACSeq

description:
Library name: Tead_Control1_ATACSeq
Genome-wide chromatin accessibility of TEAD Control1


title: Tau5, eCLIP, Ctrl 3

description:
Library name: 110-408-IP
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0375-V1]


title: P2 cerebellar cells, Insm1 mutant3, ATACSeq

description:
Library name: Insm1_Mutant3_ATACSeq
Genome-wide chromatin accessibility of INSM1 Mutant3

value: Atoh1Cre; Insm1fl/fl


title: Tau5, eCLIP, Ctrl 2

description:
Library name: 110-003-IP
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0285-V5]


title: Tau5, eCLIP, AD Low 3

description:
Library name: 110-001-IP
Tau5-eCLIP


title: P2 cerebellar cells, Insm1 mutant2, ATACSeq

description:
Library name: Insm1_Mutant2_ATACSeq
Genome-wide chromatin accessibility of INSM1 Mutant2


title: Tau5, eCLIP, Ctrl 1

description:
Library name: HBT474-IP
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0285-V3]


title: P2 cerebellar cells, Insm1 mutant1, ATACSeq

description:
Library name: Insm1_Mutant1_ATACSeq
Genome-wide chromatin accessibility of INSM1 Mutant1


title: Tau5, input, ANA 9

description:
Library name: ZA031-INPUT
Tau5-eCLIP

value: UNK


title: genomic DNA from maternal peripheral blood [0285-V2]


title: genomic DNA from maternal peripheral blood [0285-V1]


title: Tau5, input, ANA 8

description:
Library name: 13109-INPUT
Tau5-eCLIP


title: Tau5, input, ANA 7

description:
Library name: BA020-INPUT
Tau5-eCLIP


title: PanCK+, PDAC3, MGC W-004

description:
Library name: DSP-1001660021509-A-A05
PanCK+ AOI from PDAC patient PDAC3, slide: Slide3_Panck, ROI: PDAC3-MGC_W-004, area: 26766.76 um2, nuclei: 215

source_name: pancreas

value: pancreas

value: tumor cells


title: Sample 5_FL 7  b

city: Bonn

first: Muhammad Ahmer

last: Jamil

state: NRW

address: Sigmund-Freud Str. 25

department: Institute of experimental haematology and transfusion medicine

institute: University Clinic Bonn

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

source_name: Embryonic Kidney

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

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

treatment_protocol: No treatment

value: Embryonic Kidney

value: human embryonic kidney 293 cells

value: Full length FVIII


title: PanCK+, PDAC3, MGC W-005

description:
Library name: DSP-1001660021509-A-A06
PanCK+ AOI from PDAC patient PDAC3, slide: Slide3_Panck, ROI: PDAC3-MGC_W-005, area: 30296.79 um2, nuclei: 199

data_processing:
For each AOI, digital count conversion (.dcc) files were generated from fastqs using the GeoMx NGS Pipeline (version 3.1.1).
From each tissue under investigation DCC files were read into a NanoStringGeoMxSet object using the readNanoStringGeoMxSet function from GeomxTools R package (version 3.5, R version 4.3.3), and segments were assessed for sequence quality.
After generating gene-level counts, segments with high fraction of genes detected below the limit of quantification (LOQ) were removed. Count matrix, sample annotations, and feature annotations were read into a SpatialExperiment object and analyzed with standR package (version 1.6) workflow.
Genes with low expression levels were removed. Counts were normalized using the upper-quartile method from the edgeR package (version 4.0.16).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files containing raw expression values for each AOI/sample
Supplementary files format and content: DCC files containing raw probe read counts for each AOI/sample; RTS_IDs are interpretable using the accompanying PKC file


title: genomic DNA from maternal peripheral blood [0203-V5]

value: Sampled at delivery

value: Term


title: P2 cerebellar cells, Insm1 control1, ATACSeq

description:
Library name: Insm1_Control1_ATACSeq
Genome-wide chromatin accessibility of INSM1 Control1

value: Cerebelleum


title: genomic DNA from maternal peripheral blood [0203-V3]

value: Female

value: Pregnant


title: Tau5, input, ANA 6

description:
Library name: 7A025-INPUT
Tau5-eCLIP

value: hippocampus


title: Tau5, input, ANA 5

description:
Library name: OA038-INPUT
Tau5-eCLIP


title: P2 cerebellar cells, Tead1/2 mutant4, RNASeq

description:
Library name: Tead12_Mutant4_BulkRNASeq
column name in TEAD_RSEM_gene_count..txt: 2617891_T12AT6

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


title: genomic DNA from maternal peripheral blood [0203-V2]


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

description:
Library name: Tead12_Mutant3_BulkRNASeq
column name in TEAD_RSEM_gene_count..txt: 2617890_T12AT5


title: P2 cerebellar cells, Tead1/2 mutant2, RNASeq

description:
Library name: Tead12_Mutant2_BulkRNASeq
column name in TEAD_RSEM_gene_count..txt: 2617889_T12AT4


title: Tau5, input, ANA 3

description:
Library name: MA027-INPUT
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0203-V1]

value: Sampled during 11-14 weeks of gestation


title: Tau5, input, ANA 4

description:
Library name: GA029-INPUT
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0107-V5]

value: Peripheral blood

value: Preterm


title: P2 cerebellar cells, Tead1/2 mutant1, RNASeq

description:
Library name: Tead12_Mutant1_BulkRNASeq
column name in TEAD_RSEM_gene_count..txt: 2617888_T12AT1


title: genomic DNA from maternal peripheral blood [0107-V3]

value: Sampled during 26-28 weeks of gestation


title: P2 cerebellar cells, Tead1/2 control3, RNASeq

description:
Library name: Tead12_Control3_BulkRNASeq
column name in TEAD_RSEM_gene_count..txt: 2617887_T12AT9

value: Tead1fl/fl; ;Tead2fl/fl


title: Tau5, input, ANA 2

description:
Library name: 13473-INPUT
Tau5-eCLIP

value: UNK


title: Tau5, input, ANA 1

description:
Library name: RA017-INPUT
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0107-V2]

value: Sampled during 18-20 weeks of gestation


title: genomic DNA from maternal peripheral blood [0682-V3]


title: P2 cerebellar cells, Tead1/2 control2, RNASeq

description:
Library name: Tead12_Control2_BulkRNASeq
column name in TEAD_RSEM_gene_count..txt: 2617885_T12AT3


title: Tau5, eCLIP, ANA 9

description:
Library name: ZA031-IP
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [0107-V1]


title: P2 cerebellar cells, Tead1/2 control1, RNASeq

description:
Library name: Tead12_Control1_BulkRNASeq
column name in TEAD_RSEM_gene_count..txt: 2617884_T12AT2


title: Tau5, eCLIP, ANA 8

description:
Library name: 13109-IP
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [1441-V5]


title: genomic DNA from maternal peripheral blood [0029-V5]


title: P2 cerebellar cells, Insm1 control3, ATACSeq

description:
Library name: Insm1_Control3_ATACSeq
Genome-wide chromatin accessibility of INSM1 Control3


title: m6A, eCLIP, Ctrl 1

description:
Library name: 110408-m6AIP
m6A-eCLIP

value: ApoE 3/3


title: Tau5, eCLIP, ANA 7

description:
Library name: BA020-IP
Tau5-eCLIP


title: P2 cerebellar cells, Insm1 mutant4, RNASeq

description:
Library name: Insm1_Mutant4_BulkRNASeq
column name in INSM1_RSEM_gene_count.txt: 2617403_ISAT6

value: Atoh1Cre; Insm1fl/fl


title: P2 cerebellar cells, Tead mutant1, TEAD1 CUTRUN

description:
Library name: Tead_Mutant1_CUTRUN, TEAD1
TEAD1 CUTRUN of Tead_Mutant1


title: P2 cerebellar cells, Insm1 control2, ATACSeq

description:
Library name: Insm1_Control2_ATACSeq
Genome-wide chromatin accessibility of INSM1 Control2


title: MC38 (wt) tumor 3

city: Chicago

first: Lu

last: Gao

state: IL

institute: University of Chicago

description: Library name: wt3

data_processing:
Raw sequence reads were quality checked using FastQC software. Cutadapt software was used to trim poor-quality bases (<20) and Illumina universal adapter sequences from raw reads before alignment
Reads were then aligned to mm10 reference genome using the STAR aligner.
Picard tools were used to mark duplicate sequences as an additional quality control step. Raw gene expression counts were summarized with FeatureCounts.
Sample quality metrics and raw read counts were imported into R for further processing. The DESeq2 R package was used to estimate library size factors, normalize counts and perform differential expression analyses.
Assembly: mm10
Supplementary files format and content: rds file includes raw counts for each sample

source_name: xenograft tumor

growth_protocol: Cells were grown in DMEM + 10% FBS

extract_protocol:
RNAs were extracted with TRIZOL reagent.
Libraries were made using Roche KAPA RNA HyperPrep Kit

treatment_protocol: Cells were subcutaneously injected to C57BL/6 mice to induce tumor xenografts.

value: xenograft tumor

value: Colon cancer cell

value: Acss2 wt

value: subcutaneous xenograft


title: genomic DNA from maternal peripheral blood [0029-V2]

value: Female

value: Term


title: Sample 17_#83 CALR SKO - #2

data_processing:
Fastqc was used for quality analysis of the sequences. Cutadapt was used to remove the illumina universal adapter sequence in the reads. miARma-seq pipeline as used for further analysis, tophat2 with bowtie algorithm was used as a mapper whereas gtf file of genome build HG38 from ensemble was used as annotation file. Read counts were generated from miARma-seq and Qlucore omics explorer 3.6 was used to convert read counts into expression value. Trimmed mean of M-values (TMM) normalization was performed using Qlucore Omics explorer 3.5, same gtf file was used to annotate genes. Gene with less than 5 read counts in a sample were removed, also if gene is not expressed in both replicates of a sample were also removed.
Assembly: hg38
Supplementary files format and content: tab delimited text file included TMM normalized values for each sample and have ensembl gene Ids and gene symbols

growth_protocol: Different cell line with specific knockouts where cultured until about 70% confluency in six well plates

extract_protocol:
RNA was purified using the PureLink™ RNA mini kit according to manufacturer’s instructions (Invitrogen 12183018A) from the collected cell pellets
The concentration of the RNA was determined by measuring absorbance at 260 nm using NanoDrop One (ThermoFisher Scientific). The RNA and subjected to the Illumina sequencing protocol
3' RNA-seq (Illumina HiSeq 2500 V4 platform)

value: Embryonic Kidney

value: human embryonic kidney 293 cells

value: KO-CALR

value: CRISPR-KO


title: P2 cerebellar cells, Insm1 mutant3, RNASeq

description:
Library name: Insm1_Mutant3_BulkRNASeq
column name in INSM1_RSEM_gene_count.txt: 2617402_ISAT5

value: Cerebelleum


title: Tau5, eCLIP, ANA 6

description:
Library name: 7A025-IP
Tau5-eCLIP

value: hippocampus


title: P2 cerebellar cells, Wildtype3, TEAD1 CUTRUN

description:
Library name: Wildtype3_CUTRUN, TEAD1
TEAD1 CUTRUN of Wildtype3

value: Wildtype


title: genomic DNA from maternal peripheral blood [0029-V3]

value: Peripheral blood

value: Pregnant

value: Sampled during 26-28 weeks of gestation


title: Tau5, eCLIP, ANA 5

description:
Library name: OA038-IP
Tau5-eCLIP

value: UNK


title: genomic DNA from maternal peripheral blood [1213-V2]

value: Sampled during 18-20 weeks of gestation


title: genomic DNA from maternal peripheral blood [0029-V1]

value: Sampled during 11-14 weeks of gestation


title: P2 cerebellar cells, Insm1 mutant2, RNASeq

description:
Library name: Insm1_Mutant2_BulkRNASeq
column name in INSM1_RSEM_gene_count.txt: 2617401_ISAT4

value: Atoh1Cre; Insm1fl/fl


title: P2 cerebellar cells, Insm1 mutant1, RNASeq

description:
Library name: Insm1_Mutant1_BulkRNASeq
column name in INSM1_RSEM_gene_count.txt: 2617400_ISAT3


title: Tau5, eCLIP, ANA 4

description:
Library name: GA029-IP
Tau5-eCLIP


title: genomic DNA from maternal peripheral blood [4293-V5]

value: Sampled at delivery

value: Preterm


title: genomic DNA from maternal peripheral blood [0978-V5]

value: Female


title: Tau5, eCLIP, ANA 3

description:
Library name: MA027-IP
Tau5-eCLIP


title: P2 cerebellar cells, Insm1 control4, RNASeq

description:
Library name: Insm1_Control4_BulkRNASeq
column name in INSM1_RSEM_gene_count.txt: 2617399_ISAT10


title: P2 cerebellar cells, Insm1 control2, RNASeq

description:
Library name: Insm1_Control2_BulkRNASeq
column name in INSM1_RSEM_gene_count.txt: 2617397_ISAT2


title: genomic DNA from maternal peripheral blood [4293-V2]


title: P2 cerebellar cells, Insm1 control3, RNASeq

description:
Library name: Insm1_Control3_BulkRNASeq
column name in INSM1_RSEM_gene_count.txt: 2617398_ISAT8


title: Tau5, eCLIP, ANA 1

description:
Library name: RA017-IP
Tau5-eCLIP


title: P2 cerebellar cells, Insm1 control1, RNASeq

description:
Library name: Insm1_Control1_BulkRNASeq
column name in INSM1_RSEM_gene_count.txt: 2617396_ISAT1


title: genomic DNA from maternal peripheral blood [4006-V5]

value: Term


title: Jurkat/Raji BC13

city: Seattle

first: Allen Institute

last: For Immunology

state: Washington

address: 615 Westlake Ave N, Seattle, WA

institute: Allen Institute

description:
Library name: FIX00566
10x Genomics Flex Modified with Reverse Transcription Enabled TCR/CDR3 Capture

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

source_name: Blood

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

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

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

value: Blood

value: Mixed Population

tag: subject id

tag: age at_blood_drawn

value: Male

tag: ethnicity/race

tag: cmv stats

tag: treatment time

tag: batch id

tag: pool id

value: PB

tag: batch pool

tag: probe barcode_id


title: P7 cerebellar cells from Tead1/2cKO, Insm1cKO, and controls

description:
Library name: All_samples_scRNASeq
Parse Biosciences

value: Cerebelleum

value: Mixed (Controls and Mutants)


title: genomic DNA from maternal peripheral blood [4006-V3]

value: Peripheral blood

tag: status

tag: time point

tag: delivery

tag: individual