title: H9C2 cardiomyocytes, HG group, biological replicate 1

city: Changchun

first: Naixin

last: Chen

address: No. 126, Xiantai Street

institute: China-Japan Union Hospital of Jilin University

description:
Library name: HG-1.raw_1.fastq.gz, HG-1.raw_2.fastq.gz
High glucose group biological replicate 1, total RNA-seq

data_processing:
Raw sequencing data were filtered to remove low‑quality reads, adapter sequences, and contaminating sequences to obtain clean reads using Trimmomatic software.
Assembly: Rattus norvegicus (rat) reference genome Rn6 (UCSC version rn6, GCA_000001895.4)
Supplementary files format and content: 1. Raw gene count matrix: Tab‑separated values (TSV) format, containing raw read counts of each gene across all 12 samples; 2. FPKM expression matrix: TSV format, containing normalized FPKM expression values of each gene across all 12 samples; 3. Differentially expressed gene (DEG) lists: TSV format for each pairwise comparison, containing gene ID, gene name, log₂ fold change, P value, adjusted P value, and other related statistics; 4. GO and KEGG enrichment analysis results: TSV format, containing enriched term ID, term name, gene number, P value, adjusted P value, and other related statistics; 5. Visualization files: PDF format, including volcano plots, heatmaps, enrichment scatter plots, and other related figures.
Supplementary files format and content: 1. Raw gene count matrix: Tab‑separated values (TSV) format, containing raw read counts of each gene across all 12 samples; 2. FPKM expression matrix: TSV format, containing normalized FPKM expression values of each gene across all 12 samples; 3. Differentially expressed gene (DEG) lists: TSV format for each pairwise comparison, containing gene ID, gene name, log₂ fold change, P value, adjusted P value, and other related statistics; 4. GO and KEGG enrichment analysis results: TSV format, containing enriched term ID, term name, gene number, P value, adjusted P value, and other related statistics; 5. Visualization files: PDF format, including volcano plots, heatmaps, enrichment scatter plots, and other related figures.

organism: Rattus norvegicus

growth_protocol: H9C2 cardiomyocytes were purchased from the American Type Culture Collection (ATCC, Manassas, VA, USA). Cells were routinely cultured in Dulbecco’s Modified Eagle Medium (DMEM, Gibco, Thermo Fisher Scientific, USA) supplemented with 10% fetal bovine serum (FBS, Gibco, Thermo Fisher Scientific, USA) and 1% (v/v) penicillin‑streptomycin double antibiotic solution (100 U/mL penicillin, 100 μg/mL streptomycin, HyClone, GE Healthcare, USA). The cell culture environment was maintained at 37 °C in a humidified incubator containing 5% CO₂ (Thermo Fisher Scientific, USA). When cells reached approximately 80% confluence, culture medium was replaced for subsequent experiments.

extract_protocol:
Total RNA was isolated from H9C2 cells in each experimental group using Trizol reagent (Thermo Fisher Scientific, USA) according to the manufacturer’s instructions. The purity and integrity of RNA were detected by a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific, USA) and agarose gel electrophoresis, respectively. Only RNA samples with A260/A280 ratio between 1.8 and 2.0 and intact 28S and 18S rRNA bands were used for subsequent transcriptome sequencing.
Transcriptome sequencing library construction and high‑throughput sequencing were performed by Novogene Co., Ltd. (China) using the Illumina NovaSeq 6000 platform. Briefly, mRNA was enriched from total RNA using oligo(dT) beads, followed by fragmentation into short fragments. First‑strand cDNA was synthesized using random hexamer primers and reverse transcriptase, followed by second‑strand cDNA synthesis. The cDNA fragments were end‑repaired, A‑tailed, and ligated with sequencing adapters. After PCR amplification and purification, the final libraries were quality‑controlled and sequenced on the Illumina NovaSeq 6000 platform to generate 150 bp paired‑end reads.

treatment_protocol: H9C2 cells were divided into four experimental groups with three independent biological replicates per group: 1) Control group: Cells were cultured in normal glucose medium (5.5 mM D‑glucose, Sigma‑Aldrich, Merck, USA) without any drug treatment; 2) High glucose (HG) group: Cells were cultured in HG medium (100 mM D‑glucose) without any drug treatment; 3) HG + Resveratrol (Res) group: Cells were cultured in HG medium and treated with 5 μM resveratrol (MedChemExpress, MCE, USA); 4) HG + Res + SIRT7 inhibitor group: Cells were cultured in HG medium and treated with 5 μM resveratrol and 5 μM SIRT7‑specific inhibitor (SirReal2, Selleck Chemicals, USA). All cells were incubated in the above‑mentioned conditions for 48 h in a 37 °C, 5% CO₂ humidified incubator before subsequent experiments.

value: cardiomyocytes

value: Wild type (WT)

value: High glucose medium (100 mM D-glucose), no drug treatment


title: JB-161-5

status: Public on Jul 01 2026

type: SRA

city: Suita

first: Tomoaki

last: Hara

address: Yamadaoka 2-2

country: Japan

institute: The University of Osaka

description: Library name: Sample 19

library_source: transcriptomic

data_processing:
Sequencing was performed on an Illumina NovaSeqX Plus platform in a 151-base single-end mode.
The NovaSeq control software operated base calling analysis software and delivered raw sequencing data.
Sequence quality of the FASTQ files was assessed using FastQC, and reads were trimmed based on quality scores using Trimmomatic. Trimmed reads were aligned to the human reference genome sequences (GRCh38.p5) using Hisat2.
SAM files were converted to BAM format with Samtools, and gene-level read counts were generated using featureCounts.
Assembly: GRCh38.p5
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: tumor

extract_protocol:
A moderate amount of tumor was placed in ISOGEN (NIPPON GENE), crushed with a mixer, and RNA was extracted according to ISOGEN protocol.
Ribosomal RNA was depleted using Ribo-Zero Plus rRNA Depletion Kit (Illumina) and the library was prepared using a TruSeq stranded mRNA Library Prep Kit (Illumina).

tag: tissue

value: tumor

tag: treatment


title: MCF-7 Ribociclib-Resistant, Ribociclib, Day6 Hr24

city: Duarte

first: Aritro

last: Nath

state: California

address: 1500 E Duarte Rd

department: Medical Oncology & Therapeutics Research

country: USA

institute: City of Hope

description:
Library name: 40_MCF7_Ribo_Afat
40_MCF7_Ribo_Afat

data_processing:
Paired-end raw RNA-seq FASTQ files were processed using Kallisto version 0.48 to perform pseudoalignment and obtain estimates of transcript abundance. An index fo Kallisto was built using GENCODE release 43 (CRCh38.p13) trancript sequences and comprehensive gene annotations.
Assembly: GRCh38 (hg38)
Supplementary files format and content: TSV (tab-separated values) files with counts or transcripts per million. Genes in rows, samples in columns.

source_name: MCF-7 Ribociclib-Resistant

growth_protocol: CAMA-1 and MCF-7 breast cancer cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotic-antimycotic and incubated in 5% CO2 at 37°C.

extract_protocol:
Cells were collected for bulk RNA-seq on days 0, 6, 12, and 18 at 0, 6, and 24 h after media change. Cells were pooled, washed with PBS, and pellets were frozen at -80°C for subsequent RNA isolation. RNA was isolated using the Qiagen RNeasy® Plus Mini Kit (Cat. No: 74136) following the manufacturer’s protocol.
Library preparation was performed on the samples using the Illumina TruSeq Stranded mRNA Kit following the manufacturer’s protocol.

treatment_protocol: CAMA-1 cells were treated with 0.2µM ribociclib (Selleck Chemicals, Cat. No: S7440), 1.25μM afatinib (Selleck Chemicals, Cat. No: S1011), or a combination of ribociclib and afatinib. MCF-7 cells were treated with 0.5μM ribociclib, 1.5µM afatinib, or a combinatin of ribociclib and afatinib. Cells were treated for a total of 21 days with media change performed every three days.

tag: cell line

value: MCF-7 Ribociclib-Resistant

tag: cell type

value: ER+ Breast Cancer

tag: genotype

value: WT

value: Ribociclib

tag: time

value: Day6 Hr24


title: SU-DHL-8 cells, Erianin 100nM, 24h, rep3

city: Tianjin

first: Minghan

last: Qiu

state: Tianjin

address: Department of Oncology, Tianjin Union Medical Center of Nankai Univercity, 190 Jieyuan Street, Hongqiao District, Tianjin, China.

department: Department of Oncology

country: China

data_processing:
Raw reads were filtered and cleaned by fastp software (v0.23.2).
Gene expression levels were quantified with featureCounts v2.0.1,referencing the GENCODE28 annotations.
Sequences were then aligned to the GRCh38 reference genome using STAR v2.7.10.
Transcript assembly and abundance estimation were performed using StringTie v2.2.1.
R was used for visualization.
Assembly: hg38
Supplementary files format and content: table-delimited text file includes raw counts for each sample
Supplementary files format and content: table-delimited text file includes TPM values for each sample

growth_protocol: SU-DHL-8 cells were maintained  in RPMI 1640, all with 10% FBS, penicillin (100 IU/ml), and streptomycin (100 μg/ml) in a 5% CO2 atmosphere at 37°C.

extract_protocol:
Total RNA was extracted using TRIzol reagent
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: SU-DHL-8 cells were treated with 100nM Erianin for 24 hours, with an equal concentration of DMSO as the control

value: DLBCL cell

value: Erianin 100nM, 24h


title: JB-161-4

description: Library name: Sample 18


title: Patient 48 COAD 048

type: RNA

city: Seoul

first: Chungyeop

last: Lee

address: Songpagu Olympicro 43gil

country: South Korea

institute: Asan Medical Center

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software. Training cohort and validation cohort normalization were separately conducted.

source_name: Locally Advanced Rectal Cancer

label_protocol: No labeling was performed; digital barcoding system was used (NanoString).

extract_protocol: Total RNA was extracted from pretreatment FFPE biopsy tissues using the RNeasy FFPE Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol.

value: rectal cancer

tag: histology

value: Total


title: SU-DHL-8 cells, Erianin 100nM, 24h, rep2

institute: Tianjin Union Medical Center of Nankai Univercity


title: Patient 47 COAD 047

description: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software.

value: Minimal


title: JB-161-3

description: Library name: Sample 17


title: SU-DHL-8 cells, Erianin 100nM, 24h, rep1


title: MCF-7 Sensitive, Ribociclib + Afatinib, Day6 Hr24

description:
Library name: 38_MCF7_Ribo_Afat
38_MCF7_Ribo_Afat

source_name: MCF-7 Sensitive

value: MCF-7 Sensitive

value: Ribociclib + Afatinib


title: SU-DHL-8 cells, DMSO, 24h, rep3


title: JB-161-2

description: Library name: Sample 16


title: Patient 46 COAD 046


title: MCF-7 Ribociclib-Resistant, DMSO, Day6 Hr24

description:
Library name: 39_MCF7_Ribo_Afat
39_MCF7_Ribo_Afat

value: DMSO


title: Patient 45 COAD 045


title: JB-161-1

description: Library name: Sample 15


title: 39_Control_2019_01_02_3, rep3

city: Villenave d Ornon

first: mathieu

last: fouché

state: Gironde

address: 71 avenue Edouard Bourlaux

department: UMR BFP

country: France

institute: INRAE

description: Library name: 39_cold_deprivation, 39_TTACAGGA-GCTTGTCA-AHGKC2BBXY_L006

data_processing:
trimming: Trimmomatic 0.36 (Bolger et al., 2014) with following settings fa:2:10:5:1 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were mapped to the sweet cherry ‘Regina’ reference genome v.1 (Vimont et al., 2021) using STAR (Dobin et al., 2013)
Raw read count was performed using HTSeq count (Anders et al., 2015)
Assembly: sweet cherry ‘Regina’ reference genome v.1 (Le Dantec et al, 2022)
Supplementary files format and content: the format is .txt and include raw counts of each gene for each sample

organism: Prunus avium

source_name: flower bud

growth_protocol: adult potted trees

extract_protocol:
Total RNA was extracted from 100 mg of frozen and grinded flower buds using RNeasy Plant Mini kit (Qiagen) with minor modification: 1.5% PVP-40 was added in the extraction buffer RLT
Library preparation was performed on 1 μg of high quality RNA (RNA integrity number equivalent superior or equivalent to 8.5) using the TruSeq Stranded mRNA Library Prep Kit High Throughput (Illumina cat. no. RS-122-2103)

value: flower bud

value: plant

value: Regina

tag: batch


title: MCF-7 Sensitive, Afatinib, Day6 Hr24

description:
Library name: 37_MCF7_Ribo_Afat
37_MCF7_Ribo_Afat

value: Afatinib


title: MCF-7 Sensitive, Ribociclib, Day6 Hr24

description:
Library name: 36_MCF7_Ribo_Afat
36_MCF7_Ribo_Afat


title: SU-DHL-8 cells, DMSO, 24h, rep1


title: JB-157-5

description: Library name: Sample 14

value: tumor


title: MCF-7 Sensitive, DMSO, Day6 Hr24

description:
Library name: 35_MCF7_Ribo_Afat
35_MCF7_Ribo_Afat

value: ER+ Breast Cancer


title: JB-157-4

description: Library name: Sample 13


title: Patient 44 COAD 044


title: T26_0300

type: genomic

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

country: Germany

institute: Hertie-Institute for Clinical Brain Research

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hypridized to human Infinium MethylationEPIC version 2 array using standard Illumina protocols

scan_protocol: Arrays were imaged using BeadArray Reader and standard recommended Illumina scanner protocols

data_processing:
SeSAMe pipline (v1.24.0)
Average Beta values

label: Cy3 and Cy5

molecule: genomic DNA

source_name: meningioma

label_protocol: Standard Illumina Protocol

extract_protocol: Genomic DNA from human meningiomas was extracted using QIAamp DNA Blood Mini Kit

value: meningioma


title: Patient 42 COAD 042


title: MCF-7 Ribociclib-Resistant, Ribociclib + Afatinib, Day6 Hr6

description:
Library name: 34_MCF7_Ribo_Afat
34_MCF7_Ribo_Afat

value: MCF-7 Ribociclib-Resistant

value: WT

value: Day6 Hr6


title: JB-157-3

description: Library name: Sample 12


title: MCF-7 Ribociclib-Resistant, Afatinib, Day6 Hr6

description:
Library name: 33_MCF7_Ribo_Afat
33_MCF7_Ribo_Afat


title: JB-157-2

description: Library name: Sample 11


title: T26_0298


title: MCF-7 Ribociclib-Resistant, Ribociclib, Day6 Hr6

description:
Library name: 32_MCF7_Ribo_Afat
32_MCF7_Ribo_Afat

value: Ribociclib


title: SU-DHL-8 cells, DMSO, 24h, rep2

value: DLBCL cell


title: JB-157-1

description: Library name: Sample 10


title: Patient 40 COAD 040

value: rectal cancer


title: T26_0296


title: T26_0295


title: MCF-7 Ribociclib-Resistant, DMSO, Day6 Hr6

description:
Library name: 31_MCF7_Ribo_Afat
31_MCF7_Ribo_Afat


title: 5-FU-3

description: Library name: Sample 8


title: MCF-7 Sensitive, Ribociclib + Afatinib, Day6 Hr6

description:
Library name: 30_MCF7_Ribo_Afat
30_MCF7_Ribo_Afat


title: H9C2 cardiomyocytes, Ctrl group, biological replicate 1

description:
Library name: Ctrl-1.raw_1.fastq.gz, Ctrl-1.raw_2.fastq.gz
Control group (normal glucose) biological replicate 1, total RNA-seq

value: cardiomyocytes

value: Wild type (WT)

value: Normal glucose medium, no drug treatment


title: Patient 39 COAD 039

value: Minimal


title: 5-FU-2

description: Library name: Sample 7


title: Patient 37 COAD 037


title: MCF-7 Sensitive, Ribociclib, Day6 Hr6

description:
Library name: 28_MCF7_Ribo_Afat
28_MCF7_Ribo_Afat

value: MCF-7 Sensitive


title: 5-FU-1

description: Library name: Sample 6


title: T26_0293


title: Patient 36 COAD 036


title: MCF-7 Sensitive, DMSO, Day6 Hr6

description:
Library name: 27_MCF7_Ribo_Afat
27_MCF7_Ribo_Afat

value: DMSO


title: Patient 35 COAD 035


title: Control-5

description: Library name: Sample 5

value: Control-5; DMSO


title: MCF-7 Ribociclib-Resistant, Ribociclib + Afatinib, Day6 Hr0

description:
Library name: 26_MCF7_Ribo_Afat
26_MCF7_Ribo_Afat

value: Ribociclib + Afatinib

value: Day6 Hr0


title: Control-4

description: Library name: Sample 4

value: tumor

value: Control-4; DMSO


title: T26_0292

value: meningioma


title: Patient 34 COAD 034

value: Total


title: T26_0291


title: MCF-7 Ribociclib-Resistant, Afatinib, Day6 Hr0

description:
Library name: 25_MCF7_Ribo_Afat
25_MCF7_Ribo_Afat

value: MCF-7 Ribociclib-Resistant

value: ER+ Breast Cancer

value: WT

value: Afatinib


title: Control-3

description: Library name: Sample 3

value: Control-3; DMSO


title: Patient 33 COAD 033

description: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software.

value: rectal cancer

value: Near total


title: Control-2

description: Library name: Sample 2

value: Control-2; DMSO


title: Patient 32 COAD 032


title: MCF-7 Ribociclib-Resistant, DMSO, Day6 Hr0

description:
Library name: 23_MCF7_Ribo_Afat
23_MCF7_Ribo_Afat


title: Patient 31 COAD 031


title: T26_0287


title: MCF-7 Sensitive, Ribociclib + Afatinib, Day6 Hr0

description:
Library name: 22_MCF7_Ribo_Afat
22_MCF7_Ribo_Afat

value: MCF-7 Sensitive


title: T26_0273


title: Patient 30 COAD 030


title: MCF-7 Sensitive, Afatinib, Day6 Hr0

description:
Library name: 21_MCF7_Ribo_Afat
21_MCF7_Ribo_Afat


title: T26_0264


title: Patient 29 COAD 029


title: MCF-7 Sensitive, Ribociclib, Day6 Hr0

description:
Library name: 20_MCF7_Ribo_Afat
20_MCF7_Ribo_Afat

value: Ribociclib


title: Patient 28 COAD 028


title: T26_0263


title: Patient 27 COAD 027


title: T26_0260


title: Control

description: Library name: Sample 1

library_source: genomic

data_processing:
Sequencing was performed on an Illumina NovaSeqX Plus platform in a 151-base paired-end mode.
The NovaSeq control software operated base calling analysis software and delivered raw sequencing data.
ChIP-seq peaks were identified using MACS2
Assembly: GRCm38
Supplementary files format and content: narrowPeak file for each Sample

extract_protocol:
HT-29 cells were harvested, and histones were extracted from 1 × 10⁷ cells using the EpiQuik Total Histone Extraction Kit (EpigenTek) according to the manufacturer’s instructions.
The resulting chromatin solution was incubated with Histone H3 (D1H2) Rabbit mAb (Cell Signaling Technology) pre-bound to Dynabeads Protein G (Invitrogen), and immunoprecipitated DNA was recovered following the kit protocol.

value: Control; DMSO


title: MCF-7 Sensitive, DMSO, Day6 Hr0

description:
Library name: 19_MCF7_Ribo_Afat
19_MCF7_Ribo_Afat

value: DMSO


title: MCF-7 Ribociclib-Resistant, Ribociclib + Afatinib, Day0 Hr24

description:
Library name: 18_MCF7_Ribo_Afat
18_MCF7_Ribo_Afat

value: Ribociclib + Afatinib

value: Day0 Hr24


title: HCoF Young replicate 2

city: Suwon-si

first: min jung

last: sung

state: Gyeonggi-do

address: 206, World cup-ro, Yeongtong-gu

institute: ajou university

description: Library name: HCoF_Young_2

data_processing:
Raw sequencing data are provided as FASTQ files.
Raw sequencing reads were processed using fastp v0.23.1 to remove adapter sequences and low-quality reads.
Filtered reads were aligned to the reference genome using Bowtie2 v2.3.4.3.
PCR duplicate reads were removed using Picard v2.27.5. Reads mapping to mitochondrial DNA or with low mapping quality were filtered using samtools v1.17.
Reads mapping to ENCODE blacklist regions were removed. Tn5 insertion bias was corrected by adjusting read coordinates using the alignmentSieve function from deepTools v3.5.2.
Peak calling was performed using MACS2 v2.2.8. Peaks were annotated using the ChIPseeker R package v1.36.0. Differential chromatin accessibility analysis was conducted using edgeR v3.42.4 with TMM-normalized log2(CPM + 1) values. Motif enrichment analysis was performed using HOMER v4.11.1.
Assembly: Reads were aligned to the human reference genome (GRCh38/hg38).
Supplementary files format and content: Processed data files include ATAC-seq peak files in TSV format listing accessible chromatin regions and genome browser tracks in bigWig format representing normalized chromatin accessibility signals.

source_name: Colon

extract_protocol:
For ATAC-seq, 100,000 fresh cells were washed twice with cold PBS and resuspended in lysis buffer. Cells were incubated on ice for 10 minutes to isolate nuclei, followed by centrifugation at 500 g at 4°C for 10 minutes to remove the supernatant.
ATAC-seq libraries were prepared using the ATAC-Seq Library Prep Kit for Illumina (Active Motif, United States) according to the manufacturer’s instructions. Briefly, isolated nuclei were incubated with Tagmentation Master Mix at 37°C for 30 minutes with shaking at 800 rpm. Tagmented DNA was purified using the DNA purification column provided in the kit. Libraries were amplified by PCR for 10 cycles under the following conditions: 72°C for 10 minutes; 98°C for 30 seconds; followed by cycling at 98°C for 10 seconds, 63°C for 30 seconds, and 72°C for 1 minute. Amplified libraries were purified using SPRI beads to remove primer dimers. Library quality and fragment size distribution were assessed using TapeStation HS D5000 Screen Tape (Agilent Technologies). Libraries were sequenced on an Illumina NovaSeq XP platform with 150 bp paired-end reads.

value: Colon

value: HCoF

value: Colonic fibroblast

value: Wild type

tag: group

value: Young


title: T26_0230

value: meningioma


title: MCF-7 Ribociclib-Resistant, Afatinib, Day0 Hr24

description:
Library name: 17_MCF7_Ribo_Afat
17_MCF7_Ribo_Afat

value: MCF-7 Ribociclib-Resistant

value: ER+ Breast Cancer

value: WT

value: Afatinib


title: MCF-7 Ribociclib-Resistant, Ribociclib, Day0 Hr24

description:
Library name: 16_MCF7_Ribo_Afat
16_MCF7_Ribo_Afat


title: HCoF Old replicate 3

description: Library name: HCoF_Old_3

value: Old


title: Patient 25 COAD 025

value: rectal cancer

value: Total


title: Patient 24 COAD 024

value: Moderate


title: 38_Control_2019_01_02_2, rep2

description: Library name: 38_cold_deprivation, 38_CCGTGAAG-ATCCACTG-AHGKC2BBXY_L005

value: flower bud

value: plant

value: Regina


title: T26_0223


title: Patient 23 COAD 023


title: MCF-7 Ribociclib-Resistant, DMSO, Day0 Hr24

description:
Library name: 15_MCF7_Ribo_Afat
15_MCF7_Ribo_Afat

value: DMSO

value: Day0 Hr24


title: T26_0210


title: MCF-7 Sensitive, Ribociclib + Afatinib, Day0 Hr24

description:
Library name: 14_MCF7_Ribo_Afat
14_MCF7_Ribo_Afat

value: MCF-7 Sensitive

value: Ribociclib + Afatinib


title: HCoF Old replicate 1

description: Library name: HCoF_Old_1

value: Colon

value: HCoF

value: Colonic fibroblast

value: Wild type


title: T26_0204

value: meningioma


title: MCF-7 Sensitive, Afatinib, Day0 Hr24

description:
Library name: 13_MCF7_Ribo_Afat
13_MCF7_Ribo_Afat

value: ER+ Breast Cancer

value: WT

value: Afatinib


title: TBPB_1_R2_P2

city: Ottawa

first: Matthew

last: Meier

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Health Canada

country: Canada

institute: Government of Canada

description: Library name: s165

data_processing:
Reads were demultiplexed from the BCL files and processed into FASTQ files using  DRAGEN analysis v1.3.0 on the Illumina BaseSpace Sequence Hub (Illumina, Inc., San Diego, CA, USA). Processing and quality control of the FASTQ files, differential expression analysis, and exploratory statistical analyses were performed using the R-ODAF_Health_Canada pipeline (https://github.com/R-ODAF/R-ODAF_Health_Canada; accessed March 2025), which manages workflows using Snakemake v8.0 (Mölder et al. 2021) and relies on scripts in R (v.4.3.2). The preprocessing steps use fastp v0.23.2 for trimming (Chen et al. 2018), STAR v2.7.8a (Dobin et al. 2013) to perform alignment of raw reads to the reference sequence and the qCount function of the QuasR R package (v1.30.0; (Gaidatzis et al. 2015) to extract the feature counts from the aligned reads (BAM files) using features specified in a GTF file. A samples-by-probes count matrix was produced.
Assembly: Probe sequence set provided by biospyder based on Human Whole Transcriptome kit v2.1
Supplementary files format and content: Tab-delimited table containing read counts per TempO-Seq probe

source_name: Mammary

growth_protocol: MCF-7 cells (ATCC, Manassas, Virginia) were cultured in 10 cm dishes (Corning Falcon No. 353003, Corning, New York) with Dulbecco’s modified Eagle’s medium (DMEM; Gibco, Thermo Fisher Scientific, Waltham, Massachusetts) containing 10% fetal bovine serum (FBS; Wisent Bioproducts, Saint-Jean Baptiste, QC, Canada), and 1% penicillin and streptomycin (P/S; Wisent), at 37°C in a humidified atmosphere (5% CO2).

extract_protocol:
Cells were washed with phosphate-buffered saline and lysed in situ using 2x TempO-Seq lysis buffer diluted with an equal amount of PBS for TempO-Seq library building.
Gene expression was measured using the TempO-Seq Human Whole Transcriptome v2.1 kit (BioSpyder Technologies Inc, Carlsbad, California) as per the manufacturer’s instructions

treatment_protocol: For the experiment, cells were washed with phosphate-buffered saline (PBS) and the media were replaced with phenol red-free DMEM supplemented with 5% charcoal-dextran stripped FBS (CD-FBS) to eliminate estrogens present in commercial media and serum (Atlas et al. 2003) for 24 h. Cells were then seeded into clear 96-well plates (Corning Falcon No. 353075) at a density of 2.0 x 104 cells per well in phenol red-free DMEM supplemented with 5% CD-FBS and 1% P/S. After 24 h, the medium was removed and replaced with phenol red-free DMEM containing 5% CD-FBS and 1% P/S and chemicals of interest. Cells were exposed for 48 h, in quadruplicates, to BPA, the 12 chemicals of interest at eight different concentrations (0.001, 0.01, 0.1, 0.5, 1, 5, 10, 50 µM), 17β-estradiol (E2; 0.1, 1 nM) as a positive control, and at least four plate-matched solvent controls (0.1% DMSO).

value: Mammary

value: Epithelial

value: chemical exposure

tag: chemical

value: tetrabromophenol blue

tag: dose


title: Patient 21 COAD 021

value: rectal cancer

value: Moderate


title: HCoF Mid-old replicate 3

description: Library name: HCoF_Mid_old_3

value: Mid-old


title: MCF-7 Sensitive, Ribociclib, Day0 Hr24

description:
Library name: 12_MCF7_Ribo_Afat
12_MCF7_Ribo_Afat

value: MCF-7 Sensitive

value: Ribociclib

value: Day0 Hr24


title: Patient 20 COAD 020

value: Near total


title: T26_0181


title: HCoF Mid-old replicate 2

description: Library name: HCoF_Mid_old_2

value: Colon

value: HCoF

value: Colonic fibroblast


title: Patient 19 COAD 019


title: HCoF Mid-old replicate 1

description: Library name: HCoF_Mid_old_1

value: Wild type


title: T26_0179

value: meningioma


title: MCF-7 Ribociclib-Resistant, Ribociclib + Afatinib, Day0 Hr6

description:
Library name: 10_MCF7_Ribo_Afat
10_MCF7_Ribo_Afat

value: MCF-7 Ribociclib-Resistant

value: ER+ Breast Cancer

value: WT

value: Ribociclib + Afatinib

value: Day0 Hr6


title: T26_0156


title: NFs from the control mesenery_rep3

first: Young-Ho

last: Ahn

address: 25 Magokdong-ro 2-gil, Gangseo-gu

department: College of Medicine

institute: Ewha Womans University

description: Library name: NF_3

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software. In this step, clean data (clean reads) were obtained by removing reads containing adapters, reads containing ploy-N, and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean 1 reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequenceper Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes FPKM values for each sample

molecule: polyA RNA

source_name: mesentery

growth_protocol: Mesenteric inflammation-associated fibroblasts (IAFs) and normal fibroblasts (NFs) were isolated from the mesenteries of patients with Crohn’s disease (CD) and individuals with non-cancerous colonic polyps (control samples) using magnetic-activated cell sorting.

extract_protocol:
Total RNA was isolated from the cells using the XENOPURE Total RNA Purification Kit (Xenohelix, Korea) following the manufacturer’s protocol. RNA integrity was assessed using the Bioanalyzer 2100 system(Agilent Technologies, CA, USA).
Messenger RNA was purified from total RNA using poly-T oligo-attachedmagnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers followed by the secondstrand cDNA synthesis. The library was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantificationand bioanalyzer for size distribution detection.

value: mesentery

value: IAFs

value: normal fibroblasts

value: con


title: Patient 43 COAD 043

value: rectal cancer

value: Total


title: Patient 17 COAD 017

value: Near total


title: MCF-7 Ribociclib-Resistant, Afatinib, Day0 Hr6

description:
Library name: 9_MCF7_Ribo_Afat
9_MCF7_Ribo_Afat

value: Afatinib


title: NFs from the control mesenery_rep2

description: Library name: NF_2


title: Patient 16 COAD 016


title: MCF-7 Ribociclib-Resistant, Ribociclib, Day0 Hr6

description:
Library name: 8_MCF7_Ribo_Afat
8_MCF7_Ribo_Afat

value: Ribociclib


title: NFs from the control mesenery_rep1

description: Library name: NF_1


title: T26_0189


title: T26_0149


title: Patient 15 COAD 015

description: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software.


title: MCF-7 Ribociclib-Resistant, DMSO, Day0 Hr6

description:
Library name: 7_MCF7_Ribo_Afat
7_MCF7_Ribo_Afat

value: DMSO


title: IAFs from the CD mesentery_rep3

description: Library name: IAF_3

value: inflammation-associated fibroblasts

value: CD


title: T26_0145

value: meningioma


title: MCF-7 Sensitive, Ribociclib + Afatinib, Day0 Hr6

description:
Library name: 6_MCF7_Ribo_Afat
6_MCF7_Ribo_Afat

value: MCF-7 Sensitive

value: ER+ Breast Cancer


title: T26_0297


title: IAFs from the CD mesentery_rep2

description: Library name: IAF_2

value: WT


title: Patient 14 COAD 014


title: T26_0133


title: Patient 38 COAD 038

value: Moderate


title: 5-FU-4

description: Library name: Sample 9

value: tumor


title: MCF-7 Sensitive, Afatinib, Day6 Hr6

description:
Library name: 29_MCF7_Ribo_Afat
29_MCF7_Ribo_Afat

value: Day6 Hr6


title: T26_0294


title: Patient 13 COAD 013


title: MCF-7 Sensitive, Afatinib, Day0 Hr6

description:
Library name: 5_MCF7_Ribo_Afat
5_MCF7_Ribo_Afat

value: Day0 Hr6


title: IAFs from the CD mesentery_rep1

description: Library name: IAF_1

value: mesentery

value: IAFs


title: T26_0121


title: MCF-7 Sensitive, Ribociclib, Day0 Hr6

description:
Library name: 4_MCF7_Ribo_Afat
4_MCF7_Ribo_Afat


title: SK-N-BE(2) cells, IgG antibody

city: suzhou

first: yang

last: yang

address: zhongnan road

institute: soochow university

description: Library name: Sample 3

data_processing:
Filtering: Raw reads were filtered using fastp (verion 0.23.4)
Mapping: Clean reads were mapped to hg38 using bowtie2 (version 2.2.5)
Peak calling: MACS3 (version 3.0.1) was used to call peak with the significance cut-off q-value <= 0.01
Assembly: hg38
Supplementary files format and content: Read coverage in BigWig format; Narrow peaks in bed format.
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

value: Neuroblastoma cells

tag: antibody

value: IgG


title: Patient 12 COAD 012

value: rectal cancer

value: Near total


title: T26_0118


title: MCF-7 Sensitive, DMSO, Day0 Hr6

description:
Library name: 3_MCF7_Ribo_Afat
3_MCF7_Ribo_Afat

value: DMSO


title: T26_0290


title: SK-N-BE(2) cells, NUDT21 antibody, replicate 2

description: Library name: Sample 2

value: NUDT21 (Proteintech, #10322-1-AP)


title: T26_0116


title: Patient 11 COAD 011


title: T26_0154


title: Patient 10 COAD 010

value: Total


title: T26_0289

value: meningioma


title: MCF-7 Ribociclib-Resistant, Ribociclib, Day6 Hr0

description:
Library name: 24_MCF7_Ribo_Afat
24_MCF7_Ribo_Afat

value: MCF-7 Ribociclib-Resistant

value: Ribociclib

value: Day6 Hr0


title: SK-N-BE(2) cells, NUDT21 antibody, replicate 1

description: Library name: Sample 1


title: MCF-7 Ribociclib-Resistant, DMSO, Day0 Hr0

description:
Library name: 2_MCF7_Ribo_Afat
2_MCF7_Ribo_Afat

value: ER+ Breast Cancer

value: WT

value: Day0 Hr0


title: T26_0110


title: Control-1

description: Library name: Sample 1

value: tumor

value: Control-1; DMSO


title: MCF-7 Sensitive, DMSO, Day0 Hr0

description:
Library name: 1_MCF7_Ribo_Afat
1_MCF7_Ribo_Afat

value: MCF-7 Sensitive


title: T26_0101


title: CFF-16HBEge cells plasmid-transfected, 48h, rep3

city: Cork

first: Lucia

last: Nicosia

state: Co. Cork

address: College Road

country: Ireland

institute: University College Cork

description: Library name: PLAS3

data_processing:
The samples were sequenced using a 2x150 Pair-End (PE) configuration v1.5. Image analysis and base calling were conducted by the NovaSeq Control Software v1.7 on the NovaSeq instrument. Raw sequence data (.bcl files) generated from Illumina NovaSeq was converted into fastq files and de-multiplexed using Illumina bcl2fastq program version 2.20. One mismatch was allowed for index sequence identification.
After investigating the quality of the raw data, sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36. The trimmed reads were mapped to the Homo sapiens reference genome available on ENSEMBL using the STAR aligner v.2.5.2b. The STAR aligner is a splice aligner that detects splice junctions and incorporates them to help align the entire read sequences. BAM files were generated as a result of this step. Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2. Only unique reads that fell within exon regions were counted.
Assembly: Trimmed reads were mapped to the Homo sapiens GRCh38 reference genome available on ENSEMBL.
Supplementary files format and content: Excel spreadsheet (.xlsx) with raw read counts, with genes as rows and samples as columns. The first column contains Ensembl gene identifiers, columns 2-10 contain integer count values for biological triplicates of each condition (eVLP, NC, PLAS), and the final column contains gene symbols.
Supplementary files format and content: Excel spreadsheets with Differential Gene Expression and Gene Ontology analysis results.

extract_protocol:
Total RNA from each condition was extracted ~48 hours post-treatment using the Monarch® Total RNA Miniprep Kit (NEB, T2010S) according to manufacturer’s protocols.
RNA sequencing library preparation was performed using NEBNext Ultra II Directional RNA Library Prep Kit for Illumina by following the manufacturer’s recommendations (NEB, Ipswich, MA, USA). Briefly, mRNAs were first enriched with Oligo(dT) beads. Enriched mRNAs were fragmented for 15 minutes at 94 °C. First strand and second strand cDNAs were subsequently synthesized. The second strand of cDNA was marked by incorporating dUTP during the synthesis. cDNA fragments were end repaired and adenylated at 3’ ends, and universal adapters were ligated to cDNA fragments, followed by index addition and library enrichment by limited-cycle PCR. The incorporated dUTP in second strand cDNA quenched the amplification of second strand, which helped to preserve the strand specificity. Sequencing libraries were validated using NGS Kit on the Agilent 5300 Fragment Analyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by using Qubit 4.0 Fluorometer (Invitrogen, Carlsbad, CA).

value: gene edited human bronchial epithelial cells

value: CFTR G542X/G542X

value: plasmid lipofection for base editing

value: 48 hours post treatment


title: JB161

description: Library name: Sample 3


title: CFF-16HBEge cells plasmid-transfected, 48h, rep2

description: Library name: PLAS2


title: Patient 8 COAD 008

value: rectal cancer


title: JB157

description: Library name: Sample 2


title: T26_0084


title: EM (mid RA) CD8 donor 3

city: Atlanta

first: Donald

last: McGuire

state: GA

address: 1462 Clifton Road room 412

institute: Emory University School of Medicine

description: Library name: p24118-s020_483-CD8-EM-MID

data_processing:
Samples were alligned to Hg38 using Hisat2 and processed into bam files using samtools 1.13.  Count data was obtained using featurecout from the subread package.  Splicing of the PTPRC gene was done using a coustom python script using the pysam package
Assembly: Hg38
Supplementary files format and content: CSV(comma seperated values)

source_name: PBMC

extract_protocol:
1,000-10,000 T cells were flow sorted based on CD45RA and CCR7 expression into RPMI supplemented with 10% FBS.  RNA was then obtained use Qiagen DNA/RNA mini allprep kit.
cDNA libraries prepared using TakaraBio's SMART-Seq v4 Ultra Low Input RNA Kit with Illumina's Nextera XT DNA Library Preparation Kit

value: PBMC

value: CD45RA-int CCR7- CD8+ CD3+


title: Patient 9 COAD 009

value: Near total


title: CFF-16HBEge cells plasmid-transfected, 48h, rep1

description: Library name: PLAS1


title: Patient 7 COAD 007


title: EMRA CD8 donor 3

description: Library name: p24118-s021_483-CD8-EMRA

value: CD45RA+ CCR7- CD8+ CD3+


title: EM CD8 donor 3

description: Library name: p24118-s019_483-CD8-EMRO

value: CD45RA- CCR7- CD8+ CD3+


title: T26_0073

value: meningioma


title: CFF-16HBEge cells eVLP-transduced, 48h, rep2

description: Library name: eVLP2

value: eVLP transduction for base editing


title: T26_0064


title: Patient 5 COAD 005

value: Total


title: T26_0054


title: Patient 4 COAD 004


title: CFF-16HBEge cells eVLP-transduced, 48h, rep1

description: Library name: eVLP1


title: Patient 3 COAD 003


title: CFF-16HBEge cells mock-transfected, 48h

description: Library name: NC3

value: mock-transfection


title: naive CD4 donor 3

description: Library name: p24118-s015_483-CD4-N

value: CD45RA+ CCR7+ CD4+ CD3+


title: Patient 2 COAD 002


title: T26_0021


title: Patient 1 COAD 001


title: EMRA CD8 donor 2

description: Library name: p24118-s014_595-CD8-EMRA


title: T26_0159


title: Sample 80-I; Drug_Female

city: New York

first: Molly

middle: S

last: Estill

state: NY

address: 1 Gustave L. Levy Place

department: Neuroscience

institute: Mount Sinai School of Medicine

description: Library name: 80-I

data_processing:
FASTQ files were processed with the NGS-Data-Charmer pipeline (https://github.com/shenlab-sinai/NGS-Data-Charmer). In brief, adapter trimming was performed, followed by alignment to the mm10 genome build using HISAT2, and duplicate alignments were removed using the Picard ‘MarkDuplicates’ module. Peaks were called with MACS2 (v2.2.6;-f BAMPE -q 0.01 --keep-dup) using IgG as background, and annotated withChIPseeker (v1.22.1).
Assembly: mm10
Supplementary files format and content: Narrowpeak files were annotated with ChIPSeekeR. Each annotated file contains peak locations and the associated genomic annotations of the peaks.
Library strategy: CUT&Run

organism: Mus musculus

source_name: Dorsal Hippocampus

extract_protocol:
The dorsal two-thirds of the right hippocampus was sub-dissected to use for CUT&RUN analysis. CUT&RUN was performed using a primary anti-ΔFOSB antibody.
Libraries were generated using the NEB Next® Ultra™ II DNA Library Prep Kit (New England BioLabs) and sequenced on an Illumina HiSeq 4000 with a 2 × 150 bp paired-end configuration at a minimum depth of 30 million reads per sample.

treatment_protocol: 2–3-month-old Alzheimer's model mice expressing human Amyloid Precursor Protein (APP) were injected with YL0441 in the right dorsal hippocampus. YL0441 or vehicle was infused for three days into the hippocampus. Mice were then anesthetized with commercial euthanasia solution, transcardially perfused with ice-cold 0.9% saline solution, and the brains collected and hemisected.

value: Dorsal Hippocampus

tag: Sex

value: Female

value: Drug

value: APP

value: IgG


title: CFF-16HBEge cells untreated, 48h

description: Library name: NC1

value: gene edited human bronchial epithelial cells

value: CFTR G542X/G542X

value: no treatment

value: 48 hours post treatment


title: EM (mid RA) CD8 donor 2

description: Library name: p24118-s013_595-CD8-EM-MID

value: PBMC

value: CD45RA-int CCR7- CD8+ CD3+


title: SK-N-BE(2) cells, control, rep 2

description: Library name: Sample 4

data_processing:
Illumina Casava2.19 software used for basecalling.
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to hg38 whole genome and GENCODE v29 using STAR 2.7.10a with parameters --outFilterMismatchNoverReadLmax 0.04 --outFilterMultimapNmax 1
Transcripts per million (TPM) were calculated using stringtie v2.1.7. Gene differential expression were calculated using DESeq2 v1.40.2.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include read counts and expression values of each gene for each sample and differential expression values between treatment group and control group.

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol.  FastPure Cell/Tissue Total RNA Isolation Kit V2(( Vazyme , RC112-01)  was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Neuroblastoma cells

value: control


title: T26_0197

value: meningioma


title: Sample 54-I; Drug_Male

description: Library name: 54-I

value: Male


title: EM CD8 donor 2

description: Library name: p24118-s012_595-CD8-EMRO

value: CD45RA- CCR7- CD8+ CD3+


title: T26_0146


title: SK-N-BE(2) cells, control, rep 1

description: Library name: Sample 3


title: SK-N-BE(2) cells, NUDT21 knockdown, rep 2

description: Library name: Sample 2

value: NUDT21 knockdown


title: T26_0109


title: Sample 35-I; Drug_Female

description: Library name: 35-I

value: Dorsal Hippocampus


title: SK-N-BE(2) cells, NUDT21 knockdown, rep 1

description: Library name: Sample 1


title: Sample 28-I; Drug_Male

description: Library name: 28-I


title: EM CD4 donor 2

description: Library name: p24118-s010_595-CD4-EM

value: CD45RA- CCR7- CD4+ CD3+


title: Sample 27-I; Drug_Male

description: Library name: 27-I

value: Drug


title: CM CD4 donor 2

description: Library name: p24118-s009_595-CD4-CM

value: CD45RA- CCR7+ CD4+ CD3+


title: T26_0221


title: SK-N-BE(2) cells, control, replicate 2

description: Library name: Sample 4

data_processing:
Filtering: Only read 2 was used to determine PAS sites. Raw reads were trimmed to remove adapters, low-quality bases with a score below 20, more than 3 consecutive "G"s at the end of the sequence, as well as "N"s and all subsequent sequences. Reads containing no less than 30% of the bases with a quality score below 20 were filtered out. Processed reads with a remaining length greater than 20 were retained.
Removing poly(A) tract: To remove poly(A) tract, we first search for at least 8 consecutive A's from the end of the reads. If more than 2 consecutive non-A bases are encountered, the poly(A) tract and all subsequent bases are removed, retaining only those reads with a length of 12 bases or more. Next, we scan for A's starting from the 5' end of the reads; if more than 9 consecutive A's are present, the poly(A) tract and all subsequent bases are removed, with reads of 12 bases or longer retained.
Alignment: These two sets of processed reads above are then simultaneously aligned to hg38 genome and Gencode.v45 using HISAT2. For reads that align successfully under both conditions, priority is given to the alignment result corresponding to the read with a poly(A) tract at the end.
Assembly: hg38
Supplementary files format and content: BigWig files containing read coverage normalized to CPM (read count per million)

extract_protocol:
Total RNA was extracted using the FastPure Cell/Tissue Total RNA Isolation Kit V2 (Vazyme, RC112-01).
For each sample, 5 μg of total RNA was treated with RQ1 DNase (M6101,Promega, USA) to remove DNA, fragmented RNAs were used for PAS-seq library preparation. mRNAs were captured with mRNA Capture Beads kit （N401,Vazyme,Chian）. Fragmented mRNAs were used for directional PAS-seq library preparation by KAPA Stranded mRNA-Seq Kit for Illumina® Platforms (KK8544, Roche, USA). Fragmented mRNAs were converted into double strand cDNA. Following end repair and A tailing, the DNAs were ligated to Diluted Roche Adaptor (KK8726, Roche, USA). After purification of ligation product and size fractioning to 300-500 bp, the ligated products were amplified and purified, quantified and stored at -80℃ before sequencing. The strand marked with dUTP (the 2nd cDNA strand) is not amplified, allowing strand-specific sequencing. For high-throughput sequencing, the libraries were prepared following the manufacturer's instructions and applied to Illumina Novaseq Xplus system for 150 nt paired-end sequencing.


title: Sample 51-I_Batch1; Control_Female

description: Library name: 51-I_Batch1

value: Female

value: Control

value: APP

value: IgG


title: naive CD4 donor 2

description: Library name: p24118-s008_595-CD4-N

value: CD45RA+ CCR7+ CD4+ CD3+


title: SK-N-BE(2) cells, control, replicate 1

description: Library name: Sample 3


title: T26_0096


title: Sample 26-I; Control_Female

description: Library name: 26-I


title: EMRA CD8 donor 1

description: Library name: p24118-s007_9-CD8-EMRA

value: PBMC

value: CD45RA+ CCR7- CD8+ CD3+


title: SK-N-BE(2) cells, NUDT21 knockdown, replicate 2

description: Library name: Sample 2

value: Neuroblastoma cells


title: Sample 19-I; Control_Male

description: Library name: 19-I


title: EM (mid RA) CD8 donor 1

description: Library name: p24118-s006_9-CD8-EM-MID

value: CD45RA-int CCR7- CD8+ CD3+


title: T26_0055

value: meningioma


title: Sample 12-I; Control_Male

description: Library name: 12-I

value: Male


title: EM CD8 donor 1

description: Library name: p24118-s005_9-CD8-EMRO

value: CD45RA- CCR7- CD8+ CD3+


title: Jurkat T cells, stimulated (8 hours), replicate 3

city: La Jolla

first: Nathan

middle: E

last: Lewis

address: 9500 GILMAN DR

institute: University of California San Diego

description: Library name: Sample 12

data_processing:
Demultiplexing was performed with Illumina's bcl2fastq Conversion Software (Illumina).
Raw sequencing reads in FASTQ format were first assessed for quality using FastQC, followed by adapter and barcode trimming using TrimGalore.
Transcript quantification was performed by pseudoalignment with Kallisto.
Assembly: hg38
Supplementary files format and content: tab-delimited text file containing raw counts for each sample

source_name: Jurkat

growth_protocol: Jurkat T cells were cultured in RPMI 1640 supplemented with 10% fetal bovine serum and penicillin-streptomycin in humidified atmosphere with 5% CO2 at 37 C.

extract_protocol:
Total RNA was extracted using the RNeasy Plus Mini Kit (Qiagen), according to the manufacturer’s instructions.
RNA-seq libraries were generated using the Illumina® Stranded mRNA Prep kit (Illumina), following the manufacturer’s protocol.

treatment_protocol: Jurkat T cells were stimulated using the culture medium supplemented with PMA, ionomycin, PHA, and human CD3/CD28 T Cell Activator.

value: Jurkat

value: T lymphocytes

value: WT

value: PMA, Ionomycin, PHA, CD3/CD28 Abs

value: 8 hours


title: Patient 18 COAD 018

value: rectal cancer

value: Near total


title: T26_0229


title: naive CD8 donor 1

description: Library name: p24118-s004_9-CD8-N

value: CD45RA+ CCR7+ CD8+ CD3+


title: Jurkat T cells, stimulated (8 hours), replicate 2

description: Library name: Sample 11


title: T26_0217


title: Sample 54; Drug_Male

description: Library name: 54

value: Dorsal Hippocampus

value: Drug

value: APP

value: ΔFOSB antibody


title: EM CD4 donor 1

description: Library name: p24118-s003_9-CD4-EM

value: PBMC

value: CD45RA- CCR7- CD4+ CD3+


title: T26_0115

value: meningioma


title: Sample 35; Drug_Female

description: Library name: 35

value: Female


title: CM CD4 donor 1

description: Library name: p24118-s002_9-CD4-CM

value: CD45RA- CCR7+ CD4+ CD3+


title: Jurkat T cells, stimulated (6 hours), replicate 3

description: Library name: Sample 9

value: Jurkat

value: 6 hours


title: Sample 28; Drug_Male

description: Library name: 28

value: Male


title: naive CD4 donor 1

description: Library name: p24118-s001_9-CD4-N

value: CD45RA+ CCR7+ CD4+ CD3+


title: T26_0039


title: Jurkat T cells, stimulated (6 hours), replicate 2

description: Library name: Sample 8

value: T lymphocytes

value: WT

value: PMA, Ionomycin, PHA, CD3/CD28 Abs


title: KSHV PDX 323473

city: Bethesda

first: Laurie

middle: T

last: Krug

state: Maryland

address: 10 Center Drive

institute: National Cancer Institute

description: FFPE from Xenograft

data_processing:
The raw original FASTQ files were generated through 10X Visium pipeline with the respective TIFF image file using v1 probe with 5 KSHV spiked in the probes. A combined reference of HG38 with adding Human herpesvirus 8 strain GK18 (NC_009333) (spaceranger_hg38_kshv_refrence.gz) and a probe set V1 (Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38-2020-A_K.csv). To remove the ambiguous and mouse reads, previous methods were adapted to the spatial datasets that are embedded with additional barcode sequences in the reads.The preprocessing part of the Xenomake pipeline was applied, which removed the spatial barcode/UMI tag and trims adapter/polyA from the reads. Thereafter, Xenome was applied to determine if the source of the read is the graft (i.e., human) or the host (i.e., mouse).
Ambiguous or mouse reads from the paired FASTQ files were removed based on Xenome calls, keeping only the reads whose source was the human xenograft or the virus.
Processed FASTQ files were then aligned to a custom reference with KSHV genome (NC_009333.1) added using SpaceRanger    count    module (version 3.0.0)
Assembly: spaceranger_hg38_kshv_refrence
Supplementary files format and content: barcodes_coordination.tsv: list of barcodes and their coordinations
Supplementary files format and content: feature.tsv: list of gene IDs
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: Tate_Krug_8004-XL-1-*_V12U06-096.tif: Tiff file for the tissue
Supplementary files format and content: V12U06-096-*1.json: Spots informations
Library strategy: Spatial Transcriptomics

source_name: PDX

growth_protocol: We engraft two cutaneous KS patient tumors in immunodeficient mice to generate KS PDX. KS was maintained in the PDX of recipient mice for long periods, up to 272 days, supporting the consistent expansion of KSHV-infected endothelial cells across multiple donors with diverse clinical features. Spatial Transcriptomics were performed on both PDX and a matched Biopsy of the patient.

extract_protocol:
FFPE treated samples were deparaffinized with investigator placed sections, H&E stained, imaged and decrosslinked.
The tissue was permeabilized and 10X Genomics human transcriptome V1 probes were hybridized to the mRNA overnight. The probes were ligated, released from the tissue, captured on the spatially barcoded spots and subjected to extension followed by denaturation per manufacturer protocol.

treatment_protocol: No treatment was performed on the PDXs.

value: cutaneous KS tumor


title: T26_0224


title: Jurkat T cells, stimulated (6 hours), replicate 1

description: Library name: Sample 7


title: Sample 51_Batch1; Control_Female

description: Library name: 51_Batch1

value: Dorsal Hippocampus

value: Control


title: KSHV PDX 330912

description: FFPE from Xenograft


title: Jurkat T cells, stimulated (4 hours), replicate 3

description: Library name: Sample 6

value: 4 hours


title: Sample 80; Drug_Female

description: Library name: 80

value: Drug

value: APP

value: ΔFOSB antibody


title: T26_0030

value: meningioma


title: T2-intermediate asthma_8038917295

city: Oxford

first: Timothy

last: Hinks

state: United Kingdom

address: John Radcliffe Hospital, Headley Way, Oxford

department: NDM Experimental Medicine - New College

country: United Kingdom

institute: University of  Oxford

description: Library name: 8038917295

data_processing:
Sequences in fastq files (in single and pair ends) were aligned using STAR aligner (version 2.7.1a)
R package (17)Rsubread was employed for quantification of reads assigned to genes
Assembly: GRCh38
Supplementary files format and content: Raw_counts_B_BR_Pl.txt
Supplementary files format and content: Normalized_counts_B_BR_Pl.txt

source_name: BIOPSY

extract_protocol:
Total RNA was extracted from subjects biopsies and brushing using RNeasy mini kits (Qiagen).
TruSeq library preparation kits were used for RNA samples. Starting with total RNA, the messenger RNA was first purified using polyA.
Single and paired-ends library were prepared.

value: BIOPSY

tag: sample group

value: T2-intermediate asthma


title: Sample 26; Control_Female

description: Library name: 26

value: Female


title: KSHV Biopsy TB0118

description: FFPE from Patient

source_name: biopsy


title: 80_CC2NOV_2019_02_28_2, rep1

description: Library name: 80_cold_deprivation, 80_GAATGAGA-AATGCCTC-AHGKC2BBXY_L004

value: flower bud

value: plant

value: Regina


title: Jurkat T cells, stimulated (8 hours), replicate 1

description: Library name: Sample 10

value: Jurkat

value: T lymphocytes

value: 8 hours


title: Jurkat T cells, stimulated (4 hours), replicate 2

description: Library name: Sample 5

value: WT

value: PMA, Ionomycin, PHA, CD3/CD28 Abs


title: T26_0203


title: Sample 19; Control_Male

description: Library name: 19

value: Dorsal Hippocampus

value: Male

value: Control


title: KSHV Biopsy TB0134

description: FFPE from Patient

value: cutaneous KS tumor


title: T26_0038


title: Jurkat T cells, stimulated (4 hours), replicate 1

description: Library name: Sample 4

value: 4 hours


title: BM-MSC, M-Ti

city: Los Angeles

first: Karolina Elzbieta

middle: Kaczor

last: Urbanowcz

state: CA

address: 10833 Le Conte Avenue

institute: UCLA

data_processing:
The sequence data were analyzed using the RaNA-seq cloud platform.
Then, low-quality reads were removed, the data were aligned to the human genome GCHr38 and differential expression was done using the RaNA-seq cloud platform
Assembly: The Ensembl Transcripts release GRCm38.107 GTF was used for gene feature annotation. For normalization of transcripts counts, CPM normalized counts were generated by adding 1.0E-4 followed by counts per million (CPM) normalization. Differential Gene expression was determined by Partek Flow GSA algorithm (Partek® Flow® software, version 7.0 Copyright ©; 2019 Partek Inc., St. Louis, MO, USA). Gene ontology enrichment analysis for differentially expressed genes were performed using ShinyGo 0.77
Supplementary files format and content: The processed data were then further analyzed for gene ontogeny for biological pathway (BP), molecular function (MF) and cellular components (CC) as well as KEGG pathways by the use of gProfiler2

source_name: Bone Marrow

growth_protocol: BM-MSC were seeded on SiN, MTi, or ATi discs in a 24-well plate at 40,000 cells/well. After cells became confluent, cells were treated with the osteogenic medium (StemPro® Osteogenesis Differentiation kit (Thermo Fisher Scientific)). The culture medium was replaced twice a week.

extract_protocol:
Total RNA samples of BM-MSC cultured on SiN, MTi and ATi discs for 21 days were extracted using Quick RNA Miniprep kit (Zymo Research, Inc. Irvine, CA). Total RNA samples from 3 separate wells in the group were combined at the equal quantity.
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit. The workflow consists of mRNA enrichment and fragmentation, first strand cDNA synthesis using random priming followed by second strand synthesis converting cDNA:RNA hybrid to double-stranded cDNA (dscDNA), and incorporates dUTP into the second cDNA strand. cDNA generation is followed by end repair to generate blunt ends, A-tailing, adaptor ligation and PCR amplification. Different adaptors were used for multiplexing samples in one lane.

value: Bone Marrow

value: Mesenchymal Stromal Cells

value: Cultured on M-Ti disc


title: T26_0127

value: meningioma


title: Sample 12; Control_Male

description: Library name: 12

value: APP

value: ΔFOSB antibody


title: Jurkat T cells, unstimulated, replicate 3

description: Library name: Sample 3

value: 0 hours


title: T26_0267


title: Sample 51-I_Batch2; Drug_Female

description: Library name: 51-I_Batch2

value: Female

value: Drug

value: IgG


title: Jurkat T cells, unstimulated, replicate 2

description: Library name: Sample 2

value: Jurkat

value: T lymphocytes

value: WT


title: BM-MSC, A-Ti

value: Cultured on A-Ti disc


title: T26_0160


title: Sample 41-I; Drug_Female

description: Library name: 41-I

value: Dorsal Hippocampus


title: BM-MSC, SiN

value: Cultured on SiN disc


title: CAMA-1 Ribociclib-Resistant, DMSO, Day6 Hr24

description:
Library name: 39_CAMA1_Ribo_Afat
39_CAMA1_Ribo_Afat

data_processing:
Paired-end raw RNA-seq FASTQ files were processed using Kallisto version 0.48 to perform pseudoalignment and obtain estimates of transcript abundance. An index fo Kallisto was built using GENCODE release 43 (CRCh38.p13) trancript sequences and comprehensive gene annotations.
Assembly: GRCh38 (hg38)
Supplementary files format and content: TSV (tab-separated values) files with counts or transcripts per million. Genes in rows, samples in columns.

source_name: CAMA-1 Ribociclib-Resistant

extract_protocol:
Cells were collected for bulk RNA-seq on days 0, 6, 12, and 18 at 0, 6, and 24 h after media change. Cells were pooled, washed with PBS, and pellets were frozen at -80°C for subsequent RNA isolation. RNA was isolated using the Qiagen RNeasy® Plus Mini Kit (Cat. No: 74136) following the manufacturer’s protocol.
Library preparation was performed on the samples using the Illumina TruSeq Stranded mRNA Kit following the manufacturer’s protocol.

value: CAMA-1 Ribociclib-Resistant

value: ER+ Breast Cancer

value: DMSO

value: Day6 Hr24


title: IPP from animal_55

city: Tempe

first: Noah

last: Snyder-Mackler

state: Arizona

address: 214 Life Sciences C

department: School of Life Sciences

institute: Arizona State University

description:
Library name: NSM1063
3 lvl sciRNAseq

library_source: transcriptomic single cell

data_processing:
Converts base calls to fastq files with bcl2fastq/ v.2.20 (RRID:SCR_015058) (Illumina), merge read 1 which contains the barcode to read 2 files.
Removes polyA tails using Trim Galore/v.0.6.7 (RRID:SCR_011847)
Aligns trimmed reads to a reference genome with STAR/v.2.7.6 (RRID:SCR_004463)
Extracts mapped reads and removes duplicates.
Generates UMI counts for exonic and intronic regions of each gene, tabulated according to the unique three-level barcode design in sci-RNA-seq3.
Assembly: rhesus macaque reference genome (Mmul_10)
Supplementary files format and content: all_regions_cell_annotate.csv
Supplementary files format and content: all_regions_count.npz
Supplementary files format and content: all_regions_gene_annotate.csv

molecule: nuclear RNA

organism: Macaca mulatta

source_name: inferior posterior parietal cortex

growth_protocol: free-ranging population

extract_protocol:
Briefly, tissue was manually pulverized on dry ice, transferred to pre-chilled tubes, and stored at −80°C. For lysis, pulverized tissue was suspended in hypotonic lysis buffer A (0.3 M sucrose, 0.1% Triton X-100, 3 mM MgCl₂, 0.025% IGEPAL CA-630, 1% DEPC in PBS) for 10 min, filtered (40-μm), pelleted, and resuspended in SPBSTM buffer (0.3 M sucrose, 1X PBS, 0.1% TritonX-100, 3 mM MgCl₂, and 1% DEPC). Nuclei were fixed for 10 min in 1.5 mM dithiobis(succinimidyl propionate) (DSP), diluted from a 123 mM stock in DMSO into methanol. After washing in 0.3 M SPBSTM, nuclei were layered onto a 10:1 volume of 1.4 M SPBSTM, centrifuged (3,000 x g, 20 min, 4°C), and resuspended. Nuclei were filtered (20-μm), counted, aliquoted, and cryopreserved in 90% 0.3 M SPBSTM with 10% anhydrous DMSO at -80°C. One library per region was generated using the optimized sci-RNA-seq3 protocol with the following modifications: nuclei were counted using the ImageExpress Pico System (Molecular Devices), and 15,000-20,000 nuclei were loaded per reverse transcription well. Tagmentation used N7 adaptor-loaded Tn5 transposase (Diagenode, C01070010-20), with 6-9 μL of Tn5 per 550 μL of 2X TD buffer (20 mM Tris-HCl pH 7.6, 10 mM MgCl₂, 20% dimethylformamide), distributed at 5uL per well.
sci-RNA-seq3

treatment_protocol: Following veterinary euthanasia, a necropsy was immediately performed during which the brain was perfused by transcardial perfusion with sterile saline. The brain was then removed from the cranium and sagittally sectioned into left and right hemispheres. The left hemisphere was fixed in 10% formalin and not used for this study. The right hemisphere was further sectioned prior to cryopreservation. First, the cerebellum was separated from the cerebrum. The cerebrum was then placed on a custom mold and sectioned coronally into 11 ~0.5 cm-thick slices. All 12 slices (including the cerebellar hemisphere) were individually stored in Whirl-pak bags and flash frozen in a dry-ice/ethanol bath immediately before storage in ultralow (-80°C) freezers. Regions of interest were dissected in sterile, RNase-free conditions on dry ice to minimize RNA degradation. Six 1-mm tissue biopsies were then collected by biopsy punch.

value: inferior posterior parietal cortex


title: Sample 27; Drug_Male

description: Library name: 27

value: Male

value: APP


title: T26_0078

data_processing:
SeSAMe pipline (v1.24.0)
Average Beta values

extract_protocol: Genomic DNA from human meningiomas was extracted using QIAamp DNA Blood Mini Kit

value: meningioma


title: Jurkat T cells, unstimulated, replicate 1

description: Library name: Sample 1

value: PMA, Ionomycin, PHA, CD3/CD28 Abs

value: 0 hours


title: T26_0260


title: CFF-16HBEge cells eVLP-transduced, 48h, rep3

description: Library name: eVLP3

value: gene edited human bronchial epithelial cells

value: CFTR G542X/G542X

value: eVLP transduction for base editing

value: 48 hours post treatment


title: Sample 23-I; Drug_Female

description: Library name: 23-I

value: Female

value: Drug

value: IgG


title: Subject 63, EuE, ALDH-Middle

city: Houston

first: Peixin

last: Jiang

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

description:
Library name: Sample 8
EM5

data_processing:
Raw sequencing reads were preprocessed using fastp for low-quality reads filtering and adapter-trimming.
Reads were aligned to reference genome using STAR Aligner.
The gene count table was generated using featureCounts.
The raw counts were filtered, normalized, and analyzed using DESeq2.
Assembly: GRCh38
Supplementary files format and content: Tab-sperated value files.

source_name: Endometriosis lesion

extract_protocol:
We used Direct-zol RNA Miniprep Kit (Zymo Research) to extract RNA.
Library was prepared using Illumina TruSeq RNA Library Prep Kit and sequenced with Illumina Novaseq.

value: Endometriosis lesion

value: Epithelium


title: Patient 6 COAD 006

institute: Asan Medical Center

data_processing: The raw data were numerical counts of each reporter barcode that hybridized with target RNA. The raw data were normalized through NanoString nSolver software. Training cohort and validation cohort normalization were separately conducted.

source_name: Locally Advanced Rectal Cancer

extract_protocol: Total RNA was extracted from pretreatment FFPE biopsy tissues using the RNeasy FFPE Kit (Qiagen, Hilden, Germany) according to manufacturer’s protocol.

value: rectal cancer

value: Near total


title: T26_0212


title: HSF, 10nm-3

city: Shanghai

first: Xin

last: Huang

state: China

address: zhizaoju Road 639

institute: Ninth People's Hospital affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Quality control: the image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level: featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis of three conditions/groups (three biological replicates per condition) was performed using the DESeq2 R package (1.20.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate . padj<0.05 and |log2(foldchange)| > 1 were set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: BAM

source_name: not applicable

growth_protocol: HSF cells were maintained in DMEM (Gibco) supplemented with 10% fetal bovine serum (Gibco) and 1% P/S (Gibco) in humidified atmosphere with 5% CO2 at 37℃

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

treatment_protocol: HSF cells were treated with human recombinant SPP1 (MedChemExpress, HY-P70499) with concenration of 10nM for 24h. Control group of cells were treated with solvent control for 24h. Three independent experimental replicates were performed and planed for RNA-sequencing.

value: not applicable

value: HSF

value: Human skin fibroblast cell line

value: WT

value: 10nM SPP1 treatment for 24h


title: HSF, 10nm-2


title: Sample 50-I; Drug_Male

description: Library name: 50-I

value: Dorsal Hippocampus

value: Male

value: APP


title: Subject 129, EuE, ALDH-Low

description:
Library name: Sample 7
EL3


title: Sample 44-I; Drug_Male

description: Library name: 44-I


title: EM CD4 donor 3

description: Library name: p24118-s017_483-CD4-EM

value: PBMC

value: CD45RA- CCR7- CD4+ CD3+


title: T26_0199

value: meningioma


title: T26_0040


title: CM CD4 donor 3

description: Library name: p24118-s016_483-CD4-CM

value: CD45RA- CCR7+ CD4+ CD3+


title: naive CD8 donor 3

description: Library name: p24118-s018_483-CD8-N

value: CD45RA+ CCR7+ CD8+ CD3+


title: Subject 127, EuE, ALDH-Low

description:
Library name: Sample 6
EL1

value: Endometriosis lesion


title: T26_0286


title: Sample 42-I; Drug_Male

description: Library name: 42-I

value: Drug

value: IgG


title: HSF, ctrl-3

value: solvent control


title: HSF, 10nm-1

value: not applicable


title: Subject 63, EuE, ALDH-High

description:
Library name: Sample 5
EH6

value: Epithelium


title: Sample 37-I; Control_Female

description: Library name: 37-I

value: Female

value: Control


title: T26_0089


title: T26_0251


title: Sample 24-I; Control_Female

description: Library name: 24-I


title: T26_0105


title: Sample 48-I; Control_Male

description: Library name: 48-I


title: IPP from animal_52

description:
Library name: NSM1060
3 lvl sciRNAseq

value: inferior posterior parietal cortex


title: MN12_ADT

first: Laura

last: Dillon

address: Room 10CRC 6-5142, 10 Center Drive

department: Hematology Branch

institute: National Heart Lung and Blood Institute, NIH

description: Patient 12 single-cell Protein

library_source: other

data_processing:
Patient samples were analyzed using Cell Ranger version 3.1.0 (10x Genomics) to obtain the UMI counts for GEX. The number of barcode mismatches was set to be 0 to minimize the demultiplexing error. The ADT libraries were quantified by CITE-seq-Count (https://github.com/Hoohm/CITE-seq-Count) with 15000 expected cells, and cells with overlapping cell barcodes (CB) in GEX results were included in the multimodal analysis.
Assembly: Single-cell cellranger used the pre-built GRCh38 in the pipeline.
Supplementary files format and content: Single-cell processed data contain the gene and protein expression matrices with cell barcodes.

molecule: protein

source_name: Bone marrow

growth_protocol: Bone marrow (BM) aspirate was collected from 12 AML patients with known abnormalities on chr7 according to cytogenetics studies

extract_protocol:
Bone marrow mononuclear cells (BMMCs) were purified from BM aspirate using density centrifugation, cryopreserved, and stored in liquid nitrogen.
The 10x Genomics 3’v2 Single Cell Profiling platform was used for scRNAseq. After staining and cell concentration adjustment, cells were loaded onto a Chromium Chip A with master mix, gel beads, and partitioning oil according to manufacturer’s instructions. Desired number of captured cells was 3000-4000. Reverse transcription (RT) of mRNA into barcoded first strand cDNA was performed on the emulsion by incubating at 53°C for 45 min in an Eppendorf Mastercycler X50a. After RT, emulsions were broken and cDNA purified using Dynabeads MyOne SILANE. At this stage, cDNA was amplified by PCR (98°C for 45 seconds; 13 cycles of 98°C for 20 sec, 67°C for 30 sec, 72°C for 1 min; 72°C for 1 min). Additional primers were added to ensure adequate amplification of oligo tags to later generate antibody-derived tag (ADT) sequencing libraries. Amplified cDNA was mixed with 0.6X SPRIselect magnetic beads (Beckman Coulter); after magnetic separation, supernatant was transferred for ADT library generation, and the remaining pellet was used for constructing the gene expression (GEX) library. Concentration of amplified cDNA was measured at a 1:10 dilution with a High Sensitivity (HS)-D5000 chip on an Agilent Tapestation.  For the GEX library, 50ng of amplified cDNA was carried forward for library construction. Fragmentation, end-repair, and A-tailing was performed (32°C for 5 min; 65°C for 30 min), followed by double-sided size selection using SPRIselect beads. Adaptor ligation (20°C for 15 min), cleanup with SPRIselect beads, and PCR amplification with sample indexing primers (98C for 45 seconds, 14 cycles of 90C for 20 sec, 54C for 30 sec, 72°C for 20 sec; 72°C for 1 min) were performed in that order. A final double size-selection was again done using SPRIselect beads. To make ADT libraries, sample index PCR using unique indices was performed with the transferred supernatant taken immediately after initial cDNA amplification (98°C for 45 seconds; 9 cycles of 98°C for 20 sec, 54°C for 30 sec, 72°C for 20 sec; 72°C for 1 min) using Kapa HiFi Hotstart Readymix (Kapa), followed by a single sided size selection cleanup with SPRIselect beads.

treatment_protocol: No treatment

value: Bone marrow

tag: disease

value: Acute Myeloid Leukemia (AML) with Abnormalities on Chromosome 7

tag: library type

value: ADT


title: T26_0080

institute: Hertie-Institute for Clinical Brain Research

source_name: meningioma


title: Subject 44, DIE, ALDH-High

description:
Library name: Sample 2
DH8


title: MN11_ADT

description: Patient 11 single-cell Protein


title: Subject 128, DIE, ALDH-High

description:
Library name: Sample 1
DH7


title: T26_0216


title: Sample 51_Batch2; Drug_Female

description: Library name: 51_Batch2

value: Dorsal Hippocampus

value: APP

value: ΔFOSB antibody


title: T26_0129

value: meningioma


title: Sample 23; Drug_Female

description: Library name: 23


title: MN10_ADT

description: Patient 10 single-cell Protein


title: MN9_ADT

description: Patient 9 single-cell Protein


title: T26_0219


title: Neonatal rat cardiomyocyte, YAP5SA-S94A, mouse YAP antibody

city: CINCINNATI

first: Shijie

last: Zhang

state: OH

address: 3333 Burnet Ave, T4.325

department: Heart institute

institute: Cincinnati Children's hospital medical center

description: Library name: NRCMs_YAPS94A_mouse_YAP_Ab

data_processing:
For RNA seq, raw sequencing data (FASTQ files) were processed using fastp for quality control. Reads containing adapters, poly-N regions, or low-quality bases were removed. Clean reads were evaluated for quality using Q20, Q30, and GC content metrics. All downstream analyses were based on high-quality clean reads. Clean reads were aligned to the rat reference genome (rn7, Ensembl release 106) using HISAT2 (v2.2.1) with default parameters. Mapped reads were quantified at the gene level with StringTie (v2.2.1), and transcript abundances were reported as raw counts and TPM values. Raw count matrices were imported into R (v4.3.1) and processed with DESeq2 (v1.38.3). CUT&RUN libraries were sequenced and processed by trimming adapters and aligning reads to the rat reference genome (rn7) using Bowtie2. Duplicate and low-quality reads (MAPQ < 30) were removed with SAMtools. Peaks were identified using MACS v2.1.0 with a significance threshold of q-value ≤ 0.01. For quantification, consensus peak regions across replicates were generated with BEDTools. Peak scores (−log10 adjusted p-values from MACS2) were assigned to genomic intervals and summed within each gene body ±2 kb flanking regions, yielding a total peak score per gene. Mapped reads were extended to 150 bp, normalized to reads per million (RPM), and converted to bigWig format for visualization.
Assembly: rn7
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample and bigWig
Library strategy: CUT&Run

source_name: Heart

growth_protocol: M199 supplemented with 10% fetal bovine serum, 2 mM glutamine, and 1× penicillin/streptomycin. Cells were cultured at 37°C with 5% CO₂.

extract_protocol:
RNA was harvested using RNeasy Mini Plus Kit (Qiagen). 1.3 μg of total RNA was used for the construction of sequencing libraries. For CUT&RUN, DNA was released by incubation with 1/100 volume of 10% SDS and 1/80 volume of 2.5 mg/mL Proteinase K (Thermo Fisher) for at least 1 hour at 55 °C. DNA was then purified by phenol/chloroform/isoamyl alcohol extraction, followed by ethanol precipitation with glycogen, and resuspended in nuclease-free water.
For RNA seq, messenger RNA (mRNA) was purified from total RNA using poly-T oligo-attached magnetic beads. Following fragmentation, first-strand cDNA was synthesized using random hexamer primers, and second-strand cDNA synthesis was performed using dUTP instead of dTTP to maintain strand specificity. Directional libraries were prepared through a series of steps, including end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. Library quality was assessed using Qubit fluorometry, real-time PCR, and fragment size distribution by Bioanalyzer. Libraries were pooled based on effective concentration and desired sequencing depth, then subjected to Illumina sequencing.  For CUT&RUN, DNA was released by incubation with 1/100 volume of 10% SDS and 1/80 volume of 2.5 mg/mL Proteinase K (Thermo Fisher) for at least 1 hour at 55 °C. DNA was then purified by phenol/chloroform/isoamyl alcohol extraction, followed by ethanol precipitation with glycogen, and resuspended in nuclease-free water. For CUT&RUN, Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) with minor modifications. End repair was carried out for 30 minutes at 20 °C, followed by A-tailing at 65 °C for 30 minutes. After adapter ligation (30 minutes at 20 °C), DNA fragments were purified using 1.8× SPRIselect beads (Beckman Coulter), then amplified via PCR for 17 cycles using NEBNext Ultra II Q5 Master Mix (New England Biolabs). Final libraries were purified with 0.9× SPRIselect beads and quantified with the Qubit dsDNA HS Assay Kit (Agilent Technologies).

value: Heart

value: Cardiomyocyte

value: wild type


title: Neonatal rat cardiomyocyte,YAP5SA-S94A, rabbit YAP antibody

description: Library name: NRCMs_YAPS94A_rabbit_YAP_Ab


title: Sample 50; Drug_Male

description: Library name: 50

value: Male

value: Drug


title: Neonatal rat cardiomyocyte,YAP5SA, rabbit YAP antibody

description: Library name: NRCMs_YAP5SA_rabbit_YAP_Ab


title: T26_0163

first: Daniel

last: Merk

address: Otfried-Müller-Str. 27


title: Sample 44; Drug_Male

description: Library name: 44


title: Neonatal rat cardiomyocyte, YAP5SA, mouse YAP antibody

description: Library name: NRCMs_YAP5SA_mouse_YAP_Ab


title: MN7_ADT

description: Patient 7 single-cell Protein


title: T26_0020


title: Sample 42; Drug_Male

description: Library name: 42


title: MN6_ADT

description: Patient 6 single-cell Protein


title: T26_0178


title: Sample 37; Control_Female

description: Library name: 37


title: T26_0051


title: Neonatal rat cardiomyocyte, GFP, mouse YAP antibody

description: Library name: NRCMs_GFP_mouse_YAP_Ab

value: Ad-GFP


title: Sample 24; Control_Female

description: Library name: 24


title: MN5_ADT

description: Patient 5 single-cell Protein


title: MN4_ADT

description: Patient 4 single-cell Protein


title: T26_0157


title: Neonatal rat cardiomyocytes, YAP5SA-S94A overexpression, biol rep2

description: Library name: YAPS94A-5

data_processing:
For RNA seq, raw sequencing data (FASTQ files) were processed using fastp for quality control. Reads containing adapters, poly-N regions, or low-quality bases were removed. Clean reads were evaluated for quality using Q20, Q30, and GC content metrics. All downstream analyses were based on high-quality clean reads. Clean reads were aligned to the rat reference genome (rn7, Ensembl release 106) using HISAT2 (v2.2.1) with default parameters. Mapped reads were quantified at the gene level with StringTie (v2.2.1), and transcript abundances were reported as raw counts and TPM values. Raw count matrices were imported into R (v4.3.1) and processed with DESeq2 (v1.38.3). CUT&RUN libraries were sequenced and processed by trimming adapters and aligning reads to the rat reference genome (rn7) using Bowtie2. Duplicate and low-quality reads (MAPQ < 30) were removed with SAMtools. Peaks were identified using MACS v2.1.0 with a significance threshold of q-value ≤ 0.01. For quantification, consensus peak regions across replicates were generated with BEDTools. Peak scores (−log10 adjusted p-values from MACS2) were assigned to genomic intervals and summed within each gene body ±2 kb flanking regions, yielding a total peak score per gene. Mapped reads were extended to 150 bp, normalized to reads per million (RPM), and converted to bigWig format for visualization.
Assembly: rn7
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample and bigWig


title: Sample 22; Control_Female

description: Library name: 22


title: MN3_ADT

description: Patient 3 single-cell Protein


title: Neonatal rat cardiomyocytes, YAP5SA-S94A overexpression, biol rep1

description: Library name: YAPS94A-4


title: T26_0236


title: T26_0245


title: Neonatal rat cardiomyocytes, YAP5SA overexpression, biol rep2

description: Library name: YAP5SA-4


title: MN2_ADT

description: Patient 2 single-cell Protein


title: Sample 43; Control_Male

description: Library name: 43


title: Sample 48; Control_Male

description: Library name: 48


title: MN1_ADT

description: Patient 1 single-cell Protein


title: T26_0003


title: Neonatal rat cardiomyocytes, YAP5SA overexpression, biol rep1

description: Library name: YAP5SA-3


title: Whole dura, Bulk RNA-seq, 5

city: Cambridge

first: Colin

middle: YC

last: Lee

address: Wellcome Genome Campus, Hinxton

institute: Molecular Immunity Unit

data_processing:
Fastq files from sequencing libraries were trimmed of the first 3 nucleotides of the R1 strand. Contaminating adaptor sequences and poor-quality bases were removed using Trim Galore (Babraham bioinformatics). Libraries were only trimmed for quality.
Quality of resulting files were assessed by FastQC and aligned to the mm10 genome using HISAT2, followed by gene-level quantification using the Featurecount function from the Rsubread package in R.
Assembly: mm10
Supplementary files format and content: Raw counts matrix (csv) - individual libraries
Supplementary files format and content: Raw counts matrix (csv) - combined

source_name: Dura

extract_protocol:
RNA extraction was performed using RNeasy plus mico kit (Qiagen) according to the manufacturer’s instructions. Genomic DNA contamination was removed using Optimal DNA depletion columns (Qiagen).
Libraries were prepared using the SMARTer stranded total RNAseq mammalian pico input kit (Takara) according to the manufacturer’s instructions. 5 ng of total RNA was used for production of libraries.

value: Dura

value: Control / baseline


title: T26_0016


title: Restim_Ax_4_input

city: London

first: Braulio

last: Martinez De La Cruz

address: Gower Street

department: LMCB

institute: UCL

description:
Library name: S32
Column name in processed data file matches "title" in this file

data_processing:
Sequencing data was processed using nf-core/rnaseq (https://zenodo.org/records/7998767) of the nf-core collection of workflows. Reads were pre-processed including quality filtered and trimmed before being mapped to GRCm38, using a combination of fastqc, samtools, star, salmon, trimgalore (full list of software and processes in table S3) set with default parameters. Mapped reads were deduplicated and quantified to produce gene counts which were used as input for differential gene expression. Differential gene expression was performed with the SARTools pipeline using DESeq2. Differential gene expression analysis was performed using edgeR using TMM normalization. Only genes with more than 15 total counts with at least 10 counts in one of the samples were considered for further processing. Surrogate Variable Analysis was used to remove batch effects. Linear models were fitted through all eight conditions (~ SV1 + SV2 + compartment * seqmethod * treatment). Gene Ontology analysis was performed using Metascape and plots were created with ggplot2 (Wickham, 2009) on R (R Core Team, 2014).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files with raw and size normalised counts per gene for each sample

source_name: Nervous

growth_protocol: Primary sympathetic neurons from p0-p2 mice were seeded on the top compartment of trans-well membranes and cultured in "NGF medium" composed of DMEM + 10% FBS + 1% Pen/Strep + 2 mM L-Glutamine supplemented with 100 ug/ml NGF and 10 uM Ara-C for at least 14 days before treatment

extract_protocol:
Cells were washed 3x in 1x PBS, and the top and bottom of a trans-well membrane was scraped for Cell Bodies/Axonal fractions, respectively. The fractions were collected, pelleted, and PBS was replaced with cell lysis buffer from PureLink RNA Micro Kit
After saving 10% RNA for inputs, RNA was sheared into ~200 bp fragments using the NEBNext® Magnesium RNA Fragmentation Module (New England Biolabs, Cat. E6150S). After purification with AMPure XP beads (Beckman Coulter, Cat. A63880), meRIP was performed as described above. RNA size, quality, and concentration were verified via TapeStation High Sensitivity RNA ScreenTape Analysis. Using the Watchmaker RNA Library Prep Kit with Polaris available under aCC-BY-NC-ND 4.0 International license. (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made bioRxiv preprint doi: https://doi.org/10.1101/2025.09.01.671701; this version posted September 3, 2025. The copyright holder for this preprint 17 Depletion (Watchmaker Genomics, Cat. 7BK0002-024), rRNA and Goblin RNA depletion, first and second strand cDNA synthesis, sequencing library prep and amplification were performed in one continuous workflow.

treatment_protocol: Medium was removed, cells were washed 3x with 1xPBS, and medium without NGF was added for 18 hours. Cells were then restimulated by replacing medium with NGF medium for 1 hour.

value: Nervous

value: Sympathetic neurons

tag: cell subset

value: Ax

value: Wildtype

value: Restimulation with NGF after 18 hours of starvation


title: Whole dura, Bulk RNA-seq, 4

tag: tissue


title: Restim_Ax_3_input

description:
Library name: S31
Column name in processed data file matches "title" in this file

tag: treatment


title: T26_0277

city: Tübingen


title: Whole dura, Bulk RNA-seq, 3


title: MN11_GEX

description: Patient 11 single-cell RNAseq

value: Bone marrow

value: Acute Myeloid Leukemia (AML) with Abnormalities on Chromosome 7

value: mRNA


title: MN10_GEX

description: Patient 10 single-cell RNAseq


title: Restim_Ax_2_input

description:
Library name: S30
Column name in processed data file matches "title" in this file


title: Whole dura, Bulk RNA-seq, 2


title: T26_0104

value: meningioma


title: MN9_GEX

description: Patient 9 single-cell RNAseq


title: Restim_Ax_1_input

description:
Library name: S29
Column name in processed data file matches "title" in this file


title: T26_0081


title: Whole dura, Bulk RNA-seq, 1


title: MN8_GEX

description: Patient 8 single-cell RNAseq


title: Restim_CB_4_input

description:
Library name: S28
Column name in processed data file matches "title" in this file

value: CB


title: MN7_GEX

description: Patient 7 single-cell RNAseq


title: exs10KOS45 population-Rep3

city: bethesda

first: Xiang

last: Guo

state: MD

address: 50 south drive, blg50

department: NIDDK

institute: NIH

description:
S4 and S5 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.

data_processing:
Sequenced reads were trimmed for adaptor sequence,  then mapped to mouse Gencode m12  whole genome using hisat2 v2.1.0 with default parameters respectively. Multimappnig reads were filtered using samtoools 1.9, uniquely aligned reads were then mapped to gene features using Subread featureCounts v1.6.4
Differential expression between groups of samples was tested using R version 3.5.1 with DESeq2 1.20.0
Assembly: mouse GRCm38
Supplementary files format and content: tab-delimited text files include gene count values for each Sample ...

source_name: fetal livers

growth_protocol: DIS3 and EXOSC10 WT and KO mice were housed in NIDDK mouse core facility, in accordance with guidelines of the Animal Care and Use Committee of the National Institutes of Health under a Division of Intramural Research, NIDDK approved animal study protocols. Fetal livers isolated from E14.5 control and knockout mice.

extract_protocol:
Total RNA was isolated using RNeasy Plus Micro Kit and Arcturus PicoPure RNA Isolation Kit
RNA sequencing libraries were generating from 100ng-1 ug of RNA using Illumina Stranded Total RNA Rrep Ligation with Ribo-Zero Plus following manufacturer’s protocol.

value: fetal livers

tag: strain

value: exs10 KO

tag: age

value: Embryonic day 14.5


title: T26_0047


title: Restim_CB_3_input

description:
Library name: S27
Column name in processed data file matches "title" in this file

tag: cell type

tag: genotype


title: MN6_GEX

description: Patient 6 single-cell RNAseq


title: exs10KOS45 population-Rep2

description:
S4 and S5 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Restim_CB_2_input

description:
Library name: S26
Column name in processed data file matches "title" in this file


title: T26_0241


title: exs10KOS45 population-Rep1

description:
S4 and S5 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: MN5_GEX

description: Patient 5 single-cell RNAseq


title: Restim_CB_1_input

description:
Library name: S25
Column name in processed data file matches "title" in this file


title: exs10KOS3 population-Rep3

description:
S3 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: MN4_GEX

description: Patient 4 single-cell RNAseq


title: T26_0272


title: exs10KOS3 population-Rep2

description:
S3 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: MN3_GEX

description: Patient 3 single-cell RNAseq


title: Control_Ax_3_input

description:
Library name: S23
Column name in processed data file matches "title" in this file

value: Growth under NGF


title: exs10KOS3 population-Rep1

description:
S3 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: MN2_GEX

description: Patient 2 single-cell RNAseq


title: Control_Ax_4_input

description:
Library name: S24
Column name in processed data file matches "title" in this file


title: T26_0186


title: exs10KOS2 population-Rep3

description:
S2 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Control_Ax_1_input

description:
Library name: S21
Column name in processed data file matches "title" in this file


title: MN1_GEX

description: Patient 1 single-cell RNAseq


title: T26_0066


title: Control_CB_4_input

description:
Library name: S20
Column name in processed data file matches "title" in this file


title: Placenta, RNA PE+IUGR4 Rep2

first: Pradeepa

middle: M

last: Madapura

state: UK

address: 4 Newark Street, Whitechapel

institute: Queen Mary University of London

data_processing:
The reads were processed and mapped using STAR aligner. The mapped data obtained as bam files were further used for merging, sorting and indexing. The sorted bam files were converted to bigwigs via deepTools (version 3.5.1) bamCoverage tool with --skipNAs  –normalizeUsing  RPKM --smoothLength 60  --centerReads options.
PolyA RNA-seq
Assembly: GRCh38/hg38
Supplementary files format and content: bigwig containing signal for RNAseq

source_name: Placenta tissue

growth_protocol: Healthy control and preeclampsia placenta biopsies were used for performing CUT&Tag and RNA sequencing

extract_protocol:
RNA was isolated from placental biopsies using TRI reagent solution (ThermoFisher Scientific, AM9738), and genomic DNA was eliminated by treating RNA samples with Turbo RNAse free DNAse1 (ThermoFisher Scientific AM1907).
RNA sequencing library preparation using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (NEB #E7765), followed by libraries, were sequenced as 150 bp paired-end reads using Novaseq 6000.
PolyA RNA-seq

value: Placenta tissue

value: PE+IUGR


title: exs10KOS2 population-Rep2

description:
S2 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: T26_0214


title: exs10KOS2 population-Rep1

description:
S2 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Placenta, RNA PE+IUGR4 Rep1


title: Control_CB_3_input

description:
Library name: S19
Column name in processed data file matches "title" in this file


title: exs10KOS1 population-Rep3

description:
S1 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: T26_0213


title: Placenta, RNA Control6 Rep2

value: Control


title: T26_0257


title: Control_CB_2_input

description:
Library name: S18
Column name in processed data file matches "title" in this file

value: Nervous


title: T26_0052


title: exs10KOS1 population-Rep2

description:
S1 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Placenta, RNA Control6 Rep1


title: Control_CB_1_input

description:
Library name: S17
Column name in processed data file matches "title" in this file

value: Sympathetic neurons


title: T26_0182


title: Placenta, RNA Control5 Rep2


title: exs10KOS1 population-Rep1

description:
S1 population replication 1
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Restim_Ax_4

description:
Library name: S16
Column name in processed data file matches "title" in this file

data_processing:
Sequencing data was processed using nf-core/rnaseq (https://zenodo.org/records/7998767) of the nf-core collection of workflows. Reads were pre-processed including quality filtered and trimmed before being mapped to GRCm38, using a combination of fastqc, samtools, star, salmon, trimgalore (full list of software and processes in table S3) set with default parameters. Mapped reads were deduplicated and quantified to produce gene counts which were used as input for differential gene expression. Differential gene expression was performed with the SARTools pipeline using DESeq2. Differential gene expression analysis was performed using edgeR using TMM normalization. Only genes with more than 15 total counts with at least 10 counts in one of the samples were considered for further processing. Surrogate Variable Analysis was used to remove batch effects. Linear models were fitted through all eight conditions (~ SV1 + SV2 + compartment * seqmethod * treatment). Gene Ontology analysis was performed using Metascape and plots were created with ggplot2 (Wickham, 2009) on R (R Core Team, 2014).
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files with raw and size normalised counts per gene for each sample
Library strategy: MeRIP-Seq

value: Ax


title: T26_0242


title: T26_0034


title: exs10KOS0 population-Rep3

description:
S0 population replication 3
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Placenta, RNA Control5 Rep1


title: T26_0164


title: Restim_Ax_3

description:
Library name: S15
Column name in processed data file matches "title" in this file

value: Wildtype


title: T26_0280


title: Placenta, RNA Control4 Rep2


title: exs10KOS0 population-Rep2

description:
S0 population replication 2
FACs experiments with surface marker CD71/Ter119 divided the fetal liver cells into S0-S5 population from immature to mature erythroid cells.


title: Restim_Ax_2

description:
Library name: S14
Column name in processed data file matches "title" in this file

value: Restimulation with NGF after 18 hours of starvation


title: T26_0176