title: frail 24h D62

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

description:
Library name: Sample 15
Gene expression profiling of gastrocnemius muscle from a frail animal 24h after running challenge.

data_processing:
FASTQ files were aligned to mouse genome build mm10 using STAR (version 2.7.9a).
Ensembl-Gene-level counts for non-mitochondrial genes were generated using featureCounts (Subread package, version 2.0.3) and Ensembl annotation build 100 (uniquely aligned proper pairs, same strand).
FASTQ quality was assessed using FastQC (version 0.11.7), and alignment quality was assessed using RSeQC (version 3.0.0).
Variance-stabilizing transformation (VST) was accomplished using the varianceStabilizingTransformation function in the DESeq2 R package (version 1.32.0).
All analyses were performed using the R environment for statistical computing (version 4.1.2).
Assembly: mm10
Supplementary files format and content: counts.txt: TSV file containing 55450 x 15 matrix of counts produced by Subread featureCounts
Supplementary files format and content: varianceStabilizingTransformation.txt: TSV file containing 55450 x 15 matrix of variance-stabilizing-transformed (VST) expression values

source_name: gastrocnemius muscle

growth_protocol: Mice were housed in a temperature-controlled (25°C) facility on a 12-hour light/dark cycle at the Boston University vivarium, with ad libitum access to standard rodent chow and water.

extract_protocol:
~25 mg portion of powdered gastrocnemius was homogenized in 600 µL of Zymo Tri Reagent. Total RNA was isolated using a Zymo RNA Miniprep kit including an on-column DNase treatment.
Libraries were prepared using the NEBNext UltraExpress RNA Library Prep Kit according to the manufacturer's protocol.

treatment_protocol: Downhill running was performed using a six-lane motorized treadmill set to a 22° decline. The protocol began with a 6 min warm up period starting at 5 m/min with speed gradually increased to 13 m/min. After a 3 min rest, mice completed 10 stages consisting of a 1 min acceleration period followed by a 6 min run at 13 m/min and a subsequent 3 min rest. The mice were manually prodded to encourage running. If the mouse refused to run despite encouragement, they were provided a 3 min rest period before reinitiating the run.

value: gastrocnemius muscle

tag: frailty

value: frail

tag: run

tag: group

value: frail 24h


title: AKM55

status: Public on Mar 18 2026

type: SRA

city: AUBURN

first: Amit

middle: Kumar

last: Mitra

state: AL

address: HARRISON COLLEGE OF PHARMACY

department: DRUG DISCOVERY AND DEVELOPMENT

country: USA

institute: AUBURN UNIVERSITY

description: Library name: MCL36

library_source: transcriptomic

data_processing:
Partek Genomics Suite
Read count extraction were performed from raw data using Partek Flow
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized gene counts in Samples

molecule: total RNA

organism: Homo sapiens

source_name: MCL

extract_protocol:
High quality RNA was isolated using QIAshredder columns and RNAeasy Mini kit (Qiagen)
RNA-seq libraries were constructed using Illumina TruSeq RNA Library Prep Kit v2 (poly A enrichment).

tag: tissue

value: MCL

tag: cell line

tag: cell type

value: Mantle Cell Lymphoma cell line

tag: treatment


title: MC38 cells, wildtype, replicate 8

city: Shanghai

first: Chen

last: Qian

address: No. 227 Chongqing South Road, Huangpu District, Shanghai, China

country: China

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: WT_8
RNA-seq of MC38 cells with non-targeting CRISPR control

data_processing:
Raw sequencing reads were subjected to quality control to remove adaptor sequences and low-quality reads.
Clean reads were aligned to the mouse reference genome using HISAT2.
Gene-level read counts were quantified using featureCounts.
Gene expression levels were normalized and summarized to generate a gene expression matrix.
Assembly: GRCm39
Supplementary files format and content: The processed data file is provided in comma-separated values (CSV) format, with genes in rows and samples in columns. Each cell represents the raw read count mapped to the corresponding gene in each sample.

organism: Mus musculus

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

extract_protocol:
Total RNA was extracted from MC38 cells using TRIzol reagent according to the manufacturer’s instructions. RNA integrity and concentration were assessed using an Agilent Bioanalyzer.
RNA sequencing libraries were constructed using a poly(A) selection method to enrich mRNA. Libraries were prepared following the standard protocol recommended by BGI and sequenced on the DNBSEQ-T7 platform to generate paired-end reads.

treatment_protocol: MC38 cells were transduced with CRISPR-Cas9 constructs targeting RAD51D, LIMCH1, or BRD9 using gene-specific sgRNAs. A non-targeting sgRNA was used as the negative control. Stable knockout cells were selected and validated before RNA extraction.

value: colorectal cancer cell

tag: genotype

value: WT

value: CRISPR-Cas9 control

tag: batch


title: frail 24h D53

description:
Library name: Sample 14
Gene expression profiling of gastrocnemius muscle from a frail animal 24h after running challenge.

molecule: polyA RNA


title: MC38 cells, wildtype, replicate 7

description:
Library name: WT_7
RNA-seq of MC38 cells with non-targeting CRISPR control


title: frail 24h D52

description:
Library name: Sample 13
Gene expression profiling of gastrocnemius muscle from a frail animal 24h after running challenge.


title: AKM53

description: Library name: MCL34

value: CLF


title: CUT&Tag, Free_TGFb_H3K36me3_2

city: wuhan

first: Jie

last: Yao

state: 湖北

address: wuhan hubei province

institute: wuhan university

description: Library name: Sample2

library_source: genomic

data_processing:
We performed quality control using FastQC on all samples. The raw reads were trimmed using Trim-galore to remove adapters. The clean reads were mapped to mouse reference genome (mm39) using Bowtie2 with the “--end-to-end --very-sensitive -I 10 -X 700 --no-mixed" option.  Low-quality mapped reads and those mapped to mitochondrial reads were filtered using Samtools. The duplicated reads were removed using Sambamba. The Counts Per Million mapped reads (CPM) normalization method was used to transform alignment bam files into read coverage files in bigWig format on deepTools. Peak calling was performed using MACS2. Differentially accessible peaks were identified using the DiffBind. Motif enrichment analysis was performed using the HOMER.
Assembly: mm39
Supplementary files format and content: bigWig for each Sample
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: MLF

growth_protocol: Primary mouse lung fibroblasts (MLFs) were maintained in DMEM/F-12 medium supplemented with 10% FBS (LONSERA) and 1% penicillin-streptomycin (Gibco) at 37°C under 5% O₂ and 5% CO₂.

extract_protocol:
CUT&Tag assay was performed using CUT&Tag High‐Sensitivity Kit (Novoprotein, N259-YH01) according to the manufacturer’s recommendation.
CUT&Tag assay was performed using CUT&Tag High‐Sensitivity Kit (Novoprotein, N259-YH01) according to the manufacturer’s recommendation.

treatment_protocol: We transfected two KDM4A siRNAs into MLF cells. After 24 h of transfection, the cells were treated with 20 ng/mL TGF-β1 for 48 h, followed by CUT&Tag assay for H3K36me3.

value: MLF

value: Primary mouse lung fibroblasts


title: MC38 cells, wildtype, replicate 6

description:
Library name: WT_6
RNA-seq of MC38 cells with non-targeting CRISPR control


title: AKM54

description: Library name: MCL35


title: Mtb infected INPP5D Knockout macrophages 4 days post infection treated with 3AC_3

city: Ithaca

first: Nelson

middle: Victor

last: Simwela

state: NY

address: 930 Campus Rd

department: Microbiology and Immunology

institute: Cornell University

description: Library name: INPP5D_KO_host_3AC_3

data_processing:
STAR-2.7.10b
Reads were mapped to GRCm39 using STAR. Raw read counts were obtained from mapped reads using HTSeq count
Raw and normalised reads were analyzed using DESeq2
Assembly: mm10
Supplementary files format and content: txt files for both raw and normalised counts

source_name: Bone marrow macrophages

extract_protocol:
RNA was extracted using TRIZOL, total RNA from the aqueous phase was purified using the Zymo RNA clean and concentrator kit
Barcoded RNAseq libraries were generated using the Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit

value: Bone marrow macrophages

value: Macrophages

value: INPP5D knockout treated with 3AC

value: Mtb infected - 4 days


title: AKM52

description: Library name: MCL32

value: MINO-P


title: frail control D67

description:
Library name: Sample 11
Gene expression profiling of gastrocnemius muscle from a frail sedentary animal.

value: control

value: frail control


title: MC38 cells, wildtype, replicate 5

description:
Library name: WT_5
RNA-seq of MC38 cells with non-targeting CRISPR control


title: Mtb infected INPP5D Knockout macrophages 4 days post infection treated with 3AC_2

description: Library name: INPP5D_KO_host_3AC_2


title: CUT&Tag, Free_TGFb_H3K36me3_1

description: Library name: Sample1


title: frail 24h D49

description:
Library name: Sample 12
Gene expression profiling of gastrocnemius muscle from a frail animal 24h after running challenge.

value: gastrocnemius muscle

value: frail


title: MC38 cells, wildtype, replicate 4

description:
Library name: WT_4
RNA-seq of MC38 cells with non-targeting CRISPR control


title: AKM51

description: Library name: MCL31

value: MCL

value: IBR


title: frail control D25

description:
Library name: Sample 10
Gene expression profiling of gastrocnemius muscle from a frail sedentary animal.


title: MC38 cells, wildtype, replicate 3

description:
Library name: WT_3
RNA-seq of MC38 cells with non-targeting CRISPR control

value: colorectal cancer cell


title: Mtb infected INPP5D Knockout macrophages 4 days post infection treated with 3AC_1

description: Library name: INPP5D_KO_host_3AC_1


title: frail control D23

description:
Library name: Sample 9
Gene expression profiling of gastrocnemius muscle from a frail sedentary animal.


title: AKM49

description: Library name: MCL29

value: MINO-VR

value: Mantle Cell Lymphoma cell line


title: Mtb infected Scramble sgRNA macrophages 4 days post infection treated with 3AC_2

description: Library name: SC_3AC_2

value: Scramble (WT) treated with 3AC


title: MC38 cells, wildtype, replicate 2

description:
Library name: WT_2
RNA-seq of MC38 cells with non-targeting CRISPR control

value: WT

value: CRISPR-Cas9 control


title: MC38 cells, wildtype, replicate 1

description:
Library name: WT_1
RNA-seq of MC38 cells with non-targeting CRISPR control


title: AKM48

description: Library name: MCL28


title: robust 24h D66

description:
Library name: Sample 7
Gene expression profiling of gastrocnemius muscle from a robust animal 24h after running challenge.

value: robust

value: robust 24h


title: Mtb infected Scramble sgRNA macrophages 4 days post infection treated with 3AC_3

description: Library name: SC_3AC_3

value: Bone marrow macrophages

value: Macrophages


title: AKM47

description: Library name: MCL27


title: Heart, Normal, rep1

type: RNA

city: Paris

first: Jean-Sébastien

last: Hulot

address: Rue Leblanc

country: France

institute: Paris Centre de Recherche Cardiovasculaire

hyb_protocol: A total of 100 ng of RNA were incubated with the Capture and Reporter ProbeSets for 18 hours at 65 °C.

scan_protocol: Post-hybridization processing and data collection were performed using the nCounter Prep Station and Digital Analyzer (nCounter Max System) as indicated by the manufacturer.

data_processing: Raw counts of gene expression data were analyzed with the nSolver Analysis Software (version 4.0.70). Background correction was applied based on the negative controls, and the geometric means of the supplied positive controls and housekeeping genes were used to normalize the measured expression values. All the samples passed the QC metrics which were defined as binding density > 0.05 and < 2.25 probes/μm2, % fields of view > 0.75, positive control linearity > 0.95, and sufficient assay efficiency. Per-sample Level of Detection (LOD)  was defined as the mean of the counts of negative control probes for each sample and was ensured by using internal quality control reference probes. Raw gene expression data were normalized using the Remove Unwanted Variation (RUV) approach following quality control and housekeeping assessment.

label: Fluorescently barcoded nucleic acid probes

source_name: Heart

label_protocol: The customized nCounter Human Banff Organ Transplant gene panel probes were prepared by the manufacturer.

extract_protocol: RNA was extracted froms three 20 𝜇m FFPE sections using the tissue RNEasy FFPE kit #73504 (Qiagen, Hilden, Germany). The concentration and quality of isolated RNA were assessed using NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific Inc., Waltham, MA, USA).

tag: myocardial infarctus or normal

value: Normal


title: AKM46

description: Library name: MCL26


title: AKM50

description: Library name: MCL30


title: MC38 cells, RAD51D knockout, replicate 2

description:
Library name: RKO_2
RNA-seq of MC38 cells with RAD51D knockout

value: RAD51D knockout

value: CRISPR-Cas9 knockout


title: Mtb infected INPP5D knockout macrophages 4 days post infection_3

description: Library name: INPP5D_KO_host_3

value: INPP5D knockout

value: Mtb infected - 4 days


title: Mtb infected Scramble sgRNA macrophages 4 days post infection treated with 3AC_1

description: Library name: SC_3AC_1


title: robust 24h D61

description:
Library name: Sample 6
Gene expression profiling of gastrocnemius muscle from a robust animal 24h after running challenge.

value: gastrocnemius muscle


title: robust 24h D68

description:
Library name: Sample 8
Gene expression profiling of gastrocnemius muscle from a robust animal 24h after running challenge.


title: robust 24h D57

description:
Library name: Sample 5
Gene expression profiling of gastrocnemius muscle from a robust animal 24h after running challenge.


title: MC38 cells, RAD51D knockout, replicate 3

description:
Library name: RKO_3
RNA-seq of MC38 cells with RAD51D knockout


title: AKM45

description: Library name: MCL25

value: MCL

value: MINO-P


title: Mtb infected INPP5D knockout macrophages 4 days post infection_1

description: Library name: INPP5D_KO_host_1


title: Heart, Late MI, rep3

value: Late MI


title: AKM44

description: Library name: MCL24

value: Mantle Cell Lymphoma cell line


title: Mtb infected INPP5D knockout macrophages 4 days post infection_2

description: Library name: INPP5D_KO_host_2


title: MC38 cells, RAD51D knockout, replicate 1

description:
Library name: RKO_1
RNA-seq of MC38 cells with RAD51D knockout

value: colorectal cancer cell


title: robust control D11

description:
Library name: Sample 3
Gene expression profiling of gastrocnemius muscle from a robust sedentary animal.

value: control

value: robust control


title: MC38 cells, LIMCH1 knockout, replicate 4

description:
Library name: LKO_4
RNA-seq of MC38 cells with LIMCH1 knockout

value: LIMCH1 knockout


title: Heart, Early MI, rep5

value: Early MI


title: AKM43

description: Library name: MCL23


title: MC38 cells, LIMCH1 knockout, replicate 3

description:
Library name: LKO_3
RNA-seq of MC38 cells with LIMCH1 knockout


title: Mtb infected Scramble sgRNA macrophages 4 days post infection_3

description: Library name: SC_3

value: Bone marrow macrophages

value: Scramble (WT)


title: robust control D9

description:
Library name: Sample 2
Gene expression profiling of gastrocnemius muscle from a robust sedentary animal.

value: robust


title: robust control D98

description:
Library name: Sample 4
Gene expression profiling of gastrocnemius muscle from a robust sedentary animal.


title: Mtb infected Scramble sgRNA macrophages 4 days post infection_1

description: Library name: SC_1

value: Macrophages


title: Heart, Late MI, rep7


title: N-B-D11

city: Portland

first: Priya

last: Chaudhary

state: OR

address: 1225 NE 2nd Avenue

department: Devers Eye Institute

institute: Legacy Research Institute

description:
Library name: DSP-1001660033923-B-D11
spatial WTA sequencing

data_processing:
Raw sequencing data were processed using the Nanostring's pipeline to generate DCC files.
Hs_R_NGS_WTA_v1.0.pkc = 46ed2c63a88f12c64e9ba6f7841b0d27
Assembly: Human NGS Whole Transcriptome Atlas RNA version 1.0
Supplementary files format and content: .dcc and .pkc
Library strategy: Spatial transcriptomics

growth_protocol: Control and Experimental glaucoma ONH samples were used.

extract_protocol:
Paraformaldehyde fixed tissue was paraffin embedded and 5 micron sections were cut.
Spatial transcriptomics sequencing libraries were prepared using Nanostring GeoMx NGS pipeline according to manufacturer's instructions.

treatment_protocol: Laser treatment was used to induce experimental glaucoma.

tag: animal#

tag: glaucoma

value: YES


title: robust control D8

description:
Library name: Sample 1
Gene expression profiling of gastrocnemius muscle from a robust sedentary animal.


title: MC38 cells, LIMCH1 knockout, replicate 1

description:
Library name: LKO_1
RNA-seq of MC38 cells with LIMCH1 knockout

value: CRISPR-Cas9 knockout


title: MC38 cells, BRD9 knockout, replicate 4

description:
Library name: BKO_4
RNA-seq of MC38 cells with BRD9 knockout

value: BRD9 knockout


title: N-B-D10

description:
Library name: DSP-1001660033923-B-D10
spatial WTA sequencing


title: MC38 cells, BRD9 knockout, replicate 3

description:
Library name: BKO_3
RNA-seq of MC38 cells with BRD9 knockout


title: Mtb infected Scramble sgRNA macrophages 4 days post infection_2

description: Library name: SC_2

value: Mtb infected - 4 days


title: MC38 cells, LIMCH1 knockout, replicate 2

description:
Library name: LKO_2
RNA-seq of MC38 cells with LIMCH1 knockout


title: AKM42

description: Library name: MCL22

value: MCL


title: KPC4 cells treated with Gem-PSC-SU, biological replicate 3

city: Marburg

first: Mark

last: Schmitt

address: Karl-von-Frisch-Str. 2

country: Germany

institute: Institute of Pharmacology, University of Marburg

description:
Library name: Kpc_Gem_SU3
Murine KPC4 pancreatic cancer cells exposed to supernatant from PSC4 cells previously educated with gemcitabine-treated KPC4 supernatant.

data_processing:
Raw sequencing reads were assessed for quality using FastQC.
Adapter sequences and low-quality bases were trimmed using Trim Galore (v0.6.10), which internally uses Cutadapt (v5.2), with a Phred quality score cutoff of 20. Paired-end reads shorter than 20 bp after trimming were discarded.
Transcript abundance was quantified using Salmon.
Transcript-level abundance estimates were imported into R (v4.5.1) and summarized to gene-level counts using tximport. Differential gene expression analysis was performed using DESeq2 with experimental condition as the main factor. Genes with low expression were filtered prior to analysis, and p-values were adjusted using the Benjamini–Hochberg method.
Assembly: Mus musculus GRCm39
Supplementary files format and content: tab-delimited text
Supplementary files format and content: Processed data files include gene-level raw count matrices, DESeq2 differential expression result tables sorted by adjusted p value, and README files describing sample processing and analysis.

growth_protocol: Mouse pancreatic adenocarcinoma cell line KPC4 and murine pancreatic stellate cell line PSC4 were maintained in DMEM supplemented with 10% fetal bovine serum, 1% HEPES and 1% penicillin/streptomycin at 37°C with 5% CO2.

extract_protocol:
Total RNA was isolated using the QIAwave RNA Mini Kit (Qiagen, 74536) with on-column DNase I digestion (Qiagen, 79254). RNA quality and quantity were assessed using an Agilent 2100 Bioanalyzer with the RNA 6000 Pico Kit (Agilent Technologies).
RNA sequencing libraries were prepared and sequenced by Novogene using the Illumina NovaSeq X Plus platform.

treatment_protocol: For PSC4 RNA-seq, KPC4 cells were treated with 10 µM gemcitabine or vehicle for 6 h, washed, and cultured for 14 h in starvation medium to generate Gem-SU and Control-SU. PSC4 cells were then exposed to Control-SU or Gem-SU for 24 h before RNA isolation. For KPC4 RNA-seq, PSC4 cells were first exposed to Control-SU or Gem-SU for 6 h, washed, and cultured for 18 h in fresh starvation medium to generate Control-PSC-SU and Gem-PSC-SU. KPC4 cells were then exposed to PSC-derived supernatants for 24 h before RNA isolation.

value: murine pancreatic cancer cells

value: KPC4 recipient cells exposed to PSC4-derived Gem-PSC-SU


title: AKM41

description: Library name: MCL21

value: MINO-P

value: Mantle Cell Lymphoma cell line


title: AKM39

description: Library name: MCL18


title: KPC4 cells treated with Gem-PSC-SU, biological replicate 1

description:
Library name: Kpc_Gem_SU1
Murine KPC4 pancreatic cancer cells exposed to supernatant from PSC4 cells previously educated with gemcitabine-treated KPC4 supernatant.


title: KPC4 cells treated with Gem-PSC-SU, biological replicate 2

description:
Library name: Kpc_Gem_SU2
Murine KPC4 pancreatic cancer cells exposed to supernatant from PSC4 cells previously educated with gemcitabine-treated KPC4 supernatant.


title: AKM38

description: Library name: MCL17

value: BTZ


title: MC38 cells, BRD9 knockout, replicate 2

description:
Library name: BKO_2
RNA-seq of MC38 cells with BRD9 knockout

value: colorectal cancer cell


title: N-B-D09

description:
Library name: DSP-1001660033923-B-D09
spatial WTA sequencing


title: N-B-D08

description:
Library name: DSP-1001660033923-B-D08
spatial WTA sequencing


title: KPC4 cells treated with Control-PSC-SU, biological replicate 3

description:
Library name: Kpc_Control_SU3
Murine KPC4 pancreatic cancer cells exposed to supernatant from PSC4 cells previously educated with vehicle-treated KPC4 supernatant.

value: KPC4 recipient cells exposed to PSC4-derived Control-PSC-SU


title: AKM40

description: Library name: MCL20


title: AKM37

description: Library name: MCL16A


title: MC38 cells, BRD9 knockout, replicate 1

description:
Library name: BKO_1
RNA-seq of MC38 cells with BRD9 knockout


title: KPC4 cells treated with Control-PSC-SU, biological replicate 2

description:
Library name: Kpc_Control_SU2
Murine KPC4 pancreatic cancer cells exposed to supernatant from PSC4 cells previously educated with vehicle-treated KPC4 supernatant.


title: Ctrl-RNA-3

city: Tianjin

first: Bingqian

last: Chu

address: Cell and Organism Ecological Laboratory, Yuexin Dao, Haihe River

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

description: Library name: Ctrl-RNA-3

data_processing:
Raw sequencing data were quality-controlled using FastQC (v0.11.9), and adapter sequences were trimmed with Cutadapt.
High-quality reads were aligned to the mouse reference genome (GRCm39, Ensembl release) using STAR (v2.7.9a).
Transcript quantification was performed with featureCounts, and differential expression analysis was conducted using the limma package (v3.60.6) with thresholds set at |log₂FC| > 1 and FDR < 0.05.
Data consistency was assessed via Pearson correlation coefficients and coefficient of variation (CV).
Assembly: GRCm39
Supplementary files format and content: RNA_matrix.txt

source_name: Brain

extract_protocol:
Total RNA of control group was extracted using TRIzol Reagent (Invitrogen) following the manufacturer’s protocol. RNA was precipitated with isopropanol, washed with 75% ethanol, and resuspended in RNase-free water. RNA of Co-extraction group was isolated using the AllPrep DNA/RNA/Protein Mini Kit (QIAGEN) according to the manufacturer’s instructions, ensuring compatibility with subsequent proteomic and phosphoproteomic workflows.
RNA libraries were constructed using T7-based in vitro transcription amplification following the manufacturer’s protocol. Sequencing was performed on an Illumina NovaSeq 6000 platform with 150-bp paired-end reads (PE150).

value: Brain

tag: method

value: Ctrl

value: WT


title: N-B-D07

description:
Library name: DSP-1001660033923-B-D07
spatial WTA sequencing


title: N-B-D06

description:
Library name: DSP-1001660033923-B-D06
spatial WTA sequencing


title: N-B-D05

description:
Library name: DSP-1001660033923-B-D05
spatial WTA sequencing


title: Ctrl-RNA-1

description: Library name: Ctrl-RNA-1


title: Ctrl-RNA-2

description: Library name: Ctrl-RNA-2


title: AKM35

description: Library name: MCL15A


title: PSC4 cells treated with Gem-SU, biological replicate 1

description:
Library name: Psc_Gem_SU1
Murine PSC4 pancreatic stellate cells exposed to supernatant from gemcitabine-treated KPC4 cells.

value: murine pancreatic stellate cells

value: PSC4 recipient cells exposed to KPC4-derived Gem-SU


title: KPC4 cells treated with Control-PSC-SU, biological replicate 1

description:
Library name: Kpc_Control_SU1
Murine KPC4 pancreatic cancer cells exposed to supernatant from PSC4 cells previously educated with vehicle-treated KPC4 supernatant.


title: N-B-D04

description:
Library name: DSP-1001660033923-B-D04
spatial WTA sequencing

value: YES


title: All-RNA-2

description: Library name: All-RNA-2

value: AllPrep


title: AKM34

description: Library name: MCL15


title: AKM33

description: Library name: MCL14A


title: AKM36

description: Library name: MCL16


title: PSC4 cells treated with Gem-SU, biological replicate 3

description:
Library name: Psc_Gem_SU3
Murine PSC4 pancreatic stellate cells exposed to supernatant from gemcitabine-treated KPC4 cells.


title: All-RNA-3

description: Library name: All-RNA-3


title: N-B-D03

description:
Library name: DSP-1001660033923-B-D03
spatial WTA sequencing


title: N-B-D02

description:
Library name: DSP-1001660033923-B-D02
spatial WTA sequencing


title: PSC4 cells treated with Gem-SU, biological replicate 2

description:
Library name: Psc_Gem_SU2
Murine PSC4 pancreatic stellate cells exposed to supernatant from gemcitabine-treated KPC4 cells.


title: N-B-D01

description:
Library name: DSP-1001660033923-B-D01
spatial WTA sequencing


title: AKM32

description: Library name: MCL13A

value: CLF


title: PSC4 cells treated with Control-SU, biological replicate 3

description:
Library name: Psc_Control_SU3
Murine PSC4 pancreatic stellate cells exposed to supernatant from vehicle-treated KPC4 cells.

value: PSC4 recipient cells exposed to KPC4-derived Control-SU


title: KG1A-R3

type: genomic

city: Little Rock

first: Samrat

last: Roy Choudhury

state: AR

address: 13 Children's Way, Arkansas Children's Research Institute

institute: University of Arkansas for Medical Sciences

description:
207041120010_R05C01
Illumina Infinium MethylationEPIC v2.0 BeadChip (GPL33022)

hyb_protocol: Bisulfite-converted DNA was hybridized to the Illumina Infinium MethylationEPIC v2.0 BeadChip following the manufacturer's protocol (Illumina, Part # 15019519 v01). Samples were denatured and loaded onto the array using the automated Tecan system or Illumina manual procedures.

scan_protocol: Arrays were scanned using the Illumina iScan System according to the manufacturer's recommended settings. IDAT files were generated for each sample and used for downstream analysis.

data_processing:
Raw IDAT files were imported and processed using the R package minfi. Quality control and background correction were applied using standard minfi workflows. Probes failing detection p-value threshold (p > 0.01) were excluded. Probes on sex chromosomes and known cross-reactive sites were filtered out. Beta values (β-values), representing the ratio of methylated signal over the sum of methylated and unmethylated signals, were calculated for each CpG.
Processed values represent β-values, calculated as: β=MM+U+100\beta = \frac{M}{M + U + 100}β=M+U+100M, where M is the methylated signal intensity, U is the unmethylated signal intensity, and 100 is a regularization constant. Values range from 0 (completely unmethylated) to 1 (fully methylated).

label: Cy3 and Cy5

label_protocol: Genomic DNA (500 ng per sample) was bisulfite-converted using the EZ DNA Methylation Kit (Zymo Research) following the manufacturer’s standard protocol. No additional labeling step was used, as hybridization and signal detection are built into the Illumina array platform.

growth_protocol: KG1A cells were cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂. Cells were maintained in logarithmic growth phase and passaged every 2–3 days.

extract_protocol: Genomic DNA was extracted using the AllPrep DNA/RNA kit (Qiagen) according to the manufacturer’s instructions. DNA concentration and purity were assessed using a NanoDrop spectrophotometer, and DNA integrity was confirmed by agarose gel electrophoresis.

treatment_protocol: Cells were seeded at 1×10⁶ cells per well and treated with 50 nM Nanaomycin A (NanA; MedChemExpress, HY-103397) or an equivalent volume of DMSO (vehicle control) for 48 hours. Following treatment, cells were collected for DNA extraction.

value: Acute Myeloid Leukemia

value: Control (DMSO)


title: ZE6

city: Hangzhou

first: Nafei

last: Huang

address: The Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China

description: Library name: MODEL4

data_processing:
Base calling was performed using Illumina CASAVA software (v1.8.2) with default parameters. Raw FASTQ files were processed with in-house Perl scripts to remove reads containing adapter sequences, reads with >10% poly-N, and low-quality reads (Q-score < 20 in more than 50% of bases). Quality metrics (Q20, Q30, GC content, and sequence duplication levels) were calculated using FASTQC (v0.11.9).
Clean reads were aligned to the Mus musculus sapiens reference genome (GRCm39) using HISAT2 (v2.0.5) with default parameters (--rna-strandness RF). Only reads with perfect matches or up to one mismatch were retained.
Transcripts were assembled and quantified using StringTie (v1.3.3) with default settings. Gene expression levels were calculated as fragments per kilobase of transcript per million mapped reads (FPKM).
Alignment files were sorted and duplicates removed using Picard tools (v1.41) and SAMtools (v0.1.18).
Assembly: GRCm39.109
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: liver

growth_protocol: Specific-pathogen-free (SPF) C57BL/6 male mice (18-22 g, 6-8 weeks old) were purchased from Shanghai SLAC Laboratory Animal Co. Ltd.

extract_protocol:
Total RNA was extracted using Trizol and subjected to RNA sequencing.
RNA libraries for RNA-seg were prepared using Hieff NGS Ultima Dual-mode mRNA Library Prep Kit following manufacturer's protocols.

treatment_protocol: All the groups were given an improved Lieber DeCarli liquid diet without alcohol, and the mice adapted to the liquid diet for 5 days. After 5 days, the Ethanol-fed groups were given the Lieber DeCarli liquid diet for 15 days, where the alcohol concentration gradually increased from 1% to 5%.The XPQG group (15.2g/kg) was administered by gavage at the same time as modeling. All animals were dosed simultaneously during the modeling. At 8:00 a.m. on the 16th day, the Ethanol-fed groups were gavaged with 31.5% (V/V) alcohol solution.All animal specimens were collected 9 hours later.

value: liver

tag: strain

tag: sample group

value: NIAAA model


title: AKM28

description: Library name: MCL11A

value: MCL

value: Mantle Cell Lymphoma cell line

value: CON


title: N-B-C07

description:
Library name: DSP-1001660033923-B-C07
spatial WTA sequencing

value: NO


title: PSC4 cells treated with Control-SU, biological replicate 2

description:
Library name: Psc_Control_SU2
Murine PSC4 pancreatic stellate cells exposed to supernatant from vehicle-treated KPC4 cells.


title: pTh17_cKO-3

city: Wuhan

last: Sun

state: Hubei

address: Donghu Road, No. 115

department: MRI

institute: Wuhan university

description: Library name: samples8

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 adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: GCRm39
Supplementary files format and content: tab-delimited text files include raw read count

source_name: spleen and lymph nodes

extract_protocol:
Total RNA was extracted from pTh17 cells  of indicated coditions cultured for2 days using the Direct-zol RNA Microprep Kit (ZYMO Research,R2061).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-Toligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: spleen and lymph nodes

value: HMGCS1 cKO


title: pTh17_cKO-5

description: Library name: samples10


title: AKM30

description: Library name: MCL12A

value: IBR


title: All-RNA-1

description: Library name: All-RNA-1

value: Brain

value: WT


title: pTh17_cKO-4

description: Library name: samples9


title: N-B-C12

description:
Library name: DSP-1001660033923-B-C12
spatial WTA sequencing

value: YES


title: AKM29

description: Library name: MCL12


title: PSC4 cells treated with Control-SU, biological replicate 1

description:
Library name: Psc_Control_SU1
Murine PSC4 pancreatic stellate cells exposed to supernatant from vehicle-treated KPC4 cells.

value: murine pancreatic stellate cells


title: N-B-C06

description:
Library name: DSP-1001660033923-B-C06
spatial WTA sequencing


title: Heart, Normal, rep2

value: Normal


title: AKM27

description: Library name: MCL11


title: N-B-C04

description:
Library name: DSP-1001660033923-B-C04
spatial WTA sequencing


title: AKM31

description: Library name: MCL13

value: CLF


title: pTh17_WT-3

description: Library name: samples3

value: wild type


title: JD5

institute: The Second Clinical Medical College, Zhejiang Chinese Medical University

description: Library name: XPQG4

value: Xing-Pi-Qing-Gan decoction


title: pTh17_cKO-2

description: Library name: samples7


title: AKM25

description: Library name: MCL10


title: ZD17

description: Library name: MODEL2

value: liver


title: JC18

description: Library name: XPQG2


title: AKM26

description: Library name: MCL10a


title: pTh17_cKO-1

description: Library name: samples6


title: Aealbo control replicate 01

city: Hamilton

first: Lucas

last: Tirloni

state: MT

address: 903 S 4th Street

department: LB

institute: NIAID

description: Library name: Aealbo control replicate 01

data_processing:
RNA-Seq reads underwent quality control, adapter trimming, mapping, counting and differential expression analysis via the mRNAseq pipeline from the snakePipes package (v2.7.3). Mapping was performed using the software STAR (v2.7.10b) and the AalbF5 (GCF_035046485) version of the A. albopictus genome as reference. Read count for each gene was done using featureCounts (v2.0.1).
Assembly: GCF_035046485
Supplementary files format and content: aa_dmso_stm_counts.tsv

organism: Aedes albopictus

extract_protocol:
Total RNA was isolated from cells using TRIzol reagent according to the manufacturer’s instructions and analyzed with an Agilent High Sensitivity RNA ScreenTape System in an TapeStation 4150 (Agilent).
The library was constructed using the NEBNextUltraTM II (Directional) RNA with polyA selection library prep kit and sequencing was performed in an Illumina Novaseq 6000 DNA sequencer.


title: pTh17_WT-2

description: Library name: samples2


title: N-B-C02

description:
Library name: DSP-1001660033923-B-C02
spatial WTA sequencing


title: pTh17_WT-5

description: Library name: samples5


title: KG1A-50 nM-R3

description:
207041120010_R07C01
Illumina Infinium MethylationEPIC v2.0 BeadChip (GPL33022)

value: Acute Myeloid Leukemia

value: Treatment (NanA_50 nM)


title: pTh17_WT-1

description: Library name: samples1


title: Klebsiella pneumoniae control (WT), biological replicate 3

city: Please Select

first: 佳

last: 万

state: Please Select

address: 广东省广州市越秀区中山二路中山医学院科技楼301

institute: 中山医学院

description: Library name: WT-3

data_processing:
Data were employed to assemble the transcriptome using Trinity RNA-Seq software, and RNA-Seq reads were aligned according to the genome sequences of Klebsiella pneumoniae subsp. pneumoniae ATCC43816 KPPR1 (CP009208. 1) using the Subread aligner. A volcano map was constructed with R studio (version 3.6.1) to show the comprehensive differences between WT group and ΔdksA group. The differential transcription genes were mapped to KEGG database (http://geneontology.org/) and gene ontology (GO) terms (with Blast2GO software) for enrichment analysis, and the results were plotted by R studio (version 3.6.1).
DksA_RNAseq_expression_matrix.txt
WT_vs_ΔdksA_DEGs.csv
Assembly: Klebsiella pneumoniae ATCC 43816 KPPR1 (NCBI: CP009208.1)
Supplementary files format and content: WT_vs_ΔdksA_DEGs.csv : Differentially expressed gene list with columns for gene ID, log2 fold change, p-value, adjusted p-value, and gene annotation; DksA_RNAseq_expression_matrix.txt: Tab-delimited text file containing raw gene counts for all 6 samples. Rows represent genes, columns represent samples.

organism: Klebsiella pneumoniae

source_name: Bacteria

extract_protocol:
Total RNA was extracted from Klebsiella pneumoniae using TRIzol reagent (Invitrogen, USA) following the manufacturer's protocol. Genomic DNA was removed by DNase I treatment.
Sequencing libraries were constructed using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Cat# E7530L) following manufacturer's recommendations. Index codes were added to multiplex samples.

value: Bacteria

value: Klebsiella pneumoniae


title: AKM20

description: Library name: MCL7a

value: MCL

value: MINO-VR

value: Mantle Cell Lymphoma cell line


title: N-B-B12

description:
Library name: DSP-1001660033923-B-B12
spatial WTA sequencing

value: NO


title: N-B-B09

description:
Library name: DSP-1001660033923-B-B09
spatial WTA sequencing


title: d2_pTh17-1

description: Library name: samples4

extract_protocol:
Total RNA was extracted fromn pTh17 and  pTh17 cells  of indicated coditions cultured for2 days using the Direct-zol RNA Microprep Kit (ZYMO Research,R2061).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-Toligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370~420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: spleen and lymph nodes


title: BL_1

city: guiyang

first: yudan

last: zhou

address: West Campus of Guizhou University, Huaxi District

institute: Guizhou University

description:
Library name: sample 1
BL group, replicate biosample 1

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to DM 1-3 516 R44 (v6.1)  using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: DM 1-3 516 R44 (v6.1)
Supplementary files format and content: tab-delimited text file includes gene counts and fpkm for each sample

organism: Solanum tuberosum

source_name: leaf

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: leaf

value: NtGSTU10 overexpression mutant


title: AKM19

description: Library name: MCL7

value: IBR


title: N-B-B07

description:
Library name: DSP-1001660033923-B-B07
spatial WTA sequencing


title: N-A-D01

description:
Library name: DSP-1001660022236-A-D01
spatial WTA sequencing


title: Gh time(dpi):4 rep:D

city: Harpenden

first: Erika

last: Kroll

address: West Common

country: United Kingdom

institute: Rothamsted Research

description:
Library name: Gh_PDB_D
150bp paired reads

data_processing:
Read mapping with HISATv2.1.0; transcript abundance quantified with StringTie v2.1.1; gene count matrix generated with prepDE.py
Assembly: GCA_051938715.1 (Gt-19d1) and GCA_051938805.1 (Gh-2C17)
Supplementary files format and content: Raw gene count matrix csv files

organism: Gaeumannomyces hyphopodioides

source_name: Mycelium

growth_protocol: Fungal mycelium was grown up in 200 ml conical flasks containing 50 ml Potato Dextrose Broth (PDB; Formedium, UK) supplemented with 50 μg/ml kanamycin. Flasks were inoculated with 3 x mycelial plugs taken from the leading edge of a two-week old fungal colony growing on Potato Dextrose Agar (PDA; Formedium, UK) using a no.2 cork borer (5 mm). Plugs were cut up into small pieces to ensure even mycelial growth. Five flasks were set up for each fungus to provide five treatment replicates. Inoculated flasks were placed in a New Brunswick™ Innova® 44 orbital shaker (New Brunswick Scientific, UK) at 20 °C, 160 RPM for four days. Cultures were filtered through sterile Miracloth (Merck, USA) by vacuum filtration, followed by three washes with sterile water.

extract_protocol:
Samples were ground to a fine powder using a pre-cooled sterile mortar and pestle under liquid nitrogen. Samples were not allowed to thaw prior to RNA extraction. When the amount of tissue was limited (as in chapter 5), samples were ground in an RNAse-free 1.5 ml Eppendorf tube containing liquid nitrogen, using a pre-cooled RNAse-free disposable pestle (Thermo Scientific™, USA). RNA extractions were carried out using the E.Z.N.A.® Plant RNA Kit with the associated RNase-free DNase I Set (Omega-Biotek, USA) following the standard protocol provided. RNA was eluted in 30 μl RNAse free water and stored at -80 °C.
mRNA library preparation was carried out by Novogene (China) using the Novogene RNA Library Prep Set (PT042) for polyA enrichment.

value: Mycelium

value: Treatment=Gh. Time=4d. Replicate:D


title: N-B-B02

description:
Library name: DSP-1001660033923-B-B02
spatial WTA sequencing


title: Heart, Late MI, rep2

value: Late MI


title: d2_npTh17-1

description: Library name: samples1

value: wild type


title: Gh time(dpi):4 rep:C

description:
Library name: Gh_PDB_C
150bp paired reads

value: Treatment=Gh. Time=4d. Replicate:C


title: AKM15

description: Library name: MCL5

value: MINO-P


title: Heart, Late MI, rep4


title: N-B-C05

description:
Library name: DSP-1001660033923-B-C05
spatial WTA sequencing


title: JD3

description: Library name: XPQG3

value: liver

value: Xing-Pi-Qing-Gan decoction


title: N-B-A12

description:
Library name: DSP-1001660033923-B-A12
spatial WTA sequencing


title: ZE18

description: Library name: MODEL3

value: NIAAA model


title: pTh17_Hi-2

description: Library name: samples15

value: 1mM Hymeglusin


title: Gh time(dpi):4 rep:A

description:
Library name: Gh_PDB_A
150bp paired reads

value: Treatment=Gh. Time=4d. Replicate:A


title: AKM24

description: Library name: MCL9a

value: MCL

value: Mantle Cell Lymphoma cell line


title: N-B-C01

description:
Library name: DSP-1001660033923-B-C01
spatial WTA sequencing

value: NO


title: ZC11

description: Library name: MODEL1


title: pTh17_WT-4

description: Library name: samples4

value: spleen and lymph nodes


title: N-B-A11

description:
Library name: DSP-1001660033923-B-A11
spatial WTA sequencing


title: pTh17_Hi-1

description: Library name: samples14


title: pTh17_Mock-3

description: Library name: samples13


title: Control, replicate 2

city: Helsingør

first: Niels-Ulrik

last: Frigaard

address: Strandpromenaden 5

department: Department of Biology

country: Denmark

institute: University of Copenhagen

description: Library name: ECA33_2

data_processing:
RNA sequence reads (ca. 14–18 million non-rRNA, quality-filtered, paired-end reads per biological replicate) were mapped to the reference genome (RefSeq annotation GCF_000019485.1) using STAR 2.7.10b (Dobin et al. 2013) as part of the expression analysis pipeline of Eurofins (version 2.9.10).
Assembly: GCF_000019485.1
Supplementary files format and content: Raw reads were counted with Subread featureCounts v. 2.0.3 (parameter -p --countReadPairs -C --largestOverlap -s 2 -T 8 -Q 10).

organism: Picosynechococcus sp. PCC 7002

source_name: bacteria

growth_protocol: Strains were cultivated in liquid A+ HEPES medium with 30% CO2 and the inducers anhydrotetracycline (1 ng /mL) and IPTG (5 mM) in a Multi-Cultivator MC OD-1000 photobioreactor (Photon Systems Instruments, Czech Republic). Cells were harvested in the exponential phase (OD720 = 0.3–0.6) and total RNA was isolated.

extract_protocol:
Total RNA was extracted using PGTX reagent as previously described (Geissler et al. 2026).
Total RNA was depleted of rRNA and sequenced using Illumina technology (2x150 bp reads, ca. 300 bp insert size) by Eurofins Genomics (Konstanz, Germany).

value: bacteria


title: N-B-A09

description:
Library name: DSP-1001660033923-B-A09
spatial WTA sequencing


title: N-B-C03

description:
Library name: DSP-1001660033923-B-C03
spatial WTA sequencing


title: AKM22

description: Library name: MCL8a

extract_protocol:
High quality RNA was isolated using QIAshredder columns and RNAeasy Mini kit (Qiagen)
RNA-seq libraries were constructed using Illumina TruSeq RNA Library Prep Kit v2 (poly A enrichment).

value: MINO-VR


title: AKM11

description: Library name: MCL2a

value: BTZ


title: AKM23

description: Library name: MCL9

value: IBR


title: pTh17_Mock-2

description: Library name: samples12


title: Control, replicate 1

description: Library name: ECA33_1


title: BL_3

description:
Library name: sample 3
BL group, replicate biosample 3

value: leaf

value: NtGSTU10 overexpression mutant


title: N-B-B10

description:
Library name: DSP-1001660033923-B-B10
spatial WTA sequencing


title: d2_pTh17-2

description: Library name: samples5

value: wild type


title: JC17

description: Library name: XPQG1


title: AKM18

description: Library name: MCL6a

value: MINO-P


title: N-B-B11

description:
Library name: DSP-1001660033923-B-B11
spatial WTA sequencing


title: d2_pTh17-3

description: Library name: samples6


title: AKM17

description: Library name: MCL6


title: BL_2

description:
Library name: sample 2
BL group, replicate biosample 2


title: AKM21

description: Library name: MCL8


title: ndhF3 ndhF4 knockdown, replicate 1

description: Library name: ECA28_1


title: d2_npTh17-3

description: Library name: samples3


title: mouse, colonocytes, fish oil, pectin diet biol rep 3

city: College Station

first: Destiny

middle: A

last: Mullens

state: Texas

address: 2253 TAMU

department: Nutrition

institute: Texas A&M University

description:
Library name: GC782
10x Genomics for Chromium Fixed RNA Profiling from FFPE Tissue Blocks

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregaion were made using the Cell Ranger software v. 8.0.0.
To perform the mapping using the updated genome, we created an adaptation to the "Chromium Mouse Transcriptome Probe Set v1.0.1" (provided). Alternatively, samples can be mapped using 10X Genomics provided "refdata-gex-mm10-2020-A" reference with the "Chromium_Mouse_Transcriptome_Probe_Set_v1.0.1_mm10-2020-A.csv" probe list.
Assembly: GRCm39-2024-A
Assembly: Chromium_Mouse_Transcriptome_Probe_Update2024.csv
Supplementary files format and content: tab separated value files and matrix files

source_name: colon

extract_protocol:
Two 50 um sections were freshly cut from formalin-fixed paraffin-embedded colon swiss roll blocks and processed using protocols from 10x Genomics for Chromium Fixed RNA Profiling from FFPE Tissue Blocks.
Processed for the Fixed RNA Profiling (Flex) assay according to the 10x Genomics Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples protocol.

treatment_protocol: C57BL/6 mice were fed a diet of either corn oil and celluloser or fish oil and pectin for 3 weeks.

value: colon

value: fish oil, pectin


title: AKM7

city: AUBURN

last: Mitra

institute: AUBURN UNIVERSITY

description: Library name: HK_38_CRRA190002993-1a_HMHTKDSXX_L1

data_processing:
Partek Genomics Suite
Read count extraction were performed from raw data using Partek Flow
Assembly: hg38
Supplementary files format and content: tab-delimited text files include normalized gene counts in Samples


title: N-B-B08

description:
Library name: DSP-1001660033923-B-B08
spatial WTA sequencing


title: nhaS3UTEX overexpression, replicate 3

description: Library name: ECA26_3


title: N-B-A05

description:
Library name: DSP-1001660033923-B-A05
spatial WTA sequencing


title: AKM16

description: Library name: MCL5a


title: nhaS3UTEX overexpression, replicate 2

description: Library name: ECA26_2


title: N-B-A04

description:
Library name: DSP-1001660033923-B-A04
spatial WTA sequencing


title: pTh17_Hi-3

description: Library name: samples16


title: nhaS3UTEX overexpression, replicate 1

description: Library name: ECA26_1


title: N-B-A03

description:
Library name: DSP-1001660033923-B-A03
spatial WTA sequencing


title: AKM5

description: Library name: HK_36_CRRA190002991-1a_HMHTKDSXX_L1


title: ccmR knockdown, replicate 3

description: Library name: ECA16_3


title: mouse, colonocytes, fish oil, pectin diet biol rep 1

description:
Library name: GC743
10x Genomics for Chromium Fixed RNA Profiling from FFPE Tissue Blocks


title: Gh time(dpi):4 rep:E

description:
Library name: Gh_PDB_E
150bp paired reads

value: Mycelium

value: Treatment=Gh. Time=4d. Replicate:E


title: AKM4

description: Library name: HK_11_CRRA190002966-1a_HMHTKDSXX_L1

value: CLF


title: Control, replicate 3

description: Library name: ECA33_3


title: N-B-A02

description:
Library name: DSP-1001660033923-B-A02
spatial WTA sequencing


title: ccmR knockdown, replicate 2

description: Library name: ECA16_2


title: Donor_2607_LEVO_9

city: New Haven

first: Priyanka

last: Jamadagni

state: CT

address: 333 Cedar Street

department: School of Medicine

institute: Yale University

description:
Library name: Sample 58
Drug_D60_iGlut_all_featureCounts.txt

data_processing:
The downstream data was processed using DESeq2 software package
Assembly: The reads were mapped to GRCz10 genome for zebrafish and GRCh38 for the hPSC derived iGLUT cells.
Supplementary files format and content: Excel spreadsheets include raw counts for both cells and zebrafish samples, and DESeq2 processed files for zebrafish samples, for each treatment group vs control group.

source_name: hiPSCs derived D60 iGLUT

growth_protocol: Larval zebrafish were raised in fish media upto 6 days post fertilization. iGluts were raised to D60.

extract_protocol:
RNA was extracted from fish at 6 days post fertilization and from cells at D60. RNA was extracted using Qiagen Rneasy Plus Micro Kit.
For fish, NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina was used. For cells, Kapa mRNA Hyper Prep Kit Cat# KR1352 was used.

treatment_protocol: Larval zebrafish were treated with Levocarnitine or DMSO for 24 hours from 5 to 6 days post fertilization. iGluts were treated with Levocarnitine or DMSO for 48 hours.

value: wt

value: 10 µM Levocarnitine 48hrs

tag: donor id

value: Donor 2607

value: hiPSCs derived D60 iGLUT


title: N-B-B01

description:
Library name: DSP-1001660033923-B-B01
spatial WTA sequencing

value: NO


title: Gh time(dpi):4 rep:B

description:
Library name: Gh_PDB_B
150bp paired reads

value: Treatment=Gh. Time=4d. Replicate:B


title: mouse, colonocytes, corn oil, cellulose diet biol rep 2

description:
Library name: GC835
10x Genomics for Chromium Fixed RNA Profiling from FFPE Tissue Blocks

value: corn oil, cellulose


title: AKM14

first: Amit

address: HARRISON COLLEGE OF PHARMACY

description: Library name: MCL4a

value: MCL

value: Mantle Cell Lymphoma cell line


title: Donor_2607_LEVO_8

description:
Library name: Sample 57
Drug_D60_iGlut_all_featureCounts.txt


title: N-B-A10

description:
Library name: DSP-1001660033923-B-A10
spatial WTA sequencing


title: AKM13

description: Library name: MCL4


title: d2_npTh17-2

description: Library name: samples2

value: spleen and lymph nodes


title: mouse, colonocytes, corn oil, cellulose diet biol rep 1

description:
Library name: GC819
10x Genomics for Chromium Fixed RNA Profiling from FFPE Tissue Blocks


title: AKM12

description: Library name: MCL3


title: ndhF3 ndhF4 knockdown, replicate 2

description: Library name: ECA28_3

value: bacteria


title: VNIM non-lesion white matter

city: Valencia

first: Yaakov

middle: A.

last: Levine

state: CA

address: 25101 Rye Canyon Loop

institute: SetPoint Medical Corporation

description: Library name: VNSNL_5

data_processing:
Raw sequencing data were processed using the cloud-based Cell Ranger Multi v9.0.1 (10x Genomics) for demultiplexing, alignment, and UMI counting to generate gene-cell count matrices referenced to the default mm10 genome. One Sham and one VNIM lesion sample were excluded from downstream analysis due to technical errors during tissue processing; these samples had been retained through library preparation as they were already loaded on the multiplexing chip.
Gene-cell count matrices were merged and analyzed using the Seurat package (v4). Cellular trajectories and pseudotime relationships were inferred using Slingshot
Assembly: mm10
Supplementary files format and content: Feature Barcode Market Exchange Matrices (MEX) files

source_name: Spinal cord white matter

extract_protocol:
Neutral red–labeled white matter was isolated as lesion tissue. Non-lesion tissue consisted of approximately 1 cm of white matter collected 0.5 mm above and below the lesion site. In naïve animals, where no neutral red labeling was observed, approximately 2 cm of white matter from a comparable spinal cord level was collected. To obtain sufficient cell numbers, lesion and non-lesion samples were pooled from two animals of the same sex. Dissected tissue was transferred to gentleMACS C Tubes (Miltenyi Biotec) containing digestion buffer from the Adult Brain Dissociation Kit (Miltenyi Biotec) supplemented with the inhibitor cocktail and mechanically minced. Enzymatic dissociation was performed using the gentleMACS OctoDissociator (program 37C_ABDK_01). Samples were briefly centrifuged, filtered through a 70 μm strainer, washed, and subjected to debris removal by density gradient centrifugation according to the manufacturer’s instructions. Cell viability and concentration were assessed using ViaStain AOPI staining solution (1:1) and quantified using a DeNovix CellDrop FL prior to library preparation. To minimize ex vivo transcriptional and translational activation, an inhibitor cocktail containing actinomycin D (5 μg/mL; Sigma-Aldrich), triptolide (10 μM; Sigma-Aldrich), and anisomycin (27.1 μg/mL; Sigma-Aldrich) in 1x PBS without Ca2+, Mg2+, or phenol red (pH 7.4; Gibco) was applied during tissue dissection and enzymatic digestion.
Single-cell libraries were generated using the GEM-X Universal 3′ Gene Expression v4 4-plex OCM Reagent Kits (10x Genomics) according to the manufacturer’s protocol, targeting 5,000 cells per sample. Quality control for cDNA and final libraries was performed using the Agilent 2100 Bioanalyzer system using the Agilent High Sensitivity DNA quantification kit (Agilent Technologies). Libraries were sequenced by MedGenome on an Illumina NovaSeq platform using 10x Genomics-recommended read configurations, targeting 40,000–80,000 reads per cell.

treatment_protocol: Focal demyelination was induced by injection of 1% LPC at D0. At D4, animals received either VNIM (10 Hz, 0.75-1.0 mA, 1 min) or sham treatment. Naïve animals receive no injection or intervention.

value: Spinal cord white matter

value: All cells from isolated tissue

value: VNIM


title: N-B-A07

description:
Library name: DSP-1001660033923-B-A07
spatial WTA sequencing


title: Donor_2607_LEVO_7

description:
Library name: Sample 56
Drug_D60_iGlut_all_featureCounts.txt


title: AKM9

description: Library name: MCL1

value: CON


title: N-B-A06

description:
Library name: DSP-1001660033923-B-A06
spatial WTA sequencing


title: N-B-A08

description:
Library name: DSP-1001660033923-B-A08
spatial WTA sequencing


title: mouse, colonocytes, fish oil, pectin diet biol rep 4

description:
Library name: GC714
10x Genomics for Chromium Fixed RNA Profiling from FFPE Tissue Blocks

value: colon

value: fish oil, pectin


title: AKM10

description: Library name: MCL2

value: BTZ


title: Donor_2607_LEVO_6

description:
Library name: Sample 55
Drug_D60_iGlut_all_featureCounts.txt

value: wt

value: 10 µM Levocarnitine 48hrs


title: MUT5_Mice 5

city: Mineola

first: M. Mahmood

last: Hussain

state: New York

address: 101 Mineola Blvd.

department: Foundations of Medicine

institute: NYU Grossman Long Island School of Medicine

description: Library name: B5_MUT

data_processing:
Raw data in fastq format were processed by Novogene using their in-house Perl scripts  to obtain clean reads by removing adapter sequences, reads with poly-N, and low-quality reads.
Trimmed sequence reads were mapped to GRCh37/hg19 using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: mm39
Supplementary files format and content: gene_count.xlsx

source_name: Duodenum

growth_protocol: All mice were on regular chow diet thorughout the study.

extract_protocol:
Total RNA was isolated using Trizol reagent (Thermo Fisher Scientific, # 15596018) following manufacturers protocol.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using dTTP. It was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

value: Duodenum

value: Pla2g12b mutant


title: VNIM lesion white matter

description: Library name: VNSL_4


title: pTh17_Mock-1

first: Jie

description: Library name: samples11

value: wild type


title: Human_CD63_KD#1_S3

city: Seattle

first: Yuzuru

last: Sasamoto

state: WA

address: 750 Republican St

department: Ophthalmology

institute: University of Washington

description: Library name: Human sample 8

data_processing:
(1) For mouse samples: RNA-seq counts were generated by bcbio and bcbioRNASeq using salmon. Counts were imported into R using tximport and DESeq2.(2) For human samples: The reads were adaptor trimmed and aligned using the STAR program (version 2.6.1d). Transcript counts were inferred from alignment files and all transcripts with either 0 or 1 counts were removed. Gene expression was measured using EdgeR. Differential expression analyses were performed by the DESeq2.
Assembly: mm10, hg38
Supplementary files format and content: Differentially expressed gene data

source_name: Cultured limbal epithelial cells

extract_protocol:
(1) Dissociated mouse corneal epithelial cells were resuspended with2% fetal bovine serum (FBS) supplemented phosphate-buffered saline (PBS). The cells were incubated with 40μg/ml human anti-Abcb5 mAb (clone 3B9) at 37°C for 30min and subsequently incubated with Donkey Anti-Human IgG H+L (DyLight 650) on ice for 30min. To remove the hematopoietic cells, the cells were incubated with 0.1μg/ml PE-conjugated anti-CD45 mAb and 3µg/ml PE-conjugated anti-CD11b mAb on ice for 30min. To exclude the dead cells, the cells were incubated with 30nM SYTOX Green Dead Cell Stain on ice for 20min. RNA was extracted from the FACS sorted Abcb5-positive cells and Abcb5-negative cells. (2) Human donor corneas were obtained from eye banks. The central cornea was removed by an 8mm disposable biopsy punch and the corneal endothelium was removed mechanically. After 1 h incubation with PluriSTEM Dispase II Solution at 37 °C, limbal epithelial cells were scraped and incubated with TrypLE Express Enzyme at 37 °C for 30 min to dissociate. Dissociated limbal epithelial cells were cultured and treated with siRNAs (Control, CD63 knockdown#1 and CD63 knockdown#2).  On day 5, the cells were harvested for RNA extraction after siRNA transfection.
After the removal of rRNA, approximately 500 ng of total RNA underwent library preparation with the Zymo-Seq RiboFree Total RNA Library Prep Kit (Zymo Research). Sequencing was carried out by an Illumina NovaSeq to a sequencing depth of ~50-75 million read pairs (150 bp paired-end sequencing) per sample. (1) For mouse samples: SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing (Clontech Laboratories, Mountain View, CA) was used to generate mRNA libraries. (2) For human samples: Zymo-Seq RiboFree Total RNA Library Prep Kit (Zymo Research) was used to generate mRNA libraries.

value: Cultured limbal epithelial cells

value: In vitro human corneal epithelial cells

value: Sample 3, CD63 knockdown#1


title: Human_CD63_KD#2_S3

description: Library name: Human sample 9

value: Sample 3, CD63 knockdown#2


title: mouse, colonocytes, fish oil, pectin diet biol rep 2

description:
Library name: GC730
10x Genomics for Chromium Fixed RNA Profiling from FFPE Tissue Blocks


title: MUT4_Mice 4

description: Library name: B4_MUT


title: AKM8

description: Library name: HK_39_CRRA190002994-1a_HMHTKDSXX_L1

value: MCL

value: MINO-VR

value: Mantle Cell Lymphoma cell line


title: AKM6

description: Library name: HK_37_CRRA190002992-1a_HMHTKDSXX_L1

value: MINO-P


title: Sham lesion white matter

description: Library name: ShamL_2

value: Spinal cord white matter

value: All cells from isolated tissue

value: Sham


title: MUT3_Mice 3

description: Library name: B3_MUT


title: Donor_2607_LEVO_5

description:
Library name: Sample 54
Drug_D60_iGlut_all_featureCounts.txt

value: Donor 2607

value: hiPSCs derived D60 iGLUT


title: MUT1_Mice 1

description: Library name: B1_MUT


title: Naïve white matter

description: Library name: Naïve_1

value: Naïve


title: MUT2_Mice 2

description: Library name: B2_MUT

value: Duodenum


title: mouse, colonocytes, corn oil, cellulose diet biol rep 4

description:
Library name: GC703
10x Genomics for Chromium Fixed RNA Profiling from FFPE Tissue Blocks

value: colon

value: corn oil, cellulose


title: Donor_2607_LEVO_4

description:
Library name: Sample 53
Drug_D60_iGlut_all_featureCounts.txt

value: wt

value: 10 µM Levocarnitine 48hrs


title: Donor_2607_LEVO_2

description:
Library name: Sample 51
Drug_D60_iGlut_all_featureCounts.txt


title: Human_CD63_KD#1_S2

description: Library name: Human sample 5

value: Cultured limbal epithelial cells

value: In vitro human corneal epithelial cells

value: Sample 2, CD63 knockdown#1


title: SC

description: Library name: SAMPLES 2

data_processing:
Raw sequencing data were first processed using Fastp to trim primer sequences and low-quality bases. The remaining reads were then processed using the Seeksoul tools to demultiplex cellular barcodes and align reads to the mm10 reference genome (refdata-gex-mm10-2020-A), generating a feature-barcode matrix for downstream analysis.
Assembly: GRCm38
Supplementary files format and content: The processed data include the filtered gene-cell count matrix generated by the SeekRNA pipeline. The matrix is provided in the 10x Genomics-compatible Matrix Market format, which consists of three files:barcodes.tsv(.gz),features.tsv(.gz) and matrix.mtx(.gz).
Supplementary files format and content: The matrix is provided in the 10x Genomics-compatible Matrix Market format, which consists of three files:

source_name: Spinal cord

extract_protocol:
CD45+ cells were isolated from the dLNs and spinal cords of EAE-induced C57BL/6 mice by fluorescence-activated cell sorting (FACS).
Single-cell RNA-Seq libraries were prepared using SeekOne® Digital Droplet Single Cell 3' library preparation kit (SeekGene, Catalog No. K00202). Briefly, appropriate number of cells were mixed with reverse transcription reagent and then added to the sample well in SeekOne® chip S3. Subsequently Barcoded Hydrogel Beads (BHBs) and partitioning oil were dispensed into corresponding wells separately in chip S3. After emulsion droplet generation reverse transcription were performed at 42℃ for 90 minutes and inactivated at 85℃ for 5 minutes. Next, cDNA was purified from broken droplet and amplified in PCR reaction. The amplified cDNA product was then cleaned, fragmented, end repaired, A-tailed and ligated to sequencing adaptor. Finally, the indexed PCR were performed to amplify the DNA representing 3' polyA part of expressing genes which also contained Cell Barcode and Unique Molecular Index. The indexed sequencing libraries were cleanup with VAHTS DNA Clean Beads (Vazyme, N411-01), analyzed by Qubit (Thermo Fisher Scientific, Q33226) and Bio-Fragment Analyzer (Bioptic, Qsep400). The libraries were then sequenced on illumina NovaSeq 6000 with PE150 read length or DNBSEQ-T7 platform with PE150 read length.

value: Spinal cord

value: cd45+ cells


title: Human_Control_S3

description: Library name: Human sample 7

value: Sample 3 Control


title: Donor_2607_DMSO_9

description:
Library name: Sample 49
Drug_D60_iGlut_all_featureCounts.txt

value: DMSO


title: Donor_2607_LEVO_1

description:
Library name: Sample 50
Drug_D60_iGlut_all_featureCounts.txt


title: Human_Control_S2

description: Library name: Human sample 4

value: Sample 2, Control


title: dLN

description: Library name: SAMPLES 1

source_name: Draining lymph nodes

value: Draining lymph nodes


title: ADD_3_synovium_12weeks

city: Sinagawa-ku

first: Kazuhiro

last: Shibusaka

state: Tokyo-to

address: 1-5-8, Hatanodai,1st building, 343

country: Japan

institute: showa university

data_processing:
Quality control (QC) and trimming conducted using Fastp. (version 0.23.4)
Following the initial mapping process using STAR (version 2.7.10b)
The data was subsequently aggregated using RSEM (version 1.3.3).
Assembly: mm39
Supplementary files format and content: tab-delimited csv file includes raw counts for each sample
Supplementary files format and content: tab-delimited csv file includes TPM values for each sample

source_name: Synovium

extract_protocol:
Both the condyles and synovial tissues were stored at -80°C until RNA was extracted using TRIzol reagent (Invitrogen). After homogenization with zirconia beads in a TRIzol-containing tube, the mixture was incubated and then centrifuged. The supernatant was removed, RNA was isolated, and the total RNA was dissolved in RNase-free water. RNA was harvested using the Direct-zol™ RNA MicroPrep kit (ZYMO RESEARCH). A total of 0.2 μg of RNA was used for the construction of sequencing libraries
RNA libraries for RNA-seq were prepared using Optimal Dual-mode mRNA Library Prep Kit following manufacture's protocols.

value: Synovium

value: WT


title: Human_CD63_KD#2_S1

description: Library name: Human sample 3

value: Sample 1, CD63 knockdown#2


title: Human_CD63_KD#1_S1

description: Library name: Human sample 2

value: Sample 1, CD63 knockdown#1


title: Human_CD63_KD#2_S2

description: Library name: Human sample 6

value: Sample 2, CD63 knockdown#2


title: Donor_2607_DMSO_7

description:
Library name: Sample 47
Drug_D60_iGlut_all_featureCounts.txt

value: Donor 2607

value: hiPSCs derived D60 iGLUT


title: WT3_Mice 3

description: Library name: A3_WT

value: Duodenum


title: ccmR knockdown, replicate 1

description: Library name: ECA16_1

value: bacteria


title: AKM3

description: Library name: HK_10_CRRA190002965-1a_HMHTKDSXX_L1

source_name: MCL

value: MCL

value: MINO-VR

value: Mantle Cell Lymphoma cell line

value: CON


title: Donor_2607_DMSO_6

description:
Library name: Sample 46
Drug_D60_iGlut_all_featureCounts.txt

value: wt


title: Sham non-lesion white matter

description: Library name: ShamNL_3

value: Spinal cord white matter

value: All cells from isolated tissue

value: Sham


title: ADD_2_synovium_12weeks

value: Synovium


title: Pooled samples: Rb-/- Organoids ABT-737, Rb-/- Organoids Luminespib and Rb-/- Organoids Vehicle Control DMSO

city: Newcastle University

first: Majlinda

last: Lako

address: Newcastle University

institute: Newcastle University

description: Library name: Pooled samples

data_processing:
The sequencing data was aligned to GRCh38, and the reads quantified using Trailmaker (version 1.4.0). The filtered Trailmaker outputs were quality controlled to remove dead cells and debris prior to downstream analysis.  The following filtering thresholds were applied: a minimum of 5,000 counts per cell, a minimum of 3,000 detected genes per cell, and a maximum of 5% mitochondrial gene content. Each sample was processed and clustered individually using Seurat (Version 5.3.0). Cells were normalized and scaled, and highly variable features were identified. Principal component analysis (PCA) was performed for dimensionality reduction, and the top 20 principal components were used to construct a shared nearest neighbour (SNN) graph for clustering using the Louvain algorithm. Following individual clustering, samples were integrated using the Harmony (version 1.2.3) batch correction method to account for technical variation across datasets. To minimize confounding effects, gene counts, read counts, and cell cycle phase scores were regressed out during the integration process. The integrated dataset was clustered using the same approach as for individual samples, and marker genes for each cluster were identified. Cell type annotations were assigned based on the expression of known retinal marker genes.
Assembly: GRCh38
Supplementary files format and content: h5ad: scanpy objects output from the trailmaker pipeline
Supplementary files format and content: csv: csv files containing cell metadata for each sample
Supplementary files format and content: mtx: matrix files for each sample containing filtered cell counts

source_name: iPSC Retinal Organoid

growth_protocol: Sasai Retinal Organoid doi: 10.1038/nature09941

extract_protocol:
Parse Biosciences
Single Cell RNA sequencing was conducted using the Parse Evercode WT Mini V3 kit, all steps were conducted as per manufacturer’s instructions. Samples were split evenly for library preparation to ensure even representation in final solution. The two samples were run using a NovaSeq 6000 with SP 100 cycle v1.5 kit. Run parameters were 64/8/8/58 cycles and 5% PhiX control was spiked in.

value: iPSC Retinal Organoid

value: iPSC Retinal

value: Retinal

value: Rb

value: Various


title: AKM2

description: Library name: HK_8_CRRA190002963-1a_HV3NWDSXX_L1

value: MINO-P

value: CLF


title: MS_1_synovium_12weeks

value: WT


title: Donor_2607_DMSO_5

description:
Library name: Sample 45
Drug_D60_iGlut_all_featureCounts.txt

value: DMSO

value: Donor 2607

value: hiPSCs derived D60 iGLUT


title: vehicle control, replicate 9

city: Singapore

first: Jason

middle: Yongsheng

last: Chan

address: 30 Hospital Blvd

country: Singapore

institute: National Cancer Centre Singapore

description: NanoString Mouse Immunology Panel

hyb_protocol: Hybridation was performed as per manufacturer's protocol

scan_protocol: Analysed in the nCounter Digital Analyser using default protocol

data_processing: Normalization was performed using the nSolver 4.0 Advanced Analysis software using default parameters

label: not provided

source_name: EL4-C57BL6N syngeneic mouse tumor model

label_protocol: 100 ng total RNA was used as input into the hybridisation step and carried out according to the manufacturer's protocol

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen) from snap frozen EL4 cell-line derived tumors engrafted on C57BL6N mice and analyzed using the 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA).

value: vehicle control with isotype


title: Ctrl_3_synovium_12weeks


title: mouse, colonocytes, corn oil, cellulose diet biol rep 3

description:
Library name: GC840
10x Genomics for Chromium Fixed RNA Profiling from FFPE Tissue Blocks

value: colon

value: corn oil, cellulose


title: Donor_2607_DMSO_4

description:
Library name: Sample 44
Drug_D60_iGlut_all_featureCounts.txt

value: wt


title: vehicle control, replicate 8

description: NanoString Mouse Immunology Panel

value: EL4 cell-line derived tumors engrafted on C57BL6N mice


title: PTPN2+/+ SC-islet

city: Anderlecht

first: Valerie

last: Vandenbempt

state: Vlaams-Brabant

address: Lenniksebaan 808

country: Belgium

institute: Université Libre de Bruxelles

description:
Library name: Sample 1
H1WT differentiated SC-islet

data_processing:
Ambient RNA removal
Doublet removal
Assembly: Hg19
Supplementary files format and content: Cellranger output

source_name: SC-islet

growth_protocol: SC-islet differentiation

extract_protocol:
Cell dispersion
10X 3´

value: SC-islet

value: PTPN2 wild type


title: Donor_2607_DMSO_3

description:
Library name: Sample 43
Drug_D60_iGlut_all_featureCounts.txt


title: Donor_2607_DMSO_2

description:
Library name: Sample 42
Drug_D60_iGlut_all_featureCounts.txt


title: VVA11_H1WT_Cyto_N3

description: Library name: Sample 11

data_processing:
Batch correction
Assembly: Hg19
Supplementary files format and content: Raw counts

source_name: Stem cell

growth_protocol: Stem cell culture

extract_protocol:
total RNA collection
Bulk RNAsequencing

value: Stem cell

value: PTPN2 WT

value: IFN-g


title: Donor_2607_LEVO_3

description:
Library name: Sample 52
Drug_D60_iGlut_all_featureCounts.txt

value: 10 µM Levocarnitine 48hrs


title: ADD_3_condyle_12weeks

source_name: Condyle

value: Condyle


title: Donor_553_LEVO_9

description:
Library name: Sample 40
Drug_D60_iGlut_all_featureCounts.txt

value: Donor 553


title: AKM1

description: Library name: HK_7_CRRA190002962-1a_HMHTKDSXX_L2

value: MCL

value: MINO-P

value: Mantle Cell Lymphoma cell line

value: CON


title: vehicle control, replicate 3

description: NanoString Mouse Immunology Panel

value: vehicle control with isotype


title: ADD_2_condyle_12weeks

value: WT


title: VVA9_H1WT_CTL_N3

description: Library name: Sample 9

value: Control


title: Donor_553_LEVO_8

description:
Library name: Sample 39
Drug_D60_iGlut_all_featureCounts.txt

value: wt

value: hiPSCs derived D60 iGLUT


title: VVA10_H1N2_CTL_N3

description: Library name: Sample 10

value: PTPN2 KO


title: Ctrl_1_synovium_12weeks

value: Synovium


title: ADD_1_condyle_12weeks


title: Human_Control_S1

description: Library name: Human sample 1

value: Cultured limbal epithelial cells

value: In vitro human corneal epithelial cells

value: Sample 1, Control


title: WT4_Mice 4

description: Library name: A4_WT

value: Duodenum


title: VVA7_H1WT_Cyto_N2

description: Library name: Sample 7

value: Stem cell

value: PTPN2 WT

value: IFN-g


title: Single-cell RNA-seq of human iPSC-derived lung organoid

city: Seoul

first: Eun-mi

last: Kim

address: 621, Hwarang-ro

country: South Korea

institute: Seoul Women's University

description: Library name: hLO

data_processing:
Raw BCL or FASTQ files were processed using the Cell Ranger pipeline v9.0.1 (10x Genomics) with the “count” function. Reads were aligned to the human genome (GRCh38), and gene-barcode matrices (matrix.mtx, features.tsv, barcodes.tsv) were generated.
Assembly: Human GRCh38
Supplementary files format and content: Processed files include Cell Ranger output (matrix.mtx, features.tsv, barcodes.tsv)

source_name: Lung

extract_protocol:
Single-cell suspensions were obtained using enzymatic dissociation, followed by cell counting and viability assessment.
Single-cell libraries were constructed according to the manufacturer’s protocol for the Chromium Single Cell 3’ v4 kit (10x Genomics). In brief, cells and reagents were loaded onto a Chromium Chip to generate Gel Beads-in-emulsion (GEMs), where mRNAs from individual cells were barcoded during reverse transcription. Full-length cDNA was amplified, fragmented, end-repaired, and ligated to sequencing adapters. Indexed sequencing libraries were purified and quality-checked before sequencing on an Illumina platform.

value: Lung

value: Lung organoid


title: Donor_553_LEVO_6

description:
Library name: Sample 37
Drug_D60_iGlut_all_featureCounts.txt
This Sample record represents a resequencing of the 'donor_553_levo_4' sample.  In Drug_D60_iGlut_all_featureCounts.txt, there is only one column representing that sample.

value: 10 µM Levocarnitine 48hrs

value: Donor 553


title: ADD_1_synovium_12weeks

value: WT


title: anti-PD1 treated, replicate 7

description: NanoString Mouse Immunology Panel

value: anti-PD1 treated

value: EL4 cell-line derived tumors engrafted on C57BL6N mice


title: vehicle control, replicate 7

description: NanoString Mouse Immunology Panel

value: vehicle control with isotype


title: Donor_553_LEVO_5

description:
Library name: Sample 36
Drug_D60_iGlut_all_featureCounts.txt
This Sample record represents a resequencing of the 'donor_553_levo_4' sample.  In Drug_D60_iGlut_all_featureCounts.txt, there is only one column representing that sample.

value: wt

value: hiPSCs derived D60 iGLUT


title: Donor_2607_DMSO_1

description:
Library name: Sample 41
Drug_D60_iGlut_all_featureCounts.txt

value: DMSO

value: Donor 2607


title: VVA5_H1WT_CTL_N2

description: Library name: Sample 5

value: Control


title: anti-PD1 treated, replicate 6

description: NanoString Mouse Immunology Panel


title: Donor_553_LEVO_4

description:
Library name: Sample 35
Drug_D60_iGlut_all_featureCounts.txt


title: WT1_Mice 1

description: Library name: A1_WT

value: Duodenum


title: Ctrl_3_condyle_12weeks

value: Condyle


title: Donor_553_LEVO_3

description:
Library name: Sample 34
Drug_D60_iGlut_all_featureCounts.txt


title: VVA12_H1WT_Cyto_N3

description: Library name: Sample 12

value: Stem cell

value: PTPN2 KO


title: VVA4_H1N2_Cyto_N1

description: Library name: Sample 4

value: IFN-g


title: PTPN2-/- SC-islet

description:
Library name: Sample 2
H1N2 knockout differentiated SC-islet

value: SC-islet

value: PTPN2 knockout


title: anti-PD1 treated, replicate 4

description: NanoString Mouse Immunology Panel


title: VVA6_H1N2_CTL_N2

description: Library name: Sample 6


title: Donor_2607_DMSO_8

description:
Library name: Sample 48
Drug_D60_iGlut_all_featureCounts.txt


title: MS_2_condyle_12weeks


title: Ctrl_2_condyle_12weeks


title: VVA2_H1N2_CTL_N1

description: Library name: Sample 2


title: vehicle control, replicate 5

description: NanoString Mouse Immunology Panel


title: Ctrl_2_synovium_12weeks

value: Synovium


title: VVA8_H1N2_Cyto_N2

description: Library name: Sample 8


title: anti-PD1 treated, replicate 8

description: NanoString Mouse Immunology Panel


title: TgSwDI miR34a-/- [D-8]

city: Peoria

first: Ken-ichiro

last: Fukuchi

state: Illinois

address: One Illini Dr

department: Cancer Biology and Pharmacology

institute: University of Illinois College of Medicine

data_processing:
Raw reads were trimmed to remove Truseq adapters and bases from the 3’ end with quality scores less than 20 using cutadap
Trimmed reads shorter than 40bp were discarded
Trimmed reads were aligned to the mm10 genome in a splice-aware manner using the STAR aligner
Raw read counts were generated using FeatureCounts
Assembly: mm10
Supplementary files format and content: tab-delimited file includes raw counts for each sample

source_name: Mouse hippocampus

extract_protocol:
RNA was extracted from mouse hippocampus by use of Direct-zol RNAkit (Zymo) and purified from total RNA using oligo(Dt)-attached magnetic beads.
RNA library for RNA-seq were prepared using DNBSEQ Eukaryotic Stranded Transcriptome library protocol for stranded mRNA library

value: Mouse hippocampus

value: TgSwDI miR34a-/-


title: Donor_553_DMSO_6

description:
Library name: Sample 30
Drug_D60_iGlut_all_featureCounts.txt

value: Donor 553


title: vehicle control, replicate 4

description: NanoString Mouse Immunology Panel

value: vehicle control with isotype

value: EL4 cell-line derived tumors engrafted on C57BL6N mice


title: S8_M1KO

description: Library name: S8_M1KO

data_processing:
batch correction
Assembly: hg19
Supplementary files format and content: fastq files

source_name: Transplanted SC-islets

growth_protocol: SC-islet differentiation & transplantation

extract_protocol:
Total RNA collection
Bulk RNAseq

value: Transplanted SC-islets


title: WT2_Mice2

description: Library name: A2_WT

value: WT


title: anti-PD1 treated, replicate 1

description: NanoString Mouse Immunology Panel

value: anti-PD1 treated


title: Donor_553_LEVO_7

description:
Library name: Sample 38
Drug_D60_iGlut_all_featureCounts.txt

value: wt

value: 10 µM Levocarnitine 48hrs

value: hiPSCs derived D60 iGLUT


title: anti-PD1 treated, replicate 5

description: NanoString Mouse Immunology Panel


title: vehicle control, replicate 6

description: NanoString Mouse Immunology Panel


title: MS_2_synovium_12weeks


title: brincidofovir and anti-PD1 treated, replicate 9

description: NanoString Mouse Immunology Panel

value: brincidofovir and anti-PD1 treated


title: Donor_553_DMSO_5

description:
Library name: Sample 29
Drug_D60_iGlut_all_featureCounts.txt

value: DMSO


title: Ctrl_1_condyle_12weeks

value: Condyle


title: MS_3_condyle_12weeks


title: vehicle control, replicate 2

description: NanoString Mouse Immunology Panel


title: MS_3_synovium_12weeks


title: S6_M10KO

description: Library name: S6_M10KO


title: brincidofovir and anti-PD1 treated, replicate 8

description: NanoString Mouse Immunology Panel


title: TgSwDI miR34a-/- [D-2]


title: vehicle control, replicate 1

description: NanoString Mouse Immunology Panel


title: MS_1_condyle_12weeks


title: Donor_553_LEVO_2

description:
Library name: Sample 33
Drug_D60_iGlut_all_featureCounts.txt


title: S4_M1KO

description: Library name: S4_M1KO


title: Donor_553_LEVO_1

description:
Library name: Sample 32
Drug_D60_iGlut_all_featureCounts.txt


title: H9_M3WT

description: Library name: H9_M3WT

value: Wild type


title: VVA1_H1WT_CTL_N1

description: Library name: Sample 1

value: Stem cell

value: PTPN2 WT

value: Control


title: brincidofovir and anti-PD1 treated, replicate 7

description: NanoString Mouse Immunology Panel


title: Donor_553_DMSO_2

description:
Library name: Sample 26
Drug_D60_iGlut_all_featureCounts.txt


title: Donor_553_DMSO_7

description:
Library name: Sample 31
Drug_D60_iGlut_all_featureCounts.txt


title: VVA3_H1WT_Cyto_N1

description: Library name: Sample 3

value: IFN-g


title: Donor_553_DMSO_1

description:
Library name: Sample 25
Drug_D60_iGlut_all_featureCounts.txt

value: Donor 553


title: brincidofovir and anti-PD1 treated, replicate 6

description: NanoString Mouse Immunology Panel


title: Donor_553_DMSO_3

description:
Library name: Sample 27
Drug_D60_iGlut_all_featureCounts.txt


title: TgSwDI miR34a-/- [D-5]

value: Mouse hippocampus

value: TgSwDI miR34a-/-


title: S7_M4WT

description: Library name: S7_M4WT

value: Transplanted SC-islets


title: Patient GHD58-Visit-2 [EB_58_V2C]

city: Chicago

first: Ajay

last: Rana

state: IL

address: 840 S. Wood Street

department: Surgery

institute: University of Illinois at Chicago

description:
Library name: EB_58_V2C
Patient GHD58-Visit-2

data_processing:
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 ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: GRCh38,hg38
Supplementary files format and content: analysis results; AR_FPKM.xls.txt

source_name: skeletal muscle

extract_protocol:
RNA was isolated using RNAeasy mini kit (Qiagen)
The library was checked with Qubit and real-time PCR for quantification and a bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

value: skeletal muscle

tag: treatment/time point

value: after 12 months of supervised, resistance-based muscle therapy


title: TgSwDI miR34a-/- [D-3]


title: Patient GHD58-Visit-2 [EB_58_V2B]

description:
Library name: EB_58_V2B
Patient GHD58-Visit-2


title: anti-PD1 treated, replicate 2

description: NanoString Mouse Immunology Panel

value: anti-PD1 treated

value: EL4 cell-line derived tumors engrafted on C57BL6N mice


title: anti-PD1 treated, replicate 3

description: NanoString Mouse Immunology Panel


title: brincidofovir and anti-PD1 treated, replicate 3

description: NanoString Mouse Immunology Panel


title: TgSwDI miR34a-/- [D-1]


title: TgSwDI miR34a+/+ [C-4]

value: TgSwDI miR34a+/+


title: VVA12_H1WT_Cyto_N3

description: Library name: Sample 12

data_processing:
HOMER analysis
Assembly: Hg38
Supplementary files format and content: fastq reads

source_name: Stem cells

extract_protocol:
DNA extraction with T5 enzyme
ATAC-seq

treatment_protocol: with or without interferon-gamma for 24h

value: Stem cells

value: PTPN2 KO


title: TgSwDI miR34a+/+ [C-7]


title: H10_M10_WT

description: Library name: H10_M10_WT


title: TgSwDI miR34a+/+ [C-5]


title: Non-Tg miR34a-/- [B-8]

value: Non-Tg miR34a-/-


title: Non-Tg miR34a-/- [B-7]


title: brincidofovir and anti-PD1 treated, replicate 5

description: NanoString Mouse Immunology Panel

value: brincidofovir and anti-PD1 treated


title: VVA11_H1WT_Cyto_N3

description: Library name: Sample 11


title: Donor_553_DMSO_4

description:
Library name: Sample 28
Drug_D60_iGlut_all_featureCounts.txt

source_name: hiPSCs derived D60 iGLUT

value: wt

value: DMSO

value: hiPSCs derived D60 iGLUT


title: Patient GHD58-Visit-1 [EB_58_V1C]

description:
Library name: EB_58_V1C
Patient GHD58-Visit-1

value: before 12 months of supervised, resistance-based muscle therapy


title: VVA9_H1WT_CTL_N3

description: Library name: Sample 9

value: PTPN2 WT

value: CTL


title: TgSwDI miR34a+/+ [C-6]

value: Mouse hippocampus


title: TgSwDI miR34a+/+ [C-3]


title: VVA7_H1WT_Cyto_N2

description: Library name: Sample 7

value: IFN-g


title: brincidofovir treated, replicate 8

description: NanoString Mouse Immunology Panel

value: brincidofovir treated


title: Patient GHD45-Visit-2 [EB_45_V2C]

description:
Library name: EB_45_V2C
Patient GHD45-Visit-2

value: skeletal muscle

value: after 12 months of supervised, resistance-based muscle therapy


title: brincidofovir and anti-PD1 treated, replicate 1

description: NanoString Mouse Immunology Panel

value: EL4 cell-line derived tumors engrafted on C57BL6N mice


title: VVA10_H1N2_CTL_N3

description: Library name: Sample 10


title: Non-Tg miR34a-/- [B-2]


title: VVA6_H1N2_CTL_N2

description: Library name: Sample 6


title: brincidofovir and anti-PD1 treated, replicate 2

description: NanoString Mouse Immunology Panel


title: brincidofovir and anti-PD1 treated, replicate 4

description: NanoString Mouse Immunology Panel


title: Patient GHD45-Visit-2 [EB_45_V2B]

description:
Library name: EB_45_V2B
Patient GHD45-Visit-2


title: VVA5_H1WT_CTL_N2

description: Library name: Sample 5


title: Patient GHD58-Visit-1 [EB_58_V1B]

description:
Library name: EB_58_V1B
Patient GHD58-Visit-1


title: Non-Tg miR34a+/+ [A-7]

value: Non-Tg miR34a+/+


title: VVA8_H1N2_Cyto_N2

description: Library name: Sample 8

value: Stem cells


title: brincidofovir treated, replicate 9

description: NanoString Mouse Immunology Panel


title: brincidofovir treated, replicate 6

description: NanoString Mouse Immunology Panel


title: brincidofovir treated, replicate 7

description: NanoString Mouse Immunology Panel


title: Non-Tg miR34a-/- [B-4]


title: Non-Tg miR34a+/+ [A-6]


title: Patient GHD42-Visit-2 [EB_42_V2B]

description:
Library name: EB_42_V2B
Patient GHD42-Visit-2


title: Patient GHD45-Visit-1 [EB_45_V1C]

description:
Library name: EB_45_V1C
Patient GHD45-Visit-1


title: VVA2_H1N2_CTL_N1

description: Library name: Sample 2

value: PTPN2 KO


title: Patient GHD45-Visit-1 [EB_45_V1B]

description:
Library name: EB_45_V1B
Patient GHD45-Visit-1


title: Non-Tg miR34a+/+ [A-4]


title: VVA3_H1WT_Cyto_N1

description: Library name: Sample 3


title: Non-Tg miR34a-/- [B-1]

value: Non-Tg miR34a-/-


title: Patient GHD42-Visit-1 [EB_42_V1C]

description:
Library name: EB_42_V1C
Patient GHD42-Visit-1


title: Patient GHD42-Visit-2 [EB_42_V2A]

description:
Library name: EB_42_V2A
Patient GHD42-Visit-2


title: brincidofovir treated, replicate 3

description: NanoString Mouse Immunology Panel


title: brincidofovir treated, replicate 4

description: NanoString Mouse Immunology Panel


title: VVA1_H1WT_CTL_N1

description: Library name: Sample 1


title: VVA4_H1N2_Cyto_N1

description: Library name: Sample 4


title: brincidofovir treated, replicate 2

description: NanoString Mouse Immunology Panel


title: GeCas12a2_T_PFS_Screen

city: Salt Lake City

first: Emily

middle: Rose

last: Wilson

state: UT

address: 2000 Circle of Hope

department: Oncological Sciences

institute: Huntsman Cancer Institute

description: Library name: GeCas12a2 target PFS Screen

library_source: other

data_processing:
Trimmomatic v0.39 (parameters: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10, LEADING:3, TRAILING:3, SLIDINGWINDOW:4:15)
BBMerge 38.97 (qtrim=t trimq=10 minlength=20)
Motifs matching TTCCTTCAGGTGTTGCTCCA (.....) GGTGAGTTCT were extracted
Excluded sequences with N bases or Phred scores <20
depletion = sum(non-target)/sum(target) x count(target)/count(non-target)
Supplementary files format and content: csv: sequence counts
Library strategy: CRISPR Screen

molecule: other

organism: Escherichia coli

source_name: Liquid culture

growth_protocol: 37C in LB medium containing 0.1 mM IPTG and 0.2% L-arabinose

extract_protocol:
Plasmids were purified with ZymoPURE II Plasmid Midiprep Kit
PCR amplification KAPA HIFI HotStart polymerase, 20 cycles 64.5°C

treatment_protocol: Centrifugation at 4,000 g for 15 min

value: Liquid culture


title: Patient GHD35-Visit-2 [EB_35_V2A]

description:
Library name: EB_35_V2A
Patient GHD35-Visit-2


title: Patient GHD35-Visit-2 [EB_35_V2C]

description:
Library name: EB_35_V2C
Patient GHD35-Visit-2


title: GeCas12a2_NT_PFS_Screen

description: Library name: GeCas12a2 non-target PFS Screen


title: Patient GHD35-Visit-1 [EB_35_V1C]

description:
Library name: EB_35_V1C
Patient GHD35-Visit-1


title: brincidofovir treated, replicate 1

description: NanoString Mouse Immunology Panel


title: Whole blood, healthy control 6

city: Westmead

first: Nader

last: Aryamanesh

state: NSW

address: 214 Hawkesbury Rd

department: Bioinformatics

country: Australia

institute: CMRI

description: Library name: Control_6

data_processing:
RNA-Seq raw fastq files were quality checked by FastQC (version 0.11.9), and trimming of adapters and quality filtering were then performed by AdapterRemoval (version 2.3.2). Trimmed and quality filtered paired-end reads were aligned to the human GRCh38 reference genome by using STAR (version 2.7.9a) with default parameters. Gene expression was quantified by counting the number of reads aligned to each Ensembl gene model using featureCounts (version 2.0.1).
Assembly: Human hg38
Supplementary files format and content: tsv file for read count matrix from the same samples.

source_name: Whole blood

growth_protocol: Stored at -80 degrees.

extract_protocol:
This workflow includes RNA extraction from PAXgene™ blood RNA tubes, depletion of ribosomal RNA via hybrid capture (Illumina Ribo-Zero), and Illumina TruSeq Stranded Total RNA Library Preparation (input 200-1000 ng of Total RNA). The stranded RNA samples are sequenced on the Illumina NovaSeq 6000 next generation sequencing platform (2 x 150 base pair) for a depth of 50 million paired end reads. The cleaned sequence reads were aligned against the Homo sapiens genome (Build version hg38), and the STAR aligner (v2.5.3a) was used to map unique reads to the genomic sequences14.
FASTQ files were processed into gene and transcript counts

treatment_protocol: Whole blood stored at -80 degrees within 1 hour of collection.

value: Whole blood

tag: age

value: Control

tag: Sex

value: F


title: sperm, BPA lineage, male, f0 generation, biol rep2

city: Columbia

first: Ramji

last: Bhandari

state: MO

address: 1200 University Ave

department: Division of Biological Sciences

institute: University of Missouri

description: Library name: BPA lineage, f0 generation, sperm 2

data_processing:
The “nf-core/methylseq” (v1.6.1) automated bioinformatic pipeline for Methylation (Bisulfite) sequencing data was used to analyze all the samples. In particular, the “nf-core/methylseq” pipeline's "Bismark workflow" was used to align the reads on the medaka genome (assembly ASM223467v1).
The Bismark coverage files of each individual sample, which describe the methylation percentages and overall coverages of methylated and unmethylated cytosines at each CpG location, were collected for further downstream analyses using methylKit R package. The samples of all the generations (f0, f1 and f2) were processed in the same way.
Assembly: ASM223467v1
Supplementary files format and content: Bismark Coverage file (*.bismark.cov.gz) for each sample

organism: Oryzias latipes

source_name: sperm

extract_protocol:
DNA was extracted by using Quick-DNA Microprep Kit following manufacturer's protocol
DNA library was prepared by using NEBNext® Ultra™ II FS DNA Library Prep Kit for Illumina following manufacturer's protocol

value: sperm

tag: generation

value: male

value: with BPA in f0 generation


title: N2

city: Calgary

first: Tatiana

last: Maroilley

state: Alberta

address: Tarailo-Graovac

country: Canada

institute: University of Calgary

description: Library name: N2

data_processing:
Trimmomatic for adapters removal and trimming
STAR for alignment and quantification
Assembly: ce11
Supplementary files format and content: counts files (tsv)

organism: Caenorhabditis elegans

source_name: whole organism

extract_protocol:
Trizol-chloroform based RNA extraction protocol followed by in-column DNAse treatment ZYMO Research RNA Clean and Concentrato kit
Ribosomal RNA depletion

tag: tissue

value: whole organism


title: Non-Tg miR34a+/+ [A-2]

value: Mouse hippocampus


title: Non-Tg miR34a+/+ [A-3]


title: Whole blood, healthy control 7

description: Library name: Control_7

value: M


title: sperm, BPA lineage, male, f0 generation, biol rep1

description: Library name: BPA lineage, f0 generation, sperm 1


title: Whole blood, healthy control 5

description: Library name: Control_5


title: Patient GHD35-Visit-1 [EB_35_V1A]

description:
Library name: EB_35_V1A
Patient GHD35-Visit-1

value: skeletal muscle

value: before 12 months of supervised, resistance-based muscle therapy


title: BC986

description: Library name: BC986


title: sperm, BPA lineage, male, f0 generation, biol rep3

description: Library name: BPA lineage, f0 generation, sperm 3


title: Whole blood, healthy control 3

description: Library name: Control_3


title: Patient GHD42-Visit-1 [EB_42_V1B]

description:
Library name: EB_42_V1B
Patient GHD42-Visit-1


title: Patient GHD28-Visit-2 [EB_28_V2C]

description:
Library name: EB_28_V2C
Patient GHD28-Visit-2

value: after 12 months of supervised, resistance-based muscle therapy


title: sperm, control lineage, male, f0 generation, biol rep3

description: Library name: Control lineage, f0 generation, sperm 3

value: control