title: Fungus cells, Wildtype, Avicel medium, rep2

city: Auckland

first: Yapeng

last: Lai

address: 55 Wellesley Street East,  Auckland Central

department: School of Science

country: New Zealand

institute: Auckland University of Technology

description: Library name: WT_2

data_processing:
Raw reads containing adapters or low quality bases  were further filtered by fastp (version 0.18.0). An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Gene differential expression analysis was performed by DESeq2 software between two different groups.
Assembly: The Reference genome is ASM22609v1
Supplementary files format and content: xlsx file includes FPKM values for each sample

organism: Thermothelomyces thermophilus ATCC 42464

source_name: Fungus cells

growth_protocol: For analysis of MtClr-2-specific transcriptomes, conidia from the wild type (WT) and ΔMtclr-2 strains of M. thermophila were pre-grown in liquid glucose medium, and then transferred the washed mycelia into liquid medium containing 2% (w/v) Avicel as the carbon source for 48 h.

extract_protocol:
Total fungal RNAs were extracted from fresh mycelia harvested from 2% (w/v) Avicel media through vacuum filtration.Total RNAs were isolated using an RNA extraction kit TransZol Up (TransGen Biotech, Beijing, China) following the manufacturer’s protocols, and RNA extracts were assessed by electrophoresis and quantified using the NanoDrop 2000 Spectrophotometer (Thermo Scientific, Waltham, MA, USA).
After total RNA was obtained, the mRNA for each sample was enriched by Oligo (dT) beads and reversely transcribed into cDNA via the aid of NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich, MA, USA).

tag: cell type

value: Fungus cells

value: WT


title: 4DM1F1LU_S49

status: Public on Jun 01 2026

type: SRA

city: Durham

first: Scott

last: Auerbach

state: NC

address: 111 TW Alexander Drive

country: USA

institute: Division of the National Toxicology Program at NIEHS

description: Library name: 4DM1F1LU_S49_R1_001

library_source: transcriptomic

data_processing:
TempO-Seq sequences were aligned to the rat S1500+ probe sequences using Bowtie version 1.3.1. The Bowtie configuration allowed up to three mismatches and selected the single best alignment for reporting.
The aligned read counts for attenuated probes were properly readjusted to calculate unattenuated equivalent counts using the attenuation factors provided in the platform manifest.
Assembly: BioSpyder TempO-seq mouse S1500+ manifest
Supplementary files format and content: tab-delimited text file includes attenuation-adjusted raw probe counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Lung

extract_protocol:
The majority of all tissues from all animals were collected within approximately 10 minutes of euthanasia. Tissue samples were collected following organ weight measurements in the following order: lung, heart, liver (left lobe), kidney, and ovary (no ovary weights were taken) from all remaining animals on study day 5 for transcriptomic analysis. Two samples of lung, heart, liver, and kidney tissue (approximately 5 mm3) were collected and placed into cryotubes containing RNAlater. The ovaries were collected whole bilaterally (one sample) and placed into cryotubes containing RNAlater. The tissue samples were stored at 2°C to 8°C for approximately 55 hours for rats or up to 48 hours for mice. The RNAlater was then removed and the samples were stored in a −85°C to −60°C freezer until processed for RNA isolation. Tissues were homogenized in QIAzol lysis buffer (Qiagen Inc., Valencia, CA) using the TissueLyser II bead-beating system followed by RNA extraction using the RNeasy 96 QIAcube HT kits (Qiagen Inc., Valencia, CA) with a DNA digestion step.
Isolated RNA was utilized for analysis using either the Mouse S1500+ v1.2 TempO-Seq (BioSpyder, Carlsbad, CA) platform with a minimum of 500 mapped read counts/transcript and approximately 1.5 million counts/sample. Work instructions developed by Battelle using the BioSpyder User Guide (https://www.biospyder.com/s/100802-TempO-Seq-User-Guide-rev-C-r8r7.pdf) were followed.

tag: tissue

value: Lung

tag: cell line

value: B6D2F1/Crl (BDF-1)

tag: Sex

value: female

tag: age

value: 9 weeks

tag: treatment

tag: concentration (ppm)

tag: animal id

tag: sample status

value: Used in Analysis

tag: qc issue


title: scRNA-seq_WT_rep1

city: San Antonio

first: Ying

last: Guo

state: Texas

address: 8403 Floyd Curl Dr

institute: UT Health Science Center at San Antonio

data_processing:
Sequencing results from 10x Genomics were demultiplexed and converted to FASTQ format by cellranger  with a parameter of mkfastq
The FASTQ data was aligned to mouse reference genome and quantified using cellranger with default parameters
Assembly: mm10
Supplementary files format and content: h5 files of filtered counts for all genes in each cell

source_name: Bone marrow

extract_protocol:
The libraries for each single cell sample were prepared using the Chromium Single Cell Gene Expression 3’ Version 3.1 Kit (10X Genomics) with the Chromium Controller.
single-cell RNA-seq

treatment_protocol: The Lineage-cKit+ cells were purified from mouse bone marrow cells using BD FACSAria II

value: Lin-cKit+ bone marrow cells

tag: strain

tag: genotype

value: wild type


title: Fungus cells, Deletion_MtClr-2, Avicel medium, rep3

description: Library name: Deletion_MtClr-2_3

value: MtClr-2 deletion


title: Fungus cells, Wildtype, Avicel medium, rep3

description: Library name: WT_3


title: Fungus cells, Deletion_MtClr-2, Avicel medium, rep2

description: Library name: Deletion_MtClr-2_2


title: Fungus cells, Deletion_MtClr-2, Avicel medium, rep1

description: Library name: Deletion_MtClr-2_1


title: 4DM1F1KI_S43

description: Library name: 4DM1F1KI_S43_R1_001

source_name: Kidney

value: Kidney

value: Not Used in Analysis

value: Potential Tissue Contamination


title: Fungus cells, Wildtype, Avicel medium, rep1

description: Library name: WT_1


title: 4DM1F1HE_S43

description: Library name: 4DM1F1HE_S43_R1_001

source_name: Heart

value: Heart


title: 4DM1F10OV_S125

description: Library name: 4DM1F10OV_S125_R1_001

source_name: Ovary

value: Ovary


title: 4DM1F10LU_S43

description: Library name: 4DM1F10LU_S43_R1_001


title: 4DM1F10HE_S72

description: Library name: 4DM1F10HE_S72_R1_001


title: 2DM6F508OV_S92

description: Library name: 2DM6F508OV_S92_R1_001


title: 4DM1F10LI_S43

description: Library name: 4DM1F10LI_S43_R1_001

source_name: Liver Left Lobe

value: Liver Left Lobe


title: 4DM1F10KI_S72

description: Library name: 4DM1F10KI_S72_R1_001


title: 2DM6F508LU_S10

description: Library name: 2DM6F508LU_S10_R1_001


title: 2DM6F508KI_S5

description: Library name: 2DM6F508KI_S5_R1_001


title: Exp9-Patient-PBMC-BM-1000000000362318-APC-PE-negative-G5, scTCR

city: Houston

first: Jeffrey

middle: J

last: Molldrem

state: United States

address: 7435 Fannin St

department: Hematopoietic Biology & Malignancy

institute: MD Anderson Cancer Center

description: Library name: Exp9-Patient-PBMC-BM-1000000000362318-APC-PE-negative-G5-scTCR

library_source: other

data_processing:
Raw fastq files are processed by 10X CellRanger Single Cell software suite v7.0 against reference data refdata-gex-GRCh38-2020-A for scFB samples, and refdata-cellranger-vdj-GRCh38-alts-ensembl-7.0.0 for scTCR samples, with default parameters.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger Feature Barcode Matrices, MEX Format, for scFB data
Supplementary files format and content: Cell Ranger high-confidence, filtered V(D)J sequences, TSV text format, for scTCR data
Supplementary files format and content: FB.csv (feature barcode for CellRanger uses to analyze Feature Barcode (scFB) libraries), Tetramer.csv (duo feature barcodes for tetramer peptides in each scFB library), Hashtag.csv (demultiplexed patients in each scFB library)  and Dataset.csv (mapping table of dataset in paper and CITEseq Experiment like Exp# in GEO).
Library strategy: CITE-seq

molecule: other

organism: Homo sapiens

source_name: blood

extract_protocol:
Live, tetramer positive CD8 cells were sorted and run on 10X Genomics 5' Cell Immune Profiling workflow using manufacturer's instructions.
Sorted cells were loaded onto a lane of a Chromium Next GEM Chip G for GEM production using the Chromium Controller from 10X Genomics. GEM-RT, cDNA amplification and cleanup were performed using Chromium Single Cell V(D)J Reagent Kits User Guide (v1.1 Chemistry) with Feature Barcoding technology for Cell Surface Protein (RevG) workflow per 10X Genomics protocols.

value: blood

tag: sample group


title: 2DM6F508HE_S5

description: Library name: 2DM6F508HE_S5_R1_001


title: Exp9-HD-PBMC-1000000000362318-APC-PE-negative-G8, scTCR

description: Library name: Exp9-HD-PBMC-1000000000362318-APC-PE-negative-G8-scTCR


title: Exp9-Patient-PBMC-BM-1000000000362318-APC-PE-negative-G5, scFB

description: Library name: Exp9-Patient-PBMC-BM-1000000000362318-APC-PE-negative-G5-scFB


title: 2DM6F508LI_S10

description: Library name: 2DM6F508LI_S10_R1_001


title: 2DM6F507OV_S95

description: Library name: 2DM6F507OV_S95_R1_001


title: Exp9-HD-PBMC-1000000000362318-APC-PE-negative-G8, scFB

description: Library name: Exp9-HD-PBMC-1000000000362318-APC-PE-negative-G8-scFB


title: Exp7-Patients-PBMC-BM-1000000000361926-Tet-Lo, scTCR

description: Library name: Exp7-Patients-PBMC-BM-1000000000361926-Tet-Lo-scTCR


title: 2DM6F507LU_S13

description: Library name: 2DM6F507LU_S13_R1_001


title: 2DM6F507LI_S13

description: Library name: 2DM6F507LI_S13_R1_001


title: Exp7-Patients-PBMC-BM-1000000000361926-Tet-Hi, scTCR

description: Library name: Exp7-Patients-PBMC-BM-1000000000361926-Tet-Hi-scTCR


title: 2DM6F507HE_S8

description: Library name: 2DM6F507HE_S8_R1_001


title: Exp7-Patients-PBMC-BM-1000000000361926-Tet-Lo, scFB

description: Library name: Exp7-Patients-PBMC-BM-1000000000361926-Tet-Lo-scFB


title: Exp7-Patients-PBMC-BM-1000000000361926-Tet-Hi, scFB

description: Library name: Exp7-Patients-PBMC-BM-1000000000361926-Tet-Hi-scFB


title: 2DM6F507KI_S8

description: Library name: 2DM6F507KI_S8_R1_001


title: 2DM6F506ROV_S99

description: Library name: 2DM6F506ROV_S99_R1_001


title: Exp7-Patients-PBMC-BM-1000000000361926-CD8-Bulk, scTCR

description: Library name: Exp7-Patients-PBMC-BM-1000000000361926-CD8-Bulk-scTCR


title: 2DM6F506RLI_S17

description: Library name: 2DM6F506RLI_S17_R1_001


title: Exp7-Patients-PBMC-BM-1000000000361926-CD8-Bulk, scFB

description: Library name: Exp7-Patients-PBMC-BM-1000000000361926-CD8-Bulk-scFB


title: 2DM6F506RLU_S17

description: Library name: 2DM6F506RLU_S17_R1_001


title: Exp6-Patients-PBMC-BM-1000000000361921-Tet-High, scTCR

description: Library name: Exp6-Patients-PBMC-BM-1000000000361921-Tet-High-scTCR


title: 2DM6F506RKI_S12

description: Library name: 2DM6F506RKI_S12_R1_001


title: Exp6-Patients-PBMC-BM-1000000000361921-Tet-High, scFB

description: Library name: Exp6-Patients-PBMC-BM-1000000000361921-Tet-High-scFB


title: Exp6-Patients-PBMC-BM-1000000000361921-Tet-Dim, scTCR

description: Library name: Exp6-Patients-PBMC-BM-1000000000361921-Tet-Dim-scTCR


title: 2DM6F506RHE_S12

description: Library name: 2DM6F506RHE_S12_R1_001


title: 2DM6F505OV_S106

description: Library name: 2DM6F505OV_S106_R1_001


title: 2DM6F505LU_S24

description: Library name: 2DM6F505LU_S24_R1_001

value: TOTAL ALIGNMENT RATE < 40%


title: Exp5-Patients-PBMC-BM-1000000000361918-Tet-Positive, scTCR

description: Library name: Exp5-Patients-PBMC-BM-1000000000361918-Tet-Positive-scTCR


title: Exp6-Patients-PBMC-BM-1000000000361921-Tet-Dim, scFB

description: Library name: Exp6-Patients-PBMC-BM-1000000000361921-Tet-Dim-scFB


title: 2DM6F505KI_S19

description: Library name: 2DM6F505KI_S19_R1_001


title: Exp5-Patients-PBMC-BM-1000000000361918-Tet-Positive, scFB

description: Library name: Exp5-Patients-PBMC-BM-1000000000361918-Tet-Positive-scFB


title: 2DM6F505HE_S19

description: Library name: 2DM6F505HE_S19_R1_001


title: 2DM6F505LI_S24

description: Library name: 2DM6F505LI_S24_R1_001


title: Exp4-HD-PBMC-1000000000361864-Tet-Positive, scTCR

description: Library name: Exp4-HD-PBMC-1000000000361864-Tet-Positive-scTCR


title: Exp4-Patients-PBMC-BM-1000000000361864-Tet-Positive, scFB

description: Library name: Exp4-Patients-PBMC-BM-1000000000361864-Tet-Positive-scFB


title: 2DM6F504OV_S111

description: Library name: 2DM6F504OV_S111_R1_001


title: Exp4-Patients-PBMC-BM-1000000000361864-Tet-Positive, scTCR

description: Library name: Exp4-Patients-PBMC-BM-1000000000361864-Tet-Positive-scTCR


title: 2DM6F504LU_S29

description: Library name: 2DM6F504LU_S29_R1_001


title: Exp4-HD-PBMC-1000000000361864-Tet-Positive, scFB

description: Library name: Exp4-HD-PBMC-1000000000361864-Tet-Positive-scFB


title: 4DM1F2OV_S154

description: Library name: 4DM1F2OV_S154_R1_001


title: scRNA-seq_Phf6 Tg_rep1

value: Phf6R274X Tg


title: 2DM6F504LI_S29

description: Library name: 2DM6F504LI_S29_R1_001

value: SEQ DEPTH < 300000


title: Exp3-S5, scTCR

description: Library name: Exp3-S5-scTCR


title: 2DM6F504KI_S24

description: Library name: 2DM6F504KI_S24_R1_001

value: B6D2F1/Crl (BDF-1)


title: 2DM6F504HE_S24

description: Library name: 2DM6F504HE_S24_R1_001

value: female


title: 2DM6F503OV_S90

description: Library name: 2DM6F503OV_S90_R1_001

value: 9 weeks


title: Exp3-S5, scFB

description: Library name: Exp3-S5-scFB


title: Dpp9-CSPL

city: NEW HAVEN

first: Tianli

last: Xiao

state: Connecticut

address: 1 Gilbert street, TAC S570

department: Immunobiology

institute: Yale University

description: Library name: Dpp9-CSPL

library_source: transcriptomic single cell

data_processing:
Raw FASTQ files were aligned to the human reference genome GRCh38-3.0.0 using the 10x Genomics CellRanger v7.1.0 pipeline. Samples were demultiplexed based on hashtag antibodies: WT cells were labeled with TotalSeq™-B0251 anti-human Hashtag 1 antibody, and KO cells were labeled with TotalSeq™-B0252 anti-human Hashtag 2 antibody (Biolegend).
Assembly: GRCh38-3.0.0
Supplementary files format and content: CellRanger output files: feature_reference.csv, *barcodes.tsv.gz,*features.tsv.gz,*matrix.mtx.gz

source_name: bone marrow

extract_protocol:
The femur is surgically isolated and single-cell suspension of bone marrow cells are obtained through crushing the femur with a mortar and pestle and suspended in FACS buffer (PBS +2% FBS). Human CD45+ cells expressing CD34 and negative for lineage markers (CD3, CD14, CD16, CD19, CD20, CD56) and negative for mouse CD45 and mouse C-KIT are sorted on Bigfoot Spectral cell sorter. Control and DPP9KO cells are hashtagged separately and then pooled.
10,000 cells were encapsulated into droplets using 10x Chromium GEM technology. Libraries were prepared in house using the Chromium Next GEM Single Cell 3′ Reagent Kits v.3.1 with 3' feature barcode kit (10x Genomics). scRNA-seq libraries were sequenced using the Nova-Seq system (Illumina).

treatment_protocol: transplantation in MISTRG6 mice

value: bone marrow

value: Lin- CD34+ hematopoietic stem and progenitor cells

value: transplantation in MISTRG6 mice

tag: library type

value: cell surface protein library

tag: hashtag

value: WT:TotalSeq™-B0251 anti-human Hashtag 1 Antibody, KO:TotalSeq™-B0252 anti-human Hashtag 2 Antibody


title: Dpp9-GEX

description: Library name: Dpp9-GEX

value: gene expression library


title: 2DM6F503LU_S8

description: Library name: 2DM6F503LU_S8_R1_001

value: Lung

value: Used in Analysis


title: 2DM6F503LI_S8

description: Library name: 2DM6F503LI_S8_R1_001


title: 2DM6F503KI_S3

description: Library name: 2DM6F503KI_S3_R1_001

value: Kidney


title: ARPE-19 – Control 8h NEW (biol rep 1) [TRR-B1]

city: Messina

first: Luigi

last: Donato

state: Italy

address: via Consolare Valeria, 1

department: BIOMORF

country: Italy

institute: University of Messina

description:
Library name: ARPE19_CTRL_8h_NEW_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=8h; OX=No; Rep1; sequencing batch=TRR_Batch1.

data_processing:
Raw reads were quality-checked with FastQC (v0.11.9) and trimmed for adapter sequences and low-quality bases using Trimmomatic (v0.39; ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
High-quality reads were aligned to the Homo sapiens reference genome (GRCh38/hg38, Ensembl release 109) using STAR (v2.7.10a) with chimeric alignment enabled (--chimSegmentMin 10 --chimOutType Junctions SeparateSAMold) for back-splice junction detection.
Circular RNA candidates were identified from chimeric alignments using CIRI2 (v2.0.6) and/or find_circ (v1.2). Back-splice junctions supported by ≥2 reads were retained. Candidates were classified into confidence tiers (Tier 1–3) based on read support, annotation overlap, and cross-batch reproducibility.
Linear gene expression quantification was performed using featureCounts (Subread v2.0.3) on STAR-aligned BAM files against Ensembl GRCh38 release 109 GTF annotation.
Differential expression analysis of linear transcripts was carried out using DESeq2 (v1.38.0) in R (v4.2.2). Circular RNA differential expression was assessed using a negative binomial model on back-splice read counts, correcting for sequencing depth. Adjusted p-value threshold: FDR < 0.05; |log2FC| > 1.
Pathway and gene ontology (GO) enrichment analyses were performed using clusterProfiler (v4.6.0) and ReactomePA (v1.42.0) in R. circRNA–miRNA–mRNA interaction networks were constructed using miRanda and TargetScan predictions.
Assembly: Homo sapiens GRCh38 (hg38), Ensembl release 109
Supplementary files format and content: chimeric_events_tier3_all_samples.csv: rows = circular RNA loci (chr:start:end:strand); columns = samples; values = back-splice junction read counts (BSJ). Includes annotation columns: gene name, circBase ID (if available), confidence tier, genomic coordinates (GRCh38).
Supplementary files format and content: linear_counts_matrix.csv: rows = genes (Gene_name, Gene_ID); columns = 74 GEO library names; values = featureCounts-derived gene-level abundance values after downstream processing (non-integer values).

growth_protocol: ARPE-19 human retinal pigment epithelial cells (ATCC CRL-2302) were maintained in DMEM/F-12 (1:1) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin/streptomycin at 37°C in a humidified atmosphere of 5% CO2. Cells were seeded at 2×10⁵ cells/well in 6-well plates and allowed to reach 70–80% confluency before treatment.

extract_protocol:
Cells were lysed directly in culture wells using TRIzol Reagent (Thermo Fisher Scientific). Total RNA was extracted according to the manufacturer's protocol, including chloroform phase separation and isopropanol precipitation. RNA pellets were washed with 75% ethanol, air-dried, and resuspended in RNase-free water. RNA quality and quantity were assessed using an Agilent 2100 Bioanalyzer and NanoDrop 2000 spectrophotometer; samples with RNA Integrity Number (RIN) ≥ 7 were used for library preparation.
RNA-seq libraries were constructed from total RNA using a ribosomal RNA depletion strategy (Ribo-Zero Plus, Illumina) to preserve both polyadenylated and non-polyadenylated transcripts, including circular RNAs. Depleted RNA was fragmented, reverse-transcribed to cDNA, end-repaired, A-tailed, ligated to indexed adapters, and PCR-amplified following the manufacturer's protocol. Library quality was verified on an Agilent Bioanalyzer High Sensitivity DNA chip; libraries were pooled equimolarly and sequenced on an Illumina NovaSeq platform with paired-end 150 bp reads.

treatment_protocol: Oxidative stress was induced by exposing ARPE-19 cells to H2O2 (400 µM, 1 h), followed by replacement with fresh medium. QMR (Quantum Molecular Resonance) electromagnetic stimulation was delivered using a dedicated device (Tecar Winback; 4 MHz carrier, 3-min sessions) immediately after H2O2 washout. Secretome (conditioned medium) was obtained from MSC cultures and applied at 30% v/v. For combined rescue (QMR + Secretome), both treatments were applied simultaneously. Cells were harvested at 8 h, 24 h, and 72 h after the oxidative challenge. Control cells received no H2O2 and no therapeutic treatment.

value: Retinal Pigment Epithelium

value: no oxidative stress; untreated (NEW medium)


title: ARPE-19 – Secretome + Oxidative Stress 72h (biol rep 2) [WGB-B2]

description:
Library name: ARPE19_SEC_72h_OX_Rep2_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.

value: H2O2 400 µM (oxidative stress); Secretome (conditioned medium)


title: ARPE-19 – Secretome + Oxidative Stress 72h (biol rep 1) [WGB-B2]

description:
Library name: ARPE19_SEC_72h_OX_Rep1_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.


title: 2DM6F503HE_S3

description: Library name: 2DM6F503HE_S3_R1_001

value: Heart


title: ARPE-19 – Secretome + Oxidative Stress 24h (biol rep 2) [WGB-B2]

description:
Library name: ARPE19_SEC_24h_OX_Rep2_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.


title: ARPE-19 – Secretome + Oxidative Stress 24h (biol rep 1) [WGB-B2]

description:
Library name: ARPE19_SEC_24h_OX_Rep1_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.


title: 2DM6F501OV_S115

description: Library name: 2DM6F501OV_S115_R1_001

value: Ovary


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 72h (biol rep 2) [WGB-B2]

description:
Library name: ARPE19_RESSEC_72h_OX_Rep2_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation + Secretome (conditioned medium)


title: 2DM6F501LU_S33

description: Library name: 2DM6F501LU_S33_R1_001

value: B6D2F1/Crl (BDF-1)

value: female


title: 2DM6F501LI_S33

description: Library name: 2DM6F501LI_S33_R1_001

value: Liver Left Lobe

value: 9 weeks


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 72h (biol rep 1) [WGB-B2]

description:
Library name: ARPE19_RESSEC_72h_OX_Rep1_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.


title: 2DM6F501KI_S28

description: Library name: 2DM6F501KI_S28_R1_001

value: Not Used in Analysis

value: Potential Tissue Contamination


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 24h (biol rep 2) [WGB-B2]

description:
Library name: ARPE19_RESSEC_24h_OX_Rep2_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 24h (biol rep 1) [WGB-B2]

description:
Library name: ARPE19_RESSEC_24h_OX_Rep1_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.


title: 2DM6F501HE_S28

description: Library name: 2DM6F501HE_S28_R1_001


title: 2DM5F405OV_S97

description: Library name: 2DM5F405OV_S97_R1_001


title: 2DM5F405LU_S15

description: Library name: 2DM5F405LU_S15_R1_001


title: ARPE-19 – QMR Rescue + Oxidative Stress 72h (biol rep 1) [WGB-B2]

description:
Library name: ARPE19_RES_72h_OX_Rep1_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation


title: ARPE-19 – QMR Rescue + Oxidative Stress 72h (biol rep 2) [WGB-B2]

description:
Library name: ARPE19_RES_72h_OX_Rep2_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.


title: ARPE-19 – QMR Rescue + Oxidative Stress 24h (biol rep 2) [WGB-B2]

description:
Library name: ARPE19_RES_24h_OX_Rep2_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.


title: ARPE-19 – QMR Rescue + Oxidative Stress 24h (biol rep 1) [WGB-B2]

description:
Library name: ARPE19_RES_24h_OX_Rep1_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.


title: ARPE-19 – Control + Oxidative Stress 72h (biol rep 2) [WGB-B2]

description:
Library name: ARPE19_CTRL_72h_OX_Rep2_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.

value: H2O2 400 µM (oxidative stress); untreated


title: 2DM5F404OV_S87

description: Library name: 2DM5F404OV_S87_R1_001


title: ARPE-19 – Control + Oxidative Stress 72h (biol rep 1) [WGB-B2]

description:
Library name: ARPE19_CTRL_72h_OX_Rep1_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.


title: 2DM5F404LU_S5

description: Library name: 2DM5F404LU_S5_R1_001

value: Lung


title: ARPE-19 – Control + Oxidative Stress 24h (biol rep 1) [WGB-B2]

description:
Library name: ARPE19_CTRL_24h_OX_Rep1_WGB_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch2.


title: ARPE-19 – Secretome 72h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_SEC_72h_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=No; Rep1; sequencing batch=TRR_Batch2.

value: no oxidative stress; Secretome (conditioned medium)


title: 2DM5F404KI_S37

description: Library name: 2DM5F404KI_S37_R1_001

value: Kidney

value: Used in Analysis


title: ARPE-19 – Secretome 72h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_SEC_72h_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=No; Rep1; sequencing batch=TRR_Batch2.

value: Retinal Pigment Epithelium


title: ARPE-19 – Secretome + Oxidative Stress 72h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_SEC_72h_OX_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.

value: H2O2 400 µM (oxidative stress); Secretome (conditioned medium)


title: 2DM5F404HE_S37

description: Library name: 2DM5F404HE_S37_R1_001

value: Heart


title: 2DM5F403OV_S107

description: Library name: 2DM5F403OV_S107_R1_001

value: Ovary


title: ARPE-19 – Secretome + Oxidative Stress 72h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_SEC_72h_OX_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.


title: 2DM5F403LU_S25

description: Library name: 2DM5F403LU_S25_R1_001


title: ARPE-19 – Secretome 24h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_SEC_24h_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=24h; OX=No; Rep1; sequencing batch=TRR_Batch2.


title: 2DM5F403LI_S25

description: Library name: 2DM5F403LI_S25_R1_001


title: 2DM5F403KI_S20

description: Library name: 2DM5F403KI_S20_R1_001

value: Outlier based on PCA/correlation


title: ARPE-19 – Secretome 24h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_SEC_24h_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=24h; OX=No; Rep1; sequencing batch=TRR_Batch2.


title: 2DM5F403HE_S20

description: Library name: 2DM5F403HE_S20_R1_001

value: B6D2F1/Crl (BDF-1)


title: ARPE-19 – Secretome + Oxidative Stress 24h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_SEC_24h_OX_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=24h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.


title: ARPE-19 – Secretome + Oxidative Stress 24h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_SEC_24h_OX_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=24h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.


title: ARPE-19 – QMR+Secretome Rescue 72h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_RESSEC_72h_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=No; Rep1; sequencing batch=TRR_Batch2.

value: no oxidative stress; QMR electromagnetic stimulation + Secretome (conditioned medium)


title: 2DM5F402OV_S84

description: Library name: 2DM5F402OV_S84_R1_001

value: female


title: ARPE-19 – QMR+Secretome Rescue 72h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_RESSEC_72h_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=No; Rep1; sequencing batch=TRR_Batch2.


title: 2DM5F402LU_S2

description: Library name: 2DM5F402LU_S2_R1_001

value: 9 weeks


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 72h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_RESSEC_72h_OX_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation + Secretome (conditioned medium)


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 72h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_RESSEC_72h_OX_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.


title: 2DM5F402HE_S34

description: Library name: 2DM5F402HE_S34_R1_001


title: ARPE-19 – QMR+Secretome Rescue 24h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_RESSEC_24h_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=24h; OX=No; Rep1; sequencing batch=TRR_Batch2.


title: 2DM5F401OV_S116

description: Library name: 2DM5F401OV_S116_R1_001


title: 2DM5F401LU_S34

description: Library name: 2DM5F401LU_S34_R1_001


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 24h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_RESSEC_24h_OX_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.


title: 2DM5F401KI_S29

description: Library name: 2DM5F401KI_S29_R1_001

value: Not Used in Analysis

value: Potential Tissue Contamination


title: 2DM5F401LI_S34

description: Library name: 2DM5F401LI_S34_R1_001

value: Liver Left Lobe


title: ARPE-19 – QMR Rescue 72h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_RES_72h_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=No; Rep1; sequencing batch=TRR_Batch2.

value: no oxidative stress; QMR electromagnetic stimulation


title: 2DM5F401HE_S29

description: Library name: 2DM5F401HE_S29_R1_001


title: ARPE-19 – QMR Rescue 72h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_RES_72h_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=No; Rep1; sequencing batch=TRR_Batch2.


title: 2DM4F305OV_S91

description: Library name: 2DM4F305OV_S91_R1_001


title: ARPE-19 – QMR Rescue + Oxidative Stress 72h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_RES_72h_OX_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation


title: 2DM4F305LU_S9

description: Library name: 2DM4F305LU_S9_R1_001

value: Lung


title: ARPE-19 – QMR Rescue + Oxidative Stress 72h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_RES_72h_OX_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.


title: ARPE-19 – QMR Rescue 24h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_RES_24h_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=24h; OX=No; Rep1; sequencing batch=TRR_Batch2.


title: 2DM4F305LI_S9

description: Library name: 2DM4F305LI_S9_R1_001

value: Used in Analysis


title: ARPE-19 – QMR Rescue 24h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_RES_24h_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=24h; OX=No; Rep1; sequencing batch=TRR_Batch2.

value: Retinal Pigment Epithelium


title: ARPE-19 – QMR Rescue + Oxidative Stress 24h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_RES_24h_OX_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.


title: 2DM4F304OV_S86

description: Library name: 2DM4F304OV_S86_R1_001


title: NPC patient 45

type: RNA

city: Hong Kong

first: Huaping

last: Li

address: 21 Sassoon Rd, Pok Fu Lam

country: Hong Kong

institute: The University of Hong Kong

hyb_protocol: Gene expression profiling was performed using the Nanostring PanCancer Immune Profiling Panel and 20 additional custom designed gene probes,

scan_protocol: standard protocol

data_processing:
The Nanostring nCounter expression profiling is optimized for FFPE samples, around 800 genes were profiled.
data were normalized based on NanoString housekeeping probes and the geNorm algorithm using RosalindÂ® Software (https://rosalind.onramp.bio/). Fold-changes and p-values were calculated using the fast method as described in the nCounterÂ® Advanced Analysis 2.0 User Manual. P-value adjustment was performed using the Benjamini-Hochberg method of estimating false discovery rates (FDR).

label: oligonucleotide probe

source_name: locoregionally advanced NPC FFPE sample

label_protocol: Purity of End of expansion CAR-iNKT was >90%. No further label/purification step was required

extract_protocol: RNA was extracted using the RNeasy Plus Mini Kit (Qiagen) according to the manufacturer's instructions.

tag: gender

value: M

value: locoregionally advanced NPC FFPE sample


title: NPC patient 44

value: F


title: 2DM4F304LU_S4

description: Library name: 2DM4F304LU_S4_R1_001


title: NPC patient 43


title: NPC patient 42


title: 2DM5F405HE_S10

description: Library name: 2DM5F405HE_S10_R1_001

value: Heart


title: ARPE-19 – Control 72h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_CTRL_72h_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=No; Rep1; sequencing batch=TRR_Batch2.

value: no oxidative stress; untreated


title: 2DM4F304LI_S4

description: Library name: 2DM4F304LI_S4_R1_001

value: B6D2F1/Crl (BDF-1)


title: ARPE-19 – Control 72h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_CTRL_72h_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=No; Rep1; sequencing batch=TRR_Batch2.


title: 2DM4F304KI_S36

description: Library name: 2DM4F304KI_S36_R1_001

value: Kidney

value: female


title: NPC patient 39


title: ARPE-19 – Control + Oxidative Stress 72h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_CTRL_72h_OX_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.

value: H2O2 400 µM (oxidative stress); untreated


title: NPC patient 38


title: low blood glucose, high body weight at weaning, male, hypothalamus, replicate 2

status: Public on Jun 02 2026

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

data_processing:
The sequenced reads (raw reads) often contain low quality reads and adapters, which will affect the analysis quality. So it's necessary to filter the raw reads and get the clean reads. The filtering process is as follows: 1. Remove reads containing adapters. 2.  Remove reads containing N > 10% (N represents the base cannot be determined). 3. Remove reads containing low quality (Qscore<= 5) base which is over 50% of the total base.
Sequences of adaptors: 5' Adapter:   5'-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT-3'; 3' Adapter(The underlined 6bp bases is Index):  5'-GATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG-3'
Mapping with STAR version 2.7.6a
Gene-level read counts were obtained with summarizeOverlaps, mode = ’Union’, package GenomicAlignments v1.30.0
Normalization with DESeq2 (version 1.28.1)
Assembly: GRCm38.101
Supplementary files format and content: tab-delimited file with normalized linear counts. Tissues were normalized separately.

source_name: hypothalamus

growth_protocol: Male and female TallyHo/JngJ mice were housed in ventilated cages (SealsafePlus AERO IVC Greenline, Tecniplast) on a 12-h light/12-h dark cycle with ad libitum access to food and water. Room temperature was kept constant (22 +/- 1°C) and humidity (55%) was controlled. Mouse experiments were conducted in compliance with the Federation of European Laboratory Animal Science Association (FELASA) protocols. All mouse experiments were performed according to European Union directive 2010/63/EU and were approved by the responsible authorities of the government of Upper Bavaria.  Male TallyHo/JngJ mice were mated with one or two female TallyHo/JngJ mice for 5 – 7 days. Litter size adjustment or shifting of litters (pups of the same father were exchanged between mothers to achieve small or large litters) was performed within 48 hours after birth. Unless otherwise indicated, the animals for each experiment were bred in different time-shifted batches.

extract_protocol:
Total RNA (including miRNA and other small RNA molecules) was extracted from tissues (VAT, hypothalamus, liver, SAT, muscle) using the miRNeasy® Mini Kit (Qiagen), following the manufacturer’s instructions.
Directional mRNA library done by Novogene. mRNA from eukaryotic organisms is enriched using oligo(dT) beads. First, the mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, A ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

treatment_protocol: no

value: hypothalamus

value: TallyHo/JngJ

value: male

value: 18 weeks

tag: development stage

value: adult

tag: condition


title: 2DM4F304HE_S36

description: Library name: 2DM4F304HE_S36_R1_001

tag: tissue

value: 9 weeks


title: ARPE-19 – Control + Oxidative Stress 72h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_CTRL_72h_OX_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.

tag: cell line

tag: cell type


title: NPC patient 36

tag: age


title: 2DM4F303OV_S117

description: Library name: 2DM4F303OV_S117_R1_001

value: Ovary

tag: Sex

tag: treatment

value: Used in Analysis


title: NPC patient 35


title: ARPE-19 – Control 24h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_CTRL_24h_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=24h; OX=No; Rep1; sequencing batch=TRR_Batch2.

value: Retinal Pigment Epithelium


title: NPC patient 34

value: M

value: locoregionally advanced NPC FFPE sample


title: 2DM4F303LU_S35

description: Library name: 2DM4F303LU_S35_R1_001

value: Lung

tag: concentration (ppm)

tag: animal id


title: ARPE-19 – Control 24h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_CTRL_24h_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=24h; OX=No; Rep1; sequencing batch=TRR_Batch2.

value: no oxidative stress; untreated


title: NPC patient 32


title: 2DM4F303LI_S35

description: Library name: 2DM4F303LI_S35_R1_001

value: Liver Left Lobe

value: B6D2F1/Crl (BDF-1)

tag: sample status

tag: qc issue


title: NPC patient 31


title: NPC patient 30


title: ARPE-19 – Control + Oxidative Stress 24h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_CTRL_24h_OX_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=24h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.


title: NPC patient 29

value: F


title: 2DM4F303KI_S30

description: Library name: 2DM4F303KI_S30_R1_001

value: Kidney

value: female

value: Not Used in Analysis

value: Potential Tissue Contamination


title: NPC patient 28


title: ARPE-19 – Control + Oxidative Stress 24h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_CTRL_24h_OX_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=24h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.

value: H2O2 400 µM (oxidative stress); untreated


title: 2DM4F303HE_S30

description: Library name: 2DM4F303HE_S30_R1_001

value: Heart


title: NPC patient 27


title: NPC patient 26


title: ARPE-19 – Secretome + Oxidative Stress 72h (biol rep 3) [WGB-B1]

description:
Library name: ARPE19_SEC_72h_OX_Rep3_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.

value: H2O2 400 µM (oxidative stress); Secretome (conditioned medium)


title: NPC patient 25


title: NPC patient 24


title: ARPE-19 – Secretome 72h (biol rep 3) [WGB-B1]

description:
Library name: ARPE19_SEC_72h_Rep3_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=No; Rep1; sequencing batch=WGB_Batch1.

value: no oxidative stress; Secretome (conditioned medium)


title: NPC patient 23


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 72h (biol rep 3) [WGB-B1]

description:
Library name: ARPE19_RESSEC_72h_OX_Rep3_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation + Secretome (conditioned medium)


title: NPC patient 22


title: NPC patient 21


title: NPC patient 33


title: 2DM4F302LI_S7

description: Library name: 2DM4F302LI_S7_R1_001

value: 9 weeks

value: Used in Analysis


title: ARPE-19 – QMR+Secretome Rescue 72h (biol rep 3) [WGB-B1]

description:
Library name: ARPE19_RESSEC_72h_Rep3_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=No; Rep1; sequencing batch=WGB_Batch1.

value: Retinal Pigment Epithelium

value: no oxidative stress; QMR electromagnetic stimulation + Secretome (conditioned medium)


title: NPC patient 20

value: locoregionally advanced NPC FFPE sample


title: NPC patient 19

value: M


title: 2DM5F405LI_S15

description: Library name: 2DM5F405LI_S15_R1_001

value: Liver Left Lobe

value: B6D2F1/Crl (BDF-1)


title: ARPE-19 – QMR Rescue + Oxidative Stress 72h (biol rep 3) [WGB-B1]

description:
Library name: ARPE19_RES_72h_OX_Rep3_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation


title: 2DM4F302KI_S2

description: Library name: 2DM4F302KI_S2_R1_001

value: Kidney

value: female

value: Outlier based on PCA/correlation


title: NPC patient 18

value: F


title: 2DM5F405KI_S10

description: Library name: 2DM5F405KI_S10_R1_001


title: NPC patient 17


title: 2DM4F302HE_S2

description: Library name: 2DM4F302HE_S2_R1_001

value: Heart


title: 2DM5F404LI_S5

description: Library name: 2DM5F404LI_S5_R1_001


title: ARPE-19 – QMR Rescue 72h (biol rep 3) [WGB-B1]

description:
Library name: ARPE19_RES_72h_Rep3_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=No; Rep1; sequencing batch=WGB_Batch1.

value: no oxidative stress; QMR electromagnetic stimulation


title: NPC patient 16


title: NPC patient 15


title: 2DM4F301OV_S105

description: Library name: 2DM4F301OV_S105_R1_001

value: Ovary


title: 2DM4F302OV_S89

description: Library name: 2DM4F302OV_S89_R1_001


title: NPC patient 14


title: ARPE-19 – Control + Oxidative Stress 72h (biol rep 3) [WGB-B1]

description:
Library name: ARPE19_CTRL_72h_OX_Rep3_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.

value: H2O2 400 µM (oxidative stress); untreated


title: 2DM4F301LU_S23

description: Library name: 2DM4F301LU_S23_R1_001

value: Lung

value: 9 weeks


title: 2DM5F402KI_S34

description: Library name: 2DM5F402KI_S34_R1_001

value: Not Used in Analysis

value: Potential Tissue Contamination


title: 2DM5F402LI_S2

description: Library name: 2DM5F402LI_S2_R1_001

value: Used in Analysis


title: ARPE-19 – Control 72h (biol rep 3) [WGB-B1]

description:
Library name: ARPE19_CTRL_72h_Rep3_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=No; Rep1; sequencing batch=WGB_Batch1.

value: Retinal Pigment Epithelium

value: no oxidative stress; untreated


title: NPC patient 12

value: M

value: locoregionally advanced NPC FFPE sample


title: NPC patient 11


title: 2DM4F302LU_S7

description: Library name: 2DM4F302LU_S7_R1_001

value: B6D2F1/Crl (BDF-1)


title: 2DM4F301LI_S23

description: Library name: 2DM4F301LI_S23_R1_001

value: Liver Left Lobe

value: female


title: NPC patient 13


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 24h (biol rep 3) [TRR-B2]

description:
Library name: ARPE19_RESSEC_24h_OX_Rep3_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation + Secretome (conditioned medium)


title: NPC patient 10


title: ARPE-19 – QMR+Secretome Rescue 24h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_RESSEC_24h_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=24h; OX=No; Rep1; sequencing batch=TRR_Batch2.

value: no oxidative stress; QMR electromagnetic stimulation + Secretome (conditioned medium)


title: ARPE-19 – Secretome + Oxidative Stress 72h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_SEC_72h_OX_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.

value: H2O2 400 µM (oxidative stress); Secretome (conditioned medium)


title: ARPE-19 – Secretome + Oxidative Stress 72h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_SEC_72h_OX_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.


title: NPC patient 9

value: F


title: 2DM4F301KI_S18

description: Library name: 2DM4F301KI_S18_R1_001

value: Kidney


title: NPC patient 7


title: NPC patient 8


title: 2DM4F301HE_S18

description: Library name: 2DM4F301HE_S18_R1_001

value: Heart


title: ARPE-19 – Secretome 72h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_SEC_72h_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=No; Rep1; sequencing batch=WGB_Batch1.

value: no oxidative stress; Secretome (conditioned medium)


title: NPC patient 6


title: NPC patient 5


title: 2DM3F205OV_S100

description: Library name: 2DM3F205OV_S100_R1_001

value: Ovary

value: 9 weeks


title: ARPE-19 – Secretome 72h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_SEC_72h_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=No; Rep1; sequencing batch=WGB_Batch1.


title: NPC patient 4


title: 2DM4F305HE_S4

description: Library name: 2DM4F305HE_S4_R1_001

value: Used in Analysis


title: 2DM4F305KI_S4

description: Library name: 2DM4F305KI_S4_R1_001


title: NPC patient 3


title: 2DM3F205LU_S18

description: Library name: 2DM3F205LU_S18_R1_001

value: Lung


title: ARPE-19 – Secretome + Oxidative Stress 24h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_SEC_24h_OX_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.

value: Retinal Pigment Epithelium


title: NPC patient 2

value: M


title: 2DM3F205LI_S18

description: Library name: 2DM3F205LI_S18_R1_001


title: mbd8_RNAseq_rep3

city: Beijing

first: xinjian

last: he

address: No. 7, zhongguancun life science park road, changping district

country: China

institute: National Institute of Biological Sciences

description: Library name: Sample 9

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to the Arabidopsis genome (TAIR10) using STAR.  The clean reads were aligned to the Oryza sativa genome (IRGSP-1.0) using HISAT2.
The expression of genes were obtained with the R package edgeR.
Assembly: TAIR10; IRGSP-1.0
Supplementary files format and content: Tab-delimited text file include normalized reads for each sample.

organism: Arabidopsis thaliana

source_name: Arabidopsis seedlings

growth_protocol: Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates for 12 days, under a 8 h light/16 h dark photoperiod at 22°C.Oryza sativa were grown in the controlled growth chamber at 28°C, under LD conditions (14-h light/10-h dark) with 70% relative humidity.

extract_protocol:
Total RNA was extracted from 12-day-old Arabidopsis seedlings or 50-day-old Oryza sativa leaves with TRIzol reagent (Invitrogen).
Sequencing libraries were built for RNA-seq (Illumina Novaseq 6000 platform, paired-end 150bp).

value: Arabidopsis seedlings

tag: genotype

tag: time


title: ARPE-19 – Secretome + Oxidative Stress 24h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_SEC_24h_OX_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.


title: mbd8_RNAseq_rep2

description: Library name: Sample 8


title: NPC patient 1

value: locoregionally advanced NPC FFPE sample


title: ARPE-19 – QMR Rescue + Oxidative Stress 24h (biol rep 2) [TRR-B2]

description:
Library name: ARPE19_RES_24h_OX_Rep2_TRR_Batch2
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=TRR_Batch2.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation


title: 2DM3F205KI_S13

description: Library name: 2DM3F205KI_S13_R1_001

value: B6D2F1/Crl (BDF-1)

value: female


title: mbd8_RNAseq_rep1

description: Library name: Sample 7


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 72h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_RESSEC_72h_OX_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation + Secretome (conditioned medium)


title: ldl2_RNAseq_rep3

description: Library name: Sample 6


title: 2DM3F205HE_S13

description: Library name: 2DM3F205HE_S13_R1_001


title: ldl2_RNAseq_rep2

description: Library name: Sample 5


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 72h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_RESSEC_72h_OX_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.


title: 2DM3F204OV_S120

description: Library name: 2DM3F204OV_S120_R1_001


title: C24_RNAseq_rep3

description: Library name: Sample 3

value: wild type C24


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 24h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_RESSEC_24h_OX_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.


title: C24_RNAseq_rep2

description: Library name: Sample 2


title: C24_RNAseq_rep1

description: Library name: Sample 1


title: 2DM3F204LU_S38

description: Library name: 2DM3F204LU_S38_R1_001


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 24h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_RESSEC_24h_OX_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.


title: mbd8_H3K4me2_rep2

description: Library name: Sample 12

library_source: genomic

data_processing:
Basecalling performed using bcl2fastq.
The clean reads were aligned to Arabidopsis genome (TAIR10) using Bowtie2.
Assembly: TAIR10
Supplementary files format and content: bigWig files were generated using bamCoverage.

molecule: genomic DNA

growth_protocol: The Arabidopsis seedlings were grown on MS (Murashige and Skoog) medium plates with a 16 h light/8 h dark photoperiod at 22°C for 12 d.

extract_protocol:
Arabidopsis seedlings were corss-linked by 1% formaldehyde. Chromatin were clarified from sonicated nuclei and were isolated with antibody.
Libraries were built for ChIP-seq (Illumina Novaseq 6000; 150-bp pair-end sequencing)

tag: chip antibody

value: Abcam, ab7766


title: 2DM3F204LI_S38

description: Library name: 2DM3F204LI_S38_R1_001

value: Liver Left Lobe


title: mbd8_H3K4me2_rep1

description: Library name: Sample 11


title: 2DM3F204KI_S33

description: Library name: 2DM3F204KI_S33_R1_001

value: Kidney


title: ldl2_H3K4me2_rep1

description: Library name: Sample 9


title: ARPE-19 – QMR+Secretome Rescue 72h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_RESSEC_72h_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=No; Rep1; sequencing batch=WGB_Batch1.

value: no oxidative stress; QMR electromagnetic stimulation + Secretome (conditioned medium)


title: C24_H3K4me2_rep2

description: Library name: Sample 8


title: C24_H3K4me2_rep1

description: Library name: Sample 7


title: ARPE-19 – QMR Rescue + Oxidative Stress 72h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_RES_72h_OX_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.


title: ldl2_H3K4me1_rep2

description: Library name: Sample 4

value: Abcam, ab8895


title: ARPE-19 – QMR Rescue + Oxidative Stress 72h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_RES_72h_OX_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.


title: mbd8_H3K4me1_rep1

description: Library name: Sample 5


title: ldl2_H3K4me1_rep1

description: Library name: Sample 3


title: ARPE-19 – QMR Rescue 72h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_RES_72h_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=No; Rep1; sequencing batch=WGB_Batch1.

value: no oxidative stress; QMR electromagnetic stimulation


title: 2DM3F203LI_S27

description: Library name: 2DM3F203LI_S27_R1_001

value: 9 weeks

value: Not Used in Analysis

value: SEQ DEPTH < 300000


title: C24_H3K4me1_rep1

description: Library name: Sample 1


title: ARPE-19 – QMR Rescue 72h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_RES_72h_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=72h; OX=No; Rep1; sequencing batch=WGB_Batch1.

value: Retinal Pigment Epithelium


title: hb34-3

city: hangzhou

first: xiaoxiao

address: #866 Yuhangtang Rd.

institute: zhejiang university

description: Library name: hb34-rep3

data_processing:
Reads were mapped to the Arabidopsis thaliana (TAIR10) genome using Hisat2 (version 2.1.0) with default settings.
Transcripts assembled from three independent biological replicates were included in the analysis, compared using DESeq2 (version 1.30.1) with default settings.
The R package DESeq2 (version 1.30.1) in v4.0.3 was employed to identify differentially expressed genes with at least a 1.5-fold change
Assembly: TAIR10
Supplementary files format and content: text files include genecounts for each files

source_name: leaves

growth_protocol: The stratified seeds were germinated in half-strength Murashige and Skoog (MS) medium for 10 d. Plants were grown under cool white light in a long-day condition (16 h light /8 h dark, 22 ºC).

extract_protocol:
Total RNA was extracted from 10-d-old seedlings using TRIzol reagent (Invitrogen, USA) and reverse-transcribed into cDNAs using commercial kits (TOYOBO, FSQ-301) following the manufacturer's instruction. Real-time PCR was performed using SYBR Green qPCR Master Mix (TRANS, AQ601) on the C1000 Touch™ Thermal Cycler (YEASEN). The constitutively reference genes were used as the endogenous control to normalize the amount of cDNA templates.
RNA sequencing was carried out using the Illumina NovaSeq 6000 with Hiseq-PE150 strategy, conducted by Novogene Corporation (Beijing, China).

value: leaves

value: Columbia

value: hb34 mutant

value: mock


title: hb34-2

description: Library name: hb34-rep2


title: hb34-1

description: Library name: hb34-rep1


title: ARPE-19 – QMR+Secretome Rescue 72h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_RESSEC_72h_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=No; Rep1; sequencing batch=WGB_Batch1.


title: 2DM3F203HE_S22

description: Library name: 2DM3F203HE_S22_R1_001

value: Heart

value: B6D2F1/Crl (BDF-1)

value: female

value: Used in Analysis


title: mbd8_H3K4me1_rep2

description: Library name: Sample 6

value: Arabidopsis seedlings


title: ARPE-19 – QMR Rescue + Oxidative Stress 24h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_RES_24h_OX_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation


title: col-2

description: Library name: col-rep2

value: WT


title: col-1

description: Library name: col-rep1


title: ARPE-19 – Control + Oxidative Stress 8h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_CTRL_8h_OX_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=8h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.

value: H2O2 400 µM (oxidative stress); untreated


title: HB34_input

description: Library name: HB34_input

data_processing:
The clean paired-end reads were mapped to the reference genome by Bowtie2 (Version 2.3.5) and reads with low mapping quality or multiple positions on the genome were identified and removed by SAMtools (version 1.9). Only perfectly and uniquely mapped reads were retained for further analysis.
Enriched peaks were called and annotated by MACS2 (Version 2.2.8) with the following parameters: “-f BAMPE -g 119145879 -q 0.01”. Peaks that were consistently found in two replicates were selected for further analyses. The generated data were imported into the Integrative Genomics Viewer (IGV) (James T Robinson, 2011) for visualization.
ComputeMatrix, plotProfile and plotHeatmap programs in deepTools (version 3.3.0) were used to compare the average enrichment at defined loci between YB2-FLAG and WT. To assign peaks to proximal genes, regions within 1.0 kb flanking the transcription start site (TSS) were extracted.
Assembly: TAIR10
Supplementary files format and content: bw files generated from SAMtools
Supplementary files format and content: peak files generated from MACS2

growth_protocol: The stratified seeds were germinated in half-strength Murashige and Skoog (MS) medium for 10. Plants were grown under cool white light in a long-day condition (16 h light /8 h dark, 22 ºC).

extract_protocol:
Briefly, about 0.5-g 10-d-old seedlings were crosslinked with 1% formaldehyde and stopped with 125 mM glycine. Samples were ground and resuspended in the nuclei isolating buffer (10 mM Tris pH 8.0, 10 mM Sodium butyrate, 400 mM Sucrose, 0.1 mM PMSF, 5 mM β-mercaptoethanol, 1×cocktail protein inhibitor freshly). The isolated nuclei were resuspended with 1 mL lysis buffer (50 mM HEPES pH 7.5, 150 mM NaCl, 1 mM EDTA, 10 mM Sodium butyrate, 0.1% deoxycholate, 0.1% SDS, 1% Triton X-100, 1 mM PMSF and 1×protease inhibitor cocktail freshly) and sonicated into 200-500 bp fragments by Diagenode Bioruptor (high setting, 18 cycles，30s on and 30s off). Subsequently, the sonicated chromatin was incubated with GFP-antibodies (Abcam, ab290) overnight at 4°C.
The recovered DNAs in ChIP assay were used to library construction with the Scale ssDNA-seq Lib Prep Kit (ABclonal, RK20228). High-throughput sequencing was carried out using Illumina Hiseq-PE150 by Novogene Corporation (Beijing, China).


title: 2DM3F202LU_S16

description: Library name: 2DM3F202LU_S16_R1_001

value: Lung


title: ARPE-19 – Control + Oxidative Stress 8h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_CTRL_8h_OX_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=8h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.


title: HB34_IP_1

description: Library name: HB34_IP_1


title: 2DM3F202LI_S16

description: Library name: 2DM3F202LI_S16_R1_001

value: Liver Left Lobe

value: 9 weeks


title: p2k1-3 bdg-8 double mutant, ATP, rep3

city: Columbia

first: Gary

last: Stacey

state: Missouri

address: 271E Christopher S. Bond Life Sciences Center

institute: University of Missouri at Columbia

data_processing:
Cutadapt version 1.13 was used to trim adaptors from sequences and remove the read pairs that at least one of the reads was shorter than 10 nucleotides.
The quality of the trimmed reads was evaluated with MultiQC version 1.9.
The trimmed high-quality reads were then aligned against the TAIR11 Arabidopsis reference genome using STAR version 2.7.4a.
The reads were then mapped to protein-coding genes and generated count matrices via HTSeq version 0.13.5.
Assembly: TAIR11
Supplementary files format and content: Tab-delimited text files include raw counts of sequencing reads for each sample.

molecule: polyA RNA

source_name: seedling

extract_protocol:
Total RNAs were extracted using a Rneasy Plant Mini Kit (Qiagen) with on-column Dnase digestion according to the manufacturer’s instructions.
RNA-seq libraries were constructed using a poly A enrichment method and sequenced on a single NovaSeq SP PE10 flow cell following manufacturer's protocols.

value: seedling

value: p2k1-3 bdg-8 double mutant

value: 150 μM ATP for 30 min


title: ARPE-19 – Control + Oxidative Stress 72h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_CTRL_72h_OX_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.

value: Retinal Pigment Epithelium


title: p2k1-3 bdg-8 double mutant, ATP, rep2


title: 2DM3F202KI_S11

description: Library name: 2DM3F202KI_S11_R1_001

value: Kidney

value: Not Used in Analysis

value: Potential Tissue Contamination


title: p2k1-3 bdg-8 double mutant, ATP, rep1


title: ARPE-19 – Control + Oxidative Stress 72h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_CTRL_72h_OX_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.


title: p2k1-3 bdg-8 double mutant, Mock, rep3

value: Mock


title: 2DM3F202HE_S11

description: Library name: 2DM3F202HE_S11_R1_001

value: Heart

value: B6D2F1/Crl (BDF-1)

value: female


title: 2DM3F201OV_S104

description: Library name: 2DM3F201OV_S104_R1_001

value: Ovary

value: Used in Analysis


title: p2k1-3 bdg-8 double mutant, Mock, rep2


title: p2k1-3 bdg-8 double mutant, Mock, rep1


title: p2k1-3 mutant, ATP, rep3

value: p2k1-3 mutant


title: ARPE-19 – Control 72h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_CTRL_72h_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=No; Rep1; sequencing batch=WGB_Batch1.

value: no oxidative stress; untreated


title: p2k1-3 mutant, ATP, rep2


title: p2k1-3 mutant, ATP, rep1


title: ARPE-19 – Control + Oxidative Stress 24h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_CTRL_24h_OX_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.

value: H2O2 400 µM (oxidative stress); untreated


title: p2k1-3 mutant, Mock, rep3


title: PBMCs, Male, PFOA, rep2

city: Wageningen

first: Benthe

last: van der Lugt

address: Akkermaalsbos 2

country: Netherlands

institute: Wageningen University & Research

description: Library name: PFOA_M_2

data_processing:
The RNAseq reads were used to quantify transcript abundances. To this end, the tool Cutadapt (version 1.16) was used to trim adapters from the reads and HISAT2 (version 2.2.1) was used to map the reads to the GRCh38.p13 (release 42)human genome assembly-based transcriptome sequences as annotated by the GENCODE consortium. HISAT2 (version 2.2.1.) output was converted and sorted by chromosomal position using Samtools (version 1.9). RSeQC (v3.0.1) and PRINSEQ (v0.20.4) were used for quality control. HTSeq (version 0.11.2) was used to count reads in transcripts using gene-level quantification. Differential gene expression was determined using the package limma (version 3.50.3) utilizing the obtained scaled gene-level counts. Briefly, before statistical analyses, non-specific filtering of the count table was performed to increase detection power, based on the requirement that a gene should have an expression level greater than around 10 counts in at least three samples. Differences in library size were adjusted by the trimmed mean of M-values normalization method, implemented in the package edgeR (version 3.36.0).
Assembly: GRCh38.p13
Supplementary files format and content: Text file including the normalized counts for each sample.

source_name: male

growth_protocol: PBMCs were isolated from buffy coats obtained from anonymous male and female healthy donors purchased from the Niguarda Hospital (Milan, Italy). PBMCs were isolated by Ficoll gradient centrifugation and subsequently washed five times with PBS. For the experiments, PBMCs were suspended in RPMI 1640 without phenol red containing 2 mM L-glutamine, 100 IU/mL penicillin, 0.1 mg/mL streptomycin, 10 µg/mL gentamycin, 50 µM 2-mercaptoethanol, supplemented with 5% of heat-inactivated human serum (hereafter referred to as complete medium). The aforementioned cell culture medium, serum and all supplements were purchased from Sigma-Aldrich. Cells were incubated in a humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
RNA was extracted using RNeasy Mini spin columns (Qiagen, Hilden, Germany) according to the manufacturer's instructions. RNA concentration and purity were determined by measuring the absorbance of the samples at 230, 260, and 280 nm using a NanoReady F-3100 spectrophotometer (Life Real, Zhejiang, China). The optical density (OD) ratios A260/A280 and A260/A230 were used to assess RNA purity.
After poly(A) selection, library preparation was performed using the NEBNext Ultra II RNA Library Preparation kit.

treatment_protocol: PBMCs were isolated from 5 male and 5 female donors and seeded in 48-wells plates containing 1.26 x 10^6 PBMCs in 1 mL of complete medium. PBMCs were exposed either to PFOA or PFOS (at the concentration of 12.6 µg/mL), DEX (150 µg/mL) or DMSO as vehicle control (final concentration 0.1% (v/v)) and incubated for 24 hours without subsequent stimulation. Following exposure, RNA was extracted and used for RNA sequencing.

value: male

value: PBMCs

value: 12.6 μg/mL PFOA


title: PBMCs, Male, PFOA, rep4

description: Library name: PFOA_M_4


title: 2DM3F201LI_S22

description: Library name: 2DM3F201LI_S22_R1_001

value: Liver Left Lobe

value: 9 weeks


title: ARPE-19 – Control + Oxidative Stress 24h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_CTRL_24h_OX_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=24h; OX=Yes; Rep1; sequencing batch=WGB_Batch1.

value: Retinal Pigment Epithelium


title: p2k1-3 mutant, Mock, rep1

value: seedling


title: 2DM3F201KI_S17

description: Library name: 2DM3F201KI_S17_R1_001

value: Kidney


title: p2k1-3 mutant, Mock, rep2

value: Mock


title: bdg-8 mutant, ATP, rep3

value: bdg-8 mutant

value: 150 μM ATP for 30 min


title: ARPE-19 – Control 24h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_CTRL_24h_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=24h; OX=No; Rep1; sequencing batch=WGB_Batch1.


title: bdg-8 mutant, ATP, rep2


title: 2DM3F201HE_S17

description: Library name: 2DM3F201HE_S17_R1_001

value: Heart

value: B6D2F1/Crl (BDF-1)

value: female


title: bdg-8 mutant, ATP, rep1


title: ARPE-19 – Control 24h (biol rep 1) [WGB-B1]

description:
Library name: ARPE19_CTRL_24h_Rep1_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=24h; OX=No; Rep1; sequencing batch=WGB_Batch1.


title: 4DM6F503LU_S41

description: Library name: 4DM6F503LU_S41_R1_001

value: Lung

value: Used in Analysis


title: ARPE-19 – Control 72h (biol rep 2) [WGB-B1]

description:
Library name: ARPE19_CTRL_72h_Rep2_WGB_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Control; timepoint=72h; OX=No; Rep1; sequencing batch=WGB_Batch1.

value: no oxidative stress; untreated


title: PBMCs, Male, Control, rep2

description: Library name: Ctrl_M_2

value: male

value: 0.1% DMSO


title: K_marx_P8_6

city: Zapopan

first: Lorena

last: Amaya Delgado

state: Jalisco

address: Camino arenero 1227

department: Industrial Biotechnology

country: Mexico

institute: CIATEJ

description:
P8_c-tx_GEO_NCBI.txt
treatment

data_processing:
Illumina bcl2fastq software used for basecalling.
Paired-end library, reads length 100 bp
Quality control of each sample was analyzed with FASTQC
Reads were mapped to the genome of Kluyveromyces marxianus DMKU3 with SALMON
Transcriptome assembly of reads were performed with SPADES v3.15.3
ORF’s were predicted with TransDecoder v5.5.0 with default settings
ORF’s annotation was performed with the annotate module from funannotate v1.6.0
Genome_build: NCBI ID 10898
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

organism: Kluyveromyces marxianus

source_name: Kluyveromyces marxianus

growth_protocol: A defined mineral culture medium was used, containing 20.0 g L-1 glucose as the only carbon source; a mixture of salts composed of (g L-1) 1.49 Na2HPO4·2H2O, 3.0 K2HPO4, 3.0 (NH4)·2SO4 and 1.0 glutamic acid; 2.5 mL L-1 vitamin solution composed of (mg L-1) 1.0 aminobenzoic acid, 125.0 mesoinositol, 5.0 nicotinic acid, 5.0 pantothenic acid, 5.0 pyridoxine, 5.0 thiamine HCl, and 0.012 biotin; and 1 mL L-1 oligoelement solution containing (mg L-1) 410.0 MgCl2·6H2O, 19.2 ZnCl2, 0.61 CuCl2·2H2O, 4.45 MnCl2·4H2O, 0.5 CoCl2·6H2O, 17.37 CaCl2, 11.66 FeCl2·4H2O, 0.36 (NH4)6Mo7O24·4H2O, and 3.0 H3BO3. Glucose was prepared in a 700 g L-1 stock. Glucose and salts were sterilized by autoclave (121 °C for 15 min). Oligoelements and vitamins were sterilized by filtration (0.20 μm). The fermentations were carried out in a 250mL bioreactor at 150 rpm, 30 °C.

extract_protocol:
The samples for transcriptome analysis were collected in the first 3 h of fermentation and subsequent total RNA extraction was performed using an extraction protocol using Tri-Reagen (Sigma Aldrich) and the extraction kit (Promega).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: A defined mineral culture medium was used (see growth protocol), and adittionally 1 g/L of furfural was added. The fermentations were carried out in a 250mL bioreactor at 150 rpm, 30 °C.

tag: strain

value: yeast

value: Adapted


title: PBMCs, Male, Control, rep5

description: Library name: Ctrl_M_5

value: PBMCs


title: bdg-8 mutant, Mock, rep3


title: bdg-8 mutant, Mock, rep2


title: ARPE-19 – Secretome + Oxidative Stress 8h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_SEC_8h_OX_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=8h; OX=Yes; Rep1; sequencing batch=TRR_Batch1.

value: Retinal Pigment Epithelium

value: H2O2 400 µM (oxidative stress); Secretome (conditioned medium)


title: 2DM2F105OV_S88

description: Library name: 2DM2F105OV_S88_R1_001

value: Ovary

value: 9 weeks


title: bdg-8 mutant, Mock, rep1

value: seedling

value: bdg-8 mutant

value: Mock


title: ARPE-19 – Secretome 8h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_SEC_8h_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=8h; OX=No; Rep1; sequencing batch=TRR_Batch1.

value: no oxidative stress; Secretome (conditioned medium)


title: Col-0, ATP, rep2

value: 150 μM ATP for 30 min


title: Col-0, ATP, rep3


title: 2DM2F105LU_S6

description: Library name: 2DM2F105LU_S6_R1_001

value: Lung

value: B6D2F1/Crl (BDF-1)

value: female


title: 2DM2F105LI_S6

description: Library name: 2DM2F105LI_S6_R1_001

value: Liver Left Lobe

value: Not Used in Analysis

value: Outlier based on PCA/correlation


title: 2DM3F201LU_S22

description: Library name: 2DM3F201LU_S22_R1_001

value: Used in Analysis


title: Col-0, ATP, rep1


title: ARPE-19 – Secretome + Oxidative Stress 72h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_SEC_72h_OX_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=Yes; Rep1; sequencing batch=TRR_Batch1.


title: Col-0, Mock, rep3


title: 2DM2F105KI_S1

description: Library name: 2DM2F105KI_S1_R1_001

value: Kidney

value: TOTAL ALIGNMENT RATE < 40%


title: Col-0, Mock, rep2


title: ARPE-19 – Secretome 72h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_SEC_72h_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=72h; OX=No; Rep1; sequencing batch=TRR_Batch1.

value: Retinal Pigment Epithelium


title: Col-0, Mock, rep1


title: 2DM2F105HE_S1

description: Library name: 2DM2F105HE_S1_R1_001

value: Heart


title: 163_25

city: Tel Aviv

first: Hila

last: Gingold

address: 30 Haim Levanon Street

country: Israel

institute: Tel-Aviv University

description: Library name: L14

data_processing:
All bioinformatic analyses were performed using RNAlysis. For sRNA-seq data, sRNA reads were aligned to PRJNA13758 ce11 genome assembly using ShortStack111 and aligned anti-sense reads were quantified using FeatureCounts. We included all reads with > 5 RPM without imposing any constraint on the length and 5′ nucleotide. For mRNA, we pseudo-aligned reads using Kallisto. We then performed differential expression analysis using DESeq2.
Assembly: PRJNA13758 ce11
Supplementary files format and content: mRNA_kallisto_output.xlsx

organism: Caenorhabditis elegans

source_name: Whole worm

growth_protocol: C. elegans strains were maintained on standard Nematode Growth Medium (NGM) plates seeded with E. coli OP50 at 20 degree, unless stated otherwise

extract_protocol:
Total RNA was isolated from day 1 adults (~72 hours following L1 synchronization) using standard phenol-chloroform method with TRIzolTM (Invitrogen). RNA quality was accessed using Agilent 4150 BioAnalyzer instrument and High Sensitivity RNA ScreenTapes.
To sequence the mRNA, RNA libraries were prepared using NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina® coupled with NEBNext® Poly(A) mRNA Magnetic Isolation Module. The cDNA libraries were pooled and paired-end sequencing was performed on the Nextseq 2000 platform.  For sRNA sequencing, we treated the RNA samples with RNA 5′ Polyphosphatase (epicentre) and the libraries were prepared using NEBNext® Multiplex Small RNA Library Prep Set for Illumina (New England Biolabs) or TruSeq Small RNA Library Prep Kit (Illumina) according to the manufacturer’s protocol. RNA ranging from ~140 to 160 nt was size-selected by gel extraction using 4% agarose E-Gel (Life Technologies). The pooled samples were the sequenced using the Illumina HiSeq 2500 instrument.

treatment_protocol: For experiment at 25 degree, worms were move from 20 to 25 degree at L4 stage

value: Whole worm

value: pigSi3; rde-4(ne299)


title: 161_25

description: Library name: L13


title: ARPE-19 – Secretome + Oxidative Stress 24h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_SEC_24h_OX_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=24h; OX=Yes; Rep1; sequencing batch=TRR_Batch1.

value: H2O2 400 µM (oxidative stress); Secretome (conditioned medium)


title: 2DM2F104OV_S94

description: Library name: 2DM2F104OV_S94_R1_001

value: Ovary

value: 9 weeks


title: ARPE-19 – Secretome 24h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_SEC_24h_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=Secretome; timepoint=24h; OX=No; Rep1; sequencing batch=TRR_Batch1.

value: no oxidative stress; Secretome (conditioned medium)


title: N22_25

description: Library name: L12


title: 2DM2F104LU_S12

description: Library name: 2DM2F104LU_S12_R1_001

value: Lung


title: N21_25

description: Library name: L11


title: 3373_20

description: Library name: L10


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 8h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_RESSEC_8h_OX_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=8h; OX=Yes; Rep1; sequencing batch=TRR_Batch1.

value: H2O2 400 µM (oxidative stress); QMR electromagnetic stimulation + Secretome (conditioned medium)


title: 3371_20

description: Library name: L9


title: ATAC_Ascl1_QA_D0_rep1

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building (CRB)

institute: University of Pennsylvania

description: Library name: 3_ATAC_UAE_QA_D0_rep1_S7

data_processing:
Pipeline overview: data were aligned to human genome assembly hg19 and subsequent analysis was performed with CUT&RUNTools v2.0 (https://github.com/fl-yu/CUT-RUNTools-2.0) using the standard CUT&Tag pipeline.
Read trimming and alignment: reads were trimmed with trimmomatic v0.36 and aligned with bowtie2 v2.4.2.
Read shift: aligned reads were shifted +4bp and -5bp for positive and negative strand reference genome alignments, respectively, to account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase.
Filtering and peak calling: aligned reads were filtered by size and duplicates were marked; peaks were called using MACS2 v2.2.7.1.
Peak merge: peaks from individual replicates were merged where overlapping.
Track creation: ATACseq bigwig files were generated with deeptools 3.5.1  bamCoverage --normalizeUsing CPM. the nucleosome positioning analysis was performed using NucleoATAC with default settings. Bedgraphs from the smoothed NucleoATAC signals were converted into bigWig format using UCSC Genome Browser's bedGraphToBigWig utility.
Assembly: GRCh37/hg19
Supplementary files format and content: The BED file atac_filtered_clusters.bed contains all ATAC-seq peaks identified through the CUT&RUN Tools pipeline (MACS2 narrow peak calls) which were then merged if overlapping.
Supplementary files format and content: The bigwig files *.bw were generated using deeptools bamCoverage with CPM normalisation.

source_name: hBJ fibroblast

growth_protocol: The human fibrobalst cells were cultured at 37°C incubator at 5% CO2 in fibroblast medium with DMEM, 10% TET-free FBS, 2mM GlutaMax and 1x Non-essential amino acids. When  reaching 85 - 95% confluency, cells were plated at 1:3 to 1:5, and passaged every 3-5 days.

extract_protocol:
The cells were washed once with DPBS, before incubating directly on the plate with 1 ml of ice-cold ATAC-RSB buffer (10 mM Tris-HCl pH 7.6, 10mM NaCl, 3mM MgCl2) with 0.1% NP40, 0.1% Tween 20, and 0.01% Digitonin for 10 minutes on ice. The nuclei were then scaped and washed once with ATAC-RSB buffer with 0.1% Tween 20, before being pelleted at 500g for 10 minutes at 4°C. The nuclei pellet was incubated with 50 μl transposition mix (25 μl 2x TD buffer, 2.5 μl transposase (120 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl H2O) at 37°C for 30 minutes and mixed in thermomixer at 1000 RPM. The transposition was stopped by adding 250 μl (five volumes) DNA binding buffer to the transposition mix and DNA was purified with Zymo DNA Clean and Concentrator-5 Kit (D4014) and eluted in 21 μl elution buffer.
For library preparation, 5 cycle of pre-amplification was performed, and the DNA concentration was then quantified, followed by an additional 4 cycles of amplifications. The library DNA was purified with Zymo DNA Clean and Concentrator-5 Kit and eluted in 20 μl of H2O, and the library DNA were analyzed using High Sensitivity D1000 DNA ScreenTape (Agilent, 5067-5584) on Agilent Tapestation 4150.

treatment_protocol: For ATAC-seq experiments, cells were plated at 100,000 cells per 6-well, and induced with 0.5 μg/mL dox for 0, 48, 96 and 168 hrs before being colected for ATAC-seq analysis.

value: hBJ fibroblast

value: human fibroblast

value: QA

tag: replicate


title: ldl2_RNAseq_rep1

description: Library name: Sample 4

value: Arabidopsis seedlings


title: 3376_25

description: Library name: L8


title: 2DM2F104LI_S12

description: Library name: 2DM2F104LI_S12_R1_001

value: Liver Left Lobe

value: B6D2F1/Crl (BDF-1)

value: female

value: Used in Analysis


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 72h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_RESSEC_72h_OX_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=Yes; Rep1; sequencing batch=TRR_Batch1.

value: Retinal Pigment Epithelium


title: 3375_25

description: Library name: L7

value: Whole worm


title: 2DM2F104KI_S7

description: Library name: 2DM2F104KI_S7_R1_001

value: Kidney


title: 3374_25

description: Library name: L6


title: ldl2_H3K4me2_rep2

description: Library name: Sample 10

value: Abcam, ab7766


title: ARPE-19 – QMR+Secretome Rescue + Oxidative Stress 24h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_RESSEC_24h_OX_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=24h; OX=Yes; Rep1; sequencing batch=TRR_Batch1.


title: 164_25

description: Library name: L5

value: pigSi3; rde-4(ne299)


title: 2DM2F104HE_S7

description: Library name: 2DM2F104HE_S7_R1_001

value: Heart

value: 9 weeks


title: N25_25

description: Library name: L4


title: ARPE-19 – QMR+Secretome Rescue 8h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_RESSEC_8h_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=8h; OX=No; Rep1; sequencing batch=TRR_Batch1.

value: no oxidative stress; QMR electromagnetic stimulation + Secretome (conditioned medium)


title: N24_25

description: Library name: L3


title: 2DM3F204HE_S33

description: Library name: 2DM3F204HE_S33_R1_001


title: 2DM2F103OV_S118

description: Library name: 2DM2F103OV_S118_R1_001

value: Ovary


title: DonorE cells perturbed with SIK3 knockdown by CRISPRi in batch Rep1 collected 8 hrs after restimulation

city: Palo Alto

first: Lattice

last: Data Coordination

state: CA

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

description:
Library name: Tact_cluster_validation_Diff092_DonorE_Stim8hr_Rep1_SIK3
Tact_cluster_validation_Diff092_Stim8hr_Rep1_bulkRNAseq.csv

data_processing:
Quality of the fastq files was assessed using FastQC v0.12.1. Reads were then quality filtered using fastp v0.24.0 with poly-X tail trimming, 3' quality-based tail trimming, a minimum Phred quality score of 15, and a minimum length requirement of 50 bp. Quality-filtered reads were aligned to the reference genome using STAR aligner v2.7.11 with non-canonical splice junction removal and output of unmapped reads, followed by coordinate sorting using samtools v1.22.1. PCR and optical duplicates were removed using UMI-based deduplication with UMIcollapse v1.1.0. Alignment quality metrics, strand specificity, and read distribution across genomic features were assessed using RSeQC v5.0.4 and Qualimap v2.3, with results aggregated into a comprehensive quality control report using MultiQC v1.32. Gene-level expression quantification was performed using featureCounts (subread package v2.1.1) with strand-specific counting, multi-mapping read fractional assignment, exons and three prime UTR as the feature identifiers, and grouped by gene_id. Final gene counts were annotated with gene biotype and other metadata extracted from the reference GTF file.
Assembly: GRCh38, GENCODE48
Supplementary files format and content: processed data format:csv, processed data content: raw counts, normalized counts (CPM)

growth_protocol: Naive human CD4+ T cells were isolated isolated with the EasySep Human Naive CD4+ T Cell Isolation Kit (catalog no. #19555, STEMCELL Technologies) according to the manufacturer’s protocol from PBMC-enriched leukapheresis products (Leukopaks, STEMCELL Technologies, catalog no. 70500) from healthy donors, after institutional review board–approved informed written consent (STEMCELL Technologies). At day 0, primary naive human CD4+ T cells were seeded at 1 x 106 cells/ml in cXVIVO and 200 IU/ml IL-2 at 150µL/well in 96-well flat bottom plates. Cells were activated using ImmunoCult human CD3/CD28/CD2 T cell activator at 25 µl/ml. The next morning, cells were transduced with 2% v/v concentrated ZIM3KRAB-dCas9-BlastR lentivirus. In the afternoon, cells in each well were transduced with a distinct, individual single gRNA expressing lentivirus at 2% v/v. On day 3, cells were split to ~5 x 105 cells/mL and Blasticidin was added at 10 µg/mL final concentration. At day 5, cells were centrifuged and resuspended with cXVIVO supplemented with 200 IU/mL IL-2, 5 ng/mL IL-7 and 10 µg/mL blasticidin at ~5 x 105 cells/mL. At day 7, cells were counted and diluted to 1 x 106 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2, 5 ng/mL IL-7 and 10 µg/mL blasticidin. At day 8 and day 10, cells were centrifuged and resuspended at 1 x 106 cells/mL with cXVIVO supplemented with 200 IU/mL IL-2 and 5 ng/mL IL-7. On day 12 morning, cells were centrifuged and resuspended at 2 x 106 cells/ml with cXVIVO supplemented with 200 IU/mL IL-2 and 12.5 µL/mL ImmunoCult human CD3/CD28/CD2 T cell activator for 8 hours or 48 hours.

extract_protocol:
Cells were centrifuged and resuspended in DNA/RNA Shield (Zymo Research) and sent for bulk RNAseq by Plasmidsaurus.
plasmidsaurus library preparation - conversion of mRNA into complementary DNA via reverse transcription and second-strand synthesis, followed by tagmentation, library indexing, and amplification.

treatment_protocol: 200 IU/mL IL-2 and 12.5 µL/mL ImmunoCult human CD3/CD28/CD2 T cell activator for 8 hours and 48 hours.

value: blood

value: CD4-positive, alpha-beta T cells

value: 8 hour ImmunoCult™ Human CD3/CD28/CD2 T Cell Activator

tag: experimental perturbation

value: CRISPRi knockdown of SIK3

tag: donor id

tag: donor age

tag: donor weight

tag: donor height

tag: donor smoker

value: No

tag: donor blood_type

value: O+

tag: anticoagulant

value: ACDA

tag: source

value: STEMCELL technologies

tag: donor sex

value: Female

tag: donor dev_stage

value: adult stage

tag: donor living_at_sample_collection

value: TRUE

tag: donor body_mass_index

tag: donor disease

value: Normal

tag: sample preservation_method

value: Zymo DNA/RNA Shield

tag: suspension depletion_factors

value: EasySep™ Human Naïve CD4+ T Cell Isolation Kit:CD8,CD14,CD16,CD19,CD20,CD25,CD36,CD56,TCRgd,GlyA,CD61,CD66b,CD123,HLA-DR,CD45RO

tag: donor ethnicity

value: Hispanic

tag: genetic perturbation_strategy

value: CRISPRi

tag: enriched cell_types

tag: library protocol

value: Plasmidsaurus RNA-Seq

tag: batch


title: ARPE-19 – QMR+Secretome Rescue 72h (biol rep 1) [TRR-B1]

description:
Library name: ARPE19_RESSEC_72h_Rep1_TRR_Batch1
ARPE-19 human retinal pigment epithelium; total RNA; paired-end; QMR/oxidative stress perturbation study; treatment=QMR+Secretome Rescue; timepoint=72h; OX=No; Rep1; sequencing batch=TRR_Batch1.

tag: cell line

tag: cell type

value: Retinal Pigment Epithelium

tag: treatment

value: no oxidative stress; QMR electromagnetic stimulation + Secretome (conditioned medium)


title: 3375_20

description: Library name: L2

tag: tissue

value: Whole worm

tag: genotype


title: 2DM2F103LU_S36

description: Library name: 2DM2F103LU_S36_R1_001

data_processing:
TempO-Seq sequences were aligned to the rat S1500+ probe sequences using Bowtie version 1.3.1. The Bowtie configuration allowed up to three mismatches and selected the single best alignment for reporting.
The aligned read counts for attenuated probes were properly readjusted to calculate unattenuated equivalent counts using the attenuation factors provided in the platform manifest.
Assembly: BioSpyder TempO-seq mouse S1500+ manifest
Supplementary files format and content: tab-delimited text file includes attenuation-adjusted raw probe counts for each sample

source_name: Lung

extract_protocol:
The majority of all tissues from all animals were collected within approximately 10 minutes of euthanasia. Tissue samples were collected following organ weight measurements in the following order: lung, heart, liver (left lobe), kidney, and ovary (no ovary weights were taken) from all remaining animals on study day 5 for transcriptomic analysis. Two samples of lung, heart, liver, and kidney tissue (approximately 5 mm3) were collected and placed into cryotubes containing RNAlater. The ovaries were collected whole bilaterally (one sample) and placed into cryotubes containing RNAlater. The tissue samples were stored at 2°C to 8°C for approximately 55 hours for rats or up to 48 hours for mice. The RNAlater was then removed and the samples were stored in a −85°C to −60°C freezer until processed for RNA isolation. Tissues were homogenized in QIAzol lysis buffer (Qiagen Inc., Valencia, CA) using the TissueLyser II bead-beating system followed by RNA extraction using the RNeasy 96 QIAcube HT kits (Qiagen Inc., Valencia, CA) with a DNA digestion step.
Isolated RNA was utilized for analysis using either the Mouse S1500+ v1.2 TempO-Seq (BioSpyder, Carlsbad, CA) platform with a minimum of 500 mapped read counts/transcript and approximately 1.5 million counts/sample. Work instructions developed by Battelle using the BioSpyder User Guide (https://www.biospyder.com/s/100802-TempO-Seq-User-Guide-rev-C-r8r7.pdf) were followed.

value: Lung

value: B6D2F1/Crl (BDF-1)

tag: Sex

value: female

tag: age

value: 9 weeks

tag: concentration (ppm)

tag: animal id

tag: sample status

value: Used in Analysis

tag: qc issue


title: 2DM3F203OV_S109

description: Library name: 2DM3F203OV_S109_R1_001

value: Ovary