title: shCMPK2, Induced, Replicate 3

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

description: Library name: 18_shCMPK2-NaB_C3-Pos_S60

data_processing:
Reads were aligned using Bowtie2 against human (hg19) and EBV (NC007605) genome, and RNA-Seq by Expectation Maximization (RSEM) was used to quantify transcripts and estimate fragments per kilobase of transcript per million fragments mapped values using Ensembl transcriptome information.
Assembly: human genome (hg19)  and EBV (NC007605)
Supplementary files format and content: Text and RSEM raw counts

source_name: Mutu I

growth_protocol: Mutu I cells were cultured in RPMI supplemented with 10%  FBS, 2 mM L-glutamine, 100 U/ml penicillin and 100 µg/ml streptomycin and maintained in incubator at 37 C and 5% CO2

extract_protocol:
Rneasy Plus mini kit (Qiagen, 74134)
Lexogen Quantseq 3’mRNAseq version 2 Library Prep kit FWD w/ UDI cat #: 191.96

treatment_protocol: Mutu I cells were transduced with lentivirus for either shControl, shRSAD2 or shCMPK2. After transduction, cells were treated with sodium butyrate (NaB)+TPA for 24 h to induce lytic EBV reactivation. Cells not treated with NaB+TPA were also cultured alongside.

value: Mutu I

value: EBV+ B-cell line

value: CMPK2 knockdown

value: NaB+TPA treated


title: eWAT_PHx_D3_3

status: Public on Jun 01 2026

type: SRA

city: Portland

first: Teresa

last: Zimmers

state: OR

address: 2730 S Moody Ave

department: CDCB

country: USA

institute: OHSU

description:
Library name: Sample 7
RNAs cleaned up, DNaseI treated

library_source: transcriptomic

data_processing:
Raw FASTQ files were uploaded to Partek (Illumina). Pre allignment QC was applied to test quality of reads. All samples passed QC with an average trim score of 39. Reads were then trimmed and aligned using the STAR function using mm39 as a reference index. We next proceeded with post-alignement QA/QC. Uniquely paired percentage was superior than 70% in all samples, and average quality score was superior than 39 in all samples..
Reads were then quantified using Partek E/M function. Counts were filtered by excluding feature with a maximun median counts ≤1.0. Filtered counts were then normalized based on median ratio (DESeq2 only).
Differential analysis was applied, using a multitest correction by FDR-Step up
Differentailly expression genes (Hamidi et, al_Adipose_PHx_2025.xls) were obtained by comparing PHx-day3 vs Sham, and Phx-day7 vs Sham. Data was then used for subsequent analysis by applying defined Fold change and FDR cutoff.
Assembly: mm39
Supplementary files format and content: DEGs file contains gene annotations and correspoding fold change, Log2FC, P-value and FDR for each gene. Two differential gene expression were analyzed, gene expression changes in PHx-Day3 vs Sham, and gene expression changes in PHx-Day7 vs Sham.

molecule: polyA RNA

organism: Mus musculus

source_name: Day3 post 70% hepatectomy

growth_protocol: 12 to 14 weeks old male C57bl6 mice were used

extract_protocol:
Total RNAs were extracted from nitrogen frozen bulk eWAT using QIAzol lysis reagent (Qiagen, #79306). RNA cleanup and DNAse treatment were performed using the RNeasy cleanup kit (Qiagen, #74204) and DNaseI
Library construction performed at Novogene

treatment_protocol: Animals were subjected to sham surgery or 70% partial hepatectomy. On day3, and day7 post-surgery, animals were euthanized, then epididymal white adipose tissue were collected to extract total RNA for subsequent     RNA0sequencing experiment. 4 sham control animals, 5 and 3 partial hepatectomy animals were used for day3 and day7 respectively.

tag: tissue

value: eWAT


title: Differentiated HCT116 cells induced by PPARG expression

city: Nanjing

first: Ying

last: Cao

address: 12 Xuefu Rd., Pukou High-Tech Zone

country: China

institute: Nanjing University

description: Library name: HCT116_PPARG

data_processing:
CASAVA base recognition
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data, then mapped to GRCh38 whole genome using Hisat2 software.
The featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Assembly: GRCh38
Supplementary files format and content: Excel files including fpkm values for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Cell line

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS at 37°C in 5% CO2 for desired period of time when cells with forced expression of MYOD1 or PPARG underwent significant phenotypic change.

extract_protocol:
Cells were collected with trypsinization and total RNA was extract with TRIzol using the protocol from the manufacturer.
Libraries were contructed with NEBNext® Ultra™ RNA Library Prep Kit for Illumina® using the protocol from the manufacturer.

tag: cell line

tag: cell type

value: Colon cancer cell line

tag: genotype

value: Forced expression of PPARG

tag: treatment

value: HCT116 cells transfected with lentivirus for PPARG expression


title: QEIII-180

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

description: gene expression from FFPE sample

hyb_protocol: The Affymetrix Human U133 GeneChip (Affymetrix, Santa Clara, CA, USA) was used for microarray gene expression analysis

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000.

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: locoregionally advanced NPC FFPE sample

label_protocol: RNA integration using an Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA). Total RNA was amplified using an Ovation FFPE WTA System (NuGEN, San Carlos, CA, USA), and an Encore Biotin Module (NuGEN) was used for fragmentation and labeling.

growth_protocol: All paraffin was removed from freshly cut FFPE tissue before RNA purification, and the sample was briefly heated in RNeasy lysis bugger

extract_protocol: RNA was extracted from FFPE samples using the QIAGEN FFPE RNeasy kit (QIAGEN GmbH, Hilden, Germany).

treatment_protocol: The patients were recruited from seven oncology centers in Hong Kong between September 2006 and September 2012 and were treated with concurrent chemoradiotherapy plus (neo)-adjuvant chemotherapy. The median follow-up time for all patients was 8.4 years. Formalin-fixed paraffin-embedded (FFPE) samples from the nasopharynx were prospectively archived

tag: gender

value: M

tag: age


title: eWAT_PHx_D3_2

description:
Library name: Sample 6
RNAs cleaned up, DNaseI treated


title: shCMPK2, Induced, Replicate 2

description: Library name: 17_shCMPK2-NaB_C2-Pos_S59


title: Differentiated HCT116 cells induced by MYOD1 expression

description: Library name: HCT116_MYOD1

value: Forced expression of MYOD1

value: HCT116 cells transfected with lentivirus for MYOD1 expression


title: QEIII-167

description: gene expression from FFPE sample


title: eWAT_PHx_D3_1

description:
Library name: Sample 5
RNAs cleaned up, DNaseI treated


title: shCMPK2, Induced, Replicate 1

description: Library name: 16_shCMPK2-NaB_C1-Pos_S58


title: QEIII-133

description: gene expression from FFPE sample


title: WT

city: Berlin

first: Pawel

last: Lisowski

address: Hannoversche Str. 28

country: Germany

institute: Max-Delbrück-Center for Molecular Medicine (MDC) in the Helmholtz Association

description: Library name: P3163_SP200_006_H9_S15_L004

library_source: transcriptomic single cell

data_processing:
Raw sequence reads were aligned using CellRanger (version 8.0.0) against the Human genome GRCh38-2020-A reference provided by 10x Genomics. We used the filtered count matrix from the CellRanger output, which contains only barcodes associated with actual cells. Subsequent processing was performed using Scanpy (version 1.10.3; doi: 10.1186/s13059-017-1382-0). We first filtered out genes detected in fewer than 10 cells and calculated the top 2000 highly variable genes using the “seurat_v3” flavor of Scanpy. To remove doublets, we applied scVI (version 1.2.0; doi: 10.1038/s41587-021-01206-w) on this preliminary filtered matrix, using an NVIDIA RTX A4500 GPU for accelerated computation. After doublet removal, the CellRanger filtered matrix was re-imported, and barcodes classified as doublets were excluded. We then performed filtering on the re-imported matrix by removing genes present in fewer than 3 cells and cells expressing fewer than 200 genes. We excluded cells with a number of detected genes above the 98th percentile, thereby removing the top 2% of cells with the highest gene counts, which likely correspond to doublets or other artifacts. Additionally, we filtered out cells where mitochondrial gene counts constituted 20% or more of the total counts, as well as those with fewer than 40 total counts, to eliminate low-quality or dying cells. Post-clustering we identified a small cluster separating from the rest of the cells. Closer examination showed high ribosomal expression and we consequently removed this cluster since this indicates a population of stressed cells.
Assembly: GRCh38-2020-A
Supplementary files format and content: TSV (Tab-Separated Values) files including barcodes, features and and matrix tsv.gz files.

source_name: human forebrain micropatterned organoid

growth_protocol: Organoids featuring a prominent neural rosette can be generated by seeding stem cells directly on the chip from Day 0. Specifically, human pluripotent stem cells, 80–90% confluent, were dissociated to single cells with Accutase (Sigma-Aldrich, A6964-500ML)), and 450.000 cells were seeded in a dropwise manner on top of the coverslips already in pre-warmed StemFlex medium (Thermo, A3349401) supplemented with 1X antibiotic-antimycotic (Thermo, 15240062) and ROCK inhibitor CEPT cocktail (MedChemExpress, HY-K1043) which consists in 50nM Chroman 1, 5µM Emricasan, 1x Polyamine Supplement, 0.7µM trans-ISRIB. Two days after seeding, stem cell medium was replaced with neural induction medium as following: Cortical differentiation medium (CDM) I, containing DMEM-F12 No Glutamine (Thermo, 21331020), 20% Knockout Serum Replacement (KSR) (Thermo, 10828028), 0.1 mM Minimum Essential Medium non-essential amino acids (MEM-NEAA) (Thermo, 11140050), 1 mM Sodium pyruvate (Thermo, 11360070), 0.1 mM 2-mercaptoethanol (Thermo, 31350010), 100 U/ml penicillin and 100 μg/ml streptomycin (Thermo, 15140122). From day 0 to day 3, CDMI was supplemented with TGFβ inhibitor SB431542 (Tocris, 1614/10), BMP inhibitor LDN-193189 (Adooq Bioscience, A11478) and WNT inhibitor IWR1e (Sigma-Aldrich, 681669) at a final concentration of 10µM, 0.2µM and 3µM respectively. The medium was also supplemented with ROCK inhibitor (CEPT cocktail). From day 3 to day 9, we supplemented the neural induction medium only with 25nM Chroman-1. From day 9 to 18, organoids were cultured in CDM II and 25nM Chroman-1. CDM II consists in DMEM/F12, HEPES medium (Thermo, 11330032), 1mM Glutamax (Thermo, 31331028), 1% N2 supplement (Thermo, 17502001), 1% Chemically Defined Lipid Concentrate (Thermo, 11905031), 1x Antibiotic-Antimycotic (Thermo, 15240062). From day 18 to 24, medium was changed to CDM III and 25nM Chroman-1, consisting of CDM II supplemented with 10% fetal bovine serum (FBS) (Thermo, 16140071), 5 μg/ml heparin (Sigma-Aldrich, H3149-10KU). From day 24, organoids were cultured in CDM IV, consisting of CDM III supplemented with B27 supplement minus vitamin A (Thermo, A3582801). To generate organoids suitable for long-term cultures, early neural progenitors are seeded following 10 days of neural induction. Specifically, 35mm dishes (or 6 wells plates) were coated with 10 µg/ml Laminin incubated for at least 2 h at 37°C and followed by 1x wash with DPBS+/+. Human ESC cell lines (H9 and DYRK1A+/-) were seeded at a density of 1 million cells per well in StemFlex medium supplemented with 10 µM ROCK inhibitor (Y-27632; Cayman Chemical, 10005583-10) and maintained in 2D culture until the completion of neural induction (D10). Two days after seeding, the cells reach 90% confluency and the medium was replaced with Neural maintenance medium (NMM) which consists in 1:1 mixture of N-2 and B-27-containing media. N-2 medium consists of DMEM/F-12 GlutaMAX, 100 µM N2 supplement, 5 μg/ml insulin (Sigma-Aldrich, I9278-5ML), 1 mM L-glutamine (Thermo, 25030024), 100 μM MEM non-essential amino acids, 100 μM 2-mercaptoethanol, 0.5X Antibiotic-antimycotic. B-27 medium consists of Neurobasal medium (Thermo, 21103049), 1× B-27 supplement minus Vitamin A, 2.5 mM L-glutamine, 0.5X Antibiotic-antimycotic. 2-Mercaptoethanol was added after medium filtration. The neural fate was induced for 10 days through the classical Dual-SMAD inhibition targeting TGF-ß and BMP pathways, 10µM SB431542 and 0.2µM LDN193189 HCl. Afterwards, cells were passaged with gentle dissociation reagent (STEMcell Technologies, 100-1077) allowing the formation of small clumps and then seeded in 1:3 ration on micropatterned chips previously coated with 20µg ml-1 and 10µg ml-1 CellAdhere™ Laminin-521 (STEMCELL Technologies, 200-0117) and 5µM Y-27632 which is known to improve cell viability and reduce cell stress. Specifically, micropatterned glass coverslips (CYTOO chips - Arena 500A; 4Dcell coverslips 500µm) were coated with 20µg ml-1 and 10µg ml-1 CellAdhere™ Laminin-521 (STEMCELL Technologies, 200-0117) respectively. Laminin was diluted in DPBS+/+ (Gibco, 14040091) and the coverslips were placed face-down on a drop of 250µl laminin in a 10cm Petri dish covered with Parafilm. The Petri dish was then sealed with Parafilm and placed at 4°C for overnight coating or, alternatively, at least 2 h at 37°C. Prior seeding, the coverslips were washed and transferred to a 6-well plate and washed with DPBS+/+ five times with serial dilution (1:4) and two complete washes. The coverslips sit in DPBS+/+ at 37°C until seeding.  Organoids were then cultured until the desired time point and then processed according to the specific experiment (immunofluorescence, single-cell, scRNA sequencing, proteomics). To improve organoid attachment to the glass substrate, complete medium change was avoided and 60% of it was replaced instead with fresh medium. In this way, we also prevented additional stress due to forces exerted by the fluid. Exogenous ECM components were supplemented to the medium to reduce cell/organoid detachment for long-term organoid culture. Every 10 days, 500 µl of laminin-521(5µg/ml) was directly pipetted into 2.5 ml of medium.

extract_protocol:
Organoids were dissociated and fixed for single-cell RNA sequencing using manufacturer protocolsa standardized protocol [ref]. Organoids were first incubated in TrypLE Express (Thermo, 12604054) at 37°C for 10 minutes, with gentle pipetting using P1000 and P200 pipettes to obtain a single-cell suspension. Cells were passed through a 40 µm FlowMi filter (Merck, BAH136800040), washed with 0.04% BSA in DPBS, and centrifuged at 200×g for 5 minutes using a swinging-bucket rotor. The cell pellet was resuspended in fixation buffer (4% paraformaldehyde final concentration) and incubated overnight at 4°C. After fixation, cells were quenched in ice-cold quenching buffer, and an enhancer solution was added before gradual glycerol supplementation (10% final concentration) to improve stability. Fixed cells were stored at -80°C for up to six months. Before processing, samples were thawed at RT, centrifuged at 850×g, and resuspended in a post-storage buffer containing 0.2 U/µl RNase inhibitor (Thermo, EO0382). Propidium iodide (Miltenyi Biotec, 130-093-233) staining was used to assess cell viability, followed by fluorescence microscopy for quality control. The prepared single-cell suspensions were immediately processed on the 10x Chromium platform for single-cell RNA sequencing
Barcoding and cDNA amplification were carried out using the Chromium Single Cell 3'  (vNext) Reagent Kit.

value: human forebrain micropatterned organoid

value: forebrain organoid

value: WT

value: isogenic control


title: DYRK1A

description: Library name: P3163_SP200_003_DYRK1a_S14_L004

value: isogenic variant introduction


title: eWAT_Sham_4

description:
Library name: Sample 4
RNAs cleaned up, DNaseI treated

source_name: Pre 70% hepatectomy


title: QEIVB-16

description: gene expression from FFPE sample


title: shRSAD2, Induced, Replicate 3

description: Library name: 12_shRSAD2-NaB_R3-Pos_S54

value: RSAD2 knockdown


title: eWAT_Sham_3

description:
Library name: Sample 3
RNAs cleaned up, DNaseI treated


title: shRSAD2, Induced, Replicate 2

description: Library name: 11_shRSAD2-NaB_R2-Pos_S53

value: Mutu I


title: QEIVA-10

description: gene expression from FFPE sample


title: NPC, CR_2, procainimide, batch2, rna-seq

city: Shanghai

first: Chenhan

last: Liao

address: 393 Middle Huaxia Road, Pudong, Shanghai

institute: ShanghaiTech University

description:
Library name: NPC_CR_procainimide_2_batch2
CR2+P

data_processing:
Raw reads were processed to remove adapters using cutadapt version 0.6.10, after which clean reads were aligned to human genome reference (hg38) with STAR in two-pass mode. Gene-level read counts were extracted using mode of STAR (--quantMode GeneCounts).
Assembly: hg38
Supplementary files format and content: txt

source_name: NPC

growth_protocol: HeLa cells were maintained in DMEM high glucose with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃, NPC cells were  maintained in STEMdiff™ Neural Progenitor Medium (Cat. NO. 05833).

extract_protocol:
Total RNA was extracted from each sample using the RNA mini kit (Qiagen, Germany), with quality assessed by gel electrophoresis and a Qubit. 1 μg of RNA was utilized to construct libraries.
1 μg of RNA was utilized to construct libraries with the VAHTS Total RNA-seq (H/M/R) Library Prep Kit for Illumina®. Libraries were sequenced as 151-bp paired-end reads on the Illumina NovaSeq 6000 by Genergy Biotechnology Co. Ltd. (Shanghai, China), following the manufacturer's guidelines

value: NPC

value: neural progenitor cell

value: C596R heterozygous

value: ES cell differentiation + procainimide


title: shRSAD2, Induced, Replicate 1

description: Library name: 10_shRSAD2-NaB_R1-Pos_S52

value: EBV+ B-cell line

value: NaB+TPA treated


title: NPC, CR_1, procainimide, batch2, rna-seq

description:
Library name: NPC_CR_procainimide_1_batch2
CR1+P


title: eWAT_Sham_2

description:
Library name: Sample 2
RNAs cleaned up, DNaseI treated

value: eWAT


title: QEIII-117

description: gene expression from FFPE sample

value: M


title: lncRNA profile of whole blood cells - SAMPLE 2-10

first: Chunxia

last: Wang

state: Shanghai

address: No.355 Luding Road, Shanghai Children's Hospital, Shanghai Jiao Tong University School of Medicine

department: Department of Critical Care Medicine

institute: 上海交通大学附属儿童医院

hyb_protocol: Agilent Gene Expression Hybridization Kit (Agilent p/n 5188-5242) was used for hybridization followed by washing

scan_protocol: The results were scanned by Agilent Microarray Scanner (Agilent p/n G2565BA) and data were extracted by Agilent Feature Extraction software.

data_processing:
Based on the first batch result of Arraystar human LncRNA microarray using 16 cases (12 cases with bacteria sepsis vs. 4 cases with non-bacteria sepsis), we firstly revealed the potential key relationship between lncRNAs landscape and pathogen infection (Preliminary data, data not shown). Then, the other batch of Arraystar human LncRNA microarray using 40 cases (24 cases with bacteria sepsis vs. 16 cases with non-bacteria cases) were added. Totally, these two batches included 36 cases with bacterial sepsis and 20 children with non-bacterial sepsis. To remove the batch effects, we merged 2 batches results, and all analyses were conducted with R version 4.0.5 and sva packages.
Use the “limma” package to identify the differentially expressed genes (DEGs) between bacteria sepsis and non-bacteria sepsis. The screening condition were p-value<0.05 and |logFC|≥1. Differentially expressed lncRNAs and mRNAs were screened out by volcano plot.

source_name: whole blood cells

label_protocol: Arraystar Flash RNA Labeling Kit

growth_protocol: Blood samples were collected before received inpatient treatment initiation. Groups: Bacterial sepsis vs. Non-bacterial sepsis

extract_protocol: Arraystar human LncRNA/mRNA microarray was performed on whole blood samples of 36 cases with bacterial sepsis and 20 children with non-bacterial sepsis to analyze differentially expressed LncRNAs. All experimental procedures were performed following Arraystar standard protocol. Briefly, TRIzol reagent were used to prepare RNA samples from whole blood cells, and RNA quantification and quality control (QC) was performed.

treatment_protocol: EDTA-anticoagulated whole blood was collected and stored at -80oC for further microarray analysis

tag: infection group

value: Bacterial sepsis

value: whole blood cells


title: eWAT_Sham_1

description:
Library name: Sample 1
RNAs cleaned up, DNaseI treated


title: shControl, Induced, Replicate 3

description: Library name: 6_shCtrl-NaB_NC3-Pos_S48


title: QEIII-49

description: gene expression from FFPE sample

value: F


title: NPC, CR_2, NC, batch2, rna-seq

description:
Library name: NPC_CR_NC_2_batch2
CR2

value: ES cell differentiation


title: shControl, Induced, Replicate 2

description: Library name: 5_shCtrl-NaB_NC2-Pos_S47

value: WT


title: SL6394 2 NMO lesions 17 day post injection

city: Zurich

first: Marina

last: Herwerth

address: Winterthurerstrasse 190

country: Switzerland

institute: University of Zurich

description: Library name: SL6622

data_processing:
Reads were processed and aligned to the mouse reference genome (GRCm39) using Space Ranger (v3.1.3, 10x Genomics) with default parameters. Gene expression matrices were generated from the filtered feature-barcode matrices.
Assembly: GRCm39 (mm39)
Supplementary files format and content: barcodes.tsv; list of spatial barcodes
Supplementary files format and content: features.tsv; list of detected genes
Supplementary files format and content: matrix.mtx; gene expression count matrix
Supplementary files format and content: annotation.csv; comma-separated spot annotation
Supplementary files format and content: .tif; h&e image
Library strategy: Spatial Transcriptomics

source_name: Somatosensory cortex

extract_protocol:
Animals were perfused with 4% PFA supplemented with 10% formalin and tissue was embeded in paraffin, then cut at 5 um thickness
Libraries were prepared using the Visium HD Spatial Gene Expression protocol (10x Genomics) following the manufacturer’s instructions. Sequencing was performed at the Functional Genomics Center Zurich on an Illumina NovaSeq X Plus system with 150 bp paired-end reads (read configuration: 150:10:10:150) across two lanes of a 10B flow cell.

treatment_protocol: After craniotomy and durotomy, a mixture of human IgG1 recombinant AQP4-IgG antibody and human complement was injected into the somatosensory cortex of Aldh1l1-eGFP mice.

value: Somatosensory cortex

value: AQP4-IgG injection


title: NPC, CR_1, NC, batch2, rna-seq

description:
Library name: NPC_CR_NC_1_batch2
CR1


title: QEIII-159

description: gene expression from FFPE sample


title: shControl, Induced, Replicate 1

description: Library name: 4_shCtrl-NaB_NC1-Pos_S46


title: SL6392 2 NMO lesions 17 day post injection

description: Library name: SL6394


title: NPC, WT_2, NC, batch2, rna-seq

description:
Library name: NPC_WT_NC_2_batch2
WT2


title: shCMPK2, Uninduced, Replicate 3

description: Library name: 15_shCMPK2-NaB_C3-Neg_S57

value: CMPK2 knockdown

value: Untreated


title: PYIII-105

description: gene expression from FFPE sample


title: QEIII-11

description: gene expression from FFPE sample


title: SL6390 2 NMO lesions 5 day post injection

description: Library name: SL6392


title: NPC, WT_1, NC, batch2, rna-seq

description:
Library name: NPC_WT_NC_1_batch2
WT1

value: NPC


title: shCMPK2, Uninduced, Replicate 2

description: Library name: 14_shCMPK2-NaB_C2-Neg_S56

value: Mutu I


title: QEIII-116

description: gene expression from FFPE sample


title: SL6622 2 NMO lesions 5 day post injection

description: Library name: SL6390


title: PISH-mesenchymal stem cell-2

first: xin

last: wen

address: 321 Zhongshan Road, Gulou District

department: Department of Rheumatology and Immunology

description: Library name: sample4

data_processing:
Reads for each sample were first mapped to a reference genome with HISAT2 software. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: human GRCh38
Supplementary files format and content: TXT files including FPKM values for all samples

source_name: umbilical cord

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the  manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Then the libraries were constructed using VAHTS Universal V10 RNA-seq Library Prep Kit (Premixed Version) according to the manufacturer’s instructions.

value: umbilical cord

value: mesenchymal stem cell


title: shCMPK2, Uninduced, Replicate 1

description: Library name: 13_shCMPK2-NaB_C1-Neg_S55

value: EBV+ B-cell line


title: PISH-mesenchymal stem cell-1

institute: Department of Rheumatology and Immunology

description: Library name: sample3


title: QEIVB-3

description: gene expression from FFPE sample


title: SL6002 2 NMO lesions 3 day post injection

description: Library name: SL6002


title: shRSAD2, Uninduced, Replicate 3

description: Library name: 9_shRSAD2-NaB_R3-Neg_S51

value: RSAD2 knockdown


title: CCL2 deficient mesenchymal stem cell -2

description: Library name: sample2


title: QEIII-55

description: gene expression from FFPE sample


title: SL6001 1 NMO lesion 3 day post injection

description: Library name: SL6001


title: PYIII-125

description: gene expression from FFPE sample


title: SL6000 2 NMO lesions 3 day post injection

description: Library name: SL6000


title: shRSAD2, Uninduced, Replicate 2

description: Library name: 8_shRSAD2-NaB_R2-Neg_S50


title: CCL2 deficient mesenchymal stem cell -1

description: Library name: sample1


title: shRSAD2, Uninduced, Replicate 1

description: Library name: 7_shRSAD2-NaB_R1-Neg_S49


title: PYIII-96

description: gene expression from FFPE sample


title: MCF7_gata3_ko,330, rep3

city: Hangzhou

first: Yatao

last: Chen

address: 150 Dongfang Street, Xiasha Street, Qiantang District

institute: Chinese Academy of Sciences

description: Library name: 330_3

data_processing:
After quantified by Qubit 4.0, the sequencing library was performed on NovaSeq6000 platform using NovaSeq Reagent Kit.
Assembly: Tthe expression level of each transcript was calculated according to the transcripts per million reads (TPM) method. RSEM was used to quantify gene abundances.
Supplementary files format and content: txt file includes FPKM values for each Sample

source_name: cell line

growth_protocol: MCF7 cells in RPMI1640  supplemented with 10% FBS and 1% PS at 37°C and 5% CO2 in a humidified incubator.

extract_protocol:
Total RNA was extracted from the tissue using TRIzol® Reagent according the manufacturer’s instructions.Then RNA quality was determined by 5300 Bioanalyser (Agilent) and quantified using the ND-2000 (NanoDrop Technologies). Only high-quality RNA samplewas used to construct sequencing library.
RNA purification, reverse transcription, library construction, and sequencing were conducted by Suzhou GENEWIZ (Suzhou, China) in accordance with the manufacturer's instructions. The RNA - seq transcriptome library was prepared using 1μg of total RNA, following the Illumina® Stranded mRNA Prep, Ligation protocol (San Diego, CA). Messenger RNA was initially isolated using the polyA selection method with oligo (dT) beads and then fragmented using fragmentation buffer. Subsequently, double - stranded cDNA was synthesized using random hexamer primers. The synthesized cDNA underwent end - repair, phosphorylation, and adapter addition as per the library construction protocol. Libraries were size - selected to obtain cDNA target fragments of 300-400bp using magnetic beads, followed by PCR amplification for 10-15 cycles.

value: cell line

value: Human breast cancer cells

value: GATA3-R330 overexpression

value: Lentivirus infection

tag: batch


title: SL5656 2 NMO lesions 3 day post injection

description: Library name: SL5656


title: Wildtype, Mouse Achilles Tendon, Female, Cage Activity, 4

city: Ann Arbor

first: Adam

last: Abraham

state: MI

address: 2800 Plymouth Rd

department: Orthopaedic Surgery

institute: University of Michigan

description:
Library name: X9789.SNEL.36
Column name in gene_expected_count_batch2.annot.txt :  X9789.SNEL.36

data_processing:
The reads were trimmed using Cutadapt v2.3
FastQC v0.11.8 was used to ensure the quality of data
Fastq Screen v0.13.0 was used to screen for various types of contamination
Reads were mapped to the reference genome GRCm38 (ENSEMBL), using STAR v2.7.8a  and assigned count estimates to genes with RSEM v1.3.3.  Alignment options followed ENCODE standards for RNA-seq.
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw counts for each sample
Supplementary files format and content: tab delimited csv file includes FPKM for each sample

source_name: Achilles Tendon

extract_protocol:
Tissues were mechanically pulverized in TRIzol, and total RNA was isolated using spin-columns, (with on column genomic DNA digestion. RNA
RNA libraries  for RNA-seq were prepared with were prepped UltraExpress RNA Library Prep Kit following manufacters instructions

value: Achilles Tendon

value: W

value: C


title: MCF7_gata3_ko,330, rep2

description: Library name: 330_2


title: shControl, Uninduced, Replicate 3

description: Library name: 3_shCtrl-NaB_NC3-Neg_S45

value: WT


title: PYIII-57

description: gene expression from FFPE sample

value: F


title: AMPKcKO, Mouse Achilles Tendon, Male, Cage Activity, 3

description:
Library name: X9789.SNEL.34
Column name in gene_expected_count_batch2.annot.txt :  X9789.SNEL.34

value: A


title: PYIVB-5

description: gene expression from FFPE sample

value: M


title: shControl, Uninduced, Replicate 2

description: Library name: 2_shCtrl-NaB_NC2-Neg_S44

value: Untreated


title: MCF7_gata3_ko,330, rep1

description: Library name: 330_1


title: PYIVA-34

description: gene expression from FFPE sample


title: Wildtype, Mouse Achilles Tendon, Male, Wheel Runner, 3

description:
Library name: X11116.MK.9
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.9

value: R


title: MCF7_gata3_ko,308, rep3

description: Library name: 308_3

value: GATA3-X308 overexpression


title: shControl, Uninduced, Replicate 1

description: Library name: 1_shCtrl-NaB_NC1-Neg_S43

value: Mutu I


title: Wildtype, Mouse Achilles Tendon, Male, Wheel Runner, 2

description:
Library name: X11116.MK.8
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.8


title: U2OS ZAK-KO + ZAKɑ full-length rescue, replicate 2, 1 µM CC885

city: Copenhagen

first: Zhenzhen

last: Wu

address: Blegdamsvej 3B, Maersk Building,

department: Department of Cellular and Molecular Medicine

country: Denmark

institute: University of Copenhagen

description: Library name: ZAK_CC885_Rep2

library_source: genomic

data_processing:
Pulled libraries were demultiplexed based on barcoded adaptor sequences using SeqKit.
Raw reads were quality filtered and Illumina adaptor trimmed using TrimGalore.
PCR duplicates removed using SeqKit.
Barcode and UMI tags were trimmed using TrimGalore.
Reads aligned using STAR and crosllink sites identified using bedtools as described Buchbender et al.
Assembly: GRCh38/hg38
Supplementary files format and content: Bedgraph
Library strategy: iCLIP

source_name: bone

growth_protocol: DMEM, clucose concentration: 4.5g/L, with L-Glutamine, 10% fetal bovine serum, sodium pyruvate, 1x penicillin/streptomycin. U-2 OS cells were cultured at 37°C supplied with 5% CO2.

extract_protocol:
Cells were subjected to 254 nm (UVC) irradiation with a dose of 150 mJ/cm². Cell pellets were lysed and sonicated using Branson Digital Sonifier.
iCLIP2-seq libraries were prepared following the protocol described by Buchbender et al. (“Improved library preparation with the new iCLIP2 protocol,” Methods 178 (2020): 33–48), with adaptations inspired by Cordiner et al. (“Temporal-iCLIP captures co-transcriptional RNA-protein interactions,” Nat Commun 14(1):696, 2023). Cells were cultured in 15 cm dishes and harvested at ~80% confluence; two plates were used as starting material per condition. Final pooled libraries were size-selected for fragments ≥155 bp using AMPure XP beads (Beckman Coulter). Library quality was assessed with the Agilent High Sensitivity D1000 ScreenTape assay.

value: bone

value: U-2 OS

value: osteosarcoma cell

value: 1 µM CC885, 6 hour


title: PYIVA-35

description: gene expression from FFPE sample


title: MCF7_gata3_ko,308, rep2

description: Library name: 308_2

value: cell line

value: Human breast cancer cells


title: U2OS ZAK-KO + ZAKɑ full-length rescue, replicate 1, 1 µM CC885

description: Library name: ZAK_CC885_Rep1


title: Wildtype, Mouse Achilles Tendon, Male, Wheel Runner, 1

description:
Library name: X11116.MK.7
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.7

value: Achilles Tendon


title: PYIII-122

description: gene expression from FFPE sample


title: MCF7_gata3_ko,308, rep1

description: Library name: 308_1

value: Lentivirus infection


title: AMPKcKO, Mouse Achilles Tendon, Female, Wheel Runner, 4

description:
Library name: X11116.MK.5
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.5


title: U2OS ZAK-KO + ZAKɑ full-length rescue, replicate 1, 15 µM lactimidomycin

description: Library name: ZAK_LTM_Rep1_batch3

value: 15 µM lactimidomycin, 1 hour


title: MCF7_gata3_ko,2R_A, rep3

description: Library name: 2R_A_3

value: GATA3-R329R330-A overexpression


title: PYIII-35

description: gene expression from FFPE sample

value: F


title: PYIII-28

description: gene expression from FFPE sample


title: AMPKcKO, Mouse Achilles Tendon, Female, Wheel Runner, 3

description:
Library name: X11116.MK.4
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.4

value: A


title: U2OS ZAK-KO + ZAKɑ Δ417-422 + Δ611-617 rescue, replicate 2

description: Library name: ZAK_d417-422_d611-617_Rep2

value: same amount of DMSO, 15 min


title: MCF7_gata3_ko,2R_A, rep2

description: Library name: 2R_A_2


title: QEIVB-1

description: gene expression from FFPE sample

value: M


title: Wildtype, Mouse Achilles Tendon, Female, Wheel Runner, 2

description:
Library name: X11116.MK.3
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.3

value: W

value: R


title: U2OS ZAK-KO + ZAKɑ Δ417-422 + Δ611-617 rescue, replicate 1

description: Library name: ZAK_d417-422_d611-617_Rep1


title: MCF7_gata3_ko,2R_A, rep1

description: Library name: 2R_A_1


title: PYIVB-51

description: gene expression from FFPE sample


title: U2OS ZAK-KO + ZAKɑ Δ768-780 rescue, replicate 1, 0.19 µM anisomycin

description: Library name: ZAK_d768-780_AnL_Rep1

value: 0.19 µM Anisomycin, 15 min


title: AMPKcKO, Mouse Achilles Tendon, Male, Cage Activity, 2

description:
Library name: X11116.MK.25
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.25

value: C


title: MCF7_gata3_ko,WT, rep3

description: Library name: WT_3

value: GATA3-WT overexpression


title: AMPKcKO, Mouse Achilles Tendon, Male, Cage Activity, 1

description:
Library name: X11116.MK.24
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.24


title: U2OS ZAK-KO + ZAKɑ 1-713, replicate 2

description: Library name: ZAK_1-713_AnL_Rep2

value: bone

value: U-2 OS

value: osteosarcoma cell


title: PYIVB-16

description: gene expression from FFPE sample


title: MCF7_gata3_ko,WT, rep2

description: Library name: WT_2

value: cell line

value: Human breast cancer cells


title: AMPKcKO, Mouse Achilles Tendon, Female, Wheel Runner, 2

description:
Library name: X11116.MK.23
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.23

value: Achilles Tendon


title: MCF7_gata3_ko,WT, rep1

description: Library name: WT_1

value: Lentivirus infection


title: U2OS ZAK-KO + ZAKɑ 1-713, replicate 1

description: Library name: ZAK_1-713_AnL_Rep1


title: QEIII-21

description: gene expression from FFPE sample


title: Wildtype, Mouse Achilles Tendon, Male, Cage Activity, 3

description:
Library name: X11116.MK.22
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.22


title: QEIII-123

description: gene expression from FFPE sample


title: U2OS ZAK-KO + ZAKɑ full-length rescue, replicate 1, batch 3

description: Library name: ZAK_Rep1_batch3

value: same amount of DMSO as control, 15 min


title: NPC, AV_3, rna-bis-seq

description: Library name: NPC_AV_3_rna_bis_seq

data_processing:
Raw reads were trimmed using cutadapt with paired end mode. Reads shorter than 20 bp were excluded from subsequent analysis. Then, the reads were aligned to human rRNA and tRNA using meRanT.pl from meRanTK. Unmapped reads were retained for further analysis. Unmapped reads were aligned to human genome (hg38) using meRanGs.pl from meRanTK
Then, control sequence was used to calculate the bisulfite conversion rate. Methylation levels were extracted using bisulfite conversion rates and meRanCall.pl from meRanTK
Assembly: hg38
Supplementary files format and content: txt
Library strategy: RNA-BisSeq

growth_protocol: NPCs were  maintained in STEMdiff™ Neural Progenitor Medium (Cat. NO. 05833).

extract_protocol:
Total RNA was extracted from each sample using the RNA mini kit (Qiagen, Germany), with quality assessed by gel electrophoresis and a Qubit.
Watchmaker RNA Library Prep Kit was employed to deplete rRNA. Following RNase H and DNase I treatments, RNA purification was achieved using VAHTS RNA Clean Beads. The RNA was then subjected to bisulfite conversion with the EZ RNA Methylation Kit. After treatment, RNA was purified and reverse transcribed to cDNA. The cDNA was further purified and amplified using the Equinox Uracil Tolerant PCR Master Mix, with 15 cycles. Quantification of the libraries was performed using a Qubit fluorometer, after which they were sequenced on NovaSeq 6000 platform.

value: NPC

value: neural progenitor cell

value: DNMT1 A570V homozygous mutation

value: ES cell differentiation


title: Wildtype, Mouse Achilles Tendon, Male, Cage Activity, 2

description:
Library name: X11116.MK.21
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.21

value: W


title: U2OS WT, replicate 1

description: Library name: U2OS_Empty_Rep1


title: NPC, AV_2, rna-bis-seq

description: Library name: NPC_AV_2_rna_bis_seq


title: PYIII-91

description: gene expression from FFPE sample

value: F


title: Wildtype, Mouse Achilles Tendon, Male, Cage Activity, 1

description:
Library name: X11116.MK.20
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.20


title: QEIII-104

description: gene expression from FFPE sample

value: M


title: U87-R, STM2457, rep 2, m6A eCLIP

city: New Haven

first: Sigrid

last: Nachtergaele

state: CT

address: 260 Whitney Ave

department: Molecular, Cellular, and Developmental Biology

institute: Yale University

description: Library name: Sample 16

data_processing:
Trim UMIs and for quality/adaptors (umi_tools, cutadapt)
Filter repetitive elements and genome alignment (STAR)
Remove PCR duplicates (umi_tools)
CLIPper for peak calling (peak calling, input normalization, and target annotation)
PureCLIP for single nucleotide site calling (read 5' mismatch stripping, single nucleotide site calling with input normalization, and target annotation)
Assembly: hg38
Supplementary files format and content: txt files of m6A peaks and m6A crosslink sites

source_name: U87 MG, TMZ resistant

growth_protocol: U87 MG and U87-R cells were grown in EMEM with 10% fetal bovine serum and 1% penicillin/streptomycin. Growth media for U87-R cells was also supplemented with 50uM temozolomide.

extract_protocol:
Total RNA was extracted from cells using the QIAGEN RNeasy Midi Kit, according to manufacturers instructions. Total RNA was sent to Eclipse Bioinnovations for processing, IP, library preparation, and analysis.
Total RNA was processed as per EclipseBio protocols for m6A-eCLIP: polyA selection, fragmentation, m6A immunoprecipitation and crosslinking, input and IP processing, reverse transcription, and then library amplification.

treatment_protocol: Cells were treated 50uM STM2457 for 96 hours

value: U87 MG, TMZ resistant

value: glioma cultured cell line

value: 50uM STM2457, 96 hours


title: NPC, AV_1, rna-bis-seq

description: Library name: NPC_AV_1_rna_bis_seq


title: Wildtype, Mouse Achilles Tendon, Female, Wheel Runner, 1

description:
Library name: X11116.MK.2
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.2

value: R


title: U87-R, STM2457, rep 1, m6A eCLIP

description: Library name: Sample 15


title: PYIVB-8

description: gene expression from FFPE sample


title: NPC, HT_3, rna-bis-seq

description: Library name: NPC_HT_3_rna_bis_seq

value: DNMT1 A570V heterozygous mutation


title: AMPKcKO, Mouse Achilles Tendon, Female, Cage Activity, 2

description:
Library name: X11116.MK.19
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.19

value: A

value: C


title: U87-R rep 3, m6A eCLIP

description: Library name: Sample 14

value: DMSO control


title: NPC, HT_2, rna-bis-seq

description: Library name: NPC_HT_2_rna_bis_seq


title: PYIII-49

description: gene expression from FFPE sample


title: U87-R rep 2, m6A eCLIP

description: Library name: Sample 13


title: AMPKcKO, Mouse Achilles Tendon, Female, Cage Activity, 3

description:
Library name: X11116.MK.18
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.18

value: Achilles Tendon


title: NPC, HT_1, rna-bis-seq

description: Library name: NPC_HT_1_rna_bis_seq


title: AMPKcKO, Mouse Achilles Tendon, Female, Cage Activity, 1

description:
Library name: X11116.MK.17
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.17


title: PYIVA-25

description: gene expression from FFPE sample


title: U87-R rep 1, m6A eCLIP

description: Library name: Sample 12


title: NPC, WT_3, rna-bis-seq

description: Library name: NPC_WT_3_rna_bis_seq

value: WT


title: Wildtype, Mouse Achilles Tendon, Female, Cage Activity, 3

description:
Library name: X11116.MK.16
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.16


title: U87 MG rep 3, m6A eCLIP

description: Library name: Sample 11

source_name: U87 MG

value: U87 MG


title: NPC, WT_2, rna-bis-seq

description: Library name: NPC_WT_2_rna_bis_seq

value: NPC

value: neural progenitor cell


title: QEIVA-23

description: gene expression from FFPE sample


title: PYIII-101

description: gene expression from FFPE sample


title: Wildtype, Mouse Achilles Tendon, Female, Cage Activity, 2

description:
Library name: X11116.MK.15
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.15


title: U87 MG rep 2, , m6A eCLIP

description: Library name: Sample 10


title: NPC, WT_1, rna-bis-seq

description: Library name: NPC_WT_1_rna_bis_seq

value: ES cell differentiation


title: QEIVB-19

description: gene expression from FFPE sample


title: Wildtype, Mouse Achilles Tendon, Female, Cage Activity, 1

description:
Library name: X11116.MK.13
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.13

value: W


title: U87 MG rep 1, m6A eCLIP

description: Library name: Sample 9


title: NPC, HT_2, procainimide, rna-seq

description: Library name: NPC_HT_procainimide_2


title: PYIVA-15

description: gene expression from FFPE sample


title: AMPKcKO, Mouse Achilles Tendon, Male, Wheel Runner, 3

description:
Library name: X11116.MK.12
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.12


title: QEIII-124

description: gene expression from FFPE sample


title: U87-R, STM2457, rep 2, input

description: Library name: Sample 8


title: NPC, HT_1, procainimide, rna-seq

description: Library name: NPC_HT_procainimide_1


title: AMPKcKO, Mouse Achilles Tendon, Male, Wheel Runner, 2

description:
Library name: X11116.MK.11
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.11


title: U87-R, STM2457, rep 1, input

description: Library name: Sample 7


title: PYIII-130

description: gene expression from FFPE sample

value: F


title: NPC, AV_4, NC, rna-seq

description: Library name: NPC_AV_NC_4

value: DNMT1 A570V homozygous mutation


title: AMPKcKO, Mouse Achilles Tendon, Male, Wheel Runner, 1

description:
Library name: X11116.MK.10
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.10


title: U87-R rep 3, input

description: Library name: Sample 6

value: U87 MG, TMZ resistant


title: NPC, AV_3, NC, rna-seq

description: Library name: NPC_AV_NC_3


title: QEIII-15

description: gene expression from FFPE sample

value: M


title: blood RNA

city: Augsburg

first: Victoria

middle: Elisabeth

last: Fincke

address: Stenglinstraße 2

institute: Childens Cancer Center - University hospital Augsburg

description: pateint has a germline 48.46 Mb duplication of 4q31.22q35.5 and a 10.77 Mb deletion of 10q26.13q26.3

hyb_protocol: 15 µg of fragmented biotin-labeled cRNA was hybridized to Affymetrix Human Genome U13 Plus 2.0 Array

scan_protocol: Affymetrix protocol

data_processing: Affymetrix protocol

source_name: blood

label_protocol: total RNA was used to prepare biotin-labeled cRNA using the Affymetrix GeneChip Kit according to the manufacturer’s protocol

growth_protocol: Peripheral blood was collected from the patient via venipuncture using standard procedures. No in vitro culture or growth was performed.

extract_protocol: RNA extraction was performed using the blood RNA extraction kit from Qiagen

treatment_protocol: No treatment was applied prior to RNA extraction.

value: male

tag: age (months)


title: Wildtype, Mouse Achilles Tendon, Female, Wheel Runner, 3

description:
Library name: X11116.MK.1
Column name in gene_expected_count_batch2.annot.txt :  X11116.MK.1

value: R


title: U87-R rep 2, input

description: Library name: Sample 5

value: glioma cultured cell line


title: NPC, AV_2, NC, rna-seq

description: Library name: NPC_AV_NC_2


title: Wildtype, Mouse Achilles Tendon, Male, One Month, Cage Activity, 3

description:
Library name: X9789.SNEL.9
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.9

value: Wildtype


title: U87-R rep 1, input

description: Library name: Sample 4


title: NPC, AV_1, NC, rna-seq

description: Library name: NPC_AV_NC_1


title: AMPKcKO, Mouse Achilles Tendon, Female, One Month, Cage Activity, 3

description:
Library name: X9789.SNEL.8
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.8

value: AMPKcKO


title: UPN827 cells, VB-030BL Local Cohort T1D Baseline plasma

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

description: Gene expression data from UPN827 cells stimulated with T1D plasma

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

source_name: UPN827 cells stimulated with VB-030BL Local Cohort T1D Baseline plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN827 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of participant plasma  that was sampled at baseline or the 3-6 months post-baseline from six TrailNet new-onset T1D intervention trails, or from our local Recent onset T1DM cohort. Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN827 cells

tag: sample timepoint

value: Local Cohort T1D Baseline


title: U87 MG rep 3, input

description: Library name: Sample 3

value: DMSO control


title: UPN827 cells, VB-029BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-029BL Local Cohort T1D Baseline plasma


title: NPC, HT_4, NC, rna-seq

description: Library name: NPC_HT_NC_4

value: DNMT1 A570V heterozygous mutation


title: UPN827 cells, VB-028BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-028BL Local Cohort T1D Baseline plasma


title: U87 MG rep 2, input

description: Library name: Sample 2

value: U87 MG


title: AMPKcKO, Mouse Achilles Tendon, Female, One Month, Cage Activity, 2

description:
Library name: X9789.SNEL.7
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.7

value: Achilles Tendon


title: NPC, HT_3, NC, rna-seq

description: Library name: NPC_HT_NC_3

value: NPC

value: neural progenitor cell

value: ES cell differentiation


title: AMPKcKO, Mouse Achilles Tendon, Female, One Month, Cage Activity, 1

description:
Library name: X9789.SNEL.6
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.6


title: U87 MG rep 1, input

description: Library name: Sample 1


title: NPC, HT_2, NC, rna-seq

description: Library name: NPC_HT_NC_2


title: UPN827 cells, VB-027BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-027BL Local Cohort T1D Baseline plasma


title: UPN827 cells, VB-026BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-026BL Local Cohort T1D Baseline plasma


title: AMPKcKO, Mouse Achilles Tendon, male, Cage Activity, 7

description:
Library name: X9789.SNEL.37
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.37


title: U2OS ZAK-KO + ZAKɑ, KR→A in S domain rescue, replicate 2, 0.19 µM Anisomycin

description: Library name: ZAK_KRtoA_AnL_Rep2

data_processing:
Pulled libraries were demultiplexed based on barcoded adaptor sequences using SeqKit.
Raw reads were quality filtered and Illumina adaptor trimmed using TrimGalore.
PCR duplicates removed using SeqKit.
Barcode and UMI tags were trimmed using TrimGalore.
Reads aligned using STAR and crosllink sites identified using bedtools as described Buchbender et al.
Assembly: GRCh38/hg38
Library strategy: iCLIP

value: bone

value: U-2 OS

value: osteosarcoma cell

value: 0.19 µM Anisomycin, 15 min


title: NPC, HT_1, NC, rna-seq

description: Library name: NPC_HT_NC_1


title: AMPKcKO, Mouse Achilles Tendon, male, Cage Activity, 6

description:
Library name: X9789.SNEL.35
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.35


title: U2OS ZAK-KO + ZAKɑ, KR→A in S domain rescue, replicate 1, 0.19 µM Anisomycin

description: Library name: ZAK_KRtoA_AnL_Rep1


title: NPC, WT_4, NC, rna-seq

description: Library name: NPC_WT_NC_4

value: WT


title: UPN827 cells, VB-025BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-025BL Local Cohort T1D Baseline plasma


title: UPN827 cells, VB-024BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-024BL Local Cohort T1D Baseline plasma


title: NPC, WT_3, NC, rna-seq

description: Library name: NPC_WT_NC_3

source_name: NPC


title: U2OS ZAK-KO + ZAKɑ ΔYLD rescue, replicate 2, 0.19 µM anisomycin

description: Library name: ZAK_dYLD_AnL_Rep2


title: AMPKcKO, Mouse Achilles Tendon, Female, Cage Activity, 6

description:
Library name: X9789.SNEL.33
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.33


title: AMPKcKO, Mouse Achilles Tendon, Female, Cage Activity, 5

description:
Library name: X9789.SNEL.32
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.32


title: U2OS ZAK-KO + ZAKɑ ΔYLD rescue, replicate 1, 0.19 µM anisomycin

description: Library name: ZAK_dYLD_AnL_Rep1


title: NPC, WT_2, NC, rna-seq

description: Library name: NPC_WT_NC_2


title: UPN827 cells, VB-023BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-023BL Local Cohort T1D Baseline plasma


title: AMPKcKO, Mouse Achilles Tendon, male, Cage Activity, 5

description:
Library name: X9789.SNEL.30
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.30


title: U2OS ZAK-KO+ ZAKɑ ΔCTD rescue, replicate 2, 0.19 µM anisomycin

description: Library name: ZAK_dCTD_AnL_Rep2


title: NPC, WT_1, NC, rna-seq

description: Library name: NPC_WT_NC_1


title: UPN827 cells, VB-020BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-020BL Local Cohort T1D Baseline plasma


title: Wildtype, Mouse Achilles Tendon, Female, One Month, Cage Activity,3

description:
Library name: X9789.SNEL.3
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.3


title: U2OS ZAK-KO + ZAKɑ ΔCTD rescue, replicate 1, 0.19 µM anisomycin

description: Library name: ZAK_dCTD_AnL_Rep1


title: UPN827 cells, VB-019BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-019BL Local Cohort T1D Baseline plasma


title: Hela, siDNMT1_3, rna-seq

description: Library name: Hela_siDNMT1_3_rna_seq

source_name: HeLa

value: HeLa

value: epithelial cell

value: DNMT1 knockdown


title: UPN827 cells, VB-018BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-018BL Local Cohort T1D Baseline plasma

value: UPN827 cells


title: U2OS ZAK-KO + ZAKɑ full-length rescue, replicate 2, 76 µM anisomycin

description: Library name: ZAK_AnH_Rep2

source_name: bone

value: 76 µM Anisomycin, 15 min


title: Wildtype, Mouse Achilles Tendon, Male, Cage Activity, 6

description:
Library name: X9789.SNEL.27
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.27

source_name: Achilles Tendon

value: Wildtype


title: Hela, siDNMT1_2, rna-seq

description: Library name: Hela_siDNMT1_2_rna_seq


title: UPN827 cells, VB-015BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-015BL Local Cohort T1D Baseline plasma

value: Local Cohort T1D Baseline


title: Wildtype, Mouse Achilles Tendon, Male, Cage Activity, 5

description:
Library name: X9789.SNEL.25
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.25


title: Hela, siDNMT1_1, rna-seq

description: Library name: Hela_siDNMT1_1_rna_seq


title: U2OS ZAK-KO + ZAKɑ full-length rescue, replicate 1, 76 µM anisomycin

description: Library name: ZAK_AnH_Rep1


title: Wildtype, Mouse Achilles Tendon, Male, Cage Activity, 4

description:
Library name: X9789.SNEL.24
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.24


title: Hela, siNC_3, rna-seq

description: Library name: Hela_NC_3_rna_seq


title: U2OS ZAK-KO + ZAKɑ full-length rescue, replicate 2, 0.19 µM anisomycin

description: Library name: ZAK_AnL_Rep2


title: UPN827 cells, VB-011BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-011BL Local Cohort T1D Baseline plasma


title: AMPKcKO, Mouse Achilles Tendon, Female, Cage Activity, 4

description:
Library name: X9789.SNEL.23
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.23

value: AMPKcKO


title: UPN827 cells, VB-013BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-013BL Local Cohort T1D Baseline plasma


title: U2OS ZAK-KO + ZAKɑ full-length rescue, replicate 1, 0.19 µM anisomycin

description: Library name: ZAK_AnL_Rep1


title: Hela, siNC_2, rna-seq

description: Library name: Hela_NC_2_rna_seq


title: UPN827 cells, VB-010BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-010BL Local Cohort T1D Baseline plasma


title: Wildtype, Mouse Achilles Tendon, Female, One Month, Cage Activity, 2

description:
Library name: X9789.SNEL.2
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.2

value: Achilles Tendon


title: U2OS ZAK-KO + ZAKɑ mutant (K/R→A in S domain, ΔC-terminal domain) rescue, replicate 2

description: Library name: ZAK_Mut_Rep2

value: same amount of DMSO as control, 15 min


title: Hela, siNC_1, rna-seq

description: Library name: Hela_NC_1_rna_seq


title: Wildtype, Mouse Achilles Tendon, Female, Cage Activity, 5

description:
Library name: X9789.SNEL.18
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.18


title: U2OS ZAK-KO + ZAKɑ mutant (K/R→A in S domain, ΔC-terminal domain) rescue, replicate 1

description: Library name: ZAK_Mut_Rep1


title: NPC, AV_2, rrbs-seq

description: Library name: NPC_AV_2_rrbs_seq

data_processing:
Raw read adapters were trimmed using cutadapt 0.6.10 in RRBS mode (--rrbs). Clean reads were aligned to the human genome (hg38) with Batmeth2 using default parameters. Methylation levels at CpG sites were extracted using Batmeth2’s module. CpG sites with coverage below 4 reads were filtered out.
Assembly: hg38
Supplementary files format and content: bigwig

molecule: genomic DNA

extract_protocol:
Tissue or PBS-washed cells were lysed in a buffer containing 100 mM NaCl, 10 mM Tris-HCl (pH 8.0), 25 mM EDTA (pH 8.0), 0.5% SDS, and 200 µg/mL Proteinase K for 2 hours at 50°C. An equal volume of Phenol : Chloroform : Isoamyl alcohol (25:24:1) (Cat. No. P1021) was added to the lysate, and the supernatant was retained after centrifugation. This was mixed with twice the volume of pre-chilled ethanol and incubated at -20°C for 10 minutes to precipitate the DNA. After centrifugation at 13,000 rpm for 15 minutes at 4°C, the pellet was washed twice with pre-chilled 70% ethanol. The DNA was then dissolved in 10 mM Tris-HCl (pH 8.0).
10 ug of DNA were sonicated to approximately 150 bp fragments using the Covaris S220, followed by end repair and adenylation. Fragments were ligated with custom hairpin and sequence adapters. Enrichment for CG-rich fragments was performed using Msel (T/TAA) and Mluel (/AATT) restriction enzymes. Dynabeads M-280 Streptavidin were utilized to isolate fragments with successfully ligated hairpin adapters. Bisulfite conversion was conducted with the Epitect Plus DNA Bisulfite Kit following a specified temperature and time protocol (95℃ for 5min, 60℃ for 26min, 95℃ for 5min, 60℃ for 60min, 95℃ for 5min, 60℃ for 1h 25min, 95℃ for 5min, 60℃ for 2h 55min). Library concentrations were quantified using the Qubit 4.0 fluorometer. Amplification and indexing were performed using KAPA HiFi Hotstart Uracil+ReadyMix. The final libraries were size-selected for 350-550 bp fragments and subjected to paired-end sequencing on the NovaSeq 6000 platform

value: NPC

value: neural progenitor cell

value: DNMT1 A570V homozygous mutation


title: UPN827 cells, VB-009BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-009BL Local Cohort T1D Baseline plasma


title: UPN827 cells, VB-008BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-008BL Local Cohort T1D Baseline plasma


title: AMPKcKO, Mouse Achilles Tendon, Male, One Month, Cage Activity, 3

description:
Library name: X9789.SNEL.16
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.16


title: U2OS ZAK-KO + ZAKɑ full-length rescue, replicate 2

description: Library name: ZAK_Rep2

value: bone

value: U-2 OS


title: NPC, AV_1, rrbs-seq

description: Library name: NPC_AV_1_rrbs_seq

value: ES cell differentiation


title: AMPKcKO, Mouse Achilles Tendon, Male, One Month, Cage Activity, 2

description:
Library name: X9789.SNEL.15
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.15


title: NPC, HT_2, rrbs-seq

description: Library name: NPC_HT_2_rrbs_seq

value: DNMT1 A570V heterozygous mutation


title: U2OS ZAK-KO + ZAKɑ full-length rescue, replicate 1

description: Library name: ZAK_Rep1

value: osteosarcoma cell


title: UPN827 cells, VB-006BL Local Cohort T1D Baseline plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with VB-006BL Local Cohort T1D Baseline plasma


title: AMPKcKO, Mouse Achilles Tendon, Male, One Month, Cage Activity, 1

description:
Library name: X9789.SNEL.14
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.14


title: NPC, HT_1, rrbs-seq

description: Library name: NPC_HT_1_rrbs_seq


title: UPN827 cells, VB-003BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-003BL Local Cohort T1D Baseline plasma


title: Fibrosis 13

city: Orlando

first: Daria

last: Igudesman

address: 301 E Princeton St

institute: AdventHealth

description:
Library name: MODIFY74
MODIFY74

data_processing:
Raw counts were generated with the R package salmon.
Assembly: hg38 - Ensembl
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

source_name: Sigmoid colon

extract_protocol:
Total mRNAs were isolated from colonic tissues using TRIzol (Invitrogen, Carlsbad, CA) according to the manufacturer’s instructions.
cDNA library was prepared using the Invitrogen Collibri Stranded RNA library Prep Kit for Illumina with Collibri H/M/R rRNA Depletion Kit according to the manufacturer’s instructions and starting with 500ng of purified RNAs. Briefly, rRNA were first depleted, and enriched mRNAs subsequently used for fragmentation, adaptors ligation and reverse transcription. After purification, libraries were PCR-enriched, further purified, and quantified and quality-assessed on an Agilent 2100 Bioanalyzer instrument. A master library was generated from the purified products in equimolar ratios. The pooled product was quantified using Qubit and sequenced using an llumina Next-Seq sequencer (paired-end reads, 2x750 bp).

value: Sigmoid colon


title: Wildtype, Mouse Achilles Tendon, Male, One Month, Cage Activity, 2

description:
Library name: X9789.SNEL.12
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.12


title: Fibrosis 12

description:
Library name: MODIFY73
MODIFY73


title: NPC, WT_2, rrbs-seq

description: Library name: NPC_WT_2_rrbs_seq

source_name: NPC

value: WT


title: UPN827 cells, VB-002BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with VB-002BL Local Cohort T1D Baseline plasma

value: UPN827 cells


title: Wildtype, Mouse Achilles Tendon, Male, One Month, Cage Activity, 1

description:
Library name: X9789.SNEL.11
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.11


title: Fibrosis 11

description:
Library name: MODIFY70
MODIFY70


title: UPN827 cells, CHW002BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW002BL Local Cohort T1D Baseline plasma


title: NPC, WT_1, rrbs-seq

description: Library name: NPC_WT_1_rrbs_seq


title: UPN827 cells, CHW052BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW052BL Local Cohort T1D Baseline plasma


title: Wildtype, Mouse Achilles Tendon, Female, One Month, Cage Activity,1

description:
Library name: X9789.SNEL.1
Column name in gene_expected_count_batch1.annot.txt : X9789.SNEL.1


title: Fibrosis 10

description:
Library name: MODIFY68
MODIFY68


title: Hela, siDNMT1_3, rrbs-seq

description: Library name: Hela_siDNMT1_3_rrbs_seq

source_name: HeLa

value: HeLa

value: epithelial cell

value: DNMT1 knockdown


title: Wildtype, Mouse Achilles Tendon, Female, Cage Activity, 4

description:
Library name: X9789.SNEL.36
Column name in gene_expected_count_batch1.annot.txt :  X9789.SNEL.36

value: Wildtype


title: Fibrosis 9

description:
Library name: MODIFY67
MODIFY67


title: Hela, siDNMT1_2, rrbs-seq

description: Library name: Hela_siDNMT1_2_rrbs_seq


title: UPN827 cells, CHW050BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW050BL Local Cohort T1D Baseline plasma

value: Local Cohort T1D Baseline


title: UPN827 cells, CHW048BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW048BL Local Cohort T1D Baseline plasma


title: AMPKcKO, Mouse Achilles Tendon, Male, Cage Activity, 3

description:
Library name: X9789.SNEL.34
Column name in gene_expected_count_batch1.annot.txt :  X9789.SNEL.34

source_name: Achilles Tendon

value: Achilles Tendon

value: AMPKcKO


title: Fibrosis 8

description:
Library name: MODIFY66
MODIFY66


title: Hela, siDNMT1_1, rrbs-seq

description: Library name: Hela_siDNMT1_1_rrbs_seq


title: 10-day old male flies, high sucrose diet +0.25 mM AITC, rep 3

city: Gießen

first: Sonja

last: Dähn

address: Wilhelmstrasse 20

institute: Justus-Liebig-Universität Gießen

description: Library name: HAMS3

data_processing:
data processing was done by  Novogene Co., Ltd (Beijing, China).
Assembly: NCBI 7227
Supplementary files format and content: csv
Supplementary files format and content: counts and fpkm

organism: Drosophila melanogaster

source_name: whole flie

extract_protocol:
for RNA extraction, the Quick-RNA Tissue/Insect kit (Zymo Research, Freiburg, Germany) was used, according to the manufacturer’s instructions.
polyA enrichment library preparation resulting in the construction of 250-300 bp insert cDNA library, done by Novogene Co., Ltd (Beijing, China).

treatment_protocol: flies were fed 30% sucrose diet with or without 0.25 mM allyl-isothiocyanate for 10 days

value: whole flie

value: high sucrose diet+0.25 mM AITC


title: UPN827 cells, CHW047BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW047BL Local Cohort T1D Baseline plasma


title: Hela, siNC_3, rrbs-seq

description: Library name: Hela_NC_3_rrbs_seq


title: Fibrosis 6

description:
Library name: MODIFY59
MODIFY59


title: Fibrosis 7

description:
Library name: MODIFY60
MODIFY60


title: UPN827 cells, CHW046BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW046BL Local Cohort T1D Baseline plasma


title: 10-day old male flies, high sucrose diet +0.25 mM AITC, rep 2

description: Library name: HAMS2


title: Hela, siNC_2, rrbs-seq

description: Library name: Hela_NC_2_rrbs_seq


title: UPN827 cells, CHW045BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW045BL Local Cohort T1D Baseline plasma


title: 10-day old male flies, high sucrose diet +0.25 mM AITC, rep 1

description: Library name: HAMS1


title: Fibrosis 5

description:
Library name: MODIFY58
MODIFY58


title: Hela, siNC_1, rrbs-seq

description: Library name: Hela_NC_1_rrbs_seq


title: Fibrosis 4

description:
Library name: MODIFY56
MODIFY56


title: 10-day old female flies, high sucrose diet +0.25 mM AITC, rep 3

description: Library name: HAFS3


title: RNA library from 12 weeks Natural single oocyte 20

first: Eric

middle: Alejandro

last: Rhon Calderon

state: Pennsylvania

address: 3400 Civic Center Blvd, Bldg 421, Floor 9-175

department: Cell and Developmental Biology

institute: University of Pennsylvania

description:
Library name: 92_3_6
92_3_6
summary_count_12weeks_single_oocytes.txt

data_processing:
RNA-seq reads were trimmed for quality using Trimmomatic (version 0.32). Illumina TruSeq3-PE primers, leading and trailing low-quality (below quality 3) and N base calls were trimmed, and reads were scanned using a 4-bp sliding window and trimmed when the average quality per base dropped below 15. Reads of at least 30-bp in length following this quality control process were retained and used for subsequent analyses.
The resulting reads were then aligned to mm10 reference genome assembly using STAR (version 2.3.0e), allowing read pairs to align no farther than 2000-bp apart and keeping alignments with a mapping quality score (MAPQ) greater than 1 for genome-wide transcript counting.
FeatureCounts (version 1.5.0) was used to generate a matrix of mapped fragments per RefSeq annotated gene.
Analysis for differential gene expression was performed using DESeq2 with the cutoff of FDR < 0.05. Clustering and heatmaps of differentially expressed genes were generated using heatmaply R package. Chord plots were done using complexheatmap, clusterprofiler and circlize packages in R. WGCNA was done using the WGCNA package for R.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: 12 week single oocyte

growth_protocol: All animals were housed in polysulfone cages containing drinking water and chow (Laboratory Irradiated Rodent Diet 5LG4, LabDiet) ad libitum.

extract_protocol:
For tissue: RNA was extracted using Rneasy mini plus kit (Qiagen). 2 ug of total RNA was used for the construction of sequencing libraries. For single oocytes and cumulus cells: a modified SMART-seq extraction protocol was used using TCL and BME for cell lysis
For tissue: RNA libraries for RNA-seq were prepared using KAPA Stranded mRNA-Seq Kit (Illumina Platforms) and KAPA Single-Indexed adapter kit following manufacturer's protocols. For single oocytes and cumulus cells: Nextera Library prep and Nextera sequencing indexes (Illumina) were used.

treatment_protocol: E18.5 ovaries, 12 weeks ovaries, 39 weeks ovaries, 12 weeks single oocytes, 39 weeks single oocytes, 12 cumulus cells pools, 39 weeks cumulus cells pools, F2 12 weeks testis, F2 12 weeks male livers, F2 12 weeks ovaries, F2 weeks female livers awere collected, snap frozen in liquid nitrogen and stored at -80C for RNA extraction.

value: 12 week single oocyte

value: Female

value: Natural


title: RNA library from 12 weeks Natural single oocyte 18

description:
Library name: 92_3_3
92_3_3
summary_count_12weeks_single_oocytes.txt


title: ATAC_ARV-110_rep3

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

country: United Kingdom

institute: Cardiff University

description: Library name: Sample 9

data_processing:
Nextflow (v 23.10.1) was used to run the nf-core/atacseq pipeline.
The command used was: nextflow run nf-core/atacseq -profile singularity -params-file parameters.json --input samples.csv --genome GRCh38 --outdir output
Briefly, fastQ files were aligned to the 'GRCh38/hg38' genome build assembly using Bowtie2 and peak calling was performed using MACS2.
DiffBind was used to identify significant differential peak enrichment between control and experimental samples.
Assembly: hg38
Supplementary files format and content: Indexed Bigwig files (bw).

source_name: Ovarian cancer cell line

growth_protocol: OVCAR-3 cells were grown in 12-well TC plates using RPMI 1640 (20% FBS) media (Thermo Fisher Scientific).

extract_protocol:
After 48h of treatment, cells were lysed, nuclei extracted and DNA tagmented and purified using the ATAC-Seq kit (C01080002, Diagenode) following manufacturer's instructions.
DNA libraries were prepared using the unique dual indexes (UDI) for Tagmeneted libraries kit (C01011034, Diagenode). AMPure XP beads (A63880, Beckman Coulter) were used for library clean up.
DNA libraries were sequenced at Novogene (PE150).

treatment_protocol: OVCAR-3 cells were treated with GSK-J5 (control) and GSK-J4 (2.5µM) for 48h prior to chromatin extraction.

value: Ovarian cancer cell line


title: QEIII-198

description: gene expression from FFPE sample

data_processing: The data were analyzed with Robust Multichip Average (RMA) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: locoregionally advanced NPC FFPE sample

extract_protocol: RNA was extracted from FFPE samples using the QIAGEN FFPE RNeasy kit (QIAGEN GmbH, Hilden, Germany).

value: M


title: Healthy 13

description:
Library name: MODIFY54
MODIFY54

value: Sigmoid colon


title: PYIII-64

description: gene expression from FFPE sample


title: QEIII-22

description: gene expression from FFPE sample


title: 10-day old female flies, high sucrose diet +0.25 mM AITC, rep 2

description: Library name: HAFS2


title: UPN827 cells, CHW042BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW042BL Local Cohort T1D Baseline plasma


title: ATAC_ARV-110_rep2

description: Library name: Sample 8


title: UPN827 cells, CHW044BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW044BL Local Cohort T1D Baseline plasma


title: Healthy 12

description:
Library name: MODIFY53
MODIFY53

source_name: Sigmoid colon


title: 10-day old female flies, high sucrose diet +0.25 mM AITC, rep 1

description: Library name: HAFS1


title: ATAC_ARV-110_rep1

description: Library name: Sample 7


title: Healthy 11

description:
Library name: MODIFY49
MODIFY49


title: 10-day old male flies, high sucrose diet, rep 3

description: Library name: HCMS3

value: high sucrose diet


title: UPN827 cells, CHW041BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW041BL Local Cohort T1D Baseline plasma

value: UPN827 cells


title: UPN827 cells, CHW040BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW040BL Local Cohort T1D Baseline plasma


title: normal endometrium of patient4

city: Hefei

first: Yifan

last: Feng

state: Anhui

address: Jixi Road 218

institute: The Anhui Medical University

description: 10x Genomics

data_processing:
Basecalls performed using bcl2fastq V2.19.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence.
Quantify gene expression using read2 by featureCounts software
Assembly: genome/10xHuman/Ensembl_98
Supplementary files format and content: Tab-separated values files and matrix files

source_name: endometrium

extract_protocol:
Briefly, frozen tissue samples were rapidly added to the lysis buffer and homogenized into a liquid state using a tissue homogenizer.  The resulting tissue lysate was filtered through a 40 μm cell sieve to remove impurities and then transferred to a fresh 2 mL EP tube.  The sample was centrifuged at 500 g at 4°C for 5 minutes to collect the precipitate.  Subsequently, PB1, PB2, and PB3 solutions were added to the precipitate, with the nuclei positioned at the interface between PB2 and PB3 solutions.  Finally, the nuclei were resuspended by gentle pipetting into 50 μL of NB solution.  A cell counter was employed to count the nuclei (Thermo Fisher, USA)
Sequencing libraries were prepared following the manufacturer's instructions (10X Genomics, USA) and then sequenced on the NovaSeq 6000 system (Illumina, USA).

tag: pathlogy

value: normal endometrium

tag: grade

value: endometrium


title: Steatosis 13

description:
Library name: MODIFY48
MODIFY48


title: 10-day old male flies, high sucrose diet, rep 2

description: Library name: HCMS2


title: UPN827 cells, CHW039BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW039BL Local Cohort T1D Baseline plasma


title: normal endometrium of patient1

description: 10x Genomics


title: UPN827 cells, CHW038BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW038BL Local Cohort T1D Baseline plasma


title: Peyer's patch immune cells, pooled 16 mice, ScaleBio scRNA-seq multiplexed library_3

city: New Brunswick

first: Gaetan

last: Barbet

state: NJ

address: 89 French Street

department: Department of Pediatrics

institute: Rutgers University

description:
Library name: 24274FL-01-03
One multiplexed ScaleBio scRNA-seq library prepared from Peyer's patch immune cells from 16 mice (4 wild-type, 4 Trif-/-, 4 Il1r1-/-, and 4 littermate controls). Sample identity was encoded with RT barcodes (sample.csv). Run2 is additional sequencing of the same library.

data_processing:
Raw sequencing reads were processed using the ScaleBio Seq Suite: RNA pipeline. The workflow included barcode parsing, sample demultiplexing using RT barcode information in samples.csv, read trimming, genome alignment with STAR/STARsolo, transcript assignment, UMI counting, cell filtering, and generation of filtered gene expression matrices.
Mouse samples were aligned to the mm39 reference genome.
Filtered gene expression matrices were used for downstream analysis in Seurat v5.0.2.
Assembly: Mus musculus (mm39)
Supplementary files format and content: Processed data files include per-sample filtered gene-expression matrices in Matrix Market format (matrix.mtx.gz) with matching barcodes.tsv.gz and features.tsv.gz files. Sample barcode-to-biological-sample assignments are provided in sample.csv.

source_name: Peyer's patches

extract_protocol:
Trif- and Il1r1-deficient mice were crossed with wild-type C57BL/6 mice to generate F1 offspring. heterzygotes F1 were crossed to get F2 mice. Peyer's patches of Trif- and Il1r1-deficient mice and their littermate wild-type controls (4 mice per group) were digested for 15 min at 37 °C in 0.5 mg/ml collagenase D and 10 μg/ml DNase I to generate a single-cell suspension. Live cells (Zombie NIR-negative) were sorted using a Cytek Aurora CS. One million cells from each sample were fixed with the ScaleBio Sample Fixation Kit. Fixed samples were stored at -80 °C until all samples were collected.
Frozen fixed cells were thawed on ice and counted twice by hemocytometer. Using the ScaleBio Single Cell RNA Sequencing Kit v1.1 (Scale Biosciences), all 16 samples were prepared in one batch. Cells were loaded at 10,000 per well (6 wells per sample) to add RT barcodes as sample identifiers. Pooled cells were distributed across the 384-well plate for ligation barcode addition, then pooled again with 1,600 nuclei per well for second-strand synthesis. After tagmentation and indexing PCR, libraries were pooled (5 ul each), cleaned with 0.8X SPRIselect beads (Beckman Coulter B23317), and fragment size/concentration were quantified using High Sensitivity D5000 ScreenTape (Agilent).

treatment_protocol: Twelve-week-old wild-type (JAX#00664), Trif^Lps2 (JAX#005037; hereafter referred to as Trif-/-), and Il1r1-/- (JAX#003245) mice were maintained under specific pathogen-free (SPF) conditions.

value: Peyer's patches

value: immune cells

value: mixed (wild-type littermate controls, Trif-/-, and Il1r1-/-)

value: ScaleBio batch 1


title: HSC2_cells_shortRNA, C. albicans-treated 2, 6 hours

city: Szeged

first: Marton

last: Horvath

state: Csongrád

address: Közép fasor 52.

department: Microbiology

country: Hungary

institute: University of Szeged

description: Library name: H6_CA112_miR

library_source: other

data_processing:
Human sequenced reads were trimmed for standard Illumina adaptor sequences / low-quality sequences using trim-galore (v0.6.4) (parameters: -q 20 --paired --illumina), the --length cutoff was set 36 for RNA-seq and 18 for miRNA-seq samples.
Processed RNA reads were aligned using Hisat2 (v2.2.1)  (parameter: --phred33 --dta --non-deterministic --rna-strandness "RF"), sorted and indexed using Samtools (v1.20).
Mapped reads were quantified for genomic features using FeatureCounts (v2.0.6). (parameter: -p --countReadPairs -s 2)
Further analysis steps for RNA-seq samples were conducted in R, inculding differential gene expression analysis using DESeq2 (v1.46.0) packages.
Processed miRNA reads were aligned using mirdeep2 (v2.0.1.3) in two steps: mapped with the mapper.pl script (parameter: -e -h -i -j -m -k AGATCGGAAGAGCACACGTCT -l 18) and quantified with the miRDeep2.pl script.
Assembly: GRCh38 (release 96) from ENSEMBL, further references for the miRNA sequencing were downloaded from miRBase (release 22), including human mature- and hairpin sequences, and mouse and rat mature sequences for contaminant masking.
Supplementary files format and content: total_read_counts.csv
Supplementary files format and content: The 6 column miRNA quantification result tables, including detected mature-, precursor-, and normalized counts.

molecule: other

growth_protocol: HSC-2 cells were grown in EMEM medium supplemented with 10% heat inactivated FBS, 1% PS, and 4 mM L-glutamine. Cells were maintained at 37°C in the presence of 5% CO2.

extract_protocol:
After reaching 85 % confluency, total RNA and total miRNA was extracted using the miRNeasy Mini Kit, following the manufacturer’s instructions.
mRNA and miRNA sequencing libraries were prepared at Novogene (UK) Company Limited, Cambridge, UK, according to the company’s own guidelines. Briefly, mRNA was poly(A)-enriched and sequenced on an Illumina NovaSeq X Plus (2×15 bp, PE150 workflow, ≥20M read pairs/sample). miRNA libraries were sequenced on a NovaSeq 6000 (50 bp single-end, SE50 workflow, ≥10M reads/sample)

treatment_protocol: Host cells were stimulated with yeast cells at the MOI of 1:1 or 5:1 (pathogen: host ratio) in serum-free EMEM medium for 1 or 6 hours at 37C, in the presence of 5% CO2. Yeast cells were cultivated in liquid YPD medium, overnight at 30C, prior to the experiments.

value: oral epithelial

value: C.albicans MOI 1(pathogen):1(host)

tag: time

value: 6 hours


title: UPN827 cells, CHW035BLrh Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW035BLrh Local Cohort T1D Baseline plasma

value: Local Cohort T1D Baseline


title: Healthy 8

description:
Library name: MODIFY41
MODIFY41


title: normal endometrium of patient3

description: 10x Genomics


title: normal endometrium of patient2

description: 10x Genomics


title: low grade endometrioid endometrial cancer of patient1

description: 10x Genomics

source_name: endometrioid endometrial

value: endometrioid endometrial cancer

value: Low

value: endometrioid endometrial


title: Healthy 9

description:
Library name: MODIFY46
MODIFY46


title: 10-day old female flies, high sucrose diet, rep 1

description: Library name: HCFS1

source_name: whole flie

value: whole flie


title: 10-day old female flies, high sucrose diet, rep 3

description: Library name: HCFS3


title: RNA library from 12 weeks Natural single oocyte 11

city: Philadelphia

description:
Library name: 35_3_3
35_3_3
summary_count_12weeks_single_oocytes.txt

value: 12 week single oocyte

value: Female

value: Natural


title: Fibrosis 3

description:
Library name: MODIFY45
MODIFY45

value: Sigmoid colon


title: RNA library from 12 weeks Natural single oocyte 14

description:
Library name: 35_3_6
35_3_6
summary_count_12weeks_single_oocytes.txt


title: UPN827 cells, CHW036BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW036BL Local Cohort T1D Baseline plasma

value: UPN827 cells


title: DTR_2

city: Guangzhou

first: Ximin

last: Hu

address: Department of Burn and Plastic Surgery, Guangzhou First People's Hospital, South China University of Technology, Guangzhou, Guangdong

description:
Library name: Sample_10
gene_expression_473_DTR.xlsx; sample_DTR_2_fpkm

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Bray N, Pimentel H, Melsted P, et al., Near-optimal RNA-Seq quantification, 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: http://ftp.ensembl.org/pub/release-107/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.toplevel.fa.gz http://ftp.ensembl.org/pub/release-107/gtf/mus_musculus/Mus_musculus.GRCm39.107.gtf.gz http://ftp.ensembl.org/pub/release-107/gtf/mus_musculus_c57bl6nj/Mus_musculus_c57bl6nj.C57BL_6NJ_v1.107.gtf.gz
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Male and female mice (8 to 12 weeks old) were housed in individually ventilated cages under a 12-hour light/dark cycle with ad libitum access to food and water. Mice used within each experimental comparison were bred to generate littermates, cohoused under identical conditions, and randomly assigned to experimental groups by lab managers blinded to the study design.

extract_protocol:
RNA was harvested using Trizol reagent.
A total amount of 0.2 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using Fast RNA-seq Lib Prep Kit V2 （Cat.No.RK20306） following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads (PE150) were generated.

treatment_protocol: Optogenetic stimulation was performed using a 473nm 100mW diode-pumped solid-state laser (Laser and Optics Century, Shanghai, China). An optical cannula aimed at the dorsal ear was placed 1 cm from the surface of the skin. Stimulation was at a frequency of 10 Hz for 30 minutes with a power density of 8 mW/mm2 for 11 consecutive days. Both PF4Cre; Ai32 and Ai32 control mice underwent photostimulation of the dorsal ear.

value: PF4 Cre; iDTR

value: MC903 treatment


title: RNA library from 12 weeks Natural single oocyte 6

description:
Library name: 35_1_6
35_1_6
summary_count_12weeks_single_oocytes.txt


title: DTR_4

department: Department of Burn and Plastic Surgery, Guangzhou First People's Hospital

institute: Guangzhou First People's Hospital, South China University of Technology

description:
Library name: Sample_12
gene_expression_473_DTR.xlsx; sample_DTR_4_fpkm


title: RNA library from 12 weeks Natural single oocyte 2

description:
Library name: 35_1_2
35_1_2
summary_count_12weeks_single_oocytes.txt


title: RNA library from 12 weeks Natural single oocyte 3

description:
Library name: 35_1_3
35_1_3
summary_count_12weeks_single_oocytes.txt


title: middle grade endometrioid endometrial cancer of patient2

description: 10x Genomics

value: Middle


title: PYIII-14

city: Hong Kong

first: Huaping

last: Li

address: 21 Sassoon Rd, Pok Fu Lam

institute: The University of Hong Kong

description: gene expression from FFPE sample

value: M


title: Head of MZrlig1 zebrafish embryos, 5 dpf stage, bad behaviour 2

city: Konstanz

first: Fiona

middle: Sophie

last: Klusmann

address: Universitätsstrasse 10

institute: University of Konstanz

description:
Library name: KO_bad 2
K_B_2

data_processing:
Bioinformatic processing started with the download of the reference genome (Danio_rerio.GRCz11.dna_sm.primary_assembly.fa.gz) and gene annotation file (Danio_rerio.GRCz11.113.gtf.gz) from ENSEMBL (release 113). An index was generated using STAR (v.2.7.10b), and clean paired-end reads were then aligned to the reference genome using the same version of STAR. To reconstruct the transcriptome, the genome FASTA and annotation GTF files were processed with gffread (v.0.12.7). Transcript- and gene-level expression quantification was subsequently performed with Salmon (v.0.14.1) in alignment-based mode, using STAR-generated transcriptome BAM files as input.
Differential gene expression (DGE) analysis was conducted in R using the DESeq2 package (v.1.42.1)71. Transcript-level quantifications from Salmon were imported with the tximport package (v.1.30.0)72, and a DESeqDataSet object was created from the count data and corresponding experimental metadata, with ‘condition’ defined as the main factor of interest. Genes with fewer than 10 reads across all samples were excluded to reduce noise. Counts were normalised using DESeq2’s median-of-ratios method, and p-values were adjusted for multiple testing using the Benjamini–Hochberg false discovery rate (FDR).
Assembly: Danio rerio GRCz11 (Ensembl release 113)
Supplementary files format and content: Gene-level count tables (TXT format) containing raw read counts per gene
Supplementary files format and content: Normalised expression values (TXT format) generated with DESeq2.
Supplementary files format and content: Fragments per kilobase of transcript per million fragments mapped  (TXT format).
Supplementary files format and content: Differential expression results (XLSX format) with log₂FoldChange, p-value, adjusted p-value.

organism: Danio rerio

source_name: head

growth_protocol: Embryos used for developmental transcriptome profiling were raised in the dark at 28 °C. Embryos used for behavioural analysis and head transcriptome profiling were raised at 28 °C on a 14 h/10 h light/dark cycle. All embryos were collected by natural spawning and staged according to morphological criteria.

extract_protocol:
Total RNA was extracted from pools of zebrafish embryos or dissected larval heads using TRIzol™ Reagent (Invitrogen) according to the manufacturer’s instructions. For developmental profiling, samples were collected at six stages (4-cell, sphere, shield, bud, 1 dpf, 5 dpf). Per condition, 10 embryos were pooled for the 4-cell, sphere, and shield stages, and 8 embryos for the bud, 1 dpf, and 5 dpf stages. For behavioural profiling, heads from 8 larvae were pooled per sample. RNA integrity was assessed with the Bioanalyzer 2100 system (Agilent).
Poly(A)-enriched libraries were prepared according to Novogene’s standard protocol. mRNA was enriched using oligo(dT) magnetic beads, fragmented, and used for first- and second-strand cDNA synthesis. After end repair, A-tailing, and adapter ligation, fragments were size-selected, PCR amplified, and purified to generate sequencing libraries.

value: head

value: 5 dpf

value: bad behaviour


title: Steatosis 12

description:
Library name: MODIFY36
MODIFY36


title: middle grade endometrioid endometrial cancer of patient1

description: 10x Genomics


title: high grade endometrioid endometrial cancer of patient3

description: 10x Genomics

value: High


title: Head of MZrlig1 zebrafish embryos, 5 dpf stage, bad behaviour 3

description:
Library name: KO_bad 3
K_B_3


title: UPN827 cells, CHW032BL Local Cohort T1D Baseline plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with CHW032BL Local Cohort T1D Baseline plasma

value: Local Cohort T1D Baseline


title: UPN827 cells, CHW033BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW033BL Local Cohort T1D Baseline plasma


title: Healthy 7

description:
Library name: MODIFY35
MODIFY35


title: Head of MZrlig1 zebrafish embryos, 5 dpf stage, bad behaviour 1

description:
Library name: KO_bad 1
K_B_1


title: high grade endometrioid endometrial cancer of patient2

description: 10x Genomics

value: endometrioid endometrial cancer


title: Healthy 6

description:
Library name: MODIFY34
MODIFY34


title: Head of wildtype zebrafish embryos, 5 dpf stage, bad behaviour 4

description:
Library name: WT_bad 3
W_B_4

value: Wildtype


title: Healthy 5

description:
Library name: MODIFY30
MODIFY30


title: UPN827 cells, CHW031BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW031BL Local Cohort T1D Baseline plasma


title: high grade endometrioid endometrial cancer of patient1

description: 10x Genomics

value: endometrioid endometrial


title: UPN827 cells, CHW029BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW029BL Local Cohort T1D Baseline plasma


title: Steatosis 11

description:
Library name: MODIFY29
MODIFY29


title: Erythroid cells, Control, Day11, CUT&Tag

city: zhengzhou

first: Hengchao

last: Zhang

state: Henan

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zzu

data_processing:
Trim Galore version 0.6.6 was used to remove adapter and low-quality reads. Align paired-end reads using Bowtie2 version 2.5.1 with options: “--end-to-end --very-sensitive”. Peak calling uses MACS2 version 2.1.1 with threshold: q<0.01, and the differential binding sites of H3K4me3 were calculated using the DiffBind version 3.8.4 with the parameter log2foldchange >=1 and FDR <0.05 (https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/diffbind.html). Scatterplots, correlation plots, and heatmaps are displayed using deepTools version 2.5.7. Annotation of peaks is performed using an R package ChIPseeker version 1.34.1(https://www.cruk.cam.ac.uk/core-facilities/bioinformatics-core/software/ ChIPseeker.html). The CUT&Tag peak/region <1000bp from the nearest TSS was defined as the promoter. Hypergeometric Optimization of Motif Enrichment (HOMER) version 4.11 (http://homer.ucsd.edu/homer/) was used to search for the binding motif.
Assembly: GRCh38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: Cord blood

growth_protocol: CD34+ cells were puriﬁed from cord blood by positive selection using the magnetic-activated cell sorting magnetic beads system, according to the manufacturer’sinstructions. The purity of isolated CD34+ cells was 95% to 98%. The cell culture procedure was comprised of 3 phases. Composition ofthe base culture medium was Iscove’sModiﬁed Dulbecco’s Medium, 2%human peripheral blood plasma, 3% human AB serum, 200 mg/mL Holo-human transferrin, 3 IU/mL heparin, and 10 mg/mL insulin. In the ﬁrst phase(day 0 to day 6), CD34+ cells at a concentration of 105/mL were cultured inthe presence of 10 ng/mL stem cell factor, 1 ng/mL IL-3, and 3 IU/mL erythropoietin. In the second phase (day 7 to day 11), IL-3 was omitted from the culture medium. In the third phase that lasted until day 21, the cell concentration was adjusted to 106/mL on day 11 and to 5 3 106/mL on day 15, respectively, the medium for this phase was the base medium plus 3 IU/mL erythropoietin, and the concentration of transferrin was adjusted to 1mg/mL. The cells were cultured at 37°C in the presence of 5% CO2.

extract_protocol:
Cells were harvested, counted and centrifuged for 3 min at 600×g at room temperature. 1×105 cells were washed twice in 500μL wash buffer by gentle pipetting. Concanavalin A coated magnetic beads were prepared as the kit manual described, 10 µL of activated beads were added per sample and incubated at RT for 10 min. According to the kit instructions, cells were sequentially incubated with ConA Beads, primary antibody (anti-H3K4me3 antibody, secondary antibody (Goat anti-Rabbit IgG) and Hyperactive PG-TN5/PA-TN5 Transposon and then fragmented. The fragmented DNA was extracted from the samples and amplified by PCR.
CUT&Tag libraries were constructed using Hyperactive Universal CUT&Tag Assay Kit for Illumina (TD901, Vazyme, China) and sequenced on an Illumina NovaSeq platform, and 150-bp paired-end reads were generated.

treatment_protocol: Here, we set 0.5μM DZNep dosing which was an inhibitor of AHCY to inhibit AHCY activity. After treated with 0.5μM DZNep for four days, we performed a H3K4me3 CUT&Tag sequencing of DMSO and DZNep treated cells.

value: Cord blood

value: Erythroid cells

value: DMSO


title: Head of wildtype zebrafish embryos, 5 dpf stage, bad behaviour 2

description:
Library name: WT_bad 2
W_B_2


title: UPN827 cells, CHW028BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW028BL Local Cohort T1D Baseline plasma


title: Head of wildtype zebrafish embryos, 5 dpf stage, bad behaviour 1

description:
Library name: WT_bad 1
W_B_1


title: Erythroid cells, DZNep  treated 3, Day11, CUT&Tag

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

value: DZNep 0.5μM


title: Fibrosis 1

description:
Library name: MODIFY27
MODIFY27

source_name: Sigmoid colon

value: Sigmoid colon


title: Healthy 4

description:
Library name: MODIFY25
MODIFY25


title: Head of MZrlig1 zebrafish embryos, 5 dpf stage, good behaviour 3

description:
Library name: KO_good 2
K_G_3

value: good behaviour


title: UPN827 cells, CHW026BL Local Cohort T1D Baseline plasma

source_name: UPN827 cells stimulated with CHW026BL Local Cohort T1D Baseline plasma

value: UPN827 cells


title: Erythroid cells, DZNep  treated 2, Day11, CUT&Tag

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区


title: 5_473

description:
Library name: Sample_4
gene_expression_473_DTR.xlsx; sample_473_5_fpkm

value: PF4 Cre; Ai32

value: Optogenetic stimulation (473nm 100mW, Laser and Optics Century, Shanghai, China)