title: Dot1l-KO cornea, KO-2

city: tianjin

first: Lexin

last: Yang

address: tianjin

institute: Tianjin medical university

description:
Library name: Sample 4
10× Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger (version 7.1.0) for read alignment, barcode assignment, and UMI quantification. The mouse reference genome (mm10) was used. Subsequent analyses, including quality control, normalization, clustering, cell-type annotation, and differential expression analysis, were conducted using the Seurat R package (version 4.4.0).
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Dot1l-KO cornea

extract_protocol:
The eyes from 10 wild type (WT) mice and 10 Dot1l-/- mice (Dot1l-KO) were enucleated, and the corneas were carefully dissected and rinsed 2–3 times with ice-cold sterile PBS. Corneas were incubated with Dispase II (Sigma-Aldrich, 15 mg/ml) at 4 °C for 16 h to separate the epithelial layer. Following enzymatic treatment, the corneal epithelium was gently peeled away from the underlying stroma using ribbed forceps and subsequently dissociated with 0.25% trypsin/EDTA for 10 min. The remaining stromal tissue was digested with collagenase A (Sigma-Aldrich, 2.5 mg/ml) at 37 °C for 1 h. Digestion was terminated by adding an equal volume of DMEM supplemented with 10% fetal bovine serum (FBS). The resulting cell suspensions were filtered through a 40 µm cell strainer to remove large aggregates and debris. Cell viability and quality were assessed using a Luna automated cell counter, with acceptance criteria set at viability > 80%, clumping rate < 5%, and debris/fragment content < 5%. Following quality control, single-cell suspensions from WT and Dot1l-/- groups were individually pooled, resuspended, and adjusted to a concentration of 700–1200 cells/µL in preparation for 10 × Genomics single-cell RNA sequencing.
In brief, single cell was loaded onto a Chromium Single Cell Chip (Chromium Single Cell G chip Kit, 10 x Genomics, PN-1000120) to generate single-cell GEMs and construct barcoded cDNA libraries using the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (10 x Genomics, PN-1000268) following the manufacturer’s instructions. The quality of the resulting libraries was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies), and sequencing was performed on an Illumina platform (Annoroad Gene Technology Co., Ltd., Beijing, China).

value: Dot1l-KO cornea


title: Female,Adlib,Saline,Adult,rep4

status: Public on Jul 03 2026

type: SRA

city: Verdun

first: Nicholas

last: O'Toole

state: QC

address: 6875 Boulevard Lasalle

country: Canada

institute: Douglas Mental Health University Institute

description:
Library name: 16A.7_Female_Adlib_Saline_mPFC_Adult
16A.7_Female_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt

library_source: transcriptomic

data_processing:
Reads were aligned to the rat genome with STAR
Read counts per gene were computed with STAR
Assembly: Rnor_6.0
Supplementary files format and content: Ensembl gene Ids and read counts, tab delimited
Supplementary files format and content: Differential expression data, tab delimited

molecule: total RNA

organism: Rattus norvegicus

source_name: Medial prefrontal cortex

extract_protocol:
Qiagen AllPrep RNA minikit
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Medial prefrontal cortex


title: Dot1l-KO cornea, KO-1

country: China

description:
Library name: Sample 3
10× Genomics

library_source: transcriptomic single cell

molecule: polyA RNA

organism: Mus musculus


title: Sample2_PrimaryT, Untreated, rep2

city: Shanghai, China

first: Shengnan

last: She

state: Shanghai, China

address: Shanghai, China

institute: Fudan University, China

description:
Library name: Sample2
Column name in PrimaryT_count.csv: Untreated_2

data_processing:
Sequence reads were trimmed for adapters and low-quaity sequence using Trimmomatic v0.39
Trimmed sequence reads were mapped to hg38/mm39 using Hisat2 v2.2.1
Read count extraction and normalization were performed using FeatureCounts v2.0.6 (parameters- Q: 10 -p --countReadPairs -B -C)
Assembly: hg38, mm39
Supplementary files format and content: tab-delimited text file includes raw counts for samples (for Sample1 to Sample15)
Supplementary files format and content: tab-delimited text file includes raw counts for samples (for Sample16 to Sample21)

organism: Homo sapiens

source_name: lymphoid

extract_protocol:
RNA was harvested using Quick-RNA™ Microprep Kit (Zymo). 1.3 ug of total RNA was used for the construction of sequencing libraries.
mRNA was enriched by Oligo(dT) beads, and fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#7530,New England Biolabs, Ipswich, MA, USA).

value: lymphoid

tag: cell type

value: Primary T cells

tag: treatment

value: Untreated


title: Sample14_PrimaryT, PEO, rep2

description:
Library name: Sample14
Column name in PrimaryT_count.csv: PEO_2

value: PEO


title: Nthy, EZH1 Y727D, ATAC, rep2

city: Seoul

first: Hanbyeol

last: Kim

address: Daehak-ro 103

country: South Korea

institute: Seoul National University

description: Library name: Nthy_EZH1_Y727D_ATAC_rep2

library_source: genomic

data_processing:
Adapter sequences were trimmed using fastp and reads were aligned to the human (hg38) and E. coli (k12) reference genomes using Bowtie2. Mitochondrial reads and reads mapping to the ENCODE black list were removed. BAM files were normalized using RPKM to account for differences in sequencing depth. Subsequently, these values were further adjusted using scaling factors derived from reads mapping to the E. coli genome (originating from residual DNA in the Tn5 transposase preparation) were used to calculate scaling factors. Bigwig files were generated using deepTools and visualized using the Integrative Genomics Viewer (IGV). Heatmaps were generated with deepTools to visualize chromatin accessibility patterns across conditions.
Assembly: hg38
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Nthy-ori 3-1

growth_protocol: RPMI, 10% fetal bovine serum, 2mM glutamine, 1x antibiotics/antimycotics. Cells were cultured at 37°C at 5% CO2.

extract_protocol:
ATAC-seq was performed as previously described. Briefly, 50,000 cells were harvested and washed with ice-cold PBS. The supernatant was removed, and the cell pellet was resuspended in 50 µL of lysis buffer (10 mM Tris-HCl [pH 7.4], 3 mM MgCl2, 10 mM NaCl, and 0.1% NP-40). Nuclei were collected and resuspended in 50 µL of transposition reaction buffer (10 mM TAPS [pH 8.5], 5 mM MgCl2, and 10% DMF) containing adaptor-loaded Tn5 transposase. The reaction was incubated at 37°C for 30 min in a thermomixer set to 1,000 rpm. To terminate tagmentation, 10 µL of clean-up buffer (900 mM NaCl and 300 mM EDTA [pH 8.0]) was added.
Tagmented DNA was purified using the MinElute PCR Purification Kit and quantified via qPCR. Libraries were amplified using the KAPA HiFi HotStart PCR Kit with index primers and purified using SPRIselect DNA Size Selection Reagent. Sequencing was performed on an Illumina NovaSeq X (100 bp paired-end) or NovaSeq X Plus (150 bp paired-end) platform.

tag: cell line

value: Nthy-ori 3-1

value: Thyroid follicular epithelial cell

tag: genotype

value: EZH1 Y727D overexpression


title: Control cornea, WT-2

description:
Library name: Sample 2
10× Genomics

source_name: Control cornea

value: Control cornea


title: Nthy, EZH1 Y727D, ATAC, rep1

description: Library name: Nthy_EZH1_Y727D_ATAC_rep1


title: Female,Adlib,Saline,Adult,rep3

description:
Library name: 15B.7_Female_Adlib_Saline_mPFC_Adult
15B.7_Female_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH2 Q570R, ATAC, rep2

description: Library name: Nthy_EZH2_Q570R_ATAC_rep2

value: EZH2 Q570R overexpression


title: Control cornea, WT-1

description:
Library name: Sample 1
10× Genomics


title: Male,Adlib,Saline,Adult,rep4

description:
Library name: 15B.3_Male_Adlib_Saline_mPFC_Adult
15B.3_Male_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH1 Q571R, RNA, rep3

description: Library name: Nthy_EZH1_Q571R_RNA_rep3

data_processing:
For data analysis, adapter sequences were trimmed using Trimmomatic, and reads were aligned to the human reference genome (hg38) using HISAT2. Transcript assembly was performed using StringTie. Differential gene expression analysis was carried out using DESeq2, with significance defined as a p-value < 0.05 and log2 |fold change| > 1. Normalized RNA expression values were derived from DESeq2. Pathway enrichment analysis and z-scores were calculated using the limma package.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Cells were resuspended in 1 mL of TRIzol and incubated for 5 min at room temperature. After incubation, 0.2 mL of chloroform was added, and the mixture was vortexed vigorously. The samples were centrifuged at 13,000 x g for 15 min at 4°C, and the upper aqueous phase was transferred to a fresh tube. RNA was precipitated with isopropanol and washed with ice-cold 70% ethanol. The RNA pellet was resuspended in DEPC-treated water, and the concentration was measured.
Sequencing libraries were prepared using TruSeq Stranded Total RNA Ribo-Zero H/M/R Gold kit.

value: EZH1 Q571R overexpression


title: Sample13_PrimaryT, PEO, rep1

description:
Library name: Sample13
Column name in PrimaryT_count.csv: PEO_1


title: Sample1_PrimaryT, Untreated, rep1

description:
Library name: Sample1
Column name in PrimaryT_count.csv: Untreated_1


title: Nthy, EZH2 Q570R, ATAC, rep1

description: Library name: Nthy_EZH2_Q570R_ATAC_rep1


title: MΦSSIGR-ID3 + US

city: Xi’an

first: zihang

last: li

address: 277 West Yanta Road

institute: the First Affiliated Hospital of Xi’an Jiaotong University

description: Library name: Sample 3

data_processing:
The raw sequencing data included Read1, Read2, and i7 index read. Quality filtering and preprocessing of raw reads were conducted using Fastp. The filtered reads were aligned to the mouse reference genome (mm10_2020A) using MobiVision v2.1 under default parameters, and gene–cell expression matrices were generated for downstream analysis.
Assembly: mouse mm10_2020A
Supplementary files format and content: Core processed data (primary matrix files)

source_name: mouse tumor

extract_protocol:
Fresh tumor tissues were mechanically dissociated into 1–3 mm³ pieces and enzymatically digested in a mixed enzyme solution to obtain single-cell suspensions. The resulting suspensions were filtered through 40 μm cell strainers and washed 2–3 times with buffer to remove residual debris. Cell viability was assessed using trypan blue staining and a TC20 automated cell counter (Bio-rad, Hercules, CA), and only samples with >80% viability were used for downstream processing. The cell concentration was adjusted to 700–1200 cells/μL. Subsequently, the single-cell suspensions were processed and prepared for library construction using the MobiCube® High Throughput Single Cell 3' RNA-Seq Kit (v2.1, MobiDrop) according to the manufacturer’s instructions at Novogene Bioinformatics Technology Co., Ltd (Tianjing, China).
Single-cell suspensions were loaded onto a microfluidic chip from the Chip A Single Cell Kit v2.0 (MobiDrop, Cat. No. S050100201), and droplets were generated using the MobiNova-100 system (MobiDrop, Cat. No. A1A40001). Each droplet encapsulated a single cell together with a barcoded gel bead containing millions of oligonucleotides with unique cell barcodes and UMIs. The droplets were then subjected to optical disruption using the MobiNovaSP-100 device (MobiDrop, Cat. No. A2A40001) to release oligos into the reaction mix. Within the droplets, mRNAs were captured by oligo(dT)-tagged gel beads, followed by reverse transcription and barcode-labeled cDNA synthesis. Libraries were subsequently constructed using the High Throughput Single Cell 3′ RNA-Seq Kit v2.0 (MobiDrop, Cat. No. S050200201) and the 3′ Single Index Kit (Cat. No. S050300201). Paired-end sequencing (150 bp) was performed on the Illumina NovaSeq platform by Novogene Bioinformatics Technology Co., Ltd (Tianjing, China).

value: mouse tumor


title: Female,FR,Saline,Adult,rep2

description:
Library name: 15A.7_Female_FR_Saline_mPFC_Adult
15A.7_Female_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH1 Q571R, RNA, rep2

description: Library name: Nthy_EZH1_Q571R_RNA_rep2


title: Nthy, EZH2 WT, ATAC, rep2

description: Library name: Nthy_EZH2_WT_ATAC_rep2

value: EZH2 WT overexpression


title: MΦID3-OE

description: Library name: Sample 2


title: Male,FR,Saline,Adult,rep2

description:
Library name: 15A.3_Male_FR_Saline_mPFC_Adult
15A.3_Male_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH1 Q571R, RNA, rep1

description: Library name: Nthy_EZH1_Q571R_RNA_rep1


title: MΦSSIGR-ID3

description: Library name: Sample 1


title: Nthy, EZH2 WT, ATAC, rep1

description: Library name: Nthy_EZH2_WT_ATAC_rep1


title: Male,Adlib,Saline,Adult,rep3

description:
Library name: 13B.3_Male_Adlib_Saline_mPFC_Adult
13B.3_Male_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH1 WT, RNA, rep3

description: Library name: Nthy_EZH1_WT_RNA_rep3

value: EZH1 WT overexpression


title: sample 25_EV71_RD_20190916

city: Wuhan

first: Zhang

last: Kui

address: Jinlong Avenue, Jiangxia District     Wuhan Institute of Virology, Chinese Academy of Sciences     Wuhan, Hubei 430200     China

institute: Wuhan Institute of Virology

description: Library name: sample 25

data_processing:
Sample 1-18: For sequencing, circularized DNA was amplified via rolling circle amplification to produce DNA nanoballs (DNBs), which were loaded onto patterned nanoarrays. Combinatorial Probe-Anchor Synthesis (cPAS) technology (DNBSEQ platform, BGI) was employed for 150 bp paired-end sequencing. Raw reads were quality-filtered using SOAPnuke to remove low-quality bases and adapters. Clean reads were mapped to the human reference genome (GRCh38/hg38) using HISAT2. Gene expression levels were estimated with RSEM (v1.3.1) and normalized to FPKM values. Differential Expression analysis was performed using DESeq2 (v1.4.5) with hresholds of |log2FC| ≥ 1 and adjusted p-value < 0.05. Enriched KEGG pathways were identified via Hypergeometric testing (Phyper), with significance thresholds set at Q-value ≤ 0.05 after false discovery rate (FDR) correction. All analyses were conducted using the BGI Tom Multi-omics Platform (https://biosys.bgi.com).
Sample 19-22: To identify termination sites characteristic of 2'-O-methylation, raw paired-end reads were first filtered by fastp (v0.23.2) and merged using FLASH (v1.2.11, -p 33 -m 12 -M 300 -x 0.25 -z) to create longer contiguous sequences. The merged reads were then filtered to select those containing the target adapter sequence "agtctcgatttcggaGGGGGGGG", allowing for one nucleotide mismatch to account for potential sequencing errors while maintaining specificity for Nm-detection products. Adapter sequences and any downstream polyG tracts were subsequently trimmed using Cutadapt to isolate the authentic viral sequences. The processed reads were then aligned to the EV71 reference genome (BrCr-TR, GenBank # U22521.1) using Bowtie2 (v2.2.6).
Sample 23-25: Raw multi-fast5 reads were base-called using Guppy (v3.1.5) and converted to single-read fast5 files using the ont_fast5_api (v3.0.2) multi_to_single_fast5 command. Reads were then mapped to the EV71 reference genome (GenBank # JQ804832.1) using Tombo (v1.5.1).
Assembly: GRCh38/hg38,and EV71 genome (GenBank number: U22521.1 or JQ804832.1)
Supplementary files format and content: Sample 1-18: Excel files contain FPKM.
Supplementary files format and content: Sample 19-22: Excel files contain NanoNm rate.
Supplementary files format and content: Sample 23-25: Excel files contain Nm mutation rate.

source_name: embryonic rhabdomyosarcoma

growth_protocol: RD/Vero cells were maintained in DMEM supplemented with 10% fetal bovine serum(FBS)at 37 ℃ in a 5% CO2 environment

extract_protocol:
Total RNAs were extracted using TRIzol Reagent (Invitrogen, cat. NO 15596026）
Sample 1-18: For library preparation, mRNA was enriched via oligo(dT) magnetic bead-based selection, fragmented, and subjected to quality control. First- and second-strand cDNA synthesis was performed, followed by 3’ adenylation and adapter ligation. (3) cDNA ends from low-dNTP extension were amplified by nested RACE-PCR. The resulting amplicons were purified and constructed into sequencing libraries for the Illumina platform. (4) Poly(A) RNA was directly ligated to sequencing adapters without reverse transcription. The prepared library was loaded onto a Nanopore flow cell for direct RNA sequencing.  Sample 19-22: Library preparation was performed by two step PCR. First round PCR reaction was set up as follows: DNA (10 ng/μl) 2μl; amplicon PCR forward primer mix (10 μM) 1μl; amplicon PCR reverse primer mix (10 μM) 1μl; 2×PCR Ready Mix 15 μl (total 25μl) (Kapa HiFi Ready Mix). The plate was sealed and PCR performed in a thermal instrument (BIO-RAD, T100TM).The PCR products were checked using electrophoresis in 1 % (w/v) agarose gels in TBE buffer (Tris, boric acid, EDTA). Then we used AMPure XP beads to purify the amplicon product. After that, the second round PCR was performed. PCR reaction was set up as follows: DNA (10 ng/μl) 2μl; universal P7 primer with index(10 μM) 1μl; P5 primer with index(10 μM) 1μl; 2× PCR Ready Mix 15 μl (total 30μl)(Kapa HiFi Ready Mix). Then we used AMPure XP beads to purify the amplicon product. The libraries were then quantified and pooled. Paired-end sequencing of the library was performed on the NovaSeq6000 / MiSeqsequencers with MIseq PE300 model (Illumina, San Diego, CA).  Sample 23-25: Poly(A) mRNA isolation using the GenElute mRNA Miniprep Kit (Sigma-Aldrich). Direct RNA sequencing was performed according to the Oxford Nanopore DRS protocol (SQK-RNA002)

treatment_protocol: For infection, RD/Vero cells were infected with EV71, followed by incubation and harvesting at specified time points. For knockdown, RD cells were transfected with siRNA targeting FBL or control siRNA, followed by EV71 infection.

value: embryonic rhabdomyosarcoma

value: RD

value: cell line


title: APOA1 treated astrocytes, replicate 8

city: San Francisco

first: Haoyue

last: Zhou

state: CA

address: 1650 Owens St

country: USA

institute: Gladstone Institutes

description: Library name: AS.Apoa1.8

data_processing:
Initial quality control was performed using FastQC (v0.12.1) and summarized with MultiQC (v1.27)
Reads were aligned to the mouse genome (GRCm39, Ensembl release 110) using STAR (v2.7.11b) with --sjdbOverhang 49.
Gene-level quantification was performed using featureCounts (v2.0.8) with parameters for paired-end, reverse-stranded reads.
Count matrices were processed with DESeq2 (v1.44.0). Genes with <10 counts in ≥8 samples were filtered.
Assembly: Normalization and dispersion estimation were performed using the DESeq function.
Supplementary files format and content: GRCm39, Ensembl release 110
Supplementary files format and content: DESeq2_library_size_normalized_counts_physiological.txt contains library size normalized counts from the DESeq() function of the R package DESeq2 (v1.44.0)

source_name: brain

growth_protocol: 500ml DMEM+GlutaMAX + 45ml FBS + 5ml 100x pen/strep

extract_protocol:
RNA extraction with Qiagen RNeasy Mini kit with on-column DNase digestion
NEBNext Ultra II Directional RNA Library Prep, mRNA

treatment_protocol: 10 μg/mL APOA1 for 24h, PBS volume-matched control

value: brain

value: Primary Astrocyte

value: WT

value: APOA1 treated


title: Nthy, EZH1 WT, RNA, rep2

description: Library name: Nthy_EZH1_WT_RNA_rep2


title: Female,Adlib,Saline,Adult,rep2

description:
Library name: 12A.7_Female_Adlib_Saline_mPFC_Adult
12A.7_Female_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt

value: Medial prefrontal cortex


title: OEcdgR_3

first: Yiling

state: Hubei

address: Nr.7 Donghu south road

institute: Chinese Academy of Sciences, Institute of Hydrobioloy

description:
Library name: sample9
column name in read_count.xlsx: OEcdgR6

data_processing:
To gain high quality sequence (clean data) for subsequent analysis,  Trimmomatic (v0.36) was employed to filter the original sequencing data. Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced (FPKM) was used to standardize the expression.
HISAT2 (v2.2.1) was used to map the filtered reads to the reference genome.
StringTie (v2.2.1) statistics was used to compare the read count values on each gene as the original expression of the gene.
Difference expression genes (DEGs) were analyzed by DESeq2 (1.34.0) with filter criteria as follows: |log2 (foldchange)| > 1 and false discovery rate (FDR)<0.05.
GO (gene ontology), and KEGG (kyoto encyclopedia of genes and genomes) pathway enrichment analyses were performed using clusterProfiler (v4.9.0.2).
Assembly: ASM972v1
Supplementary files format and content: Excel file (.xlsx) contain raw counts  for each samples
Supplementary files format and content: Excel file (.xlsx) contain FPKM and TPM values for each samples

organism: Synechocystis sp. PCC 6803

growth_protocol: The wild type, ∆cdgR and WT_OE cdgR were streaked onto BG11 plates and cultured under continuous light at an intensity of 30 μmol photons m-2s for one week. Subsequently, the cells were harvested from the plates, diluted 60-fold, and measured for OD750. Further dilution was carried out to achieve an OD of 15 using BG11 liquid medium, and aliquots were spotted onto the surface of BG11 agar medium (0.6% agar) in 10 cm square plates supplemented with 0.3 µM CuSO4 and 2 mM theophylline . The spots were placed in the middle row, approximately 7 cm from the bottom of the plate.

extract_protocol:
Trizol Reagent (Invitrogen Life Technologies) was used to isolate total RNA，the RNA concentrations were measured using Qubit 4 Fluorometer (Thermo Fisher Scientific, DE, USA).
Sequencing libraries were constructed using the VAHTS Universal V8 RNA-seq Library Prep Kit for MGI (NRM605, Vazyme, Nanjing, China) following the manufacturer's protocol.

treatment_protocol: Each plate was spotted with 50 µl of the diluted culture until completion, and three plates were prepared for each sample. The plates were then exposed to lateral white LED lamps with an intensity of approximately 50 μmol photons m-2s-1 for 5 days.

tag: strain

value: cdgR overexpression

value: grown on 0.6% BG11 agar plate under lateral illumination


title: Male,Adlib,Saline,Adult,rep2

description:
Library name: 12A.3_Male_Adlib_Saline_mPFC_Adult
12A.3_Male_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: APOA1 treated astrocytes, replicate 7

description: Library name: AS.Apoa1.7


title: OEcdgR_2

description:
Library name: sample8
column name in read_count.xlsx: OEcdgR5


title: Nthy, EZH1 WT, RNA, rep1

description: Library name: Nthy_EZH1_WT_RNA_rep1

value: Nthy-ori 3-1

value: Thyroid follicular epithelial cell


title: Female,Adlib,Saline,Adult,rep1

description:
Library name: 11B.7_Female_Adlib_Saline_mPFC_Adult
11B.7_Female_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: APOA1 treated astrocytes, replicate 6

description: Library name: AS.Apoa1.6


title: Nthy, EZH1 Q571R, CUT&Tag, HK36me2, rep2

description: Library name: Nthy_EZH1_Q571R_CUT_Tag_H3K36me2_rep2

data_processing:
For data analysis, adapter sequences were trimmed using Cutadapt, and reads were aligned to the human (hg38) and Drosophila (dm6) reference genomes using Bowtie2. Potential PCR duplicates were removed using Picard tools. BAM files were initially normalized using CPM to account for sequencing depth. To correct for experimental variability, the data were further normalized using scaling factors derived from reads mapping to the Drosophila genome. Peak calling for H3K27me3 and H3K36me2 was performed using SICER2 with a window size of 1,000 bp and a gap size of 100,000 bp. Bigwig files and heatmaps were generated using deepTools.
Assembly: hg38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was performed following the EpiCypher protocol. In brief, 50,000 nuclei were mixed with Drosophila melanogaster nuclei and incubated with ConA-conjugated magnetic beads in bead activation buffer (20 mM HEPES-NaCl [pH 7.9], 10 mM KCl, 1 mM CaCl2, and 1 mM MnCl2) for 10 min at room temperature. The nuclei-bound beads were incubated overnight at 4°C with primary antibodies against H3K27me3 or H3K36me2, alongside an anti-H2Av antibody, diluted in antibody buffer (20 mM HEPES-NaCl [pH 7.9], 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, 2 mM EDTA, and protease inhibitors) on a nutator. The following day, the complexes were washed twice with Digitonin-150 buffer (20 mM HEPES-NaCl [pH 7.9], 150 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, and protease inhibitors) and incubated with secondary antibody diluted in Digitonin-150 buffer for 30 min at room temperature. After two washes, 2.5 µL pAG-Tn5 diluted in Digitonin-300 buffer (20 mM HEPES-NaCl [pH 7.9], 300 mM NaCl, 0.5 mM spermidine, 0.01% digitonin, and protease inhibitors) was added and incubated for 1 h at room temperature. Complexes were washed twice with Digitonin-300 buffer and then incubated in Digitonin-300 buffer supplemented with 10 mM MgCl2 for 1 h at 37°C for tagmentation. The reaction was stopped by washing with TAPS buffer (10 mM TAPS [pH 8.5] and 0.2 mM EDTA). To release the tagmented DNA, SDS release buffer (10 mM TAPS [pH 8.5] and 0.1% SDS) was added, and the mixture was incubated at 58°C for 1 h. SDS was quenched by the addition of 0.67% Triton X-100.
Libraries were amplified by PCR using a non-hot start 2x PCR master mix with i5 and barcoded i7 primers. PCR products were purified using AMPure XP beads.


title: OEcdgR_1

description:
Library name: sample7
column name in read_count.xlsx: OEcdgR4


title: APOA1 treated astrocytes, replicate 5

description: Library name: AS.Apoa1.5


title: Male,Adlib,Saline,Adult,rep1

description:
Library name: 11B.3_Male_Adlib_Saline_mPFC_Adult
11B.3_Male_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: cdgR_3

description:
Library name: sample6
column name in read_count.xlsx: cdgR6

value: cdgR deletion


title: Female,FR,Saline,Adult,rep1

description:
Library name: 11A.7_Female_FR_Saline_mPFC_Adult
11A.7_Female_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: Nthy, EZH1 Q571R, CUT&Tag, HK36me2, rep1

description: Library name: Nthy_EZH1_Q571R_CUT_Tag_H3K36me2_rep1

value: EZH1 Q571R overexpression


title: Nthy, EZH1 Q571R, CUT&Tag, HK27me3, rep2

description: Library name: Nthy_EZH1_Q571R_CUT_Tag_H3K27me3_rep2


title: cdgR_2

description:
Library name: sample5
column name in read_count.xlsx: cdgR5


title: APOA1 treated astrocytes, replicate 3

description: Library name: AS.Apoa1.3


title: Male,FR,Saline,Adult,rep1

description:
Library name: 11A.3_Male_FR_Saline_mPFC_Adult
11A.3_Male_FR_Saline_mPFC_Adult
Adult_mPFC_counts.txt


title: APOA1 treated astrocytes, replicate 4

description: Library name: AS.Apoa1.4


title: APOA1 treated astrocytes, replicate 2

description: Library name: AS.Apoa1.2


title: cdgR_1

description:
Library name: sample4
column name in read_count.xlsx: cdgR4


title: Nthy, EZH1 Q571R, CUT&Tag, HK27me3, rep1

description: Library name: Nthy_EZH1_Q571R_CUT_Tag_H3K27me3_rep1


title: DRG, Sham_solvent_3

city: 武汉

first: Bang

last: Hu

address: 昙华林特1号

institute: 湖北中医药大学

data_processing:
Valid sequences were obtained by removing adapter self-links and low-quality bases and reads. The raw sequences obtained from sequencing were firstly removed from sequences containing two indeterminate bases, and then FASTX-toolkit (version 0.0.13) was used to filter the low-quality reads containing the adjoined and low-quality reads inside, and the sequences below 16 in length were removed to obtain valid sequences (clean reads).
Based on the characteristics of the genome, HISAT2 software was run to compare the clean reads to the reference genome (reference genome version number: mRatBN7.2), and the reads with unique positioning on the genome (uniquely mapped reads) were counted in each region.
The distribution of uniquely mapped reads in each region of the genome was calculated using FPKM, and the number of genes with FPKM>0 and FPKM≥1 were counted.
Differential expression analysis of genes is performed using DESeq2 software
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: dorsal root ganglion

extract_protocol:
Total RNA was extracted with TRIZOL (Ambion). the RNA was further purified by two phenol-chloroform treatments and then treated with RQ1 DNase (Promega, Madison, WI, USA) to remove DNA. the quality and quantity of purified RNA was further verified by measuring the absorbance at 260 nm/280 nm (A260). The quality and quantity of purified RNA was redetermined by measuring absorbance at 260 nm/280 nm (A260/A280) using Nanodrop one (Thermo). The integrity of RNA was further verified by 1.0% agarose gel electrophoresis.
1μg of total RNA that passed the assay was taken for RNA-seq library preparation. DNA was removed using RQ1 DNA enzyme (Promega), total RNA was mRNA captured by VAHTS mRNA capture beads (Vazyme, N401) and RNA was purified by RNA clean beads, followed by final fragmentation using KAPA strand mRNA-Seq Kit (KK8544 The RNA-seq library was prepared using Illumina Novaseq 6000 in PE150 mode for high-throughput sequencing. sequencing.

value: dorsal root ganglion

tag: disease state

value: Sham

value: solvent


title: Nthy, EZH1 Q571R, CUT&Tag, IgG, rep1

description: Library name: Nthy_EZH1_Q571R_CUT_Tag_IgG_rep1


title: DRG, Sham_solvent_2


title: WT_3

description:
Library name: sample3
column name in read_count.xlsx: WT3


title: APOA1 treated astrocytes, replicate 1

description: Library name: AS.Apoa1.1


title: Nthy, EZH1 WT, CUT&Tag, HK36me2, rep2

description: Library name: Nthy_EZH1_WT_CUT_Tag_H3K36me2_rep2

value: EZH1 WT overexpression


title: Untreated astrocytes, replicate 8

description: Library name: AS.Ctrl.8

value: Untreated


title: WT_2

description:
Library name: sample2
column name in read_count.xlsx: WT2


title: WT_1

description:
Library name: sample1
column name in read_count.xlsx: WT1


title: AP d3, rep 3

city: Cambridge

first: Timotheus

last: Halim

address: University of Cambridge Li Ka Shing Centre, Robinson Way

department: CRUK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

data_processing:
Initial mapping and counting of 10x Genomics scRNA-seq reads was performed using Cell Ranger v3.1.0.
Assembly: GRCm38.p6
Supplementary files format and content: Cell Ranger output containing barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files

source_name: Pancreas

extract_protocol:
Single-cell encapsulation was performed using the Chromium Single Cell B Chip Kit (10x Genomics, PN-1000073).
Library preparation was performed using the Chromium Single Cell 3’ GEM Library & Gel Bead Kit v3 (10x Genomics, PN-1000075).

treatment_protocol: Mice were treated with PBS (n=3) or repeated hourly doses of 75ng/g body weight of caerulein for 6 hours, and taken down at day 1 (n=2), day 3 (n=3), or day 7 (n=2).

value: Pancreas

value: Caerulein


title: Untreated astrocytes, replicate 7

description: Library name: AS.Ctrl.7

value: brain

value: Primary Astrocyte


title: Nthy, EZH1 WT, CUT&Tag, HK36me2, rep1

description: Library name: Nthy_EZH1_WT_CUT_Tag_H3K36me2_rep1


title: DRG, Sham_herb_3

value: herb


title: DRG, Sham_solvent_1


title: Prunus mongolica seedling combined alkali salt and cadmium stress with GABA biological replicate 3

city: Hohhot,Inner Mongolia

first: Lei

last: Wang

address: Daxue East Street, Saihan District

institute: Inner Mongolia Agricultural University

description:
Library name: SCdG_3
Combined alkali salt and cadmium stress with GABA treatment sample, biological replicate 3. Column name in expression matrices: SCdG_3

data_processing:
Raw sequencing reads were preprocessed and filtered using Cutadapt to remove adaptor sequences and low-quality reads, generating clean reads.
Quality control of sequencing reads was performed using FastQC v0.10.1.
Clean reads were mapped to the Prunus mongolica reference genome using HISAT2 v2.2.1.
Transcript assembly and gene/transcript expression quantification were performed using StringTie v2.1.6, and expression levels were reported as raw read counts and FPKM values.
Differential expression analysis was performed using DESeq2 v1.22.2 and edgeR v3.22.5, with p-values adjusted using the Benjamini-Hochberg method. Differentially expressed genes were identified according to the thresholds used in this study.
Assembly: Prunus mongolica reference genome assembly from NGDC Genome Warehouse, Assembly ID 34295; reference genome accessions include GWHBQDV00000001.1.
Supplementary files format and content: 1_genes_fpkm_expression.txt: tab-delimited text file containing gene-level annotation and expression information for all samples, including gene IDs, genomic positions, functional annotations, FPKM values, and raw read counts.
Supplementary files format and content: 2_transcripts_fpkm_expression.txt: tab-delimited text file containing transcript-level annotation and expression information for all samples, including transcript IDs, transcript classification, genomic positions, FPKM values, and raw read counts.
Supplementary files format and content: gene_count_matrix.txt: tab-delimited matrix containing raw read counts for genes across all samples, with genes as rows and samples as columns.
Supplementary files format and content: transcript_count_matrix.txt: tab-delimited matrix containing raw read counts for transcripts across all samples, with transcripts as rows and samples as columns.

organism: Prunus mongolica

source_name: leaf

growth_protocol: Healthy and uniformly sized Prunus mongolica seeds were selected, surface-sterilized in 0.05% KMnO4 for 25 min, rinsed six times with sterile distilled water, and pre-soaked in distilled water for 12 h. Sinking seeds were selected for germination and seedling culture. The growth substrate consisted of a fertilized white peat-based seedling medium mixed with perlite at a volume ratio of 3:1. Before use, the substrate was disinfected with 0.3% KMnO4, sealed for 12 h, and exposed to sunlight for 8 h. Seeds were sown in disinfected black polypropylene seedling trays with 32 cells, each with an approximate volume of 110 mL.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Thermo Fisher, 15596018) according to the manufacturer's protocol. RNA quantity and purity were assessed using a NanoDrop ND-1000 spectrophotometer (NanoDrop, Wilmington, DE, USA), and RNA integrity was evaluated using an Agilent Bioanalyzer 2100 (Agilent, CA, USA). RNA samples with concentration >50 ng/μL, RIN >7.0, and total RNA amount >1 μg were used for downstream library construction.
Poly(A)+ mRNA was enriched from total RNA using oligo(dT) magnetic beads (Dynabeads Oligo (dT), cat. 25-61005, Thermo Fisher, USA) through two rounds of purification. The captured mRNA was fragmented at 94°C for 5–7 min using the NEBNext Magnesium RNA Fragmentation Module (cat. E6150S, USA). First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen, cat. 1896649, CA, USA). Second-strand cDNA synthesis was performed using E. coli DNA polymerase I (NEB, cat. M0209, USA) and RNase H (NEB, cat. M0297, USA), with dUTP incorporated into the second strand. After end repair, A-tailing, adapter ligation, size selection, and purification, the second strand was digested using UDG enzyme (NEB, cat. M0280, MA, USA). PCR amplification was performed under the following conditions: 95°C for 3 min; 8 cycles of 98°C for 15 s, 60°C for 15 s, and 72°C for 30 s; followed by a final extension at 72°C for 5 min. Strand-specific libraries with an insert size of approximately 300 ± 50 bp were constructed and sequenced on an Illumina NovaSeq X Plus platform by LC Bio Technology Co., Ltd. (Hangzhou, China) using paired-end 150 bp sequencing.

treatment_protocol: Based on the physicochemical properties of different soil types in Wuhai City, Inner Mongolia Autonomous Region, China, the simulated alkali-salt stress pH was adjusted to 8.50–8.80 to better reflect local ecological restoration conditions. Prunus mongolica seedlings were subjected to eight treatments: control (CK), exogenous GABA treatment (G), alkali-salt stress (S), cadmium stress (Cd), combined alkali-salt and cadmium stress (SCd), alkali-salt stress with exogenous GABA treatment (SG), cadmium stress with exogenous GABA treatment (CdG), and combined alkali-salt and cadmium stress with exogenous GABA treatment (SCdG). Alkali-salt stress was simulated using a 10.00 mmol/L mixed alkali-salt solution prepared with 0.81 g/L NaHCO3 and 0.036 g/L Na2CO3, with the pH adjusted to 8.50–8.80. Cadmium stress was applied using a 0.5 mmol/L cadmium solution prepared from 97.00 mg/L CdCl2·H2O. Exogenous GABA was applied at 0.90 mmol/L, prepared using 92.8 mg/L gamma-aminobutyric acid. These concentrations were selected based on preliminary experiments showing that alkali-salt and cadmium treatments inhibited seed germination and seedling growth, whereas exogenous GABA promoted germination and seedling development.

value: leaf

value: wild type

tag: batch

value: batch 1


title: Untreated astrocytes, replicate 6

description: Library name: AS.Ctrl.6

value: WT


title: Nthy, EZH1 WT, CUT&Tag, HK27me3, rep2

description: Library name: Nthy_EZH1_WT_CUT_Tag_H3K27me3_rep2

value: Nthy-ori 3-1

value: Thyroid follicular epithelial cell


title: Nthy, EZH1 WT, CUT&Tag, HK27me3, rep1

description: Library name: Nthy_EZH1_WT_CUT_Tag_H3K27me3_rep1


title: Prunus mongolica seedling combined alkali salt and cadmium stress with GABA biological replicate 2

description:
Library name: SCdG_2
Combined alkali salt and cadmium stress with GABA treatment sample, biological replicate 2. Column name in expression matrices: SCdG_2


title: DRG, Sham_herb_2


title: Control 1

city: Stockholm

first: Danai

last: Zareifi

address: Nobels väg 6

department: Medicine Huddinge

country: Sweden

institute: Karolinska Institutet

description: Library name: P23101_1045

data_processing:
Library preparation and sequencing were conducted on an Illumina platform, generating reads with Phred scores consistently above Q30. Quality and adapter trimming of reads was performed using Cutadapt (v2.8). Sample quality was assessed using FastQC (v0.11.8) and MultiQC (v1.7). Reads were aligned to the Ensembl GRCh38 reference genome using STAR (v2.7.9a). Counts for each gene were obtained using featureCounts (v1.5.1).
Assembly: Ensembl GRCh38
Supplementary files format and content: txt file contains raw counts for all samples

source_name: human adipocytes

extract_protocol:
RNA isolation, cDNA synthesis and quantitative real-time PCR (qPCR) were performed as previously described11. Briefly, total RNA was purified using the NucleoSpin RNA kit (Macherey-Nagel #740955) and quantified with a NanoDrop 2000 spectrophotometer (Thermo Fisher Scientific). Reverse transcription and qPCR were performed using iScript (Bio-Rad #1708891) and iQ SYBR Green Supermix (Bio-Rad #1708882), respectively. Relative mRNA levels were calculated using the comparative 2-DDct method. Where indicated, z-score analysis was applied using the formula: (observed value - mean) / standard deviation.
The library pool was prepared with Illumina mRNA stranded ligation protocol.

value: human adipocytes

tag: Sex

value: male

value: control


title: Untreated astrocytes, replicate 5

description: Library name: AS.Ctrl.5


title: DRG, Sham_herb_1

value: dorsal root ganglion

value: Sham


title: Prunus mongolica seedling combined alkali salt and cadmium stress with GABA biological replicate 1

description:
Library name: SCdG_1
Combined alkali salt and cadmium stress with GABA treatment sample, biological replicate 1. Column name in expression matrices: SCdG_1


title: Untreated astrocytes, replicate 4

description: Library name: AS.Ctrl.4

value: Untreated


title: Nthy, EZH1 WT, CUT&Tag, IgG, rep1

description: Library name: Nthy_EZH1_WT_CUT_Tag_IgG_rep1

value: EZH1 WT overexpression


title: DRG, NPP_solvent_3

value: NPP

value: solvent


title: Nthy, EZH1 Q571R, ChIP, EZH1, rep2

description: Library name: Nthy_EZH1_Q571R_ChIP_EZH1_rep2

data_processing:
For data analysis, adapter sequences were trimmed using Cutadapt, and reads were aligned to the human reference genome (hg38) using Bowtie2. EZH1 peaks were called using MACS2 in narrow peak mode with a q-value threshold of 0.05. For downstream analysis, BAM files were normalized using CPM to account for differences in sequencing depth. BigWig files and heatmaps were generated with deepTools.
Assembly: hg38
Supplementary files format and content: bigWig

extract_protocol:
Approximately 5x10^6 cells were harvested and crosslinked with 2 mM disuccinimidyl glutarate (DSG) for 35 min, followed by fixation with 1% formaldehyde for an additional 10 min. The crosslinking reaction was quenched with 125 mM glycine, and the cell pellet was washed with PBS. After fixation, nuclei were isolated using nuclei isolation buffer (20 mM HEPES-NaCl [pH 7.9], 10 mM KCl, 0.1% Triton X-100, 20% glycerol, 0.5 mM spermidine, and protease inhibitors). The nuclei were resuspended in 130 μL of 1% SDS lysis buffer (50 mM Tris-HCl [pH 8.0], 10 mM EDTA, 1% SDS, and protease inhibitors) and sonicated using a Covaris S220 focused-ultrasonicator (175 peak incident power, 10% duty factor, 200 cycles per burst) for 430 s. The sheared chromatin was diluted in ChIP dilution buffer (16.7 mM Tris-HCl [pH 8.0], 0.01% SDS, 1.1% Triton X-100, 16.7 mM NaCl, 1.2 mM EDTA, and protease inhibitors) and centrifuged at 13,000 x g for 15 min at 4°C to collect the soluble chromatin fraction. Chromatin was incubated overnight at 4°C with Dynabeads Protein A conjugated with an anti-EZH1 antibody. The following day, the beads were washed three times with Wash Buffer A (140 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate, and 10 mM Tris-HCl [pH 8.0]), twice with Wash Buffer B (300 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 1% Triton X-100, 0.2% SDS, 0.1% sodium deoxycholate, and 10 mM Tris-HCl [pH 8.0]), and once with Wash Buffer C (250 mM LiCl, 10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5% NP-40, and 0.5% sodium deoxycholate). The beads were resuspended in 10 mM Tris-HCl [pH 8.0] and incubated with 5 μg of RNase A for 30 min at 37°C, followed by incubation with 100 μg proteinase K overnight at 65°C for reverse crosslinking. The supernatant was transferred to new tubes, and DNA fragments around 200 bp were purified and size-selected using SPRIselect beads.
Library preparation was performed using the NEBNext Ultra II DNA Library Prep Kit. Libraries were sequenced on an Illumina NovaSeq 6000 (100 bp paired-end) or NovaSeq X Plus (150 bp paired-end) platform.

value: EZH1 Q571R overexpression


title: Prunus mongolica seedling cadmium stress with GABA biological replicate 3

description:
Library name: CdG_3
Cadmium stress with GABA treatment sample, biological replicate 3. Column name in expression matrices: CdG_3

value: cadmium stress with GABA


title: Untreated astrocytes, replicate 3

description: Library name: AS.Ctrl.3

value: brain

value: Primary Astrocyte


title: Prunus mongolica seedling cadmium stress with GABA biological replicate 2

description:
Library name: CdG_2
Cadmium stress with GABA treatment sample, biological replicate 2. Column name in expression matrices: CdG_2

value: leaf

value: wild type

value: batch 1


title: DRG, NPP_solvent_2


title: Nthy, EZH1 Q571R, ChIP, EZH1, rep1

description: Library name: Nthy_EZH1_Q571R_ChIP_EZH1_rep1

value: Nthy-ori 3-1

value: Thyroid follicular epithelial cell


title: Untreated astrocytes, replicate 2

description: Library name: AS.Ctrl.2

value: WT


title: DRG, NPP_solvent_1


title: Nthy, EZH1 Q571R, ChIP, IgG, rep1

description: Library name: Nthy_EZH1_Q571R_ChIP_IgG_rep1


title: Prunus mongolica seedling cadmium stress with GABA biological replicate 1

description:
Library name: CdG_1
Cadmium stress with GABA treatment sample, biological replicate 1. Column name in expression matrices: CdG_1


title: Untreated astrocytes, replicate 1

description: Library name: AS.Ctrl.1


title: DRG, NPP_herb_3

value: herb


title: Nthy, EZH1 WT, ChIP, EZH1, rep2

description: Library name: Nthy_EZH1_WT_ChIP_EZH1_rep2


title: APOA1 treated astrocytes (with A-beta), replicate 8

description: Library name: AS.Aβ.Apoa1.8

data_processing:
Initial quality control was performed using FastQC (v0.12.1) and summarized with MultiQC (v1.27)
Reads were aligned to the mouse genome (GRCm39, Ensembl release 110) using STAR (v2.7.11b) with --sjdbOverhang 49.
Gene-level quantification was performed using featureCounts (v2.0.8) with parameters for paired-end, reverse-stranded reads.
Count matrices were processed with DESeq2 (v1.44.0). Genes with <10 counts in ≥8 samples were filtered.
Assembly: Normalization and dispersion estimation were performed using the DESeq function.
Supplementary files format and content: GRCm39, Ensembl release 110
Supplementary files format and content: DESeq2_library_size_normalized_counts_AD.txt contains library size normalized counts from the DESeq() function of the R package DESeq2 (v1.44.0)

value: APOA1 treated


title: DRG, NPP_herb_2

value: dorsal root ganglion


title: Prunus mongolica seedling alkali-salt stress with GABA biological replicate 3

description:
Library name: SG_3
Alkali salt stress with GABA treatment sample, biological replicate 3. Column name in expression matrices: SG_3

value: alkali salt stress with GABA


title: Prunus mongolica seedling alkali-salt stress with GABA biological replicate 2

description:
Library name: SG_2
Alkali salt stress with GABA treatment sample, biological replicate 2. Column name in expression matrices: SG_2


title: Nthy, EZH1 WT, ChIP, EZH1, rep1

description: Library name: Nthy_EZH1_WT_ChIP_EZH1_rep1

value: EZH1 WT overexpression


title: APOA1 treated astrocytes (with A-beta), replicate 7

description: Library name: AS.Aβ.Apoa1.7


title: DRG, NPP_herb_1

value: NPP


title: Nthy, EZH1 Y727D, ChIP, EZH1, rep2

description: Library name: Nthy_EZH1_Y727D_ChIP_EZH1_rep2

value: EZH1 Y727D overexpression


title: Prunus mongolica seedling alkali-salt stress with GABA biological replicate 1

description:
Library name: SG_1
Alkali salt stress with GABA treatment sample, biological replicate 1. Column name in expression matrices: SG_1


title: Nthy, EZH1 WT, ChIP, IgG, rep1

description: Library name: Nthy_EZH1_WT_ChIP_IgG_rep1


title: DRG, Ctrl_solvent_3

value: Ctrl

value: solvent


title: mm468_scChIC_h3k27me3

city: Paris

first: Céline

last: Vallot

address: 26 Rue D'Ulm

country: France

institute: Institut Curie

description: Library name: mm468_scChIC_h3k27me3

data_processing:
Fastq files were generated by the Single Cell Core of the Hubrecht Institute according to (Zeller et al. 2023; PMID: 36539617) and transformed into the 10X-like format using a custom script (see Moutaux & Schwager et al 2025). The transformed fastq files were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Assembly: hg38
Supplementary files format and content: fragment files of DNA counts :  chic_h3k27me3.fragments_prefixed.tsv.gz
Supplementary files format and content: fragment file indexes: chic_h3k27me3.fragments_prefixed.tsv.gz.tbi
Supplementary files format and content: Pseudobulk bigwig (CPM-normalized):chic_h3k27me3.bigwig

growth_protocol: MDA-MB-468 cells (American Type Culture Collection (ATCC), HTB-132) were maintained in DMEM (Gibco-BRL, 11966025) supplemented with 10% heat-inactivated fetal bovine serum (Gibco, 10500064) and cultured in a humidified 5% CO2 atmosphere at 37 °C.

extract_protocol:
500 000 MDA-MB-468 cells were fixed with 70% Ethanol
scChIC-seq was performed by the Single Cell Core of the Hubrecht Institute according to (Zeller et al. 2023; PMID: 36539617).

value: epithelial

value: no

tag: library type

value: DNA


title: APOA1 treated astrocytes (with A-beta), replicate 6

description: Library name: AS.Aβ.Apoa1.6

value: brain

value: Primary Astrocyte


title: Prunus mongolica seedling combined alkali salt and cadmium stress biological replicate 3

description:
Library name: SCd_3
Combined alkali salt and cadmium stress treatment sample, biological replicate 3. Column name in expression matrices: SCd_3

value: leaf

value: wild type

value: combined alkali salt and cadmium stress

value: batch 1


title: APOA1 treated astrocytes (with A-beta), replicate 4

description: Library name: AS.Aβ.Apoa1.4

value: WT

value: APOA1 treated


title: mm468_scChIP_h3k27me3

description: Library name: mm468_scChIP_h3k27me3

data_processing:
Raw fastq files were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Assembly: hg38
Supplementary files format and content: fragment files of DNA counts : D937C02_MM468-H3K27me3_2000c.fragments.tsv.gz
Supplementary files format and content: fragment file indexes: D937C02_MM468-H3K27me3_2000c.fragments.tsv.gz.tbi
Supplementary files format and content: Pseudobulk bigwig (CPM-normalized): D937C02.bigwig

extract_protocol:
MDA-MB-468 cells were labeled with CFSE staining and resuspended in cell suspension buffer (30% Percoll, 0.1% Pluronic F-68, 25mM Hepes pH 7.4, 50mM NaCl) before encapsulation in droplets, with lysis/digestion buffer using homemade microfluidic chips as described in (Grosselin et al. 2019; ; PMID: 31152164)
scChIP-seq was performed according to (Grosselin et al 2019; PMID: 31152164)


title: APOA1 treated astrocytes (with A-beta), replicate 5

description: Library name: AS.Aβ.Apoa1.5


title: DRG, Ctrl_solvent_1

value: dorsal root ganglion


title: Prunus mongolica seedling combined alkali salt and cadmium stress biological replicate 1

description:
Library name: SCd_1
Combined alkali salt and cadmium stress treatment sample, biological replicate 1. Column name in expression matrices: SCd_1


title: APOA1 treated astrocytes (with A-beta), replicate 3

description: Library name: AS.Aβ.Apoa1.3


title: DRG, Ctrl_3


title: Siglec10-2-P

city: nantong

first: chuang

last: miao

state: jiangsu

address: No. 20 Xisi Road

department: Department of General Surgery

institute: Affiliated Hospital of Nantong University

description:
Library name: Siglec10-2-P
P group, replicate biosample 2

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes gene counts for each sample by tpm analysis

source_name: colon

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: colon

value: SIGLEC10 postive


title: APOA1 treated astrocytes (with A-beta), replicate 2

description: Library name: AS.Aβ.Apoa1.2


title: Prunus mongolica seedling cadmium stress biological replicate 3

description:
Library name: Cd_3
Cadmium stress stress treatment sample, biological replicate 3. Column name in expression matrices: Cd_3

value: cadmium stress


title: DRG, Ctrl_2

value: Ctrl


title: Siglec10-1-P

description:
Library name: Siglec10-1-P
P group, replicate biosample 1


title: APOA1 treated astrocytes (with A-beta), replicate 1

description: Library name: AS.Aβ.Apoa1.1


title: Prunus mongolica seedling cadmium stress biological replicate 2

description:
Library name: Cd_2
Cadmium stress stress treatment sample, biological replicate 2. Column name in expression matrices: Cd_2


title: DRG, Ctrl_1


title: Siglec10-3-N

description:
Library name: Siglec10-3-N
N group, replicate biosample 3

value: SIGLEC10 negative


title: Prunus mongolica seedling cadmium stress biological replicate 1

description:
Library name: Cd_1
Cadmium stress stress treatment sample, biological replicate 1. Column name in expression matrices: Cd_1


title: Untreated astrocytes (with A-beta), replicate 8

description: Library name: AS.Aβ.8

value: Untreated


title: IL33_ILC2_rep5

data_processing:
Quality of raw sequence data was assessed using FastQC (version 0.11.9)
Raw sequence was trimmed for adapter content using Trimmomatic (version 0.39)
Reads were aligned to the GRCm38.p6 genome using STAR (v 2.7.7a)
Alignment quality was assess using Picard’s CollectAlignmentMetrics, CollectRnaSeqMetrics, MarkDuplicates and CollectInsertSizeMetrics tools (v 2.27.3)
Quantification of gene expression was performed using Salmon (v 1.6.0) in mapping-based mode versus the Ensembl release 102 transcriptome
Assembly: GRCm38.p6
Supplementary files format and content: Raw and DESeq2-normalised counts matrix (as .csv file)

extract_protocol:
RNA was extracted using RNeasy plus micro kit (Qiagen) and 5 to 15 ng used as input material for library preparation.
Libraries were generated with the NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (NEB) according to manufacturer's instructions. The pooled libraries were quantified with KAPA Library Quantification Kit for Illumina (Kapa Biosystems) and sequenced (paired end 150nt) on an Illumina NovaSeq 6000 system (Illumina).

value: Pancreas


title: Siglec10-2-N

description:
Library name: Siglec10-2-N
N group, replicate biosample 2


title: Prunus mongolica seedling alkali-salt stress biological replicate 3

description:
Library name: S_3
Alkali salt stress treatment sample, biological replicate 3. Column name in expression matrices: S_3

value: alkali salt stress


title: Female,Adlib,Saline,Adult,rep9

description:
Library name: 8B.4_Female_Adlib_Saline_mPFC_Adult
8B.4_Female_Adlib_Saline_mPFC_Adult
Adult_mPFC_counts.txt

data_processing:
Reads were aligned to the rat genome with STAR
Read counts per gene were computed with STAR
Assembly: Rnor_6.0
Supplementary files format and content: Ensembl gene Ids and read counts, tab delimited
Supplementary files format and content: Differential expression data, tab delimited

extract_protocol:
Qiagen AllPrep RNA minikit
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Medial prefrontal cortex


title: IL33_ILC2_rep4


title: Untreated astrocytes (with A-beta), replicate 7

description: Library name: AS.Aβ.7

value: brain

value: Primary Astrocyte


title: Prunus mongolica seedling alkali-salt stress biological replicate 2

description:
Library name: S_2
Alkali salt stress treatment sample, biological replicate 2. Column name in expression matrices: S_2

value: leaf

value: wild type


title: Untreated astrocytes (with A-beta), replicate 6

description: Library name: AS.Aβ.6


title: Siglec10-1-N

description:
Library name: Siglec10-1-N
N group, replicate biosample 1


title: IL33_ILC2_rep3


title: mm468_onecell_multiome_h3k27me3

description: Library name: mm468_onecell_multiome_h3k27me3

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Raw transcriptomic data were processed using the scRNA-smartseq3 Nextflow pipeline of Curie Institute (https://github.com/bioinfo-pf-curie/scRNA-SmartSeq3).
Assembly: hg38
Supplementary files format and content: fragment files (chromatin)
Supplementary files format and content: full-length and umi-only count matrices (rna)
Library strategy: CUT&Tag

source_name: mammary gland

growth_protocol: MDA-MB-468 cells (American Type Culture Collection (ATCC), HTB-132) were maintained in DMEM (Gibco-BRL, 11966025) supplemented with 10% heat-inactivated fetal bovine serum (Gibco, 10500064) and cultured in a humidified 5% CO2 atmosphere at 37 °C. MDA-MB-468 cells were sorted into plates using CellenONE dispenser (Scienion).

extract_protocol:
The plate was subjected to the multiome OneCell CUT&Tag protocol, as described in (Schwager, Moutaux et al., 2026)
Combination of OneCell CUT&Tag with single-cell full-length transcriptomics, as described in (Schwager, Moutaux et al., 2026)

value: mammary gland

value: epithelial

value: no

value: DNA


title: Prunus mongolica seedling alkali-salt stress biological replicate 1

description:
Library name: S_1
Alkali salt stress treatment sample, biological replicate 1. Column name in expression matrices: S_1

value: batch 1


title: Untreated astrocytes (with A-beta), replicate 5

description: Library name: AS.Aβ.5

value: WT


title: IL33_ILC2_rep2


title: sample 22_EV71_901

description: Library name: sample 22

library_source: other

molecule: other

value: embryonic rhabdomyosarcoma

value: RD

value: cell line


title: Prunus mongolica seedling GABA treatment biological replicate 3

description:
Library name: G_3
Exogenous GABA treatment sample, biological replicate 3. Column name in expression matrices: G_3

value: GABA


title: sample 21_EV71_789

description: Library name: sample 21


title: Untreated astrocytes (with A-beta), replicate 4

description: Library name: AS.Aβ.4

value: Untreated


title: IL33_ILC2_rep1

value: Pancreas


title: Untreated astrocytes (with A-beta), replicate 3

description: Library name: AS.Aβ.3


title: naïve_ILC2_rep4

value: PBS


title: sample 20_EV71_421

description: Library name: sample 20


title: Untreated astrocytes (with A-beta), replicate 2

description: Library name: AS.Aβ.2

value: brain


title: Prunus mongolica seedling GABA treatment biological replicate 1

description:
Library name: G_1
Exogenous GABA treatment sample, biological replicate 1. Column name in expression matrices: G_1


title: Prunus mongolica seedling GABA treatment biological replicate 2

description:
Library name: G_2
Exogenous GABA treatment sample, biological replicate 2. Column name in expression matrices: G_2


title: sample 19_EV71_295

description: Library name: sample 19


title: naïve_ILC2_rep3


title: naïve_ILC2_rep2


title: Prunus mongolica seedling control biological replicate 3

description:
Library name: CK_3
Control sample, biological replicate 3. Column name in expression matrices: CK_3

value: control


title: frozen_pdx_OneCell_CUT&Tag_h3k4me1_rep2

description: Library name: frozen_pdx_OneCell_CUT_Tag_h3k4me1_rep2

data_processing:
Raw single-cell epigenomics data were pre-processed using the sc-epigenome pipeline of Curie institute (v2.0.0, https://github.com/bioinfo-pf-curie/scepigenome)
Assembly: hg38
Supplementary files format and content: fragment files of DNA counts : L512_PDX_BC152_P1_H3K4me1.fragments.tsv.gz, L512_PDX_BC152_P3_H3K4me1.fragments.tsv.gz
Supplementary files format and content: fragment file indexes: L512_PDX_BC152_P1_H3K4me1.fragments.tsv.gz.tbi, L512_PDX_BC152_P3_H3K4me1.fragments.tsv.gz.tbi
Supplementary files format and content: Pseudobulk bigwig (CPM-normalized): L512_PDX_BC152_P1_H3K4me1.bigwig, L512_PDX_BC152_P3_H3K4me1.bigwig
Library strategy: CUT&Tag

source_name: mammary gland tumor

growth_protocol: HBCx-14 PDX model was established from a primitive triple-negative breast cancer sample at the Curie Institute with patient informed consent on female Swiss nude mice.

extract_protocol:
Nuclei were extracted from frozen human tumors as described in (Marsolier et al 2022; PMID: 35410383). Single nuclei were distributed using a SH800 Sony Cytometer in a 384 well-plate filled with 5µl NP-40 buffer (20mM Hepes pH 7.5, 150mM NaCl, 0.5mM Spermidine, 1x Protease Inhibitor Cocktail, 1% BSA, 0.01% digitonin, 0.1% NP-40, 2mM EDTA).
Manual OneCell CUT&Tag, as described in (Moutaux & Schwager et al., 2025)

value: mammary gland tumor


title: Prunus mongolica seedling control biological replicate 2

description:
Library name: CK_2
Control sample, biological replicate 2. Column name in expression matrices: CK_2

value: leaf

value: wild type


title: Untreated astrocytes (with A-beta), replicate 1

description: Library name: AS.Aβ.1

value: Primary Astrocyte


title: sample 24_EV71_Vero_20190822

description: Library name: sample 24

data_processing:
Sample 1-18: For sequencing, circularized DNA was amplified via rolling circle amplification to produce DNA nanoballs (DNBs), which were loaded onto patterned nanoarrays. Combinatorial Probe-Anchor Synthesis (cPAS) technology (DNBSEQ platform, BGI) was employed for 150 bp paired-end sequencing. Raw reads were quality-filtered using SOAPnuke to remove low-quality bases and adapters. Clean reads were mapped to the human reference genome (GRCh38/hg38) using HISAT2. Gene expression levels were estimated with RSEM (v1.3.1) and normalized to FPKM values. Differential Expression analysis was performed using DESeq2 (v1.4.5) with hresholds of |log2FC| ≥ 1 and adjusted p-value < 0.05. Enriched KEGG pathways were identified via Hypergeometric testing (Phyper), with significance thresholds set at Q-value ≤ 0.05 after false discovery rate (FDR) correction. All analyses were conducted using the BGI Tom Multi-omics Platform (https://biosys.bgi.com).
Sample 19-22: To identify termination sites characteristic of 2'-O-methylation, raw paired-end reads were first filtered by fastp (v0.23.2) and merged using FLASH (v1.2.11, -p 33 -m 12 -M 300 -x 0.25 -z) to create longer contiguous sequences. The merged reads were then filtered to select those containing the target adapter sequence "agtctcgatttcggaGGGGGGGG", allowing for one nucleotide mismatch to account for potential sequencing errors while maintaining specificity for Nm-detection products. Adapter sequences and any downstream polyG tracts were subsequently trimmed using Cutadapt to isolate the authentic viral sequences. The processed reads were then aligned to the EV71 reference genome (BrCr-TR, GenBank # U22521.1) using Bowtie2 (v2.2.6).
Sample 23-25: Raw multi-fast5 reads were base-called using Guppy (v3.1.5) and converted to single-read fast5 files using the ont_fast5_api (v3.0.2) multi_to_single_fast5 command. Reads were then mapped to the EV71 reference genome (GenBank # JQ804832.1) using Tombo (v1.5.1).
Assembly: GRCh38/hg38,and EV71 genome (GenBank number: U22521.1 or JQ804832.1)
Supplementary files format and content: Sample 1-18: Excel files contain FPKM.
Supplementary files format and content: Sample 19-22: Excel files contain NanoNm rate.
Supplementary files format and content: Sample 23-25: Excel files contain Nm mutation rate.

organism: Chlorocebus sabaeus

source_name: kidney

value: kidney

value: Vero


title: naïve_ILC2_rep1


title: Prunus mongolica seedling control biological replicate 1

description:
Library name: CK_1
Control sample, biological replicate 1. Column name in expression matrices: CK_1

value: batch 1


title: Prunus mongolica seedling combined alkali salt and cadmium stress biological replicate 2

description:
Library name: SCd_2
Combined alkali salt and cadmium stress treatment sample, biological replicate 2. Column name in expression matrices: SCd_2

value: combined alkali salt and cadmium stress


title: DRG, Ctrl_solvent_2

value: dorsal root ganglion

value: Ctrl

value: solvent


title: sample 23_EV71_Vero_20190714

description: Library name: sample 23

value: cell line


title: Vancomycin-PO-Replicate-6

status: Public on Jul 02 2026

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St

country: Israel

institute: Bar-Ilan University

description: Library name: V6

data_processing:
Data were processed using the RASflow package, DOI: 10.1186/s12859-020-3433-x
Trimming: Reads were trimmed using Trim Galore version: 0.6.2 and adapters removed using Cutadapt version: 3.5. Quality Phred score cutoff: 20. Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected). Maximum trimming error rate: 0.1 (default). Minimum required adapter overlap (stringency): 1 bp. Minimum required sequence length before a sequence gets removed: 20 bp.
Mapping: Reads were mapped to the transcriptome (Mus_musculus.GRCm39) using Salmon. The normalized values are estimated Transcripts Per Million (TPM) from Salmon and are scaled using the average transcript length over samples and then the library size by “tximport”. Any missing gene names (using mmusculus_gene_ensembl) are replaced with gene IDs. We filtered out sparse genes, which we defined as those with over 50% zero values. We started with 35,534 genes and removed 15,077 sparse genes, leaving us with 20,457 genes. We normalized each sample’s reads to 1M reads.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: Tab-delimited text file includes both ENSMUSG and gene name identifiers, and normalized expression levels per gene.

source_name: Whole colon

growth_protocol: C57BL6/J mice were bred and maintained under a 12-hour light/dark cycle and fed standard chow in SPF conditions at the Azrieli Faculty of Medicine of the Bar-Ilan University. 8- to 12-week-old mice were used for all experiments.

extract_protocol:
RNA from flash frozen colonic tissues was extracted using RNeasy Plus Universal mini kit (Qiagen). The integrity of the isolated RNA was analyzed using the Agilent TS HS RNA Kit and TapeStation 4200 at the Genome Technology Center at the Azrieli Faculty of Medicine, Bar-Ilan University. 1000 ng of total RNA was treated with the NEBNext poly (A) mRNA Magnetic Isolation Module (NEB, #E7490L).
RNA sequencing libraries were produced by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L).  Quantification of the library was performed using a dsDNA HS Assay Kit and Qubit (Molecular Probes, Life Technologies) and qualification was done using the Agilent TS D1000 kit and TapeStation 4200. 250nM of each library was pooled together and diluted to 4nM according to the NextSeq manufacturer’s instructions. 1.6pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced with the Illumina NextSeq 550 platform with single-end reads of 75 cycles according to the manufacturer's instructions.

treatment_protocol: Mice were randomly divided into either control or antibiotic treatment groups. Mice were treated twice a day for 3 days, and once more on the 4th day, via either oral gavage, intraperitoneal or intravenous injection. Mice received 2.5mg of either ampicillin, metronidazole, neomycin, vancomycin or a mix of all four antibiotics, in 100µl of PBS. Control mice received 100µl of PBS. Four hours after the last treatment mice were euthanized and tissues extracted.

value: Whole colon

value: WT

value: Vancomycin-PO


title: frozen_pdx_OneCell_CUT&Tag_h3k4me1_rep1

description: Library name: frozen_pdx_OneCell_CUT_Tag_h3k4me1_rep1

value: no

value: DNA


title: Vancomycin-PO-Replicate-5

description: Library name: V5


title: Vancomycin-PO-Replicate-4

description: Library name: V4


title: Vancomycin-PO-Replicate-3

description: Library name: V3


title: Vancomycin-PO-Replicate-2

description: Library name: V2


title: Siglec10-3-P

description:
Library name: Siglec10-3-P
P group, replicate biosample 3

value: colon

value: SIGLEC10 postive


title: Vancomycin-PO-Replicate-1

description: Library name: V1


title: Vancomycin-IV-Replicate-4

description: Library name: V17

value: Vancomycin-IV


title: Vancomycin-IV-Replicate-5

description: Library name: V18


title: Vancomycin-IV-Replicate-3

description: Library name: V16


title: Vancomycin-IV-Replicate-2

description: Library name: V15


title: Vancomycin-IP-Replicate-4

description: Library name: V9

value: Vancomycin-IP


title: Vancomycin-IP-Replicate-3

description: Library name: V8


title: Vancomycin-IP-Replicate-2

description: Library name: V7


title: Vancomycin-IP-Replicate-1

description: Library name: V12


title: PBS-PO-Replicate-6

description: Library name: C6

value: PBS-PO


title: Vancomycin-IV-Replicate-1

description: Library name: V13


title: PBS-PO-Replicate-5

description: Library name: C5


title: PBS-PO-Replicate-4

description: Library name: C4


title: PBS-PO-Replicate-3

description: Library name: C3


title: PBS-PO-Replicate-2

description: Library name: C2


title: SB1_sequences.fastq.gz

description: Library name: SB1_sequences

data_processing:
The 16S rRNA sequencing data were analyzed using QIIME2. Raw single-end sequences were imported, demultiplexed, and processed with DADA2 for quality control and denoising, generating amplicon sequence variants (ASVs). Taxonomic classification of ASVs was performed using a pre-trained Naive Bayes classifier specific to the V4 region, based on the Greengenes2 database (version 2022.10). The feature table was exported in BIOM format for downstream analyses.
Assembly: OTHER
Supplementary files format and content: Tab-delimited text files include taxon ID and read counts.

source_name: Feces

extract_protocol: DNA was extracted from mouse fecal samples using the PureLink Microbiome DNA Purification Kit (Invitrogen) and Mobio PowerSoil DNA Extraction Kit (Mo Bio). The V4 region of the bacterial 16S rRNA gene was amplified by polymerase chain reaction (PCR) using the 515F (AATGATACGGCGACCACCGAGATCTACACGCT) barcoded and 806R (TATGGTAATTGTGTGYCAGCMGCCGCGGTAA) primers. A reaction containing a final concentration of 0.04% of each primer and 0.5% of PrimeSTAR Max DNA Polymerase (TaKaRa) 50μl total volume. PCR reactions were carried out by 30-35 cycles of denaturation (95°C), annealing (55°C) and extension (72°C), with final elongation at 72°C. PCR products were purified using AMPure magnetic beads (Beckman Coulter) and quantified using a Denovix spectrophotometer. Samples were then pooled at equal amounts, loaded on 2% agarose E-Gel (Thermo Fisher), purified and sent for sequencing using the Illumina MiSeq platform (Genomic center, Azrieli Faculty of Medicine, BIU, Israel).

value: Feces

tag: group


title: PBS-PO-Replicate-1

description: Library name: C1


title: SB1_barcodes.fastq.gz

description: Library name: SB1_barcodes


title: PBS-IV-Replicate-5

description: Library name: C17

value: PBS-IV


title: ok122_sequences.fastq.gz

description: Library name: ok122_sequences


title: ok122_barcodes.fastq.gz

description: Library name: ok122_barcodes


title: PBS-IV-Replicate-3

description: Library name: C15


title: PBS-IV-Replicate-4

description: Library name: C16


title: 34158_HepG2_HNF4A_BX_rep1-1

city: Ithaca

first: B. Franklin

last: Pugh

state: NY

address: 465 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

description: Library name: 34158_HepG2_HNF4A_BX_rep1-1

data_processing:
Reads were aligned using BWA-MEM.
Remove duplicate reads (Picard MarkDuplicates and Samtools).
Tally coverage of read1 5' tag using deeptools
Assembly: hg38
Supplementary files format and content: BigWig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: BigWig for reverse strand -- coverage of 5' end of Read 1 across the genome

growth_protocol: K562 cells were grown in suspension at ~0.5-1.0 x 106 cell/mL in complete IMDM with ~10% FBS and ~1% PenStrep at 5% CO2 and 37oC.

extract_protocol:
Cells were crosslinked in methanol-free formaldehyde (final 1% concentration in IMDM media) at 25 °C for 10 min. 1 mole of formaldehyde was quenched with 3 mole extra Tris (pH 8.0) at 25 °C for 5 min. Fixed cells were washed with PBS and stored at -80 oC. 25 million (M) formaldehyde crosslinked K562 were lysed by incubating with 1 mL Lysis Buffer F (20 mM Tris, pH 8.0, 85 mM KCl, 0.5% NP-40, 0.5% Triton X-100) for 20 min at 4°C, then with 1 mL RIPA Buffer M (1x PBS 1.0% NP40, 0.5% NaDeoxycholate, 0.1% SDS) for 20 min at 4°C. Nuclei (25 M) were incubated in 500 ul Benzonase Digestion Buffer (10 mM Tris, pH 8, 10 mM NaCl, 2 mM MgCl2) at a Benzonase concentration of 100 U/ml for 10 min at 25 °C. Reactions were quenched by adding 500 ul Benzonase Quench Buffer (10 mM Tris, pH 8, 800 mM NaCl, 20 mM EDTA), The quenched reactions were centrifuged at 14,000 rpm for 10 minutes to collect Benzonase-solubilized chromatin in the supernatant. Nuclei pellets were sonicated in a Bioruptor PICO model sonicator (Diagenode) for 8 cycles (30-on/ 30-off). Sonicated material was centrifuged at 13.2K rpm for 15 minutes using a Microfuge (Eppendorf 5415R). Solubilized chromatin supernatant was collected. Benzonase solubilized and sonication chromatin were collected for incubation with pAG Mag Sepharose ™ (Cytiva™) preloaded with 3 ug of antibody overnight. Following antibodies were used according to the manufacturer’s instructions to prepare ChIP-exo libraries: SMC3 (ab9263, Sigma), P300 (HPA003128, Atlas), NFIA (HPA008884, Atlas), WDR5 (HPA047182, Atlas), GABPA (HPA003258, Atlas), SP1 (HPA001853, Atlas), RAD21(HPA020044, Atlas), GTFIIB (HPA061626, Atlas), P300(A300-358A, Bethyl labs), RbBP5 (A300-109A, Bethyl labs), and CTCF (07-729, Millipore). TBP (Pugh lab). The immunoprecipitated chromatin was then processed through Lambda exonuclease digestion, first adapter ligation, cross-link reversal, second adapter ligation, and PCR for final high-throughput sequencing.
Illumina or Element library prep

tag: pegr id

tag: source

tag: method

value: Benzonase ChIP-exo (v6)

tag: target

tag: antibody

tag: biological replicate

tag: resequencing replicate


title: 29010_K562_CTCF_nonXLBX_rep2-1

description: Library name: 29010_K562_CTCF_nonXLBX_rep2-1

value: K562 nonXL

value: CTCF


title: PBS-IV-Replicate-2

description: Library name: C14

tag: tissue


title: PBS-IV-Replicate-1

description: Library name: C13

tag: treatment


title: 29009_K562_CTCF_nonXLBX_rep1-1

description: Library name: 29009_K562_CTCF_nonXLBX_rep1-1

tag: cell line


title: PBS-IP-Replicate-4

description: Library name: C8

tag: genotype

value: PBS-IP


title: PBS-IP-Replicate-3

description: Library name: C7


title: Terminal Mapping, SIVmac251 construct, Jurkat-b, Illumina, replicate 2

city: Scarborough

first: Guillaume

last: Filion

state: ON

address: 1265 Military Trail

institute: University of Toronto

description: Library name: SIVmac251_Jurkat-b_Illumina_rep_2

data_processing:
For Illumina reads. The ends of the LTRs were trimmed by seeq (https://github.com/ezorita/seeq) allowing 5 errors (HIV-1 target sequence: CTTGTCTTCGTTGGGAGTGAATTAGCCCTTCCA, or SIVmac251 target sequence: TCTATGTCTTCTTGCACTGTAATAAATCCCTTCCA), leaving 34 nucleotides (plus or minus errors) for mapping the read into the host genome. Mapping insertion sites in the host genome. Processed Nanopore reads were mapped using bwa  with options bwa mem `-t8 -L0 -x pacbio` in an index containing the human genome (hg38), the genome of phage PhiX174, and the sequence of the HIV and SIV constructs. The added reference sequences accelerate the mapping. Following alignment, parsed SAM files were processed to identify high-confidence integration sites. Alignments containing hard clipping (secondary alignments) or exhibiting more than 5 bp of soft clipping at the 5’ end were discarded to ensure the sequencing read began immediately at the host-virus junction.
For Oxford Nanopore Technology reads. Viral genomic segments were extracted from FASTQ files using a custom Python parser based on seeq for approximate DNA/RNA matching via Levenshtein distance (https://github.com/ezorita/seeq). Sequencing reads and their reverse complements were scanned for the so-called anchor consisting of the adapter and the added poly-A tail with a maximum tolerance of 6 errors including indels (target sequence: AAAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC). Identified reads were split around the anchor, using the prefix to find an insertion site in the genome, and recursively repeating the process above on the suffix. The reason for recursively searching for insertion sites in the same read is that independent molecules are routinely ligated together to form concatemers during the adapter ligation step, so a single read may contain multiple amplicons. For each prefix, the specific viral motif from the LTR was identified with a maximum tolerance of 5 errors including indels (HIV-1 target sequence: CTTGTCTTCGTTGGGAGTGAATTAGCCCTTCCA, SIVmac251 target sequence: TCTATGTCTTCTTGCACTGTAATAAATCCCTTCCA). The sequence located between the viral LTR and the closest poly-A tract was isolated (20 As with a maximum tolerance of 3 errors including indels) and kept for further analyses.
For both Illumina and Oxford Nanopore Technology reads. Genomic coordinates were determined based on alignment orientation: for positive strand matches, the integration site was defined by the alignment start position, whereas for negative strand matches, it was defined by the alignment end (start position plus alignment length derived from the CIGAR string). To correct for sequencing or mapping imprecision, insertion sites on the same chromosome located within a 15 bp window were collapsed into a single insertion located at the mode of the cluster. Reads mapping to the internal controls (HIV, SIV, and PhiX174 genomes) were filtered out at this stage. Finally, the representative integration site for each cluster was assigned to the coordinate with the highest read count.
For Oxford Nanopore Technology reads. The number of independent capture events was estimated by quantifying unique poly-A termination sites (separated by 5 bp or more) associated with every insertion.
Assembly: hg38
Supplementary files format and content: Tab-separated values (tsv) indicating insertions with columns: chromosome, location, strand and number of reads. For Oxford Nanopore Technology reads, an additional column indicates the number of unique poly-A termination sites.

source_name: Thymus

growth_protocol: RPMI 1640 medium (Gibco, 11875-093), 10% fetal bovine serum, 1% GlutaMAX (Gibco, 35050-061), 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Genomic DNA from Jurkat T cell pools was extracted 21 days post-transduction with PureLink Genomic DNA Kit (Invitrogen, K1820-01).
500 ng genomic DNA from transduced Jurkat T cells were linear-amplified using 0.02 μM of a specific primer (annealing to the HIV-1 5′ LTR and to the SIVmac251 5′ LTR, respectively) and 1.1x Red Taq DNA Polymerase Master Mix (VWR Life science, 733-2544) in a 50 μL final volume. The cycling conditions were as follows: 95°C for 5 min; 95°C for 30 s, 55°C for 1 min and 72°C for 15 s (100 cycles); and 72°C for 5 min. Following linear amplification, 25 μL single-stranded DNA product in the Taq DNA Polymerase Master Mix were mixed with 0.4 μM of a biotinylated primer annealing to HIV-1 SIVmac251 and hybridized by gradual cooling. The mixture was denatured at 95°C for 2 min, followed by slow cooling from 95°C to 15°C at a rate of 0.1°C/s. The temperature was held at 15°C for 10 min to ensure complete annealing. Biotinylated single-stranded DNA was then purified using streptavidin-coated magnetic beads (Cytiva, 30152103010350) according to the manufacturer’s instructions. Bead-bound DNA was washed thoroughly three times with 1x High salt wash buffer containing 10 mM Tris HCl pH 8.0, 1 M NaCl and 0.5 mM EDTA. The purified single-stranded DNA was eluted in 20 μL Elution Buffer (Qiagen, 19086) preheated to 95°C. The mixture was incubated at 95°C for 5 min to disrupt biotin-streptavidin interactions. The beads were then magnetically separated, and the supernatant containing the eluted DNA was collected. To catalyze the addition of poly(A) tails to the 3′ ends of DNA fragments, terminal deoxynucleotidyl transferase (TdT) reaction was performed using the 20 μL eluted DNA, 5 μL 10x  Terminal Transferase Reaction Buffer, 0.25 mM CoCl2, 1 μL 10 mM dATP, and 20 units TdT enzyme (New England Biolabs Inc., M0315) in a 50 μL final volume. The reaction mixture was incubated at 37°C for 30 min, followed by enzyme inactivation at 70°C for 10 min. For exponential amplification by PCR, 25 μL of TdT reaction products were directly added in 50 μL standard Taq DNA polymerase reaction mix (GeneBio Systems Inc., P3004) with 0.2 μM forward primer (annealing to the poly(A) tail with Illumina R2 Seq Primer overhang) and 0.2 μM reverse primer (annealing to the HIV-1 5′ LTR and to the SIVmac251 5′ LTR, respectively; with Illumina R1 Seq Primer overhang). The cycling conditions were as follows: 95°C for 5 min; 95°C for 30 s, 53°C for 1 min and 72°C for 1 min (30 cycles); and 72°C for 5 min. For each condition, at least four tubes were pooled and purified using a silica column-based purification kit (Qiagen, 28104) according to the manufacturer’s instructions and eluted in 20 μL Elution Buffer. Finally, 4 μL of the purified product were diluted to 50 μL of standard Taq DNA polymerase reaction mix with 0.2 μM of a primer annealing to the Illumina PE1.0 primer and an indexing primer annealing to the Illumina PE2.0 primer. The cycling conditions were as follows: 95°C for 5 min; 95°C for 30 s, 56°C for 1 min and 72°C for 1 min (6 cycles); and 72°C for 5 min.

treatment_protocol: Cells were transduced with viral stocks serially diluted 2-fold (from 10x to 80x) in a total volume of 1 mL of complete RPMI 1640 medium containing 8 μg of Polybrene (MilliporeSigma, TR-1003). The plates were centrifuged at 1,000 g at 32 °C for 90 min. At 48 hours post transduction, the efficiency of transduction was analyzed by the proportion of GFP (+) cells using a flow cytometer (Becton Dickinson, LSRFortessa). Following this, the RIU / mL was calculated using dilutions resulting in < 20% infection to minimize multiple infection events per cell, using the formula: RIU / mL = [cell number x ratio of GFP (+) cells x dilution factor] / volume (mL). Subsequently, the multiplicity of infection (MOI) was defined as the ratio of the RIU to the number of host cells at the time of transduction experiment (MOI = RIU / cells). For all subsequent experiments, the volume of viral supernatant required to achieve a target MOI 0.1 was adjusted based on this calculated functional titer to ensure consistent infection efficiency across replicates. Jurkat T cells were sorted two days post transduction with pseudotyped reporter viruses at an MOI of 0.1 with a cell sorter (Becton Dickinson, FACSAria III). Before sorting, cells were washed and resuspended in PBS (Gibco, 10010-023) containing 1% FBS and 5 μL of Hoechst dye (Thermo Scientific, 62249) at a concentration of 1 μg / mL. Results shown throughout the chapter correspond to representative data from experiments repeated at least twice.

value: Thymus

value: Jurkat

tag: cell type

value: CD4+ T cell

value: viral transduction


title: Terminal Mapping, SIVmac251 construct, Jurkat-b, Illumina, replicate 1

description: Library name: SIVmac251_Jurkat-b_Illumina_rep_1


title: PBS-IP-Replicate-2

description: Library name: C12

value: Whole colon

value: WT


title: Terminal Mapping, HIV-1 construct, Jurkat-b, Illumina, replicate 2

description: Library name: HIV-1_Jurkat-b_Illumina_rep_2


title: Terminal Mapping, HIV-1 construct, Jurkat-b, Illumina, replicate 1

description: Library name: HIV-1_Jurkat-b_Illumina_rep_1


title: Neomycin-PO-Replicate-6

description: Library name: N6

value: Neomycin-PO


title: PolyI:C stimulated cells_3

type: RNA

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

country: Germany

institute: University Heidelberg

description: Gene expression data from T24/83 uropithelial cells estimulated with polyI:C

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 7, from SAS. Gene expression profiling was performed using arrays of human Hugene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

label: Biotin

source_name: T24/83 cell line

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: T24/83 cells were infected in McCoy medium without FCS, antibiotics or cycloheximid. 2h post infection FCS (10%) was added.

extract_protocol: RNA was prepared using the Quiagen RNeasy kit (#74104) according to the manufacturer's protocol

treatment_protocol: T24/83 cells were infected with C. trachomatis serovar D (MOI 5) for 4h or 24h or stimulated with polyI:C (5 µg/ml) or LPS (1 µg/ml) for 4h

value: uropithelial

tag: agent

value: PolyI:C stimulated cells


title: PBS-IP-Replicate-1

description: Library name: C11


title: PolyI:C stimulated cells_2


title: PolyI:C stimulated cells_1


title: Terminal Mapping, HIV-1 construct, Jurkat-a, Illumina

description: Library name: HIV-1_Jurkat-a_Illumina

value: Unknown


title: LPS pllus TLR4 stimulated Cells_2

description: Gene expression data from T24/83 uropithelial cells estimulated with LPS plust TLR4 inhibitor

value: LPS pllus TLR4 stimulated Cells


title: Neomycin-PO-Replicate-5

description: Library name: N5


title: LPS pllus TLR4 stimulated Cells_1


title: LPS stimulated cells_2

description: Gene expression data from T24/83 uropithelial cells estimulated with LPS

value: LPS stimulated cells


title: LPS stimulated cells_3


title: 38476_K562_SMC3_rep2-1

data_processing:
Reads were aligned using BWA-MEM.
Remove duplicate reads (Picard MarkDuplicates and Samtools).
Tally coverage of read1 5' tag using deeptools
Assembly: hg38
Supplementary files format and content: BigWig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: BigWig for reverse strand -- coverage of 5' end of Read 1 across the genome
Library strategy: Benzonase ChIP-exo (6.1)

extract_protocol:
Cells were crosslinked in methanol-free formaldehyde (final 1% concentration in IMDM media) at 25 °C for 10 min. 1 mole of formaldehyde was quenched with 3 mole extra Tris (pH 8.0) at 25 °C for 5 min. Fixed cells were washed with PBS and stored at -80 oC. 25 million (M) formaldehyde crosslinked K562 were lysed by incubating with 1 mL Lysis Buffer F (20 mM Tris, pH 8.0, 85 mM KCl, 0.5% NP-40, 0.5% Triton X-100) for 20 min at 4°C, then with 1 mL RIPA Buffer M (1x PBS 1.0% NP40, 0.5% NaDeoxycholate, 0.1% SDS) for 20 min at 4°C.  Nuclei (25 M) were incubated in 500 ul Benzonase Digestion Buffer (10 mM Tris, pH 8, 10 mM NaCl, 2 mM MgCl2) at a Benzonase concentration of 100 U/ml for 10 min at 25 °C. Reactions were quenched by adding 500 ul Benzonase Quench Buffer (10 mM Tris, pH 8, 800 mM NaCl, 20 mM EDTA), The quenched reactions were centrifuged at 14,000 rpm for 10 minutes to collect Benzonase-solubilized chromatin in the supernatant. Nuclei pellets were sonicated in a Bioruptor PICO model sonicator (Diagenode) for 8 cycles (30-on/ 30-off). Sonicated material was centrifuged at 13.2K rpm for 15 minutes using a Microfuge (Eppendorf 5415R). Solubilized chromatin supernatant was collected.
Benzonase solubilized and sonication chromatin were collected for incubation with pAG Mag Sepharose ™ (Cytiva™) preloaded with 3 ug of antibody overnight. Following antibodies were used according to the manufacturer’s instructions to prepare ChIP-exo libraries: SMC3 (ab9263, Sigma), P300 (HPA003128, Atlas), NFIA (HPA008884, Atlas), WDR5 (HPA047182, Atlas), GABPA (HPA003258, Atlas), SP1 (HPA001853, Atlas), RAD21(HPA020044, Atlas), GTFIIB (HPA061626, Atlas), P300(A300-358A, Bethyl labs), RbBP5 (A300-109A, Bethyl labs), and CTCF (07-729, Millipore). TBP (Pugh lab). The immunoprecipitated chromatin was then processed through Lambda exonuclease digestion, first adapter ligation, cross-link reversal, second adapter ligation, and PCR for final high-throughput sequencing.

tag: growthmedia

value: IMDM

value: Benzonase ChIP-exo (6.1)


title: 37449_K562_IgG_rep10-1

value: IgG


title: Neomycin-PO-Replicate-4

description: Library name: N4


title: Neomycin-PO-Replicate-3

description: Library name: N3


title: 36900_K562_IgG_rep9-1


title: Neomycin-PO-Replicate-2

description: Library name: N2


title: LPS stimulated cells_1


title: PolyI:C plus TLR3 stimulated cells_3

description: Gene expression data from T24/83 uropithelial cells estimulated with polyI:C plust TLR3 inhibitor

value: PolyI:C plus TLR3 stimulated cells


title: PolyI:C plus TLR3 stimulated cells_2


title: LPS pllus TLR4 stimulated Cells_3


title: C. thrachomatis infected plus TLR4 4h_3

description: Gene expression data from T24/83 uropithelial cells infected with C. thrachomatis  plus TLR4 inhibitor at 4 h

value: C. thrachomatis infected plus TLR3

tag: time point


title: PolyI:C plus TLR3 stimulated cells_1


title: 36713_K562_IgG_rep8-1


title: Neomycin-PO-Replicate-1

description: Library name: N1


title: C. thrachomatis infected plus TLR4 4h_2


title: C. thrachomatis infected plus TLR4 4h_1


title: 34668_K562_IgG_rep7-1


title: Neomycin-IV-Replicate-5

description: Library name: N17

value: Neomycin-IV


title: C. thrachomatis infected plus TLR3 4h_2

description: Gene expression data from T24/83 uropithelial cells infected with C. thrachomatis  plus TLR3 inhibitor at 4 h


title: C. thrachomatis infected plus TLR3 4h_3


title: 34469_K562_IgG_rep6-1


title: C. thrachomatis infected plus TLR3 4h_1


title: Neomycin-IV-Replicate-4

description: Library name: N16


title: Neomycin-IV-Replicate-3

description: Library name: N15


title: 34175_K562_IgG_rep5-1


title: 34055_K562_IgG_rep4-1


title: Neomycin-IV-Replicate-2

description: Library name: N14


title: C. thrachomatis infected 4h_2

description: Gene expression data from T24/83 uropithelial cells infected with C. thrachomatis at 4 h

value: C. thrachomatis


title: C. thrachomatis infected 4h_3


title: uninfected cells 4h_2

description: Gene expression data from T24/83 uropithelial cells uninfected gathered at 4 h


title: C. thrachomatis infected 4h_1


title: uninfected cells 4h_1


title: Neomycin-IV-Replicate-1

description: Library name: N13


title: 33963_K562_IgG_rep2-1


title: C. thrachomatis infected plus TLR4 24h_3

description: Gene expression data from T24/83 uropithelial cells infected with C. thrachomatis  plus TLR4 inhibitor at 24 h


title: Neomycin-IP-Replicate-6

description: Library name: N9

value: Neomycin-IP


title: C. thrachomatis infected plus TLR4 24h_2


title: C. thrachomatis infected plus TLR3 24h_2

description: Gene expression data from T24/83 uropithelial cells infected with C. thrachomatis  plus TLR3 inhibitor at 24 h


title: Neomycin-IP-Replicate-5

description: Library name: N8


title: C. thrachomatis infected plus TLR4 24h_1


title: 33925_K562_IgG_rep1-1


title: 38479_K562_FOXA2_rep2-1


title: C. thrachomatis infected plus TLR3 24h_3


title: Neomycin-IP-Replicate-4

description: Library name: N7


title: C. thrachomatis infected 24h_3

description: Gene expression data from T24/83 uropithelial cells infected with C. thrachomatis at 24 h


title: C. thrachomatis infected plus TLR3 24h_1


title: 32659_K562_FOXA2_rep1-1


title: C. thrachomatis infected 24h_2


title: Neomycin-IP-Replicate-3

description: Library name: N12


title: C. thrachomatis infected 24h_1


title: 38478_K562_FOXA1_rep2-1


title: Neomycin-IP-Replicate-2

description: Library name: N11


title: 38477_K562_FOXA1_rep1-1


title: uninfected cells 24h_3

description: Gene expression data from T24/83 uropithelial cells uninfected gathered at 24 h


title: uninfected cells 24h_1


title: Neomycin-IP-Replicate-1

description: Library name: N10


title: uninfected cells 24h_2


title: Hippocampal neural stem cells from HFCS-fed offspring, rep. 3

city: Fuchinobe

first: EIji

last: Munetsuna

country: Japan

institute: Azabu University

description: Gene expression profiling of hippocampal neural stem cells isolated from HFCS-fed offspring at E20.5.

hyb_protocol: Following fragmentation, labeled cDNA was hybridized to Affymetrix Clariom S Rat Arrays according to the manufacturer’s instructions.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner system.

data_processing: Raw CEL files were processed using Affymetrix Transcriptome Analysis Console (TAC) software with default settings, and CHP files were generated for downstream analyses.

label: biotin

source_name: Rat hippocampal neural stem cells

label_protocol: Biotin-labeled cRNA was prepared according to the standard Affymetrix protocol.

growth_protocol: Pregnant Sprague-Dawley rats were administered either distilled water or 20% high-fructose corn syrup (HFCS) solution throughout gestation. Hippocampal neural stem cells (NSCs) were isolated from male offspring at embryonic day 20.5 (E20.5) and cultured for 7 days in neural stem cell medium supplemented with EGF and bFGF under undifferentiated conditions.

extract_protocol: Total RNA was extracted using the RNeasy Kit according to the manufacturer’s instructions.

treatment_protocol: NSCs were isolated from offspring of control or maternal HFCS-fed rats. No additional treatment was applied during primary culture before RNA extraction.

value: Hippocampal neural stem cells

tag: gender

value: male

tag: age


title: 34174_K562_CTCF_rep1-1

tag: pegr id

value: CTCF


title: Hippocampal neural stem cells from HFCS-fed offspring, rep. 1


title: Hippocampal neural stem cells from HFCS-fed offspring, rep. 2


title: 34031_K562_IgG_rep3-1


title: Mix-PO-Replicate-6

description: Library name: X6

value: Whole colon

value: WT

value: Mix-PO


title: 38483_HepG2_IgG_rep3-1

value: DMEM


title: Mix-PO-Replicate-5

description: Library name: X5


title: Hippocampal neural stem cells from Control offspring, rep. 3

description: Gene expression profiling of hippocampal neural stem cells isolated from control offspring at E20.5.


title: Player 9 post-soccer match

city: Bethesda

first: Iago

last: Pinal-Fernandez

state: MARYLAND

address: 50 South Drive, Room 1142, Building 50, MSC 8024

department: NIAMS

institute: NIH

description: Library name: player_9_socpost

data_processing:
RNA-seq reads were demultiplexed using bcl2fastq/2.20.0 and preprocessed with fastp/0.23.4. Gene abundance was quantified with Salmon/1.5.2.
Assembly: GENCODE Release 39 based on GRCh38
Supplementary files format and content: csv text file includes the counts for each sample

source_name: muscle

extract_protocol:
RNA was extracted using TRIzol (Thermo Fisher Scientiﬁc)
Libraries were prepared using the NEBNext Poly(A) mRNA Magnetic Isolation Module and Ultra™ II Directional RNA Library Prep Kit for Illumina (New England BioLabs, #E7490 and #E7760)

value: muscle


title: Mix-PO-Replicate-4

description: Library name: X4


title: 38482_HepG2_IgG_rep2-1


title: Player 9 pre-soccer match

description: Library name: player_9_socpre


title: Hippocampal neural stem cells from Control offspring, rep. 1

source_name: Rat hippocampal neural stem cells,


title: Hippocampal neural stem cells from Control offspring, rep. 2


title: Hippocampal neural stem cells from Control offspring, rep. 4


title: Player 8 post-soccer match

description: Library name: player_8_socpost


title: 38481_HepG2_IgG_rep1-1


title: Mix-PO-Replicate-3

description: Library name: X3


title: Player 8 pre-soccer match

description: Library name: player_8_socpre


title: Player 7 post-soccer match

description: Library name: player_7_socpost


title: 38480_HepG2_FOXA2_rep2-1


title: Mix-PO-Replicate-2

description: Library name: X2


title: Player 7 pre-soccer match

description: Library name: player_7_socpre


title: 32467_HepG2_FOXA2_rep1-1


title: Mix-PO-Replicate-1

description: Library name: X1


title: Player 6 post-soccer match

description: Library name: player_6_socpost


title: Player 5 post-soccer match

description: Library name: player_5_socpost


title: 32354_HepG2_FOXA1_rep1-1


title: Player 4 post-soccer match

description: Library name: player_4_socpost


title: Player 5 pre-soccer match

description: Library name: player_5_socpre


title: Mix-IV-Replicate-6

description: Library name: X18

value: Mix-IV


title: Mix-IV-Replicate-5

description: Library name: X17


title: Player 4 pre-soccer match

description: Library name: player_4_socpre


title: Player 6 pre-soccer match

description: Library name: player_6_socpre