title: PBS3

description:
Library name: PBS-Rep3
PBS training macrophages from healthy control PBMCs replicate 3

data_processing:
The adaptors and low quality bases assessed using FASTQC 0.11.3 were trimmed by Trimmomatic 0.39 using the following options: TRAILING:20, MINLEN:235 and CROP:235. Trimmed reads were then aligned to the ensembl 79 (GRCh38.p2) reference genome using STAR 2.4.0.1. FeatureCounts 1.6.2 was subsequently employed to convert aligned short reads into read counts for each sample. Genes with less than ten counts in two or more samples were removed. The data were then analyzed using R 3.4.4 and DEseq2 1.18.1. Differentially expressed genes of each disease group were identified using Wald statistics test, with fold-change > 2 and Benjamini–Hochberg (BH)-adjusted P < 0.1 as compared to NC group77. Cluster analysis and visualization was performed using the pheatmap Bioconductor package (v1.0.12).
Assembly: GRCh38.p2
Supplementary files format and content: counts

source_name: Macrophages from healthy control PBMCs

extract_protocol:
Human monocytes were used for total RNA extraction with RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed using a Nanodrop ND-2000 (Thermo Scientific), and each RNA sample had an A260:A280 ratio above 1.8 and A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies), and each sample had the RNA Integrity Number (RIN) above 7.0. The ribosomal RNAs (rRNAs) were removed using Ribo-Zero rRNA Removal Kits (Illumina).
RNA libraries were then constructed by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) and evaluated using the Agilent 2200 TapeStation and Qubit® 2.0 (Life Technologies). Sequencing was performed by RiboBio Co., Ltd. on an Illumina NovaSeq 6000 machine with paired-end 150-bp reads.

value: Macrophages from healthy control PBMCs

value: PBS


title: DSID01 Whole maternal blood after delivery

status: Public on Nov 27 2025

type: SRA

city: Chicago

first: William

last: Ackerman

state: Illinois

address: 820 South Wood Street, MC 808, Dept. of Obstetrics & Gynecology

department: Obstetrics and Gynecology

country: USA

institute: University of Illinois Chicago College of Medicine

description: Library name: DSID01_WBafter

library_source: genomic

data_processing:
Sequenced reads were mapped to the SILVA 132 database using QIIME2-2017.2. An operational taxonomic units (OTU) table was generated which contained the OTUs identified in each sample along with the number of sequence reads and the taxonomic classification of each OTU. The classification was further collapsed at either genera, family, order or phylum level for subsequent analyses using the MicrobialAnalyst web-based platform. Because blood samples were expected to have low number of reads, we thought it more important to be inclusive of low abundance taxa even if these could represent sequencing errors, therefore the default R code was modified to exclude the abundance filters. The Chao-1 index (measure of α-diversity) was used to estimate OTU richness in different types of samples. Enrichment of taxa between groups was further analyzed by LEfSe (linear discriminant analysis effect size) and EdgeR methods built within the platform. These computational algorithms designed primarily for highly multidimensional data, employ a combination of statistical tests to extract features (e.g. OTU) that show significant differences in abundance (enrichment) in different samples while accounting for the effect size of the differences.
Assembly: SILVA_132 reference database
Supplementary files format and content: OTU counts for each sample (tab delimited) and corresponding OTU table

molecule: genomic DNA

organism: human blood metagenome

source_name: whole blood

extract_protocol:
All specimens were collected using sterile gloves, and all procedures were carried out under strict sterile conditions. For sequencing of 16S RNA genes and microbial community analysis, genomic DNA was extracted and the 16S rRNA amplified using V4 primers. 16S amplicon multiplex libraries were sequenced on Illumina platform at the Sequencing Facility of the Argonne National Laboratory.
Genomic DNA was amplified using primers targeting the V4 region of the 16S rRNA gene with Illumina overhang adapters. Amplicon PCR was performed with KAPA HiFi HotStart ReadyMix under the following conditions: 95 °C for 3 min; 25 cycles of 95 °C for 30 s, 55 °C for 30 s, 72 °C for 30 s; final extension at 72 °C for 5 min. PCR products were purified using AMPure XP beads (0.8× ratio). Dual indices and Illumina sequencing adapters were added in a second PCR (8 cycles) using Nextera XT index primers, followed by another AMPure XP bead cleanup. Libraries were quantified with Qubit and validated for size using Bioanalyzer. Equimolar pooling was performed prior to sequencing on an Illumina MiSeq platform (paired-end).

tag: tissue

value: whole blood


title: PBS1

city: beijing

first: lu

last: z

state: - 选择 -

address: beijing

country: China

institute: institution of microbology

description:
Library name: PBS-Rep1
PBS training macrophages from healthy control PBMCs replicate 1

library_source: transcriptomic

molecule: polyA RNA

organism: Homo sapiens

tag: cell type

tag: treatment


title: dna_cdca7acdca7bhet_rep2

city: Los Angeles

first: Shuya

last: Wang

state: California

address: 610 Charles E Young Dr S

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

description: Library name: dna_cdca7acdca7bhet_rep2

data_processing:
WGBS were filtered and Illumina adaptors were removed using Trim Galore (v 0.6.7, Babraham Institute). Reads with three or more consecutively methylated CHH sites were treated as non-converted reads and filtered out. Bismark (v 0.19.1, Babraham Institute) was used to map the reads to the Arabidopsis reference genome (TAIR10) and Col-Cen-v1.2 genome assembly. ViewBS (v 0.1.11) was used to generate the plots.
Assembly: TAIR10/Col-Cen-v1.2
Supplementary files format and content: bed: methylation level

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis thaliana plants in this study were Col-0 ecotype and were grown under 16h light: 8h dark condition (on soil), or under constant light (on plates).

extract_protocol:
14-day old seedlings were harvested from Col-0, cdca7a, cdca7b, cdca7a cdca7b+/-, cdca7a cdca7b, h1.1 h1.2, h1.1 h1.2 cdca7a cdca7b, and ddm1-2. Samples were immediately frozen in liquid nitrogen. DNA were extracted using the DNeasy Plant Mini kit (Qiagen). RNA was extracted using the Direct-zol RNA MiniPrep kit (Zymo Research).
A total of 100ng DNA from was sheared to ~200bp using the Covaris S2 (Covaris). Then the libraries were constructed using the Ovation Ultralow Methyl-seq kit (NuGEN), and bisulfite conversion was achieved using the Epitect Bisulfite Conversion kit (QIAGEN). Finally, the libraries were sequenced on Illumina Novaseq X plus instruments.

value: seedling

tag: genotype


title: dna_cdca7acdca7b_rep2

description: Library name: dna_cdca7acdca7b_rep2


title: ExoTB1

description:
Library name: ExoTB-Rep1
Exosomes from TB training macrophages from healthy control PBMCs replicate 1

value: Exosomes from TB


title: dna_cdca7a_rep2

description: Library name: dna_cdca7a_rep2


title: dna_cdca7acdca7bhet_rep1

description: Library name: dna_cdca7acdca7bhet_rep1


title: dna_cdca7acdca7b_rep1

description: Library name: dna_cdca7acdca7b_rep1


title: PBS2

description:
Library name: PBS-Rep2
PBS training macrophages from healthy control PBMCs replicate 2


title: ExoTB2

description:
Library name: ExoTB-Rep2
Exosomes from TB training macrophages from healthy control PBMCs replicate 2


title: ExoTB3

description:
Library name: ExoTB-Rep3
Exosomes from TB training macrophages from healthy control PBMCs replicate 3


title: rna_h1.1h1.2cdca7acdca7b_rep3

description: Library name: rna_h1.1h1.2cdca7acdca7b_rep3

data_processing:
RNA-seq reads were filtered and Illumina adaptors were trimmed using Trim Galore (v 0.6.7, Babraham Institute). Left reads were mapped to the Arabidopsis reference genome (TAIR10) using STAR (v 2.7.11a). Uniquely mapped reads with less than 5% of mismatches were kept. For visualization, bigwig files were generated using deeptools (v 3.0.2) bamCoverage with the options -- normalizeUsing RPGC and --binSize 10. HTSeq (v 0.13.5) was used to obtain the read counts for genes and TE. DESeq2 (v 1.42.0). Differential analysis was used perform via DESeq2 (v 1.42.0) with the cutoff padj < 0.05 and |log2FC| >= 1. Eventually, ggplot2 (v 3.4.4) was sued to generate all the related plots.
Assembly: TAIR10
Supplementary files format and content: bw: transcript level
Supplementary files format and content: genecounts: gene transcript level

extract_protocol:
14-day old seedlings were harvested from Col-0, cdca7a, cdca7b, cdca7a cdca7b+/-, cdca7a cdca7b, h1.1 h1.2, h1.1 h1.2 cdca7a cdca7b, and ddm1-2. Samples were immediately frozen in liquid nitrogen. DNA were extracted using the DNeasy Plant Mini kit (Qiagen). RNA was extracted using the Direct-zol RNA MiniPrep kit (Zymo Research).
500ng of total RNA from seedling tissues were used for RNA-seq library preparation with TruSeq Stranded mRNA kit (Illumina). The final library was sequenced on Illumina Novaseq X plus instruments.


title: ExoRSTR3

description:
Library name: ExoRSTR-Rep3
Exosomes from TB resister training macrophages from healthy control PBMCs replicate 3

value: Exosomes from TB resister


title: ExoRSTR2

description:
Library name: ExoRSTR-Rep2
Exosomes from TB resister training macrophages from healthy control PBMCs replicate 2


title: ExoRSTR1

description:
Library name: ExoRSTR-Rep1
Exosomes from TB resister training macrophages from healthy control PBMCs  replicate 1


title: rna_h1.1h1.2cdca7acdca7b_rep2

description: Library name: rna_h1.1h1.2cdca7acdca7b_rep2


title: rna_h1.1h1.2cdca7acdca7b_rep1

description: Library name: rna_h1.1h1.2cdca7acdca7b_rep1


title: dna_ddm1_rep1

description: Library name: dna_ddm1_rep1


title: ExoLTBI3

description:
Library name: ExoLTBI-Rep3
Exosomes from latent tuberculosis infection training macrophages from healthy control PBMCs replicate 3


title: rna_h1.1h1.2_rep3

description: Library name: rna_h1.1h1.2_rep3


title: ExoLTBI1

description:
Library name: ExoLTBI-Rep1
Exosomes from latent tuberculosis infection training macrophages from healthy control PBMCs  replicate 1


title: rna_h1.1h1.2_rep2

description: Library name: rna_h1.1h1.2_rep2


title: ExoLTBI2

description:
Library name: ExoLTBI-Rep2
Exosomes from latent tuberculosis infection training macrophages from healthy control PBMCs  replicate 2


title: rna_h1.1h1.2_rep1

description: Library name: rna_h1.1h1.2_rep1


title: ExoHC3

description:
Library name: ExoHC-Rep3
Exosomes from healthy control training macrophages from healthy control PBMCs replicate 3

value: Exosomes from healthy control


title: rna_Col0_rep2

description: Library name: rna_Col0_rep2


title: rna_Col0_rep3

description: Library name: rna_Col0_rep3


title: ExoHC1

description:
Library name: ExoHC-Rep1
Exosomes from healthy control training macrophages from healthy control PBMCs replicate 1


title: PDCD1_Supplier_C

city: Memphis

first: Shengdar

last: Tsai

state: TN

address: 262 Danny Thomas Pl

department: Department of Hematology

institute: St Jude Children's Research Hospital

description:
Library name: VK2279_PDCD1_Supplier_C
gRNA sequencing for ABE targets

library_source: other

data_processing:
Paired-end reads were merged using FLASH with an expected fragment length of 100bp. Scaffold specific primer (3’-end) was trimmed using cutadapt (v4.1) and read with length than 20bp were removed. The percentage of target gRNA and full-length product (target gRNA + scaffold sequence) was calculated based on an exact string match. Merged reads were aligned to the expected full-length product using bowtie2 to identify indels in the sequencing data. Source code available at https://github.com/tsailabSJ/gRNA_sequencing.
Supplementary files format and content: csv

molecule: other

organism: synthetic construct

source_name: synthetic construct

extract_protocol:
guide RNAs were chemically modified and commercially synthesized by multiple sources (Suppliers A, B and C)
Pooled index library 2.2 nM (+10% Phix) was sequenced on MiSeq (Illumina) with a MiSeq v.2 micro kit using paired-end sequencing with 101-8-8-101 cycles.

value: synthetic construct


title: rna_Col0_rep1

description: Library name: rna_Col0_rep1


title: rna_cdca7acdca7b_rep3

description: Library name: rna_cdca7acdca7b_rep3


title: CIITA_Supplier_C

description:
Library name: VK2278_CIITA_Supplier_C
gRNA sequencing for ABE targets


title: CD7_Supplier_C

description:
Library name: VK2277_CD7_Supplier_C
gRNA sequencing for ABE targets


title: CBLB_Supplier_C

description:
Library name: VK2276_CBLB_Supplier_C
gRNA sequencing for ABE targets


title: dna_cdca7a_rep1

description: Library name: dna_cdca7a_rep1


title: B2M_Supplier_C

description:
Library name: VK2275_B2M_Supplier_C
gRNA sequencing for ABE targets


title: rna_cdca7acdca7b_rep2

description: Library name: rna_cdca7acdca7b_rep2


title: PDCD1_Supplier_B

description:
Library name: VK2274_PDCD1_Supplier_B
gRNA sequencing for ABE targets


title: CBLB_Supplier_B

description:
Library name: VK2272_CBLB_Supplier_B
gRNA sequencing for ABE targets


title: HEK_RNAseqThumpD1KO1

city: Frederick

first: Colin

last: Wu

state: MD

department: RNA Biology Laboratory

institute: NCI

description: Library name: HEK_RNAseqThumpD1KO1

data_processing:
Reads  were processed using a standard pipeline.
Assembly: hg19
Supplementary files format and content: Differential expression of genes

molecule: total RNA

growth_protocol: DMEM+ 10FBS+ 2mM Gln

extract_protocol:
total RNAs extracted for RNAseq
Libraries were constructed using a Zymo-Seq RiboFree total RNA library kit

tag: cell line

value: kidney embryonic

value: KO

tag: batch

value: paired-end


title: HEK_RNAseqThumpD1KO2

description: Library name: HEK_RNAseqThumpD1KO2


title: CIITA_Supplier_A_Batch_1

description:
Library name: VK2270_CIITA_Supplier_A_Batch_1
gRNA sequencing for ABE targets


title: HEK_RNAseqWT2

description: Library name: HEK_RNAseqWT2

value: WT


title: P1

city: BeiJing

first: Yue

last: Zhang

address: North Lishi Road

institute: Fuwai Hospital, Chinese Academy of Medical Sciences

description:
Library name: Sample4
10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw gene expression matrices were generated for each sample by the Cell Ranger (Version 6.1.2) Pipeline coupled with human reference version GRCh38-2020-A. The output-filtered gene expression matrices were analyzed by R software (Version 4.1.2) with the Seurat package (Version 4.1.1). A custom R script was used to combine the expression data and metadata from all libraries corresponding to a single batch, and cells with fewer than 200 Features were removed. The expression data matrix was filtered to retain genes with >5 UMI counts and then loaded into a Seurat object along with the library metadata for downstream processing. The percentage of mitochondrial transcripts for each cell (percent. mt) was calculated and added as metadata to the Seurat object. Cells were further filtered before dimensionality reduction (nGene-min. 200; percent. mt-max. 10%). Low-quality libraries identified were removed from the dataset. Expression values were then scaled to 10,000 transcripts per cell and Log-transformed. Effects of variable (percent. mito) were estimated and regressed out using a GLM (ScaleData function, model.use=” linear”), and the scaled and centered residuals were used for dimensionality reduction and clustering. Before the clustering, we first applied Canonical correlation analysis (CCA) implemented in Seurat to correct the batch effects among the experiments and integrate the gene expression matrix of all samples into a whole matrix
Assembly: Human GRCh38-2020-A
Supplementary files format and content: TSV

molecule: nuclear RNA

organism: Sus scrofa

source_name: heart

extract_protocol:
Nuclei were isolated as previously described [35] with minor modifications. Briefly, 400 mg of frozen myocardial tissue per sample was thawed on ice, rinsed with cold phosphate-buffered saline (PBS), and minced into small pieces in 1 mL lysis buffer (composition: 0.32 M sucrose, 1.5 mM CaCl₂, 0.9 mM magnesium acetate (C₄H₆MgO₄), 0.75 mM ethylene glycol tetraacetic acid (EGTA), 3 mM Tris-HCl (pH 8.0), 0.6 mM ethylenediaminetetraacetic acid (EDTA), 0.1 mM phenylmethylsulfonyl fluoride (PMSF), 0.3 mM dithiothreitol (DTT), and 20 U/μL RNase inhibitor (RI)). Next, the tissue was homogenized in 15 mL lysis buffer using a T-25 Ultra-Turrax probe homogenizer (IKA, Staufen, Germany) at 24,000 rpm for 20 seconds, then diluted to 30 mL with additional lysis buffer. Homogenates were further disrupted using a 40 mL glass dounce homogenizer (10 strokes) to release nuclei, then filtered sequentially through 100 μm and 70 μm cell strainers. Filtrates were centrifuged at 700 × g for 10 minutes at 4 °C; pellets were resuspended in 23 mL sucrose buffer (2.1 M sucrose, 0.9 mM magnesium acetate, 3 mM Tris-HCl (pH 8.0), 0.2 mM DTT, 20 U/μL RI). A 7 mL sucrose buffer cushion (pre-incubated with 1% bovine serum albumin [BSA]) was layered in a 50 mL centrifuge bottle (Beckman Coulter cat no. 357003), over which 23 mL of the resuspended pellet was carefully layered. The bottle was centrifuged at 13,000 rpm for 1 hour at 4 °C (Beckman Avanti J-26XPI centrifuge). Supernatants were discarded, and nuclei pellets resuspended in 1 mL 1% BSA (containing 200 U/mL RI). Nuclei were counted using trypan blue staining, adjusted to 700–1000 nuclei/μL, and processed for single-nucleus RNA sequencing (snRNA-seq) following the 10x Genomics protocol.
Isolated nuclei were stained with acridine orange/propidium iodide (AO/PI) and counted using a fluorescence-based automated cell counter. Nuclei concentration was adjusted to 800–1200 nuclei/μL and ~20,000 nuclei per sample were loaded onto a Chromium Controller (10x Genomics) for gel bead emulsion formation. Libraries were prepared using the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 (10x Genomics cat. no. PN-1000121) according to the manufacturer’s instructions. Libraries were sequenced on the Illumina PE150 platform at a depth of ~40,000 reads per nucleus.  All samples’ libraries were within the range of 200-2000 bp. No additional peaks were observed below 200 bp, ensuring that the libraries were qualified.

value: heart

value: cardiomyocytes


title: PDCD1_Supplier_A_Batch_1

description:
Library name: VK2271_PDCD1_Supplier_A_Batch_1
gRNA sequencing for ABE targets


title: CIITA_Supplier_B

description:
Library name: VK2273_CIITA_Supplier_B
gRNA sequencing for ABE targets


title: P2

description:
Library name: Sample5
10x Genomics


title: CD7_Supplier_A_Batch_1

description:
Library name: VK2269_CD7_Supplier_A_Batch_1
gRNA sequencing for ABE targets


title: CBLB_Supplier_A_Batch_1

description:
Library name: VK2268_CBLB_Supplier_A_Batch_1
gRNA sequencing for ABE targets


title: ExoHC2

description:
Library name: ExoHC-Rep2
Exosomes from healthy control training macrophages from healthy control PBMCs replicate 2


title: B2M_Supplier_A_Batch_1

description:
Library name: VK2267_B2M_Supplier_A_Batch_1
gRNA sequencing for ABE targets


title: Female, Fecal sequence, HfiD feed 5w, HFD feed 0w

city: Huddinge

first: Zhi

last: Peng

state: Stockholm

address: Blickagången 16

department: MedH

country: Sweden

institute: Karolinska Institutet

description:
Library name: HfiD_HFD0w_female
Female

data_processing:
High quality paired-end reads were assigned to samples based on the barcode using Fast Length Adjustment of Short reads (FLASH v1.2.11). Data filtering was performed with fastp (v0.23.1). Chimera sequences were identified based on the Silva database (16S/18S) and were subsequently removed using vsearch (v2.16.0). Denoise and species annotation were performed with QIIME2 (vQIIME2-202202). Absolute abundance of amplicon sequence variants was normalized to the sequence number of the sample with the least reads and before using for alpha and beta diversity analysis. Clustering was performed using the ade4 and ggplot2 package in R (v4.0.3).
Assembly: Silva Database(QIIME2)
Supplementary files format and content: Feature table in groups and samples
Library strategy: 16S rRNA-seq

organism: Mus musculus

source_name: Fecal

extract_protocol:
Fecal pellets were collected and stored at -80°C until DNA extraction. DNA extraction was performed using the Magnetic Soil and Stool DNA Kit (TianGen, Cat# DP712) and verified on a 2% agarose gel for band at around 310 bp.
Primers 515F (GTGCCAGCMGCCGCGGTAA) and 806R (GGACTACHVGGGTWTCTAAT) with barcode were used for bacterial hypervariable V4 region amplification. Sequencing libraries were built with the NEB Next® Ultra™ II FS DNA PCR- free Library Prep Kit (New England Biolabs, Cat# E7430L) and validated with Qubit and real-time qPCR before sequencing with the NovaSeq 6000 system (Illumina).

value: Fecal


title: Female, Fecal sequence, HfiD feed 5w, HFD feed 8w

description:
Library name: HfiD_HFD8w_female
Female


title: Female, Fecal sequence, HfiD feed 5w, HFD feed 4w

description:
Library name: HfiD_HFD4w_female
Female


title: PDCD1_Supplier_A_Batch_2

description:
Library name: VK2266_PDCD1_Supplier_A_Batch_2
gRNA sequencing for ABE targets


title: Male, Fecal sequence, HfiD feed 5w, HFD feed 8w

description:
Library name: HfiD_HFD8w
Male


title: CIITA_Supplier_A_Batch_2

description:
Library name: VK2265_CIITA_Supplier_A_Batch_2
gRNA sequencing for ABE targets


title: Female, Fecal sequence, CD feed 5w, HFD feed 4w

description:
Library name: CD_HFD4w_female
Female


title: CBLB_Supplier_A_Batch_2

description:
Library name: VK2263_CBLB_Supplier_A_Batch_2
gRNA sequencing for ABE targets


title: Female, Fecal sequence, CD feed 5w, HFD feed 0w

description:
Library name: CD_HFD0w_female
Female


title: Male, Fecal sequence, HfiD feed 5w, HFD feed 4w

description:
Library name: HfiD_HFD4w
Male


title: B2M_Supplier_A_Batch_2

description:
Library name: VK2262_B2M_Supplier_A_Batch_2
gRNA sequencing for ABE targets


title: Male, Fecal sequence, HfiD feed 5w, HFD feed 0w

description:
Library name: HfiD_HFD0w
Male


title: HEK_RNAseqWT1

description: Library name: HEK_RNAseqWT1


title: IP_ZT6_SD_4_R1_liver

city: Lausanne

first: Carlos

middle: Eduardo Sousa

last: Neves

state: Vaud

address: Genopode, UNIL-Sorge

department: Faculté de biologie et de médecine

country: Switzerland

institute: University of Lausanne

description:
Library name: IP_ZT6SD4_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 6 from SD animals

data_processing:
Read were aligned to the reference genome using bowtie2
Peak calling was performed using Genrich accounting for black- and gray-listed regions and sample replicates
Reads matchingthe identified regions were counted and normalised using diffbind R package
Assembly: mouse genome Dec 2011 (GRCm38/mm10) assembly
Supplementary files format and content: diffbind  (R package) output as RDS

source_name: liver

extract_protocol:
Samples rapidly dissected, flash-frozen in liquid nitrogen and stored at −140°C. Enrichment for BMAL1-bound chromatin regions was accessed using the previously described ChIPmentation protocol (Schmidl, C. Nat Methods 2015) with anti-BMAL1 antibody (ABCAM, AB3350).
Libraries were prepared from purified DNA fragments using Nextera dual index primers. For practical reasons, input samples were sequenced at one third of the depth and the result pooled together as an average for each condition and ZT.

value: liver

tag: strain

value: SD


title: IP_ZT6_SD_3_R1_cortex

description:
Library name: IP_ZT6SD3_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 6 from SD animals

source_name: cortex

value: cortex


title: IP_ZT6_SD_3_R1_liver

description:
Library name: IP_ZT6SD3_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 6 from SD animals


title: Male, Fecal sequence, CD feed 5w, HFD feed 0w

description:
Library name: CD_HFD0w
Male


title: rna_cdca7acdca7b_rep1

description: Library name: rna_cdca7acdca7b_rep1


title: IP_ZT6_NSD_3_R1_cortex

description:
Library name: IP_ZT6NSD3_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 6 from NSD animals

value: NSD


title: IP_ZT6_SD_1_R1_liver

description:
Library name: IP_ZT6SD1_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 6 from SD animals


title: IP_ZT6_SD_1_R1_cortex

description:
Library name: IP_ZT6SD1_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 6 from SD animals


title: IP_ZT6_NSD_2_R1_liver

description:
Library name: IP_ZT6NSD2_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 6 from NSD animals


title: CD7_Supplier_A_Batch_2

description:
Library name: VK2264_CD7_Supplier_A_Batch_2
gRNA sequencing for ABE targets


title: IP_ZT6_NSD_4_R1_liver

description:
Library name: IP_ZT6NSD4_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 6 from NSD animals


title: IP_ZT6_NSD_2_R1_cortex

description:
Library name: IP_ZT6NSD2_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 6 from NSD animals


title: Female, Fecal sequence, CD feed 5w, HFD feed 8w

description:
Library name: CD_HFD8w_female
Female


title: IP_ZT6_NSD_1_R1_cortex

description:
Library name: IP_ZT6NSD1_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 6 from NSD animals


title: IP_ZT2_SD_4_R1_cortex

description:
Library name: IP_ZT2SD4_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 2 from SD animals


title: Male, Fecal sequence, CD feed 5w, HFD feed 8w

description:
Library name: CD_HFD8w
Male


title: Male, Fecal sequence, CD feed 5w, HFD feed 4w

description:
Library name: CD_HFD4w
Male


title: IP_ZT2_SD_3_R1_cortex

description:
Library name: IP_ZT2SD3_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 2 from SD animals


title: IP_ZT2_NSD_3_R1_liver

description:
Library name: IP_ZT2NSD3_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 2 from NSD animals


title: IP_ZT2_SD_1_R1_cortex

description:
Library name: IP_ZT2SD1_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 2 from SD animals


title: IP_ZT2_NSD_3_R1_cortex

description:
Library name: IP_ZT2NSD3_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 2 from NSD animals


title: IP_ZT2_SD_3_R1_liver

description:
Library name: IP_ZT2SD3_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 2 from SD animals


title: IP_ZT2_NSD_2_R1_cortex

description:
Library name: IP_ZT2NSD2_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 2 from NSD animals


title: IP_ZT2_SD_1_R1_liver

description:
Library name: IP_ZT2SD1_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 2 from SD animals


title: IP_ZT6_SD_2_R1_cortex

description:
Library name: IP_ZT6SD2_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 6 from SD animals


title: IP_ZT2_NSD_1_R1_liver

description:
Library name: IP_ZT2NSD1_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 2 from NSD animals


title: IP_ZT2_NSD_1_R1_cortex

description:
Library name: IP_ZT2NSD1_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 2 from NSD animals


title: IP_ZT22_SD_4_R1_cortex

description:
Library name: IP_ZT22SD4_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 22 from SD animals


title: SM_AZD_1

city: Beijing

first: Jinhua

last: Qin

address: Taiping Road

institute: Beijing Institute of Transfusion

description: Library name: BulkRNA-seq_SM_AZD_1

data_processing:
For scRNA-seq, FASTQ files of 3 samples were processed by using Cell Ranger (v7.1.0) count pipeline coupled with human genome reference (Homo sapiens.GRCh38.100.chr) to generate feature-barcode matrices, respectively. The raw digital gene expression matrix data were further filtered by Seurat package (v4.4.0) with R software (v4.3.1) as follows: genes expressed in at least 3 cells and cells detected gene number ranged from 200 to 10,000 were kept for further analysis; low-quality cells were also removed if >=20% UMIs derived from the mitochondrial genome; double cells were removed.
For bulk RNA-seq, bioinformatics analysis included quality control with FastQC, read alignment using HISAT2 against the GRCh38 reference genome, and gene expression quantification. Differential expression analysis was conducted with DESeq2, applying thresholds of |log2FC| >1 and FDR <0.05.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Blood

extract_protocol:
For scRNA-seq,cryopreserved cord blood CD3+ T cells (day 0) and viable cells from the iMK induction culture on day 7 and day 14 were collected and analyzed using the Chromium system (10X Genomics) according to the manufacturer’s instructions for an expected capture rate of approximately 10,000 single cells per sample.  For bulk RNA-seq, total RNA was extracted using RNeasy Mini Kit (Qiagen), and quality was assessed using NanoDrop and Bioanalyzer to ensure high integrity (RIN >7).
For scRNA-seq,cryopreserved cord blood CD3+ T cells (day 0) and viable cells from the iMK induction culture on day 7 and day 14 were collected and analyzed using the Chromium system (10X Genomics) according to the manufacturer’s instructions for an expected capture rate of approximately 10,000 single cells per sample.  For bulk RNA-seq, sequencing libraries were prepared using the MGIEasy RNA Library Prep Kit, employing oligo(dT) beads for mRNA enrichment. Single-end sequencing (SE50) was performed on the DNBSEQ-G400 platform.

value: Blood

value: T cells cultured in basic medium containing 4M and AZD4205 for 7 days


title: SM_AZD_2

description: Library name: BulkRNA-seq_SM_AZD_2


title: SM_3

description: Library name: BulkRNA-seq_SM_3

value: T cells cultured in basic medium containing four small molecules (4M:Bix01294, RG108, PD0325901, and VPA) for 7 days


title: SM_1

description: Library name: BulkRNA-seq_SM_1


title: IP_ZT2_SD_4_R1_liver

description:
Library name: IP_ZT2SD4_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 2 from SD animals


title: IP_ZT22_SD_2_R1_liver

description:
Library name: IP_ZT22SD2_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 22 from SD animals


title: SM_2

description: Library name: BulkRNA-seq_SM_2


title: AZD_3

description: Library name: BulkRNA-seq_AZD_3

value: T cells cultured in basic medium containing AZD4205 for 7 days


title: IP_ZT22_SD_3_R1_liver

description:
Library name: IP_ZT22SD3_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 22 from SD animals


title: IP_ZT22_SD_2_R1_cortex

description:
Library name: IP_ZT22SD2_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 22 from SD animals


title: IP_ZT22_SD_1_R1_cortex

description:
Library name: IP_ZT22SD1_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 22 from SD animals


title: IP_ZT22_NSD_3_R1_liver

description:
Library name: IP_ZT22NSD3_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 22 from NSD animals


title: AZD_2

description: Library name: BulkRNA-seq_AZD_2


title: IP_ZT22_SD_1_R1_liver

description:
Library name: IP_ZT22SD1_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 22 from SD animals


title: Con_3

description: Library name: BulkRNA-seq_Con_3

value: T cells cultured in basic medium for 7 days:StemSpan SFEM II medium with SCF, TPO, IL-3, and IL-6


title: AZD_1

description: Library name: BulkRNA-seq_AZD_1


title: IP_ZT22_NSD_3_R1_cortex

description:
Library name: IP_ZT22NSD3_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 22 from NSD animals


title: IP_ZT22_NSD_2_R1_liver

description:
Library name: IP_ZT22NSD2_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 22 from NSD animals


title: Con_1

description: Library name: BulkRNA-seq_Con_1


title: IP_ZT22_NSD_2_R1_cortex

description:
Library name: IP_ZT22NSD2_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 22 from NSD animals


title: SM_AZD_3

description: Library name: BulkRNA-seq_SM_AZD_3


title: Con_2

description: Library name: BulkRNA-seq_Con_2


title: IP_ZT22_NSD_1_R1_liver

description:
Library name: IP_ZT22NSD1_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 22 from NSD animals


title: IP_ZT22_NSD_1_R1_cortex

description:
Library name: IP_ZT22NSD1_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 22 from NSD animals


title: IP_ZT2_NSD_2_R1_liver

description:
Library name: IP_ZT2NSD2_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 2 from NSD animals


title: T_iMK_D14_2

description: Library name: BulkRNA-seq_T_iMK_D14_2

value: cells  induced from T cells with five small molecules (5M:Bix01294, RG108, PD0325901, VPA and AZD4205)  for 14 days


title: T_iMK_D14_1

description: Library name: BulkRNA-seq_T_iMK_D14_1


title: IP_ZT18_SD_4_R1_cortex

description:
Library name: IP_ZT18SD4_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 18 from SD animals


title: T_iMK_D7_3

description: Library name: BulkRNA-seq_T_iMK_D7_3

value: cells  induced from T cells with five small molecules (5M:Bix01294, RG108, PD0325901, VPA and AZD4205)  for 7 days


title: T_iMK_D7_2

description: Library name: BulkRNA-seq_T_iMK_D7_2


title: IP_ZT18_SD_2_R1_liver

description:
Library name: IP_ZT18SD2_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 18 from SD animals


title: IP_ZT18_SD_2_R1_cortex

description:
Library name: IP_ZT18SD2_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 18 from SD animals


title: T_iMK_D0_3

description: Library name: BulkRNA-seq_T_iMK_D0_3

value: CD3+ T cells


title: IP_ZT18_SD_1_R1_liver

description:
Library name: IP_ZT18SD1_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 18 from SD animals


title: T_iMK_D0_2

description: Library name: BulkRNA-seq_T_iMK_D0_2


title: IP_ZT18_NSD_3_R1_liver

description:
Library name: IP_ZT18NSD3_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 18 from NSD animals


title: CDDO-Im+_IFN-gamma rep3_IFN-gamma group

city: Sendai

first: Masayuki

last: Yamamoto

state: Miyagi

address: 2-1 Seiryo-cho, Aoba-ku

country: Japan

institute: Tohoku University Graduate School of Medicine

description: Library name: Sample 24

data_processing:
Salmon quant
Assembly: GRCm38/hg38
Supplementary files format and content: tabular
Supplementary files format and content: The differential gene expression analysis between 2 groups

growth_protocol: HMC3 cells (CRL-3304) were maintained in Eagle’s Minimum Essential Medium (EMEM; 051-07615, FUJIFILM Wako) supplemented with 10% fetal bovine serum, 1 mM sodium pyruvate, non-essential amino acids, 70 mg/L penicillin G, and 100 mg/L streptomycin (FUJIFILM Wako). Cells were cultured in a humidified incubator at 37°C with 95% humidity and 5% CO₂.

extract_protocol:
Total RNA was extracted from HMC3 cells using Sepasol®-RNA I Super G. RNA quantity and purity were assessed using NanoPhotometer® NP800 (Implen) and RNA integrity (RIN) was evaluated using a TapeStation®(Agilent). The RIN vaules are between 8.5-10.
Ribosomal RNA (rRNA) was depleted using the MGIEasy rRNA Depletion Kit®(MGI). Double-stranded DNA (dsDNA) libraries were constructed from the rRNA-depleted RNA using the MGIEasy RNA Directional Library prep Kit®(MGI). Sequencing was performed on a DNBSEQ-G400RS®(MGI) platform using the DNBSEQ-G400RS High-Throughput Sequencing Kit V1.0 (MGI) to generate 150 paired-end reads.

treatment_protocol: HMC3 cells were treated with IFN-gamma (0.3µg/ml) or Amyloid beta (5 µM) with or without CDDO-Im (30 nM) for 24 hours.

value: CDDO-Im and IFN-gamma treated


title: IP_ZT18_NSD_3_R1_cortex

description:
Library name: IP_ZT18NSD3_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 18 from NSD animals


title: T_iMK_D0_1

description: Library name: BulkRNA-seq_T_iMK_D0_1


title: IP_ZT18_SD_1_R1_cortex

description:
Library name: IP_ZT18SD1_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 18 from SD animals


title: T_iMK_D14_3

description: Library name: BulkRNA-seq_T_iMK_D14_3


title: IP_ZT18_NSD_2_R1_liver

description:
Library name: IP_ZT18NSD2_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 18 from NSD animals


title: IFN-gamma rep3_IFN-gamma group

description: Library name: Sample 21

value: DMSO and IFN-gamma treated


title: IP_ZT18_NSD_1_R1_liver

description:
Library name: IP_ZT18NSD1_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 18 from NSD animals


title: IP_ZT18_NSD_2_R1_cortex

description:
Library name: IP_ZT18NSD2_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 18 from NSD animals


title: IP_ZT18_NSD_1_R1_cortex

description:
Library name: IP_ZT18NSD1_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 18 from NSD animals


title: CDDO-Im+_IFN-gamma rep1_IFN-gamma group

description: Library name: Sample 22


title: IP_ZT14_SD_5_R1_liver

description:
Library name: IP_ZT14SD5_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 14 from SD animals


title: CDDO-Im rep2_IFN-gamma group

description: Library name: Sample 17

value: CDDO-Im treated


title: IP_ZT14_SD_5_R1_cortex

description:
Library name: IP_ZT14SD5_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 14 from SD animals


title: IFN-gamma rep2_IFN-gamma group

description: Library name: Sample 20


title: IP_ZT14_SD_4_R1_cortex

description:
Library name: IP_ZT14SD4_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 14 from SD animals


title: CDDO-Im rep1_IFN-gamma group

description: Library name: Sample 16


title: IP_ZT18_SD_3_R1_liver

description:
Library name: IP_ZT18SD3_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 18 from SD animals


title: IFN-gamma rep1_IFN-gamma group

description: Library name: Sample 19


title: CDDO-Im rep3_IFN-gamma group

description: Library name: Sample 18


title: control rep3_IFN-gamma group

description: Library name: Sample 15

value: DMSO treated


title: IP_ZT14_SD_2_R1_cortex

description:
Library name: IP_ZT14SD2_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 14 from SD animals


title: CDDO-Im+_IFN-gamma rep2_IFN-gamma group

description: Library name: Sample 23


title: control rep2_IFN-gamma group

description: Library name: Sample 14


title: IP_ZT14_SD_1_R1_liver

description:
Library name: IP_ZT14SD1_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 14 from SD animals


title: CDDO-Im+Amyloid beta rep3_Amyloid beta group

description: Library name: Sample 12

value: CDDO-Im and Amyloid beta treated


title: control rep1_IFN-gamma group

description: Library name: Sample 13


title: IP_ZT14_NSD_3_R1_cortex

description:
Library name: IP_ZT14NSD3_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 14 from NSD animals


title: CDDO-Im+Amyloid beta rep1_Amyloid beta group

description: Library name: Sample 10


title: Amyloid beta rep2_Amyloid beta group

description: Library name: Sample 8

value: DMSO and Amyloid beta treated


title: IP_ZT14_NSD_1_R1_liver

description:
Library name: IP_ZT14NSD1_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 14 from NSD animals

value: liver


title: CDDO-Im+Amyloid beta rep2_Amyloid beta group

description: Library name: Sample 11


title: IP_ZT14_NSD_2_R1_liver

description:
Library name: IP_ZT14NSD2_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 14 from NSD animals


title: IP_ZT14_NSD_1_R1_cortex

description:
Library name: IP_ZT14NSD1_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 14 from NSD animals

value: cortex


title: Amyloid beta rep3_Amyloid beta group

description: Library name: Sample 9


title: IP_ZT14_NSD_2_R1_cortex

description:
Library name: IP_ZT14NSD2_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 14 from NSD animals

value: NSD


title: IP_ZT10_SD_3_R1_liver

description:
Library name: IP_ZT10SD3_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 10 from SD animals

value: SD


title: Amyloid beta rep1_Amyloid beta group

description: Library name: Sample 7


title: IP_ZT14_SD_2_R1_liver

description:
Library name: IP_ZT14SD2_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 14 from SD animals


title: CDDO-Im rep3_Amyloid beta group

description: Library name: Sample 6


title: CDDO-Im rep2_Amyloid beta group

description: Library name: Sample 5


title: IP_ZT10_SD_2_R1_cortex

description:
Library name: IP_ZT10SD2_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 10 from SD animals


title: HC10

city: hangzhou

first: zhu

last: rui

address: jinghuilu 300

institute: zhejiang university

description: Library name: Sample20

data_processing:
1) First, the original data of high-throughput sequencing were preliminatively screened according to sequence quality; Retest and retest the problem samples.  2) The library and samples were divided according to the index and Barcode information of the original sequence of quality preliminary screening, and the barcode sequence was removed.  3) Sequence denoising or OTU clustering is performed according to QIIME2 dada2 analysis process or Vsearch software analysis process.  4) Display the specific composition of each sample (group) at different species taxonomic levels to understand the overall situation.  5) According to the distribution of ASV/OTU in different samples, the Alpha diversity level of each sample was assessed, and the sparse curve reflected whether the sequencing depth was appropriate.  6) At the ASV/OTU level, the distance matrix of each sample was calculated, and the difference and significance of beta diversity between different samples (groups) were measured by a variety of unsupervised sorting and clustering methods combined with corresponding statistical testing methods.  7) At the level of species taxonomic composition, various unsupervised and supervised ranking, clustering and modeling methods, combined with corresponding statistical testing methods, were used to further measure the differences in species abundance composition among different samples (groups), and try to find marker species.  8) According to the composition distribution of species in each sample, construct the correlation network, calculate the topological index, and try to find the key species.  9) According to the results of 16S rRNA, 18S rRNA and ITS gene sequencing, it can also predict the bacterial flora metabolic function of the sample, find out the difference pathway, and obtain the species composition of the specific pathway.  10) On the basis of the above results, draw a chart with the publication level of the paper, and conduct statistical test and analysis. The analysis result documents can be found in the appendix.
Supplementary files format and content: HDF5
Library strategy: 16S rRNA-seq

organism: human saliva metagenome

source_name: saliva

extract_protocol:
1. Add 0.8 times the volume of Vazyme VAHTSTM DNA Clean Beads into 25 μl PCR products, and after full suspension by shaking, adsorb them on the magnetic rack for 5 min, and carefully use the pipette to absorb the supernatant;  2. Add 20μl 0.8 times magnetic bead washing liquid, suspend fully after shaking, place on the magnetic rack for 5 min, and carefully suck out the supernatant;  3. Add 200μl 80% ethanol, place it on the magnetic rack in reverse, and adsorb it to the other side of the PCR tube with magnetic beads, and absorb the supernatant after full adsorption;  4, put it at room temperature for 5 minutes, until the alcohol volatilization is complete, the magnetic beads can be cracked;  5. Add 25μl Elution Buffer for elution;  6. Put the PCR tube on the adsorption rack for 5 min, fully adsorb, and remove the supernatant into a clean 1.5ml centrifuge tube for storage.
llumina's TruSeq Nano DNA LT Library Prep Kit was used to prepare sequencing libraries.  1) The amplified products were repaired at the End of the sequence first. The protruding base at the 5 'end of the DNA sequence was removed through End Repair Mix 2 in the kit, and a phosphate group was added to supplement the missing base at the 3' end.  2) Add A base to the 3 'end of the DNA sequence to prevent the DNA segment from self-connecting, while ensuring that the target sequence can be connected to the sequencing connector (the 3' end of the sequencing connector has a prominent T base);  3) A sequencing connector containing a library specific tag (i.e., Index sequence) is added to the 5 'end of the sequence, so that DNA molecules can be fixed on the Flow Cell;  4) BECKMAN AMPure XP Beads were used to remove the joint self-connecting segments through magnetic bead screening and purify the library system after adding the joint;  5) PCR was performed on the DNA fragments connected with the above connectors to enrich the sequencing library template, and BECKMAN AMPure XP Beads were used to purify the enriched products of the library again.  6) The final fragment selection and purification of the library was performed by 2% agarose gel electrophoresis.

value: saliva

tag: diagnosis

value: healthy control


title: IP_ZT14_NSD_3_R1_liver

description:
Library name: IP_ZT14NSD3_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 14 from NSD animals


title: IP_ZT10_SD_3_R1_cortex

description:
Library name: IP_ZT10SD3_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 10 from SD animals


title: IP_ZT10_SD_2_R1_liver

description:
Library name: IP_ZT10SD2_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 10 from SD animals


title: HC8

description: Library name: Sample18


title: control rep3_Amyloid beta group

description: Library name: Sample 3


title: HC9

description: Library name: Sample19


title: HC6

description: Library name: Sample16


title: HC7

description: Library name: Sample17


title: IP_ZT10_SD_1_R1_liver

description:
Library name: IP_ZT10SD1_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 10 from SD animals


title: HC5

description: Library name: Sample15


title: IP_ZT10_SD_1_R1_cortex

description:
Library name: IP_ZT10SD1_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 10 from SD animals


title: HC4

description: Library name: Sample14


title: IP_ZT10_NSD_5_R1_liver

description:
Library name: IP_ZT10NSD5_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 10 from NSD animals


title: HC2

description: Library name: Sample12


title: control rep1_Amyloid beta group

description: Library name: Sample 1


title: control rep2_Amyloid beta group

description: Library name: Sample 2


title: Sample_112

type: genomic

city: Szczecin

first: Tomasz

middle: K

last: Wojdacz

state: Zachodniopomorskie

address: Unii Lubelskiej 1

department: Independent Clinical Epigenetics Laboratory

country: Poland

institute: Pomeranian Medical University

description: DNA extracted from peripheral blood of BRCA1 mutation carriers

hyb_protocol: Bisulfite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

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

data_processing: Data were processed in R, normalized using BMIQ normalization.

label: Cy5 and Cy3

source_name: BRCA1 mutation carrier

label_protocol: Standard Illumina Protocol

extract_protocol: The DNA from the whole blood samples was extracted using salting out method.

value: Peripheral Blood

tag: age

tag: Sex

value: F


title: HC1

description: Library name: Sample11


title: IP_ZT10_NSD_3_R1_liver

description:
Library name: IP_ZT10NSD3_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 10 from NSD animals


title: SZ10

description: Library name: Sample10

value: Schizophrenia


title: Sample_111


title: IP_ZT10_NSD_3_R1_cortex

description:
Library name: IP_ZT10NSD3_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 10 from NSD animals


title: CDDO-Im rep1_Amyloid beta group

description: Library name: Sample 4


title: SZ8

description: Library name: Sample8


title: SZ9

description: Library name: Sample9


title: Sample_110


title: T_iMK_D7_1

description: Library name: BulkRNA-seq_T_iMK_D7_1

value: Blood

value: cells  induced from T cells with five small molecules (5M:Bix01294, RG108, PD0325901, VPA and AZD4205)  for 7 days


title: HC3

description: Library name: Sample13


title: SZ5

description: Library name: Sample5


title: Sample_109


title: SZ6

description: Library name: Sample6


title: IP_ZT10_NSD_1_R1_liver

description:
Library name: IP_ZT10NSD1_R1_liver
BMAL1 immunoprecipitated liver sample at ZT 10 from NSD animals


title: Sample_108


title: SZ4

description: Library name: Sample4


title: IP_ZT10_NSD_2_R1_cortex

description:
Library name: IP_ZT10NSD2_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 10 from NSD animals


title: Sample_107


title: INPUT_ZT6_SD_R1_liver

description:
Library name: INPUT_ZT6SD_R1_liver
Input control liver sample at ZT 6 from SD animals


title: SZ3

description: Library name: Sample3


title: Hypo3

first: Raphaël

last: Roduit

address: Avenue de France 15

department: Lausanne University Ophtalmology

institute: Jules-Gonin Eye Hospital

description:
Library name: Hypo3
Isolated retinal ganglion cells (RGCs) maintained in hypoglycemic condition for 5 hours

data_processing:
Sequencing data were demultiplexed using the bcl2fastq2 Conversion Software (v. 2.20, Illumina).
Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8, Martin 2011). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065, Davis et al. 2013).
Reads were aligned against Mus musculus.GRCm38.92 genome using STAR (v. 2.5.3a, Dobin et al. 2013).
The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.92 gene annotation.
Quality of the RNA-seq data alignment was assessed using RSeQC (v. 2.3.7, Wang et al. 2012)
Statistical analysis was performed for genes in R (R version 4.0.3 (2020-10-10)). Genes with zero counts in all samples as well as non-protein-coding transcripts were pre-filtered out. Normalization and differential expression were performed using DESeq2 ( version 1.28.1, Love et al. 2014).
Data were variance stabilized with the function vsd() from the DESeq2 package before plotting. Plots were generated from hierarchical clustering and from principal components analysis (PCA).
Differential expression was performed using the Bioconductor package DESeq2. DESeq2 uses negative binomial GLM fitting and Wald-statistics. Parameter settings: Default settings were used for estimateSizeFactors and estimateDispersions functions. The Cooks distance cutoff parameter, cooksCutoff, was set to the default value. This sets the p-values of those genes where one or more samples have a cooks distance above the threshold to NA (only fold changes but no p-values are reported for these genes). Independent filtering was turned off. Log fold-change shrinkage was not applied.
Assembly: Mus musculus.GRCm38.92
Supplementary files format and content: RetinalHypo_htseq_genes_counts.xlsx. Raw counts per gene and per sample data matrix from htseq-count, excel format

source_name: Retina

extract_protocol:
Isolated tissues were transferred to 100 mL of lysis buffer (RNAqueous™-Micro Total RNA Isolation Kit, Thermo Fisher, AM1931) and stored at -80°C before processing for mRNA preparation. Six retinal mouse samples (isolated RNA)—3 Hypo and 3 Eugly—were evaluated for RNA quality and subjected to RNA-Seq analysis.
RNA quality was assessed on a Fragment Analyzer (Agilent Technologies) and all RNAs had a RQN between 3.8 and 5.5 and . RNA-seq libraries were prepared using 500 ng of total RNA with the Illumina TruSeq Stranded mRNA reagents (Illumina; San Diego, California, USA) following manufacturer’s recommendations. Libraries were quantified by a fluorimetric method and their quality assessed on a Fragment Analyzer (Agilent Technologies). Cluster generation was performed with 2 nM of an equimolar pool from the resulting libraries using the Illumina HiSeq 3000/4000 SR Cluster Kit reagents and sequenced on the Illumina HiSeq 4000 using HiSeq 3000/4000 SBS Kit reagents for 150 cycles.

treatment_protocol: Three eyes each from Eugly and Hypo mice were used for LCM. Firstly, retinal sections were placed on Zeiss membrane slides (MembraneSlide 1.0 PET, 415190-9051-000), irradiated with UV light at 254 nm for 30 min, and coated with 0.1% w/v poly-lysine (Sigma Aldrich, P8920). Each retinal slide (10 mm) was first incubated for 30 s in 70% EtOH and then stained with cresyl violet solution for 2 min; the sections were then dehydrated using successive cold EtOH baths (30 s each at 70%, 95%, and 100%) and observed under a microscope.

value: Retina

value: Hypoglycemic


title: SZ1

description: Library name: Sample1


title: Hypo2

description:
Library name: Hypo2
Isolated retinal ganglion cells (RGCs) maintained in hypoglycemic condition for 5 hours


title: SZ2

description: Library name: Sample2


title: INPUT_ZT6_NSD_R1_liver

description:
Library name: INPUT_ZT6NSD_R1_liver
Input control liver sample at ZT 6 from NSD animals


title: Sample_106


title: Sample_105


title: WH1

description:
Library name: Sample6
10x Genomics

organism: Steno bredanensis

value: heart

value: cardiomyocytes


title: SZ7

description: Library name: Sample7


title: Eugly3

description:
Library name: Eugly3
Isolated retinal ganglion cells (RGCs) maintained in euglycemic condition for 5 hours

value: Euglycemic


title: scRNA-seq_TiMK-D14

description: Library name: scRNA-seq_TiMK-D14

value: cells  induced from T cells with 5M for 14 days


title: Input_ZT6_NSD_R1_cortex

description:
Library name: Input_ZT6NSD_R1_cortex
Input control cortex sample at ZT 6 from NSD animals


title: Eugly2

description:
Library name: Eugly2
Isolated retinal ganglion cells (RGCs) maintained in euglycemic condition for 5 hours


title: Sample_103


title: Eugly1

description:
Library name: Eugly1
Isolated retinal ganglion cells (RGCs) maintained in euglycemic condition for 5 hours


title: Sample_101


title: Input_ZT6_SD_R1_cortex

description:
Library name: Input_ZT6SD_R1_cortex
Input control cortex sample at ZT 6 from SD animals


title: Sample_104


title: scRNA-seq_T

description: Library name: scRNA-seq_T

value: CD3+ T cells


title: scRNA-seq_TiMK-D7

description: Library name: scRNA-seq_TiMK-D7

value: cells  induced from T cells with 5M for 7 days


title: Input_ZT2_SD_R1_cortex

description:
Library name: Input_ZT2SD_R1_cortex
Input control cortex sample at ZT 2 from SD animals

value: cortex


title: IP_ZT10_NSD_1_R1_cortex

description:
Library name: IP_ZT10NSD1_R1_cortex
BMAL1 immunoprecipitated cortex sample at ZT 10 from NSD animals

value: NSD


title: INPUT_ZT2_NSD_R1_liver

description:
Library name: INPUT_ZT2NSD_R1_liver
Input control liver sample at ZT 2 from NSD animals

value: liver


title: Sample_100

description: DNA extracted from peripheral blood of BRCA1 mutation carriers


title: Sample_102


title: INPUT_ZT2_SD_R1_liver

description:
Library name: INPUT_ZT2SD_R1_liver
Input control liver sample at ZT 2 from SD animals

value: SD


title: WH2

description:
Library name: Sample7
10x Genomics


title: Hypo1

description:
Library name: Hypo1
Isolated retinal ganglion cells (RGCs) maintained in hypoglycemic condition for 5 hours


title: Nf1 KO distal stump 3, D14 following sciatic neve injury

city: Zürich

first: Salome

last: Stierli

address: Winterthurerstrasse 190

department: Institute of Anatomy

institute: University of Zurich

description:
Library name: Nf1 Ko distal 3
12-NF1_flfl_distal_3_TCCGCGAA-GTCAGTAC

data_processing:
Basecalling and de-multiplexing of the indexed reads was performed using CASAVA version 1.8.2. The raw fastq files were trimmed using Cutadapt version 1.2.1 (Martin, 2011). Low quality bases were removed from the reads by using Sickle version 1.200 with a minimum window quality score of 20. After trimming was completed, reads shorter than 10 bp were removed. The reads were mapped to mouse genome (mm10) and read counts per gene calculated.
The mapped count data are normalised and lists of differentially expressed genes are generated. A filtering step is applied to remove low expression genes. Analysis of the RNA seq data was performed using R software (Team, 2014), Bioconductor (Gentleman et al., 2004) packages including DESeq2 (Anders and Huber, 2010; Love et al., 2014) and the SARTools package developed at PF2 (Institute Pasteur). Normalization and differential analysis were performed according to the DESeq2  model and package.
@Christina this package  performs the differential expression analysis, which package did the PCA?
Assembly: mm10
Supplementary files format and content: tab-delimited text file including raw counts for each sample and gene names

source_name: Regenerating distal stump

extract_protocol:
6 nerve fragments (each fragment had a size of 0.5mm) were combined from multiple mice for each sample. 3 independent samples were obtained for each region and genotype of interest. Samples were then crushed and homogenised on dry ice and lysed using 200µL Trizol reagent. A further 300µL of Trizol reagent was then added and incubated for 5 mins at RT. After lysis, 100µL of chloroform was added, the samples vortexed for 2 mins, and centrifuged for 15 mins at 4˚C. The upper RNA phase was transferred to a fresh tube and 70% ethanol added in a 1:1 mix (final ethanol concentration of 35%). RNA was then extracted using PureLink RNA Micro Scale kit columns (Invitrogen, 12183016) according to the manufacturer’s instructions.  An additional DNA removal step was performed to eliminate genomic DNA using a RNase-free DNase kit (Qiagen), according to the manufacturer’s instructions. RNA was eluted in nuclease-free H2O, and quantified by Nanodrop measurement.
Ribosomal RNA (rRNA) was depleted with the Ribo-Zero Gold Kit (Illumina) and extent of rRNA depletion was analysed with Bioanalyzer RNA pico chip. The NEB Ultra Directional RNA Library Preparation Kit (NEB, E7420) was used to prepare the RNA-Seq libraries from the enriched material. All of the enriched material was used and following 15 cycles of amplification, the RNA was purified using AMPure XP beads (Beckman Coulter, A63882) The libraries were quantified using Qubit and the size distribution was analysed using the Agilent 2100 Bioanalyser. The final libraries were pooled in equimolar amounts.

treatment_protocol: Tmx induced loss of Nf1 in myelinaing Schwann cells (Nf1 KO samples).

value: Regenerating distal stump

value: Nf1 KO


title: Input_ZT2_NSD_R1_cortex

description:
Library name: Input_ZT2NSD_R1_cortex
Input control cortex sample at ZT 2 from NSD animals


title: Nf1 KO distal stump 1, D14 following sciatic neve injury

description:
Library name: Nf1 KO distal 1
4-NF1_flfl_distal_1_CGGCTATG-GTCAGTAC


title: P_13

city: Shiyan

first: Qin

last: Shanshan

address: Renmin Road 30, Maojian District

institute: Institute of Basic Medical Sciences, School of Basic Medical Sciences, Hubei University of Medicine

description: Library name: Sample 13

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file:https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count and FPKM values for each sample

source_name: SKIN

growth_protocol: After obtaining the patient's informed consent and approval from the ethical review, we collected 6 normal skin tissues and 8 psoriatic skin tissues, which were stored in liquid nitrogen.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The tissues were added trizol to harvested total RNA for transcriptomic sequencing.

value: SKIN

value: Psoriasis


title: Sample_99

value: Peripheral Blood

value: F


title: Sample_98


title: INPUT_ZT22_SD_R1_liver

description:
Library name: INPUT_ZT22SD_R1_liver
Input control liver sample at ZT 22 from SD animals


title: Nf1 KO bridge 3, D14 following sciatic neve injury

description:
Library name: Nf1 KO bridge 3
11-NF1_flfl_Bridge_3_TCCGCGAA-ACGTCCTG

source_name: Regenerating sciatic nerve bridge

value: Regenerating sciatic nerve bridge


title: Sample_97


title: Input_ZT22_SD_R1_cortex

description:
Library name: Input_ZT22SD_R1_cortex
Input control cortex sample at ZT 22 from SD animals


title: Input_ZT22_NSD_R1_cortex

description:
Library name: Input_ZT22NSD_R1_cortex
Input control cortex sample at ZT 22 from NSD animals


title: Nf1 KO bridge 2, D14 following sciatic neve injury

description:
Library name: Nf1 KO bridge 2
7-NF1_flfl_Bridge_2_TCCGCGAA-AGGATAGG


title: CTL distal stump 3, D14 following sciatic neve injury

description:
Library name: CTL distal 3
10-WT_distal_3_TCCGCGAA-TAAGATTA

value: CTL


title: P_14

description: Library name: Sample 14


title: Sample_96


title: P_11

description: Library name: Sample 11


title: P_09

description: Library name: Sample 9


title: P_10

description: Library name: Sample 10


title: INPUT_ZT22_NSD_R1_liver

description:
Library name: INPUT_ZT22NSD_R1_liver
Input control liver sample at ZT 22 from NSD animals


title: Nf1 KO distal stump 2, D14 following sciatic neve injury

description:
Library name: Nf1 Ko distal 2
8-NF1_flfl_distal_2_TCCGCGAA-TCAGAGCC


title: Nf1 KO bridge 1, D14 following sciatic neve injury

description:
Library name: Nf1 KO bridge 1
3-NF1_flfl_Bridge_1_CGGCTATG-ACGTCCTG


title: P_12

description: Library name: Sample 12


title: Sample_94


title: INPUT_ZT18_SD_R1_liver

description:
Library name: INPUT_ZT18SD_R1_liver
Input control liver sample at ZT 18 from SD animals


title: Sample_93


title: P_07

description: Library name: Sample 7


title: P_08

description: Library name: Sample 8


title: Input_ZT18_SD_R1_cortex

description:
Library name: Input_ZT18SD_R1_cortex
Input control cortex sample at ZT 18 from SD animals


title: Sample_92

description: DNA extracted from peripheral blood of BRCA1 mutation carriers


title: CTL bridge 3, D14 following sciatic neve injury

description:
Library name: CTL bridge 3
9-WT_bridge_3_TCCGCGAA-CTTCGCCT


title: N_06

description: Library name: Sample 6

value: Normal


title: Input_ZT18_NSD_R1_cortex

description:
Library name: Input_ZT18NSD_R1_cortex
Input control cortex sample at ZT 18 from NSD animals


title: Sample_95


title: CTL bridge 2, D14 following sciatic neve injury

description:
Library name: CTL bridge 2
5-WT_bridge_2_TCCGCGAA-AGGCTATA


title: Sample_90


title: Sample_91


title: N_03

description: Library name: Sample 3


title: N_05

description: Library name: Sample 5


title: Sample_88


title: INPUT_ZT14_NSD_R1_liver

description:
Library name: INPUT_ZT14NSD_R1_liver
Input control liver sample at ZT 14 from NSD animals


title: EN273.7_RNAseq_ESC_IAA_96h_rep3

city: San Francisco

first: Karissa

middle: Lynn

last: Hansen

state: CA

address: 555 Mission Bay Blvd S, 312

department: CVRI

institute: UCSF

data_processing:
Reads were trimmed to 100 base pairs as needed using cutadapt.
Alignment of raw RNA-seq data was produced using STAR version 2.7.7a with default parameters and basic two-pass mapping in mm10. GENCODE VM23 (GRCm38.p6) was used as the reference gene set.
bigWig files were generated using bamCoverage (deepTools) separated by strand with BPM normalization.
Assembly: mm10
Supplementary files format and content: Tab delimited text file includes raw counts for each sample
Supplementary files format and content: bigWigs separated by forward and reverse strand and normalized using BPM

growth_protocol: Parental WT E14Tg2a (karyotype 19, XY, 129/Ola isogenic background) mouse ESCs and subclones were cultured in 2iSL medium [DMEM + GlutaMAX + sodium pyruvate (ThermoFisher 10569044) supplemented with 15% fetal bovine serum, 550 µM 2-mercaptoethanol (ThermoFisher 21985-023), 1X nonessential amino acids (ThermoFisher 11140-050), 104 U of Leukemia Inhibitory Factor (Millipore ESG1107), 1µM PD0325901 (Apex Bio/Fischer A3013-25), and 3µM CHIR99021 (Apex Bio/Fischer A3011-100)]. Cells were maintained at a density of 0.2-1.5 x 105 cells/cm2 by passaging using TrypLE (ThermoFisher 12605010) every 24-48 hours on 0.1% gelatin-coated dishes (Sigma-Aldrich G1890-100G) at 37 °C and 7% CO2. The medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 3-4 months and tested negative.

extract_protocol:
Cells were washed with PBS and lysed directly with 1 mL TRIzol (Thermo Fisher 15596-018), transferred to a 1.5 mL tube, vortexed, and incubated at room temperature for 5 minutes. After incubation, mixture was supplemented with 250 µL Chloroform, vortexed again, and centrifuged at 12,000g at 4ºC for 15 minutes. Upper phase was transferred to a new tube, mixed with an equal volume of isopropanol, and spun at 12,000g at 4ºC for 15 minutes. Pellet was washed with 70% ethanol, air dried, and resuspended in 25 µL water.
100-500ng of DNase-treated total RNA was used as input for polyA+ capture and library preparation using the Illumina Stranded mRNA kit (Illumina 20040532)

treatment_protocol: FKBP12 depletion was triggered using 500 nM of PROTAC dTAG-13 (dTAG) (Sigma-Aldrich SML2601) final, diluted in culture medium. AID depletion was triggered using 500 mM of Indole-3-Acetic Acid sodium salt (IAA, auxin analog) (Tocris Bioscience 7932) final, diluted in culture medium.

value: embryonic stem cells

value: eGFP-AID-Nipbl, Tir1-2A-PuroR (Tigre), Rad21-HaloTag


title: CTL distal stump 1, D14 following sciatic neve injury

description:
Library name: CTL distal 1
2-WT_distal_1_CGGCTATG-TAAGATTA


title: Sample_89


title: N_02

description: Library name: Sample 2


title: CTL distal stump 2, D14 following sciatic neve injury

description:
Library name: CTL distal 2
6-WT_distal_2_TCCGCGAA-GCCTCTAT


title: INPUT_ZT18_NSD_R1_liver

description:
Library name: INPUT_ZT18NSD_R1_liver
Input control liver sample at ZT 18 from NSD animals


title: N_01

description: Library name: Sample 1


title: Sample_87


title: N_04

description: Library name: Sample 4


title: INPUT_ZT14_SD_R1_liver

description:
Library name: INPUT_ZT14SD_R1_liver
Input control liver sample at ZT 14 from SD animals


title: Sample_86


title: Input_ZT14_SD_R1_cortex

description:
Library name: Input_ZT14SD_R1_cortex
Input control cortex sample at ZT 14 from SD animals


title: EN273.7_RNAseq_ESC_IAA_96h_rep2


title: EN273.7_RNAseq_ESC_IAA_48h_rep3


title: Input_ZT10_SD_R1_cortex

description:
Library name: Input_ZT10SD_R1_cortex
Input control cortex sample at ZT 10 from SD animals


title: INPUT_ZT10_SD_R1_liver

description:
Library name: INPUT_ZT10SD_R1_liver
Input control liver sample at ZT 10 from SD animals


title: DAC_50_rep2

description: Library name: Sample 6

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (https://ftp.ensembl.org/pub/release-112/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2 with default parameters.
HTSeq v0.13.5 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. GTF file: https://ftp.ensembl.org/pub/release-112/gtf/homo_sapiens/Homo_sapiens.GRCh38.112.gtf.gz.
Assembly: GRCh38
Supplementary files format and content: File include Count and FPKM values for each sample

growth_protocol: The HaCaT cells were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The HaCaT cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
After DAC treatment for 72 hours, HaCaT cells were collected into Trizol for RNA extraction. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The HaCaTcell lines were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 80%, cells were treated with 0 μM, 25 μM, and 50μM DAC respectively. After 72 hours, cells were harvested for RNA sequencing.

value: HaCaT

value: keratinocyte

value: 50 μM DAC treatment


title: DAC_50_rep1

description: Library name: Sample 5


title: EN273.7_RNAseq_ESC_IAA_96h_rep1


title: EN273.7_RNAseq_ESC_IAA_48h_rep2


title: INPUT_ZT10_NSD_R1_liver

description:
Library name: INPUT_ZT10NSD_R1_liver
Input control liver sample at ZT 10 from NSD animals

value: NSD


title: CTL bridge 1, D14 following sciatic neve injury

description:
Library name: CTL bridge 1
1-WT_bridge_1_CGGCTATG-CTTCGCCT


title: Sample_82


title: EN273.7_RNAseq_ESC_IAA_48h_rep1


title: Sample_84


title: DAC_25_rep1

description: Library name: Sample 3

value: 25 μM DAC treatment


title: Sample_80


title: Sample_81


title: EN273.7_RNAseq_ESC_IAA_12h_rep3


title: DAC_25_rep2

description: Library name: Sample 4


title: D7_post-FAI, scRNA-seq

city: Hangzhou

first: Zhewen

state: ZHE JIANG

address: kaixuan street

institute: Zhejiang University School of Medicine

description: 10x Genomics

data_processing:
The sequencing data were processed into gene expression matrix with the CellRanger (version 7.2.0, 10x Genomics).
Downstream analysis of the data was performed with the R package Seurat (version 5.0.1).
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix fiiles

source_name: Arterial cells

extract_protocol:
Arterial cells were isolated from murine femoral arteries at 2 (D2) and 7 (D7) days post wire injury surgery or Sham operation. The resuspended cells were stained with 10 μg/mL DAPI (#BL105A, Biosharp, 1:1000) and filtered through a 40-μm cell strainer prior to fluorescence-activated cell sorting (FACS) using a Cytek Aurora CS for singlets isolation. Alive single cells from 6 mice were pooled for preparing the sample for each group.
Library was conducted using the Chromium Single Cell 3’ Reagent Kits v3 (10X Genomics) in accordance with the manufacturer’s protocol. Cells with a viability of over 85% were washed with 0.04% BSA in DPBS and resuspended to a concentration of 700–1200 cells/μL. The cells were then encapsulated in droplets, each containing a uniquely barcoded bead, enabling the reverse transcription of mRNA into cDNA. The cDNA libraries were subsequently amplified and sequenced on the Illumina NovaSeq platform.

treatment_protocol: 8-week-old male mice subjected to femoral artery injury surgery were sacrificed at the indicated time points. Femoral arteries were harvested for further processing.

value: Arterial cells

value: WT

value: FAI

tag: time

value: 7 days


title: NC_rep2

description: Library name: Sample 2

extract_protocol:
After 48 hours, remove the medium and directly add 800μL Trizol into the 6-well plate to harvest samples. Total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions. The RNA purity and concentration was checked using the NanoPhotometer spectrophotometer (IMPLEN, CA, USA).
A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: The HaCaTcell lines were seeded into 6-well plates and grown overnight. The next day, when the cell plating density reached 20%-30%, cells were transfected with letivirus (Genechem) to establish TCN1-overexpression cell line. After validation of the overexpression efficiency of TCN1, cells were harvested for RNA sequencing.

value: SKIN

value: negative control


title: NC_rep1

description: Library name: Sample 1


title: PDGFRb+ MSCs, FAI_3

data_processing:
Reads were quality controlled with FastQC (Version 0.12.1)
Cutadapt was used to trim low quality sequences
RNA STAR (Version 2.7.11a) was used to map reads to the mouse reference genome
Gene expression quantification was performed using featureCounts (Version 2.0.3)
Differential expression analysis was conducted with the DESeq2 package (version 1.42.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text files include gene counts for each sample

source_name: mesenchymal stromal cells

extract_protocol:
Total RNA was extracted using TRIzol reagent (#15596018CN, Thermo Fisher) from cells isolated from the femoral artiries using FACS, and was eluted in 10 µl of sterile water.
SMARTer Ultra Low RNA Kit (Takara, Janpan, Catalog #: 634936) was used to synthesize cDNA. After library amplification, cDNA was tagmented and bar coded using TruePrep DNA Library Prep Kit V2 (vazyme TD503-02). The quantity and quality of final libraries were evaluated using the Qubit 2.0 Fluorometer and Agilent 2100 bioanalyzer.

value: mesenchymal stromal cells


title: Input_ZT14_NSD_R1_cortex

description:
Library name: Input_ZT14NSD_R1_cortex
Input control cortex sample at ZT 14 from NSD animals

value: cortex


title: EN273.7_RNAseq_ESC_IAA_12h_rep2


title: Sham, scRNA-seq

description: 10x Genomics

value: sham


title: EN273.7_RNAseq_ESC_IAA_24h_rep3


title: EN273.7_RNAseq_ESC_IAA_24h_rep2


title: NC_rep2

description: Library name: Sample 2


title: Sample_79

value: Peripheral Blood

value: F


title: EN273.7_RNAseq_ESC_IAA_24h_rep1

value: embryonic stem cells

value: eGFP-AID-Nipbl, Tir1-2A-PuroR (Tigre), Rad21-HaloTag


title: D2_post-FAI, scRNA-seq

description: 10x Genomics

value: 2 days


title: Sample_85


title: Input_ZT10_NSD_R1_cortex

description:
Library name: Input_ZT10NSD_R1_cortex
Input control cortex sample at ZT 10 from NSD animals


title: Sample_78


title: TCN1_rep1

description: Library name: Sample 3

value: HaCaT

value: keratinocyte


title: Sample_83


title: Multiplexed sample: Control_1 (BC_001), Control_2 (BC_002), CCR4KO_1 (BC_003), and CCR4KO_2

city: Kobe

first: Takuo

last: Emoto

state: Hyogo

address: 7-5-1 Kusunoki-cho, Chuo-ku

department: Division of Cardiovascular Medicine, Department of Internal Medicine

institute: Kobe University Graduate School of Medicine

description:
Library name: Combined data files of scRNA-seq
10X genomics

data_processing:
Libraries were sequenced on an Illumina NovaSeq X with paired-end dual-indexing. Raw base call files from the Novaseq sequencer were demultiplexed into FASTQ files for each library. FASTQ files were processed with Cell Ranger v7.0.1 (10x Genomics) against the GRCm38 mouse reference genome with the default parameter.
Assembly: GRCm38
Supplementary files format and content: 10X Cellranger format

source_name: aortas

growth_protocol: not applicabel

extract_protocol:
Abdominal aortas were isolated from angiotensin II-infused Apoe-/- or Ccr4-/-Apoe-/- mice and frozen in liquid nitrogen within 6 hours after sample collection.
the libraries were prepared as according to the 10x Genomics Chromium Fixed RNA Profiling for Multiplexed Samples v1 guidelines (CG000527).

treatment_protocol: not applicabel

value: aortas

value: total cells


title: TCN1_rep2

description: Library name: Sample 4


title: PDGFRb+ MSCs, FAI_2

value: WT


title: Sample_77

description: DNA extracted from peripheral blood of BRCA1 mutation carriers


title: EN273.7_RNAseq_ESC_untreated_rep2

value: untreated


title: NC_rep1

description: Library name: Sample 1


title: Sample_75


title: Sample_76


title: PDGFRb+ MSCs, sham_4


title: Donor5, Th2 cells, Veh treated, Activated

city: Davos

first: Abhijeet

last: Kulkarni

address: Herman-Burchard-Strasse 9

institute: SIAF

description: Library name: D5_Veh_Act

data_processing:
fastp (v0.23.4) used for trimming + filtering of raw data
Kallisto (0.46.1) used for transcript expression quantification
Assembly: GRCh38.p13
Supplementary files format and content: Tab delimited text files of transcript abundances

source_name: In vitro long differentiated Th2 cells

growth_protocol: In vitro long differentiated Th2 cells were maintained in RPMI+10% Fetal Calf Serum+100IU recombinant human IL-2 in 5%CO2 at 37C.

extract_protocol:
Total RNA was extracted using RNEasy micro kit (Qiagen) using manufacturer instructions. RNA quality was determined using RNA ScreenTape Analysis (Agilent) and manufacturer instructions. All samples had a RIN score > 9.8. 400ng of RNA was used for subsequent analysis.
Illumina Stranded mRNA Prep, Ligation protocol was used according to manufacturer instructions.

treatment_protocol: L-phenylalanine was supplemented at 1mM to Phe-treated cells. Final concentration of L-phenylalanine in the medium is 1.090mM

value: In vitro long differentiated Th2 cells


title: Sample_74


title: Donor5, Th2 cells, 1mM Phe treated, Not Activated

description: Library name: D5_Phe_NotAct


title: Donor5, Th2 cells, Veh treated, Not Activated

description: Library name: D5_Veh_NotAct


title: EA18.1_RNAseq_ASC_dTAG13_48h_rep1

value: NPC-derived astrocyte differentiation


title: Donor5, Th2 cells, 1mM Phe treated, Activated

description: Library name: D5_Phe_Act


title: PDGFRb+ MSCs, sham_3


title: EA18.1_RNAseq_ASC_dTAG13_48h_rep3


title: PDGFRb+ MSCs, sham_2


title: Sample_73


title: Donor4, Th2 cells, Veh treated, Activated

description: Library name: D4_Veh_Act


title: Sample_72


title: EN273.7_RNAseq_ESC_untreated_rep3


title: Donor4, Th2 cells, Veh treated, Not Activated

description: Library name: D4_Veh_NotAct


title: Sample_71


title: PDGFRb+ MSCs, sham_1


title: EA18.1_RNAseq_ASC_DMSO_48h_rep2


title: EA18.1_CUTTag_Exit_H3K27me3_dTAG13_2d_rep2

description: CUT&Tag samples have bw and bed files.

data_processing:
Fastq files for CUT&Tag samples were processed using Nextflow and the nf-core CUT&RUN pipeline v3.1. In brief, adapters were trimmed using Trim Galore. Paired-end alignment was performed using Bowtie2 and peaks were called using SEACR with a peak threshold of 0.05 with spike in normalization performed using the E. coli genome K12.
Peaks in ENCODE blacklisted regions (Amemiya et al., 2019) were removed using the intersect function in bedtools2 v2.30.0.
Assembly: mm10
Supplementary files format and content: bigWig files for individual replicates and the average of two replicates, SEACR consensus peak lists
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag was conducted using the protocol from Kaya-Okur et al. 2020 with the following modifications: freshly collected cells were bound to Concanavalin A beads at a ratio of 2e5 cells/7 μL beads in CR wash at RT. At least 1e5 cells were used as input per sample. Bead-bound cells were then incubated rotating overnight at 4°C in CT Antibody buffer (CR Wash with 0.05% Digitonin, 2 mM EDTA, 1 mg/mL BSA) containing primary antibody. After primary, samples were washed 3 times for 5 minutes each using CR Dig-wash buffer and resuspended in 1:100 secondary antibody (Guinea pig anti-rabbit, Antibodies Online #ABIN101961) in CR Dig-wash buffer at 4°C for 1 hour rotating at 4°C. Samples were then incubated for 1 hour at 4°C with 50 μL of approximately 25 nM homemade pA-Tn5 in CT Dig300 wash buffer (20 mM HEPES, 300 mM NaCl, 0.01% Digitonin, 0.5 mM Spermidine with Roche cOmplete protease inhibitors added). Recombinant Tn5 was purified and loaded with adapters as previously described (Kaya-Okur et al. 2019). After Tn5 incubation, samples were washed 3 times for 5 minutes each with CT Dig300 wash buffer. Tagmentation was then initiated for 1hr at 37°C in a thermocycler by adding MgCl2 to 10 mM final concentration in 50 μL volume. The tagmentation reaction was quenched immediately afterwards by adding 1.6 μL l of 0.5 M EDTA, 1 μL of 10 mg/mL Proteinase K, and 1 μL of 5% SDS. Samples were then incubated at 55°C for 2 hours in a thermocycler to denature Tn5 and solubilize tagmented chromatin. After incubation, samples were magnetized, and the supernatant was transferred to new wells where SPRI bead purification was performed using homemade beads to select all DNA fragment lengths larger than 100 bp. Samples were eluted in 0.1X TE
Approximately half of each sample was used for library preparation using NEBNext HIFI Polymerase with custom indices synthesized by IDT. An appropriate number of cycles for each target was chosen to prevent overamplification bias. After amplification, libraries were purified with 1.2X homemade SPRI beads to select for fragments >250 bp and eluted in 0.1X TE.

value: ESC exit from pluripotency differentiation

tag: antibody

value: H3K27me3 (Cell Signaling 9733)


title: EA18.1_CUTTag_Exit_H3K27me3_DMSO_2d_rep2

description: CUT&Tag samples have bw and bed files.


title: EN273.7_RNAseq_ESC_untreated_rep1


title: PDGFRb+ MSCs, FAI_1

value: mesenchymal stromal cells

value: FAI


title: Donor4, Th2 cells, 1mM Phe treated, Not Activated

description: Library name: D4_Phe_NotAct


title: Donor4, Th2 cells, 1mM Phe treated, Activated

description: Library name: D4_Phe_Act


title: EA18.1_RNAseq_ASC_DMSO_48h_rep1


title: EA18.1_RNAseq_ASC_dTAG13_48h_rep2


title: Sample_69

description: DNA extracted from peripheral blood of BRCA1 epimutation carriers

source_name: BRCA1 epimutation carrier

value: Peripheral Blood


title: EA18.1_CUTTag_ESC_H3K27me3_DMSO_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_ASC_DMSO_48h_rep3


title: Sample_68

value: F


title: EA18.1_CUTTag_ESC_H3K27me3_dTAG13_1d_rep2

description: CUT&Tag samples have bw and bed files.

value: embryonic stem cells


title: Donor3, Th2 cells, Veh treated, Activated

description: Library name: D3_Veh_Act


title: Sample_65


title: Donor3, Th2 cells, 1mM Phe treated, Activated

description: Library name: D3_Phe_Act


title: EA18.1_CUTTag_Exit_H3K27ac_dTAG13_2d_rep2

description: CUT&Tag samples have bw and bed files.

value: H3K27ac (Abcam ab4729)


title: EA18.1_RNAseq_NPC_dTAG13_48h_rep2

value: neural progenitor cells


title: EA18.1_RNAseq_NPC_DMSO_48h_rep3


title: Sample_66


title: EA18.1_RNAseq_NPC_dTAG13_48h_rep1


title: EA18.1_CUTTag_Exit_H3K27ac_DMSO_2d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_ESC_H3K27ac_DMSO_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_NPC_DMSO_48h_rep2


title: Donor3, Th2 cells, 1mM Phe treated, Not Activated

description: Library name: D3_Phe_NotAct


title: Sample_67


title: Sample_64


title: Donor2, Th2 cells, Veh treated, Not Activated

description: Library name: D2_Veh_NotAct


title: Sample_70


title: EA18.1_CUTTag_ESC_H3K27ac_dTAG13_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_NPC_DMSO_48h_rep1


title: Donor2, Th2 cells, Veh treated, Activated

description: Library name: D2_Veh_Act


title: EA18.1_CUTTag_Exit_H3K27me3_dTAG13_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: Sample_63


title: Donor3, Th2 cells, Veh treated, Not Activated

description: Library name: D3_Veh_NotAct


title: EA18.1_CUTTag_Exit_H3K27me3_DMSO_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_Exit_dTAG13_48h_rep3


title: Sample_62


title: Donor2, Th2 cells, 1mM Phe treated, Activated

description: Library name: D2_Phe_Act


title: EA18.1_RNAseq_Exit_dTAG13_48h_rep2


title: EA18.1_CUTTag_ESC_H3K27me3_dTAG13_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: Donor2, Th2 cells, 1mM Phe treated, Not Activated

description: Library name: D2_Phe_NotAct


title: EA18.1_RNAseq_Exit_DMSO_48h_rep3


title: Sample_58


title: Sample_61


title: Sample_60


title: EA18.1_RNAseq_Exit_dTAG13_48h_rep1


title: EA18.1_CUTTag_ESC_H3K27me3_DMSO_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: Sample_59


title: Donor1, Th2 cells, Veh treated, Not Activated

description: Library name: D1_Veh_NotAct


title: Donor1, Th2 cells, 1mM Phe treated, Not Activated

description: Library name: D1_Phe_NotAct


title: EA18.1_RNAseq_Exit_DMSO_48h_rep2


title: EA18.1_CUTTag_Exit_H3K27ac_DMSO_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: Sample_57


title: Donor1, Th2 cells, 1mM Phe treated, Activated

description: Library name: D1_Phe_Act


title: EA18.1_RNAseq_NPC_dTAG13_48h_rep3


title: EA18.1_CUTTag_ESC_H3K27ac_dTAG13_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_Exit_DMSO_48h_rep1


title: EA18.1_RNAseq_ESC_dTAG13_48h_rep3


title: EA18.1_CUTTag_Exit_H3K27ac_dTAG13_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: KH150.1_RAD21-AID_del-SRR2_IAA_3h30_rep2

description: Library name: KH4C65-66

data_processing:
To generate DpnII/Csp6I fragment maps, the mm10 mouse genome was scanned for restriction enzyme recognition sites using the Biostrings package. Only fragments containing both the primary (DpnII) and secondary (Csp6I) enzyme site were retained. Sequencing reads from different viewpoints were demultiplexed by scanning raw reads for viewpoint-specific primer sequences using the Biostrings package, allowing up to two mismatches, and trimming the reads up to the DpnII restriction site. Trimmed reads were aligned to the mm10 genome using bwa-aln (v0.7.17-r1188) and filtered for uniquely mapped reads using samtools (v1.19.2). Fragment-level read counts were calculated by requiring exact matches between read start or end positions and fragment boundaries. Library size normalization was performed by scaling read counts to counts per million, based on the total number of mapped reads per library. The normalized counts were then smoothed using a rolling mean with a window size of 21 fragments.
Assembly: mm10
Supplementary files format and content: bigWig files for each 4C viewpoint.
Library strategy: 4C-Seq

growth_protocol: Parental WT E14Tg2a (karyotype 19, XY, 129/Ola isogenic background) mouse embryonic stem cells (ESCs) and subclones were cultured in 2iSL medium [DMEM + GlutaMAX + sodium pyruvate (ThermoFisher 10569044) supplemented with 15% fetal bovine serum (Gibco SKU A5256701), 550 µM 2-mercaptoethanol (ThermoFisher 21985-023), 1X nonessential amino acids (ThermoFisher 11140-050), 10^4 U/mL of Leukemia Inhibitory Factor (Millipore ESG1107), 1 µM PD0325901 (Apex Bio/Fischer A3013-25), and 3 µM CHIR99021 (Apex Bio/Fischer A3011-100)]. Cells were maintained at a density of 0.2-1.5 x 10^5 cells/cm^2 by passaging using TrypLE (ThermoFisher 12605010) every 24-48 hours on 0.1% gelatin-coated dishes (Sigma-Aldrich G1890-100G in 1XPBS) at 37 °C and 5% CO2. The medium was changed daily when cells were not passaged. Cells were checked for mycoplasma infection every 6 months and tested negative.

extract_protocol:
4C was performed as previously described (Krijger et al., 2020). MboI was used for the first digestion and Csp6I was used for the second digestion.
4C was performed using a two-step PCR method for indexing.

treatment_protocol: Degradation of proteins tagged with the Auxin-Inducible Degron [44 amino-acid AID* truncation with residues 71–114] was induced by adding Indole-3-acetic acid sodium (IAA, Sigma Cat #I5148-2G) to a final concentration of 500 μM (from a 1000X filter-sterilized stock diluted in water). Degradation of proteins tagged with the FKBP degron [FKBP12-F36V] was induced by adding dTAG-13 (abbreviated dTAG; Sigma Cat, SML2601) to a final concentration of 500 nM (from a 1000X filter-sterilized stock diluted in DMSO).

value: embryonic stem cell

value: RAD21-AID-eGFP; Tir1-2A-PuroR(Tigre); SRR2 KO


title: EA18.1_CUTTag_ASC_H3K27me3_dTAG13_2d_rep2

description: CUT&Tag samples have bw and bed files.


title: Sample_56


title: Sample_55


title: KH150.1_RAD21-AID_del-SRR2_unt_rep2

description: Library name: KH4C63-64


title: EA18.1_CUTTag_ASC_H3K27me3_DMSO_2d_rep2

description: CUT&Tag samples have bw and bed files.


title: Donor1, Th2 cells, Veh treated, Activated

description: Library name: D1_Veh_Act


title: EN272.2_RAD21-AID_WT-SRR2_IAA_3h30_rep2

description: Library name: KH4C58-62

value: RAD21-AID-eGFP; Tir1-2A-PuroR(Tigre)


title: EA18.1_RNAseq_ESC_dTAG13_24h_rep4


title: Sample_54


title: Sample_53


title: EA18.1_RNAseq_ESC_dTAG13_24h_rep2


title: EA18.1_CUTTag_NPC_H3K27me3_DMSO_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: EN272.2_RAD21-AID_WT-SRR2_unt_rep2

description: Library name: KH4C53-57


title: KH128.3_NIPBL-FKBP_del-SRR2_DMSO_24h_rep2

description: Library name: KH4C49-50

value: BlastR-T2A-2xHA-FKBP12-Nipbl; SRR2 KO


title: KH128.3_NIPBL-FKBP_del-SRR2_dTAG13_24h_rep2

description: Library name: KH4C51-52


title: EA18.1_CUTTag_ASC_H3K27ac_DMSO_2d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_ESC_DMSO_24h_rep4


title: Sample_51


title: EA18.1_CUTTag_ASC_H3K27ac_dTAG13_2d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_CUTTag_ESC_H3K27ac_DMSO_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: Sample_50


title: EA18.1_NIPBL-FKBP_WT-SRR2_dTAG13_24h_rep2

description: Library name: KH4C44-48


title: EA18.1_RNAseq_ESC_DMSO_24h_rep2


title: Sample_52


title: EA18.1_RNAseq_ESC_dTAG13_48h_rep2


title: EA18.1_CUTTag_NPC_H3K27ac_dTAG13_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_ESC_dTAG13_48h_rep1


title: EA18.1_RNAseq_ESC_DMSO_24h_rep1


title: EA18.1_CUTTag_NPC_H3K27ac_DMSO_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: Sample_48


title: KH150.1_RAD21-AID_del-SRR2_IAA_3h30_rep1

description: Library name: KH4C32-33


title: EA18.1_NIPBL-FKBP_WT-SRR2_DMSO_24h_rep2

description: Library name: KH4C39-43


title: E14_RNAseq_ESC_dTAG13_24h_rep4

value: WT


title: EA18.1_CUTTag_NPC_H3K27me3_dTAG13_1d_rep2

description: CUT&Tag samples have bw and bed files.


title: EA18.1_RNAseq_ESC_dTAG13_24h_rep1


title: EA18.1_CUTTag_ASC_H3K27me3_dTAG13_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: Sample_47


title: Sample_49


title: KH150.1_RAD21-AID_del-SRR2_unt_rep1

description: Library name: KH4C30-31

value: untreated


title: E14_RNAseq_ESC_dTAG13_24h_rep3


title: EA18.1_CUTTag_ASC_H3K27me3_DMSO_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: Sample_45


title: HU3

description:
Library name: Sample3
10x Genomics

data_processing:
Raw gene expression matrices were generated for each sample by the Cell Ranger (Version 6.1.2) Pipeline coupled with human reference version GRCh38-2020-A. The output-filtered gene expression matrices were analyzed by R software (Version 4.1.2) with the Seurat package (Version 4.1.1). A custom R script was used to combine the expression data and metadata from all libraries corresponding to a single batch, and cells with fewer than 200 Features were removed. The expression data matrix was filtered to retain genes with >5 UMI counts and then loaded into a Seurat object along with the library metadata for downstream processing. The percentage of mitochondrial transcripts for each cell (percent. mt) was calculated and added as metadata to the Seurat object. Cells were further filtered before dimensionality reduction (nGene-min. 200; percent. mt-max. 10%). Low-quality libraries identified were removed from the dataset. Expression values were then scaled to 10,000 transcripts per cell and Log-transformed. Effects of variable (percent. mito) were estimated and regressed out using a GLM (ScaleData function, model.use=” linear”), and the scaled and centered residuals were used for dimensionality reduction and clustering. Before the clustering, we first applied Canonical correlation analysis (CCA) implemented in Seurat to correct the batch effects among the experiments and integrate the gene expression matrix of all samples into a whole matrix
Assembly: Human GRCh38-2020-A
Supplementary files format and content: TSV

extract_protocol:
Nuclei were isolated as previously described [35] with minor modifications. Briefly, 400 mg of frozen myocardial tissue per sample was thawed on ice, rinsed with cold phosphate-buffered saline (PBS), and minced into small pieces in 1 mL lysis buffer (composition: 0.32 M sucrose, 1.5 mM CaCl₂, 0.9 mM magnesium acetate (C₄H₆MgO₄), 0.75 mM ethylene glycol tetraacetic acid (EGTA), 3 mM Tris-HCl (pH 8.0), 0.6 mM ethylenediaminetetraacetic acid (EDTA), 0.1 mM phenylmethylsulfonyl fluoride (PMSF), 0.3 mM dithiothreitol (DTT), and 20 U/μL RNase inhibitor (RI)). Next, the tissue was homogenized in 15 mL lysis buffer using a T-25 Ultra-Turrax probe homogenizer (IKA, Staufen, Germany) at 24,000 rpm for 20 seconds, then diluted to 30 mL with additional lysis buffer. Homogenates were further disrupted using a 40 mL glass dounce homogenizer (10 strokes) to release nuclei, then filtered sequentially through 100 μm and 70 μm cell strainers. Filtrates were centrifuged at 700 × g for 10 minutes at 4 °C; pellets were resuspended in 23 mL sucrose buffer (2.1 M sucrose, 0.9 mM magnesium acetate, 3 mM Tris-HCl (pH 8.0), 0.2 mM DTT, 20 U/μL RI). A 7 mL sucrose buffer cushion (pre-incubated with 1% bovine serum albumin [BSA]) was layered in a 50 mL centrifuge bottle (Beckman Coulter cat no. 357003), over which 23 mL of the resuspended pellet was carefully layered. The bottle was centrifuged at 13,000 rpm for 1 hour at 4 °C (Beckman Avanti J-26XPI centrifuge). Supernatants were discarded, and nuclei pellets resuspended in 1 mL 1% BSA (containing 200 U/mL RI). Nuclei were counted using trypan blue staining, adjusted to 700–1000 nuclei/μL, and processed for single-nucleus RNA sequencing (snRNA-seq) following the 10x Genomics protocol.
Isolated nuclei were stained with acridine orange/propidium iodide (AO/PI) and counted using a fluorescence-based automated cell counter. Nuclei concentration was adjusted to 800–1200 nuclei/μL and ~20,000 nuclei per sample were loaded onto a Chromium Controller (10x Genomics) for gel bead emulsion formation. Libraries were prepared using the Chromium Next GEM Single Cell 3′ GEM, Library & Gel Bead Kit v3.1 (10x Genomics cat. no. PN-1000121) according to the manufacturer’s instructions. Libraries were sequenced on the Illumina PE150 platform at a depth of ~40,000 reads per nucleus.  All samples’ libraries were within the range of 200-2000 bp. No additional peaks were observed below 200 bp, ensuring that the libraries were qualified.

value: heart

value: cardiomyocytes


title: EA18.1_CUTTag_NPC_H3K27me3_DMSO_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: Sample_46


title: KH128.3_NIPBL-FKBP_del-SRR2_dTAG13_24h_rep1

description: Library name: KH4C18-19


title: HU2

description:
Library name: Sample2
10x Genomics


title: KH128.3_NIPBL-FKBP_del-SRR2_DMSO_24h_rep1

description: Library name: KH4C16-17


title: EN272.2_RAD21-AID_WT-SRR2_IAA_3h30_rep1

description: Library name: KH4C25-29


title: EA18.1_CUTTag_ASC_H3K27ac_DMSO_2d_rep1

description: CUT&Tag samples have bw and bed files.

value: NPC-derived astrocyte differentiation


title: EA18.1_CUTTag_ASC_H3K27ac_dTAG13_2d_rep1

description: CUT&Tag samples have bw and bed files.


title: Sample_44


title: Sample_43


title: E14_RNAseq_ESC_dTAG13_24h_rep1


title: EA18.1_NIPBL-FKBP_WT-SRR2_dTAG13_24h_rep1

description: Library name: KH4C11-15


title: EA18.1_CUTTag_NPC_H3K27ac_dTAG13_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: EN272.2_RAD21-AID_WT-SRR2_unt_rep1

description: Library name: KH4C20-24


title: Sample_41


title: Control_cells_rep2

city: Macao Special Administrative Region of China

first: GAO

middle: SHAN

last: SHAN

address: MACAU UNIVERSITY STREE

country: Macau

institute: MACAU UNIVERSITY

description: Library name: H2

data_processing:
CLC Genomics Workbench v 11.0.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: files include FPKM values for each Sample
Assembly: human reference genome (GRCh38)

source_name: hCMEC

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: hCMEC


title: Control_cells_rep3

description: Library name: H3


title: EA18.1_CUTTag_NPC_H3K27ac_DMSO_1d_rep1

description: CUT&Tag samples have bw and bed files.


title: Sample_40

description: DNA extracted from peripheral blood of healthy women with neither BRCA1 mutation nor epimutation (Controls)

source_name: Healthy woman with neither BRCA1 mutation nor epimutation (Control)


title: EA18.1_NIPBL-FKBP_WT-SRR2_DMSO_24h_rep1

description: Library name: KH4C6-10


title: EA18.1_CUTTag_NPC_H3K27me3_dTAG13_1d_rep1

description: CUT&Tag samples have bw and bed files.

value: H3K27me3 (Cell Signaling 9733)


title: E14_RNAseq_NPC_dTAG13_24h_rep4


title: E14_WT_unt_rep1

description: Library name: KH4C1-5


title: Control_cells_rep1

description: Library name: H1


title: OGD_R_treatment_rep3

description: Library name: OGD_R3


title: HU1

description:
Library name: Sample1
10x Genomics

source_name: heart


title: OGD_R_treatment_rep2

description: Library name: OGD_R2


title: E14_RNAseq_NPC_dTAG13_24h_rep3