title: RGCs from Tgfbr1flx/flx;Vglut2+/+ mice, Sample1


title: ICN1_GSI_exp14_SUPT1

status: Public on Aug 31 2025

type: SRA

city: Toulouse

first: Olivier

last: Cuvier

address: 118 route de Narbonne

department: LBME

country: France

institute: CNRS

library_source: genomic

data_processing:
Raw reads quality control perfomed with Fastqc (version 0.11.5)
Reads alignment with BWA (0.7.16a) on hg38 human genome version
Bigwig files were generated using deeptools bamCompare and normalized by the correponding input using SES normalization
Genome_build: hg38
Supplementary_files_format_and_content: bigwig files containing ChIP-seq coverage for each sample normalized by the corresponding input

molecule: genomic DNA

organism: Homo sapiens

source_name: T-cell

growth_protocol: SupT1 cells were routinely maintained in RPMI 1640 Medium (Lonza) supplemented with 10% (v/v) heat-inactivated fetal calf serum (Lonza), 1000 U.mL-1 penicillin/streptomycin (Lonza) and 20 mM Ultraglutamine (Lonza).

extract_protocol:
ChIP experiments were performed in SupT1 T-ALL cells using the ChIP IP High Sensitivity (Active Motif 53040).
ChIP-seq librairies were constructed using the Next Gen DNA Library Kit (Active Motif 53216 and 53264).

treatment_protocol: Notch signaling was inhibited by treating SupT1 T-ALL cells with the γ-secretase inhibitor (GSI) compound E at the final concentration of 1µM for two days.

tag: cell type

value: T-cell lymphoma cell line

tag: strain

tag: treatment

value: GSI

tag: passages

tag: chip antibody

value: ICN1 (Cell Signaling 4147)


title: MTA2_GSI_exp14_SUPT1

value: MTA2 (Bethyl A300-395A)


title: peripheral blood sample of donor8

city: Chengdu

first: Yujun

last: Deng

address: No. 17, Section 3, Renmin South Road, Chengdu

country: China

institute: Sichuan University

description:
Library name: donor8-1
10x Genomics
5'scRNA + scTCRseq

library_source: transcriptomic

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0 or v6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: transcript files :Tab-separated values files and matrix files; TCR files :comma-separated values files

molecule: total RNA

source_name: peripheral blood

extract_protocol:
Human thymus samples were collected and transferred to RPMI1640 medium supplied with 10% FBS on ice, the tissues were cut into small pieces to release thymocytes. After thymocytes were collected, the remaining tissues were washed with RPMI1640 for 2-3 times and subjected to digestion with pre-warmed RPMI1640 containing 0.1g/mL collagenase and 100ug/mL DNase at 37ºC for 30-40 mins. The cell suspension was passed through 70m cell strainer and combined with thymocytes collected previously. The cells were centrifuged at 500g for 6min and suspended with RPMI1640 medium for cell counting, staining and sorting.  PBMCs were isolated from peripheral blood using Lymphocyte Separation Medium (LTS1077, TBD). Briefly, blood was added into 15mL tube containing equal volume of Lymphocyte Separation Medium gently and centrifuged at 2000 rpm for 20 min at room temperature with brake off. The PBMCs layer located at the interface were collected and washed with PBS plus 5% FBS.  For scRNA-seq, fresh cells isolated from human thymus were sorted as 7-AAD-CD235a-CD45+ and 7-AAD-CD235a-CD45- cells and combined with ratio at 6:4, or sorted as CD34+ cells or EpCAM+ cells. The sorted cells were applied for 10X single cell RNA-sequencing, TCR repertoire sequencing or cellular indexing of transcriptomes and epitopes sequencing.
For 10X single cell RNA-sequencing and 5’-TCR repertoire sequencing, 20,000 live sorted thymic cells or PBMCs were loaded on to each of the Chromium Controller (10X Genomics). Single cell cDNA and unique molecular identifier (UMI) tagged scRNA-Seq libraries and TCR repertoire Seq libraries were prepared using 10X Genomics platform.

tag: tissue

value: peripheral blood

value: PBMC

tag: age

value: 35 years

tag: Sex

value: Female


title: creeping fat 3 (CF3)

city: 济南市

first: xiaofen

last: lv

address: 107 Wenhua West Road

institute: Shandong University

data_processing:
These libraries were sequenced on the Illumina sequencing platform (HiSeqTM 2500 or other platform) and 150 bp/125bp paired-end reads were generated.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each sample

organism: Mus musculus

source_name: adipose tissue

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis.
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

value: adipose tissue

tag: genotype

value: WT

value: repeated colonic cautery injury


title: MTA2_DMSO_exp14_SUPT1

value: DMSO


title: thymus sample of donor7

description:
Library name: donor7-2
10x Genomics
5'scRNA + scTCRseq

source_name: thymus

value: thymus

value: combined CD45+ and CD45- cells (6:4)

value: 56 years


title: ICN1_DMSO_exp14_SUPT1


title: HDAC1_GSI_exp05_SUPT1

value: HDAC1 (Bethyl A300-713A)


title: peripheral blood sample of donor7

description:
Library name: donor7-1
10x Genomics
5'scRNA + scTCRseq


title: 16hr_dex_3_clv3

city: Mohali

first: Hasthi

last: Ram

address: Sector 81

department: Agriculture biotechnology

country: India

institute: NABI (National Agri-Food Biotechnology Institute)

data_processing:
The quality of the sequencing data was assessed using FastQC
bases with fluctuating GC content were trimmed off with cutadapt
Genome mapping was performed using TopHat
A gene expression count table was generated from the aligned dataset using HTSeq
Assembly: TAIR10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Arabidopsis thaliana

source_name: SAM

growth_protocol: Plants were grown under long day conditions till flowering

extract_protocol:
Rneasy Mini kit (Qiagen) was used according to manufacturer’s instruction
the libraries were prepared with 1μg of total RNA using ‘TruSeq Stranded mRNA Library Prep Kit from Illumina’.

treatment_protocol: For inducible gene perturbations in the IM, 10 μMDEX solution containing 0.015% Silwet L-77 was applied once to the IM and tissues were collected after required time point for RNA-Seq

value: SAM

value: pUBQ10>>mir165a in clv3

value: Dex 16hr

tag: time


title: 16hr_dex_2_clv3


title: RGCs from Tgfbr1flx/flx;Vglut2Cre/+ mice, Sample1

city: Changsha

first: Yuerong

last: Ren

address: Renmin Road No.139

institute: central south university

data_processing:
The libraries were sequenced on a llumina Novaseq 6000 platform and 150 bp paired-end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low-quality reads were removed to obtain the clean reads, which were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis was performed using R (v 3.2.0) to evaluate the biological duplication of samples. Differential expression analysis was performed using the DESeq2. Q-value <0.05 and |log2FC| > 1 was set as the threshold for significantly differential expression genes (DEGs). Hierarchical cluster analysis of DEGs was performed using R (v 3.2.0) to demonstrate the expression pattern of genes in different groups and samples. Based on the hypergeometric distribution, GO pathway enrichment analysis of DEGs was performed to screen the significantly enriched term using R (v 3.2.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: retinal ganglion cell

extract_protocol:
The total RNA of each sample was extracted by RNeasy Micro Kit (QIAGEN). The purity and quantification of RNA were assessed with Nanodrop 2000 (Thermo Scientific). The integrity of RNA was evaluated by Agilent 2100 Bioanalyzer (Agilent Technologies). 1ng of total RNA was used for the construction of sequencing libraries.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: retinal ganglion cell


title: creeping fat 2 (CF2)


title: BMI1_GSI_exp14_SUPT1

value: T-cell lymphoma cell line

value: GSI

value: BMI1  (Active Motif 39993)


title: creeping fat 1 (CF1)


title: thymus sample of donor6

description:
Library name: donor6
10x Genomics
5'scRNA + scTCRseq

value: 35 years


title: MDA-436-200f4

city: Guelph

first: Roger

last: Moorehead

address: 50 Stone Rd E

department: Biomedical Sciences

country: Canada

institute: University of Guelph

description: MDA-MB-436 cells infected with a lentivirus containing the miR-200c/141 cluster + a lentivirus containing the miR-200b/200a/429 cluster and grown as 2D culture, sample 4

data_processing:
adapters removed, reads containing N>10% removed, Qscore<=5 removed by Novogene
data was provided by Novogene as .fq.gz files
data was analyzed using Genialis software and the standard RNA-seq pipeling
Assembly: Homo sapiens annotation (ENSEMBL 100)
Supplementary files format and content: xlsx file containing featurecounts data

source_name: human TNBC cell line MDA-MB-436

growth_protocol: All cells were maintained in DMEM media (GIBCO, Burlington, ON) supplemented with 10% FBS, 2% glutamine, 1% sodium pyruvate, 1% 4-(2-hydroxyethyl)-1-piper- azineethanesulfonic acid (HEPES), and 1% antibiotic/antimycotic. MDA-436EV cells were cultured with 20ug/ml puromycin while MDA-436-200f cells were cultured with 20ug/ml puromycin + 200ug/ml hygromycin Antibiotics were obtained from InvivoGen, San Diego, CA).

extract_protocol:
Total RNA was extracted using the miRVana miRNA extraction kit from Thermo Fisher Scientific
libraries were created by Novogene using Illumina kits

treatment_protocol: MDA-MB-436 cells were infected with lentiviral particles containing the pLV[Exp]-EGFP:T2A:Puro-EF1A>mCherry (vector ID: VB160109-10005, VectorBuilder Inc., Chicago, IL, USA) to create MDA-436EV cells. To create MDA-436-200f cells, MDA-MB-436 cells were infected with lentiviral particles containing pLV[Exp]-mCherry:T2A:Hygro-CMV>[Ex_miR200c-141] and lentiviral particles containing pLenti 4.1 Ex_miR200b-200a-429

value: human TNBC cell line MDA-MB-436

tag: cell line

value: triple negative breast cancer

value: overexpress miR-200c/141 and miR-200b/200a/429 cluster

value: lentivirus with miR-200c/141 + lentivirus with miR-200b/200a/429


title: MDA-436-200f3

description: MDA-MB-436 cells infected with a lentivirus containing the miR-200c/141 cluster + a lentivirus containing the miR-200b/200a/429 cluster and grown as 2D culture, sample 3


title: BMI1_DMSO_exp14_SUPT1

value: DMSO


title: 9hr_dex_3_clv3

value: Dex 9hr


title: thymus sample of donor5

description:
Library name: donor5
10x Genomics
5'scRNA + scTCRseq

value: thymus

value: combined CD45+ and CD45- cells (6:4)

value: 12 years

value: Female


title: thymus sample of donor8

description:
Library name: donor8-2
10x Genomics
5'scRNA + scTCRseq


title: thymus sample of donor4

description:
Library name: donor4
10x Genomics
5'scRNA + scTCRseq

value: 5 years


title: MDA-436-200f2

description: MDA-MB-436 cells infected with a lentivirus containing the miR-200c/141 cluster + a lentivirus containing the miR-200b/200a/429 cluster and grown as 2D culture, sample 2


title: input_GSI_exp14_SUPT1


title: 9hr_dex_2_clv3

value: SAM

value: pUBQ10>>mir165a in clv3


title: thymus sample of donor3

description:
Library name: donor3
10x Genomics
5'scRNA + scTCRseq

value: 24 years


title: 9hr_dex_1_clv3


title: MDA-436-200f1

description: MDA-MB-436 cells infected with a lentivirus containing the miR-200c/141 cluster + a lentivirus containing the miR-200b/200a/429 cluster and grown as 2D culture, sample 1


title: HDAC1_DMSO_exp05_SUPT1

value: T-cell lymphoma cell line

value: HDAC1 (Bethyl A300-713A)


title: thymus sample of donor2

description:
Library name: donor2
10x Genomics
5'scRNA + scTCRseq

value: 48 years


title: input_DMSO_exp14_SUPT1


title: 4hr_dex_3_clv3

value: Dex 4hr


title: input_GSI_exp05_SUPT1

value: GSI


title: MDA-436EV3

description: MDA-MB-436 cells infected with control lentivirus and grown as 2D culture, sample 3

value: human TNBC cell line MDA-MB-436

value: triple negative breast cancer

value: control

value: control lentivirus


title: 16hr_dex_1_clv3

value: Dex 16hr


title: input_DMSO_exp05_SUPT1

value: DMSO


title: KD-TFRC_3

city: Dali

first: Zhiqiang

last: Ma

state: Yunnan

address: No.35 Renmin South Road

institute: Dali Bai Autonomous Prefecture People's Hospital

data_processing:
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file includes RPKM for each Sample

source_name: Thyroid cancer cell line

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Thyroid cancer cell line

value: TFRC Knockdown


title: MDA-436EV1

description: MDA-MB-436 cells infected with control lentivirus and grown as 2D culture, sample 1


title: 4hr_dex_1_clv3


title: thymus sample of donor1

description:
Library name: donor1
10x Genomics
5'scRNA + scTCRseq

value: thymus

value: combined CD45+ and CD45- cells (6:4)

value: 56 years

value: Female


title: PHx_4

city: Kunming

first: Liyan

last: Li

address: No. 1168, Chunrong West Road

department: Institute of Neuroscience

institute: Kunming Medical University

description: Library name: Sample8

data_processing:
Raw reads of fastq form atwere firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then clean reads for each sample were retained for subsequent analyses. The cleanreads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R(v 3.2.0) to evaluate the biological duplication of samples
Assembly: mRatBN7.2
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Rattus norvegicus

source_name: Liver

value: Liver

value: WT

value: PHx


title: MDA-436EV2

description: MDA-MB-436 cells infected with control lentivirus and grown as 2D culture, sample 2


title: control3_clv3

value: SAM


title: KD-TFRC_1


title: 4hr_dex_2_clv3

value: pUBQ10>>mir165a in clv3

value: Dex 4hr


title: PHx_2

description: Library name: Sample6


title: control2_clv3


title: KD-TFRC_2


title: D28_52_DC

city: Stockholm

first: Keying

last: Zhu

state: -- select state --

address: L8:04, Center for Molecular Medicine, Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

data_processing:
Data were processed by the Bioinformatics and Expression Analysis (BEA) core facility at Karolinska Institutet. To ensure that all sequenced data meets our guarantee of data quality and quantity, a number of standardised bioinformatics quality control checks are performed before delivery. These include checking the yield, sequence read quality and cross-sample contamination.
Assembly: Ensembl Mus_musculus.GRCm38.101
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
SMART-Seq v4 Ultra Low Input RNA Kit
Nextera XT kit

value: primary cell

value: microglia

value: Tgfbr2 ko


title: KD-NC_3


title: D28_52_G


title: control1_clv3


title: KD-NC_2


title: PHx_1

description: Library name: Sample5


title: 16hr_dex_3

data_processing:
The quality of the sequencing data was assessed using FastQC
bases with fluctuating GC content were trimmed off with cutadapt
Genome mapping was performed using TopHat
A gene expression count table was generated from the aligned dataset using HTSeq
Assembly: TAIR10
Supplementary files format and content: count

growth_protocol: Arabidopsis were grown  at 22 degrees C in  continuous  light with 60% humidity.

value: pUBQ10>>mir165a in ap1cal

value: Dex 16hr


title: WT_4_VC

value: wildtype


title: Sham_4

description: Library name: Sample4

value: Sham


title: KD-NC_1

value: Thyroid cancer cell line


title: 16hr_dex_2


title: WT_4_DC


title: H9 CCR7KO TO-2, CCR7 KO, biol rep2

city: St Louis

first: Sabine

last: Dietmann

state: MO

address: 4565 McKinley Avenue

country: USA

institute: Washington University School of Medicine

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were converted to fastq format using the cellranger mkfastq command (v.5.0.0).
Assembly: Raw sequencing reads were aligned to the human genome reference genome (GRCh38, UCSC hg38) and quantified using the CellRanger count command on GENCODE basic annotations (release 44) considering protein-coding genes only
Supplementary files format and content: Processed data files contain matrix with counts, barcodes and features provided as standard output by cellranger

source_name: CCR7 KO H9

extract_protocol:
Day 10 WT and CCR7 KO hTOs from two independent experiments were used for the scRNA-seq. For scRNA-seq sample preparation, organoids were washed two times with PBS and then incubated in ice cold cell recovery solution for 30 min. The organoids released from Matrigel were spined down with short pulse function of centrifuge and washed twice with Advanced DMEM/F12. hTOs were transferred to 1.5 mL microtubes containing 500 μL ice cold HBSS and washed three times with cold HBSS. Organoids were then treated with 400 μL of activated Papain solution [9 μL Papain enzyme (MP Biomedicals, 100921), 391 μL of (2.5 mM Cysteine, 0.5 mM EDTA in HEPES)] in 37oC water bath for 10 min, with the tube gently inverted every 2 min. 600 μL 10% FBS in DMEM was added per sample and gently triturated 3-5 times with a P1000 pipette. 10 μL of RNase free DNase I (NEB, M0303) was added and incubated for 5 min in 37oC. 3- 5 more times gentle trituration were applied and centrifuged at 4000 rpm for 30 seconds. Single cell dissociated hTO cells were strained through a 40 μm filter at a concentration of approximately 1,000 cells/μL.
The libraries  was generated using the Chromium Single Cell 3’ Reagents kit v3.1 following the manufacture’s instruction. Single cell libraries were sequenced on a NovaSeq6000 S4 and the target sequencing depth was 50,000 reads/cell for all samples.

value: CCR7 KO H9

value: H9 Trophoblast organoid

value: mutant


title: 16hr_dex_1


title: WT_4_G


title: Sham_3

description: Library name: Sample3

value: Liver


title: Sham_2

description: Library name: Sample2

value: WT


title: D28_52_VC


title: PHx_3

description: Library name: Sample7

value: PHx


title: WT_3_VC


title: H9 CCR7KO TO-1, CCR7 KO, biol rep1


title: Sham_1

description: Library name: Sample1


title: 12hr_dex_3

value: SAM

value: Dex 12hr


title: H9 TO-2, WT, biol rep2


title: 12hr_dex_1


title: WT_3_DC


title: H9 TO-1, WT, biol rep1


title: 12hr_dex_2


title: Larval fish - 7 days old, PFDoDA low 6

city: Gainesville

first: Christopher

last: Martyniuk

state: FL

address: 8891 SW 79th Avenue

institute: University of Florida

description: Library name: Sample 9

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
DESeq2 was used for differential expression analysis between the control and treatments.
Assembly: ensembl_danio_rerio_grcz11_gca_000002035_4
Supplementary files format and content: PFDoDA LowvsDMSO excel sheet containing read count, fpkm, log2 fold change, p-value
Supplementary files format and content: PFDoDA HighvsDMSO excel sheet containing read count, fpkm, log2 fold change, p-value

organism: Danio rerio

source_name: Larval fish - 7 days old

extract_protocol:
Total RNA for each sample was extracted from zebra fish larvae using TRIzol. RNA concentration was determined using the Qubit® 2.0 Fluorometer (ThermoFisher/Invitrogen, Grand Island, NY) after clean up the samples from any genomic contamination using  RNA samples with a measured 28S/18S > 1 and RNA integrity number determined RNAseq library construction.
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library"
Total RNA was used for mRNA isolation using the NEBNext Ploy(A) mRNA Magnetic Isolation module (New England Biolabs, catalog # E7490). RNA library construction was then performed with the NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina® (New England Biolabs, catalog #E7760) according to the manufacturer's user guide. Individually prepared libraries were pooled by equimolar and sequenced by NovoSeq6000 (Illumina Inc., CA, U.S.A). Sequencing was performed by Novogene.

value: Larval fish - 7 days old

value: Low dose


title: WT_3_G

value: primary cell

value: microglia


title: Larval fish - 7 days old, PFDoDA low 5

description: Library name: Sample 8


title: T06

city: nanjing

first: yuanfeng

last: wang

state: jiangsu

address: 101 Longmian Avenue, Jiangning Campus

institute: Nanjing Medical University

description: overexpression sample 3

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, GC-content and sequence duplication level of the clean data were calculated. All the downstream analyses were based on clean data with high quality.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. HISAT2 tools software were used to map to reference genome.
Gene function was annotated based on the following databases: NR(NCBI non-redundant protein sequences database);Nt (NCBI non-redundant nucleotide sequences);Pfam (The database of Homologous protein family);COG (The database of Clusters of Protein homology);Swiss-Prot (A manually annotated non-redundant protein sequence database);KOG(The database of Clusters of protein homology); KEGG(The database of Kyoto Encyclopedia of Genes and Genomes);GO (Gene Ontology database).
Picard - tools v1.41 and samtools v0.1.18 were used to sort, remove duplicated reads and merge the bam alignment results of each sample. GATK2 or Samtools software was used to perform SNP calling. Raw vcffiles were filtered with GATK standard filter method and other parameters ( clusterWindowSize: 10; MQ0 >= 4 and (MQ0/(1.0*DP)) > 0.1; QUAL < 10; QUAL < 30.0 or QD < 5.0 or HRun > 5), and only SNPs with distance > 5 were retained.
The adaptor sequences and low-quality sequence reads were removed from the data sets. Raw sequences were transformed into clean reads after data processing. These clean reads were then mapped to the reference genome sequence. Only reads with a perfect match or one mismatch were further analyzed and annotated based on the reference genome. HISAT2 tools software were used to map to reference genome.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes different expression genes

source_name: Ligamentum flavum

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent.NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB #E7775L) was used with 0.4 ug of total RNA for the construction of sequencing libraries.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase. Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H . Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 240 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 μl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37°C for 15 min followed by 5 min at 95°C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Ligamentum flavum


title: WT_2_VC


title: 9hr_dex_3

value: pUBQ10>>mir165a in ap1cal

value: Dex 9hr


title: Larval fish - 7 days old, PFDoDA low 4

description: Library name: Sample 7


title: T05

description: overexpression sample 2


title: WT_2_DC

value: wildtype


title: 9hr_dex_2


title: Larval fish - 7 days old, PFDoDA high 3

description: Library name: Sample 6

value: High dose


title: T04

description: overexpression sample 1


title: 9hr_dex_1


title: WT_2_G


title: Larval fish - 7 days old, PFDoDA high 2

description: Library name: Sample 5


title: 6hr_dex_3

value: Dex 6hr


title: Larval fish - 7 days old, PFDoDA high 1

description: Library name: Sample 4


title: T03

description: control sample3


title: D28_54_VC

value: Tgfbr2 ko


title: T02

description: control sample2


title: D28_54_DC


title: 6hr_dex_2


title: 6hr_dex_1


title: T01

description: control sample1


title: Larval fish - 7 days old, Control 3

description: Library name: Sample 3

value: Control


title: control3

source_name: control


title: D28_54_G


title: A23

city: Beijing

first: Jinming

last: Zhao

state: Beijing

address: No.1, Dongjiaominxiang, Dongcheng District

institute: Beijing Tongren Hospital, Capital Medical University

description: s15-LZW-human peripheral blood

data_processing: Differential expression analysis was performed between two comparisons via the DESeq2 R package (1.16.1). DESeq2 provides statistical procedures to determine differential expression in digital gene expression data using a model based on a negative binomial distribution. The method of Benjamini and Hochberg was used to adjust the P value to control the error detection rate. Genes with adjusted P < 0.05 were considered DE according to DESeq2. For each sequenced library, the read count was adjusted via a scale normalization factor in the edgeR package prior to differential expression analysis. Differential expression analysis of the two conditions was performed via the edgeR software package. The Benjamini and Hochberg methods were used to adjust the P values. After correction, the P value and fold change were used as thresholds for significant differential expression.

source_name: blood

extract_protocol:
Blood samples were collected in 5-ml EDTA vacuum tubes, and the leukocytes were separated via red blood cell lysis solution (Solarbio, R1010). Total RNA was extracted from leukocytes with Tri®-Reagent (Sigma, T9424) within 2 hours.
All procedures were performed according to the manufacturer’s instructions. An RNA-seq library was constructed and sequenced by Novogene Company Limited. The NEBNext® UltraTM RNA Library Prep Kit (New England Biolabs) was used for library construction. After the library was constructed, an Agilent 2100 Bioanalyzer (Agilent Technologies) was used to determine the size of the library insert. Reverse transcription‒quantitative polymerase chain reaction (RT‒qPCR) was used to quantify the effective concentration of the library accurately to ensure quality. After qualified library inspection, Illumina sequencing was performed for the different pooled libraries according to the requirements of the effective concentration and target onboard data amount, and a 150-bp matching end reading was produced. The basic principle of sequencing is sequencing by synthesis.

value: blood

value: leukocytes

value: female

tag: disease

value: HDM-induced AR


title: D28_84_VC


title: Larval fish - 7 days old, Control 2

description: Library name: Sample 2


title: control2

value: SAM


title: Larval fish - 7 days old, Control 1

description: Library name: Sample 1

value: Larval fish - 7 days old


title: A22

description: s97-RHJ-human peripheral blood

value: male


title: control1-1


title: D28_84_G

value: primary cell


title: PFBA high 4

description: Library name: Sample 15

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.
Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
DESeq2 was used for differential expression analysis between the control and treatments.
Assembly: ensembl_danio_rerio_grcz11_gca_000002035_4
Supplementary files format and content: PFBA0_1vsDMSO excel files containing read count, fpkm, log2 fold change, p-value
Supplementary files format and content: PFBA1vsDMSO excel files containing read count, fpkm, log2 fold change, p-value
Supplementary files format and content: PFBA10vsDMSOexcel files containing read count, fpkm, log2 fold change, p-value

value: PFBA - 10 ug/L


title: A21

description: s93-YP-human peripheral blood


title: D28_84_DC

value: microglia


title: A20

description: s92-WCW-human peripheral blood


title: PFBA high 3

description: Library name: Sample 14


title: D18_98_DC


title: D18_98_VC


title: PFBA high 2

description: Library name: Sample 13


title: D18_98_G


title: A19

description: s79-CQ-human peripheral blood


title: PFBA high 1

description: Library name: Sample 12


title: hDPSCs Treatment Rep3

city: Bangkok

first: Ajjima

last: Chansaenroj

address: 34 Henri-Dunant Road

department: Anatomy

country: Thailand

institute: Faculty of Dentistry, Chulalongkorn University

data_processing:
Cutadapt (V1.9.1, phred cutoff: 20, error rate: 0.1, adapter overlap: 1bp, min. length: 75, proportion of N: 0.1) to be high quality clean data.
Clean data were aligned to reference genome via software Hisat2 (v2.2.1).
HTSeq (v0.6.1) estimated gene and isoform expression levels from the pair-end clean data.
Differential expression analysis used the DESeq2 Bioconductor package
Assembly: Firstly, reference genome sequences and gene model annotation files of relative species were downloaded from genome website, such as UCSC, NCBI, ENSEMBL. Secondly, Hisat2 (v2.2.1) was used to index reference genome sequence. Finally, clean data were aligned to reference genome via software Hisat2 (v2.2.1).
Supplementary files format and content: Microsoft excel 97
Supplementary files format and content: Microsoft excel 97

source_name: Dental pulp

growth_protocol: The dental pulp tissues were gently removed from the teeth and minced into small pieces (size 2x2 mm). The tissues were placed on the 35-mm tissue culture dishes filled with 1000 µl growth medium. The growth medium was composed of Dulbecco’s Modified Eagle Medium (DMEM, cat. no. 11960, Gibco, USA) supplemented with 10% fetal bovine serum (FBS, cat. no. 10270, Gibco, USA), 1% L-glutamine (GlutaMAX-1, cat. no. 35050, Gibco, USA), 100 unit/mL penicillin, 100 µg/mL streptomycin, and 250 ng/mL amphotericin B (Antibiotic–Antimycotic, cat. no. 15240, Gibco, USA). After confluence, the cells were trypsinised and seeded on the 60-mm tissue culture dishes and this population was considered passage 1. Subculturing was performed at a 1:3 ratio when the cells reached confluence. All cell culture experiments were maintained in an incubator in a 5% CO2 humidified atmosphere at 37oC.

extract_protocol:
1 μg total RNA was used for following library preparation. The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated.
Then libraries with different indexs were multiplexed and loaded on an Illumina HiSeq/ Illumina Novaseq/ MGI2000 instrument for sequencing using a 2x150 paired-end (PE) configuration according to manufacturer’s instructions.

treatment_protocol: The cells were treated with 1.25 μg/mL CBD for 24h.

value: Dental pulp

value: hDPSCs

value: CBD


title: hDPSCs Treatment Rep2


title: D18_94_VC


title: PFBA medium 4

description: Library name: Sample 11

value: PFBA - 1 ug/L


title: A16

description: s61-LLD-human peripheral blood


title: D18_94_DC


title: PFBA high 5

description: Library name: Sample 16


title: hDPSCs Control Rep3


title: D18_94_G


title: PFBA medium 3

description: Library name: Sample 10


title: hDPSCs Treatment Rep1


title: A15

description: s5-JXR-human peripheral blood


title: hDPSCs Control Rep2


title: PFBA medium 2

description: Library name: Sample 9


title: A14

description: s56-SYN-human peripheral blood


title: A13

description: s50-WY-human peripheral blood


title: PFBA medium 1

description: Library name: Sample 8


title: WT_1_VC

value: wildtype


title: hDPSCs Control Rep1


title: WT_1_DC


title: A12

description: s48-JJQ-human peripheral blood


title: PFBA low 3

description: Library name: Sample 7

value: PFBA - 0.1 ug/L


title: A18

description: s75-HXW-human peripheral blood


title: WT_1_G


title: U87-GRIK1-siRNA3

city: shanghai

first: hou

middle: guo

last: qiang

address: 160 pujian road

department: Neurosurgery

institute: Department of Neurosurgery, Renji Hospital, Shanghai Jiaotong University, Shanghai, China

data_processing:
Cutadapt v 1.9.1
sequence reads were trimmed foradaptor sequence/low-quality sequence using cutadapt(error rate:0.1)
trimmed sequence reads were mapped to NCBI using Hisat2
read count extraction and normalization were performed using HTSeq
Assembly: GRCh38.107
Supplementary files format and content: raw counts and FPKM for each Sample

extract_protocol:
RNA was harvested using trizol（Invitrogen)。1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Illumina VAHTS® Universal V8 RNA-seq Library Prep Kit fowllowing manufacturer's protocols.

value: glioma

value: GRIK1 knockdown


title: PFBA low 2

description: Library name: Sample 6


title: A11

description: s47-LZ-human peripheral blood

value: blood

value: leukocytes


title: U87-GRIK1-siRNA2


title: PFBA low 1

description: Library name: Sample 5


title: A10

description: s45-YQY-human peripheral blood

value: HDM-induced AR


title: U87-GRIK1-siRNA1


title: D18_88_DC

value: Tgfbr2 ko


title: Control 4

description: Library name: Sample 4

value: Larval fish - 7 days old

value: Control


title: U87-NC-3


title: Control 3

description: Library name: Sample 3


title: D18_6_VC

value: primary cell


title: A8

description: s34-CHL-human peripheral blood

value: male


title: U87-NC-2


title: D18_88_G

value: microglia


title: A9

description: s40-CL-human peripheral blood


title: D18_6_DC


title: A6

description: s136-DHQ-human peripheral blood

value: female


title: Control 1

description: Library name: Sample 1


title: D18_6_G


title: Long descending propriospinal neurons 5

city: Berlin

first: Niccolò

last: Zampieri

address: Robert-Rössle-Straße 10

country: Germany

institute: MDC

description: Library name: LDPNs 5

data_processing:
Data processing was done in R version 4.4.2 (R Foundation for Statistical Computing, Vienna, Austria) and Seurat version 4.
In order to create a unique identity per cell we pulled together the unique (per plate) well/cell barcode and the number of the plate. The plate number is appended to the barcode sequence. e.g.,  ACCAAC_8 means that it's the well with barcode ACCAAC of the 8th plate, plate_8.
Assembly: mm10
Supplementary files format and content: Tab separated value files

molecule: nuclear RNA

source_name: Cervical spinal cord

extract_protocol:
Mice that received lumbar or cervical bilateral injections of Rabies-H2BCherry were sacrificed by decapitation. The cervical (C1 to T1) or lumbar segments (L1 to L6) of the spinal cord were cut into small pieces and placed in a Dounce homogenizer filled with ice-cold homogenization buffer. The tissue was manually homogenized with five strokes of the loose pestle, followed by 10–15 strokes of the tight pestle. Subsequently, the solution containing the dissociated nuclei was filtered through a 40 μm filter into a sorting tube and DAPI was added to a final concentration of 1 μM to label the nuclear population. Nuclear mCherry+/DAPI+ neurons were sorted into 96-well plates using BD FACSAria Fusion
Single-nucleus RNA libraries were prepared following the CEL-Seq2 protocol (https://doi.org/10.1186/s13059-016-0938-8.)

value: Cervical spinal cord

value: Spinal neurons

value: Postnatal day 8

tag: plate number


title: U87-NC-1

data_processing:
Cutadapt v 1.9.1
sequence reads were trimmed foradaptor sequence/low-quality sequence using cutadapt(error rate:0.1)
trimmed sequence reads were mapped to NCBI using Hisat2
read count extraction and normalization were performed using HTSeq
Assembly: GRCh38.107
Supplementary files format and content: raw counts and FPKM for each Sample
Supplementary files format and content: tab-delimited text files includes RPKM values for each Sample

value: wildtype


title: Long descending propriospinal neurons 4

description: Library name: LDPNs 4


title: A7

description: s22-AYF-human peripheral blood


title: D18_88_VC


title: A5

description: s134-SYG-human peripheral blood


title: OB7d

city: Jiujiang

first: Tao

last: Wang

address: No. 551, Qianjin East Road

institute: Jiujiang University

description: Library name: sample4

data_processing:
Raw data were generated after sequencing, image analysis, base calling and quality filtering on Illumina sequencer. Firstly, Q30 was used to perform quality control.
The adaptor sequences were trimmed and the adaptor-trimmed-reads (>= 16nt) were left by cutadapt software (v1.9.3).
Then, the raw counts of each tRF&tiRNA (MINTbase v2.0) was calculated for all samples, defined as the raw expression levels of that tRF&tiRNA.
The raw counts were normalized by TPM and differentially expressed tRF&tiRNAs between two groups were calculated by TPM and filtered by Fold Change and P-value.
Assembly: GRCh37/hg19
Supplementary files format and content: This file contains the raw counts and normalized counts of tRF&tiRNA identified form each sample.

source_name: hBMSCs

extract_protocol:
Total RNA was extracted using Trizol reagent.
High throughput sequencing service was provided by CloudSeq Biotech (Shanghai, China). Total RNA of each sample was used to prepare the tRF&tiRNA sequencing library, which included the following steps: 1) 3'-adaptor ligation; 2) 5'-adaptor ligation; 3) cDNA synthesis; 4) PCR amplification; 5) Size selection of ~150 bp PCR amplicons The libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 50 cycles on Illumina HiSeq sequencer following the manufacturer's instructions.

value: hBMSCs

tag: batch


title: D18_2_DC


title: A4

description: s12-LJN-human peripheral blood


title: D18_2_VC


title: A17

description: s6-ZWY-human peripheral blood


title: A3

description: s110-YX-human peripheral blood


title: D18_2_G


title: Long descending propriospinal neurons 2

description: Library name: LDPNs 2


title: Long descending propriospinal neurons 3

description: Library name: LDPNs 3


title: Control 2

description: Library name: Sample 2


title: OB-0d

description: Library name: sample1


title: A2

description: s108-XY-human peripheral blood


title: Pancreatic bud, TBZ_3

city: Yokohama

first: Airi

last: Inoue

state: Kanagawa

address: 4259 Nagatsuta-cho, Midori-ku

country: Japan

institute: Tokyo institute of technology

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through in-house scripts.  In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data.  At the same time, Q20, Q30 and GC content of the clean data were calculated.  All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly.  Paired-end clean reads were aligned to the reference genome using the Spliced Transcripts Alignment to a Reference (STAR) software, which is based on a previously undescribed RNA-seq alignment algorithm that uses sequential maximum mappable seed search in uncompressed suffix arrays followed by seed clustering and stitching procedure.  STAR exhibits better alignment precision and sensitivity than other RNA-seq aligners for both experimental and simulated data.
HTSeq was used to count the read numbers mapped of each gene.  And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.  RPKM, Reads Per Kilobase of exon model per Million mapped reads, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels (Mortazavi et al., 2008).
Assembly: mm10
Supplementary files format and content: txt file representing FPKMs and counts

source_name: Pancreatic bud

growth_protocol: Pancreatic bud at E12.5 was cultured in M199 no phenol red containing 10% fetal bovine serum with 0.1 % DMSO for 2 days.

extract_protocol:
RNA was extracted using Rneasy micro kit (Qiagen).
A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations.  Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.  Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.  Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-).  Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.  Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities.  After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization.  In order to select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA).  Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor- ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR.  Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer.  At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system (with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using PE Cluster Kit cBot-HS (Illumina) according to the manufacturer’s instructions.  After cluster generation, the library preparations were sequenced on an Illumina platform (Novaseq 6000PE150) and paired-end reads were generated.カキハ オクッテイタダイタ ガイヨウニ シュッテン ヨウ ヨウカクニン オソラク コンカイハ

treatment_protocol: 0.1μM TBZ was added for whole culture period.

value: Pancreatic bud

value: TBZ


title: A1

description: s101-ZS-human peripheral blood

value: blood


title: Long ascending propriospinal neurons 5

description: Library name: LAPNs 5

source_name: Lumbar spinal cord

value: Lumbar spinal cord


title: Pancreatic bud, TBZ_1


title: Long descending propriospinal neurons 1

description: Library name: LDPNs 1


title: OB-21d

description: Library name: sample3


title: CD14+CD16+ monocytes, Young Adult with co-morbid conditions,WGP stimulated -3

city: New Haven

first: Heidi

last: Zapata

address: 300 Cedar St

institute: Yale University

data_processing:
The raw FASTQ files were executed for adaptor trimming and quality trimming using Cutadapt v1.18.
The trimmed fastq files were aligned to human genome reference (GRCh38.primary assembly) by using STAR/ 2.7.3a-foss-2018b
Raw counts were obtained using Subread/2.0.0-GCC-7.3.0-2.30 featureCounts package
Assembly: Human GRCh38.primary assembly
Supplementary files format and content: tab-delimited text file "count_None_WGP.txt" include the raw count values for all samples

source_name: CD14+CD16+ monocytes

extract_protocol:
RNA was harvested using Rneasy kit (Qiagen).
RNA libraries for RNA-seq were prepared using Illumina Nextra Xt DNA Library Kit following manufacturer's protocols.

treatment_protocol: CD14+CD16+ monocytes were isolated were isolated from PBMCs and stimulated with whole glucan particle (10mg/ml) for 18 hours at 37°C in a 5% CO2 humidified environmen

tag: sample type

value: PBMC

value: CD14+CD16+ monocytes

value: Whole Glucan Particle


title: Pancreatic bud, TBZ_2


title: OB-14d

description: Library name: sample2


title: Long ascending propriospinal neurons 4

description: Library name: LAPNs 4


title: Long ascending propriospinal neurons 2

description: Library name: LAPNs 2


title: HSPSeq_019_01_RNA_fibroblasts

city: Boston

first: Darius

last: Ebrahimi-Fakhari

state: Massachusetts

address: Center for Life Sciences Building CL12160.6

department: Neurobiology

institute: Boston Children's Hospital

data_processing:
Image analysis and base calling conducted by the Control software. Raw sequence data (.bcl files) generated by the sequencer were converted into fastq files and de-multiplexed using Illumina’s bcl2fastq 2.17 software. One mismatch was allowed for index sequence identification.
Reads were aligned to the human reference genome GRCh38 using STAR aligner v2.7.3a. SAMtools v.1.13 was used for indexing and picard to mark duplicates. Post-alignment, normalized bigWig files were generated for visualization, and quality control was performed using RSeQC.
Assembly: GRCh38
Supplementary files format and content: bigWig, mapped and normalized sequencing reads, for visualization

source_name: skin

growth_protocol: Cells were maintained in DMEM (Corning 10-013-CV) supplemented with 10% FBS (Life Technologies 10439-024), penicillin 100U/ml and streptomycin 100μg/ml (Gibco, #15140122), L-Glutamine (Thermo Fisher scientific, 25-030-08) with final concentration of 2mM, sterile filtered by 0.22 μm PES-Filter (Celltreat, 229707). Cells were maintained in the media described above at 37°C and 5 % CO2 in 10 cm culture dishes.

extract_protocol:
For RNA sequencing, cells were processed as described previously until centrifugation. The cell pellet was snap-frozen in PBS using liquid nitrogen.
RNA sequencing libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina using the manufacturer’s instructions (New England Biolabs).

value: skin

value: fibroblasts


title: C17

description: C35-LMY-human peripheral blood

value: leukocytes

value: male

value: healthy control


title: Control_RNA

value: control


title: Pancreatic bud, Control_3

value: DMSO


title: C18

description: C36-LY-human peripheral blood


title: Long ascending propriospinal neurons 3

description: Library name: LAPNs 3

value: Spinal neurons

value: Postnatal day 8


title: C19

description: C38-WY-human peripheral blood

value: female


title: CD14+CD16+ monocytes, Young Adult with co-morbid conditions,WGP stimulated -2


title: CD14+CD16+ monocytes, Young Adult with co-morbid conditions,WGP stimulated -1


title: Pancreatic bud, Control_2

value: Pancreatic bud


title: C16

description: C32-LZP-human peripheral blood


title: Long ascending propriospinal neurons 1

description: Library name: LAPNs 1


title: Pancreatic bud, Control_1


title: CD14+CD16+ monocytes, Young Adult with co-morbid conditions, Control - 3


title: C15

description: C31-ZY-human peripheral blood


title: r22_r38_CD45+_salivary glands_scRNAseq

city: Shinjuku-ku

first: Mana

last: Iizuka

address: 35 Shinanomachi

institute: Keio University School of Medicine

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.2.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Salivary glands

extract_protocol:
For isolation of CD45+ cells in the salivary glands, tissue was cut into small pieces, digested by 2 mg/ml collagenase type II (Worthington Biochemical Corp) and homogenized. The suspension was purified by centrifugation using Lympholyte-M solution (Cedarlane) according to the manufacturer’s protocol. Totalseq-Hashtag antibody (BioLegend) was incubated with each sample, and CD45+ cells were sorted by FACSAriaIII (Becton Dickinson).
Libraries were prepared according to the protocol of the Chromuim Next GEM Single Cell 5' Reagent Kits v2 (10x Genomics) using a Chromium controller (10x Genomics).

value: Salivary glands

value: primary cell


title: CD14+CD16+ monocytes, Young Adult with co-morbid conditions, Control - 2


title: CD14+CD16+ monocytes, Young Adult with co-morbid conditions, Control - 1


title: KO BMDMS LPS24H-3

first: zilong

last: xiao

address: Xietu Road1609, Xuhui District

department: cardiology

institute: fudan university

data_processing:
Raw reads of fastq format were firstly processed using fastp 1 and the low quality reads were removed to obtain the clean
The clean reads were mapped to the reference genome using HISAT2
FPKM3 of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample
Supplementary files format and content: tab-delimited text file includes Counts values for each sample

source_name: BMDMs

growth_protocol: BMDMs were maintained in DMEM Supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin.

extract_protocol:
RNAs were extracted with TRIzol reagent. 1.5ug of total RNA was used for the constriction of sequencing libraries
VAHTS Total RNA-seq (H/M/R) Library Prep Kit (Vazyme, China)  was used to construct RNA-seq strand-specific libraries

treatment_protocol: BMDMs were activated with LPS for 24 hours

value: BMDMs

value: bone marrow-derived macrophages


title: C14

description: C30-DK-human peripheral blood

value: blood


title: EED KO+F-C-KR EED EBday2_FLAG_rep2

first: Shinsuke

last: Ito

address: 1-7-22 Suehirocho

department: IMS

institute: RIKEN

description: Library name: Sample 16

data_processing:
Reads were aligned to UCSC mm9 or UCSC mm10 using bowtie2. The SAM files were converted to the BAM format using Samtools. The PCR duplicates were removed by Picardtools. The BAM files were converted to bigwig files by deepTools2 for visualization. The bigwig files were normalized to reads per million mapped sequence reads (RPKM).
Assembly: mm9
Supplementary files format and content: bigwig

source_name: mouse embryonic stem cells

growth_protocol: Embryonic stem cells were cultured in DMEM supplemented with 20% fetal bovine serum, GlutaMax, MEM nonessential amino acids, 2-mercaptoethanol, GlutaMax and LIF on MEF feeder layers at 37°C in a 5% CO2 incubator.

extract_protocol:
For mESCs, 10^6-10^7 cells were cross-linking by 1% formaldehyde for 10 min at room temperature. Cross-linked cells were washed once with PBS, added swelling buffer (0.1% NP-40, 1 mM DTT in PBS) and chilled on ice for 10 minutes. After centrifuge, pellets were suspended with RIPA buffer (10 mM Tris-HCl pH8.0, 1mM EDTA, 140 mM NaCl, 1%Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate), and then were sonicated by using a BioRuptor sonicator (Diagenode).  On the other hand, protein A/G beads were prepared as washed twice with beads blocking buffer and suspended with beads blocking buffer with approximately 5 µg of antibody and incubated at 4ºC for more than 2 hours. Then, antibody attached beads were washed twice with beads blocking buffer and the chromatin samples were added to those antibody-attached-beads. After overnight incubation at 4ºC, chromatin samples bound beads were washed with RIPA for 2 times, RIPA high salt buffer(10 mM Tris-HCl pH8.0, 1mM EDTA, 500 mM NaCl, 1%Triton X-100, 0.1% SDS, 0.1% Sodium Deoxycholate) twice, LiCl buffer (10 mM Tris-HCl pH8.0, 1 mM EDTA, 250 mM LiCl, 0.5% NP-40, 0.5% Sodium Deoxycholate) twice and TE twice. The chromatins were eluted with elution buffer (10 mM Tris-HCl pH8.0, 5 mM EDTA, 300 mM NaCl, 0.1 % SDS) overnight at 65ºC and treated with RNase for 30 min for 37°C and further incubation with Proteinase K for 1 hour at 37ºC. Then DNA samples were purified and used for further  ChIP-seq.
ChIP-seq libraries were prepared by using NEBNext Ultra II FS DNA prep kit (NEB E7805) following manufacturer’s instruction.

treatment_protocol: For induction of conditional KO ESCs, 800 nM (final concentration) 4-OH Tamoxifen (SIGMA) dissolved in ethanol was added into the culture medium.  To inhibit the proteasome activity, 10 µM MG132 was added to ES medium for 3 hours.

value: mouse embryonic stem cells

value: Tamoxifen+

value: EED KO

value: anti-FLAG (Sigma, F7425)


title: C13

description: C29-MZZ-human peripheral blood

value: leukocytes

value: male


title: KO BMDMS LPS24H-1


title: EED KO+F-C-KR EED EBday2_FLAG_rep1

description: Library name: Sample 15


title: C11

description: C26-MXY-human peripheral blood

value: healthy control


title: WT BMDMS LPS24H-3

value: WT


title: C12

description: C28-PYW-human peripheral blood


title: KO BMDMS LPS24H-2


title: CD14+CD16+ monocytes, Older Adult with co-morbid conditions,WGP stimulated -2

value: PBMC

value: CD14+CD16+ monocytes

value: Whole Glucan Particle


title: C10

description: C25-LGZ-human peripheral blood


title: EED KO+F-WT EED EBday2_FLAG_rep1

description: Library name: Sample 11


title: CD14+CD16+ monocytes, Older Adult with co-morbid conditions,WGP stimulated -4


title: WT BMDMS LPS24H-2


title: EED KO+F-WT EED EBday2_FLAG_rep2

description: Library name: Sample 12


title: EED KO+F-N-KR EED EBday2_FLAG_rep1

description: Library name: Sample 13


title: CD14+CD16+ monocytes, Older Adult with co-morbid conditions,WGP stimulated -1


title: C9

description: C24-WBQ-human peripheral blood


title: EED fl/fl EBday2 FLAG_rep2

description: Library name: Sample 10

value: Tamoxifen-


title: WT BMDMS LPS24H-1


title: CD14+CD16+ monocytes, Older Adult with co-morbid conditions, Control - 4


title: EED fl/fl EBday2_FLAG_rep1

description: Library name: Sample 9


title: C8

description: C23-LJ-human peripheral blood


title: lung nornal organoids cells, Control, 7 days_scATAC

first: Carle

middle: F.

last: Kim

state: MA

address: 300 Longwood Avenue

library_source: genomic single cell

data_processing:
Cellranger-arc (v 2.0.1) mkfastq was used to demultiplexes raw base call data to fastq files, and then cellranger-arc count program was used to map single-cell RNA and single-cell ATAC reads to the mm10 mouse reference genome. The cell-by-gene expression matrix was generated for the scRNA-seq data and the fragment files were generated for the scATAC-seq data as the outputs.
The scRNA-seq matrix was loaded into Seurat (v4.0, Ref: pmid 34062119) package in R for further quality control and processing. We applied the following filtrations at the per-cell level to keep the high-quality cells: number of gene > 200 & number of reads > 2500 & percent of mitochondrial reads < 10%. Cell cycle scores were regressed out during data scaling following the vignette of Seurat. For clustering, we took the first 2000 variable genes and performed PCA dimension reduction, followed by graph-based clustering and UMAP visualization using the top 60 principal components.
For the scATAC analysis, we utilized the ArchR package (v1.0, Ref: pmid 33633365) to read in the fragment files, and then performed quality controls by requiring the minimal number of fragments to be 1000 and the minimal TSS enrichment to be 4. Dimension reduction was carried out using iterative LSI (Latent Semantic Indexing) with the 500 bp tile matrix generated by ArchR. The parameters of iterative LSI were set as follows: iterations=3, resolution=0.2 and varFeatures= 50000. The ATAC cells were visualized using UMAP with the first 30 PCs from iterative LSI. Cell states annotation was based on both scRNA and scATAC signature as described in the main text.
Assembly: mm10
Supplementary files format and content: RNA gene-by-cell matrix
Supplementary files format and content: ATAC fragments

source_name: lung normal organoids

extract_protocol:
Cells were resuspended in 3D media (Dulbecco’s Modified Eagle’s Medium/F12 (Invitrogen) supplemented with 10% FBS, penicillin/streptomycin, 1 mM HEPES, and insulin/transferrin/selenium (Corning)) at a concentration to be 100,000cells/1ml. Neonatal lung mesenchymal cells were used as supporting cells as previously described. The mesenchymal cells were suspended in growth factor reduced (GFR) Matrigel at a concentration of 1000,000cells/1ml. Mix the same volume of cell/3D media mixture and mesenchymal cell/Matrigel mixture and pipetted several times before adding 100µl mixture into a Transwell (Corning). Solidify the mixture for 20 min at 37°C, 5% CO2. Add 500µl 3D media into the bottom of the transwell. Change the media every other day.
Single cells from tumor organoids were used for nuclei isolation. Then the nuclei suspension was incubated with Transposition mix (10X Genomics) for DNA fragmentation in the open chromatin region. Then the transposed Nuclei were encapsulated on a 10X Genomics Chromium Controller with Chromium Next GEM Chip J. After pre-amplification, the RNA library and ATAC library are prepared separately. Quality control of RNA and ATAC libraries were run on the Agilent TapeStation High Sensitivity D5000 ScreenTape System, performed by Biopolymers Facility at Harvard Medical School. Libraries were sequenced by Bauer Core Facility of Harvard university using NovaSeq 6000 System.

value: lung normal organoids

value: Normal alveolar type 2 cells

value: wildtype

value: Infected with Adeno-CMV-Empty


title: CD14+CD16+ monocytes, Older Adult with co-morbid conditions, Control - 3


title: EED KO+F-C-KR EED ES_FLAG_rep2

description: Library name: Sample 8


title: CD14+CD16+ monocytes, Older Adult with co-morbid conditions,WGP stimulated -3


title: EED KO+F-N-KR EED EBday2_FLAG_rep2

description: Library name: Sample 14


title: CD14+CD16+ monocytes, Older Adult with co-morbid conditions, Control - 2


title: C6

description: C21-GPH-human peripheral blood

value: blood


title: CD14+CD16+ monocytes, Older Adult with co-morbid conditions, Control - 1


title: Lung tumor organoids cells, Cre induced, 7days_scRNA

source_name: lung tumor organoids

value: lung tumor organoids

value: induced alveolar type 2 cells

value: Infected with Adeno-CMV-Cre


title: Lung tumor organoids cells, Cre induced, 7days_scATAC


title: C4

description: C18-YP-human peripheral blood


title: EED KO+F-N-KR EED ES_FLAG_rep1

description: Library name: Sample 5

value: mouse embryonic stem cells

value: Tamoxifen+

value: EED KO

value: anti-FLAG (Sigma, F7425)


title: C5

description: C20-ZDD-human peripheral blood

value: leukocytes

value: female

value: healthy control


title: CD14+CD16+ monocytes, HIV infected Young Adult, WGP stimulated - 3

value: PBMC

value: CD14+CD16+ monocytes

value: Whole Glucan Particle


title: EED KO+F-WT EED ES_FLAG_rep2

description: Library name: Sample 4


title: CD14+CD16+ monocytes, HIV infected Young Adult, WGP stimulated - 4


title: Bone marrow - Txnip-KO3

city: Shanghai

first: Xiankun

last: Cao

address: Zhizaoju load No.639

department: orthopedic

institute: Shanghai Ninth People's Hospital affiliated to Shanghai Jiao tong University School of Medicine

description: 10x Genomics

data_processing:
Basecalls performed using CASAVA version 1.8
cellranger (v6.1.1) was utilized to calculate the feature-barcode matrices. Cells contained over 200 expressed genes and mitochondria UMI rate below 20%  passed the cell quality filtering and mitochondria genes were removed in the expression table.   Seurat package (version: 2.3.4 , https://satijalab.org/seurat/) was used for cell normalization and regression based on the expression table according to the UMI counts of each sample and percent of mitochondria rate to obtain the scaled data.   PCA was constructed based on the scaled data with top 2000 high variable genes and top 10 principals  were used for tSNE construction and UMAP construction. Utilizing graph-based cluster method, we acquired the unsupervised cell cluster result based the PCA top 10  principal and we calculated the marker genes by FindAllMarkers function with wilcox rank sum test algorithm under following criteria:1. lnFC > 0.25; 2. pvalue<0.05; 3. min.pct>0.1.
Assembly: GRCm38Ensembl100
Supplementary files format and content: MTX file and TSV file contain counts for each barcodes and genes

source_name: Bone marrow

growth_protocol: Bones were harvested, samples were first washed with phosphate-buffered saline (PBS), bone marrow was flushed, samples were sieved through a 70µm cell strainer, and centrifuged at 300g for 5 min

extract_protocol:
Single-cell gel beads in emulsion (GEMs) were generated on a GemCode Single Cell Instrument (10x Genomics). Single-cell RNA-seq cDNA libraries were prepared using Chromium™ Single Cell 3’ V3.1 Reagent Kits (10x Genomics) according to manufacturer's protocol.
RNA libraries were generated by 10xGenomics Single Cell 3’ V3 Library Gel Bead Kit and prepared for sequencing using standard Illumina protocols

treatment_protocol: Bone marrow cells were then sieved, enriched, and finally isolated by Fluorescence-activated cell sorting (FACS) to get specific cells that we were interested in.

value: Bone marrow

value: Txnip-KO


title: CD14+CD16+ monocytes, HIV infected Young Adult, WGP stimulated - 2


title: C2

description: C15-SDZ-human peripheral blood

value: male


title: CD14+CD16+ monocytes, HIV infected Young Adult, WGP stimulated - 1


title: Bone marrow - Txnip-KO1

description: 10x Genomics


title: Bone marrow - Txnip-KO2

description: 10x Genomics


title: EED KO+F-WT EED ES_FLAG_rep1

description: Library name: Sample 3


title: C7

description: C22-ZXS-human peripheral blood

value: blood


title: lung nornal organoids cells, Control, 7 days_scRNA

value: lung normal organoids

value: Normal alveolar type 2 cells

value: wildtype

value: Infected with Adeno-CMV-Empty


title: C1

description: C13-LXY-human peripheral blood


title: Bone marrow - WT3

description: 10x Genomics


title: EED KO+F-C-KR EED ES_FLAG_rep1

description: Library name: Sample 7

value: mouse embryonic stem cells

value: Tamoxifen+


title: EED fl/fl ES_FLAG_rep1

description: Library name: Sample 1

value: Tamoxifen-

value: WT

value: anti-FLAG (Sigma, F7425)


title: J.gamma1, USP20, CUT&Tag rep2

city: Suzhou

first: Zimu

last: Zhang

state: Jiangsu

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
*library strategy: CUT&Tag
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. CUT&Tag reads were trimmed using Fastp v0.23.2 with default settings, and were aligned to the UCSC hg38 genome using Bowtie2 version v2.4.4 with parameter --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Peaks were identified using MACS3 (v3.0.0a6) with the significance cut-off FDR<0.01
bigWig files were generated using bedGraphToBigWig tool. narrowPeak files were generated using MACS v3 with default settings.
Assembly: hg38
Supplementary files format and content: bigwig files

source_name: cell line

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

value: cell line

value: T-ALL cells

tag: antibody

value: USP20(Proteintech, #17491-1-AP)


title: CD14+CD16+ monocytes, HIV infected Young Adult, Control - 3

value: PBMC

value: CD14+CD16+ monocytes


title: EED KO+F-N-KR EED ES_FLAG_rep2

description: Library name: Sample 6

value: EED KO


title: Bone marrow - WT2

description: 10x Genomics

value: Bone marrow


title: J.gamma1, USP20, CUT&Tag rep1


title: C3

description: C17-ZYQ-human peripheral blood

value: blood

value: leukocytes

value: male

value: healthy control


title: Bone marrow - WT1

description: 10x Genomics

value: wildtype


title: CD14+CD16+ monocytes, HIV infected Young Adult, Control - 2


title: CD14+CD16+ monocytes, HIV infected Young Adult, Control - 1


title: CD14+CD16+ monocytes, HIV infected Older Adult, WGP stimulated - 4

value: Whole Glucan Particle


title: J.gamma1 shUSP20_rep2 [USP20]

data_processing:
Illumina Casava2.19 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using hisat2 v2.2.0 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Transcripts per Kilobase of exon model per Million mapped reads (TPM) were calculated using a methodology adapted from the StringTie software. In brief, all isoforms of a gene were assembled and merged to generate a composite transcript model. The number of reads mapped to the exonic regions of this composite transcript model was tallied and subsequently normalized. Normalization was achieved by dividing the read count by the length of the composite transcript model (in kilobases) and then scaling the result by the size of the total mapped library (in millions of reads).
Assembly: hg38
Supplementary files format and content: Tab-delimited text file includes readcount values for each Sample.

extract_protocol:
Cells were harvested, and total RNA was extracted with TRIzol (Invitrogen) according to the manufacturer's protocol. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols.


title: CD14+CD16+ monocytes, HIV infected Older Adult, WGP stimulated - 3


title: J.gamma1 shUSP20_rep1 [USP20]


title: MLCKtg-5-CONV

city: Taipei

first: Linda

last: Yu

address: 1 Jen-Ai Rd. Sec. 1

country: Taiwan

institute: National Taiwan University

data_processing:
The library was loaded onto the instrument with Sequel Sequencing Kit 2.1 (4 rxn) (Part Number PB 101-310-500) and a Sequel™ SMRT® Cell 1M v2 Tray (4 cells) (Part Number PB101-008-000) for sequencing.
Library strategy: 16S ribosomal RNA (rRNA) metagenome

source_name: feces metagenome

extract_protocol:
Fecal pellets were collected aseptically and placed in sterile eppendorf. Immediately freezing stool in liquid nitrogen (LN) and store at -80°C. Extract stool bacterial DNA followed by QIAamp Fast DNA Stool Kit  protocol
For the PacBio library construction and sequencing, 16S rRNA was amplified by using primer set 27F: AGRGTTYGATYMTGGCTCAG and 1492R: RGYTACCTTGTTACGACTT followed by purification via binding to pre-washed AMPure PB beads (Part Number PB100-265-900)

treatment_protocol: Untreated

value: MLCKtg

value: Ten weeks old, conventionally raised

value: Untreated


title: CD14+CD16+ monocytes, HIV infected Older Adult, WGP stimulated - 2


title: J.gamma1 shNC_rep2 [USP20]

value: shNC


title: MLCKtg-4-CONV


title: EED fl/fl ES_FLAG_rep2

description: Library name: Sample 2

value: mouse embryonic stem cells

value: Tamoxifen-

value: WT

value: anti-FLAG (Sigma, F7425)


title: CD14+CD16+ monocytes, HIV infected Older Adult, WGP stimulated - 1

value: PBMC

value: CD14+CD16+ monocytes


title: J.gamma1 shNC_rep1 [USP20]

value: T-ALL cells


title: CD14+CD16+ monocytes, HIV infected Young Adult, Control - 4


title: MLCKtg-3-CONV


title: CD14+CD16+ monocytes, HIV infected Older Adult, Control - 4


title: MLCKtg-2-CONV


title: A549 cells,Overexpression,PGC-1α

city: Dalian

first: Tianyi

address: No. 9, West Section of Lvshun South Road

institute: The First Affiliated Hospital of Dalian Medical University

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 on containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the down stream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
The mapped reads of each sample were assembled by both Scripture (beta2) (Guttman et al. 2010) and Cufflinks (v2.1.1) (Trapnell et al. 2010) in a reference-based approach. Both methods use spliced reads to determine exons connectivity, but with two different approaches. Scripture uses a statistical segmentation model to distinguish expressed loci from experimental noise and uses spliced reads to assemble expressed segments. It reports all statistically expressed isoforms in a given locus. Cufflinks uses a probabilistic model to simultaneously assemble and quantify the expression level of a minimal set of isoforms that provides a maximum likelihood explanation of the expression data in a given locus (Cabili et al. 2011). Scripture was run with default parameters, Cufflinks was run with ‘min-frags-per-transfrag=0’ and ‘--library-type’, other parameters were set as default.
Cuffdiff (v2.1.1) was used to calculate FPKMs of both lncRNAs and coding genes in each sample (Trapnell, C. et al. 2010). Gene FPKMs were computed by summing the FPKMs of transcripts in each gene group. FPKM means fragments per kilo-base of exon per million fragments mapped, calculated based on the length of the fragments and reads count mapped to this fragment.
Cuffdiff provides statistical routines for determining differential expression in digital transcript or gene expression data using a model based on the negative binomial distribution (Trapnell, C. et al. 2010). Transcripts with an P-adjust <0.05 were assigned as differentially expressed.
Assembly: human NCBI genome build 38
Supplementary files format and content: raw counts for each Sample
Supplementary files format and content: FPKM values for each Sample

source_name: lung

growth_protocol: A549 cells were maintained at standard culture conditions (37°C, 5% CO2) in F12K medium with 10% FBS.

extract_protocol:
RNA was harvested using TRIzol and cleaned using RNAeasy Kit (Qiagen). 4 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung

value: lung cancer cells

value: PGC-1alpha overexpression


title: MLCKtg-1-CONV


title: J.gamma1, HIF1a, CUT&Tag rep2

value: cell line

value: HIF1a(Proteintech, #20960-1-AP)


title: A549 cells,Overexpression,Control

value: control


title: CD14+CD16+ monocytes, HIV infected Older Adult, Control - 2


title: MCF-7, siCOL18AS-5 (siBNAT1 #B)

type: RNA

city: Hidaka

first: Kazuhiro

last: Ikeda

state: Saitama

address: 1397-1 Yamane

institute: Saitama Medical University

description: MCF-7 cells treated with siRNA targeting BNAT1/COL18A1-AS1 (siBNAT1 #B/siCOL18AS-5)

hyb_protocol: Following fragmentation, 4 micrograms of cRNA were hybridized for 16 hr at 45C on Affymetrix GeneChip (Clariom D Assay, human). GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: The samples were scanned on a GeneChip Scanner 3000 7G (Affymetrix).

data_processing: The microarray data were preprocessed with Affymetrix Expression Console software using Affymetrix default Robust Multichip Analysis (RMA) sketch algorithm workflow.

label: biotin

source_name: breast cancer MCF7 cells

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 150 ng total RNA.

growth_protocol: Human breast cancer MCF7 cells were maintained in Dulbecco's modified Eagle's medium (DMEM).

extract_protocol: Total RNA was extracted using ISOGEN reagent (Nippon Gene, Japan).

treatment_protocol: MCF7 cells were transfected with siRNAs targeting BNAT1/COL18AS (siCOL18AS-1 and siCOL18AS-5, or siBNAT1 #A and #B, respectively) or control siRNA (siCtrl) for 48 hours.

value: siBNAT1 #B


title: J.gamma1, HIF1a, CUT&Tag rep1


title: IHESCs, NMI Knockdown, IFNα treatment, Replicate 3

city: HOUSTON

first: Sang

middle: Jun

last: Han

state: Texas

address: One Baylor Plaza

department: Molecular Cellular Biology

institute: Baylor College of Medicine

data_processing:
Galaxy version 23.1.rc1
Sequence reads were trimmed for adpotor sequence/low-quality sequence using Galaxy version 23.1.rc1
Trimmed sequence reads were mapped to hg38 using Galaxy version 23.1.rc1
Read count extraction normalization were performed using Galaxy version 23.1.rc1
Assembly: hg83
Supplementary files format and content: tab-delimited text file includes raw count for each sample.

source_name: IHESCs

growth_protocol: The cells were maintained in F12/DMEM supplemented with 10% FBS and antibiotics in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was extracted using Rneasy plus mini kit (Qiagen). 100ng of RNA was used to prepare sequencing libraries.
The Sample Quality was checked by using the NanoDrop spectrophotometer, Invitrogen Qubit 2.0 quantitation assay and Agilent Bioanalyzer. Library was prepared by using Illumina TruSeq Stranded mRNA library preparation protocol.

treatment_protocol: Cells were treated with vehicle or IFNA for 24hours.

value: IHESCs

value: Human endometriotic stromal cells

value: NMI knockdown

value: IFNα


title: ChIP_seq_pSTAT3_Olap

city: Xiamen

first: Qing

last: Li

address: School of Life Sciences, Xiang'an Campus, Xiamen University, Xiang'an District

institute: xiamen university

data_processing:
Basecalling was performed using CASAVA version 1.4
Sequenced reads were aligned to the Hg38 human reference genomes using Bowtie2 (v2.3.4.1) and generated SAM files were converted to BAM files using Samtools (v.1.9)  using the view function.
Samtools was used to further sort, index and Picard tool MarkDuplicates (http://picard.sourceforge.net) was used to remove potential PCR duplicates from BAM files with the default parameters which were converted to BigWig files using Deeptools. BigWig files were visualized using the Integrative Genomics Viewer (Broad Institute).
HOMER suit of tools was used. Aligned bam files were subjected to peak calling using findPeaks tools with the -style factor.
Assembly: hg38
Supplementary files format and content: BigWig files were generated using deeptools and were visualized using the Integrative Genomics Viewer (Broad Institute).

growth_protocol: SUM159 cells were cultured in Ham’s F12 medium supplemented with 10% FBS, 5 mg/mL insulin and 1 mg/mL hydrocortisone in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were washed once with cold PBS prior to cross-linking with 2 mM DSG for 45 minutes followed by 1% formaldehyde (28908, Thermo) for 15 min at room temperature (except for the etoposide ChIP of TOP2A, cells were treated with 100mM etoposide for 10min). To quench the cross-linking reaction, 2.5 M glycine dissolved in PBS was added and cells were incubated at room temperature for a further 5 minutes. Cells were washed twice with ice-cold PBS and lysed using cell lysis buffer (50 mM Tris pH 8.0, 0.5% NP40, 50 mM NaCl) to remove the cytoplasmic proteins. The pellet was resuspended in nuclear lysis buffer (1% Triton X-100, 2 mM EDTA pH 8.0, 400 mM NaCl, 20 mM Tris pH 8.0, 0.1% SDS). Chromatin DNA was sheared to 300–500 bp average in size through sonication using a Bioruptor instrument (Diagenode). Fragmented chromatin was diluted 1:1 with dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100) and immunoprecipitated with IgG or indicated specific antibodies overnight at 4°C, followed by incubation with protein A/G magnetic Dynabeads for 4 h. Dynabeads were washed once each with ChIP wash buffer 1 (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100) and ChIP wash buffer 2 (20 mM Tris pH 8.0, 400 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100) and washed twice with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA pH 8.0). After washing and elution, the protein–DNA complex was reversed by heating overnight at 65°C. Immunoprecipitated DNA was purified by QIAquick spin columns. Sequencing libraries were prepared using the KAPA DNA HyperPrep Kit and subjected to high-throughput sequencing.
Sequencing libraries were prepared using the KAPA DNA HyperPrep Kit and subjected to high-throughput sequencing. Briefly, Chip DNA was end-blunted and added with an ‘A’ base. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

treatment_protocol: Cells were infected with indicated lentivirus and/or treated with indicated drugs.

value: breast cancer

value: Phospho-Stat3 (Tyr705)  (CST, 9145)

value: 10 μM Olaparib

value: 3 days


title: MCF-7, siControl

description: MCF-7 cells treated with control siRNA (siCtrl).

value: siCtrl


title: CD14+CD16+ monocytes, HIV infected Older Adult, Control - 1

value: PBMC

value: CD14+CD16+ monocytes


title: B6-4-CONV

value: Ten weeks old, conventionally raised

value: Untreated


title: CD14+CD16+ monocytes, Healthy Young, WGP stimulated - 4

value: Whole Glucan Particle


title: B6-3-CONV


title: WGS_Case5_post

data_processing:
Basecalling was performed using CASAVA version 1.4
Sequenced reads were mapped to the Hg38 human reference genomes using BWA (v0.7.17) and generated SAM files were converted to BAM files using Samtools (v.1.5) using the view function.
Samtools was used to further sort, index and Picard tool MarkDuplicates (http://picard.sourceforge.net) was used to remove potential PCR duplicates from BAM files with the default parameters.
Mapped reads were processed using GATK (v4.1.7) pipeline commands HaplotypeCaller, VariantFiltration, SelectVariants, BaseRecalibrator, ApplyBQSR, and HaplotypeCaller to identify variants. High quality SNPs were filtered using the filter expression: “QD < 2.0 || MQ < 40.0 || FS >60.0 || SOR> 3.0 || MQRankSum < −12.5 || ReadPosRankSum <−8.0”, High quality Indels were filtered using the filter expression: “QD < 2.0 || FS > 200.0 || SOR > 10.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0” (McKenna et al., 2010).
Variants were annotated with Annovar (table_annovar.pl; ensGene, cytoBand, genomicSuperDups, rmsk, exac03, esp6500siv2_all, avsnp147, ALL.sites.2015_08, clinvar_202). Putative SNVs were then filtered using the following parameters: 1000G_ALL < 0.01, ExAC_ALL < 0.01, ESP6500siv2_ALL < 0.01, genomicSuperDups score < 0.9. Only mutations with nonsynonymous, stop/gain and stop/loss in exonic and splicing regions were kept as final SNVs.
CNVkit (v0.9.3) was used to call copy number from sorted BAM files. Copy number was called using batch mode with the drop-low-coverage option against the GRCh38.97 reference. Copy numbers were reported in log2 scale. Thresholds for calling copy number changes for homozygous and amplification were log2(0.2/2) and log2(8/2).
Assembly: hg38
Supplementary files format and content: csv files include mutation data for each Sample,cns files include copy number data for each sample.
Library strategy: Whole-genome seq

source_name: ovarian cancer tissue

extract_protocol:
Genomic DNA samples were extracted by TIANamp Genomic DNA kit.
A total amount of 0.2 μg DNA per sample was used as input material for the DNA library preparations. Sequencing library was generated using NEB Next® Ultra™ DNA Library Prep Kit for Illumina (NEB, USA) following manufacturer’s recommendations and index codes were added to each sample. Briefly, genomic DNA sample was fragmented by sonication to a size of 350 bp. Then DNA fragments were endpolished, A-tailed, and ligated with the full-length adapter for Illumina sequencing, followed by further PCR amplification. After PCR products were purified by AMPure XP system (Beckman Coulter, Beverly, USA), DNA concentration was measured by Qubit®3.0 Flurometer (Invitrogen, USA), libraries were analyzed for size distribution by NGS3K/Caliper and quantified by real-time PCR (3 nM). The clustering of the index-coded samples was performed on a cBot Cluster Generation System using Illumina PE Cluster Kit (Illumina, USA) according to the manufacturer’s instructions.

value: ovarian cancer tissue

value: PARPi-treatment (Niraparib)


title: WGS_Case5_pre

value: PARPi-naive


title: MCF-7, siCOL18AS-1 (siBNAT1 #A)

description: MCF-7 cells treated with siRNA targeting BNAT1/COL18A1-AS1 (siBNAT1 #A/siCOL18AS-1)

value: siBNAT1 #A


title: CD14+CD16+ monocytes, Healthy Young, WGP stimulated - 2


title: CD14+CD16+ monocytes, HIV infected Older Adult, Control - 3


title: B6-2-CONV


title: IHESCs, NMI Knockdown, Vehicle , Replicate 2

value: IHESCs

value: Human endometriotic stromal cells

value: Vehicle


title: B6-5-CONV


title: B6-1-CONV


title: WES_PDX_A5002

data_processing:
Basecalling was performed using CASAVA version 1.4
Sequenced reads were mapped to the Hg38 human reference genomes using BWA (v0.7.17) and generated SAM files were converted to BAM files using Samtools (v.1.5) using the view function.
Samtools was used to further sort, index and Picard tool MarkDuplicates (http://picard.sourceforge.net) was used to remove potential PCR duplicates from BAM files with the default parameters.
Mapped reads were processed using GATK (v4.1.7) pipeline commands HaplotypeCaller, VariantFiltration, SelectVariants, BaseRecalibrator, ApplyBQSR, and HaplotypeCaller to identify variants. High quality SNPs were filtered using the filter expression: “QD < 2.0 || MQ < 40.0 || FS >60.0 || SOR> 3.0 || MQRankSum < −12.5 || ReadPosRankSum <−8.0”, High quality Indels were filtered using the filter expression: “QD < 2.0 || FS > 200.0 || SOR > 10.0 || MQRankSum < -12.5 || ReadPosRankSum < -8.0” (McKenna et al., 2010).
Variants were annotated with Annovar (table_annovar.pl; ensGene, cytoBand, genomicSuperDups, rmsk, exac03, esp6500siv2_all, avsnp147, ALL.sites.2015_08, clinvar_202). Putative SNVs were then filtered using the following parameters: 1000G_ALL < 0.01, ExAC_ALL < 0.01, ESP6500siv2_ALL < 0.01, genomicSuperDups score < 0.9. Only mutations with nonsynonymous, stop/gain and stop/loss in exonic and splicing regions were kept as final SNVs.
CNVkit (v0.9.3) was used to call copy number from sorted BAM files. Copy number was called using batch mode with the drop-low-coverage option against the GRCh38.97 reference. Copy numbers were reported in log2 scale. Thresholds for calling copy number changes for homozygous and amplification were log2(0.2/2) and log2(8/2).
Assembly: hg38
Supplementary files format and content: csv files include mutation data for each Sample,cns files include copy number data for each sample.
Library strategy: Whole-exome seq

source_name: pancreatic cancer tissue

growth_protocol: OC316, HCC1937 cells were cultured in  RPMI1640 medium supplemented with 10% FBS in humidified atmosphere with 5% CO2 at 37C.

treatment_protocol: Cells were treated with indicated drugs.

value: pancreatic cancer tissue


title: CD14+CD16+ monocytes, Healthy Young, WGP stimulated - 1


title: IHESCs, NMI Knockdown, IFNα treatment, Replicate 2

value: NMI knockdown

value: IFNα


title: IHESCs, WT, IFNα treatment, Replicate 3

value: WT


title: CD14+CD16+ monocytes, Healthy Young, Control - 4


title: IHESCs, NMI Knockdown, Vehicle , Replicate 1


title: Albino type skin-2

city: Luoyang

first: Yanjie

last: Guo

state: Henan

address: 6# jiqing road

institute: Luoyang normal university

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic software.
Trinity was used to splice the clean reads.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Andrias davidianus

source_name: Skin

extract_protocol:
For mRNA sequencing, A total amount of 1.5 μg RNA per sample was used as input material for rRNA removal using the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA).
Sequencing libraries were generated using NEBNextR UltraTM Directional RNA Library Prep Kit for IlluminaR (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Skin

value: Albino type


title: ChIP_seq_pSTAT3_DMSO

value: breast cancer

value: Phospho-Stat3 (Tyr705)  (CST, 9145)

value: DMSO

value: 3 days


title: CD14+CD16+ monocytes, Healthy Young, Control - 3

data_processing:
The raw FASTQ files were executed for adaptor trimming and quality trimming using Cutadapt v1.18.
The trimmed fastq files were aligned to human genome reference (GRCh38.primary assembly) by using STAR/ 2.7.3a-foss-2018b
Raw counts were obtained using Subread/2.0.0-GCC-7.3.0-2.30 featureCounts package
Assembly: Human GRCh38.primary assembly
Supplementary files format and content: tab-delimited text file "count_None_WGP.txt" include the raw count values for all samples

value: PBMC

value: CD14+CD16+ monocytes


title: WES_PDX_USTC11

source_name: breast cancer tissue

value: breast cancer tissue


title: IHESCs, NMI Knockdown, IFNα treatment, Replicate 1


title: CD14+CD16+ monocytes, Healthy Young, WGP stimulated - 3

source_name: CD14+CD16+ monocytes

value: Whole Glucan Particle


title: IHESCs, NMI Knockdown, Vehicle , Replicate 3

value: IHESCs


title: Albino type skin-1


title: IHESCs, WT, IFNα treatment, Replicate 2

value: Human endometriotic stromal cells


title: CD14+CD16+ monocytes, Healthy Young, Control - 2


title: Wild type skin-1

value: Wild type


title: WES_PDX_A9007

value: pancreatic cancer tissue


title: CD14+CD16+ monocytes, Healthy Young, Control - 1


title: IHESCs, WT, IFNα treatment, Replicate 1


title: WES_HCC1937_SENS

value: 2-3 months


title: RNA-seq of Ywhaz-KO blastocysts (replicate 2)

city: Wuhan

first: Yuehan

address: No. 1095, Jiefang Ave.

institute: Huazhong University of Scicence and Technology

description:
Library name: si_Ywhaz_2
Pooled 5 Ywhaz-KO blastocysts, replicate 2 (si_Ywhaz_2_fpkm)

data_processing:
Raw reads were filtered using fastp (v0.18.0) to remove adapter sequences, low-quality reads (Q < 20), and reads with >10% unknown bases (N). rRNA contamination was removed by aligning to an rRNA database using Bowtie2 (v2.2.8). Clean reads were mapped to the mouse reference genome (GRCm39) using HISAT2 (v2.1.0). Gene expression quantification was performed using StringTie (v1.3.1) and RSEM to calculate FPKM values. Differential expression analysis between Ywhaz-KO and control groups was performed using DESeq2, and differentially expressed genes (DEGs) were identified using FDR < 0.05 and |log2FC| > 1 as the cutoff. Functional enrichment of DEGs was conducted using KEGG and Gene Ontology (GO) databases. Transcription factor annotation was also included.
Assembly: Mus musculus GRCm39 (Ensembl release)
Supplementary files format and content: Excel file (Ctrl-vs-si.all.annot.xls) containing FPKM values for each sample (Control_1, Control_2, si_Ywhaz_1, si_Ywhaz_2), along with log2 fold change, P value, FDR, gene symbols, annotations (KEGG/GO/TF). Each row represents a gene.

molecule: polyA RNA

source_name: embryo (blastocyst)

growth_protocol: Female C57BL/6 mice were superovulated, mated with males of the same strain, and embryos were harvested at the blastocyst stage. Embryos were cultured in vitro before RNA extraction.

extract_protocol:
Total RNA was extracted from each group of five blastocysts using the Trizol reagent (Life Technologies), following the manufacturer’s instructions. Homogenized embryos were lysed in 1 mL Trizol, followed by phase separation with chloroform and RNA precipitation using isopropanol. RNA quality was assessed by NanoDrop spectrophotometry and Agilent 2100.
RNA libraries were constructed using the Hieff NGS® Ultima Dual-mode mRNA Library Prep Kit (Yeasen, Cat#12309ES). mRNA was enriched using oligo(dT) magnetic beads, fragmented, and reverse transcribed into cDNA. After second-strand synthesis, cDNA was end-repaired, ligated with sequencing adapters, PCR amplified, and size-selected. Library quality was assessed using the Agilent DNA 1000 or High Sensitivity DNA assay kit.

treatment_protocol: Embryos in the knockout group were generated by CRISPR-Cas9 targeting of Ywhaz at the zygote stage. Control embryos were injected with Cas9 protein only.

value: embryo (blastocyst)

value: blastocyst

value: C57BL/6 Ywhaz knockout

value: CRISPR


title: IHESCs, WT, Vehicle, Replicate 2

value: WT

value: Vehicle


title: RNA-seq of Ywhaz-KO blastocysts (replicate 1)

description:
Library name: si_Ywhaz_1
Pooled 5 Ywhaz-KO blastocysts, replicate 1 (si_Ywhaz_1_fpkm)


title: WES_OC316_RES

value: ovarian cancer

value: 10 microM Olaparib


title: WES_PDX_LTL-313HR

source_name: prostate cancer tissue

value: prostate cancer tissue


title: ΔydcI replicate 3, sample 24

city: Cologne

first: Karin

last: Schnetz

address: Zuelpicher Str. 47a

department: Institute for Genetics

institute: University of Cologne

description: Library name: E.coli K12 strain U505 replicate 3

data_processing:
Galaxy platform was used for all data processing steps (https://usegalaxy.org/)
Sequences were aligned with Bowtie2 (Galaxy version 2.3.4.2) and default settings
Reads mapping to genes were counted with Htseq (Galaxy version 0.9.1) in union mode and a minimum alignment quality of 10 in addition to default settings
Differential expression of genes was tested using DESeq2 (Galaxy version 2.11.40.2) and default settings.
Assembly: GCA_000005845.2_ASM584v2
Supplementary files format and content: tab-delimited text file includes raw counts fo each sample

organism: Escherichia coli K-12

growth_protocol: For RNA extraction 10 ml of tryptone medium was inoculated to an OD600 of 0.05 using fresh overnight cultures, and grown at 37°C, while shaking, to OD600 of 0.8. 1.5 ml were harvested for RNA isolation.

extract_protocol:
Total RNA was extracted from 1.5 ml of culture using RNAprotect Bacteria Reagent (Qiagen, cat. No 76506) and RNeasy Mini Kit (Qiagen, cat. No 74134) with on column DNase I digestion (Qiagen, cat. No 79254), according to the manufacturer’s instructions (Qiagen, Germany).
Illumina TruSeq RNA Library Kit (with ribo-depletion, without Poly-A selection)

value: U4 delta-ydcI


title: IHESCs, WT, Vehicle, Replicate 3


title: ΔydcI replicate 2, sample 19

description: Library name: E.coli K12 strain U505 replicate 2


title: RNA-seq of WT blastocysts (replicate 2)

description:
Library name: Control_2
Pooled 5 WT blastocysts, replicate 2 (Control_2_fpkm)

value: C57BL/6 wild type


title: ΔydcI replicate 1, sample 14

description: Library name: E.coli K12 strain U505 replicate 1


title: Gut DBA/1_SpAD, biological rep3

city: Chihuahua

first: Susana

middle: Aideé

last: González-Chávez

state: Chihuahua

address: Circuito Universitario Campus II

department: Facultad de Medicina

country: Mexico

institute: Universidad Autónoma de Chihuahua

description: Gene expression data fromileocolic junction  of DBA/1 mice with Spontaneous arthritis

hyb_protocol: Following fragmentation, 5500 ng of fragmented and labeled ss-cDNA was hybridized for 16 or 18hr at 45°C on GeneChips Clariom™ D Assay, mouse. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using Affymetrix GeneChip Scanner 3000.

data_processing: The data were analyzed with the Transcriptome Analysis Console (TAC) using Affymetrix default analysis settings and global scaling as normalization method.

source_name: DBA/1 mice with Spontaneous arthritis

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 200 ng total RNA according User Guide: GeneChip WT PLUS Reagent Kit Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays.

extract_protocol: RNeasy Lipid Tissue Mini Kit extraction of total RNA was performed according to the manufacturer's instructions.

tag: condition

value: Spontaneous arthritis

value: 30 weeks

value: Ileocolic junction


title: IHESCs, WT, Vehicle, Replicate 1

value: IHESCs

tag: cell type

value: Human endometriotic stromal cells


title: Wild type skin-2

value: Skin

value: Wild type


title: RNA-seq of WT blastocysts (replicate 1)

description:
Library name: Control_1
Pooled 5 WT blastocysts, replicate 1. (Control_1_fpkm)

value: embryo (blastocyst)

value: blastocyst


title: WES_OC316_SENS

value: DMSO

value: 2-3 months


title: Gut DBA/1_SpAD, biological rep1

description: Gene expression data from ileocolic junction of DBA/1 mice with Spontaneous arthritis

tag: strain


title: WES_Case4_post

value: ovarian cancer tissue

tag: treatment

value: PARPi-treatment (Niraparib)


title: Gut DBA/1_SpAD, biological rep2


title: WES_Case4_pre

value: PARPi-naive


title: ΔlrhA replicate 2, sample 18

description: Library name: E.coli K12 strain U504 replicate 2

value: U4 delta-lrhA


title: WES_HCC1937_RES

value: breast cancer

value: 10 microM Olaparib