title: Single-cell 5' gene expressio  of Homo sapiens: ATL patient 3

status: Public on Apr 16 2025

city: Kumamoto

first: Osama

last: Hussein

state: Kumamoto Prefecture

address: 1-1-1 Honjo, Chuo-ku, Kumamoto City, Kumamoto Prefecture

department: Department of Haematology, Rheumatology, and Infectious Diseases

country: Japan

institute: Kumamoto University

description:
Library name: ATL3 5GE
10x Genomics

data_processing:
Demultiplexing was performed using Cell Ranger software. Gene expression analysis was carried out by aligning the reads to the human GRCh38 reference genome to which the HTLV-1 virus genome was added as an extra chromosome using the Cell Ranger Count pipeline. The TCR V(D)J dataset was analyzed using the Cell Ranger V(D)J pipeline, wherein the reads were aligned to the human GRCh38 reference dataset.
Assembly: Human GRCh38
Supplementary files format and content: Tab-seperated values file and matrix files

source_name: Blood

extract_protocol:
Blood samples were collected from ATL patients, and peripheral blood mononuclear cells (PBMCs) were isolated using Ficoll-Paque Plus (Cytiva). The isolated PBMCs were subsequently cryopreserved in liquid nitrogen for future analysis.
Single-cell gene expression and TCR immune profiling were performed using the Chromium Next GEM Single Cell 5' Reagent Kits v2 Dual Index (10x Genomics), following the manufacturer's protocols. Initially, thawed patient PBMCs were washed with complete RPMI medium supplemented with 10% FBS, counted, and resuspended in 1X PBS + 0.04% BSA at a final concentration of 1,000–1,200 cells/μl. GEMs were generated using Chromium Next GEM Single Cell 5ʹ Gel Bead Kit (Cat # PN-1000267) in the Chromium Controller using the Chromium Next GEM Chip K Single Cell Kit (Cat # PN-1000287). After GEM formation, the gel bead was dissolved and any co-partitioned cell was lysed. The transcripts present in the beads were barcoded and reverse-transcribed into full-length cDNA using Chromium Next GEM Single Cell 5' GEM Kit v2, (Cat # PN-1000266). The 10x barcoded, full-length cDNA was amplified by PCR, and the size distribution and the DNA concentration of the amplified cDNA were assessed using the Agilent Bioanalyzer High Sensitivity dsDNA kit. The amplified full-length cDNA was subsequently used for V(D)J amplification using the Chromium Single Cell Human TCR Amplification Kit (Cat # PN-1000252). Finally, both the 5' gene expression and the TCR V(D)J libraries were prepared using the Library Construction Kit (Cat # PN-1000196) following the manufacturer's protocols. The resulting libraries were sequenced using the DNBSEQ-G400RS platform.

value: Blood

value: PBMCs


title: Single-cell TCR V(D)J of Homo sapiens: ATL patient 3

type: SRA

description:
Library name: ATL3 TCR
10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell type

tag: age

tag: Sex

value: Male


title: Single-cell TCR V(D)J of Homo sapiens: ATL patient 2

description:
Library name: ATL2 TCR
10x Genomics


title: Iso-seq_Yeast_SynAZFa

city: Tianjin

first: Yue

last: Liu

address: 92 Weijin Road, Nankai District

country: China

institute: Tianjin University

description:
Iso-seq of SynAZFa in yeast.
Saccharomyces_R64_plasmid.fa

library_source: transcriptomic

data_processing:
The adapter and low-quality reads were filtered out through Trimmomatic (version 0.36). Clean reads were mapped to the reference genome by HISAT2 (version 2.1.0). PCR duplicates were removed using Samtools (version 1.3.1) and MACS2 software (version 2.1.1.20160309) was used to call peaks. The final mapped bam files were converted to the Bigwig format using bamCoverage for visualization in IGV.
Assembly: S288C with SynAZFa
Supplementary files format and content: tdf file
*data processing step
Library strategy: Iso-Seq

organism: Saccharomyces cerevisiae

extract_protocol:
ToFU (Transcript isOforms: Full-length and Unassembled; see Gordon et al. (2015)) was used for Iso-seq library preparation and sequencing to generate a de novo transcriptome.
RNA-seq library preparation followed standard procedures (for Illumina and PacBio, respectively).

tag: cell line


title: Single-cell 5' gene expressio of Homo sapiens: ATL patient 1

description:
Library name: ATL1 5GE
10x Genomics

value: Female


title: coculture 3

city: Shanghai

first: Chunyi

last: Shao

state: Shanghai

address: Number 639, Zhizaoju Road

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample3
Treg 3 in manuscript

data_processing:
Illumina Casava1.7 software used for basecalling.
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: GRCh38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: corneal limbus stem cells

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions

treatment_protocol: LSCs were cocultured with or without Tregs for 24 hours

value: corneal limbus stem cells

tag: treatment

value: cocultured with Tregs


title: coculture 2

description:
Library name: Sample2
Treg 2 in manuscript


title: control 1

description:
Library name: Sample4
control 1 in manuscript

value: control


title: control 3

description:
Library name: Sample6
control 3 in manuscript


title: disc cells, NT5

city: Shenzhen

first: Eric

last: Sun

address: 1120 Lianhua Rd

institute: Peking University Shenzhen Hospital

description: Library name: Sample11

data_processing:
Raw data (raw reads) of FASTQ format were firstly processed through BerryGenomics perl scripts.
Clean reads were obtained by removing following reads: (1) reads with adapter; (2) reads with more than 3 N; (3) reads with more than 20% nucleotides with Qphred<=5;
Map the clean reads to the silva database to remove the rRNA.
Assembly: GRCH38
Supplementary files format and content: Gene read counts excel for all samples

source_name: disc cells

growth_protocol: The disc cells were maintained in high glucose DMEM containing 10% fetal bovine serum supplemented with antibiotics. Cells at passage 4 were conditioned in alginate for re-differentiation prior to the treatment.

extract_protocol:
Total RNA was isolated from the cells using TRIzol plus RNA purification kit.
Library was prepared using SMARTER mRNA-seq Library Prep Kit

treatment_protocol: Serum starvation was performed for 24h prior to TGF-β1 (10ng/mL) treatment.

value: disc cells

tag: genotype

value: scramble


title: disc cells, MT8

description: Library name: Sample15

value: MMP12 knockdown


title: disc cells, MT5

description: Library name: Sample14


title: coculture 1

description:
Library name: Sample1
Treg 1 in manuscript


title: disc cells, NT2

description: Library name: Sample10


title: disc cells, MT2

description: Library name: Sample13


title: disc cells, N5

description: Library name: Sample8

value: untreated


title: disc cells, NT8

description: Library name: Sample12


title: K562_SRSF1_CUTnRUN_2_(20241016_WW1249_241007)

status: Public on Apr 17 2025

city: Seattle

first: Jorja

last: Henikoff

state: WA

address: 1100 Fairview AV N, A1-162

department: Basic Sciences

country: USA

institute: Fred Hutchinson Cancer Research Center

description:
Library name: K562_SRSF1_CUTnRUN_2
CUT&RUN targeting SRSF1  in K562

library_source: genomic

data_processing:
1. We used cutadapt 2.9 with parameters "-j 8 --nextseq-trim 20 -m 20 -a  AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -Z" to trim adapters from 50bp paired-end reads.
2. We used Bowtie2 2.4.4 with options "--very-sensitive-local --soft-clipped-unmapped-tlen --dovetail --no-mixed --no-discordant -q --phred33 -I 10 -X 1000" to map the paired-end 50bp reads to the hg19 Homo sapiens reference sequence obtained from UCSC.
3. We used samtools 1.14 "view" to extract properly paired reads from the hg19 alignments.
4. We made tracks in one of three ways with bedtools 2.30.0 "genomecov": (i) Fraction of counts at each base pair scaled by the size of the hg19 reference sequence (3095693983) so that if the counts were uniformly distributed across the reference sequence there would be one at each position (Supplementary file .hg19.bw) or (ii) Calibrated number of counts using a scaling factor of 10000/(number of fragments mapped to E.coli GCF_000005845.2_ASM584v2) (Supplementary file .hg19.spike.bw) or (iii) Raw number of counts using scaling factor of 1 which is the number of fragments aligned at each position (Supplementary file .hg19.raw_counts.bw).
Assembly: hg19
Supplementary files format and content: bigwig
Library strategy: CUT&Run

molecule: genomic DNA

tag: antibody

value: Fortis Life Sciences,  #A302-052A


title: mng_bap1_06

type: genomic

city: Heidelberg

first: Daniel

last: Schrimpf

address: Im Neuenheimer Feld 224

department: Neuropathology

country: Germany

institute: University Hospital Heidelberg, Intitute of Pathology

hyb_protocol: Illumina protocol

scan_protocol: Illumina iScan System according to the manufacturer's protocol

data_processing: Bioconductor (Version 3.3) package minifi (Version 1.18) using function 'preprocessIllumina'  Average beta

source_name: MNG BAP1

label_protocol: Illumina protocol

extract_protocol: Illumina protocol

treatment_protocol: An automated extraction was done with a Maxwell system (Promega, Fitchburg, WI, USA) and the Maxwell 16 FFPE Plus LEV DNA Purification Kit according to the manufacturer’s instructions.

tag: material

value: FFPE

tag: disease state

value: progressive

tag: outcome

value: dead


title: disc cells, T8

description: Library name: Sample6

value: WT


title: disc cells, T2

description: Library name: Sample4


title: disc cells, C8

description: Library name: Sample3


title: disc cells, T5

description: Library name: Sample5


title: disc cells, C5

description: Library name: Sample2


title: disc cells, C2

description: Library name: Sample1


title: Single-cell TCR V(D)J of Homo sapiens: ATL patient 1

description:
Library name: ATL1 TCR
10x Genomics


title: Single-cell 5' gene expressio  of Homo sapiens: ATL patient 2

description:
Library name: ATL2 5GE
10x Genomics


title: Huh 7 cell, PDCoV, 24 h, rep3

city: Jinzhong

first: Bo

last: Yang

state: Shanxi

address: No.1 Mingxian South Road，Taigu District, Jinzhong City, Shanxi Province

institute: Shanxi Agricultural University

description: Library name: Sample 6

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS(llumia) according to the manufacturer's instructions. After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Raw data (raw reads) offastq format were firstly processed through in-house perl scripts. Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built  and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
FeatureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: hg38
Supplementary files format and content: text file includes FPKM values for each sample

source_name: Liver, gallbladder

extract_protocol:
RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in 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 fiagments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments ofpreferentially 370~420 bp in length, the library fiagments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). 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: Liver, gallbladder

value: Huh 7

tag: infection

value: PDCOV


title: control 2

description:
Library name: Sample5
control 2 in manuscript


title: Huh 7 cell, PDCoV, 24 h, rep1

description: Library name: Sample 4


title: Huh 7 cell, PDCoV, 24 h, rep2

description: Library name: Sample 5


title: Huh 7 cell, Control, 24 h, rep3

description: Library name: Sample 3

value: NC


title: RNAseq_48h_INTS8_AID_Auxin_Plus_R3

city: Boston

first: Apoorva

last: Baluapuri

state: MA

address: 45 Shattuck St.

department: Biological Chemistry and Molecular Pharmacology

institute: Harvard Medical School

description: Library name: RNAseq_48h_INTS8_AID_Auxin_Plus_R3

data_processing:
Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 150 nt.
Samples were mapped to the Drosophila dm6 (spike) genome, and nonmapping reads subsequently mapped to hg38 using STAR 2.7.3a (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
Assembly: hg38
Supplementary files format and content: DESeq2 size normalized bigwigs and spreadsheets with normalized counts and associated analysis from DEseq2

source_name: embryonic kidney

growth_protocol: HEK293T cells were maintained in 5% FBS, 5% P/S DMEM

extract_protocol:
Cells were collected in Trizol, RNA was extracted, and genomic DNA contamination removed using DNAse.
rRNA depleted RNA was used as input to the NEB Next Ultra II Directional library prep kit using the manufacturer's protocol.

treatment_protocol: +/- Auxin (100 µM) 48h or untreated

value: embryonic kidney

value: homozygous miniAID

value: Auxin


title: Huh 7 cell, Control, 24 h, rep2

description: Library name: Sample 2


title: Huh 7 cell, Control, 24 h, rep1

description: Library name: Sample 1


title: RNAseq_48h_INTS8_AID_Auxin_Plus_R2

description: Library name: RNAseq_48h_INTS8_AID_Auxin_Plus_R2


title: RNAseq_48h_INTS8_AID_Auxin_Plus_R1

description: Library name: RNAseq_48h_INTS8_AID_Auxin_Plus_R1


title: disc cells, N8

description: Library name: Sample9


title: RNAseq_48h_INTS8_AID_Auxin_Minus_R3

description: Library name: RNAseq_48h_INTS8_AID_Auxin_Minus_R3


title: RBm24_3

city: Zhengzhou

first: Wang

last: Shuyuan

state: Hennan

address: 100 Science Avenue, High-tech Zone, Zhengzhou, China

department: Academy of Medical Sciences,

institute: Zhengzhou University

description: Library name: Sample 6

data_processing:
Raw reads containing more than 2-N bases were first discarded. Then adaptors and low-quality bases were trimmed from raw sequencing reads using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt were also dropped.
Clean reads were aligned to the GRCh38 genome by HISAT2, allowing four mismatches
Uniquely mapped reads were used for gene reads number counting and FPKM calculation (fragments per kilobase of transcript per million fragments mapped).
The alternative splicing events (ASEs) and regulated alternative splicing events (RASEs) between the samples were defined and quantified using the ABLas pipeline
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: CAL27 cells

extract_protocol:
Total RNA was extracted from the samples using Trizol reagent (Yeasan,China) as described in previous studies. These RNA samples were further purified using chloroform and isopropanol and then treated with RQ1 DNase (Promega) to remove DNA. Utilizing a Smartspec Plus (BioRad) instrument, the absorbance at 260/280 nm (A260/A280) was measured in order to assess the purity and quantity of the RNA.
Following the manufacturer's instructions,cDNA libraries were prepared for high-throughput sequencing and applied to the Illumina Novaseq 6000 system for 150 nt paired-end sequencing.

value: CAL27 cells

value: RBM24 overexpression in CAL27 cells


title: RNAseq_48h_INTS8_AID_Auxin_Minus_R1

description: Library name: RNAseq_48h_INTS8_AID_Auxin_Minus_R1


title: Ctrl_3

description: Library name: Sample 3

value: CAL27 cell(control plasmid)


title: RBm24_1

description: Library name: Sample 4


title: RNAseq_48h_INTS8_AID_Auxin_Minus_R2

description: Library name: RNAseq_48h_INTS8_AID_Auxin_Minus_R2


title: Ctrl_1

description: Library name: Sample 1


title: RBm24_2

description: Library name: Sample 5


title: RBM24_IP-2

description: Library name: Sample 4

data_processing:
Illumina NovaSea 6000 software used for basecalling
Adaptors and lowvquality bases were sheared using FASTX-Toolkit (Version 0.0.13) and reads less than 16 nt were filtered after discard more than 2-N bases from raw sequencing reads.
After reads were aligned onto the genome with HISAT2, the unique comparison on the genome was finally obtained, and the comparison result of PCR duplicate was removed
Then two software programs, Piranha and ABLIRC, were used to perform peak calling
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include reads counts for each Sample
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: CAL27 cells(IP)

extract_protocol:
CAL27 cells were irradiated once for 400 mJ/cm2, and lysed in ice-cold wash buffer. Cells lysis was performed in cold Wash buffer (1× PBS, 0.5% SDS, 0.5% NP-40 and 0.5% sodium deoxycholate) supplemented with a 400 U/mL RNase inhibitor (Takara) and protease inhibitor cocktail (Bimake) and incubate on ice for 30 min. Clear cell lysate by centrifugation at 10,000 rpm for 10 min at 4°C. Add RQ I (Promega, 1U/μl) to a final concentration of 0.1 U/μl and incubate in a heat block for 30 min at 37°C. Immediately afterward, a stop solution was added to the lysates to quench DNase. The mixture was then vibrated vigorously and centrifuged at 13,000 x g at 4℃ for 15 min to remove cell debris. Then RNA digestion by MNase (Thermo Scientific) was performed.
cDNA libraries were prepared with the KAPA RNA Hyper Prep Kit (KAPA, KK8541). According to the manufacturer's instructions, the libraries were constructed and used for 150 nt paired-end sequencing through the Illumina NovaSeq system.


title: Ctrl_2

description: Library name: Sample 2


title: RBM24_IP-1

description: Library name: Sample 3


title: disc cells, N2

description: Library name: Sample7

value: disc cells

value: scramble


title: RBM24_input-2

description: Library name: Sample 2

source_name: CAL27 cells(input)


title: RBM24_input-1

description: Library name: Sample 1


title: T2D.1.Isl.CD206+

city: Uppsala

first: Anders

middle: Roger

last: Hedin

state: Uppland

address: Dag Hammarskjölds väg 20.

department: Clinical immunology

country: Sweden

institute: Uppsala University

data_processing:
Read alignment with reference genome GRCh38 and quantification was performed at NGI Stockholm, using the Nextflow-based nf-core/RNAseq pipeline( doi: 10.5281/zenodo.1400710 ,doi: 10.1038/s41587-020-0439-x.., doi: 10.1038/nbt.3820. ).  Briefly summarized; FASTQ-files were merged and subsampled with fq. Strandness was inferred using Salmon(doi: 10.1038/nmeth.4197) and quality checked with FastQC(Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online].). UMIs were removed using UMI-tools(doi: 10.1101/gr.209601.116.) and adapter and quality trimming was performed using Trim Galore. Genome contaminants and ribosomal RNA were removed with BBSplit and SortMeRNA(doi: 10.1093/bioinformatics/bts611.) respectively. Reads were then aligned using STAR52 and quantified using Salmon53. In post-processing, SAMtools   (doi.org/10.1093/gigascience/giab008 ) was used to sort and index the reads, Picard MarkDuplicates was used to mark duplicate reads and BEDtools(doi: 10.1093/bioinformatics/btq033) genomecov was used to create bigWig coverage files. Transcript assembly and quantification was then carried out using StringTie(doi: 10.1186/s13059-019-1910-1.). Final QC was conducted using RSeQC(doi: 10.1093/bioinformatics/bts356.), Preseq(doi: 10.1038/nmeth.2375. ), Qualimap(doi: 10.1093/bioinformatics/btv566. Epub 2015 Oct 1.), dupRadar(doi: 10.1186/s12859-016-1276-2.), DESeq2(PMID: 25516281) and MultiQC(doi: 10.1093/bioinformatics/btw354.).
Salmon transcript abundance estimates were converted to estimated raw counts using DeSeq2. The estimated counts were rounded to the closest integer values. Estimated counts were analyzed using R (version 4.12) in RStudio.
Assembly: GRCh38
Supplementary files format and content: comma separated file(csv) that contains the estimated counts for each transcript and sample

source_name: Pancreatic Islet

extract_protocol:
Islet- and exocrine cell suspensions were washed in PBS followed by dissociation in 10 mL of Accutase for 20 minutes at room temperature. Cell clusters were frequently mechanically disaggregated with a P1000 pipette during dissociation. Cells were passed through a 40µm filter, collected in CMRL-1066 medium supplemented with human serum (10%) and DNase I (100 units/mL), and then washed in washing buffer (PBS with 2.5% FCS and 1mM EDTA). Cells were incubated with anti-CD64 antibody at 4 °C for 10 minutes. FC-receptor blocking agent was added at 4 °C for 10 minutes. Cells were incubated with anti-CD45, anti-HLA-DR and anti-CD206 antibodies at 4 °C for 30 minutes followed by two washes. Cells were then passed through a 20µm-filter. To evaluate pre-sorting CD206 expression and estimate total cell number, small aliquots of input samples were analyzed using a BD FACSVerse instrument. The remaining cells were resuspended in Tyto Running Buffer and loaded into a MacsQuant Tyto cartridge at an estimated concentration of 800,000 cells/mL. FACS data were analyzed using FlowJo software. Macrophages were identified by low-to-medium side scatter and positive staining for HLA-DR, CD45, and CD64. Macrophage subgroups were sorted sequentially using a MacsQuant Tyto instrument. First, CD206- macrophages were sorted from the islet- or exocrine sample, followed by reloading of the flow-through material and sorting of the CD206+ macrophage population. Starting tissue was alternated between donors. Cells passed through a 20 µm-filter within the sorting cartridge. The blue channel (HLA-DR staining) was used as trigger channel; the purple channel (CD45 staining) was used as speed channel. Samples were sorted at 8 °C and were then stored at 4 °C while the rest of the samples from the same donor were sorted. After all samples from one donor had been sorted, post-sorting analyses were performed using a BD FACSVerse instrument, consuming some cells (roughly 25% per sample). The remaining cells were lysed in buffer RLT+ (a component of the Qiagen Allprep DNA/RNA Micro kit), homogenized using QIAshredder spin-columns and stored at -70 °C prior to RNA extraction.
Library generation and sequencing was performed at NGI Stockholm (National Genomics Infrastructure facility, Stockholm node). Libraries were generated using the SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian kit. Libraries were sequenced using a NovaSeq 6000 instrument.

value: Pancreatic Islet

value: CD206+ macrophages

tag: status

value: T2D(Type 2 Diabetes)


title: ND.5.Isl.CD206+

value: ND(Non- diabetic)


title: ND.3.Isl.CD206+


title: ND.8.Isl.CD206+


title: T1D.1.Isl

value: Islet cells, low macrophage purity after sorting

value: T1D(Type 1 Diabetic)


title: ND.8.Isl.CD206-

value: CD206- macrophages


title: ND.5.Isl.CD206-


title: ND.3.Isl.CD206-


title: T2D.1.Isl.CD206-


title: T1D.1.Exo.CD206+

source_name: Exocrine Pancreas

value: Exocrine Pancreas


title: ND.8.Exo.CD206+


title: ND.5.Exo.CD206+


title: ND.3.Exo.CD206+


title: T2D.1.Exo.CD206+


title: ND.8.Exo.CD206-


title: T1D.1.Exo.CD206-


title: ND.5.Exo.CD206-


title: T2D.1.Exo.CD206-


title: T2D.3.Isl.CD206+


title: T2D.2.Isl.CD206+


title: ND.7.Isl.CD206-


title: IGM.2.Isl.CD206+

value: IGM(Intermediate glycemic status)


title: ND.7.Isl.CD206+


title: ND.1.Isl.CD206+


title: IGM.2.Isl.CD206-


title: PE001

city: Changchun

first: Shu

last: Zheng

state: 吉林Jilin

address: Xinmin Road

institute: Jilin University

data_processing:
(1) Alignment: We aligned Illumina-generated FASTQ files to the human reference genome (GRCh38) using the STAR algorithm. (2) Data Aggregation: To account for sequencing depth differences across libraries, we aggregated and down-sampled the data using Cell Ranger Aggregate. This step resulted in gene-barcode matrices for each sample. (3) Quality Control and Downstream Analysis: We performed quality control and downstream analysis of single-cell RNA-seq data using Seurat.
Assembly: hg38
Supplementary files format and content: Tab-separated values and matrix files

source_name: placenta

extract_protocol:
After collecting placental tissues, they were immediately processed into single-cell suspensions. The process involved washing, cutting, digesting, filtering, lysing red blood cells, removing dead cells, staining, and finally suspending the cells in a solution. The single-cell suspension was loaded onto the Chromium Controller to generate single-cell gel beads, followed by single-cell RNA sequencing using the Illumina Novaseq6000 sequencer.
The single-cell suspension was loaded onto the Chromium Controller according to the manufacturer's instructions (10X Genomics) to generate single-cell gel beads. After the generation of single-cell gel beads, single-cell RNA-seq libraries were constructed using the single-cell 3' library and gel bead kit V3.1 on an Illumina Novaseq6000 sequencer, employing a paired-end strategy with 150 bp read lengths, to generate sequencing data of at least 150 gigabases per sample.

value: placenta

value: early onset preeclampsia


title: T2D.2.Isl.CD206-


title: ND.1.Isl.CD206-


title: ND.7.Exo.CD206+


title: IGM.2.Exo.CD206+


title: T2D.2.Exo.CD206+


title: ND.1.Exo.CD206+


title: T2D.3.Exo.CD206-


title: IGM.2.Exo.CD206-


title: ND.1.Exo.CD206-


title: T2D.2.Exo.CD206-


title: ND.9.Isl.CD206+


title: ND.4.Isl.CD206+


title: ND.2.Isl.CD206+


title: ND.6.Isl.CD206+


title: ND.3.Exo.CD206-


title: T2D.3.Isl.CD206-


title: ND.9.Isl.CD206-


title: ND.6.Isl.CD206-


title: ND.4.Isl.CD206-


title: ND.2.Isl.CD206-


title: IGM.1.Isl.CD206+


title: ND.4.Exo.CD206+


title: T2D.3.Exo.CD206+


title: ND.7.Exo.CD206-


title: IGM.1.Exo.CD206-


title: ND.6.Exo.CD206+


title: ND.9.Exo.CD206-


title: IGM.1.Exo.CD206+


title: ND.4.Exo.CD206-


title: ND.2.Exo.CD206+


title: ND.2.Exo.CD206-


title: METTL3 iKO hEPSC in P2, rep2

city: Ithaca

first: Weiyu

last: Zhang

state: NY

address: 215 Tower Rd, Biotechnology Building

department: MBG

institute: Cornell University

data_processing:
Illumina RTA software used for image identification and basecalling.
Raw reads were trimmed using Trim Galore (v0.6.10) , filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs.
Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with parameter “--very-sensitive”.
Bigwig files were generated by bamCoverage from Deeptools (v3.5.1).
Assembly: hg38
Supplementary files format and content: BigWig files containing the merged signals of two replicates.

extract_protocol:
50,000 cells were collected and washed twice in pre-cold PBS without DNase. Nuclei were then isolated, lysed and incubated with Tn5 transposase according to manufacturer’s protocol (Vazyme, TD501).
Libraries were prepared by amplifying DNA for 12 cycles using TruePrep DNA Library Prep Kit (Vazyme).

value: embryonic stem cells

value: METTL3 inducible knockout


title: EPSC in P2, H3K27me3, CUT&Tag

data_processing:
Illumina RTA software used for image identification and basecalling.
Raw reads were trimmed using Trim Galore (v0.6.10) , filtering out reads with a quality score lower than 20 and read lengths shorter than 30 base pairs.
Alignment to the human genome (GRCh38 assembly) was performed using Bowtie2 (v2.4.5) with the parameter “--very-sensitive”. Duplicated reads were removed using MarkDuplicates from Picard (v3.0.0).
Genome coverage bigwig files  were generated using bamCompare from Deeptools (v3.5.1) with spike-in normalization.
Assembly: hg38
Supplementary files format and content: BigWig files normalized by splike-in
Library strategy: CUT&Tag

extract_protocol:
Cells were harvested after feeder layer removal and fixed with 1% formaldehyde. Then cells were lysed and sonicated using Diagenode BioruptorPico UltraSonication System so that length of the majority of DNA fragments is between 100 to 500bp.
ChIP-seq library will be generated using NEBNext® UltraTM IIDNA Library Prep Kit

value: expanded potential stem cells


title: METTL3 iKO hEPSC in P2, rep1


title: EPSC in P0, H3K27me3, CUT&Tag

value: DOX


title: METTL3 iKO hEPSC in P0, rep2


title: METTL3 iKO hEPSC in P0, rep1


title: GT0000451

city: Durham

first: Brian

last: Bennett

address: 111 T.W. Alexander Drive

institute: NIEHS

data_processing:
Aligned using STAR v2.6.0c
Counts generated with featureCounts and GENCODE v38
Assembly: hg38
Supplementary files format and content: tab-delimited text: column 1 = gene, column 2 = counts

source_name: peripheral whole blood

extract_protocol:
Total RNA was isolated from whole blood collected into PAXgene tubes and was subsequently stored at -80°C
Whole-transcriptome sequencing libraries were prepared from blood-derived RNA using an efficient workflow (TruSeq Stranded Total RNA with Ribo-Zero Globin) that removes ribosomal RNA and globin mRNA in a single step

value: peripheral whole blood

tag: idili causality_score

value: Probable 50-75%

tag: idili severity

value: Fatal

tag: self-reported race

value: White or Caucasian

tag: self-reported latino

value: No

tag: exclusion notes

value: Excluded from high-causality analysis (incorrect severity)


title: IGM.1.Isl.CD206-

tag: tissue

value: Pancreatic Islet

tag: cell type


title: GT0000466

value: Moderate-hospitalized


title: GT0000422

value: Severe


title: GT0000464

value: Definite Greater than 95%

value: Black or African American

value: Yes

value: Excluded from all analysis (unique race)


title: GT0000416

value: Mild


title: ND.9.Exo.CD206+

value: Exocrine Pancreas

value: CD206+ macrophages

value: ND(Non- diabetic)


title: GT0000406

value: peripheral whole blood


title: GT0000391

value: Possible 25-50%


title: GT0000362

value: Highly likely 75-95%


title: ND.6.Exo.CD206-

value: CD206- macrophages


title: GT0000354

value: White or Caucasian

value: No


title: GT0000334

value: Probable 50-75%


title: GT0000322

value: Moderate

value: Excluded from all analysis (from separate batch)


title: GT0000309


title: GT0000303


title: GT0000296

value: Moderate-hospitalized


title: GT0000275


title: GT0000259


title: GT0000281

value: Other/Multiracial


title: GT0000288

value: Unlikely Less than 25%


title: GT0000472

value: Fatal

value: Yes


title: GT0000235


title: GT0000243

value: Black or African American


title: GT0000229

value: Severe

value: Excluded from all analysis (unique race)


title: GT0000230

value: peripheral whole blood


title: GT0000233


title: GT0000201


title: GT0000400


title: GT0000202


title: GT0000231

value: Mild


title: GT0000228

value: Highly likely 75-95%

value: Excluded from high-causality analysis (incorrect severity)


title: GT0000186

value: Possible 25-50%

value: Asian


title: GT0000168

value: White or Caucasian


title: GT0000196

value: Excluded from all analysis (too few reads)


title: GT0000396

value: Probable 50-75%

value: No


title: GT0000185

value: Moderate-hospitalized


title: GT0000161

value: Unlikely Less than 25%

tag: autoimmune hepatitis


title: GT0000157


title: GT0000156


title: GT0000119


title: GT0000150


title: GT0000152


title: GT0000149

value: Definite Greater than 95%


title: GT0000136


title: GT0000132


title: GT0000115


title: GT0000200


title: GT0000114


title: GT0000106

value: Fatal


title: GT0000104

value: Black or African American


title: GT0000110


title: GT0000102

value: Severe


title: GT0000099


title: GT0000089


title: GT0000076


title: GT0000073


title: GT0000070


title: GT0000072

value: Other/Multiracial

value: Yes


title: GT0000069

value: peripheral whole blood


title: GT0000057

value: Moderate


title: GT0000058


title: GT0000061


title: GT0000067

value: Mild


title: GT0000054


title: GT0000056

value: Possible 25-50%


title: GT0000053


title: GT0000049


title: GT0000039

value: Highly likely 75-95%


title: GT0000035


title: GT0000046

value: White or Caucasian


title: GT0000113


title: GT0000022


title: GT0000028


title: GT0000036

value: Excluded from all analysis (malignancy)


title: GT0000021

value: Probable 50-75%


title: GT0000014


title: DILIN0016


title: GT0000003

value: No


title: GT0000094

value: Moderate-hospitalized


title: NB4_Realgar_rep3

city: Padova

first: Mattia

last: Forcato

address: Via Ugo Bassi, 58/B

country: Italy

institute: University of Padova

data_processing:
Raw reads were aligned using STAR version 2.7.9a to build version hg38 of the human genome.
Counts for UCSC annotated genes were calculated from the aligned reads using featureCounts function of the Rsubread R package and R (version 4.1.1)
Normalization and differential analysis were carried out using edgeR R package.
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: blood

growth_protocol: Cells were maintained at a concentration of 0.25–0.5 × 10E6 cells/mL in RPMI + 10% FCS + 1% penicillin/streptomycin

extract_protocol:
RNA was isolated from 5x10E6 cells using the SV Total RNA Isolation System (Promega #Z3100).
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. The library was prepared through end repair, A-tailing, adapter ligation, size selection, amplification, and purification.The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Cells were incubated for 24h with solvent (NaOH pH 12.7), 0.5 μM realgar or 0.5 μM arsenic trioxide. After 24h total RNA was extracted and used for RNA-Seq.

value: blood

tag: cell line

value: Myeloid

value: Acute promyelocytic leukemia cell line

value: 0.5 uM realgar


title: NB4_Realgar_rep2

tag: treatment


title: GT0000078


title: NB4_NaOH_rep3

tag: genotype

value: NaOH (solvent)


title: NB4_NaOH_rep2


title: NB4_ATO_rep3

value: 0.5 uM arsenic trioxide


title: NB4_NaOH_rep1


title: NB4_ATO_rep1


title: Jurkat_NaOH_rep3

value: Jurkat E6.1

value: T lymphoblast

value: acute T-cell leukemia cell line


title: Jurkat_Realgar_rep3


title: Jurkat_NaOH_rep1


title: Jurkat_ATO_rep3


title: Jurkat_Realgar_rep2


title: Jurkat_NaOH_rep2


title: Jurkat_Realgar_rep1


title: Jurkat_ATO_rep2


title: Jurkat_ATO_rep1


title: Parental_R3_Unperturbed

data_processing:
Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 42 nt.
Samples were mapped to the Drosophila dm6 (spike) genome, and nonmapping reads subsequently mapped to hg38 using STAR 2.7.3a (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
Assembly: hg38
Supplementary files format and content: Spreadsheets with normalized counts and associated analysis from DEseq2

extract_protocol:
Cells were collected in Trizol, RNA was extracted, and genomic DNA contamination removed using DNAse.
rRNA depleted RNA was used as input to the Illumina TruSeq stranded total RNA kit or NEB Next Ultra II Directional library prep kit using the manufacturer's protocol.
Stranded RNA-seq, dUTP

treatment_protocol: +/- Auxin (500 µM) 4h, 12h or untreated

value: embryonic kidney

value: Parental


title: Parental_R1_Unperturbed


title: CONTROL

first: Peng

last: Xu

state: Jilin

address: No.1 Xinmin Street

institute: The First Hospital of Jilin University

data_processing:
(1) Alignment: We aligned Illumina-generated FASTQ files to the human reference genome (GRCh38) using the STAR algorithm. (2) Data Aggregation: To account for sequencing depth differences across libraries, we aggregated and down-sampled the data using Cell Ranger Aggregate. This step resulted in gene-barcode matrices for each sample. (3) Quality Control and Downstream Analysis: We performed quality control and downstream analysis of single-cell RNA-seq data using Seurat.
Assembly: hg38

value: placenta


title: GDMM1


title: GDMMINS


title: GDMM2


title: Parental_R2_Unperturbed


title: INTS1_R3_Unperturbed

value: homozygous miniAID


title: INTS1_R1_Unperturbed


title: RDD, scRNA-seq

city: Nanjing

first: Xinyi

last: Xia

state: Jiangsu

address: 138 XianLin Road, Nanjing, JiangSu, China

institute: Nanjing University of Chinese Medicine

description: single cell RNA-seq

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the Cell Ranger software
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: RDD lesion

extract_protocol:
RDD tissues were dissociated using 2mg/ml Collagenase II (Sigma, C2-28-100MG) for 1h in 37℃ water bath. Digestion was terminated by wash with 5ml DMEM twice. Cells were passed through 40μm cell strainer to get single cell suspension. Cell viability were confirmed using AO/PI reagent (Absin, abs9727-100T). Then, single cell suspension was washed and resuspended in DPBS containing 0.02%BSA for single cell RNA-seq library construction.
Construction of single cell RNA-seq library for RDD was performed using 10x Genomics Chromiun Single-Cell 3’ kit(V3) according to the manufacturer’s instructions. Briefly, cells were loaded onto the 10x Genomics single-cell-A chip for a target capture of 8000 cells. After droplet generation, sample were transferred into a PCR tube and performed reverse transcription and library construction.

value: RDD lesion


title: INTS1_R2_Unperturbed


title: ABCF1-1-3,rep3

city: Taizhou

first: yin

last: yuan

state: jiangsu

address: 210 Yingchun Road, Hailing District, Taizhou City, Jiangsu Province

institute: Nanjing Medical University Affiliated Taizhou People's Hospital

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FRKM) . StringTie was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts and RPKM values for each Sample

source_name: liver

extract_protocol:
RNA was harvested using Trizol reagent. 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

value: liver


title: ABCF1-1-2,rep2


title: NB4_ATO_rep2


title: ABCF1-1-1,rep1


title: NC-1-3,rep3


title: NC-1-2,rep2


title: NB4_Realgar_rep1


title: RDD, Spatial transcriptome

description: Spatial transcriptome

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the Cell Ranger software
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics

extract_protocol:
RDD tissue was embedded in OCT and cut into 20μm sections.
Library was prepared with 10x Genomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer’s instructions.


title: NC-1-1,rep1


title: IP

data_processing:
ChIP-seq reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks with the sonicated input as a control
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0)

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

tag: antibody

value: Flag


title: control-3,rep3

data_processing:
ATAC-seq reads were aligned to the hg38 reference genome using Bowtie2(2.4.1)
Sam files were converted to Bam format using Samtools and used for peak calling
MACS2 (2.2.7.1) was used to call peaks
Assembly: GRCh38
Supplementary files format and content: bigwig files were generated using Deeptools(3.5.0)

extract_protocol:
The ATAC experiments were performed as described (Buenrostro et al., 2013).
Cells were  vehicle treated and then collected and treated with transposase Tn5 (Nextera DNA Library Preparation Kit, Illumina). DNA was purified using MinElute PCR Purification Kit (Qiagen). All samples were then amplified by PCR using NEBNextHigh-Fidelity 2× PCR Master Mix (New Englands Labs) with primers containing a barcode to generate libraries. DNA was again purified using AMPure Beads.DNA libraries for ATAC-seq were prepared using NextEra Library Prep Kit following manufacturer's protocols.


title: input


title: control-2,rep2


title: control-1,rep1


title: H3K9me2-3,rep3


title: CD4TCR-exCD8_0hr_DonorC

city: Bethesda

first: Kazusa

last: Ishii

state: MD

address: 10 Center Drive, Building 10, Room 5B05

institute: National Cancer Institute, National Institutes of Health

data_processing:
NovaSeq 6000 SP, Illumina Stranded mRNA Prep and paired-end sequencing.
The samples have 35 to 68 million pass filter reads with more than 89% of bases above the quality score of Q30. Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg38) and annotaged transcripts using STAR.
The mapping statistics were calculated using Picard software.
Library complexity was measured in terms of unique fragments in the mapped reads using Picrad's MarkDuplicate utility.
STAR 2.7.0f for alignment, RSEM 1.3.1 for Quantification.
Assembly: hg38
Supplementary files format and content: Tab delimited txt file of raw count data.

source_name: lymphocyte

extract_protocol:
RNA was extracted using Qiagen RNesy Mini Plus Kit (Qiagen) following manufacture's protocol.
RNA libraries for RNA-seq were prepared with Illumina Stranded mRNA Prep.

tag: individual

value: DonorC

value: lymphocyte

value: T cells

tag: cell subset

tag: transduction

value: TCR-ex

value: No stimulation


title: CD4TCR_0hr_DonorC

value: TCR


title: CD4CAR_0hr_DonorC

value: CAR


title: CD4TCR-exCD8_0hr_DonorB

value: DonorB


title: CD4CAR_0hr_DonorB


title: CD4TCR_0hr_DonorB


title: CD4CAR_0hr_DonorA

value: DonorA


title: CD4TCR_0hr_DonorA


title: CD8TCR_0hr_DonorC


title: CD4TCR-exCD8_0hr_DonorA


title: CD8TCR-exCD8_0hr_DonorC


title: CD8CAR_0hr_DonorB


title: CD8TCR_0hr_DonorB


title: CD8CAR_0hr_DonorA


title: CD8TCR-exCD8_0hr_DonorA


title: CD8TCR_0hr_DonorA


title: CD8CAR_0hr_DonorC


title: CD4CAR_6hr_DonorC

value: antigen stimulation


title: CD4TCR_6hr_DonorC


title: CD4TCR_6hr_DonorB


title: CD4TCR_6hr_DonorA


title: H3K9me2-2,rep2


title: CD4TCR-exCD8_6hr_DonorA


title: CD4CAR_6hr_DonorB


title: CD4TCR-exCD8_6hr_DonorB


title: H3K9me2-1,rep1


title: CD8TCR-exCD8_6hr_DonorC


title: CD4CAR_6hr_DonorA


title: CD8TCR_6hr_DonorC


title: CD8TCR-exCD8_6hr_DonorB


title: CD8TCR-exCD8_0hr_DonorB


title: CD8TCR_6hr_DonorB


title: NB4_Orpiment_rep2

description: Library name: NB4_Orpiment_rep2

extract_protocol:
RNA was isolated from 5x10E6 cells using the SV Total RNA Isolation System (Promega #Z3100).
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. The library was prepared through end repair, A-tailing, adapter ligation, size selection, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection. Quantified libraries will be pooled and sequenced on Illumina platforms, according to effective library concentration and data amount.

treatment_protocol: Cells were incubated for 48h with solvent (NaOH pH 12.7), 0.5 μM realgar or 0.5 μM arsenic trioxide or 0.5 μM orpiment. After 48h total RNA was extracted and used for RNA-Seq.

value: blood

value: Myeloid

value: Acute promyelocytic leukemia cell line

value: 0.5 μM orpiment


title: NB4_NaOH_rep4

description: Library name: NB4_NaOH_rep4

value: NaOH (solvent)


title: CD4TCR-exCD8_6hr_DonorC


title: NB4_NaOH_rep5

description: Library name: NB4_NaOH_rep5


title: NB4_Orpiment_rep1

description: Library name: NB4_Orpiment_rep1


title: Jurkat_Orpiment_rep2

description: Library name: Jurkat_Orpiment_rep2

value: Jurkat E6.1

value: T lymphoblast

value: acute T-cell leukemia cell line


title: CD8CAR_6hr_DonorB

value: lymphocyte


title: Jurkat_Orpiment_rep1

description: Library name: Jurkat_Orpiment_rep1


title: Sample 029, Ercc1 d/-, aortic arch, male, 22 weeks, DR

city: Rotterdam

first: Sanne

last: Stefens

address: Dr. Molewaterplein 40

department: Molecular Genetics

country: Netherlands

institute: Erasmus MC

description:
Library name: 104707-001-029
029

data_processing:
Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.
UMI-Tools v1.1.2 was used to move the UMI barcodes from separate files to the read pair headers. File R2 contains the UMI. Files R1 and R3 contain the paired reads
The raw fastq files were pre-processed with  fastp v0.23.213.
Reads were mapped to the reference sequence Mus_Musculus_GRCm39 with ENSEMBL v107 annotation using STAR v2.7.10a.
Read counts were generated using htseq-count v2.0.2.
Differential expression analysis was performed with DESeq2 v1.34.0
Assembly: Mus_Musculus_GRCm39
Supplementary files format and content: TSV file including raw counts for each sample

organism: Mus musculus

source_name: Aortic arch

growth_protocol: Ercc1Δ/- mice were generated by crossing Ercc1Δ/+ (in a pure C57BL6J or FVB background) with Ercc1+/- mice (in a pure FVB or C57BL6J background respectively), resulting in Ercc1Δ/- offspring with a genetically uniform F1 C57BL6J/FVB hybrid background. Wildtype (WT) F1 littermates served as controls. All animals were bred and maintained on AIN93G synthetic pellets (Research Diet Services B.V.; gross energy content 4.9 kcal/g dry mass, digestible energy 3.97 kcal/g). Dietary restriction (DR) was initiated at 7 weeks of age by 10% food reduction (g/day). DR was increased weekly with 10% (g/day), until reaching 30% DR from 9 weeks of age onward. Mice in the ad libitum (AL) group were allowed unlimited access to AIN93G pellets. Mice were kept on an adjusted light-dark schedule (light from 12 pm to 12 am and dark from 12 am to 12 pm) to facilitate feeding just before the start of the dark (active) period, in order to avoid disruptions in the biological clock. Mice were individually housed to control food intake. At 6 weeks and 22 weeks of age, mice were sacrificed by CO2 inhalation.

extract_protocol:
Total RNA and µRNA was obtained from the aortic arch using the miRNeasy Mini Kit (Qiagen).
Library preparation, sequencing and primary data analysis were performed at GenomeScan B.V. (Genomescan B.V., Leiden, The Netherlands). The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the samples. The sample preparation was performed according to the protocol  according to the protocol "NEBNext Ultra II Directional RNA Library Prep Kit for Illumina" (NEB #E7760S/L).

value: Aortic arch

tag: Sex

value: M

tag: age (weeks)

value: DR


title: Sample 014, Ercc1 d/-, aortic arch, female, 22 weeks, DR

description:
Library name: 104707-001-014
014

value: F


title: Sample 016, Ercc1 d/-, aortic arch, male, 22 weeks, DR

description:
Library name: 104707-001-016
016


title: Sample 022, Ercc1 d/-, aortic arch, female, 22 weeks, DR

description:
Library name: 104707-001-022
022


title: CD8TCR_6hr_DonorA

value: T cells

value: TCR


title: Sample 026, Ercc1 d/-, aortic arch, male, 22 weeks, AL

description:
Library name: 104707-001-026
026

value: AL


title: Jurkat_NaOH_rep5

description: Library name: Jurkat_NaOH_rep5


title: CD8TCR-exCD8_6hr_DonorA

value: DonorA

value: TCR-ex

value: antigen stimulation


title: Sample 004, Ercc1 d/-, aortic arch, female, 22 weeks, AL

description:
Library name: 104707-001-004
004


title: UCD4 EWD replicate 3

city: Aurora

first: Jessica

last: Finlay-Schultz

state: CO

department: Pathology

institute: University of Colorado Denver Anschutz Medical Campus

data_processing:
Adapter trimming was done using cutadapt
Expression quantification was done using Salmon on trimmed fastq files
DESeq2 was used for differential analysis
Assembly: GRCh38
Supplementary files format and content: Tab seperated file containing Transcript per million (TPM) quantificantion for each isoforms

source_name: UCD4 EWD cells

growth_protocol: T47D cells were maintained in minimal Eagle’s medium, 5% FBS, 1X NEAA, 10^-9 M insulin, 0.1 mg/mL sodium pyruvate, and 2 mM L-glutamine. UCD4 cells were maintained in DMEM/F12 supplemented with 10% FBS, 100 ng/mL choleratoxin, and 10^–9 M insulin. Phenol red free base media and charcoal-stripped serum were used for EWD cells.

extract_protocol:
Extraction of total RNA was performed using the Qiagen miRNeasy Mini Kit with DNase treatment according to manufacturer protocols.
Libraries were prepared for sequencing using the New England Biolabs NEBNext Ultra II Directional RNA Library Prep Kit for Illumina and multiplex oligo set 1 according to manufacturer protocols.

treatment_protocol: Cells were treated with increasing doses of tamoxifen or fulvestrant until cells could be maintained at 1 uM tamoxifen or 100 nM fulvestrant. EWD cells were kept in phenol red free media until growth could be maintained.

value: UCD4 EWD cells


title: UCD4 EWD replicate 2


title: L-EVs, replicate 1, single EV RNAseq

city: Trento

first: Francesca

last: Demichelis

state: TN

address: Via Sommarive, 9

department: Department for Cellular, Computational and Integrative Biology - CIBIO

institute: University of Trento

description: 10x Genomics

data_processing:
Data was analyzed using CellRanger (version 6.0.1) with option --expect-cells=10000
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Prostate

extract_protocol:
PC3 cells were plated into 150mm tissue culture dishes (n=18 per cell line) and allowed to proliferate in serum-supplemented media for at least 48h. After cells reached ~90% confluency, they were washed twice in PBS, and placed in serum-free media for 24hours before EV enrichment. The conditioned media was centrifuged three times at 300g, for 5minutes each to pellet down floating cells. This was followed by centrifugation at 2,800g for 10minutes to collect the 2.8K fraction. The supernatant was spun in an ultracentrifuge at 10,000g for 30minutes (k-factor 2547.2) to collect L-EVs. All differential centrifugation steps were performed at 4°C. L-EVs were then subjected to iodixanol (Optiprep™, Sigma) density gradient purification. Freshly pelleted L-EVs were resuspended in 0.2µm-filtered PBS and deposited at the bottom of an ultracentrifuge tube (Cat#344058, Beckman Coulter). Next, 30% (4.3mL, 1.20g/mL), 25% (3mL, 1.15g/mL), 15% (2.5mL, 1.10g/mL), and 5% (6mL, 1.08g/mL) iodixanol solutions were sequentially layered at decreasing density to form a discontinuous gradient. Separation was performed by ultracentrifugation at 100,000g for 230minutes (4°C, k-factor 254.7) after which L-EVs separated into the 1.10–1.15g/mL density fractions. Purified L-EVs were then washed in PBS (100,000g, 60min, 4°C) and resuspended in 0.2µm-filtered PBS. All ultracentrifugation spins were performed in a SW28 swinging rotor (Beckman Coulter).
L-EVs were isolated from the PC3 cell conditioned medium, purified by iodixanol density gradient, and the number of particles quantified as described above. To enable encapsulation of single L-EVs into individual droplets, the EV sample was diluted to contain 10,000 particles total. A 10x Genomics Chromium machine was used for single-EV capture. cDNA preparations were obtained according to the Single Cell 3’ Protocol recommended by the manufacturer. Silane magnetic beads and solid-phase reversible immobilization (SPRI) beads were used to clean up the GEM reaction mixture, and the barcoded cDNA was then amplified in a PCR step. The P7 and R2 primers were added during the GEM incubation and the P5, and R1 during library construction via end repair, A-tailing, adaptor ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification. Sequencing was carried out on an Illumina Novaseq 6000 with paired-end with read lengths of 28 and 91 bp for read 1 and read 2, respectively.

value: Adenocarcinoma, Grade IV (epithelial)

value: Prostate

tag: age

value: Derived from 62-year old white male

tag: sample type

value: Large EVs


title: CD8CAR_6hr_DonorA

value: CAR


title: UCD4 EWD replicate 1


title: Sample 013, Ercc1 d/-, aortic arch, male, 22 weeks, AL

description:
Library name: 104707-001-013
013


title: UCD4 FulvR replicate 3

source_name: UCD4 FulvR cells

value: UCD4 FulvR cells


title: UCD4 FulvR replicate 2


title: CD8CAR_6hr_DonorC

value: DonorC

value: lymphocyte


title: UCD4 FulvR replicate 1


title: FD2047

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

institute: Ulm University and Ulm University Medical Center

description: Splenomegaly, FFPE

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina HumanMethylation 450 Beadchip using standard Illumina protocol.

scan_protocol: The arrays were scanned using a iScan device.

data_processing: Raw idat files were read into the statistical program R (version 4.3.0) using the minfi package (version 1.46.0). Normalization was performed with the preprocessIllumina() function against the intrinsic controls and without background correction.

label: biotin

source_name: spleen

label_protocol: Standard Illumina Protocol

extract_protocol: genomic DNA was extracted and purified according to commercially available kits from Qiagen according to standard instructions

value: spleen


title: Sample 005, Ercc1 d/-, aortic arch, female, 22 weeks, AL

description:
Library name: 104707-001-005
005

value: Aortic arch

value: F


title: Sample 006, Ercc1 d/-, aortic arch, male, 22 weeks, DR

description:
Library name: 104707-001-006
006

value: M

value: DR


title: FD2046

description: Splenomegaly, FFPE


title: UCD4 TamR2 replicate 3

source_name: UCD4 TamR cells

value: UCD4 TamR cells


title: FD2045

description: Splenomegaly, FFPE


title: UCD4 TamR2 replicate 1


title: UCD4 TamR2 replicate 2


title: FD2044

description: Splenomegaly, FFPE


title: Jurkat_NaOH_rep4

description: Library name: Jurkat_NaOH_rep4

value: blood

value: Jurkat E6.1

value: T lymphoblast

value: acute T-cell leukemia cell line

value: NaOH (solvent)


title: UCD4 parental replicate 3

source_name: UCD4 parental cells

value: UCD4 parental cells


title: UCD4 parental replicate 1


title: UCD4 parental replicate 2


title: Sample 028, Ercc1 +/+, aortic arch, male, 22 weeks, DR

description:
Library name: 104707-001-028
028


title: Sample 010, Ercc1 +/+, aortic arch, male, 22 weeks, DR

description:
Library name: 104707-001-010
010


title: FD2042

description: Splenomegaly, FFPE


title: T47D FulvR replicate 3

source_name: T47D FulvR cells

value: T47D FulvR cells


title: Sample 017, Ercc1 +/+, aortic arch, female, 22 weeks, DR

description:
Library name: 104707-001-017
017


title: Sample 007, Ercc1 +/+, aortic arch, male, 22 weeks, DR

description:
Library name: 104707-001-007
007


title: FD2043

description: Splenomegaly, FFPE


title: T47D FulvR replicate 2


title: T47D TamR replicate 2

source_name: T47D TamR cells

value: T47D TamR cells


title: T47D FulvR replicate 1


title: 5_09312

description: immunodeficiency-associated Burkitt lymphoma, FFPE, EBV-positive

source_name: lymph node

value: lymph node


title: Sample 020, Ercc1 +/+, aortic arch, male, 22 weeks, AL

description:
Library name: 104707-001-020
020

value: AL


title: 4_09112


title: 3_01212


title: T47D TamR replicate 1


title: Sample 018, Ercc1 +/+, aortic arch, female, 22 weeks, AL

description:
Library name: 104707-001-018
018


title: Sample 021, Ercc1 +/+, aortic arch, female, 22 weeks, DR

description:
Library name: 104707-001-021
021


title: 7_09612

description: immunodeficiency-associated Burkitt lymphoma, FFPE, EBV-negative

source_name: ileon

value: ileon


title: T47D parental replicate 3

source_name: T47D parental cells

value: T47D parental cells


title: Sample 025, Ercc1 +/+, aortic arch, male, 22 weeks, AL

description:
Library name: 104707-001-025
025

value: Aortic arch


title: Sample 012, Ercc1 +/+, aortic arch, male, 22 weeks, AL

description:
Library name: 104707-001-012
012


title: Triple species biofilmes_mGTS, biol rep 2

city: Braga

first: Ângela

last: França

address: Campus de Gualtar

department: Biological Engineering

country: Portugal

institute: University of Minho

data_processing:
FastQ files were generated via Illumina bcl2fastq2 (v 2.17.1.14) starting from raw sequencing reads. The quality of individual sequences was evaluated using FastQC software after adapter trimming with cutadapt software (v 1.18).
Adapter trimmed data was further analysed by CLC Genomics Workbench v 21.99.
Sequence data were trimmed for low quality using CLC Genomics Workbench (parameter - quality limit: 0.05 and Maximum number of ambiguities allowed: 2).
Trimmed sequences read were mapped to either G. vaginalis NCTC 10287, F. vaginae FDAARGOS_934 or P. bivia DSM 20514 using CLC Genomics Workbench (parameters-Mismatch cost: 2, insertion cost; deletion cost: 3; length fraction 0.8, similarity fraction: 0.8 and maximum number of hits for a read: 10).
Differential expression analysis was performed using CLC Genomics Workbench, upon normalisation to RPKM. Baggerley statistical test was used to identify significant alterations in gene transcription. Only alterations with fold-changes > 2 and a false discovery rate (FDR)-adjusted P value < 0.05 were used for further bioinformatics analyses.
Assembly: G. vaginalis NCTC 10287 (NZ_LR134385.1), F. vaginae FDAARGOS_934 (CP065631.1) and P. bivia DSM 20514 (scaffolds NZ_JH660658.1; NZ_JH660659.1; NZ_JH660660.1)
Supplementary files format and content: The tab-delimited text files present RPKM values of the three replicas performed of G. vaginalis, F. vaginae and P. bivia mixed biofilms grown in both NYCIII and mGTS.

organism:
Gardnerella vaginalis
Prevotella bivia
Fannyhessea vaginae

source_name: Bacteria

growth_protocol: Triple-species biofilms of G. vaginalis, F. vaginae, and P. bivia were formed on 24-well culture plates (Orange Scientific, Braine-l’Alleud, Belgium), using the competitive model previously described (Rosca et al., 2022), in either NYCIII or mGTS medium. For the biofilms formed in NYCIII medium, first, an inoculum of each species was prepared and incubated at 37°C in anaerobic conditions for 24 h. For the mGTS biofilms, a suspension of each species was prepared from bacterial biomass growing on CBA plates on the same day of biofilm formation. Thereafter, for both protocols, the bacterial concentration was adjusted to 9x107 CFU/mL by reading the optical density at 620 nm (Castro et al., 2021). The bacterial suspensions were then dispensed on the plate wells for a total volume of 1 mL and a final concentration of 1x107 CFU/mL for each species, and incubated for 48 h at 37°C and in anaerobic conditions. Thereafter, the medium was removed and the biofilms were washed once with 1x phosphate-buffered saline (PBS) solution (Thermo Fisher Scientific). Following the washing step, RNA Protect bacteria reagent (Qiagen, MD, USA), diluted 2:1 in PBS, was dispensed on the biofilms and the biofilms were detached from the plate. The samples were then centrifuged at 5000 g for 10 min at room temperature. These experiments were repeated at least three times.

extract_protocol:
Twelve triple-species biofilms formed in either NYCIII or mGTS were pooled to obtain samples with enough RNA concentration for further analysis. RNA extraction was performed using the RNeasy Mini Kit (Qiagen), according to the manufacturer’s instructions, with some brief modifications as optimized before (França et al., 2012). First, cells were suspended in 600 μL of lysis buffer RLT and the volume was transferred to a tube with 0.1 mm zirconium beads (Merck, Darmstadt, Germany). Cells were lysed using the BeadBug 6 Microtube Homogenizer (Benchmark Scientific, NJ, USA) at maximum speed for 35 s. The cycle was repeated four times and the samples were kept on ice for 5 min between cycles. Then, the samples were centrifuged, and the supernatant was recovered into a new tube. Ethanol at 70% (Thermo Fisher Scientific) was added in the same proportion (vol:vol) to the supernatant and the solution was transferred to an RNeasy Mini spin column. After the washing steps in the column, the RNA was eluted in RNase-free water (Grisp). RNA was treated with Turbo DNase (Invitrogen, Waltham, Massachusetts, USA) to degrade genomic DNA following the manufacturer’s instructions for rigorous protocol. RNA quality was assessed using the Agilent 2100 Bioanalyzer (Agilent, CA, USA) and only samples with RNA quality indicators above 7 were used.
RNA-seq libraries were prepared by Lexogen (outsourced) using Lexogen’s CORALLTM Total RNA-seq kit with 100 ng of total RNA. Before RNA-seq, rRNA was removed using the RiboCop for Bacteria (Mixed Bacterial Samples META) rRNA Depletion kit (Lexogen). Sequencing libraries were evaluated for quality on a Fragment Analyzer System (Agilent) and quantified with QubitTM dsDNA HS Assay Kit (Invitrogen). Data were generated using Illumina NextSeq2000 Sequencing from single-end reads (SR100).

treatment_protocol: Not applicable

value: Bacteria


title: Triple species biofilmes_mGTS, biol rep 3


title: 2_01012

source_name: appendix

value: appendix


title: Triple species biofilmes_mGTS, biol rep 1


title: T47D TamR replicate 3


title: Triple species biofilmes_NYC III, biol rep 1


title: Sample 027, Ercc1 d/-, aortic arch, male, 6 weeks, AL

description:
Library name: 104707-001-027
027

value: M


title: Triple species biofilmes_NYC III, biol rep 3


title: Disease Relative

city: L'Hospitalet de Llobregat

first: Alessandra

last: Giorgetti

state: Barcelona

address: Avinguda de la Granvia de l’Hospitalet, 199

department: PCMRC

country: Spain

institute: IDIBELL

data_processing: Data was processed and analyzed using the shinyÉPICo (33416853) R package (http://bioconductor.org/packages/shinyepico/). The shinyÉPICo package was employed to conduct differential methylation analysis and generate graphical representations of the results. Quality control measures, such as visual inspection of methylation patterns, were performed to confirm the integrity of the data. Outputs included tables of differentially methylated positions and associated visualizations. The analysis was conducted using version 1.12.0 of the shinyÉPICo package.

label: Cy5 and Cy3

source_name: Peripheral blood

extract_protocol: Genomic DNA was extracted and purified from bone marrow and peripheral blood samples using Qiagen DNeasy Kit according to standard instructions

value: Peripheral blood

tag: disease state

value: Disease Relative


title: T47D parental replicate 2


title: Healthy Relative 2

value: Healthy Relative


title: F6 with TRF3-HA, IAA, Pol III, rep2

city: Vancouver

first: Sheila

last: Teves

state: BC

address: 2350 Health Sciences Mall

department: Biochemistry

country: Canada

institute: Life Science Institute

data_processing:
Quality Assurance was done using FastQC to check metrics
CUT&Tag reads were aligned to the mouse mm10 or fly dm6 genome using bowtie2 with parameters: --no-unal –local –very-sensitive-local –no-discordant –no-mixed –contain –overlap –dovetail –phred33 -I 10 -X 9999 with PCR duplicates being kept
bigwig generation was done using the D.melanogaster normalization factor determined from Bowtie2 mapping of dm6
Heatmaps, IGV tracks, and other downstream analysis were generated from bigwig files using Deeptools/ComputeMatrix
Read counts were generated using featureCounts (for DGE analysis) or bedtools multicov (for scatterplot analysis). DGE read counts were normalized to TMM and Scatterplot read counts were normalized to s2 scaling factor
Assembly: mm10 and dm6
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: embryonic stem cell

growth_protocol: Cells were cultured on gelatin-coated plates in ESC media (Knockout DMEM, 15% FBS, 0.1mM MEM non essential amino acids, 2mM GlutaMAX, 0.1mM 2-mercaptoethanol and 1000 units/ml of ESGRO. ES cells are fed daily, cultured at 37C in a 5% CO2 incubator and passaged every two days via trypsinization.)

extract_protocol:
Extract protocol was done following the CUT&Tag published protocol where cells and DNA were sheared using 10uL 0.5M EDTA, 3uL 10% SDS, 2.5uL 20mg/mL Proteinase followed by phenol chloroform isoamyl extracted
Librarires were prepared following the CUT&Tag protocol. Briefly 21uL(out of 30uL) was used with 2uL Universal i5 primer (10uM) +2uL uniquely barcoded i7 primers (10uM) using a different unique barcode for each sample. 25UL of NEBNext HiFi 2x PCR Master mix (NEB M0541L) was used for the PCR reaction following the PCR protocol for CUT&Tag using 12 cycles. Library was cleaned up using Ampure XP beads using 1.1x volume and samples were pooled by volume and bead cleaned again before sequencing

treatment_protocol: mESCs were treated with IAA (6 hours or 24 hours, 500uM final IAA concentration), Heat shock (30 minutes at 42C), Heat shock + IAA (24 hours, 500uM final IAA concentration followed by an extra 30 minutes of HS + IAA)

value: embryonic stem cell


title: Sample 023, Ercc1 d/-, aortic arch, female, 6 weeks, AL

description:
Library name: 104707-001-023
023

value: F


title: F6 with TRF3-HA, IAA, Pol II, rep2


title: Sample 015, Ercc1 d/-, aortic arch, male, 6 weeks, AL

description:
Library name: 104707-001-015
015


title: F6 with TRF3-HA, IAA, Pol II, rep1


title: T47D parental replicate 1


title: F6 with TRF3-HA, IAA, HA, rep2


title: Healthy Relative 1


title: F6 with TRF3-HA, IAA, HA, rep1


title: Sample 008, Ercc1 d/-, aortic arch, female, 6 weeks, AL

description:
Library name: 104707-001-008
008


title: F6 with TRF3-HA, DMSO, Pol II, rep2


title: Symptomatic Stage 2

value: Symptomatic Stage


title: Sample 002, Ercc1 d/-, aortic arch, male, 6 weeks, AL

description:
Library name: 104707-001-002
002


title: Sample 003, Ercc1 +/+, aortic arch, female, 22 weeks, AL

description:
Library name: 104707-001-003
003


title: F6 with TRF3-HA, DMSO, Pol II, rep1


title: Triple species biofilmes_NYC III, biol rep 2


title: 1_00114

source_name: unkown

value: unkown


title: Symptomatic Stage 1


title: F6 with TRF3-HA, DMSO, Pol III, rep1


title: Sample 009, Ercc1 +/+, aortic arch, male, 6 weeks, AL

description:
Library name: 104707-001-009
009

source_name: Aortic arch


title: F6 with TRF3-HA, DMSO, HA, rep2


title: F6 with TRF3-HA, DMSO, Pol III, rep2


title: F6 with TRF3-HA, IAA, Pol III, rep1


title: F6 with TRF3-HA, DMSO, HA, rep1


title: Asymptomatic Stage

value: Asymptomatic Stage


title: F6 with TRF3c-HA, IAA, Pol III, rep2


title: Healthy Donor 3

value: Healthy Donor


title: Sample 011, Ercc1 +/+, aortic arch, female, 6 weeks, AL

description:
Library name: 104707-001-011
011


title: Sample 019, Ercc1 +/+, aortic arch, male, 6 weeks, AL

description:
Library name: 104707-001-019
019


title: F6 with TRF3c-HA, IAA, Pol II, rep2


title: F6 with TRF3c-HA, IAA, HA, rep2


title: Healthy Donor 2


title: Healthy Donor 1


title: F6 with TRF3c-HA, IAA, Pol II, rep1


title: F6 with TRF3c-HA, IAA, HA, rep1


title: Sample 024, Ercc1 +/+, aortic arch, female, 6 weeks, AL

description:
Library name: 104707-001-024
024


title: F6 with TRF3c-HA, DMSO, Pol III, rep1


title: F6 with TRF3c-HA, DMSO, Pol III, rep2


title: Krt5-CreERT2-Negative Sample 1

city: San Francisco

first: Sugandh

last: Kumar

state: California

address: N431, 2340 Sutter St

department: Computational Biology

institute: University of California San Francisco (UCSF)

description:
Library name: A20WT-Mouse-1
RNASeq profiling of ear epidermal sheets derived from 8 week old A20F/F Krt5-CreERT2+ (A20KIKO) and A20F/F Krt5-CreERT2- (A20WT) mice (four distinct mice in each group) 1 week after first intraperitoneal tamoxifen injection.

data_processing:
Reads were mapped to the mouse genome (GRCm38.p5, with Gencode v25 annotation) using STAR v2.4.2a (Dobin et al. 2013). Picard-tools v1.139 (http://broadinstitute.github.io/picard) was used to compile mapping statistics for the resulting alignments, and a table of counts of each gene from each sample was generated with HTSeq v0.6.1p1 (Anders et al. 2015).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Skin

growth_protocol: A20WT and A20KIKO mice at 8 weeks of age

extract_protocol:
Ear skin was split and floated on 0.25% trypsin-EDTA overnight. Epidermal sheets were manually removed with tweezers and lysed in Qiagen RLT with bead beating. RNA was purified using Qiagen RNEasy kit.
Mouse epidermal sheet RNA from four A20WT and four A20KIKO mice was used to construct sequencing libraries using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara Clontech cat. 634894). Reverse transcription was performed on poly-adenylated RNA from cell lysate for up to 1000 cells followed by second strand synthesis to make full length cDNA. cDNA was then later amplified by PCR using cycle numbers determined by cell numbers. Amplified cDNA was purified by AMPure XP beads (Beckman Coulter) and followed by Qubit quantification. Sequencing libraries were constructed using the Illumina Nextera DNA kit 0.3 ng of cDNA synthesized from RNA. The sizes of constructed libraries were evaluated by Illumina Bioanalyzer High Sensitivity DNA Assay to ensure library sizes range between 300bp to 500bp. The libraries were quantified using NEBNext Library Quant Kit for Illumina (NEB #E7630) to ensure equal molar concentrations of sequenceable libraries were pooled. Sequencing reactions were performed on Illumina Novaseq with pair-end 150 bp reads.  An average of 22 million reads were generated per sample.

treatment_protocol: Mice were injected intraperitoneally with 1mg of Tamoxifen on 2 consecutive days. 7 Days after the first tamoxifen injection, mice were sacrificed.

value: Skin

value: Epidermal

value: Tamoxifen


title: sample 283_genomic DNA from blood sample S1625

city: Shinjuku-ku, Tokyo

first: Yae

last: Kanai

address: 35, Shinano-machi

institute: Keio University School of Medicine

hyb_protocol: Standard Illumina Protocol

scan_protocol: Standard Illumina Protocol

data_processing:
Initial quality control was performed using GenomeStudio Methylation software. The raw intensity data files were imported into the R environment using the Bioconductor minfi package. Data satisfying detection P-values are 0.05 or more was regarded not applicable. Background correction with dye-bias normalization was performed using the normal-exponential out-of-band preprocessing method.
matrix processed value definition: Normalized Average Beta

source_name: blood sample of control patient

extract_protocol: The genomic DNA was extracted from all blood samples using a Maxwell® 16 Blood DNA Purification Kit (Promega, Madison, WI, USA).

value: normal

value: female

tag: age bracket

tag: blood sample id


title: F6 with TRF3c-HA, DMSO, Pol II, rep2


title: F6 with TRF3c-HA, DMSO, Pol II, rep1


title: Krt5-CreERT2-Negative Sample 2

description:
Library name: A20WT-Mouse-2
RNASeq profiling of ear epidermal sheets derived from 8 week old A20F/F Krt5-CreERT2+ (A20KIKO) and A20F/F Krt5-CreERT2- (A20WT) mice (four distinct mice in each group) 1 week after first intraperitoneal tamoxifen injection.

tag: tissue


title: F6 with TRF3c-HA, DMSO, HA, rep2

tag: cell type


title: F6 with TRF3c-HA, DMSO, HA, rep1


title: sample 280_genomic DNA from blood sample S1575


title: Krt5-CreERT2-Negative Sample 3

description:
Library name: A20WT-Mouse-3
RNASeq profiling of ear epidermal sheets derived from 8 week old A20F/F Krt5-CreERT2+ (A20KIKO) and A20F/F Krt5-CreERT2- (A20WT) mice (four distinct mice in each group) 1 week after first intraperitoneal tamoxifen injection.


title: C64 with TRF2 KO, IAA, Pol III, rep2


title: sample 282_genomic DNA from blood sample S1617


title: sample 279_genomic DNA from blood sample S1567


title: sample 281_genomic DNA from blood sample S1600

source_name: blood sample of patient with major depressive disorder

value: major depressive disorder


title: Sample 001, Ercc1 +/+, aortic arch, male, 6 weeks, AL

description:
Library name: 104707-001-001
001

value: Aortic arch

value: AL


title: C64 with TRF2 KO, IAA, Pol III, rep1


title: B8 with TRF2-HA, IAA, Pol III, rep2


title: F6 with TRF3c-HA, IAA, Pol III, rep1


title: Krt5-CreERT2-Positive Sample 1

description:
Library name: A20KIKO-Mouse-1
RNASeq profiling of ear epidermal sheets derived from 8 week old A20F/F Krt5-CreERT2+ (A20KIKO) and A20F/F Krt5-CreERT2- (A20WT) mice (four distinct mice in each group) 1 week after first intraperitoneal tamoxifen injection.


title: B8 with TRF2-HA, IAA, Pol III, rep1


title: sample 278_genomic DNA from blood sample S1552


title: B8 with TRF2-HA, DMSO,Pol III, rep1


title: Krt5-CreERT2-Positive Sample 2

description:
Library name: A20KIKO-Mouse-2
RNASeq profiling of ear epidermal sheets derived from 8 week old A20F/F Krt5-CreERT2+ (A20KIKO) and A20F/F Krt5-CreERT2- (A20WT) mice (four distinct mice in each group) 1 week after first intraperitoneal tamoxifen injection.


title: B8 with TRF2-HA, DMSO,Pol III, rep2


title: C64 with TRF2 KO, DMSO, Pol III, rep2


title: sample 277_genomic DNA from blood sample S1545


title: C64 with TRF2 KO, DMSO, Pol III, rep1


title: sample 276_genomic DNA from blood sample S1532


title: Krt5-CreERT2-Positive Sample 3

description:
Library name: A20KIKO-Mouse-3
RNASeq profiling of ear epidermal sheets derived from 8 week old A20F/F Krt5-CreERT2+ (A20KIKO) and A20F/F Krt5-CreERT2- (A20WT) mice (four distinct mice in each group) 1 week after first intraperitoneal tamoxifen injection.


title: C94 with HA-yTBP, IAA, Pol III, rep2


title: Krt5-CreERT2-Positive Sample 4

description:
Library name: A20KIKO-Mouse 4
RNASeq profiling of ear epidermal sheets derived from 8 week old A20F/F Krt5-CreERT2+ (A20KIKO) and A20F/F Krt5-CreERT2- (A20WT) mice (four distinct mice in each group) 1 week after first intraperitoneal tamoxifen injection.


title: C94 with HA-yTBP, IAA, Pol II, rep1


title: sample 274_genomic DNA from blood sample S1512


title: C94 with HA-yTBP, HSIAA, Pol II, rep2


title: DSS-treated vagal neurons 5

city: Manhasset

first: timothy

last: Morgan

state: New York

address: 350 Community Drive

department: Feinstein Institutes

institute: Northwell

description:
Library name: DSS5
Bulk RNA-seq on DSS-treatedvagal ganglia neurons

data_processing:
Raw reads were quality-trimmed using Trim Galore (v0.5.0).
Trimmed reads were aligned to the mouse transcriptome (GRCm38.91) using STAR (v2.6.1a)
Duplicates were marked and removed using Picard tools.
Expression quantification was performed using RSEM (v1.3.1) to calculate TPM and FPKM values based on Ensembl GRCm38.91 annotations.
Quality control of raw and trimmed reads was performed using FastQC (v0.11.8).
Assembly: GRCm38.91 (Ensembl)
Supplementary files format and content: Tab-delimited text files containing TPM and FPKM values for genes and isoforms, generated using RSEM.
Supplementary files format and content: Each sample includes two files: one for gene-level expression and one for isoform-level expression.

source_name: vagal ganglia

growth_protocol: Mice were housed under standard conditions with ad libitum access to food and water. Animals were monitored daily for health and weight.

extract_protocol:
On Day 7 or 8, mice were euthanized and the left and right nodose ganglia were harvested. Ganglia were enzymatically dissociated using collagenase/dispase, filtered, centrifuged, and the cell pellet flash-frozen in liquid nitrogen. Samples were submitted to SingulOmics for library generation.
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio), pooled by concentration and data volume, and sequenced on an Illumina NovaSeq 6000 with 150 bp paired-end reads..

treatment_protocol: Mice received either normal drinking water (control group) or 4% Dextran Sodium Sulfate (DSS) in drinking water for 7 consecutive days to induce colitis.

value: vagal ganglia

value: neurons

value: VGLUT2-ires-Cre; Ai95D (ROSA26-GCaMP6f)

value: DSS

tag: batch


title: C94 with HA-yTBP, HSIAA, Pol II, rep1

value: embryonic stem cell


title: Krt5-CreERT2-Negative Sample 4

description:
Library name: A20WT-Mouse-4
RNASeq profiling of ear epidermal sheets derived from 8 week old A20F/F Krt5-CreERT2+ (A20KIKO) and A20F/F Krt5-CreERT2- (A20WT) mice (four distinct mice in each group) 1 week after first intraperitoneal tamoxifen injection.


title: DSS-treated vagal neurons 11

description:
Library name: DSS11
Bulk RNA-seq on DSS-treated vagal ganglia neurons


title: sample 273_genomic DNA from blood sample S1507

value: male


title: C94 with HA-yTBP, HSIAA, HA, rep2


title: C94 with HA-yTBP, HSIAA, HA, rep1


title: sample 272_genomic DNA from blood sample S1489


title: sample 271_genomic DNA from blood sample S1483


title: C94 with HA-yTBP, IAA, HA, rep1


title: C94 with  HA-yNTD-mTBPc, IAA, Pol III, rep2


title: C94 with  HA-yNTD-mTBPc, IAA, Pol III, rep1


title: DSS-treated vagal neurons 10

description:
Library name: DSS10
Bulk RNA-seq on DSS-treated vagal ganglia neurons


title: C94 with HA-yTBP, IAA, HA, rep2


title: sample 270_genomic DNA from blood sample S1482


title: Control mouse vagal neurons 3

description:
Library name: Control3
Bulk RNA-seq on vagal ganglia neurons

value: control


title: sample 269_genomic DNA from blood sample S1475


title: Control mouse vagal neurons 1

description:
Library name: Control1
Bulk RNA-seq on vagal ganglia neurons


title: C94 with  HA-yNTD-mTBPc, HSIAA, Pol II, rep1


title: sample 275_genomic DNA from blood sample S1521


title: C94 with HA-yTBP, IAA, Pol II, rep2


title: C94 with  HA-yNTD-mTBPc, HSIAA, Pol II, rep2


title: C94 with HA-yTBP, IAA, Pol III, rep1


title: C94 with  HA-yNTD-mTBPc, HSIAA, HA, rep2


title: sample 268_genomic DNA from blood sample S1460


title: C94 with HA-yNTD-mTBPc, HSIAA, HA, rep1


title: Naive-MS4

city: Columbia

first: Rajiv

middle: R

last: Mohan

state: Missouri

address: 1520 East Rollins University of Missouri

department: Department of Veterinary Medicine and Surgery

institute: University of Missouri

description:
Library name: Sample 16
Gene count

data_processing:
Standard protocol using R-Programming
Quality check using FastQC
Read alignment using HISAT2
Gene counts using StringTie and StringTie Merge
Differential gene expression using DESeq2
Assembly: GRCm38
Supplementary files format and content: Tab-delimited txt files, gen counts

source_name: Cornea

extract_protocol:
Total RNA was isolated from mouse corneas via RNeasy Mini Kit according to the manufacturer’s instructions (QIAGEN, Hilden, Germany). For each sample, a total of 2 μg of RNA was taken for RNA-seq library preparation.
RNA-seq library preparation via a KAPA Stranded RNA-Seq Library Prep Kit (Roche) using manufacturer's protocol

value: Cornea

value: Male

tag: time

tag: strain

value: Naïve


title: C94 with  HA-yNTD-mTBPc, IAA, HA, rep2


title: sample 267_genomic DNA from blood sample S1456


title: C94 with HA-yNTD-mTBPc, IAA, HA, rep1


title: Naive-MS2

description:
Library name: Sample 14
Gene count

tag: treatment


title: C94 with HA-mTBP, IAA, Pol III, rep2


title: C94 with  HA-yNTD-mTBPc, IAA, Pol II, rep2


title: C94 with HA-mTBP, IAA, Pol III, rep1


title: sample 265_genomic DNA from blood sample S1360


title: C94 with HA-yNTD-mTBPc, IAA, Pol II, rep1


title: sample 264_genomic DNA from blood sample S1348


title: C94 with HA-mTBP, HSIAA, Pol II, rep2


title: C94 with HA-mTBP, HSIAA, Pol II, rep1


title: Naive-FS4

description:
Library name: Sample 12
Gene count

value: Female


title: Naive-MS3

description:
Library name: Sample 15
Gene count


title: Naive-FS3

description:
Library name: Sample 11
Gene count


title: sample 263_genomic DNA from blood sample S1310


title: C94 with HA-mTBP, HSIAA, HA, rep2


title: Naive-FS2

description:
Library name: Sample 10
Gene count


title: C94 with HA-mTBP, IAA, HA, rep2


title: Control mouse vagal neurons 2

description:
Library name: Control2
Bulk RNA-seq on vagal ganglia neurons

tag: genotype


title: C94 with HA-mTBP, HSIAA, HA, rep1


title: C94 with HA-mTBP, IAA, Pol II, rep2


title: sample 262_genomic DNA from blood sample S1302


title: Naive-FS1

description:
Library name: Sample 9
Gene count


title: C94 with HA-mTBP, IAA, HA, rep1


title: C94 with HA-mTBPc, IAA, Pol III, rep1


title: C94 with HA-mTBPc, IAA, Pol III, rep2


title: BLAST-MS4

description:
Library name: Sample 8
Gene count

value: OFBI


title: sample 261_genomic DNA from blood sample S1293

value: normal


title: Naive-MS1

description:
Library name: Sample 13
Gene count


title: sample 266_genomic DNA from blood sample S1423


title: C94 with HA-mTBPc, IAA, Pol II, rep2


title: C94 with HA-mTBP, IAA, Pol II, rep1


title: C94 with HA-mTBPc, IAA, Pol II, rep1


title: BLAST-MS3

description:
Library name: Sample 7
Gene count


title: C94 with HA-mTBPc, HSIAA, Pol II, rep2


title: sample 260_genomic DNA from blood sample S1251

value: female


title: sample 258_genomic DNA from blood sample S1219

value: major depressive disorder


title: BLAST-MS2

description:
Library name: Sample 6
Gene count


title: sample 259_genomic DNA from blood sample S1243


title: C94 with HA-mTBPc, HSIAA, Pol II, rep1


title: C94 with HA-mTBPc, HSIAA, HA, rep2


title: C94 with HA-mTBPc, HSIAA, HA, rep1


title: BLAST-MS1

description:
Library name: Sample 5
Gene count


title: sample 257_genomic DNA from blood sample M0413


title: C94 with HA-mTBPc, IAA, HA, rep2


title: C94 with HA-mTBPc, IAA, HA, rep1


title: sample 256_genomic DNA from blood sample M0142


title: C94, DMSO, IgG, rep2


title: BLAST-FS4

description:
Library name: Sample 4
Gene count


title: BLAST-FS3

description:
Library name: Sample 3
Gene count


title: C94, IAA, Pol III, rep2


title: C94, DMSO, IgG, rep1


title: C94, IAA, Pol III, rep1


title: C94, IAA, Pol II, rep1


title: C94, IAA, Pol II, rep2


title: sample 254_genomic DNA from blood sample M0047


title: C94, HS, IAA, Pol II, rep2


title: sample 253_genomic DNA from blood sample M0025


title: C94, HS, IAA, Pol II, rep1


title: CatSmo51_embryo3

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

description: 10x Genomics

data_processing:
Demultiplexing and preprocessing of the scRNA data was conducted with CellRanger v2.0.2 for KK21-M-074 to KK21-M-077. Similarly, CellRanger v3.0.2 was used for the cell line data (KK21-M-005 to KK21-M-009), and CellRanger v6.0.2 for the E18.5 samples KK22-M-198, KK22-M-199, KK22-M-200, KK22-M-273, KK22-M-274 and KK22-M-278.
After converting the raw 10X data to fastq format with CellRanger's mkfastq, the data was aligned against the murine reference transcriptome mm10 with the CellRanger count function using default values.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: fore-/midbrain

extract_protocol:
Cell dissociation using papain/DNAse solution, with incubation for 30min for primary tumors. Cell dissociation of 2D culture using Accutase and Trypsin EDTA for all conditions. All primary tumor samples were FACS sorted for live cells before taken for scRNA-seq.
Approximately 10,000 vital single-cells of each sample were processed for single-cell RNA sequencing using the Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1, the Chromium Next GEM Chip G and the Single Index Kit T Set A (10X Genomics) according to the manufacturer's instructions. In brief, single-cell GEM (Gel Beads-in-Emulsion) were generated by the Chromium Controller, followed by GEM-RT (reverse transcription), Dynabeads cleanup, cDNA amplification, SPRIselect beads cleanup and Library construction. Quality, purity, size and concentrations of cDNA and libraries were assured by measurement on a Tapestation 2200 (Agilent Technologies). Indexed libraries were sequenced separately by the Illumina NextSeq500 sequencing platform.
scRNA-seq with Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1

value: fore-/midbrain

value: hGFAP-cre; Ctnnb1(ex3)Fl/+SmoM2Fl/+

value: cre+

value: Etoposide 5mg/kg i.p

tag: treatment time

value: from E14.5 to E16.5


title: BLAST-FS1

description:
Library name: Sample 1
Gene count


title: sample 251_genomic DNA from blood sample C1423


title: 5T_CatSmo_Tu E18.5

description: 10x Genomics

value: corn oil i.p


title: sample 250_genomic DNA from blood sample C1421


title: CatSmo51_embryo1

description: 10x Genomics


title: 4T_CatSmo_Tu E18.5

description: 10x Genomics


title: MC3T3-E1 cells, SAS, 1

city: Jinan

first: Jingwei

last: Liu

state: State...

address: Wenhuaxi Rd 107#, Lixia District

institute: Qilu Hospital of Shandong University

description:
Library name: Sample4
SAS1_FPKM

data_processing:
Analysis of RNA-sequencing data The original data format for offline is fastq, and the software fastp(v0.23.0,https://github.com/OpenGene/fastp) is used to remove joints and low-quality sequences from the data to obtain CleanData. Use HISAT2(v2.2.1,http://daehwankimlab.github.io/hisat2/)to compare the obtained CleanData to the genome and obtain the bam file. Quantify genes using HTSeq(v0.13.5,http://htseq.readthedocs.io/en/release_0.9.1) software and calculate the FPKM value of genes using a self-designed Python script. Perform significant difference analysis between samples using R package edgeR(https://bioconductor.org/packages/release/bioc/html/edgeR.html), and define genes with difference multiples FC>2 times or FC<0.5 times and FDR<0.05 as differential genes. Using R package clusterProfiler(v4.2.0,http://bioconductor.org/packages/release/bioc/html/clusterProfiler.html) for GO (Gene Ontology, http://geneontology.org/) enrichment analysis and KEGG (Kyoto Encyclopedia of Genes and Genomes, http://www.kegg.jp/) enrichment analysis of differentially expressed genes, pathways with p<0.05 were considered significantly enriched.
Assembly: mm39
Supplementary files format and content: xls files include FPKM values and basemean (average normalized count values) for each sample

source_name: MC3T3-E1 cells

growth_protocol: MC3T3-E1 preosteoblast cells were maintained in α-MEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atomsphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was extracted using RNAprep Pure Plant Plus Kit (DP441, TIANGEN) and purified by RNAClean XP Kit (A63987, Beckman Coulter) and RNase-Free DNase Set (79254, Qiagen).
Libraries were constructed using U-mRNAseq Library Prep Kit (AT4221, KAITAI-BIO) with Ribo-off rRNA Depletion Kit (Bacteria) (N407, Vazyme). Libraries were pooled and sequenced using the Illumina NovaSeq machine as 150-bp paired-end sequencing reads.

treatment_protocol: MC3T3-E1 cells were treated with 200μM sulfasalazine for 24 hours before RNA extraction for the SAS group. Cells in the control group (CTL group) were left untreated.

tag: cell line

value: MC3T3-E1 cells

value: Preosteoblast cells

value: WT

value: 200μM sulfasalazine

value: 24 hours


title: MC3T3-E1 cells, SAS, 2

description:
Library name: Sample5
SAS2_FPKM


title: MC3T3-E1 cells, SAS, 3

description:
Library name: Sample6
SAS3_FPKM


title: sample 249_genomic DNA from blood sample C1411

value: male


title: sample 255_genomic DNA from blood sample M0073


title: MC3T3-E1 cells, CTL, 3

description:
Library name: Sample3
CTL3_FPKM


title: 3T_ CatSmo_Tu E18.5

description: 10x Genomics


title: MC3T3-E1 cells, CTL, 2

description:
Library name: Sample2
CTL2_FPKM


title: J259B HCC+adjacent NextSeq

city: Pittsburgh

first: Shuchang

state: PA

address: 203 Lothrop Street

institute: University of Pittsburgh

description:
Library name: sample 1
J259B HCC+adjacent

data_processing:
BCL basecalling and demultiplexing was performed by spaceranger mkfastq function (10X Genomics)
For each tissue section and corresponding library, the whole slide brightfield image and CytAssist image were aligned manually using the Loupe Browser.
FASTQ and imaging files were imported to Spaceranger count function (10X Genomics) for alignment and gene quantification
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: cell barcode
Supplementary files format and content: features.tsv.gz: gene list
Supplementary files format and content: matrix.mtx.gz: gene by cell expression matrix file
Supplementary files format and content: tissue_hires_image.png: imaging files with high resolution
Supplementary files format and content: tissue_lowres_image.png: imaging files with low resolution
Library strategy: Spatial Transcriptomics

source_name: liver

extract_protocol:
The cancer and benign liver regions were identified by a board-certified pathologist. The slides were deparaffinized, Hematoxylin/Eosin stained.
The slides underwent Visium cassette assembly, probe hybridization/ligation, tissue transfer to Visium slide, DNA isolation, clean-up, and ligation probe amplification based on the manufacturer's manual.

value: liver

value: HCC+adjacent


title: sample 248_genomic DNA from blood sample C1386

value: normal


title: BLAST-FS2

description:
Library name: Sample 2
Gene count

value: Cornea

value: Female

value: OFBI


title: J259X HCC NextSeq

description:
Library name: sample 2
J259X HCC

value: HCC


title: RNAseq_12h_INTS1_AID_Auxin_Plus_R2

city: Boston

first: Apoorva

last: Baluapuri

state: MA

address: 45 Shattuck St.

institute: Harvard Medical School

description:
Merged.DEseq.xlsx
RNAseq_12h_Plus_Auxin_F.bw
RNAseq_12h_Plus_Auxin_R.bw

data_processing:
Sequencing reads were filtered (requiring a mean quality score ≥ 20) and trimmed to 42 nt.
Samples were mapped to the Drosophila dm6 (spike) genome, and nonmapping reads subsequently mapped to hg38 using STAR 2.7.3a (parameters: outFilterMismatchNmax 4 outMultimapperOrder Random outFilterType BySJout alignSJoverhangMin 8 outFilterIntronMotifs RemoveNoncanonicalUnannotated).
Assembly: hg38
Supplementary files format and content: Spreadsheets with normalized counts and associated analysis from DEseq2

source_name: embryonic kidney

extract_protocol:
Cells were collected in Trizol, RNA was extracted, and genomic DNA contamination removed using DNAse.
rRNA depleted RNA was used as input to the Illumina TruSeq stranded total RNA kit or NEB Next Ultra II Directional library prep kit using the manufacturer's protocol.
Stranded RNA-seq, dUTP

value: embryonic kidney

value: homozygous miniAID

value: 12h, Auxin_Plus


title: MC3T3-E1 cells, CTL, 1

description:
Library name: Sample1
CTL1_FPKM


title: RNAseq_12h_INTS1_AID_Auxin_Plus_R1


title: RNAseq_12h_INTS1_AID_Auxin_Plus_R3


title: sample 252_genomic DNA from blood sample C1427


title: RNAseq_12h_INTS1_AID_Auxin_Minus_R3

description:
Merged.DEseq.xlsx
RNAseq_12h_Minus_Auxin_F.bw
RNAseq_12h_Minus_Auxin_R.bw

value: 12h, Auxin_Minus


title: CatSmo51_embryo2

description: 10x Genomics

value: fore-/midbrain

value: hGFAP-cre; Ctnnb1(ex3)Fl/+SmoM2Fl/+

value: cre+

value: Etoposide 5mg/kg i.p

value: from E14.5 to E16.5


title: RNAseq_12h_INTS1_AID_Auxin_Minus_R2


title: sample 246_genomic DNA from blood sample C1349

value: major depressive disorder

value: male


city: Shanghai

first: Heyu

last: Zhao

address: No.131 Dongan Road

institute: Fudan University

description:
Library name: sample27
20210415CZL-V60-3_BKDL210020494-1a-AK24345-N506

data_processing:
The transcriptomics data were processed by removing low-quality reads and calculating Q20, Q30, and GC content. Transcriptome data were aligned to the Mus musculus reference genome (GRCm38/mm10) using HISAT2.
Assembly: mm10
Supplementary files format and content: xlsx files

source_name: VTA Postnatal day 60_3

extract_protocol:
Cell samples for transcriptome sequencing were prepared according to the SMART-seq2 protocol. RNA integrity was assessed using the RNA Nano 6000 Assay Kit (Agilent Technologies, CA, USA).
The library was sequenced using an Illumina NovaSeq sequencer (Illumina, Inc., CA, USA), generating 150 bp paired end reads. A single sample generated raw data of approximately 6 GB. The RNA-seq samples were sent to Novogene Co., Ltd. (Beijing, China) for processing, library construction, and sequencing.

value: brain

value: dopaminergic neuron


title: RNAseq_12h_INTS1_AID_Auxin_Minus_R1


description:
Library name: sample26
20210415CZL-V60-2_BKDL210020494-1a-AK24346-N506

source_name: VTA Postnatal day 60_2


title: RNAseq_4h_INTS1_AID_Auxin_Plus_R3

description:
Merged.DEseq.xlsx
RNAseq_4h_Plus_Auxin_F.bw
RNAseq_4h_Plus_Auxin_R.bw

value: 4h, Auxin_Plus


title: sample 245_genomic DNA from blood sample C1347

value: normal

value: female


title: RNAseq_4h_INTS1_AID_Auxin_Plus_R2


description:
Library name: sample25
20210415CZL-V60-1_BKDL210020494-1a-AK23147-N506

source_name: VTA Postnatal day 60_1


title: RNAseq_4h_INTS1_AID_Auxin_Plus_R1


description:
Library name: sample24
20210415CZL-S60-4_BKDL210020494-1a-AK13862-N506

source_name: SNC Postnatal day 60_4


title: sample 244_genomic DNA from blood sample C1340