title: Chronic Sample4 HTO

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

data_processing:
The mRNA data was mapped to the mm10 genome using the STARsolo framework (STAR version 2.7.10a) (Dobin et al. 2013).
Gene quantification made use of a custom GFT file based on the ensembl gene annotation (version 102) and is filtered to only include transcripts of biotypes "protein_coding", "lncRNA" and all B- and T-cell receptor gene transcripts. The cell barcode whitelist used for STAR is the file 737K-august-2016.txt provided by 10x. Other non-standard command line options for STAR included "--outFilterType BySJout --outFilterMultimapNmax 10 --outSAMmultNmax 1 --outSAMtype BAMSortedByCoordinate --outSAMunmapped Within --soloType CB_UMI_Simple --soloStrand Reverse --outFilterScoreMin 30 --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIlen 10 --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter None". --soloMultiMappers EM --soloBarcodeReadLength 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloFeatures Gene --outSAMattributes NH HI AS nM CR CY UR UY GX GN CB UB".
The cell hashtag (HTO) data was also mapped and quantified with STAR, by using the same cell barcode whitelist. The genome index was build from the HTO sequences as well as the GTF file used for quantification. Additional command line options included "--outSAMtype BAM SortedByCoordinate --outSAMunmapped Within --soloType CB_UMI_Simple --soloStrand Forward --soloCBmatchWLtype 1MM_multi_Nbase_pseudocounts --soloUMIlen 10 --soloUMIfiltering MultiGeneUMI_CR --soloUMIdedup 1MM_CR --soloCellFilter None --soloBarcodeReadLength 0 --soloCBstart 1 --soloCBlen 16 --soloUMIstart 17 --soloFeatures Gene".
Assembly: mm10
Supplementary files format and content: Three files per sample which are the raw output of STARsolo: 1. gene counts (<sample_id>_matrix.mtx), 2. tab separated text file with gene/HTO IDs (<sample_id>_features.tsv), 3. tab separated text file with cell barcodes (<sample_id>_barcodes.tsv)

molecule: protein

source_name: Spleen

growth_protocol: 1. Experimental group, "neonat.":Neonatal, intercranial infection (within first 24h after birth) with artLCMV (Kallert et al., Nat.Comm., 2017) leading to life long virus carriage, harvest of splenocytes 8 weeks post infection. 8 biological replicates; 2. Experimental group, "chronic": Intra venous (i.v.) infection of adult animals at 7 weeks age with LCMV(Cl13/WE-GP) leading to chronic infection, harvest of splenocytes 24 days post infection. 6 biological replicates;

extract_protocol:
From splenocytes, LCMV GP66-77 (PE) tetramer positive, CD44(hi), CD4+T cells were isolated and enriched; First, CD4+T cells were negatively selected (Stemcell), followed by anti-PE positive selection of LCMV GP66-77 (PE) tetramer+ cells (Stemcell). Purified cells were barcoded (Biolegend) to identify the affiliated, individual animal for each cell. Cells were pooled accordingly and LCMV GP66-77(PE) tetramer+, CD44hi, CD4+T cells were then FACS sorted and loaded onto a Chromium NextGEM Chip K (10xGenomics). Two channels of the chip were used for each condition (neonat.; adult) following the manufacturer’s instructions.
The library was constructed according the manufacturers instructions of the Chromium Next GEM Single Cell 5' v2 Dual Index Kit (10xGenomics)

value: Spleen

value: CD4 T cells

value: HTO


title: bulk SLAM-seq of heart with 50mM of 4sU IT injected (6h labeling in total), sample 1

status: Public on Mar 30 2026

type: SRA

city: Berlin

first: Janita

last: Mintcheva

address: Robert-Rössle-Str. 10

country: Germany

institute: Max-Delbrück Center for Molecular Medicine

description:
Library name: SLAM-seq 50mM IT, sample 1
nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

library_source: transcriptomic

data_processing:
demultiplexing performed with bcl2fastq, mapping performed with STAR v2.7.8a (SLAM-seq time course) or STAR v2.7.3 (remaining samples)
Assembly: Danio rerio genome version GRCz11, release 92 for SLAM-seq time course; Danio rerio GRCz11, release 95 for remaining samples.
Supplementary files format and content: tab delimited text files containing nucleotide counts and SLAM specific nucleotide conversion counts for SLAM-seq analysis.

molecule: polyA RNA

organism: Danio rerio

source_name: heart

extract_protocol:
zebrafish hearts were homogenised and RNA extracted with TRIzol.
Thiol modification with iodoacetamide, followed by library construction based on a modified CEL-seq protocol. Detailed instructions can be found in the source publication.

tag: tissue

value: heart

tag: genotype

value: AB


title: bulk SLAM-seq of heart with 200mM of 4sU IT injected, 6hpci cryoinjured (7h labeling in total), sample 1

description:
Library name: SLAM-seq 200mM IT, 6hpci, sample 1
nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: bulk SLAM-seq of heart with 100mM of 4sU IT injected (6h labeling in total), sample 2

description:
Library name: SLAM-seq 100mM IT, sample 2
nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: Neonatal Infected Sample2 HTO

library_source: other

organism: Mus musculus

tag: cell type

tag: library type


title: IOSE-523-Replicate 2

city: Melbourne

first: Kathleen

last: Pishas

state: Victoria

address: 305 Grattan Street

department: Cancer Research

country: Australia

institute: Peter MacCallum Cancer Centre

description:
Library name: Sample 8
Column name in raw_counts_All_Samples.csv: 8-IOSE-523-Rep-2_S85

data_processing:
Libraries were indexed for multiplex sequencing, and RNA sequencing was performed using the Illumina NovaSeq X10 platform, generating 100 bp paired-end reads. A sequencing depth of 50 million reads per sample was targeted to ensure comprehensive transcriptome coverage. Raw sequencing data were processed using a Python-based RNA-seq analysis framework. Quality control and adapter trimming were conducted with Trimmomatic, followed by alignment to the human reference genome (hg38) using STAR.
Assembly: Normalization of gene expression was performed using counts per million (CPM), and differential expression analysis was conducted with DESeq2, implemented within Python.
Supplementary files format and content: CSV files include gene-level raw counts for each sample.

molecule: total RNA

organism: Homo sapiens

growth_protocol: Duplicate independent samples of LGSOC cell lines were grown for 72 hours (reaching 70–80%) with cell pellets collected. Cell lines were maintained in a 1:1 mixture of M199 and MCDB105 media (Sigma-Aldrich) supplemented with 10% HyClone FBS and 1% Penicillin-Streptomycin (Sigma-Aldrich). Cells were cultured at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol, which included on-column DNase treatment to remove residual genomic DNA. 1ug of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared by the Molecular Genomics Core (Peter MacCallum Cancer Centre, Australia) using the NEBNext Ultra II Directional RNA Library Prep Kit (New England BioLabs), incorporating rRNA depletion to enhance the detection of low-abundance transcripts.

treatment_protocol: Cell media only.

tag: cell line

value: Normal Ovary


title: VOA-1056-Replicate 1

description:
Library name: Sample 13
Column name in raw_counts_All_Samples.csv: 13-VOA-1056-Rep-1_S88

value: Low Grade Serous Ovarian

value: NRAS (Q61R)


title: Chronic Sample3 HTO


title: VOA-7681-Replicate 1

description:
Library name: Sample 10
Column name in raw_counts_All_Samples.csv: 10-VOA-7681-Rep-1_S86

value: KRAS (G12V)


title: VOA-7681-Replicate 2

description:
Library name: Sample 11
Column name in raw_counts_All_Samples.csv: 11-VOA-7681-Rep-2_S87


title: bulk SLAM-seq  of heart with 100mM of 4sU IT injected (6h labeling in total), sample 1

description:
Library name: SLAM-seq 100mM IT, sample 1
nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: RHI157_hg38

city: Singapore

first: Jinyue

last: Liu

address: 60 Biopolis Street

country: Singapore

institute: Genome Institute of Singapore

data_processing:
Reads were aligned to reference genome (hg38) using STAR.
Transcript abundances were quantified using RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files containing TPM and FPKM values for each sample

source_name: 33-day old forebrain organoid

extract_protocol:
RNA was extracted from three to five 33-day-old brain organoids per line using DirectZol RNA miniprep Plus kit (Zymo Research, R2051) as per manufacturer’s recommendations.
Library preparation (Illumina RiboZero, human) and sequencing (Illumina HiSeq4000) was performed at the Next-Generation Sequencing Platform (NGSP), Genome Institute of Singapore (GIS), A*STAR, Singapore.

tag: gender

value: M

tag: diagnosis

value: control


title: Neonatal Infected Sample1 HTO


title: RHI156_hg38

value: case


title: RHI159_hg38

value: F


title: Chronic Sample4 GEX

library_source: transcriptomic single cell

value: GEX


title: Mouse, Lung,  Silica_2, scATAC

city: Chengdu

first: Ruijie

last: Hou

address: Renmin South Road

country: China

institute: State Key Laboratory of Biotherapy

description: Library name: Silica_2

library_source: genomic single cell

data_processing:
The cellranger pipeline (version 3.1.0, 10X Genomics) was used to process raw sequencing output.
Assembly: mm10
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: genomic DNA

source_name: lung

extract_protocol:
The homogenized lung tissues were suspended in DMEM medium (C11995500BT, GIBCO) containing 1 mg/mL type I collagenase (C8140，Solarbio), 1 mg/mL type IV collagenase (C8160，Solarbio), 1 mg/mL Dispase II (D6430，Solarbio), and 0.2 mg/mL DNAase (D8071, Solarbio) at 37°C for 30 min. The digested lung tissues were filtered through a 70 μm filter membrane (BS-70-XBS, biosharp), and the filtrate was centrifuged and treated with red blood cell lysis buffer (R1010, Solarbio) for 10 min, centrifuged again under the same conditions, the pellet was washed once with sterile PBS (C10010500BT, GIBCO), and centrifuged again under the same conditions. Cell pellet was resuspended again with MACS mixture (2 mM EDTA, 0.1% BSA, 1% penicillin/streptomycin/antimitotic in DPBS) to obtain lung single cell suspension.
Single-cell ATAC sequencing (scATAC-seq) was performed using the 10X Chromium 3′ v3 kit (10X Genomics, Pleasanton, CA) according to the manufacturer's instructions.

value: lung


title: VOA-14202-Replicate 2

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.csv: 5-VOA-14202-Rep-2_S83


title: Chronic Sample3 GEX


title: Mouse, Lung,  Silica_3, scATAC

description: Library name: Silica_3


title: RHI158_hg38


title: Mouse, Lung,  Silica_1, scATAC

description: Library name: Silica_1


title: RHI155_hg38


title: VOA-14202-Replicate 1

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.csv: 4-VOA-14202-Rep-1_S82


title: IOSE-523-Replicate 1

description:
Library name: Sample 7
Column name in raw_counts_All_Samples.csv: 7-IOSE-523-Rep-1_S84


title: Neonatal Infected Sample1 GEX


title: Neonatal Infected Sample2 GEX


title: RHI154_hg38


title: RHI153_hg38


title: VOA-3723-Replicate 1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.csv: 1-VOA-3723-Rep-1_S71

value: MAPK Wildtype


title: RHI152_hg38


title: Chronic Sample3 VDJ

data_processing:
10x TCR sequencing data was analysed with the cellranger software (version 6.1.2). The cellranger vdj command with option "--chain TR" was run for each of the four samples separately using the vdj-GRCm38-alts-ensembl-5.0.0 references provided by 10x.
Assembly: vdj-GRCm38-alts-ensembl-5.0.0
Supplementary files format and content: comma separated text file with filtered contig annotations (for file format description see: https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/outputs/cr-5p-outputs-annotations-vdj)
Library strategy: TCR-seq

value: VDJ


title: Mouse, Lung,  Saline_2, scATAC

description: Library name: Saline_2


title: Chronic Sample4 VDJ

value: Spleen


title: Mouse, Lung,  Saline_3, scATAC

description: Library name: Saline_3


title: Mouse, Lung,  Bleomycin_3, scATAC

description: Library name: Bleomycin_3


title: scSLAM-seq of adult zebrafish hearts, sham injured, 6hps replicate 2

description: Library name: Hr60

data_processing:
Demultiplexing and mapping was performed using CellRanger v4.0.0
Assembly: Danio rerio genome GRCz11, release 92 with RFP gene added
Supplementary files format and content: tab separates values filex, matrix files and R object rds files

extract_protocol:
Zebrafish hearts were dissociated in HBSS supplemented with Pluronic-F68 and liberase (Roche). The cell suspension was then fixed in methanol and thiol modification performed by incubation in iodoacetamide overnight. A detailed protocol can be found in the source publication.
Libraries were constructed following manufacturers instructions of the 10X Genomics 3' GEX NextGEM v3.1 protocol.

tag: treatment

value: sham injury


title: WT_DOX_R2

city: Porto

first: Bruno

last: Pereira

address: Rua Alfredo Allen, 208

country: Portugal

description:
Library name: MEX3A-hyperADARcd_DOX_rep2
Column name in raw counts_All samples.xlsx: WT_DOX_R2

data_processing:
Sequence reads were trimmed using Trimmomatic version 0.39, with the following non-default settings recommended for the HyperTRIBE pipeline (https://github.com/rosbashlab/HyperTRIBE): Head-Crop: 6; Number of leading bases for trimming: 25; Number of trailing bases for trimming: 25; Average quality of 3 consecutive bases: 25; Minimum length 19; Adapters trimming (using TruSeq3 adapters): TruSeq3-PE.fa:2:30:10:2:keepBothReads.
Alignment of the paired-end RNA-seq reads to the human genome assembly was performed using STAR aligner (v2.7.8a). Besides default options, the following were applied specifically for HyperTRIBE: outFilterMismatchNoverLmax: 0.07; outFilterMatchNmin: 16; outFilterMultimapNmax: 1.  The aligned reads were outputted in BAM format sorted by coordinates. Aligned reads were further filtered in samtools (v1.12), considering only alignments with a mapping Phred quality score above 10. Duplicate marking of reads was carried out in MarkDuplicates (Picard) tool using the “REMOVE_DUPLICATES” option.
The GATK workflow was followed for variant calling to identify mutations in the aligned reads. Prior to the variant calling step, as per the GATK recommendations, a base quality recalibration step was carried out in order to detect and fix systematic errors on the quality scores.
HyperTRIBE specific analysis was restricted to mutations within annotated RNA transcripts, retrieved from the NCBI RNA reference sequence (RefSeq) collection, calling out A-to-G mutations in transcripts encoded by the forward strand and T-to-C mutations in transcripts encoded by the reverse strand. The filtered sets of RNA editing events from RNA-seq libraries of the same experimental condition were combined and the number of reads containing the reference (A or T) and alternative (G or C) alleles from each library at each site were counted.
Assembly: Human reference genome, build GRCh38 (patch release 12)
Supplementary files format and content: Tab-delimited excel file includes annotated transcripts' raw counts for each sample

growth_protocol: Human colorectal carcinoma cell line SW480 (ATCC CCL-228) was maitained in DMEM supplemented with 10% (v/v) fetal bovine serum (FBS) and 1% Pen/Strep in humidified atmosphere with 5% CO2 at 37ºC.

extract_protocol:
Total RNA was extracted using TRI Reagent according to the manufacturer’s instructions (Merck).
RNA samples were processed for rRNA removal using the Ribo-Zero kit (Illumina). Then, mRNA was randomly fragmented by adding fragmentation buffer and cDNA synthesized using random hexamers, after which a custom second-strand synthesis step was performed. This was followed by purification with AMPure XP beads, terminal repair, polyadenylation, sequencing adapter ligation, size selection and degradation of second-strand U-contained cDNA by the USER enzyme. After the final PCR enrichment, a strand-specific cDNA library was generated using the NEBNext Ultra II Directional RNA Library Prep kit for Illumina (New England Biolabs).

treatment_protocol: SW480 HyperTRIBE stable cell lines were plated for system induction with 1µg/mL doxycycline (DOX). After 48h of treatment, TurboRFP+ cells were collected by fluorescence activated cell sorting, along with non-induced cells, pelleted and stored at -80ºC for downstream analysis.

value: Colorectal cancer cell line

tag: genetic modification

value: MEX3A-hyperADARcd construct

value: DOX

tag: time


title: Neonatal Infected Sample2 VDJ

value: CD4 T cells


title: RHI151_hg38


title: ChIP_input

city: Chiba

first: Atsushi

last: Sasaki

state: Chiba

address: Chuo ku Inohana 1-8-1

department: Immunology

country: Japan

institute: Chiba University

description: Library name: input_1

library_source: genomic

data_processing:
FASTQ files were aligned to mm10 using Bowtie2.
PCR duplicates were removed using samtools.
Peaks were called using MACS2.
Peak annotation was performed using HOMER.
Motif analysis was conducted using MEME/HOMER.
Assembly: Mus musculus mm10 (GRCm38).
Supplementary files format and content: Raw count matrix (FPKM), BigWig coverage tracks

source_name: spleen

growth_protocol: Splenic CD4⁺ T cells were isolated from wild-type mice.

extract_protocol:
Chromatin was extracted from transduced Th2 cells for ChIP-seq using anti-Epas1 antibody. Input controls were processed in parallel.
ChIP DNA libraries were prepared using Illumina-compatible adapters following end repair, A-tailing, and PCR amplification.

treatment_protocol: Cells were differentiated into Th2 cells and transduced with empty vector, Epas1-WT, or Epas1-TM constructs. Cells were cultured under normoxic or hypoxic conditions.

value: spleen

value: Th2 cell

value: wild-type

value: input DNA

tag: batch


title: Mouse, Lung,  Bleomycin_2, scATAC

description: Library name: Bleomycin_2


title: Neonatal Infected Sample1 VDJ


title: MUT_DOX_R1

description:
Library name: MEX3ADKH-hyperADARcd_DOX_rep1
Column name in raw counts_All samples.xlsx: MUT_DOX_R1

value: MEX3ADKH-hyperADARcd construct


title: WT_NIC_R2

description:
Library name: MEX3A-hyperADARcd_NIC_rep2
Column name in raw counts_All samples.xlsx: WT_NIC_R2


title: WT_DOX_R1

description:
Library name: MEX3A-hyperADARcd_DOX_rep1
Column name in raw counts_All samples.xlsx: WT_DOX_R1


title: HiC_S7WT_rep2

city: Piscataway

first: Joshua

middle: K

last: Thackray

state: NEW JERSEY

address: 145 Bevier Road

department: Human Genetics Institute of New Jersey

country: USA

institute: Rutgers University

data_processing:
Reads were trimmed using cutadapt with the options–adaptor = AAGCTTAAGCTT (HindIII ligation junction) and–minimum-length = 20.
Reads of each pair were individually mapped to the mus (Xi) and cas (Xa) reference genomes using Bowtie2 and merged into Hi-C summary files and filtered using HOMER.
Hi-C contact maps were generated from reads in the filtered HOMER mus and cas tag directories using the ‘pre’ command of Juicer tools with the genomeID mm10.
The resulting Hi-C contact maps in .hic format were visualized and normalized with the ‘Coverage Square Root’ option in Juicebox version 1.8.8.
Principal component analysis (PCA) was done using the runHiCpca.pl command of HOMER with the filtered HOMER Hi-C tag directory as input and the options -res 250000 -superRes 250000 -genome mm10.
Pearson correlation maps were also computed by HOMER using the analyzeHiC command with the filtered HOMER Hi-C tag directory as input and the options -chr chrX -res 250000 –corr.
Assembly: mm10
Supplementary files format and content: *.hic files contain Hi-C contact maps generated from reads in the filtered HOMER mus and cas tag directories using the ‘pre’ command of Juicer tools with the genomeID mm10.
Supplementary files format and content: *.corr-*.txt files contain pearson correlation maps at the indicated resolution as computed by HOMER using the analyzeHiC command with the filtered HOMER Hi-C tag directory as input and the options -chr chrX -res 250000 –corr.
Supplementary files format and content: *.bedGraph files contain PC1 scores obtained from Principal component analysis (PCA) using the runHiCpca.pl command of HOMER with the filtered HOMER Hi-C tag directory as input and the options -res 250000 -superRes 250000 -genome mm10.

source_name: TTF

extract_protocol:
5 to10 million TTF cells were scrapped and resuspended in their culture medium supplemented with 10% FBS and 2% formaldehyde (Thermo Fisher #28908), followed by an incubation of 10 minutes rotating at room temperature to fixate the cells. The formaldehyde was quenched by adding cold glycine at a final concentration of 0.125M and incubating the cells for a further 5 minutes rotating at room temperature and 15 minutes on ice. The cells were washed twice with cold 1X PBS and nuclei were extracted by resuspending the cells in 1 ml of lysis buffer containing 10 mM Tris-HCl pH 8.0, 10 mM NaCl, 0.2% IGEPAL CA630 (SIGMA-ALDRICH #18896-50ML), 1× cOmplete EDTA-free protease inhibitor cocktail (Merck #11873580001) and incubating the cells for 30 minutes on ice. Afterwards, the nuclei were washed with 1.25X NEBuffer 2 (NEB #B7002S) and resuspended in 358 μl of the same buffer. 11 μl of 10% SDS (AppliChem #A0676,0250) was added to remove proteins not crosslinked and the samples were incubated for 1 hour at 37ºC, followed by the addition of 75 μl of 10% Triton X-100 (AppliChem #A4975,0100) to quench the SDS and another 1 hour incubation at 37ºC. The chromatin was then digested overnight at 37ºC by adding 1500 U of HindIII (NEB #R0104T). The following day, the DNA ends were filled in with dCTP, dGTP, dTTP and biotin-14-dATP (Invitrogen #19524-016). In-nucleus ligation was then performed by adding 25 U of T4 DNA ligase (Thermo Fisher #15224025), 100 μl of 10× ligation buffer (NEB #B0202S), 10 μl of 10 mg/ml BSA (NEB # B9001S) and 170.5 μl of nuclease-free water and incubating the sample for 4 hours at 16ºC. 12.5 μl of RNase A was added and the nuclei were further incubated for 30 minutes at 37ºC. To reverse crosslinking, the samples were incubated overnight at 65ºC with 60 μl of 10 mg/ml Proteinase K (Roche #03115879001). The DNA was subsequently purified using a phenol : chloroform : isoamyl alcohol 25:24:1 extraction and ethanol precipitation. Non-informative biotins at the DNA ends were removed by incubating the samples with dATP and T4 DNA polymerase for 4 hours at 20ºC. The DNA was again purified using a phenol : chloroform : isoamyl alcohol 25:24:1 extraction and ethanol precipitation and quantified. 10 ug of DNA were sonicated using a Covaris M220 focused ultrasonicator in 130 μl cuvettes (70 s, Duty Factor 10%, Peak Incidence Power 50, Cycles per Burst 200). The sheared DNA ends were repaired by adding dNTPs, T4 DNA polymerase (NEB #M0203L), T4 PNK (NEB #M0201L) and Klenow enzyme (NEB #M0210L) and dATP-tailed by purifying the DNA using CleanNGS SPRI beads (CleanNA #CNGS-0050) and adding dATP and Klenow exo-enzyme (NEB #M0212L).
The enrichment of informative DNA ligation products was carried out by pulling down those DNA fragments that contained a biotin using Dynabeads MyOne Streptavidin C1 paramagnetic beads (Thermo Fisher #65001) according to the manufacturer’s instructions. The bead-bound DNA fragments were resuspended in 50 μl of 1x ligation buffer (NEB #B0202S) and the NGS library was constructed by adding 4 μl of 15 uM pre-annealed adapter mix (Illumina Truseq system, see supplementary Table 9 for sequences), 1μl of T4 DNA ligase (NEB #M0202T) and incubating the mix for 2 hours at room temperature. After washing the bead-bound DNA fragments with the adapters ligated, the library was amplified using illumine Truseq PCR primers (see Supplementary Table 9 for sequences) and Phusion high-fidelity PCR master mix with HF buffer (NEB #M0531L) for 8 cycles following the program: 98 °C for 40 s, followed by 8 cycles of 10 s at 98 °C, 30 s at 62 °C, and 30 s at 72 °C, and final extension for 10 min at 72 °C. Last, the library-containing supernatant was recovered from the beads, and the library size distribution was delimited between 300-800 bp using CleanNGS SPRI beads double-sided selection (0.4-1 volumes; CleanNA #CNGS-0050). Concentration and size distribution were assessed by automated electrophoresis (Agilent Tapestation platform with high sensitivity D1000 ScreenTape).

tag: Sex

value: Female

value: TTF

value: WT


title: VOA-3723-Replicate 2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.csv: 2-VOA-3723-Rep-2_S81

value: Low Grade Serous Ovarian


title: scSLAM-seq of adult zebrafish hearts, sham injured, 6hps replicate 1

description: Library name: Hr43

value: heart

value: AB


title: scSLAM-seq of adult zebrafish hearts, injured, 6hpci replicate 2

description: Library name: Hr59

value: cryoinjury


title: HiC_S7KO_rep2


title: ChIP_Empty_2

description: Library name: ChIP_Empty_2

value: Empty + anti-Myc ChIP


title: ChIP_Epas1 TM_2

description: Library name: ChIP_Epas1 TM_2

value: Epas1TM-Myc + anti-Myc ChIP


title: adult zebrafish heart, healthy,#3

description:
Library name: Hr50
10X Genomics

data_processing:
Demultiplexing and mapping was performed using CellRanger v4.0.0
Assembly: Danio rerio genome GRCz11, release 92 with RFP gene added
Supplementary files format and content: tab separates values filex and matrix files

extract_protocol:
Zebrafish hearts were dissociated in HBSS supplemented with Pluronic-F68 and liberase (Roche). A detailed protocol can be found in the source publication.
Libraries were constructed following manufacturers instructions of the 10X Genomics 3' GEX NextGEM v3.1 protocol.


title: ChIP_Epas1 TM_1

description: Library name: ChIP_Epas1 TM_1


title: ChIP_Empty_1

description: Library name: ChIP_Empty_1


title: HiC_S7WT_rep1


title: HiC_S7KO_rep1


title: SC Islets HNF1A-MODY 2 scRNA-seq

city: Bergen

first: Lucas

last: Unger

address: Haukelansbakken 15

country: Norway

institute: University of bergen

description: Library name: Sample 4

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.4.
Assembly: GRCh38 (version refdata-gex-GRCh38-2020-A, 10X Genomics)
Supplementary files format and content: filtered_feature_bc_matrix

source_name: Stem cell islets

extract_protocol:
The harvested stem cell islets were treated with Triple solution for 30 minutes at 37 °C with shaking at 95 rpm. Following treatment, the islets were washed with 1× DPBS and viability was assessed, ensuring a viability rate of over 90%. The cells were then stored in a buffer containing PBS supplemented with 1% w/v BSA. Subsequently, the Single Cell 3.1 protocol was initiated immediately.
Library construction was performed according to the manufacturer’s instructions (Chromium Single Cell 3' v3.1 protocol, 10x Genomics). Briefly, single cells were resuspended in the master mix and loaded into the Chromium Controller with partitioning oil and barcoded Gel Beads to generate Gel Bead-in-Emulsion (GEMs). Within each GEM, the poly-A RNA from the cell lysate was reverse transcribed into cDNA. This cDNA contained the Illumina R1 primer sequence, a Unique Molecular Identifier (UMI), and the 10x barcode. The pooled barcoded cDNA was cleaned using Silane DynaBeads, then amplified by PCR. The appropriate fragment sizes were selected using SPRIselect reagent to ensure the cDNA was suitable for library construction. During the library construction, the Illumina R2 primer sequence, paired-end constructs with P5 and P7 adapters, and a sample index were added to each fragment for sequencing.

value: Stem cell islets

value: induced pluripotent stem cells

value: Differentiation to stem cell islets


title: WT_NIC_R1

description:
Library name: MEX3A-hyperADARcd_NIC_rep1
Column name in raw counts_All samples.xlsx: WT_NIC_R1

value: Colorectal cancer cell line

value: MEX3A-hyperADARcd construct


title: SC Islets HNF1A-MODY 1 scRNA-seq

description: Library name: Sample 3


title: MUT_DOX_R2

description:
Library name: MEX3ADKH-hyperADARcd_DOX_rep2
Column name in raw counts_All samples.xlsx: MUT_DOX_R2

value: DOX


title: RNA-seq_S7WT_Rep3_d0

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with HISAT2 (version 2.1.0, option --dta) and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
StringTie (version 1.3.3) was used to estimate transcript abundance using the Ensembl GRCm38 reference GTF file (obtained from the Illumina iGenomes).
Differential expression was analyzed with DESeq2 (version 1.32.0)
Assembly: mm10
Supplementary files format and content: csv files contain count matricies estimated by StringTie.
Supplementary files format and content: BigWig files contain Counts Per Million RNA-seq read signal

source_name: ES cells

extract_protocol:
RNA was extracted with TRIZOL reagent (Thermo Fisher, #15596026) following the manufacturer instructions.
PolyA selection was performed with NEBNext Poly(A) mRNA Magnetic Isolation kit (NEB, #E7490), and libraries constructed with NEBNext® Multiplex Oligos for Illumina® (Index Primers Set 1, NEB, #E7335S) following manufacturer instructions.

treatment_protocol: mouse ES cells were treated with LIF through day 0, after which LIF was withdrawn.

value: ES cells

tag: strain

value: C57BL6/CAST hybrid

tag: timepoint

value: day 0


title: Epas1 TM_1

description: Library name: Epas1 TM_1

value: spleen

value: Th2 cell

value: wild-type

value: Epas1 TM


title: bulk SLAM-seq of zebrafish hearts labeled for 24h with 4sU, sample 2

description:
Library name: SLAM-seq timecourse 24h, sample 2
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

value: heart

value: AB


title: bulk SLAM-seq of zebrafish hearts labeled for 24h with 4sU, sample 3

description:
Library name: SLAM-seq timecourse 24h, sample 3
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: SC Islets Non carrier  2 scRNA-seq

description: Library name: Sample 2

value: non carrier


title: RNA-seq_S7WT_Rep2_d0

value: Female

value: WT

value: LIF


title: RNA-seq_S7WT_Rep2_d7

value: day 7


title: RNA-seq_S7WT_Rep3_d7


title: Epas1 WT_2

description: Library name: Epas1 WT_2

value: Epas1 WT


title: scSLAM-seq of adult zebrafish hearts, injured, 6hpci replicate 1

description: Library name: Hr44

value: cryoinjury


title: bulk SLAM-seq of zebrafish hearts labeled for 24h with 4sU, sample 1

description:
Library name: SLAM-seq timecourse 24h, sample 1
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: Empty_2

description: Library name: Empty_2

value: Empty


title: Epas1 WT_1

description: Library name: Epas1 WT_1


title: adult zebrafish heart, healthy,#2

description:
Library name: Hr49
10X Genomics


title: RNA-seq_S7WT_Rep1_d7

value: ES cells


title: SC Islets Non carrier  1 scRNA-seq

description: Library name: Sample 1

value: Stem cell islets

value: induced pluripotent stem cells

value: Differentiation to stem cell islets


title: 8-week forebrain organoid XHI061

data_processing:
Sequencing reads were aligned to hG38 reference using Cell Ranger from 10x Genomics.
Feature-barcode matrices were generated using Cell Ranger from 10x Genomics.
Assembly: hG38
Supplementary files format and content: cellranger output (filtered feature barcode matrices)

source_name: 8-week forebrain organoid

growth_protocol: On Day 0, hiPSC colonies were lifted using Collagenase type IV and transferred onto ultra-low attachment six-well plates containing DMEM/F12, 20% KOSR, 1x GlutaMAX, 1x MEM-NEAA, 0.1mM 2-Mercaptoethanol, 1x Penicillin/Streptomycin, 2µM Dorsomorphin, 2µM A-83. On Day 5 and 6, 50% medium was replaced with DMEM/F12, 1x N2 supplement, 1x GlutaMAX, 1x MEM-NEAA, 1x Penicillin/Streptomycin, 1µM CHIR-99021, 1µM SB-431542. On Day 7, organoids were embedded in growth factor reduced (GFR)-Matrigel. On Day 14, organoids were mechanically dissociated from GFR-Matrigel and cultured with shaking in DMEM/F12, 1x N2 supplement, 1x B27 supplement, 1x GlutaMAX, 1x MEM-NEAA, 1x Penicillin/Streptomycin, 0.1mM 2-Mercaptoethanol, 2.5µg/ml Insulin. Medium was supplemented with 0.5% (v/v) GFR-Matrigel from Day 35 onwards.

extract_protocol:
Two to three ~56-day-old brain organoids were collected per hiPSC line, rinsed with Earle's Balanced Salt Solution (EBSS), chopped in pre-warmed papain solution (Worthington, LS003126) and incubated at 37oC for 30 minutes with gentle shaking. Cell suspension was gently triturated, strained and inactivated with ovomucoid solution (Worthington, LS003087). Cells were re-suspended to ~1000 cells/ul. More than 90% cell viability was obtained.
Singlecell libraries were prepared using 10x Genomics Chromium Single Cell 3' Kit v3 according to manufacturer's instructions at Spatial and Single Cell Genomics Platform (S2GP), GIS to obtain a targeted 8000 cells per sample and sequenced on Illumina NovaSeq 6000 at NGSP. At least 80,000 mean reads per cell was obtained.

value: 8-week forebrain organoid

value: case


title: RNA-seq_S7WT_Rep1_d0

value: C57BL6/CAST hybrid

value: day 0


title: bulk SLAM-seq of zebrafish hearts labeled for 12h with 4sU, sample 3

description:
Library name: SLAM-seq timecourse 12h, sample 3
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

value: heart

value: AB


title: Epas1 TM_2

description: Library name: Epas1 TM_2

value: spleen

value: Th2 cell

value: wild-type

value: Epas1 TM


title: Empty_1

description: Library name: Empty_1


title: 8-week forebrain organoid XHI058

value: Male


title: Hypoxia_3

description: Library name: Hypoxia_3

data_processing:
FASTQ files were quality-checked using FastQC.
Reads were aligned to mm10 using STAR.
Gene-level counts were generated using featureCounts.
Differential expression analysis was performed using DESeq2.
Gene set enrichment analysis (GSEA) was conducted using MSigDB signatures.
Assembly: Mus musculus mm10 (GRCm38).
Supplementary files format and content: Raw count matrix (FPKM)

growth_protocol: Naïve CD4⁺ T cells were isolated from spleens of BALB/c mice maintained under SPF conditions.

extract_protocol:
Total RNA was extracted from normoxic and hypoxic Th2 cells using TRIzol followed by column purification.
Bulk RNA-seq libraries were prepared using poly(A) mRNA enrichment and Illumina-compatible library construction kits.

treatment_protocol: Cells were differentiated into Th2 cells under standard Th2-polarizing conditions. Cells were cultured under normoxia (21% O₂) or hypoxia (1% O₂).

value: hypoxia


title: bulk SLAM-seq of zebrafish hearts labeled for 12h with 4sU, sample 1

description:
Library name: SLAM-seq timecourse 12h, sample 1
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: RNA-seq_S7KO_Rep3_d7

value: Female

value: LIF

value: day 7


title: 8-week forebrain organoid XHI060


title: 8-week forebrain organoid XHI059


title: RNA-seq_S7KO_Rep2_d7

value: ES cells


title: bulk SLAM-seq of zebrafish hearts labeled for 6h with 4sU, sample 3

description:
Library name: SLAM-seq timecourse 6h, sample 3
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: bulk SLAM-seq of zebrafish hearts labeled for 12h with 4sU, sample 2

description:
Library name: SLAM-seq timecourse 12h, sample 2
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: 8-week forebrain organoid XHI057

value: control


title: Hypoxia_2

description: Library name: Hypoxia_2


title: RNA-seq_S7KO_Rep3_d0


title: bulk SLAM-seq of zebrafish hearts labeled for 6h with 4sU, sample 2

description:
Library name: SLAM-seq timecourse 6h, sample 2
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: RNA-seq_S7KO_Rep1_d7


title: 8-week forebrain organoid XHI055

value: 8-week forebrain organoid


title: RNA-seq_S7KO_Rep2_d0


title: bulk SLAM-seq of zebrafish hearts labeled for 3h with 4sU, sample 3

description:
Library name: SLAM-seq timecourse 3h, sample 3
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: INPUT_H3K36Ac_S7WT_d7_Rep2

data_processing:
Raw read quality was first assessed with FastQC (version 0.11.3), followed by adapter clipping and quality trimming with Trimmomatic (version 0.36).
Reads were then aligned to the mouse (UCSC mm10) reference genome with Bowtie2 (version 2.2.9) with options --n 2 --k 10 and converted to BAM format with SAMtools (version 0.1.19).
SNPsplit (version 0.3.4) was used to sort aligned reads into three categories based on informative SNPs using the command `SNPsplit`: A) reads from mus musculus [genome1]; B) reads from mus Castaneus [genome2]; or C) unassignable reads [unassigned]. The resulting BAM files were then sorted by position and indexed using samtools (version 0.1.19).
BigWig ChIP signal files were generated from BAM data using deepTools (version 2.4.2) using a bin size of 50 bp, scaled with SES, and normalized by INPUT.
Peak calling was performed using MACS (version 2.2.7.1) by providing ChIP as --treatment and matched Input as --control. Peak calling was performed in --broad mode with --broad-cutoff 0.1 --qvalue 0.1 --scale-to small.
Assembly: mm10
Supplementary files format and content: BigWig signal files contain INPUT normalized ChIP-seq read counts using a bin size of 50bp and scaled with SES.
Supplementary files format and content: BroadPeak files contain broad peaks as called by MACS.

extract_protocol:
cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with 0.2 M glycine for 5 min and washed once with cold PBS. Nuclei were resuspended in 300 μl Lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, and cOmplete protease inhibitors) and incubated on ice for 30 min. Chromatin was sonicated to an average fragment size range of 300-500bp and subsequently centrifugated at 12,000 x g at 4°C for 15 min. Supernatants were diluted with Dilution Buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, and cOmplete protease inhibitors). SNAP-ChIP Spike-ins controls for K-AcylStat and K-MetStat (EpiCypher, #19-1001, #19-3001) were added for quantitative normalization and antibody validation purposes by following the manufacturer's instructions.  ChIP-grade protein A/G magnetic beads (Pierce, 26162) were conjugated for at least 3 hours in 1X PBS and 0.05% NP-40 with anti-H3K36ac (EpiCypher, #13-0035, Cell Signaling, #27683). Chromatin samples and antibody-conjugated magnetic beads were incubated overnight at 4°C on a rotator. Magnetic beads were then washed 3 times with ice-cold RIPA buffer (1% NP-40, 0.7% Na-deoxycholate, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 M LiCl2, and complete protease inhibitors) and once with Buffer TE (0.1 mM EDTA, 10 mM Tris-HCl pH 8.0). Magnetic beads and input samples (1% of total chromatin) were resuspended in freshly prepared RC buffer (0.1 M NaHCO3 and 1% SDS) in the presence of proteinase K for 5 hours at 60°C on a thermomixer with 900 rpm. DNA was purified using a Binding Buffer NTB and Nucleospin PCR Clean-up Kit from Macherey-Nagel.
library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.

tag: chip antibody

value: WT


title: bulk SLAM-seq of zebrafish hearts labeled for 3h with 4sU, sample 2

description:
Library name: SLAM-seq timecourse 3h, sample 2
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: 8-week forebrain organoid XHI056


title: RNA-seq_S7KO_Rep1_d0

value: C57BL6/CAST hybrid


title: 8-week forebrain organoid XHI054


title: bulk SLAM-seq of zebrafish hearts labeled for 6h with 4sU, sample 1

description:
Library name: SLAM-seq timecourse 6h, sample 1
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: Normoxia_1

description: Library name: Normoxia_1

value: normoxia


title: Hypoxia_1

description: Library name: Hypoxia_1


title: Xenobot, 4 hours after ATP stimulus, sample 3

city: Medford

first: Vaibhav

middle: P

last: Pai

state: MA

address: 200 Boston Ave suite 4600

department: Biology

institute: Tufts University

description:
Library name: Xenobot_ATP_Stimulus_4 hour_S3
column name in rsem_gene_counts.tsv: rsem/S17_ATP_4_hrs.genes.results

data_processing:
Trim adapter and polyX tails: The RNAseq raw reads are single-end reads. The reads were trimmed for adapter “CTGTCTCTTATACACATCTCCGAGCCCACGAGAC” and polyX tails, then filtered by sequencing Phred quality (>= Q15) using fastp (Chen et al., 2018).
Generating genome indexes: Xenopus laevis genome sequences and gene annotation were downloaded from the NCBI genome database, version 10.1. GenomeGenerate module of the STAR aligner (Dobin et al., 2013) was used to generate the genome indexes. STAR aligner option was set to sjdbOverhang = 75 for 76-bp reads, as was ideal.
Aligning reads to the genome: Adapter-trimmed reads were aligned to the genome using STAR aligner with the two-pass option. Reads were mapped across the genome to identify novel splice junctions in the first-pass. These new annotations were then incorporated into the reference indexes and reads were re-aligned with this new reference in the second pass. While more time-intensive, this step could aid in aligning across these junctions, especially in organisms where the transcriptome was not as well annotated. The resulting gene count table is at rsem_gene_counts.tsv
Estimate expression: Gene expression was estimated from the gene alignments using RSEM tool for accurate quantification of gene and isoform expression from RNA-Seq data (Li and Dewey, 2011).The resulting gene count table is at rsem_gene_counts.tsv
Filtering, normalization, and transformation: To filter out low expressing genes, we kept genes that had counts per million (CPM) more than 0.6 in at least 3 samples. There were 28009 genes after filtering. We then normalized counts by weighted trimmed mean of M-values (TMM) (Robinson and Oshlack 2010). If no normalization is needed, all the normalization factors would be 1. Here the normalization factors were between 0.78 and 1.28. To use linear models in the following analysis, we performed Voom transformation (Law et al. 2014) to transform counts into logCPM.
Differential expression analysis: To discover the differential genes, we use limma, an R package that powers differential expression analyses (Ritchie et al. 2015). We performed moderated t-tests to detect genes that were differentially expressed
Assembly: Xenopus laevis (NCBI genome database, version 10.1)
Supplementary files format and content: tab-delimited file includes a gene count table
Supplementary files format and content: tab-delimited file includes logCPM normalized values

organism: Xenopus laevis

source_name: derived from embryonic ectoderm

growth_protocol: Xenopus laevis embryos were fertilized in vitro according to standard protocols in 0.1X Marc's Modified Ringer's (MMR) solution and kept at 14oC. At stage 9 embryos were transferred to 0.75X MMR solution and the ectodermal animal cap tissue was cut out of the embryos. This tissue was allowed to heal and develop for 7 days in 0.75X MMR at 14oC leading to formation of autonomously-moving Xenobots.

extract_protocol:
A sample of Xenobot consisted of 50 pooled Xenobots and each was repeated 3 times. Total RNA was extracted from tissue using TRI Reagent (Molecular Research Center, Inc - MRC) as per the manufacturer’s protocol, and total RNA quality and quantity was assessed using a NanoDrop spectrophotometer (Thermo Fisher Scientific).
RNA library preparation was done with the Illumina Stranded Total RNA with Ribo-Zero Plus. Libraries were then multiplexed, and an rRNA depletion run using single-end, 75-nucleotide sequencing was performed on NextSeq 550 High Output 75 cycles.

treatment_protocol: Embryo extract was prepared by placing three stage 8/9 Xenopus embryos into 100 µls of 0.75X MMR in an Eppendorf tube. Embryos were homogenized using a sterile pestle, followed by vigorously pipetting to generate a uniform extract. For experiments, 10 µls of this concentrated extract was added per 14 mL of 0.75X MMR as a final concentration. Adenosine triphosphate (ATP) (Sigma-Aldrich, A1852) is unstable in aqueous solutions; therefore, it was dissolved in 0.75X MMR at a stock concentration of 100 mM, aliquoted into single use portions, and stored at -20oC. For experiments, aliquots were thawed immediately before use, and 10 µL of stock solution was added per 4 mL of 0.75X MMR to achieve a final concentration of 250 µM.

value: derived from embryonic ectoderm

value: epidermal

value: ATP


title: INPUT_H3K36Ac_S7WT_d0_Rep2

value: day 0


title: bulk SLAM-seq of zebrafish hearts labeled for 3h with 4sU, sample 1

description:
Library name: SLAM-seq timecourse 3h, sample 1
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

value: heart

value: AB


title: 8-week forebrain organoid XHI050

value: Male

value: case


title: bulk SLAM-seq of zebrafish hearts labeled for 1h with 4sU, sample 3

description:
Library name: SLAM-seq timecourse 1h, sample 3
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: INPUT_H3K36Ac_S7KO_d7_Rep2

value: Female


title: INPUT_H3K36Ac_S7KO_d0_Rep2

value: LIF


title: Normoxia_3

description: Library name: Normoxia_3

value: spleen

value: Th2 cell

value: wild-type


title: Normoxia_2

description: Library name: Normoxia_2


title: Xenobot, immediately after ATP stimulus, sample 3

description:
Library name: Xenobot_ATP_Stimulus_0 hour_S3
column name in rsem_gene_counts.tsv: rsem/S16_ATP_0_hrs.genes.results


title: 8-week forebrain organoid XHI049

value: 8-week forebrain organoid

value: control


title: Xenobot, 4 hours after ATP stimulus, sample 2

description:
Library name: Xenobot_ATP_Stimulus_4 hour_S2
column name in rsem_gene_counts.tsv: rsem/S11_ATP_4_hrs.genes.results

value: WT


title: ChIP_H3K36Ac_S7WT_d7_Rep2

value: ES cells

value: C57BL6/CAST hybrid

value: day 7


title: 8-week forebrain organoid, XHI022

data_processing:
Sequencing reads were aligned to hG38 reference using Cell Ranger from 10x Genomics.
Feature-barcode matrices were generated using Cell Ranger from 10x Genomics.
Genome_build: hG38
Supplementary_files_format_and_content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

extract_protocol:
Two to three ~56-day-old brain organoids were collected per hiPSC line, rinsed with Earle's Balanced Salt Solution (EBSS), chopped in pre-warmed papain solution (Worthington, LS003126) and incubated at 37oC for 30 minutes with gentle shaking. Cell suspension was gently triturated, strained and inactivated with ovomucoid solution (Worthington, LS003087). Cells were re-suspended to ~1000 cells/ul. More than 90% cell viability was obtained.
Singlecell libraries were prepared using 10x Genomics Chromium Single Cell 3' Kit v3 according to manufacturer's instructions at Spatial and Single Cell Genomics Platform (S2GP), GIS to obtain a targeted 8000 cells per sample and sequenced on Illumina NovaSeq 6000 at NGSP. At least 80,000 mean reads per cell was obtained.
single-cell RNA-seq


title: 8-week forebrain organoid XHI052


title: 8-week forebrain organoid XHI053


title: 8-week forebrain organoid XHI051


title: Xenobot, immediately after ATP stimulus, sample 1

description:
Library name: Xenobot_ATP_Stimulus_0 hour_S1
column name in rsem_gene_counts.tsv: rsem/S04_ATP_0_hrs.genes.results

value: derived from embryonic ectoderm

value: epidermal

value: ATP


title: bulk SLAM-seq of zebrafish hearts labeled for 0.5h with 4sU, sample 2

description:
Library name: SLAM-seq timecourse 0.5h, sample 2
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

data_processing:
demultiplexing performed with bcl2fastq, mapping performed with STAR v2.7.8a (SLAM-seq time course) or STAR v2.7.3 (remaining samples)
Assembly: Danio rerio genome version GRCz11, release 92 for SLAM-seq time course; Danio rerio GRCz11, release 95 for remaining samples.
Supplementary files format and content: tab delimited text files containing nucleotide counts and SLAM specific nucleotide conversion counts for SLAM-seq analysis.

value: heart

value: AB


title: 8-week forebrain organoid, XHI021

value: case


title: bulk SLAM-seq of zebrafish hearts labeled for 0.5h with 4sU, sample 1

description:
Library name: SLAM-seq timecourse 0.5h, sample 1
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: 8-week forebrain organoid, XHI020

value: Male


title: ChIP_H3K36Ac_S7KO_d7_Rep2

value: Female


title: Xenobot, 4 hours after ATP stimulus, sample 1

description:
Library name: Xenobot_ATP_Stimulus_4 hour_S1
column name in rsem_gene_counts.tsv: rsem/S05_ATP_4_hrs.genes.results


title: bulk SLAM-seq of zebrafish hearts labeled for 1h with 4sU, sample 1

description:
Library name: SLAM-seq timecourse 1h, sample 1
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: ChIP_H3K36Ac_S7KO_d0_Rep2

value: LIF

value: day 0


title: bulk SLAM-seq of zebrafish hearts labeled for 1h with 4sU, sample 2

description:
Library name: SLAM-seq timecourse 1h, sample 2
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: bulk SLAM-seq of zebrafish hearts labeled for 0.5h with 4sU, sample 3

description:
Library name: SLAM-seq timecourse 0.5h, sample 3
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: bulk SLAM-seq of healthy, uninjected zebrafish hearts, sample 3

description:
Library name: SLAM-seq timecourse 0h, sample 3
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: Xenobot, 4 hours after Extract stimulus, sample 3

description:
Library name: Xenobot_Ext_Stimulus_4 hour_S3
column name in rsem_gene_counts.tsv: rsem/S15_Ext_4_hrs.genes.results

value: Embryo extract


title: INPUT_H3K27me3_S7WT_ES_d7_Rep2

extract_protocol:
cells were crosslinked with 1% formaldehyde for 10 min at room temperature and then quenched with 0.2 M glycine for 5 min and washed once with cold PBS. Nuclei were resuspended in 300 μl Lysis buffer 2 (1% SDS, 10 mM EDTA, 50 mM Tris-HCl pH 8.0, and cOmplete protease inhibitors) and incubated on ice for 30 min. Chromatin was sonicated to an average fragment size range of 300-500bp and subsequently centrifugated at 12,000 x g at 4°C for 15 min. Supernatants were diluted with Dilution Buffer (1% Triton X-100, 2 mM EDTA, 20 mM Tris-HCl pH 8.0, 150 mM NaCl, and cOmplete protease inhibitors). SNAP-ChIP Spike-ins controls for K-AcylStat and K-MetStat (EpiCypher, #19-1001, #19-3001) were added for quantitative normalization and antibody validation purposes by following the manufacturer's instructions.  ChIP-grade protein A/G magnetic beads (Pierce, 26162) were conjugated for at least 3 hours in 1X PBS and 0.05% NP-40 with anti-H3K27me3 (Cell Signaling, #9733). Chromatin samples and antibody-conjugated magnetic beads were incubated overnight at 4°C on a rotator. Magnetic beads were then washed 3 times with ice-cold RIPA buffer (1% NP-40, 0.7% Na-deoxycholate, 50 mM Tris-HCl pH 8.0, 1 mM EDTA, 0.5 M LiCl2, and complete protease inhibitors) and once with Buffer TE (0.1 mM EDTA, 10 mM Tris-HCl pH 8.0). Magnetic beads and input samples (1% of total chromatin) were resuspended in freshly prepared RC buffer (0.1 M NaHCO3 and 1% SDS) in the presence of proteinase K for 5 hours at 60°C on a thermomixer with 900 rpm. DNA was purified using a Binding Buffer NTB and Nucleospin PCR Clean-up Kit from Macherey-Nagel.
library preparation was performed using NEBNext® Ultra II DNA Library Prep Kit for Illumina® (NEB) according to manufacturer instructions.


title: ChIP_H3K36Ac_S7WT_d0_Rep2


title: Xenobot, immediately after ATP stimulus, sample 2

description:
Library name: Xenobot_ATP_Stimulus_0 hour_S2
column name in rsem_gene_counts.tsv: rsem/S10_ATP_0_hrs.genes.results


title: 8-week forebrain organoid, XHI015

value: 8-week forebrain organoid


title: bulk SLAM-seq of healthy, uninjected zebrafish hearts, sample 2

description:
Library name: SLAM-seq timecourse 0h, sample 2
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate

extract_protocol:
zebrafish hearts were homogenised and RNA extracted with TRIzol.
Thiol modification with iodoacetamide, followed by library construction based on a modified CEL-seq protocol. Detailed instructions can be found in the source publication.


title: Xenobot, 4 hours after Extract stimulus, sample 2

description:
Library name: Xenobot_Ext_Stimulus_4 hour_S2
column name in rsem_gene_counts.tsv: rsem/S09_Ext_4_hrs.genes.results


title: 8-week forebrain organoid, XHI016


title: bulk SLAM-seq of healthy, uninjected zebrafish hearts, sample 1

description:
Library name: SLAM-seq timecourse 0h, sample 1
bam file contains MD and MT tag used for later T>C conversion calling, nucleotide_counts and mutation_occurrences are used for calculation of bulk labeling rate


title: Xenobot, 4 hours after Extract stimulus, sample 1

description:
Library name: Xenobot_Ext_Stimulus_4 hour_S1
column name in rsem_gene_counts.tsv: rsem/S03_Ext_4_hrs.genes.results


title: INPUT_H3K27me3_S7WT_ES_d0_Rep2


title: INPUT_H3K27me3_S7KO_ES_d7_Rep2


title: Xenobot, immediately after Extract stimulus, sample 3

description:
Library name: Xenobot_Ext_Stimulus_0 hour_S3
column name in rsem_gene_counts.tsv: rsem/S14_Ext_0_hrs.genes.results


title: 8-week forebrain organoid, XHI014

value: control


title: wild type and hamp-/-, 24 hpf, CMO

city: Shanghai

first: mingjian

last: peng

address: No. 999 Hucheng Ring Road

institute: Shanghai Ocean University

description: 10x Genomics multiplexing

data_processing:
We performed the cellranger multi pipeline of Cell Ranger(7.1.0) to analyze 3' Cell Multiplexing data, and implement Seurat’s HTOdemux to further differentiate CMOs.
Assembly: GRCz11 (Ensemble release 108)
Supplementary files format and content: barcodes.tsv.gz contains the captured cell barcode,  features.tsv.gz contains the genes on the alignment,  matrix.mtx.gz contains the gene expression matrix.

source_name: embryo

extract_protocol:
For the experiment, 50 embryos were used to generate each sample. Zebrafish embryos were grown to the indicated times and chorions were removed by incubating in 10 ml 1mg/mL PronaseE (Sigma P5147-1G) for about 10 min. Then added 1 ml FBS to terminate digestion followed washing in 0.5x Danieau’s solution. Next, added deyolking buffer and pipette up and down about 10 times with the P1000 pipette until the yolk has dissolved and only the bodies of the embryos are visible. Zebrafish embryos were dissociated with trypsin-EDTA until the torso was invisible, then the digestion was stopped with FBS and filtered with 30 um cell strainer. Resuspended cells with 0.04%BSA-DPBS. Here was the single cell needed to get on the machine.
Library was performed according to the manufacter’s instructions (single cell 3’cellplexing v3.1 protocol, 10x Genomics). After cell lysis, Gel Beads automatically dissolved and released a large number of primer sequences, and reversely transcribed with mRNA with PolyA to generate the first strand of cDNA with 10x Barcode and UMI information. After the GEM was broken, a strand of cDNA was purified by magnetic beads and amplified by PCR to obtain a stable cDNA. Then the amplified cDNA was digested and segmented to screen the appropriate length fragment. The 3-terminal expression profile library containing P5 and P7 adaptors and double-end index was constructed by end repair, adding A and connecting Read2 sequencing primers.

value: embryo

value: WT/hamp knockdown

tag: age

value: 24 hpf

value: CMO


title: 8-week forebrain organoid, XHI007


title: INPUT_H3K27me3_S7KO_ES_d0_Rep2

value: ES cells

value: C57BL6/CAST hybrid


title: ChIP_H3K27me3_S7WT_ES_d7_Rep2

value: WT

value: day 7


title: Xenobot, immediately after Extract stimulus, sample 2

description:
Library name: Xenobot_Ext_Stimulus_0 hour_S2
column name in rsem_gene_counts.tsv: rsem/S08_Ext_0_hrs.genes.results

value: derived from embryonic ectoderm

value: epidermal


title: wild type and hamp-/-, 36 hpf, CMO

description: 10x Genomics multiplexing

value: 36 hpf


title: 8-week forebrain organoid, XHI013

value: Female

value: case


title: ChIP_H3K27me3_S7KO_ES_d7_Rep2


title: Xenobot, before stimulus, sample 2

description:
Library name: Xenobot_before_stimulus_S2
column name in rsem_gene_counts.tsv: rsem/S07_Ctrl.genes.results


title: Xenobot, before stimulus, sample 1

description:
Library name: Xenobot_before_stimulus_S1
column name in rsem_gene_counts.tsv: rsem/S01_Ctrl.genes.results


title: 8-week forebrain organoid, XHI008

value: Male


title: wild type and hamp-/-, 24 hpf, GEX

description: 10x Genomics multiplexing

value: GEX


title: 8-week forebrain organoid, XHI006

value: 8-week forebrain organoid


title: Xenobot, before stimulus, sample 3

description:
Library name: Xenobot_before_stimulus_S3
column name in rsem_gene_counts.tsv: rsem/S13_Ctrl.genes.results


title: wild type and hamp-/-, 12 hpf, CMO

description: 10x Genomics multiplexing

value: 12 hpf


title: ChIP_H3K27me3_S7WT_ES_d0_Rep2

value: LIF

value: day 0


title: Xenobot, immediately after Extract stimulus, sample 1

description:
Library name: Xenobot_Ext_Stimulus_0 hour_S1
column name in rsem_gene_counts.tsv: rsem/S02_Ext_0_hrs.genes.results

value: Embryo extract


title: 8-week forebrain organoid, XHI002

value: control


title: Mesenchymal cells, CLAD_line_4, C/EBPD siRNA

status: Public on Mar 29 2026

city: Ann Arbor

first: Lu

last: Lu

state: MI

address: 100 Washtenaw Ave.

department: Department of Computational Medicine and Bioinformatics

institute: University of Michigan, Ann Arbor

description: Novogene

data_processing:
Raw RNA-seq reads from both treated and control groups were aligned to the GRCh38 reference genome using STAR (v.2.7.11a) with default parameters. STAR produced sorted BAM files, which were used as the input for HTSeq-count (v.2.0.8) to generate gene-level read counts.
Assembly: GRCh38
Supplementary files format and content: The processed data files are in .txt format, containing two columns: the first column lists gene names, and the second column provides the corresponding gene counts.

source_name: Mesenchymal cells

extract_protocol:
CLAD MCs treated with either scrambled (non-targeting) control siRNA or C/EBPD siRNA were harvested 24h post-transfection. Total RNA was isolated using the RNeasy Mini Plus Kit (Qiagen) according to the manufacturer’s instructions.
RNA was quantified via measuring absorbance at 260/280nm using a NanoDrop 2000 (ThermoFisher) prior to submission to the Emory Integrated Genomics Core (EIGC). After RNA quality assessment was performed using a TapeStation system (Agilent Technologies), all mRNA was sent to a sequencing company (Novogene, China). Bulk RNA-seq (Eukaryotic RNA-Seq, non-directional, stranded library) was conducted by Novogene using the Illumina NovaSeq PE150 platform that employs a paired-end sequencing technology yielding 150-bp read lengths, with all raw reads first cleared of adapter sequences.

value: Mesenchymal cells

value: mRNA


title: ChIP_H3K27me3_S7KO_ES_d0_Rep2

value: ES cells

value: C57BL6/CAST hybrid


title: 8-week forebrain organoid, XHI004


title: Mesenchymal cells, CLAD_line_3, C/EBPD siRNA

description: Novogene


title: Mesenchymal cells, CLAD_line_2, Scr siRNA

description: Novogene


title: Mesenchymal cells, CLAD_line_4, Scr siRNA

description: Novogene


title: Mesenchymal cells, CLAD_line_2, C/EBPD siRNA

description: Novogene


title: wild type and hamp-/-, 36 hpf, GEX

description: 10x Genomics multiplexing

value: embryo

value: WT/hamp knockdown


title: Mesenchymal cells, CLAD_line_3, Scr siRNA

description: Novogene


title: Mesenchymal cells, CLAD_line_1, C/EBPD siRNA

description: Novogene


title: 1441-1.TCR.SamplePool.rs104946

city: Beaverton

first: Benjamin

middle: N

last: Bimber

state: OR

address: 505 NW 185th Ave

description: Library name: 104946

data_processing:
CellRanger count
DropletUtils emptyDrops
Seurat Normalize/Scale/PCA
Assembly: GCA_003339765.3
Supplementary files format and content: Sparse count matrix (RDS file)
Supplementary files format and content: Seurat Object (RDS file)

organism: Macaca mulatta

source_name: PBMC

extract_protocol:
10x Genomics 5' VDJ scRNA-seq
10x Genomics 5' VDJ scRNA-seq

value: PBMC


title: Mesenchymal cells, CLAD_line_1, Scr siRNA

description: Novogene


title: wild type and hamp-/-, 12 hpf, GEX

description: 10x Genomics multiplexing


title: 1441-1.GEX.SamplePool.rs104945

description: Library name: 104945


title: 1441-2.GEX.SamplePool.rs104949

description: Library name: 104949


title: 1422-2.TCR.SamplePool.rs103997

description: Library name: 103997


title: 1441-2.HTO.SamplePool.rs104947

description: Library name: 104947


title: 1422-1.TCR.SamplePool.rs103993

description: Library name: 103993


title: 1441-1.HTO.SamplePool.rs104943

description: Library name: 104943


title: 1422-2.HTO.SamplePool.rs103994

description: Library name: 103994


title: 1422-2.GEX.SamplePool.rs103996

description: Library name: 103996


title: 1441-2.TCR.SamplePool.rs104950

description: Library name: 104950


title: 1411-2.GEX.SamplePool.rs103820

description: Library name: 103820


title: 1411-2.HTO.SamplePool.rs103818

description: Library name: 103818


title: 1422-1.GEX.SamplePool.rs103992

description: Library name: 103992


title: 729-1.HTO.SamplePool.rs87634

description: Library name: 87634


title: 1411-1.TCR.SamplePool.rs103817

description: Library name: 103817


title: 1422-1.HTO.SamplePool.rs103990

description: Library name: 103990


title: 1411-1.GEX.SamplePool.rs103816

description: Library name: 103816


title: 1411-2.TCR.SamplePool.rs103821

description: Library name: 103821


title: 740-8.HTO.37012.rs79993

description: Library name: 79993

source_name: Bone marrow,MesLN,PLN,Spleen

value: Bone marrow,MesLN,PLN,Spleen


title: 1411-1.HTO.SamplePool.rs103814

description: Library name: 103814


title: 740-5.HTO.SamplePool.rs79981

description: Library name: 79981


title: 740-1.HTO.SamplePool.rs87626

description: Library name: 87626


title: 740-2.HTO.38089.rs79969

description: Library name: 79969


title: 740-6.HTO.36562.rs79985

description: Library name: 79985


title: 698-1.GEX.SamplePool.rs86150

description: Library name: 86150


title: 729-3.HTO.36131.rs74390

description: Library name: 74390


title: 698-1.TCR.SamplePool.rs82126

description: Library name: 82126


title: 729-4.HTO.SamplePool.rs74392

description: Library name: 74392


title: 729-5.HTO.SamplePool.rs87610

description: Library name: 87610


title: 729-8.HTO.SamplePool.rs74400

description: Library name: 74400


title: 740-7.HTO.36683.rs79989

description: Library name: 79989


title: 681-13.TCR.SamplePool.rs73280

description: Library name: 73280


title: 681-10.TCR.37163.rs73268

description: Library name: 73268


title: 681-2.TCR.37163.rs73236

description: Library name: 73236


title: 681-6.TCR.37167.rs73252

description: Library name: 73252


title: 729-7.HTO.SamplePool.rs74398

description: Library name: 74398


title: 740-4.HTO.35547.rs79977

description: Library name: 79977


title: 681-16.TCR.37448.rs73292

description: Library name: 73292


title: 740-3.HTO.38090.rs87614

description: Library name: 87614


title: 681-14.TCR.37167.rs73284

description: Library name: 73284


title: 681-1.TCR.SamplePool.rs73232

description: Library name: 73232


title: 681-9.TCR.SamplePool.rs73264

description: Library name: 73264


title: 681-15.TCR.36590.rs73288

description: Library name: 73288


title: 671-16.TCR.36622.rs73228

description: Library name: 73228


title: 681-12.TCR.37166.rs73276

description: Library name: 73276


title: 671-14.TCR.36497.rs73220

description: Library name: 73220


title: 671-9.TCR.SamplePool.rs73200

description: Library name: 73200


title: 681-11.TCR.38180.rs73272

description: Library name: 73272


title: 729-2.HTO.SamplePool.rs74388

description: Library name: 74388


title: 671-11.TCR.37636.rs73208

description: Library name: 73208


title: 671-10.TCR.37374.rs73204

description: Library name: 73204


title: 671-6.TCR.36497.rs73188

description: Library name: 73188


title: 681-8.TCR.37448.rs73260

description: Library name: 73260


title: 681-5.TCR.SamplePool.rs73248

description: Library name: 73248


title: 681-7.TCR.36590.rs73256

description: Library name: 73256


title: 681-3.TCR.38180.rs73240

description: Library name: 73240


title: 681-4.TCR.37166.rs73244

description: Library name: 73244


title: 671-15.TCR.36135.rs73224

description: Library name: 73224


title: 671-1.TCR.SamplePool.rs73168

description: Library name: 73168


title: 671-13.TCR.SamplePool.rs73216

description: Library name: 73216


title: 671-2.TCR.37374.rs73172

description: Library name: 73172


title: 698-1.HTO.SamplePool.rs71102

description: Library name: 71102


title: 671-16.GEX.36622.rs71069

description: Library name: 71069


title: 671-4.TCR.35644.rs73180

description: Library name: 73180


title: 671-12.TCR.35644.rs73212

description: Library name: 73212


title: 671-16.HTO.36622.rs71067

description: Library name: 71067


title: 671-8.TCR.36622.rs73196

description: Library name: 73196


title: 671-7.TCR.36135.rs73192

description: Library name: 73192


title: 671-15.HTO.36135.rs71064

description: Library name: 71064


title: 671-3.TCR.37636.rs73176

description: Library name: 73176


title: 671-11.HTO.37636.rs71052

description: Library name: 71052


title: 671-13.HTO.SamplePool.rs71058

description: Library name: 71058


title: 671-14.HTO.36497.rs71061

description: Library name: 71061


title: 671-13.GEX.SamplePool.rs71060

description: Library name: 71060


title: 671-15.GEX.36135.rs71066

description: Library name: 71066


title: 671-9.GEX.SamplePool.rs71048

description: Library name: 71048


title: 671-12.GEX.35644.rs71057

description: Library name: 71057


title: 671-5.TCR.SamplePool.rs73184

description: Library name: 73184


title: 671-12.HTO.35644.rs71055

description: Library name: 71055


title: 671-10.HTO.37374.rs71049

description: Library name: 71049


title: 671-11.GEX.37636.rs71054

description: Library name: 71054


title: 671-10.GEX.37374.rs71051

description: Library name: 71051


title: 671-14.GEX.36497.rs71063

description: Library name: 71063


title: 671-7.GEX.36135.rs71042

description: Library name: 71042


title: 671-5.GEX.SamplePool.rs71036

description: Library name: 71036


title: 671-6.GEX.36497.rs71039

description: Library name: 71039


title: 671-9.HTO.SamplePool.rs71046

description: Library name: 71046


title: 671-5.HTO.SamplePool.rs71034

description: Library name: 71034


title: 671-6.HTO.36497.rs71037

description: Library name: 71037


title: 671-3.HTO.37636.rs71028

description: Library name: 71028


title: 671-1.GEX.SamplePool.rs71024

description: Library name: 71024


title: 671-8.GEX.36622.rs71045

description: Library name: 71045


title: 671-3.GEX.37636.rs71030

description: Library name: 71030


title: 671-4.GEX.35644.rs71033

description: Library name: 71033


title: 671-8.HTO.36622.rs71043

description: Library name: 71043


title: 740-8.TCR.37012.rs79996

description: Library name: 79996


title: 671-1.HTO.SamplePool.rs71022

description: Library name: 71022


title: 740-7.TCR.36683.rs79992

description: Library name: 79992


title: 740-4.TCR.35547.rs79980

description: Library name: 79980


title: 671-7.HTO.36135.rs71040

description: Library name: 71040


title: 740-1.TCR.SamplePool.rs79968

description: Library name: 79968


title: 740-2.TCR.38089.rs79972

description: Library name: 79972


title: 740-5.GEX.SamplePool.rs79983

description: Library name: 79983


title: 671-2.HTO.37374.rs71025

description: Library name: 71025


title: 729-8.TCR.SamplePool.rs79884

description: Library name: 79884


title: 740-5.TCR.SamplePool.rs79984

description: Library name: 79984


title: 729-6.TCR.SamplePool.rs79876

description: Library name: 79876


title: 729-8.GEX.SamplePool.rs79883

description: Library name: 79883


title: 740-3.TCR.38090.rs79976

description: Library name: 79976


title: 729-5.TCR.SamplePool.rs79872

description: Library name: 79872


title: 729-7.TCR.SamplePool.rs79880

description: Library name: 79880


title: 729-4.TCR.SamplePool.rs79868

description: Library name: 79868


title: 729-4.GEX.SamplePool.rs79867

description: Library name: 79867


title: 740-6.TCR.36562.rs79988

description: Library name: 79988


title: 671-4.HTO.35644.rs71031

description: Library name: 71031


title: 671-2.GEX.37374.rs71027

description: Library name: 71027


title: 729-3.TCR.36131.rs79864

description: Library name: 79864


title: 729-6.GEX.SamplePool.rs79875

description: Library name: 79875


title: 729-1.TCR.SamplePool.rs79856

description: Library name: 79856


title: 729-2.TCR.SamplePool.rs79860

description: Library name: 79860


title: 729-2.GEX.SamplePool.rs79859

description: Library name: 79859


title: 718-8.TCR.SamplePool.rs79788

description: Library name: 79788


title: 718-7.TCR.36590.rs79784

description: Library name: 79784


title: 718-6.GEX.SamplePool.rs79779

description: Library name: 79779


title: 718-6.TCR.SamplePool.rs79780

description: Library name: 79780


title: 718-3.TCR.SamplePool.rs79768

description: Library name: 79768


title: 718-4.TCR.SamplePool.rs79772

description: Library name: 79772


title: 718-5.TCR.SamplePool.rs79776

description: Library name: 79776


title: 713-6.TCR.SamplePool.rs79748

description: Library name: 79748


title: 713-5.TCR.SamplePool.rs79744

description: Library name: 79744


title: 713-7.TCR.SamplePool.rs79752

description: Library name: 79752


title: 718-4.HTO.SamplePool.rs74344

description: Library name: 74344


title: 718-2.TCR.SamplePool.rs79764

description: Library name: 79764


title: 703-8.TCR.37012.rs73356

description: Library name: 73356


title: 713-1.TCR.SamplePool.rs79728

description: Library name: 79728


title: 718-3.HTO.SamplePool.rs74342

description: Library name: 74342


title: 703-7.TCR.36683.rs73352

description: Library name: 73352


title: 713-3.TCR.SamplePool.rs79736

description: Library name: 79736


title: 718-1.TCR.SamplePool.rs79760

description: Library name: 79760


title: 713-8.TCR.SamplePool.rs79756

description: Library name: 79756


title: 713-2.TCR.SamplePool.rs79732

description: Library name: 79732


title: 729-3.GEX.36131.rs79863

description: Library name: 79863


title: 718-6.HTO.SamplePool.rs74348

description: Library name: 74348


title: 703-7.GEX.36683.rs73351

description: Library name: 73351


title: 703-8.GEX.37012.rs73355

description: Library name: 73355


title: 718-2.HTO.SamplePool.rs74340

description: Library name: 74340


title: 703-6.TCR.36562.rs73348

description: Library name: 73348


title: 703-5.GEX.SamplePool.rs73343

description: Library name: 73343


title: 703-4.GEX.35547.rs73339

description: Library name: 73339


title: 703-5.TCR.SamplePool.rs73344

description: Library name: 73344


title: 703-6.GEX.36562.rs73347

description: Library name: 73347


title: 703-3.GEX.38090.rs73335

description: Library name: 73335


title: 703-4.TCR.35547.rs73340

description: Library name: 73340


title: 703-2.GEX.38089.rs73331

description: Library name: 73331


title: 703-1.TCR.SamplePool.rs73328

description: Library name: 73328


title: 703-3.TCR.38090.rs73336

description: Library name: 73336


title: 703-2.TCR.38089.rs73332

description: Library name: 73332


title: 698-8.GEX.36767.rs73323

description: Library name: 73323


title: 698-3.GEX.36131.rs73303

description: Library name: 73303


title: 698-4.GEX.37246.rs73307

description: Library name: 73307


title: 681-12.GEX.37166.rs73275

description: Library name: 73275


title: 698-6.GEX.37826.rs73315

description: Library name: 73315


title: 681-13.GEX.SamplePool.rs73279

description: Library name: 73279


title: 681-9.GEX.SamplePool.rs73263

description: Library name: 73263


title: 698-5.GEX.SamplePool.rs73311

description: Library name: 73311


title: 681-6.GEX.37167.rs73251

description: Library name: 73251


title: 681-3.GEX.38180.rs73239

description: Library name: 73239


title: 681-1.GEX.SamplePool.rs73231

description: Library name: 73231


title: 681-14.GEX.37167.rs73283

description: Library name: 73283


title: 698-7.GEX.36686.rs73319

description: Library name: 73319


title: 681-11.GEX.38180.rs73271

description: Library name: 73271


title: 681-4.GEX.37166.rs73243

description: Library name: 73243


title: 681-15.GEX.36590.rs73287

description: Library name: 73287


title: 698-2.GEX.35112.rs73299

description: Library name: 73299


title: 703-4.HTO.35547.rs71124

description: Library name: 71124


title: 681-7.GEX.36590.rs73255

description: Library name: 73255


title: 681-5.GEX.SamplePool.rs73247

description: Library name: 73247


title: 681-2.GEX.37163.rs73235

description: Library name: 73235


title: 698-7.HTO.36686.rs71114

description: Library name: 71114


title: 703-8.HTO.37012.rs71132

description: Library name: 71132


title: 698-3.HTO.36131.rs71106

description: Library name: 71106


title: 703-5.HTO.SamplePool.rs71126

description: Library name: 71126


title: 703-3.HTO.38090.rs71122

description: Library name: 71122


title: 703-1.GEX.SamplePool.rs73327

description: Library name: 73327


title: 703-7.HTO.36683.rs71130

description: Library name: 71130


title: 703-2.HTO.38089.rs71120

description: Library name: 71120


title: 703-6.HTO.36562.rs71128

description: Library name: 71128


title: 698-2.HTO.35112.rs71104

description: Library name: 71104


title: 681-16.HTO.37448.rs71100

description: Library name: 71100


title: 681-12.HTO.37166.rs71092

description: Library name: 71092


title: 698-4.HTO.37246.rs71108

description: Library name: 71108


title: 681-8.HTO.37448.rs71084

description: Library name: 71084


title: 698-8.HTO.36767.rs71116

description: Library name: 71116


title: 698-5.HTO.SamplePool.rs71110

description: Library name: 71110


title: 681-15.HTO.36590.rs71098

description: Library name: 71098


title: 681-7.HTO.36590.rs71082

description: Library name: 71082


title: 681-3.HTO.38180.rs71074

description: Library name: 71074


title: 681-11.HTO.38180.rs71090

description: Library name: 71090


title: 681-13.HTO.SamplePool.rs71094

description: Library name: 71094


title: 681-1.HTO.SamplePool.rs71070

description: Library name: 71070


title: 681-14.HTO.37167.rs71096

description: Library name: 71096


title: 681-4.HTO.37166.rs71076

description: Library name: 71076


title: 681-5.HTO.SamplePool.rs71078

description: Library name: 71078


title: 681-9.HTO.SamplePool.rs71086

description: Library name: 71086


title: 681-10.HTO.37163.rs71088

description: Library name: 71088


title: 586-8.GEX.37012.rs57310

description: Library name: 57310


title: 586-6.TCR.36562.rs57303

description: Library name: 57303


title: 586-7.HTO.36683.rs57304

description: Library name: 57304

source_name: MesLN,Spleen

value: MesLN,Spleen


title: 586-5.GEX.SamplePool.rs57298

description: Library name: 57298


title: 586-8.TCR.37012.rs57311

description: Library name: 57311


title: 586-7.TCR.36683.rs57307

description: Library name: 57307


title: 586-5.HTO.SamplePool.rs57296

description: Library name: 57296


title: 681-2.HTO.37163.rs71072

description: Library name: 71072


title: 586-8.HTO.37012.rs57308

description: Library name: 57308


title: 681-6.HTO.37167.rs71080

description: Library name: 71080


title: 586-7.GEX.36683.rs57306

description: Library name: 57306


title: 586-6.GEX.36562.rs57302

description: Library name: 57302


title: 586-5.TCR.SamplePool.rs57299

description: Library name: 57299


title: 586-6.HTO.36562.rs57300

description: Library name: 57300


title: 570-6.TCR.37826.rs57198

description: Library name: 57198

source_name: MesLN,PLN,Spleen

value: MesLN,PLN,Spleen


title: 586-4.TCR.35547.rs57295

description: Library name: 57295

source_name: Bone marrow,MesLN

value: Bone marrow,MesLN


title: LICs, KO1

city: guangzhou

first: Songqi

last: Zhu

state: guangdong

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: Sun Yat-sen University

description: Library name: Sample3

data_processing:
RNA-seq reads were aligned to mouse genome mm10 and gene annotation from the Ensembl database.
Low quality reads were removed and the adaptor sequences were trimmed by Trim Galore (v0.5.0).
The remaining pair-end reads were mapped to the mouse genome (GRCm39, Ensembl) via subread (v2.0.6) and bedtools (v2.31.1),
The remaining pair-end reads were mapped to the reference genome by by featureCounts (v2.0.6).
Assembly: GRCm39
Supplementary files format and content: bigwig

source_name: Bone Marrow

extract_protocol:
In brief, intact bone marrows from mice at the age of 6-8weeks were flushed from mouse femora and tibiae. Bone marrow cells by pipetting with 1 mL syringe, and then underwent red blood cell lysis using 0.16 M ammonium chloride solution.
Nuclear isolation:a. Wash cells with PBS, centrifuge at 1000g for 5 min at 4 °C, and remove the supernatant. b. add 200μL of pre-chilled lysis buffer to the washed cells, gently pipette to resuspend, and incubate on ice for 10 min. c. Centrifuge at 500g for 10 min, then add 1mL of washing buffer and invert to mix three times. d. Centrifuge at 500g for 10 min at 4°C to collect the nuclei.Transposase digestion and library construction:a. Add 50 μL of transposase reaction mix to the nuclear pellet and resuspend the nuclei by gentle pipetting.b. Incubate in a thermal cycler at 37 °C for 30 min, then hold at 4 °C.c. Purify the DNA using 2× DNA clean beads.d. Amplify for 15 cycles using P5 and P7 adapter primers to obtain the primary library.

value: Bone Marrow

value: leukemia-initiating cells

value: HMGCS2 KO


title: 586-4.GEX.35547.rs57294

description: Library name: 57294


title: 570-5.TCR.SamplePool.rs57194

description: Library name: 57194


title: 586-3.GEX.38090.rs57290

description: Library name: 57290


title: 586-4.HTO.35547.rs57292

description: Library name: 57292


title: 586-3.HTO.38090.rs57288

description: Library name: 57288


title: 586-3.TCR.38090.rs57291

description: Library name: 57291


title: LICs, WT1

description: Library name: Sample1


title: 586-2.TCR.38089.rs57287

description: Library name: 57287

source_name: Bone marrow

value: Bone marrow


title: JJ0357, control, Post-Restriction

city: Bethesda

first: Mark

middle: R

last: Cookson

state: MD

address: NIHBC 35 - PNRC I BG RM 1A-116

institute: National Institutue on Aging, NIH

description: Library name: KC48

data_processing:
Raw sequencing reads were processed with fastp to remove adapters and low-quality bases. Cleaned reads were aligned to the mouse reference genome (mm39) using STAR with the GENCODE vM34 annotation. Transcript abundances were quantified with Salmon, and transcript counts were imported into R and summarized to the gene level using the tximport package
Assembly: mm39
Supplementary files format and content: compressed tab-delimited raw counts on gene for each sample

source_name: brain (one hemisphere)

extract_protocol:
At the pre-determined brain collection points, mice were euthanized with carbon dioxide followed by rapid decapitation. The brains were immediately dissected and split into two hemispheres. One hemisphere from each brain was placed in liquid nitrogen then stored at −80 °C. In total, 48 half brains were sent to AmpSeq for RNA extraction and mRNA sequencing (poly-A selection, 20 million reads).
RNA-seq libraries were prepared using the VAHTS Universal V10 RNA-seq Library Prep Kit (Illumina-compatible). Library concentration was quantified with Qubit and qPCR, and fragment size distribution was evaluated using Qseq.

treatment_protocol: Adult female and male Grin1 conditional knockout and control mice were randomly assigned to undergo either 1) no food restriction (Pre-Restriction), 2) two consecutive nights of food restriction (Post-Restriction), or 3) two consecutive nights of food restriction followed by three consecutive days of free access to food (Free Feed). Regardless of feeding condition, mice were moved from group housing to individual cages with access to standard rodent chow and water. Mice in the Pre-Restriction group were singly housed for approximately 48 hours before their brains were collected. The brains of mice in the Post-Restriction group were collected after two nights of food restriction. Between the two overnight food restriction periods, standard rodent chow was provided. The mice in the Free Feed group underwent two nights of food restriction before an automatic feeding device provided free access to grain-based pellets. After 72 hours of free access to food via the feeding devices, the mouse brains from the Free Feed group were collected.

value: brain (one hemisphere)

value: F

value: 5.5 months

value: Post-Restriction


title: JJ0408, control, Post-Restriction

description: Library name: KC47

value: 7 months


title: JJ0407, control, Post-Restriction

description: Library name: KC46


title: 586-2.GEX.38089.rs57286

description: Library name: 57286


title: 570-8.TCR.36767.rs57206

description: Library name: 57206


title: LICs, KO2

description: Library name: Sample4


title: JJ0456, Grin1_KO, Post-Restriction

description: Library name: KC45

value: M

value: 6.5 months


title: 570-8.HTO.36767.rs57203

description: Library name: 57203


title: 570-6.GEX.37826.rs57197

description: Library name: 57197


title: LICs, WT2

description: Library name: Sample2


title: 570-4.HTO.37246.rs57187

description: Library name: 57187

source_name: Bone marrow,MesLN,Spleen

value: Bone marrow,MesLN,Spleen


title: 570-5.HTO.SamplePool.rs57191

description: Library name: 57191

value: PBMC


title: JJ0381, Grin1_KO, Post-Restriction

description: Library name: KC43

value: 8 months


title: JJ0458, control, Post-Restriction

description: Library name: KC42


title: 570-3.TCR.36131.rs57186

description: Library name: 57186

value: Bone marrow,MesLN,PLN,Spleen


title: 586-2.HTO.38089.rs57284

description: Library name: 57284


title: 570-4.TCR.37246.rs57190

description: Library name: 57190


title: 570-6.HTO.37826.rs57195

description: Library name: 57195

value: MesLN,PLN,Spleen


title: JJ0403, control, Post-Restriction

description: Library name: KC41


title: 570-5.GEX.SamplePool.rs57193

description: Library name: 57193


title: IRF8

city: Cambridge

first: Akash

last: Gupta

address: 500 Main Street, Building 76

institute: Massachusetts Institute of Technology

description: Library name: D25-7811

data_processing:
Output data was processed using 10X Genomics cell ranger using default configuration. scRNAseq data was processed by Bioinformatics & Computing Core Facility. Single‐cell RNA sequencing (scRNA‐seq) data were generated on the 10X Genomics Chromium platform from four independent mouse samples which were annotated as “FFL,” “PBS,” “NIK,” and “IRF8,” respectively.
Assembly: mm10-2020-A
Supplementary files format and content: filtered_feature_bc_matrix.tar.gz is archived and compressed folder that contains the gene expression count matrix along with corresponding gene (features) and cell barcode annotations for each sample.
Supplementary files format and content: singlet.integrated.filtered.rds.gz is fully processed and annotated integrated Seurat object.

source_name: immune cells

growth_protocol: B16-F10 and B16-F10-Luc2 were purchased from ATCC. B16-OVA, MC38, and MB49 were purchased from Millipore-Sigma. THP-1 IRF reporter cells were obtained from These cells were routinely screened for murine pathogens and mycoplasma contamination. Cells were cultured in DMEM supplemented with 4.5 g/L D-glucose, GlutaMAX, and 10% fetal bovine serum (FBS) (ThermoFisher). BMDCs were cultured by isolating bone marrow from the femur and tibia of mice. Bone marrow cells were then cultured in RPMI-1640 supplemented with GlutaMAX (ThermoFisher), 10% FBS (ThermoFisher), 100 U/mL penicillin (ThermoFisher), 100 μg/mL streptomycin (ThermoFisher), 50 μM β-mercaptoethanol (Millipore), 200 ng/mL Flt3L-Fc (R&D Systems), and 20 ng/mL GM-CSF (R&D Systems). On day 9, non-adherent cells were harvested and used immediately.

extract_protocol:
Native TE buffer (ThermoFisher) or denaturing TE buffer + 0.5% Triton-X 100 (Millipore-Sigma)
3' RNA libraries were prepared from ~5k cells on using 10X Genomics 3'RNA (GEM-X) chemistry on a ChromiumX using 12 cycles of PCR.

treatment_protocol: Human dendritic cells were differentiated from human primary bone marrow CD34+ cell using a Mouse-OP9 co-culture method as reported in previously established protocols.83 Mouse OP9 cell line (ATCC, Cat no CRL-2749)_were cultured in T75 flasks in OP9 medium (αMEM, 20% FCS, penicillin-streptomycin) at 37 °C and 5% CO₂ and maintained at a density of 4 × 10³–1 × 10⁴ cells/cm² with medium changes every 3–4 days. For plating, OP9 cells were seeded into 96-well U-bottom plates at 5,000 cells/well. Human primary bone marrow CD34⁺ cells (ATCC PCS-800-012) were resuspended at 1.5 × 10⁴ cells/ml in DC differentiation medium (αMEM supplemented with 10% FCS, 1% penicillin–streptomycin, 100 ng/ml Flt3L, 20 ng/ml SCF, and 20 ng/ml GM-CSF). OP9 medium was gently removed and replaced with 200 µl of CD34⁺ cell suspension (3,000 cells/well). Cultures were maintained with half-medium changes on day 6 and subsequently on days 12 and 18. Differentiated cells were harvested on day 19 by gentle pipetting, filtered through 50 µm strainers, and resuspended in appropriate buffers for flow cytometric analysis. Immature human DCs were treated with human NIK, IRF8 and Fluc (control) mRNAs on day 6, 12, and 18 followed by analysis on day 19.

value: immune cells


title: 570-2.TCR.35112.rs57182

description: Library name: 57182


title: JJ0443, Grin1_KO, Post-Restriction

description: Library name: KC40


title: 570-1.TCR.SamplePool.rs57178

description: Library name: 57178


title: 570-2.GEX.35112.rs57181

description: Library name: 57181


title: 570-4.GEX.37246.rs57189

description: Library name: 57189


title: 570-3.HTO.36131.rs57183

description: Library name: 57183


title: 570-2.HTO.35112.rs57179

description: Library name: 57179


title: JJ0434, Grin1_KO, No Restriction

description: Library name: KC38

value: No Restriction


title: JJ0436, control, No Restriction

description: Library name: KC36


title: JJ0404, Grin1_KO, Post-Restriction

description: Library name: KC44


title: 570-1.HTO.SamplePool.rs57175

description: Library name: 57175


title: 570-1.GEX.SamplePool.rs57177

description: Library name: 57177


title: 570-3.GEX.36131.rs57185

description: Library name: 57185


title: JJ0358, control, No Restriction

description: Library name: KC37


title: 568-6.HTO.37167.rs54949

description: Library name: 54949


title: JJ0405, Grin1_KO, No Restriction

description: Library name: KC32


title: JJ0444, control, No Restriction

description: Library name: KC35

value: 8.5 months


title: 568-8.HTO.37448.rs54957

description: Library name: 54957


title: 568-5.HTO.SamplePool.rs54945

description: Library name: 54945


title: 568-4.HTO.37166.rs54941

description: Library name: 54941


title: JJ0416, Grin1_KO, No Restriction

description: Library name: KC34


title: JJ0442, Grin1_KO, No Restriction

description: Library name: KC39


title: 568-8.TCR.37448.rs54960

description: Library name: 54960


title: 568-3.HTO.38180.rs54937

description: Library name: 54937


title: JJ0345, Grin1_KO, Refeeding

description: Library name: KC25

value: Refeeding


title: 568-8.GEX.37448.rs54959

description: Library name: 54959


title: JJ0454, Grin1_KO, No Restriction

description: Library name: KC33


title: 568-6.GEX.37167.rs54951

description: Library name: 54951


title: 568-5.TCR.SamplePool.rs54948

description: Library name: 54948


title: JJ0455, control, No Restriction

description: Library name: KC30


title: JJ0457, control, No Restriction

description: Library name: KC31


title: 568-1.HTO.SamplePool.rs54929

description: Library name: 54929


title: JJ0500, Grin1_KO, Refeeding

description: Library name: KC27

value: 7.5 months


title: JJ0415, control, No Restriction

description: Library name: KC29

value: brain (one hemisphere)


title: JJ0343, Grin1_KO, Refeeding

description: Library name: KC26

value: F


title: JJ0377, Grin1_KO, Post-Restriction

description: Library name: KC20


title: 568-7.HTO.36590.rs54953

description: Library name: 54953


title: JJ0331, Grin1_KO, Post-Restriction

description: Library name: KC19


title: 568-2.HTO.37163.rs54933

description: Library name: 54933


title: 568-7.TCR.36590.rs54956

description: Library name: 54956


title: JJ0351, control, Refeeding

description: Library name: KC23


title: JJ0329, control, Refeeding

description: Library name: KC22


title: JJ0392, control, Refeeding

description: Library name: KC24


title: 568-6.TCR.37167.rs54952

description: Library name: 54952


title: JJ0459, control, Post-Restriction

description: Library name: KC17


title: JJ0354, Grin1_KO, No Restriction

description: Library name: KC16


title: JJ0391, Grin1_KO, Refeeding

description: Library name: KC28


title: 568-2.TCR.37163.rs54936

description: Library name: 54936


title: JJ0376, Grin1_KO, No Restriction

description: Library name: KC15


title: 568-5.GEX.SamplePool.rs54947

description: Library name: 54947


title: 555-7.HTO.36135.rs47690

description: Library name: 47690


title: 568-4.TCR.37166.rs54944

description: Library name: 54944


title: 568-2.GEX.37163.rs54935

description: Library name: 54935


title: JJ0390, control, Post-Restriction

description: Library name: KC12


title: JJ0353, Grin1_KO, Post-Restriction

description: Library name: KC18


title: 555-5.HTO.SamplePool.rs47682

description: Library name: 47682


title: 568-3.GEX.38180.rs54939

description: Library name: 54939


title: JJ0344, control, No Restriction

description: Library name: KC14


title: 568-3.TCR.38180.rs54940

description: Library name: 54940


title: 555-8.HTO.36622.rs47694

description: Library name: 47694


title: JJ0389, Grin1_KO, Post-Restriction

description: Library name: KC13


title: 555-6.HTO.36497.rs47686

description: Library name: 47686


title: JJ0379, control, Post-Restriction

description: Library name: KC11


title: 568-1.TCR.SamplePool.rs54932

description: Library name: 54932


title: JJ0328, control, Refeeding

description: Library name: KC21


title: 555-1.HTO.SamplePool.rs47666

description: Library name: 47666


title: 555-8.TCR.36622.rs47697

description: Library name: 47697


title: JJ0387, Grin1_KO, Refeeding

description: Library name: KC7


title: JJ0420, Grin1_KO, Refeeding

description: Library name: KC5


title: 555-4.HTO.35644.rs47678

description: Library name: 47678


title: 555-7.GEX.36135.rs47692

description: Library name: 47692


title: JJ0399, Grin1_KO, Refeeding

description: Library name: KC8


title: JJ0422, Grin1_KO, No Restriction

description: Library name: KC9


title: 555-7.TCR.36135.rs47693

description: Library name: 47693


title: 555-3.HTO.37636.rs47674

description: Library name: 47674


title: JJ0378, control, No Restriction

description: Library name: KC10


title: JJ0388, control, Refeeding

description: Library name: KC2


title: JJ0419, control, Refeeding

description: Library name: KC4


title: 555-6.GEX.36497.rs47688

description: Library name: 47688


title: JJ0380, control, Refeeding

description: Library name: KC3


title: 555-6.TCR.36497.rs47689

description: Library name: 47689


title: 555-5.TCR.SamplePool.rs47685

description: Library name: 47685


title: 555-5.GEX.SamplePool.rs47684

description: Library name: 47684


title: JJ0400, control, Refeeding

description: Library name: KC1


title: JJ0421, Grin1_KO, Refeeding

description: Library name: KC6


title: Female Down syndrome,fetal brain

city: Chongqing

first: Kai

last: Guo

address: 1 Youyi Road, Yuzhong District

institute: Chongqing Medical University

description:
Library name: A21st-1
BGI DNBSEQ-T7

data_processing:
Raw base calls were demultiplexed to FASTQ files.Reads were aligned and quantified using 10x Genomics Cell Ranger (cellranger count) with default parameters unless otherwise stated. --include-introns=true, --chemistry=auto (Single Cell 3' v4), and BAM file generation enabled. UMI counting and gene-barcode matrix generation were performed by Cell Ranger(8.0.0).
Assembly: GRCh38,Ensembl release 104
Supplementary files format and content: Tab-separated values files and matrix files

source_name: fetal brain

extract_protocol:
Human fetal brain tissue (24 GW) or organoid (2.5 months culture) are minced and homogenized using a Dounce homogenizer on ice, then washed and filtered through a 40 μm mesh to generate a clean nuclear suspension ready for the 10x Genomics Chromium platform.
snRNA seq libraries were prepared using the 10× Genomics Chromium Controller and Chromium Single Cell 3′ V3.1 reagent kit (10× Genomics, Pleasanton, USA). Isolated nuclei were adjusted to a concentration of 1000 nuclei per uL and loaded onto the Chromium chip to generate single-nucleus Gel Bead-In-Emulsions (GEMs). Reverse transcription was performed within GEMs, followed by GEM disruption and recovery of barcoded cDNA, which was then purified and amplified. The amplified cDNA was fragmented, a tailed, adaptor ligated, and further enriched by index PCR. Library concentration was determined using the Qubit High Sensitivity DNA assay (Thermo Fisher Scientific, USA), and fragment size distribution was assessed with a High Sensitivity DNA chip on a 2100 Bioanalyzer (Agilent, USA). All libraries were sequenced on a NovaSeq 6000 platform (Illumina, USA) using a 150 bp paired end configuration.

value: fetal brain

value: single nucleus

value: Trisomy 21


title: Female Control,fetal brain

description:
Library name: A95
BGI DNBSEQ-T7

value: Euploid


title: Female Down syndrome with XIST,doxycycline-treated6,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3U-Poly-A36_N_B
BGI DNBSEQ-T7
X2-12ALL-Dox-6

data_processing:
Raw FASTQ data were preprocessed using Trim Galore to remove low-quality reads (containing adapter sequences, reads with Phred scores <20, or N base proportions >10%), yielding high-quality clean reads for downstream analysis.
Assembly: tab-delimited text file include raw counts for each sample
Supplementary files format and content: csv files include FPKM values for each sample

source_name: brain

extract_protocol:
Total RNA was extracted from cells and tissues using TRIzol reagent.
RNA quality was evaluated using an Agilent 2200 Bioanalyzer, and only samples with an RNA integrity number >8.0 were used for library construction. After rRNA depletion, RNA was fragmented to 150–200 bp, and single‑end cDNA libraries were generated using the Ion Total RNA‑Seq Kit v2.0 (Life Technologies) following reverse transcription, adapter ligation, and PCR enrichment. Library concentration was quantified using an Agilent 2200 Bioanalyzer. Sequencing was performed at NovelBio Corp. Laboratory (Shanghai) on an Ion Proton system using Ion PITM Template OT2 200 Kit v2.0 and Ion PI Sequencing 200 Kit v2.0 (Life Technologies).

value: brain

value: female

value: induced pluripotent stem cell

value: doxycycline


title: 555-1.TCR.SamplePool.rs47669

description: Library name: 47669

value: PBMC


title: 555-2.GEX.37374.rs47672

description: Library name: 47672

value: Bone marrow,MesLN,PLN,Spleen


title: 555-3.TCR.37636.rs47677

description: Library name: 47677


title: 555-2.TCR.37374.rs47673

description: Library name: 47673


title: 555-4.TCR.35644.rs47681

description: Library name: 47681

value: MesLN,PLN,Spleen


title: Female Down syndrome with XIST,doxycycline-treated1,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3P-Poly-A31_N_B
BGI DNBSEQ-T7
X2-12ALL-Dox-1


title: Female Down syndrome with XIST,doxycycline-treated4,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3S-Poly-A34_N_B
BGI DNBSEQ-T7
X2-12ALL-Dox-4


title: 555-2.HTO.37374.rs47670

description: Library name: 47670


title: Female Down syndrome with XIST,doxycycline-treated3,iPSC [E250027128]

description:
Library name: E250027128_L01_N_B_N4A14-3R-Poly-A33_N_B
BGI DNBSEQ-T7
X2-12ALL-Dox-3


title: 555-1.GEX.SamplePool.rs47668

description: Library name: 47668