title: GFP-; mApple+ rep1, GCP

city: Nashville

first: Lei

last: Chen

state: TN

address: 465 21st Ave. South

department: Department of Cell and Developmental Biology

institute: Vanderbilt University

description: Library name: GFP-; mApple+_1

data_processing:
For RNA-seq data, the FASTQ files were initially processed using Trim Galore to remove sequencing adapters, followed by alignment of the sequences to the Mus musculus mm10 genome with HISAT2.
Samtools was employed to convert the mapping results into BAM format and generate corresponding indices.
Quantification of read counts for all genes was performed using HTSeq-count, resulting in a matrix correlating samples with gene count numbers. Two biological replicates were examined.
Assembly: mm10
Supplementary files format and content: Reads count

extract_protocol:
After the removal of the meninges from the cerebellar tissue, it was sectioned into small pieces approximately 0.5 mm in size. Subsequently, these fragments were digested with a cold protease cocktail solution, which contained 10 mg/ml protease from bacillus licheniformis (Sigma-Aldrich) and 2.25 mg/ml deoxyribonuclease I from bovine pancreas (Sigma-Aldrich), for 15 minutes in a water bath maintained at 6℃, with gently pipetting to mechanically dissociate the tissues every five minutes during this period. After dissociation, the digestion enzyme mixtures were passed through a 40μm filter (Miltenyi Biotech) and washed twice by 1XPBS solution. The BD FACS Aria III cell sorter was used to purify GCPs based on the intensity of Atoh1-GFP fluorescence at the single-cell level. A total of 1,000 Atoh1-GFP-positive GCPs were isolated from Sin3ACKO and Control mice to generated RNA-seq sequencing libraries.
Cellular RNA was extracted and cDNA was generated using the SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takarabio) according to manufacturer’s instructions. NEBNext Ultra II DNA Library Prep Kit for Illumina (New England Biolabs) was utilized to construct libraries from cDNA. All libraries are sequenced and performed at multiplex Paired-End 150 bp on an Illumina NovaSeq 600 at Vanderbilt Technologies for Advanced Genomics.

value: Mouse Granule cell precursors

value: Cntn2 mApple/+; Atoh1 M1GFP/+

value: postnatal day 6


title: GFP-; mApple+ rep2, GCP

status: Public on Jun 23 2026

type: SRA

country: USA

description: Library name: GFP-; mApple+_2

library_source: transcriptomic

molecule: polyA RNA

organism: Mus musculus

source_name: Cerebella

tag: tissue

value: Cerebella

tag: cell type

tag: genotype

tag: age


title: GFP+; mApple- rep1, GCP

description: Library name: GFP+; mApple-_1


title: P0 Wildtype rep1, Cerebellum, Hdac1 (ChIP)

description: Library name: Cerebellum_P0_Wildtype_Hdac1_rep1, ChIP

library_source: genomic

data_processing:
ChIP-seq reads were initially processed using Cutadapt to remove sequencing adapter sequences, followed by alignment of the sequences to the mouse mm10 genome with Bowtie2.
The aligned results were then converted into BAM files using Samtools and filtered to exclude reads aligning to mitochondrial DNA and regions on the blacklist.
PCR duplicates were removed utilizing Picard's MarkDuplicates tool.
Peaks were called in comparison with IgG ChIP-seq controls using MACS2.
Reproducible peaks were identified using the Irreproducible Discovery Rate method.
Assembly: mm10
Supplementary files format and content: BigWig (except for IgG and Input samples)

molecule: genomic DNA

extract_protocol:
Cerebellar tissue  was sectioned into small pieces approximately 0.5 mm in size. Subsequently, these fragments were digested with a cold protease cocktail solution, which contained cold protease (Sigma-Aldrich) (5mg/ml) and Dnase (Sigma-Aldrich) (2.5mg/ml), for 15 minutes in a water bath maintained at 6℃, with gently pipetting to mechanically dissociate the tissues every five minutes during this period. After dissociation, the digestion enzyme mixtures were passed through a 40μm filter (Miltenyi Biotech) and washed twice by 1XPBS solution. The BD FACS Aria III cell sorter was used to purify GCPs based on the intensity of Atoh1-GFP fluorescence at the single-cell level.
ChIP-seq was followed by the ChIPmentation protocol(Xu et al., 2020). In brief, purified cells were cross-linked with 1% formaldehyde/PBS solution at room temperature for 15 minutes before quenching with 250 mM glycine. For co-repressor(Sin3A and Hdac1) ChIP assays, an additional protein cross-linking step using 2mM disuccinimidyl glutarate was incorporated. Chromatin was subsequently fragmented to the size of 200~1000bp by sonication for 21 seconds using a Diagenode One device (Diagenode, NJ). Soluble chromatin was then obtained and incubated overnight at 4°C with the target antibody. Afterward, Dynabeads Protein A/G (10001D/10003D, Thermo Fisher Scientific, MA) were added for two hours to capture the antibody-chromatin complexes. Unbound chromatin were removed through multiple washes following a high-salt buffter, low-salt buffer, LiCl buffer, and 10mM Tris buffter sequence to ensure specificity of binding to the beads. Subsequently, an on-bead tagmentation step were performed using transposase Tn5 (20034197, Illumina, CA) to facilitate the ligation of sequencing adapters to the DNA. The DNA was then eluted from the beads and purified using AMPure XP Beads (A63880, Beckman Coulter, IN). Finally, the ChIP DNA was amplified to generate a sequencing library with Illumina Nextera DNA CD Indexes (20018707, Illumina, CA). All libraries are sequenced and performed at multiplex Paired-End 150 bp on a Illumina NovaSeq 600 at Vanderbilt Technologies for Advanced Genomics.

value: Mouse Cerebellar Cells

value: Wildtype


title: P0 Wildtype rep2, Cerebellum, Sin3a (ChIP)

description: Library name: Cerebellum_P0_Wildtype_Sin3A_rep2, ChIP


title: Wildtype rep2, GFP-; mApple+, Sin3a (ChIP)

description: Library name: GFP-; mApple+_Control_Sin3a, ChIP


title: P0 Wildtype rep1, Cerebellum, Sin3a (ChIP)

description: Library name: Cerebellum_P0_Wildtype_Sin3A_rep1, ChIP


title: Wildtype rep1, GFP+; mApple-, Sin3a (ChIP)

description: Library name: GFP+; mApple-_Control_Sin3a, ChIP


title: Carotid body bifurcation_Mecp2 knockout_4

city: Storrs

first: Daniel

last: Mulkey

state: Connecticut

address: 69 North Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

description: Library name: Sample 8

data_processing:
Raw data were trimmed with Trimmomatic v0.38
Trimmed data were aligned to the reference with hisat2 v2.2.1
Gene counts were generated with htseq-count v0.13.5
Assembly: GRCm39
Supplementary files format and content: column 1 = gene name, column 2 = count

molecule: total RNA

source_name: Bilateral carotid body bifurcations

extract_protocol:
RNA was harvested using TRIzol reagent
Total RNA samples were prepared for mRNA sequencing using the Illumina Stranded mRNA Ligation Sample Preparation kit following the manufacturer’s protocol (Illumina, San Diego, CA, USA). Libraries were sequenced on the NovaSeq 6000, version 1.5 chemistry.

value: Bilateral carotid body bifurcations

tag: Sex

value: Male

tag: postnatal day

tag: diurnal cycle

value: dark cycle


title: Carotid body bifurcation_Mecp2 knockout_3

description: Library name: Sample 7


title: Carotid body bifurcation_Mecp2 knockout_2

description: Library name: Sample 6


title: Carotid body bifurcation_wildtype control_4

description: Library name: Sample 4


title: Carotid body bifurcation_wildtype control_1

description: Library name: Sample 1


title: Mutant E14.5 Face 2

city: Columbus

first: Rolf

last: Stottmann

state: OHIO

address: 575 Children's Crossroads

department: Pediatrics

institute: Nationwide Children's Hospital

description:
Library name: 189_4_F
Column name in AllData_RNASeq_Results.xlsx: Raw_189_4_F
Column name in AllData_RNASeq_Results.xlsx: Norm_189_4_F

data_processing:
Bbduk (v37.64) was used to trim adapter sequences and low-quality reads (q<10).
Bbduk (v37.64) was also used to remove contaminants (Ribosomal RNA, Illumina PhiX and PCR products, Mycoplasma, and Globin genes).
Reads were then aligned to the NCBI Mus musculus assembly (GRCm38.p6) using the STAR aligner (v2.6.0c). Default values were used for most parameters; these are the default filter values:outFilterType: Normal, outFilterMultimapNmax: 10, outFilterMultimapScoreRange: 1, outFilterScoreMin: 0, outFilterScoreMinOverLread: 0.66, outFilterMatchNmin: 0, outFilterMatchNminOverLread: 0.66, outFilterMismatchNmax: 10, outFilterMismatchNoverLmax: 0.3, outFilterMismatchNoverReadLmax: 1, outFilterIntronMotifs: None, outFilterIntronStrands: RemoveInconsistentStrands
Mapped reads were quantified using featureCounts (subread v1.6.3) and the Gencode (vM19) annotation.
Transcript quantification of the contaminant filtered reads was done with salmon (v0.14) and Gencode (vM19).
The assigned reads from the featureCounts step were used for the DESeq2 (v1.26.0) differential gene expression analysis.
Assembly: GRCm38.p6
Supplementary files format and content: excel files contain raw and normalized values.

source_name: Face

extract_protocol:
RNA was extracted from wildtype and Tusc3 deletion brain and craniofacial tissues at E14.5 using TRIZOL reagent method.
NEBNext® Ultra™ II Directional RNA Library Prep Kit with NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat)

value: Face


title: Mutant E14.5 Face 1

description:
Library name: 186_6_F
Column name in AllData_RNASeq_Results.xlsx: Raw_186_6_F
Column name in AllData_RNASeq_Results.xlsx: Norm_186_6_F


title: Control E14.5 Face 3

description:
Library name: 189_9_F
Column name in AllData_RNASeq_Results.xlsx: Raw_189_9_F
Column name in AllData_RNASeq_Results.xlsx: Norm_189_9_F

value: Control


title: Control E14.5 Face 2

description:
Library name: 189_2_F
Column name in AllData_RNASeq_Results.xlsx: Raw_189_2_F
Column name in AllData_RNASeq_Results.xlsx: Norm_189_2_F


title: Control E14.5 Face 1

description:
Library name: 170_7_F
Column name in AllData_RNASeq_Results.xlsx: Raw_170_7_F
Column name in AllData_RNASeq_Results.xlsx: Norm_170_7_F


title: Mutant E14.5 Brain 3

description:
Library name: 189_5_B
Column name in AllData_RNASeq_Results.xlsx: Raw_189_5_B
Column name in AllData_RNASeq_Results.xlsx: Norm_189_5_B

source_name: Brain

value: Brain


title: Mutant E14.5 Brain 2

description:
Library name: 189_4_B
Column name in AllData_RNASeq_Results.xlsx: Raw_189_4_B
Column name in AllData_RNASeq_Results.xlsx: Norm_189_4_B


title: Mutant E14.5 Brain 1

description:
Library name: 186_6_B
Column name in AllData_RNASeq_Results.xlsx: Raw_186_6_B
Column name in AllData_RNASeq_Results.xlsx: Norm_186_6_B


title: Control E14.5 Brain 3

description:
Library name: 189_9_B
Column name in AllData_RNASeq_Results.xlsx: Raw_189_9_B
Column name in AllData_RNASeq_Results.xlsx: Norm_189_9_B


title: Control E14.5 Brain 1

description:
Library name: 170_7_B
Column name in AllData_RNASeq_Results.xlsx: Raw_170_7_B
Column name in AllData_RNASeq_Results.xlsx: Norm_170_7_B


title: Control E14.5 Brain 2

description:
Library name: 189_2_B
Column name in AllData_RNASeq_Results.xlsx: Raw_189_2_B
Column name in AllData_RNASeq_Results.xlsx: Norm_189_2_B


title: Liver tumor, Slc1a5flox/flox, replicate 1

city: Wuhan

first: Wenlong

last: Jia

address: 1095 Jiefang Avenue

country: China

institute: Tongji Hospital

description: Library name: Slc1a5flox_flox_rep1

library_source: transcriptomic single cell

data_processing:
Raw sequencing reads were processed using the manufacturer-recommended ABcellar analysis pipeline to perform demultiplexing, barcode correction, unique molecular identifier counting, and generation of cell-by-gene expression matrices.
Downstream quality control, normalization, dimensionality reduction, clustering, cell-type annotation, and differential expression analyses were performed using Seurat.
Assembly: Mus musculus GRCm38/mm10
Supplementary files format and content: Processed data include barcode files, feature/gene annotation files, and matrix market files containing cell-by-gene unique molecular identifier count matrices for each sample.

source_name: liver tumor

growth_protocol: Male mice were housed under specific-pathogen-free conditions.DEN/CCl₄-induced liver tumors were generated in control and hepatocyte-specific Slc1a5-deficient mice.

extract_protocol:
Tumor tissues were mechanically and enzymatically dissociated into single-cell suspensions. Dead cells and debris were removed, and live cells were sorted or enriched as indicated for each sample. RNA capture was performed from single cells during single-cell 3′ RNA-seq library preparation.
Single-cell 3′ RNA-seq libraries were constructed using the ABcellar Pro Single Cell 3′ RNA-seq Lib Prep Kit (ABclonal, RK20380) according to the manufacturer’s protocol.

treatment_protocol: Liver tumors were collected from DEN/CCl₄-induced hepatocellular carcinoma models. Tumors were dissociated into single-cell suspensions, and live CD45+ immune cells and/or unsorted tumor cell suspensions were processed for single-cell RNA-seq.

value: liver tumor

value: tumor and immune cells

tag: treatment

value: DEN/CCl₄-induced HCC


title: LN6_IFN_Tumor

city: Rotterdam

first: Anneloes

last: van Krimpen

state: Zuid-Holland

address: Doctor Molewaterplein 40

department: Pulmonary Medicine

country: Netherlands

institute: Erasmus MC

description:
Library name: St_ME9_S9
10X Genomics

data_processing:
Sequencing reads were aligned to the murine mm39 [GRCm39-2024-A] reference genome and quantified using Cellranger (10X Genomics, version 9.01), using GEM-X Universal Multiplex Barcodes (3’ GEM-X Universal Multiplex) for demultiplexing of 4 replicates per sample.
Output was loaded into R using Seurat (version 5.3.0) and filtered (200-6000 features per cell, <15% mitochondrial DNA). Next, counts were log-normalized, variable features were called (nfeatures = 3000) and the data was scaled. Next, a PCA was run and a sample batch correction was performed using Harmony (version 1.2.3). Clusters were identified based on shared nearest neighbour (SNN) clustering using the first 30 principal components, with a resolution of 0.3 and k = 30. The first 30 PCs were then used to generate UMAP projections with a minimum distance of 0.3. Clusters were annotated using known gene markers: T cells (Cd3e, Cd3g, Cd3d, Cd4, Cd8a, Cd8b), B cells (Ms4a1, Cd19), Dendritic cells (Cst3, Flt3), Macrophages (Cd68, Csf1r), Neutrophils (S100a9), NK cells (Klrb1c), Tumour (Stmn1). Additionally, FindMarkers with a Wilcoxon Rank Sum test and an absolute log2 fold change cut-off of 1 was used to identify cluster marker genes and further stratify cell annotation. Previously published gene signatures of DCs and macrophage populations were used to validate the identity of myeloid subsets.
Assembly: GRCm39-2024-A
Supplementary files format and content: scRNAseq_mouse_PLA2G2D.rds
Supplementary files format and content: Metadata_scRNAseq_TDLN_mouse_PLA2G2D.csv
Supplementary files format and content: RAW_scRNAseq_TDLN_mouse_PLA2G2D.csv

source_name: Tumor

growth_protocol: C57BL/6 and Balb/C mice were purchased from Jackson Laboratory, Flt3l-/- mice were bred and maintained in-house, and all were housed in specific pathogen-free conditions and fed ad libitum. Pla2g2d-/- mice were generated by  CRISPR/Cas9-mediated gene editing, in which deletion of exon 2 of the Pla2g2d gene results in loss of function through a frameshift from exon 1 to exon 3. Proximal (5’-CGAAAACCTAAGAGCCTGCG-3’) and distal (5’-TAGGTGGCTGGAACAACCAT-3’) Pla2g2d guide RNAs and Cas9 protein were injected into C57BL/6NTac zygotes using established methods. PLA2G2D-humanized mice on a C57BL/6 background were generated by Ozgene using gene targeting via homologous recombination. Briefly, the murine Pla2g2d genomic locus from residues L21 within exon 2 to the stop codon in exon 4 was replaced with human cDNA encoding residues I22 through to the stop codon. Gene targeting was performed on C57BL/6 ES cells. LN6-987AL and B16F0 cells were kindly provided by dr. Reticker-Flynn (Stanford University, USA) and cultured in DMEM medium. MC38 and B16-F10 (ATCC) tumor cell lines were cultured in DMEM medium, and E.G7-OVA and CT26 (ATCC) tumor cell lines were cultured in RPMI medium. All media were supplemented with Glutamax, gentamycin (50 μg/ml) and 10% fetal bovine serum (FBS).

extract_protocol:
At day 12, tumours, TDLNs and non-draining LNs were harvested, single cell suspensions were prepared and stained for extracellular antibodies. Single-cell suspensions of (TD)LNs were prepared by mechanically dispersing the lymph nodes through a 100-μm nylon mesh cell strainer. For tumours, single cells were prepared using the Tumour Dissociation Kit (Miltenyi). Using a FACSAria III (BD Biosciences), cells were pooled from 4 sorted (TD)LN populations that were mixed in equal ratios: i) alive ii) CD45- iii) CD45+CD3+CD44+ iv) combined CD45+CD3-CD11b+ and CD45+CD3-CD11c+ cells. From processed tumours, cells were pooled and mixed from 3 sorted fractions: i) alive ii)CD45+CD3+CD44+ iii) CD45+CD3-CD11b+ or CD45+CD3-CD11c+ cells. Next, pooled cell fractions were encapsulated for cDNA synthesis and barcoded with multiplexed runs on a Chromium X using the GEM-X 3’ OCM Chip (On Chip Multiplexing).
Sequencing libraries were generated following the instructions of the 1061 GEM-X Universal 3’ Gene Expression v4 4-plex user guide (CG000768). Sequencing was performed on a Novaseq 6000 platform (Illumina) using an S2 (100 cycle) flowcell with a 28-10-10-90 cycle setting. The target sequencing depth of each library was > 25.000 reads/cell.

treatment_protocol: To prepare for tumour inoculation, mice were shaved on the right flank. B16F0-tdTomato or LN6-987AL-tdTomato (2x105 cells) were harvested and washed twice with PBS before subcutaneous inoculation in 100μL PBS. Mice were monitored daily, and  tumours were measured by caliper every 3-4 days. When tumours reached 50-150 mm3 and were palpable, mice were randomized into groups and antibodies or proteins were administered intraperitoneally every 3-4 days for a total of four doses. Mice with palpable tumours were injected with anti-PLA2G2D, anti-IFNy (BioXCell) or isotype control antibodies (all 10 mg/kg) in 200 μL PBS. Anti-mouse PD-1 antibody (Clone RMP1-14, Leinco) was dosed at 5 mg/kg using the same schedule. Recombinant PLA2G2D-Fc protein was administered intraperitoneally at 50 μg in 100 μL PBS per dose every 4 days for a total of 4 doses.

value: Tumor

tag: tumor cell_line

value: aIFNy

tag: batch


title: LN6_PLA_Tumor

description:
Library name: St_ME8_S8
10X Genomics


title: LN6_unt_Tumor

description:
Library name: St_ME7_S7
10X Genomics

value: untreated


title: LN6_PD1_TDLN

description:
Library name: St_ME5_S5
10X Genomics

source_name: TDLN

value: TDLN


title: B16_unt_Tumor

description:
Library name: St_ME6_S6
10X Genomics


title: PC149_GEX

status: Public on Jun 24 2026

city: Morgantown

first: Gangqing

last: Hu

state: WV

address: 64 Medical Center Drive

institute: West Virginia University

description: Library name: PC149_GEX

data_processing:
The snMultiome datasets was processed by cellranger-arc version 2.0.2. The reference genome was GRCh38. cellranger-arc count was used to generated the gene and peaks feature for the libraries.
Assembly: GRCh38
Supplementary files format and content: *.filtered_feature_bc_matrix.h5 : Filtered feature barcode matrix stored as a CSC sparse matrix in hdf5 format. The rows consist of all the gene and peak features concatenated together (identical to raw feature barcode matrix) and the columns are restricted to those barcodes that are identified as cells.

molecule: nuclear RNA

organism: Homo sapiens

source_name: Pancreas

extract_protocol:
Isolation procedure was adapted from nuclei isolation from complex tissues for Single Cell Multiome ATAC + Gene Expression Sequencing (CG000375). Nuclei were isolated from 50 mg of frozen tissue cut into five small sections with a razor blade. The tissue pieces were homogenised for 1.5 min with a tissue homogeniser and pestle in 10 mM Tris–HCl, 10 mM NaCl, 3 mM MgCl2, .1% Nonidet P40 substitute and 1 mM dithiothreitol (DTT) in nuclease-free water. Tissue was dissociated in lysis buffer for 5 min before passing through a 70 μm cell strainer. The solution was then centrifuged (500 × g, 4°C, 5 min). The supernatant was removed and replaced with 1 mL 1% BSA in DPBS and allowed to incubate for 5 min before resuspension. The nuclei were centrifuged again (500 × g, 4°C, 5 min). The pellet was resuspended in 1 mL 1% BSA in DPBS and passed through a 30 μm cell strainer. All steps were performed on ice. Nuclei were stained with 7-aminoactinomycin D (7-AAD) readymade solution 1:100 (Sigma, SML-1633) and sorted with a FACSAria III Cell Sorter. Nuclei were collected into 10% BSA. For snMultiomics, 1 U/mL RNase inhibitor (Sigma–Aldrich, 03335402001) was added to all final solutions.
Prepared per manufacturer's instructions (10X Genomics, 1000283; CG000338 Rev E)

value: Pancreas

value: nonresponder

value: Gem/Abraxane


title: KP cells, WT, replicate 2

city: Shanghai

first: Kan

last: Huang

address: 130, Dongan Road

institute: Fudan University

description: Library name: HA_ctrl_rep2

data_processing:
Low quality reads and sequencing adaptors of the CUT&Tag reads were trimmed using fastp v0.24.0 with the parameter of "-T 1 -5 -l 50 -q 20 -u 50 -g -c --detect_adapter_for_pe -w 9"
CUT&Tag reads were local-aligned to the mouse mm10 genome and the DNA Spike-in sequence seperately using bowtie2 v2.5.4 with the parameter of "-p 9 -q --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700"
Scaling factors of each sample were calculated as 10,000 / (fragments mapped to Spike-in sequence). Normalized coverage for each sample was calculated as the primary genome coverage multiplied by the scaling factor.
Peaks were called using MACS v3.0.3 with the significance cut-off q-value <= 0.01.
BigWig files were generated using the bamCoverage function of deeptools v3.5.6. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: mm10
Supplementary files format and content: bigWig (except for IgG sample)
Library strategy: CUT&Tag

source_name: lung adenocarcinoma

growth_protocol: KP lung adenocarcinoma cells were maintained in RPMI1640 supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5% CO2 at 37℃

extract_protocol:
CUT&Tag experiment was conducted using CUT&Tag kit complemented with  Hyperactive TF Enhancer Module  from Vazyme (TD904-C2). Briefly, cells were collected and treated with TF enhancer. Subsequently, cells were bound with Concanavalin A-coated magnetic beads, and the plasma membrane was permeabilized with digitonin. Through the use of a primary antibody targeting HA or non-targeting IgG control, a corresponding secondary antibody, and Protein A/G, the transposase fused to Protein A/G was guided to precisely cleave DNA sequences near the target protein. During cleavage, adaptor sequences were added to both ends of the DNA fragments, which were then amplified by PCR to generate libraries for high-throughput sequencing.
CUT&Tag libraries were prepared using the CUT&Tag kit complemented with  Hyperactive TF Enhancer Module  (TD904-C2) and TruePrep Index Kit V2 for Illumina (TD202) from Vazyme. All of the cleaved DNA extracted using CUT&Tag kit was used as starting material for anti-HA and anti-IgG samples. Before PCR anplification, 0.05 pg DNA Spike-in was added into each sample as a reference standard, primarily for inter-sample normalization of the sequencing data. Libraries were then amplified using 16 cycles on the thermocycler. Libraries ere validated using the Fragment Analyzer 5300 system.

value: lung adenocarcinoma

tag: cell line

value: KP

value: lung adenocarcinoma cells

value: WT


title: LN6_IFN_TDLN

description:
Library name: St_ME4_S4
10X Genomics


title: U073_healthy donor

city: London

first: PATPONG

last: RONGKARD

address: Du Cane Rd

department: National Heart and Lung Institute

country: United Kingdom

institute: Imperial College London

description: Library name: U073

data_processing:
Raw sequencing data (FASTQ files) were pre-processed and quality checked by the service. The FASTQ files were mapped using human reference genome UCSC hg38.p2 version 20201using STAR aligner (version 2.6.1d). Raw counts (uniquely mapped reads) were generated from the mapped read files (.bam) using featureCounts function of Subread package (version 1.6.2) as tab-delimited text files.
Assembly: UCSC hg38.p2 version 20201
Supplementary files format and content: tab-delimited text files inlcudes raw counts for each sample

source_name: Whole blood

extract_protocol:
For the melioidosis cohort, we isolated total RNA from whole blood sample of 81 melioidosis patients and 29 uninfected control participants (DM control, n=15; healthy donor, n=14) collected in Tempus blood RNA tube using the Tempus Spin RNA. A ribozero library preparation and the globin depletion workflow were performed by the Oxford Genomics Centre, Wellcome Centre for Human Genetics, University of Oxford.
Ribozero library preparation with globin depletion workflow (HTG 384 UDI RNA-Seq Ribozero) was performed by  the Oxford Genomics Centre, Wellcome Centre for Human Genetics, University of Oxford. And the samples were sequenced for 75-base pair pair-end, 50 million reads.

value: Whole blood

tag: group

value: Male

tag: 28day mortality

value: survivor


title: LN6_unt_TDLN

description:
Library name: St_ME2_S2
10X Genomics


title: LN6_PLA_TDLN

description:
Library name: St_ME3_S3
10X Genomics


title: Liver tumor, Slc1a5Hep, replicate 1

description: Library name: Slc1a5Hep_rep1

value: liver tumor


title: LN6_PLA_LN

description:
Library name: St_ME12_S12
10X Genomics

source_name: Lymph node

value: Lymph node


title: LN6_PD1_Tumor

description:
Library name: St_ME10_S10
10X Genomics


title: B16_unt_LN

description:
Library name: St_ME11_S11
10X Genomics


title: B16_unt_TDLN

description:
Library name: St_ME1_S1
10X Genomics


title: D10-CSDS3

first: Jinmei

last: Ye

state: Shanghai

address: NO.600 Wanping Nan Road,Shanghai

institute: shanghai mental health center

description: Library name: Sample 24

data_processing:
Illumina Casava1.7 software used for basecalling.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count
Assembly: GRCm39
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: Matrix table with FPKM values for every gene and every sample

source_name: LS

growth_protocol: Male C57BL/6J mice (8 weeks old) were housed in groups of 5 per cage under a 12-hour light/dark cycle (lights on at 07:00) at 22–25°C with ad libitum access to food and water. All animal procedures were approved by the Institutional Animal Care Committee and performed in accordance with the guidelines of Shanghai Mental Health Center.

extract_protocol:
Total RNA was extracted from mouse lateral septum (LS) tissue using TRIzol reagent (Invitrogen). RNA purity and concentration were verified using a NanoDrop spectrophotometer (260/280 ratio between 1.8 and 2.1). RNA integrity was confirmed before library preparation.
Poly(A) RNA was enriched and used to construct RNA-seq libraries. Sequencing libraries were generated using a standard directional mRNA-seq library preparation protocol. Libraries were sequenced on an Illumina NovaSeq 6000 platform to generate 150 bp paired-end reads.

treatment_protocol: Mice were subjected to chronic social defeat stress (CSDS) for 10 consecutive days. On each day, experimental mice were exposed to an aggressive CD-1 mouse for 10 minutes, then separated by a plexiglass barrier until the next session. Control mice were housed under identical conditions without defeat stress.

value: LS

tag: strain

value: male

value: 8-14 weeks old

tag: condition


title: Adipose tissue, Aged_control_3

city: Hamilton

first: Punit

last: Bhattachan

state: Ontario

address: 20 Copeland Avenue

department: Surgery

country: Canada

institute: McMaster University

description:
Library name: Sample9
Columnname in raw_counts_Aged_Samples.txt: Aged_control_3

data_processing:
Galaxy
The quality of FASTQ files was examined by FastQC and MultiQC. Cutadapt tool was used to trim the reads.
The trimmed reads were maped to the mouse genome mm10/GRC38 using HISAT2 tool.
The featureCounts tool was used to generate count matrix.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for Adult Samples
Supplementary files format and content: tab-delimited text file includes raw counts for Aged Samples

source_name: Adipose tissue

extract_protocol:
Total RNA was extracted from the adipose tissue using Trizol reagent according to manufacture's protocols and mRNA was isolated by NEBNext poly(A) kit.
NEBNext Ultra II directional RNA library kit was used for the library construction.

treatment_protocol: Adult mice with 30% and aged mice with 20% TBSA was subjected to scald burn injury. A water bath was set to 98 oC and mouse was immersed for 10 seconds on the dorsal side to get 20% TBSA and only 2 seconds on ventral side for additional 10% TBSA. Buprenorphine (0.01-0.5 mg/kg) was used for the pain management.

value: Adipose tissue

tag: time

value: Day 7

value: Untreated


title: D10-CSDS2

description: Library name: Sample 23


title: D10-Ctrl3

description: Library name: Sample 21


title: D10-Ctrl1

description: Library name: Sample 19


title: D10-Ctrl2

description: Library name: Sample 20


title: D7-CSDS3

description: Library name: Sample 18


title: Adipose tissue, Adult_burn_2

description:
Library name: Sample5
Columnname in raw_counts_Adult_Samples.txt: Adult_burn_2

value: Scald burn injury


title: A-C-9

city: guangzhou

first: Lu

last: Xiao

state: Please Select

address: No. 601 Huangpu Avenue West

institute: The First Affiliated Hospital of Jinan University

description:
Library name: sample5
A-C-9

data_processing:
CLC Genomics Workbench v 11.0.1
Assembly: mm10
Supplementary files format and content: processed data files format all.xlsx

source_name: liver

extract_protocol:
RNA was harvested using Trizol. 0.2 ug of total RNA was used for the construction of sequencing libraties
RNA libraries for RNA-seq were prepared using Novogene fast RNA-seq Library Perp Kit V2 following manufacturer's protocols

value: liver

value: hepatocyte


title: D7-CSDS2

description: Library name: Sample 17


title: PC149_ATAC

description: Library name: PC149_ATAC

library_source: genomic single cell

value: Pancreas

value: nonresponder

value: Gem/Abraxane


title: D7-CSDS1

description: Library name: Sample 16


title: D7-Ctrl3

description: Library name: Sample 15


title: D10-CSDS1

description: Library name: Sample 22


title: D7-Ctrl2

description: Library name: Sample 14


title: D7-Ctrl1

description: Library name: Sample 13


title: D4-CSDS3

description: Library name: Sample 12


title: D4-CSDS1

description: Library name: Sample 10


title: D4-CSDS2

description: Library name: Sample 11


title: D4-Ctrl3

description: Library name: Sample 9


title: D4-Ctrl2

description: Library name: Sample 8


title: D1-CSDS3

description: Library name: Sample 6


title: D4-Ctrl1

description: Library name: Sample 7


title: D055_diabetes control

description: Library name: D055

value: Whole blood


title: D1-CSDS2

description: Library name: Sample 5


title: D1-CSDS1

description: Library name: Sample 4


title: D1-Ctrl3

description: Library name: Sample 3


title: D1-Ctrl2

description: Library name: Sample 2


title: D1-Ctrl1

description: Library name: Sample 1


title: KOH2

city: Beijing

first: Zhenyu

last: Zhu

state: Beijing

address: 38 Xueyuan Road, Haidian

institute: Peking University

description:
Library name: sample 8
Column name in KO_WT_count.txt: KOH2_count

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition.
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv file includes FPKM values for each Sample

source_name: Hippocampus

extract_protocol:
RNA was purified using Trizol reagent and the integrity was assessed by the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system
The trancriptome libraries were prepared using Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) and sequenced by the Illumina NovaSeq 6000

value: Hippocampus

value: PTENd knockout


title: 8505c_shCtrl_Vehicle_1

city: Bethesda

first: Myriem

last: Boufraqech

state: Maryland

address: NIH campus, building 10 room 7S261

department: CCR

institute: NCI

description: Library name: MB_01_S1_001

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CutAdapt v1.18 (parameters: --pair-filter=any nextseq-trim=2 --trim-n -n 5 -O 5 -q 10,10 -m 35:35)
Trimmed reads were mapped to hg38 reference genome using STAR 2.7.0f aligner
Read count extraction was performed using RSEM v1.3.0
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes RSEM counts for each sample

source_name: thyroid

extract_protocol:
RNA were extracted using RNAeasy kit (Qiagen)
We used 230 ng of total RNA samples to generate the library (Poly A selected) with 12 PCR cycles. The kits used for the library prep were NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB #E7490), NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB #E7760) and NEBNext® Multiplex Oligos for Illumina® (96 Unique Dual Index Primer Pairs, NEB, E6440) as described in the manufacturer’s manual. Sequencing was carried out in the Illumina NextSeq2000 instrument with NextSeq™ 2000 P4 XLEAP-SBS™ Reagent Kit (200 Cycles) 101x101 pair end configuration. The demultiplexing was carried out with the illumina DRAGEN BCL convert software version 4.2.7.

value: thyroid

value: ATC cell line

value: shC


title: GFP+; mApple- rep2, GCP

description: Library name: GFP+; mApple-_2

value: Cerebella

value: Mouse Granule cell precursors

value: Cntn2 mApple/+; Atoh1 M1GFP/+

value: postnatal day 6


title: Mouse cerebella, control, rep 1

city: Hong Kong

first: Kin Ming

last: Kwan

address: Room EG03, Science Center East Block, The Chinese University of Hong Kong

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

description: Library name: Control 1

data_processing:
Raw sequencing files were checked with FastQC version 0.11.8 to confirm the absence of adapters. Quality trimming was performed using Trimmomatic version 0.39. The trimmed reads were aligned to the mouse reference genome GRCm38 using STAR version 2.7.1a. Gene expression quantification was conducted with the featureCounts function in Rsubread version 2.0.0 using GENCODE vM23 annotation. Normalization and differential expression analysis were performed using DESeq2 version 1.26.0.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample
Supplementary files format and content: Tab-delimited text file includes DESeq2 normalized counts for each sample

extract_protocol:
Total cerebellum RNA from control and cKO mutant mice was extracted using TRIzol reagent (Life Technologies), following the previously established protocol (doi:10.1101/pdb.prot5439) followed by ribosomal RNA (rRNA) depletion. The RNA dissovled in RNase-free ddH2O and the concentration was checked by Qubit.
Strand-specific, rRNA depletion

value: Pcp2 Cre/+; Yy1 fx/+


title: KOH1

description:
Library name: sample 7
Column name in KO_WT_count.txt: KOH1_count


title: WTH2

description:
Library name: sample 6
Column name in KO_WT_count.txt: WTH2_count

value: WT


title: M212_melioidosis

description: Library name: M212

value: Female

value: survivor


title: KOC2

description:
Library name: sample 4
Column name in KO_WT_count.txt: KOC2_count

source_name: PFC

value: PFC


title: WTH1

description:
Library name: sample 5
Column name in KO_WT_count.txt: WTH1_count


title: WTC1

description:
Library name: sample 1
Column name in KO_WT_count.txt: WTC1_count


title: WTC2

description:
Library name: sample 2
Column name in KO_WT_count.txt: WTC2_count


title: KOC1

description:
Library name: sample 3
Column name in KO_WT_count.txt: KOC1_count


title: Jejunum, WT doxorubicin day 3, mouse 144

type: RNA

city: Odense

first: Mark

last: Burton

address: J.B. Winsløvsvej 4

department: Clinical Genetics

country: Denmark

institute: Odense University Hospital

description: Jejunum; one array per animal.

hyb_protocol: Hybridisation, washing and staining were performed automatically on the Affymetrix GeneTitan instrument according to the manufacturer's protocol for the Mouse Transcriptome Array 1.0 (fluidics/staining protocol FS450_0001).

scan_protocol: Arrays were scanned automatically in the Affymetrix GeneTitan instrument.

data_processing: CEL files were summarised at gene (transcript-cluster) level using Signal Space Transformation RMA (SST-RMA) in the Affymetrix Expression Console / Transcriptome Analysis Console (TAC) v3.0; the accompanying matrix contains log2 SST-RMA signal. Differential expression was assessed by ANOVA in TAC v3.0 (FDR < 0.05).

label: biotin

source_name: jejunum

label_protocol: Biotinylated sense-strand cDNA targets were prepared from total RNA using the Affymetrix GeneChip WT PLUS reagent kit according to the manufacturer's protocol.

growth_protocol: Adult 10-12-week-old female Sftpd-/- (KO) mice, backcrossed >10 generations onto the C57BL/6N background, and Sftpd+/+ (WT) littermates were bred in-house. Genotypes were confirmed by DNA PCR.

extract_protocol: Total RNA was isolated from jejunum using TRIzol (Invitrogen) per the manufacturer's instructions; quantity/purity assessed by NanoDrop (all A260/280 >= 1.8) and integrity verified on an Agilent 2100 Bioanalyzer (RNA 6000 Nano kit).

treatment_protocol: At day 0 mice received a single intraperitoneal injection of doxorubicin 20 mg/kg (Doxorubicin Accord) or an equal volume of isotonic saline, and were sacrificed on day 3 or day 7. The small intestine was removed and the jejunum (middle segment) was sampled.

value: Sftpd+/+ (wild-type)

tag: agent

value: doxorubicin (20 mg/kg, single i.p.)

value: day 3


title: P0 Wildtype rep2, Cerebellum, Hdac1 (ChIP)

description: Library name: Cerebellum_P0_Wildtype_Hdac1_rep2, ChIP

source_name: Cerebella

tag: tissue

value: Mouse Cerebellar Cells

value: Wildtype


title: LD_442

city: Los Angeles

first: Valentina

last: Villani

state: CA

address: 4661 Sunset blvd

department: Urology

institute: Children's Hospital Los angeles

description: Library name: Sample 10

data_processing:
Raw data (raw reads) of fastq format were first processed through in-house (Novogene) perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low-quality reads from raw data.
Data were further processed onto Partek Flow (Illumina)
Sequences were aligned to the reference Mus musculus-mm39 genome using STAR. Gene expression levels were determined by a “Quantify to annotation model (Partek E/M)” mapping aligned reads to the GencodeM32 (Ensembl) embedded in Partek to obtain gene counts and transcript counts. Features were filtered to exclude features where maximum count was <= 10 and normalized by counts per million (CPM+0.0001 offset).
Assembly: mm39
Supplementary files format and content: tab-delimited text files includes normalized counts (CPM+0.0001 offset) for each sample

extract_protocol:
RNA was extracted using Rneasy mini plus kit (Qiagen). ≥200ng (≥10ml; 20ng/ml) of RNA was used for the contraction of the sequencing libraries.
Libraries were generated by Novogene. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library. For the non-directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, amplification, and purification. For the directional library, it was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification.

treatment_protocol: 25-month old HET3 female mice were fed for 5 months with either a standard diet (SD) or a Longevity diet (LD).

value: liver

value: female

value: Longevity diet


title: LD_515

description: Library name: Sample 9


title: LD_406

description: Library name: Sample 8


title: LD_405

description: Library name: Sample 6


title: SD_500

description: Library name: Sample 5

value: standard diet


title: LD_513

description: Library name: Sample 7


title: SD_646

description: Library name: Sample 4


title: SD_501

description: Library name: Sample 2


title: SD_502

description: Library name: Sample 3


title: SD_403

description: Library name: Sample 1


title: Salr OE, fat body, rep1

city: Helsinki

first: Ville

last: Hietakangas

address: Viikinkaari 9

country: Finland

institute: University of Helsinki

description: Library name: A010

data_processing:
FastQC v.0.11.2 was used for quality assessment and Trimmomatic v.0.33 for trimming the data. The minimum read length of 36 bases was required. Minimum read quality score of 20 was used. The reads were scanned with 4-base sliding window and trimmed when the average quality per base dropped below 15.
The reads were mapped with TopHat (v.2.1.0) to the D. melanogaster reference genome (FlyBase R6.10). Transcription was quantified strand-specifically with HTSeq (v.2.7.6) on the level of annotated exons (Flybase) with reads below quality score of 10 discarded.
The differential expression among different samples and conditions was quantified with limma package (v.3.28.8) implemented in R/Bioconductor with Benjamini–Hochberg correction for adjusting p values. The genes with very low counts (cpm < 1 in more than one replicate per condition) were filtered.
Assembly: Flybase R6.10
Supplementary files format and content: fastq files and tab delimited txt files consisting log2cpm values of all samples along with coefficient, t, p, adjusted p values for each gene

organism: Drosophila melanogaster

source_name: fat body

growth_protocol: 1st instar larvae were collected 24 hours after egg laying and grown on standard Drosophila medium at equal density (30/vial).

extract_protocol:
Fat body tissues of early third instar larvae were dissected, and RNA extraction was done using Nucleospin RNA II kit (Macherey-Nagel) following the manufacturer’s guidelines.
RNA libraries were prepared using the TruSeq Stranded mRNA kit (Illumina), and sequenced on the Illumina NextSeq500 system to achieve an average depth of 20 million reads per sample, utilizing the 75bp cycle kit (Illumina).

value: fat body

tag: developmental stage

value: early third-instar


title: Carotid body bifurcation_Mecp2 knockout_1

description: Library name: Sample 5

source_name: Bilateral carotid body bifurcations

value: Bilateral carotid body bifurcations

value: Male

tag: genotype

value: dark cycle


title: w1118, fat body, rep2

description: Library name: A008


title: Salr OE, fat body, rep3

description: Library name: A012


title: w1118, fat body, rep1

description: Library name: A007


title: w1118, fat body, rep3

description: Library name: A009


title: Salr OE, fat body, rep2

description: Library name: A011


title: Trip Ctrl, fat body, rep3

description: Library name: A003

value: CG-Gal4>Trip Control


title: Salr RNAi (BTN 29549), fat body, rep2

description: Library name: A005

value: CG-Gal4>Salr RNAi (29549)


title: Trip Ctrl, fat body, rep1

description: Library name: A001


title: TRAP-enriched excitatory neuron RNA from mice cortex and hippocampus at P21, replicate 1 [3w-Cre-1]

first: Jue

last: Wang

address: No.10, Xi Tou Tiao, Youanmen wai, Fengtai District

department: School of Basic Medical Sciences

institute: Capital Medical University

description:
Library name: Sample 9
3w-Cre-1

data_processing:
Raw sequencing reads were processed using fastp (v1.0.1) for quality control, adapter trimming, and filtering of low-quality reads.
Transcript-level abundance was quantified using Salmon (v1.10.0) against the mouse reference transcriptome (Assembly: mm39, GENCODE vM37 annotation).
Transcript-level quantifications were summarized to the gene level (Ensembl IDs) using the R package tximport (v1.34.0). The resulting gene-level Transcripts Per Million (TPM) matrix is provided as the processed data file.
Differential gene expression analysis was performed using the R package DESeq2 (v1.46.0), utilizing the raw counts aggregated by tximport.
Assembly: mm39
Supplementary files format and content: The processed data file is a tab-separated values (TSV) matrix containing gene-level abundance estimates. Values represent Transcripts Per Million (TPM) calculated by tximport from Salmon quantifications. Rows correspond to individual genes, identified by Ensembl Gene IDs (with version numbers removed). Columns correspond to individual samples, and the column headers exactly match the annotations in the "Description"  field.
Library strategy: Ribo-seq

source_name: cortex and hippocampus

growth_protocol: All the mice were of specific pathogen-free (SPF) grade and were housed in a laminar flow animal facility with a constant temperature of 24 °C, a humidity level of 30%-70%, and a 12-hour day-night cycle.

extract_protocol:
Upon tissue collection, whole brains were rapidly removed on ice, and the cerebral cortex and hippocampus were carefully dissected. Tissues were homogenized in salt lysis buffer supplemented with RNase inhibitor, DTT, cycloheximide, and protease inhibitors. After clarification by centrifugation, a portion of the lysate was saved as the Input fraction, while the remaining lysate was incubated with anti-GFP magnetic beads to immunoprecipitate eGFP-Rpl10a–associated ribosomes. Following several washes with high-salt buffer, ribosome-associated RNA from the IP fraction was isolated using the RNeasy Micro Kit for subsequent RNA sequencing.
Library construction was performed using the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (#NR605). Fragmented mRNA was reverse-transcribed into first-strand cDNA using random primers and M-MuLV reverse transcriptase, followed by second-strand synthesis. After end repair, A-tailing, and adaptor ligation, ~250-300 bp fragments were size-selected with VAHTS DNA Clean Beads and PCR-amplified. Library quality was assessed using a Qubit 3.0 Fluorometer and an Agilent 2100 Bioanalyzer, and libraries with an effective concentration >2 nM were sequenced on an NovaSeq X Plus platform.

treatment_protocol: NEX-RiboTag mice (generated by crossing NEX-Cre mice on a C57BL/6J background with RiboTag reporter mice) were maintained under standard housing conditions until tissue collection. Cortex and hippocampus tissues were collected at postnatal day 7 (P7), postnatal day 14 (P14), and postnatal day 21 (P21). Two P7 whole-tissue lysate samples were used as Input-RNA controls, while three TRAP-enriched IP-RNA biological replicates were collected at each developmental stage.

value: cortex and hippocampus

tag: cell type

value: Excitatory Neurons

tag: age


title: TRAP-enriched excitatory neuron RNA from mice cortex and hippocampus at P21, replicate 3 [3w-Cre-3]

description:
Library name: Sample 11
3w-Cre-3


title: TRAP-enriched excitatory neuron RNA from mice cortex and hippocampus at P14, replicate 3 [2w-Cre-3]

description:
Library name: Sample 8
2w-Cre-3


title: Trip Ctrl, fat body, rep2

description: Library name: A002


title: TRAP-enriched excitatory neuron RNA from mice cortex and hippocampus at P14, replicate 2 [2w-Cre-2]

description:
Library name: Sample 7
2w-Cre-2


title: TRAP-enriched excitatory neuron RNA from mice cortex and hippocampus at P21, replicate 2 [3w-Cre-2]

description:
Library name: Sample 10
3w-Cre-2


title: TRAP-enriched excitatory neuron RNA from mice cortex and hippocampus at P14, replicate 1 [2w-Cre-1]

description:
Library name: Sample 6
2w-Cre-1


title: Whole-tissue lysate RNA from mice cortex and hippocampus at P7, replicate 2 [1w-WT-Input]

description:
Library name: Sample 2
1w-WT-Input

data_processing:
Raw sequencing reads were processed using fastp (v1.0.1) for quality control, adapter trimming, and filtering of low-quality reads.
Transcript-level abundance was quantified using Salmon (v1.10.0) against the mouse reference transcriptome (Assembly: mm39, GENCODE vM37 annotation).
Transcript-level quantifications were summarized to the gene level (Ensembl IDs) using the R package tximport (v1.34.0). The resulting gene-level Transcripts Per Million (TPM) matrix is provided as the processed data file.
Differential gene expression analysis was performed using the R package DESeq2 (v1.46.0), utilizing the raw counts aggregated by tximport.
Assembly: mm39
Supplementary files format and content: The processed data file is a tab-separated values (TSV) matrix containing gene-level abundance estimates. Values represent Transcripts Per Million (TPM) calculated by tximport from Salmon quantifications. Rows correspond to individual genes, identified by Ensembl Gene IDs (with version numbers removed). Columns correspond to individual samples, and the column headers exactly match the annotations in the "Description"  field.

value: whole tissue


title: TRAP-enriched excitatory neuron RNA from mice cortex and hippocampus at P7, replicate 1 [1w-Cre-1]

description:
Library name: Sample 3
1w-Cre-1


title: Whole-tissue lysate RNA from mice cortex and hippocampus at P7, replicate 1 [1w-Cre-Input]

description:
Library name: Sample 1
1w-Cre-Input


title: TRAP-enriched excitatory neuron RNA from mice cortex and hippocampus at P7, replicate 2 [1w-Cre-2]

description:
Library name: Sample 4
1w-Cre-2


title: TRAP-enriched excitatory neuron RNA from mice cortex and hippocampus at P7, replicate 3 [1w-Cre-3]

description:
Library name: Sample 5
1w-Cre-3


title: Lung organoid d6

city: Guangzhou

first: Ruifang

last: Zhang

state: Guangdong

address: Haizhu District

institute: Guangzhou Laboratory

description:
Library name: Sample 1
10x Genomics

data_processing:
The Alignment and gene counting  were made using the STAR software.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lung organoids

extract_protocol:
Single-cell suspension preparation. Discard the culture medium of BLOs, wash twice with PBS, and aspirated BLOs into a 6cm dish, using insulin syringe needle (328421) to remove matrigel from BLOs. The BLOs were digested by preheated 10 U/mL Papain (Worthington, LS003126) at 37 °C for 20 min in the incubator. Once the digestion was completed, an equivalent 10% FBS was added for termination. Cell suspensions were filtered through a 40-μm strainer (Falcon, 352340) and collected into a new LoBind tube on ice. After centrifugation at 300× g for 5 min at 4 °C, removed supernatant and resuspended with PBS plus 0.04% BSA to prepare for scRNA-seq library construction. Meanwhile, 0.04% trypan blue was introduced to determine cell viability via cell staining.
Single-cell RNA library preparation and sequencing. Single-cell suspensions from each sample were loaded onto 10× Genomics Chromium v3.1 system to generate single-cell gel beads-in-emulsion (GEMs), where all generated full-length cDNA share a common 10× barcode. After incubation, GEMs were disrupted and cDNA was amplified via PCR. The single-cell 3’ gene expression libraries were constructed using 10 μL cDNA and purified with SPRIselect. Libraries were quality controlled by Qsep100 for sized distribution and by Qubit 4.0 fluorometer for concentration quantification. Finally, sequencing was Illumina NovaSeq X Plus Sequencing,which provided by ANNOROAD GENE TECHNOLOGY.

value: lung organoids

value: E10.5 lung tip-derived branching organoids (Day 6)


title: E11.5_lung_organoids_day11

description:
Library name: Sample 9
10x Genomics

value: E11.5 lung tip-derived branching organoids (Day 11)


title: E12.5_lung_organoids_day9

description:
Library name: Sample 10
10x Genomics

value: E12.5 lung tip-derived branching organoids (Day 9)


title: C57_lung_organoids_day11

description:
Library name: Sample 8
10x Genomics

value: E10.5 lung tip-derived branching organoids (Day 11)


title: Lung organoid d4

description:
Library name: Sample 6
10x Genomics

value: E10.5 lung tip-derived branching organoids (Day 4)


title: Lung organoid d2

description:
Library name: Sample 5
10x Genomics

value: E10.5 lung tip-derived branching organoids (Day 2)


title: 90dpt-endogenous

description:
Library name: Sample 4
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Single-cell suspension preparation. Discard the culture medium of BLOs, wash twice with PBS, and aspirated BLOs into a 6cm dish,using insulin syringe needle (328421)to remove matrigel from BLOs. The BLOs were digested by preheated 10 U/mL Papain (Worthington, LS003126) at 37 °C for 20 min in the incubator. Once the digestion was completed, an equivalent 10% FBS was added for termination. Cell suspensions were filtered through a 40-μm strainer (Falcon, 352340) and collected into a new LoBind tube on ice. After centrifugation at 300× g for 5 min at 4 °C, removed supernatant and resuspended with PBS plus 0.04% BSA to prepare for scRNA-seq library construction. Meanwhile, 0.04% trypan blue was introduced to determine cell viability via cell staining.
Single-cell RNA library preparation and sequencing. Single-cell suspensions from each sample were loaded onto 10× Genomics Chromium v3.1 system to generate single-cell gel beads-in-emulsion (GEMs), where all generated full-length cDNA share a common 10× barcode. After incubation, GEMs were disrupted and cDNA was amplified via PCR. The single-cell 3’ gene expression libraries were constructed using 10 μL cDNA and purified with SPRIselect. Libraries were quality controlled by Qsep100 for sized distribution and by Qubit 4.0 fluorometer for concentration quantification. Finally, sequencing was Illumina NovaSeq X Plus Sequencing,which provided by ANNOROAD GENE TECHNOLOGY.


title: 180dpt-Donor-derived

description:
Library name: Sample 5
10x Genomics


title: ALL-VC_r2

description:
Library name: Sample 40
total RNAseq

data_processing:
RNA-seq reads were aligned to the mm10 using RSEM, bowtie2.
Assembly: mm10
Supplementary files format and content: csv files include TPM values for each Sample.

extract_protocol:
BLOs total RNA Isolation. Discard the culture medium of BLOs, wash twice with PBS, and aspirate BLOs into a 1.5 ml centrifuge tube using a 1 ml pipette tip. After centrifugation at 300× g for 5 min, remove supernatant. Add 500 μl TRIzol Reagent (TR118) to extract total RNA following the product instructions.
After total RNA was isolated. Sequencing libraries were prepared according to the VAHTS mRNA-seq v2 Library Prep Kit for Illumina (NR605, Vazyme). Library sequencing used Illumina NovaSeq X Plus Sequence,which provided by ANNOROAD GENE TECHNOLOGY.

value: Lung-organoid-ALL-factor


title: ALL-MTG_r1

description:
Library name: Sample 37
total RNAseq


title: ALL-VC_r1

description:
Library name: Sample 39
total RNAseq


title: ALL_r2

description:
Library name: Sample 34
total RNAseq


title: ALL_r1

description:
Library name: Sample 33
total RNAseq


title: ALL

description:
Library name: Sample 32
total RNAseq


title: 2C+VC

description:
Library name: Sample 31
total RNAseq


title: 2C+MTG

description:
Library name: Sample 30
total RNAseq


title: 2C

description:
Library name: Sample 28
total RNAseq


title: 2C+F10

description:
Library name: Sample 29
total RNAseq


title: Lung organoid d19

description:
Library name: Sample 3
10x Genomics

data_processing:
The Alignment and gene counting were made using the STAR software.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

value: E10.5 lung tip-derived branching organoids (Day 19)


title: Lung organoid d8

description:
Library name: Sample 1
10x Genomics

value: E10.5 lung tip-derived branching organoids (Day 8)


title: 28dpt-Donor-derived

description:
Library name: Sample 1
10x Genomics


title: organoid_E14_24d

description:
Library name: Sample 28
totol RNAseq

source_name: lung


title: organoid_E9.5_13d

description:
Library name: Sample 29
totol RNAseq


title: organoid_E14_11d

description:
Library name: Sample 27
totol RNAseq


title: organoid_E13.5_30d

description:
Library name: Sample 26
totol RNAseq


title: organoid_E13.5_11d

description:
Library name: Sample 24
totol RNAseq


title: organoid_E11.5_11d

description:
Library name: Sample 23
totol RNAseq


title: organoid_E10.5_18d

description:
Library name: Sample 21
totol RNAseq


title: E13.5_Tip

description:
Library name: Sample 19
totol RNAseq

value: lung epithelium

value: lung tip epithelium cells


title: E12.5_Tip

description:
Library name: Sample 18
totol RNAseq

value: lung tip epithelial cells


title: E11.5_Tip

description:
Library name: Sample 17
totol RNAseq


title: E10.5_Tip

description:
Library name: Sample 16
totol RNAseq


title: Salr RNAi (BTN 29549), fat body, rep3

description: Library name: A006

value: fat body

value: CG-Gal4>Salr RNAi (29549)

value: early third-instar


title: Salr RNAi (BTN 29549), fat body, rep1

description: Library name: A004


title: up-half-right (6)

description:
Library name: Sample 15
totol RNAseq

value: lung organoid


title: up-half-left (5)

description:
Library name: Sample 14
totol RNAseq

value: lung organoids


title: up-half (1)

description:
Library name: Sample 13
totol RNAseq


title: right-half (4)

description:
Library name: Sample 12
totol RNAseq


title: left-half (3)

description:
Library name: Sample 11
totol RNAseq


title: intact(0)

description:
Library name: Sample 10
totol RNAseq


title: down-half-right (8)

description:
Library name: Sample 9
totol RNAseq


title: E10.5 Tip

description:
Library name: Sample 4
10x Genomics

value: lung

value: E10.5 lung tip


title: down-half-left (7)

description:
Library name: Sample 8
totol RNAseq


title: 180dpt-endogenous

description:
Library name: Sample 6
10x Genomics


title: ALL-FGF10_r1

description:
Library name: Sample 35
total RNAseq


title: ALL-FGF10_r2

description:
Library name: Sample 36
total RNAseq


title: down-half (2)

description:
Library name: Sample 7
totol RNAseq


title: ALL-MTG_r2

description:
Library name: Sample 38
total RNAseq


title: 90dpt-Donor-derived

description:
Library name: Sample 3
10x Genomics


title: LO_day11

description:
Library name: Sample 2
totol RNAseq


title: LO_day18

description:
Library name: Sample 3
totol RNAseq


title: LO_day11_DCI

description:
Library name: Sample 4
totol RNAseq


title: LO_day8

description:
Library name: Sample 1
totol RNAseq


title: Pd biol rep 8

city: Boston

first: Jimmy

middle: W.

last: Crott

state: Massachusetts

address: 670 Albany Street

department: Pathology and Laboratory Medicine

institute: Boston University School of Medicine

description:
Library name: Sample 18
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Pd_13

data_processing:
Quality control performed using FastQC (v0.12.1).
Reads aligned to Drosophila melanogaster reference genome (BDGP6.54, Ensembl Metazoa) using STAR (v2.7.11b).
Gene-level read counts generated using featureCounts from Subread package (v2.1.0) with Ensembl GTF annotations (Drosophila_melanogaster.BDGP6.54.61.gtf).
Assembly: Drosophila melanogaster BDGP6.54 (Ensembl)
Supplementary files format and content: CSV file with raw counts for all samples.
Supplementary files format and content: CSV file with DESeq2-normalized counts for all samples.

source_name: Gut

growth_protocol: Virgin female w1118 Drosophila were maintained on either Control or Parabacteroides distasonis-supplemented diets and harvested at 45 days of age.

extract_protocol:
Guts were dissected from virgin female flies and immediately placed into RNAlater (Invitrogen). Total RNA was isolated using Trizol (Thermo Fisher) with glycogen to enhance yield. RNA was quantified using a Fragment Analyzer (Agilent). Fifty ng of total RNA was used for library construction.
RNA libraries were prepared using Stranded Total RNA Prep with Ribo-Zero Plus kit (Illumina) following manufacturer's protocols.

value: Gut

value: Parabacteroides distasonis diet


title: Pd biol rep 7

description:
Library name: Sample 17
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Pd_11


title: Pd biol rep 6

description:
Library name: Sample 16
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Pd_10


title: Pd biol rep 5

description:
Library name: Sample 15
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Pd_9


title: Lung organoid d11

description:
Library name: Sample 2
10x Genomics

value: E10.5 lung tip-derived branching organoids (Day 11)


title: Pd biol rep 2

description:
Library name: Sample 12
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Pd_6


title: Pd biol rep 4

description:
Library name: Sample 14
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Pd_8


title: Pd biol rep 1

description:
Library name: Sample 11
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Pd_2


title: Pd biol rep 3

description:
Library name: Sample 13
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Pd_7


title: Control biol rep 10

description:
Library name: Sample 10
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Control_14

value: Control diet


title: 28dpt-endogenous

description:
Library name: Sample 2
10x Genomics


title: Control biol rep 9

description:
Library name: Sample 9
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Control_13


title: Control biol rep 8

description:
Library name: Sample 8
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Control_12


title: Control biol rep 6

description:
Library name: Sample 6
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Control_10


title: Control biol rep 5

description:
Library name: Sample 5
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Control_8


title: Control biol rep 7

description:
Library name: Sample 7
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Control_11


title: Control biol rep 4

description:
Library name: Sample 4
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Control_7


title: organoid_E13.5_19d

description:
Library name: Sample 25
totol RNAseq


title: Control biol rep 3

description:
Library name: Sample 3
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Control_5


title: Control biol rep 2

description:
Library name: Sample 2
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Control_4


title: 8082_Pleg_low_312

type: protein

city: Silver Spring

first: Lakshmi Manasa

middle: Sakuntala

last: Chekka

address: 10903 New Hampshire Avenue

department: DARS, CDER

institute: U.S. FDA

hyb_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).

data_processing:
https://www.mcgill.ca/genepi/files/genepi/bqc19_jgh_prt_tech_note_0.pdf. R package Biobase and SomaDataIO were used to extract and read the adat files along with the manifest files.
Read out is relative flourescent units (RFU) which is directly proportional to the amount of target protein in the initial sample, as informed by a standard curve generate for each protein-SOMAmer pair. Raw RFU is normalized as described in the data processing step above.

label: 5’ fluorophore, photocleavable linker, and biotin

molecule: protein

source_name: EDTA plasma

growth_protocol: EDTA Plasma from healthy subjects was collected and stored at -80 degrees centigrade.

extract_protocol: EDTA plasma from whole blood

treatment_protocol: Subjects were randomized between IFNβ-1a (7.5 µg) and pegIFNβ-1a (31.25 µg).

tag: drug group

tag: delivery

value: SC

tag: dose

tag: timepoint


title: 8082_Pleg_low_144

scan_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).


title: 8082_Pleg_low_216

label_protocol: https://mohanlab.bme.uh.edu/wp-content/uploads/2017/02/SSM-002-Rev-4-SOMAscan-Technical-White-Paper.pdf); SomaLogic, Boulder, Colorado; PMID: 22022604; https://pubmed.ncbi.nlm.nih.gov/22022604/; https://somalogic.com/technology/).


title: Control biol rep 1

description:
Library name: Sample 1
Column name in raw_counts.csv and DESeq2_normalized_counts.csv:  Control_3

tag: treatment


title: 8082_Pleg_low_120


title: 8082_Pleg_low_96


title: organoid_E10.5_32d

description:
Library name: Sample 22
totol RNAseq


title: 8082_Pleg_low_72


title: 8082_Pleg_low_32


title: 8082_Pleg_low_8


title: 8082_Pleg_low_16


title: 8082_Pleg_low_3


title: 8082_Pleg_low_48


title: 8082_Pleg_low_0


title: 8079_Avonex_low_120

value: IM


title: organoid_E10.5_11d

description:
Library name: Sample 20
totol RNAseq


title: 8079_Avonex_low_96


title: 8079_Avonex_low_144


title: 8079_Avonex_low_72


title: 8079_Avonex_low_48


title: 8079_Avonex_low_32


title: 8079_Avonex_low_8


title: 8079_Avonex_low_3


title: 8079_Avonex_low_16


title: 8079_Avonex_low_0


title: 8075_Pleg_low_216


title: 8075_Pleg_low_312


title: 8075_Pleg_low_144


title: 8075_Pleg_low_120


title: 8075_Pleg_low_96


title: 8075_Pleg_low_48


title: 8075_Pleg_low_72


title: 8075_Pleg_low_16


title: 8075_Pleg_low_8


title: 8075_Pleg_low_32


title: 8075_Pleg_low_3


title: 8075_Pleg_low_0


title: 8071_Avonex_low_144


title: 8071_Avonex_low_72


title: 8071_Avonex_low_96


title: 8071_Avonex_low_16


title: 8071_Avonex_low_3


title: 8071_Avonex_low_0


title: 8068_Pleg_low_312


title: 8068_Pleg_low_216


title: 8068_Pleg_low_144


title: 8068_Pleg_low_120


title: 8068_Pleg_low_72


title: 8068_Pleg_low_96


title: 8068_Pleg_low_48


title: 8068_Pleg_low_16


title: 8068_Pleg_low_8


title: 8068_Pleg_low_3


title: 8062_Pleg_low_312


title: 8068_Pleg_low_0


title: 8062_Pleg_low_216


title: 8062_Pleg_low_144


title: 8062_Pleg_low_120


title: 8062_Pleg_low_72


title: 8062_Pleg_low_48


title: 8062_Pleg_low_96


title: 8062_Pleg_low_16


title: 8062_Pleg_low_8


title: 8062_Pleg_low_0


title: 8061_Avonex_low_144


title: 8061_Avonex_low_120


title: NR3_clone54.2

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415/420 Clinical Research Building (CRB)

institute: University of Pennsylvania

description: Library name: NR3_clone54.2

data_processing:
Pipeline overview: data were aligned to human genome assembly hg38 and subsequent analysis was performed with CUT&RUNTools v2.0 (https://github.com/fl-yu/CUT-RUNTools-2.0) using the standard CUT&Tag pipeline.
Read trimming and alignment: reads were trimmed with trimmomatic v0.36 and aligned with bowtie2 v2.4.2. bowtie2 --very-sensitive-local --phred33 -I 10 -X 700
Filtering: unmapped/unpaired reads were filtered out using samtools v1.1 view -bS -h -f 3 -F 4 -F 8
PCR duplicates removal were performed using PICARD: picard.jar MarkDuplicates REMOVE_DUPLICATES=True ASSUME_SORT_ORDER=queryname
Read shift: aligned reads were shifted +4bp and -5bp for positive and negative strand reference genome alignments, respectively, to account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase.
Peak calling: peaks were called using MACS2 v2.2.7.1.
Peak merge: peaks from individual replicates were merged where overlapping.
Track creation: ATACseq bigwig files were generated with deeptools 3.5.1  bamCoverage --normalizeUsing CPM.
Assembly: hg38/GRCh38
Supplementary files format and content: The BED file union_peaks_clean_named.bed contains all ATAC-seq peaks from MACS2 narrow peak calls and were then merged if overlapping.
Supplementary files format and content: The bigwig files *.bw were generated using deeptools bamCoverage with CPM normalisation.

source_name: Primary human skin fibroblasts

growth_protocol: Primary human skin fibroblasts were obtained from commercial sources, obtained from neonatal male donors (Cascade Biologics, #C0045C). Cells were cultured in DMEM (ThermoFisher, #11995065),  supplemented with 10% fetal bovine serum (FBS) and 5% penicillin/streptomycin (Invitrogen, #15140122). Cells were passaged every 3-4 days using 0.05% trypsin-EDTA (Invitrogen, #25300054). Cell cultures tested negative for mycoplasma.

extract_protocol:
We performed ATAC sequencing according to the protocol of Corces et al., 2017 (PMID: 28846090). In short, we lysed cells and set up the transposition reaction with the Tn5 transposase at 37 C for 30 minutes. Next, we isolated transposed and adaptor-ligated genomic DNA with the Zymo DNA Clean and Concentrator Kit (Zymo, #D4014).
We amplified the library using custom-made primers (Supplemental Table 2, available on BioRxiv), originally designed by the William Greenleaf lab at Stanford University.

treatment_protocol: Cells used for ATAC-seq analysis were untreated.

value: human skin fibroblasts

tag: replicate


title: 8061_Avonex_low_96


title: 8061_Avonex_low_72


title: 8061_Avonex_low_48


title: NR2_clone42.2

description: Library name: NR2_clone42.2


title: NR2_clone42.1

description: Library name: NR2_clone42.1


title: R3_clone38.2

description: Library name: R3_clone38.2


title: 8061_Avonex_low_32


title: 8061_Avonex_low_16


title: 8061_Avonex_low_3


title: 8061_Avonex_low_0


title: R2_clone10.2

description: Library name: R2_clone10.2


title: 8057_Avonex_low_144


title: R2_clone10.1

description: Library name: R2_clone10.1


title: NR1_clone6.2

description: Library name: NR1_clone6.2


title: 8057_Avonex_low_120


title: 8057_Avonex_low_96


title: R1_clone3.2

description: Library name: R1_clone3.2


title: 8057_Avonex_low_72


title: R1_clone3.1

description: Library name: R1_clone3.1


title: PC_culture.2

description: Library name: PC_culture.2


title: 8057_Avonex_low_32


title: 8071_Avonex_low_120


title: PC_culture.1

description: Library name: PC_culture.1


title: 8071_Avonex_low_8


title: 8071_Avonex_low_32


title: 8071_Avonex_low_48


title: 8057_Avonex_low_16


title: SD45 Vehicle

city: La Jolla

first: Brian

middle: A

last: Aguado

address: 2880 Torrey Pines Scenic Dr

institute: University of California San Diego

description: Library name: BV9

data_processing:
Quality control using fastqc v0.12.1.
Confirmed adaptor sequence content with fastqc. If adaptor sequence content exceeded <5%, trimmomatic (v0.39) was performed.
Alignment using HISAT2-2.2.1.
Gene counts quantified using featureCounts  using the Sus_scrofa.Sscrofa11.1.111.gtf annotation file.
Assembly: Sus scrofa 11.1 (Ensembl) Sus_scrofa.Sscrofa11.1.dna_sm.toplevel.fa.gz
Supplementary files format and content: Tab delimited text includes raw counts for each sample

organism: Sus scrofa

source_name: Porcine aortic valve

growth_protocol: Valvular interstitial cells (VICs) were seeded onto stiff hydrogels and cultured with Media 199, 1% human serum, antibiotic and antifungal supplements.

extract_protocol:
Total RNA was isolated using Qiagen Rneasy Micro kit, following manufacturer protocol. A minimum of 100 ng of RNA per sample was used for library preparation.
RNA library for RNA-seq was prepared using Illumina's stranded mRNA kit.

treatment_protocol: VICs were treated with either DMSO (vehicle), Evogliptin at 5.4 nM, or Evogliptin at 5.4 nM with 1 ug/mL neutraizing insulin-like growth factor binding protein 2 antibody. After 2 days, VICs were lysed for RNA collection.

value: Porcine aortic valve

value: Aortic valvular interstitial cell

tag: serum sample

value: DMSO control


title: 8057_Avonex_low_8


title: 8068_Pleg_low_32


title: SD30 Vehicle

description: Library name: BV8


title: 8057_Avonex_low_3


title: SD26 Vehicle

description: Library name: BV7


title: 8057_Avonex_low_0


title: 8056_Pleg_low_312


title: 8056_Pleg_low_216


title: 8056_Pleg_low_144


title: 8056_Pleg_low_120


title: SD45 Evogliptin + IGFBP2 Antibody

description: Library name: BV3

value: Evogliptin + IGFBP2 Antibody


title: SD30 Evogliptin + IGFBP2 Antibody

description: Library name: BV2


title: SD26 Evogliptin + IGFBP2 Antibody

description: Library name: BV1


title: 8056_Pleg_low_72


title: 8056_Pleg_low_48


title: Human, NEpiC, DMSO, 2h_3

city: Fukuoka

first: Keisuke

last: Ikegami

address: Nishi-ku Motooka 744

country: Japan

institute: Kyushu University

description:
Library name: HNEpiC_Veh2h_3
20220602 HNPEpiC DMSO vs Dex2h DESeq2 wald local 0.1 non-paired_Counts.xlsx

data_processing:
FASTQ files were received from the sequencing provider.
Quality control, mapping, and differential gene expression analysis were performed using RaNAseq and BioJupies.
Differentially expressed genes were identified by comparing NE- or DEX-treated samples with vehicle-treated control samples at the corresponding exposure time points.
Assembly: To be confirmed based on the reference genome used for mapping in RaNAseq/BioJupies.
Supplementary files format and content: Processed data files contain gene-level expression values and differential expression analysis results generated from the RNA-seq data.

source_name: ciliary body

growth_protocol: Human Non-Pigmented Ciliary Epithelial Cells (HNPCEpiC; ScienCell, Cat. No. 6580) were plated in Type I collagen-coated 6-well plates and cultured until they reached 80–90% confluence. The medium was then replaced with serum-free Epithelial Cell Medium (EpiCM), and cells were incubated for 24 hours before treatment.

extract_protocol:
At the indicated time points, culture medium was aspirated, and cells were gently washed with 1 mL of ice-cold PBS. Cells were lysed by adding 0.2 mL of lysis reagent from the NucleoSpin RNA/Protein kit (Takara Bio) and detached using a cell scraper. RNA was extracted according to the manufacturer's protocol and quantified using a NanoDrop One spectrophotometer.
RNA sequencing library preparation and sequencing were performed by an external service provider using the submitted RNA samples.

treatment_protocol: After 24 hours in serum-free EpiCM, cells were treated with norepinephrine (NE; final concentration, 1 µM) or dexamethasone (DEX; final concentration, 0.1 µM). Vehicle-treated control cells received DMSO. Cells were harvested 1 or 2 hours after treatment.

value: ciliary body

value: nonpigmented ciliary epithelial cell type

value: DMSO, 2h


title: Human, NEpiC, DMSO, 2h_2

description:
Library name: HNEpiC_Veh2h_2
20220602 HNPEpiC DMSO vs Dex2h DESeq2 wald local 0.1 non-paired_Counts.xlsx


title: 8056_Pleg_low_32


title: Human, NEpiC, DEX, 2h_3

description:
Library name: HNEpiC_DEX2h_3
20220602 HNPEpiC DMSO vs Dex2h DESeq2 wald local 0.1 non-paired_Counts.xlsx

value: DEX, 2h


title: 8056_Pleg_low_16


title: Human, NEpiC, DEX, 2h_2

description:
Library name: HNEpiC_DEX2h_2
20220602 HNPEpiC DMSO vs Dex2h DESeq2 wald local 0.1 non-paired_Counts.xlsx


title: Human, NEpiC, DEX, 2h_1

description:
Library name: HNEpiC_DEX2h_1
20220602 HNPEpiC DMSO vs Dex2h DESeq2 wald local 0.1 non-paired_Counts.xlsx


title: 8056_Pleg_low_8


title: 8056_Pleg_low_3


title: 8056_Pleg_low_96


title: Human, NEpiC, DMSO, 1h_2

description:
Library name: HNEpiC_Veh1h_2
20220602 HNPEpiC DMSO vs NE1h DESeq2 wald local 0.1 non-paired_Counts.xlsx

value: DMSO, 1h


title: Mutant E14.5 Face 3

city: Columbus

first: Rolf

last: Stottmann

address: 575 Children's Crossroads

institute: Nationwide Children's Hospital

description:
Library name: 189_5_F
Column name in AllData_RNASeq_Results.xlsx: Raw_189_5_F
Column name in AllData_RNASeq_Results.xlsx: Norm_189_5_F

data_processing:
Bbduk (v37.64) was used to trim adapter sequences and low-quality reads (q<10).
Bbduk (v37.64) was also used to remove contaminants (Ribosomal RNA, Illumina PhiX and PCR products, Mycoplasma, and Globin genes).
Reads were then aligned to the NCBI Mus musculus assembly (GRCm38.p6) using the STAR aligner (v2.6.0c). Default values were used for most parameters; these are the default filter values:outFilterType: Normal, outFilterMultimapNmax: 10, outFilterMultimapScoreRange: 1, outFilterScoreMin: 0, outFilterScoreMinOverLread: 0.66, outFilterMatchNmin: 0, outFilterMatchNminOverLread: 0.66, outFilterMismatchNmax: 10, outFilterMismatchNoverLmax: 0.3, outFilterMismatchNoverReadLmax: 1, outFilterIntronMotifs: None, outFilterIntronStrands: RemoveInconsistentStrands
Mapped reads were quantified using featureCounts (subread v1.6.3) and the Gencode (vM19) annotation.
Transcript quantification of the contaminant filtered reads was done with salmon (v0.14) and Gencode (vM19).
The assigned reads from the featureCounts step were used for the DESeq2 (v1.26.0) differential gene expression analysis.
Assembly: GRCm38.p6
Supplementary files format and content: excel files contain raw and normalized values.

source_name: Face

extract_protocol:
RNA was extracted from wildtype and Tusc3 deletion brain and craniofacial tissues at E14.5 using TRIZOL reagent method.
NEBNext® Ultra™ II Directional RNA Library Prep Kit with NEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat)

value: Face


title: 8056_Pleg_low_0


title: 8053_Avonex_low_144


title: Human, NEpiC, DMSO, 1h_1

description:
Library name: HNEpiC_Veh1h_1
20220602 HNPEpiC DMSO vs NE1h DESeq2 wald local 0.1 non-paired_Counts.xlsx


title: 8053_Avonex_low_120


title: 8053_Avonex_low_96


title: Human, NEpiC, NE, 1h_2

description:
Library name: HNEpiC_NE1h_2
20220602 HNPEpiC DMSO vs NE1h DESeq2 wald local 0.1 non-paired_Counts.xlsx

value: NE, 1h


title: Human, NEpiC, NE, 1h_3

description:
Library name: HNEpiC_NE1h_3
20220602 HNPEpiC DMSO vs NE1h DESeq2 wald local 0.1 non-paired_Counts.xlsx


title: 8053_Avonex_low_72


title: Human, NEpiC, NE, 1h_1

description:
Library name: HNEpiC_NE1h_1
20220602 HNPEpiC DMSO vs NE1h DESeq2 wald local 0.1 non-paired_Counts.xlsx


title: 8053_Avonex_low_48


title: Human, NEpiC, DEX, 1h_3

description:
Library name: HNEpiC_DEX1h_3
20250722 HNPEpiC DMSO vs Dex1h DESeq2 wald local 0.1 non-paired_Counts.xlsx

value: DEX, 1h


title: 8053_Avonex_low_16


title: Human, NEpiC, DEX, 1h_1

description:
Library name: HNEpiC_DEX1h_1
20250722 HNPEpiC DMSO vs Dex1h DESeq2 wald local 0.1 non-paired_Counts.xlsx


title: 8053_Avonex_low_8


title: ADT library of ATO iPS-T cells Day 49

city: Kyoto

first: Shin

last: Kaneko

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: Center for iPS Cell Research and Applications

institute: Kyoto University

description:
Library name: ATO_Day49_CITE
10x Genomics Single Cell 5' gene expression library

library_source: other

data_processing:
Base calling was performed using Illumina Real-Time Analysis (RTA) software.
Fastq generation and demultiplexing were performed using Cell Ranger mkfastq.
Reads were aligned to the human reference genome (GRCh38) with GFP and EGFP sequences and gene expression/V(D)J usage was quantified using Cell Ranger (v7.1.0) pipeline.
For GEX, low-quality cells were filtered based on mitochondrial percentage and gene counts. Doublets were removed.
Downstream analysis including normalization, dimensionality reduction, and clustering was performed using Seurat v5. CITE-seq data was normalized using the CLR method. Batch correction was performed using Harmony.
Assembly: GRCh38 reference (the official GRCh38-2020-A) and GFP and EGFP sequences
Supplementary files format and content: Filtered feature-barcode matrix generated by Cell Ranger (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz). Content includes gene expression counts and antibody capture counts.
Supplementary files format and content: Cell Ranger output files for TCR V(D)J analysis: 'filtered_contig_annotations.csv' (per-cell contig annotations) and 'clonotypes.csv' (clonotype summary sequences and frequencies).

molecule: other

source_name: cell culture

growth_protocol: iPSCs (TKT3V1-7) were maintained on feeder-free conditions. For T cell differentiation, cells were cultured in the specific differentiation medium supplemented with cytokines as described in the manuscript. Feeder-free differentiation was performed using immobilized DLL4 and retronectin, while ATO differentiation was performed using artificial thymic organoids.

extract_protocol:
Single-cell suspensions were prepared and loaded onto the 10x Genomics Chromium Controller. scRNA-seq and scTCR-seq libraries were prepared using the Chromium Next GEM Single Cell 5' Reagent Kits (10x Genomics) according to the manufacturer's instructions.
Libraries were constructed for Gene Expression (GEX), TCR V(D)J (using Human T Cell Enrichment Kit), and Surface Protein (CITE-seq) from the same cDNA source. All libraries were prepared according to 10x Genomics protocols and sequenced on an Illumina platform.

treatment_protocol: Cells were harvested at specified time points (Day 21, 29, 33, 37 for Feeder-free; Day 21, 35, 49 for ATO) and prepared for single-cell analysis.

value: cell culture

tag: cell line

value: iPSC-derived T cell

value: ATO culture


title: scTCR-seq library of ATO iPS-T cells Day 49

description:
Library name: ATO_Day49_TCR
10x Genomics Single Cell V(D)J enriched library


title: 8053_Avonex_low_3

value: IM


title: 8045_Avonex_low_144


title: scRNA-seq library of ATO iPS-T cells Day 49

description:
Library name: ATO_Day49_GEX
10x Genomics Single Cell 5' gene expression library


title: scTCR-seq library of ATO iPS-T cells Day 35

description:
Library name: ATO_Day35_TCR
10x Genomics Single Cell V(D)J enriched library


title: 8045_Avonex_low_120


title: 8045_Avonex_low_96


title: scRNA-seq library of ATO iPS-T cells Day 35

description:
Library name: ATO_Day35_GEX
10x Genomics Single Cell 5' gene expression library


title: 8045_Avonex_low_72


title: scTCR-seq library of ATO iPS-T cells Day 21

description:
Library name: ATO_Day21_TCR
10x Genomics Single Cell V(D)J enriched library


title: 8045_Avonex_low_48


title: ADT library of ATO iPS-T cells Day 21

description:
Library name: ATO_Day21_CITE
10x Genomics Single Cell 5' gene expression library


title: 8045_Avonex_low_32


title: Human, NEpiC, DMSO, 1h_3

description:
Library name: HNEpiC_Veh1h_3
20220602 HNPEpiC DMSO vs NE1h DESeq2 wald local 0.1 non-paired_Counts.xlsx


title: 8045_Avonex_low_16


title: scTCR-seq library of Feeder-free iPS-T cells Day 37

description:
Library name: FF_Day37_TCR
10x Genomics Single Cell V(D)J enriched library

value: Feeder-free culture


title: 8045_Avonex_low_8


title: 8045_Avonex_low_3


title: ADT library of Feeder-free iPS-T cells Day 37

description:
Library name: FF_Day37_CITE
10x Genomics Single Cell 5' gene expression library


title: scRNA-seq library of Feeder-free iPS-T cells Day 37

description:
Library name: FF_Day37_GEX
10x Genomics Single Cell 5' gene expression library


title: 8045_Avonex_low_0


title: 8053_Avonex_low_32


title: Human, NEpiC, DEX, 1h_2

description:
Library name: HNEpiC_DEX1h_2
20250722 HNPEpiC DMSO vs Dex1h DESeq2 wald local 0.1 non-paired_Counts.xlsx


title: 8044_Pleg_low_312

value: SC


title: ADT library of Feeder-free iPS-T cells Day 33

description:
Library name: FF_Day33_CITE
10x Genomics Single Cell 5' gene expression library


title: scTCR-seq library of Feeder-free iPS-T cells Day 33

description:
Library name: FF_Day33_TCR
10x Genomics Single Cell V(D)J enriched library


title: 8044_Pleg_low_216


title: 8053_Avonex_low_0


title: scRNA-seq library of Feeder-free iPS-T cells Day 33

description:
Library name: FF_Day33_GEX
10x Genomics Single Cell 5' gene expression library


title: 8044_Pleg_low_144


title: scTCR-seq library of Feeder-free iPS-T cells Day 29

description:
Library name: FF_Day29_TCR
10x Genomics Single Cell V(D)J enriched library


title: 8044_Pleg_low_120


title: 8062_Pleg_low_32


title: ADT library of Feeder-free iPS-T cells Day 29

description:
Library name: FF_Day29_CITE
10x Genomics Single Cell 5' gene expression library


title: 8044_Pleg_low_96


title: scRNA-seq library of Feeder-free iPS-T cells Day 29

description:
Library name: FF_Day29_GEX
10x Genomics Single Cell 5' gene expression library


title: 8062_Pleg_low_3


title: ADT library of ATO iPS-T cells Day 35

description:
Library name: ATO_Day35_CITE
10x Genomics Single Cell 5' gene expression library


title: 8044_Pleg_low_72


title: scTCR-seq library of Feeder-free iPS-T cells Day 21

description:
Library name: FF_Day21_TCR
10x Genomics Single Cell V(D)J enriched library


title: 8044_Pleg_low_48


title: 8044_Pleg_low_32


title: ADT library of Feeder-free iPS-T cells Day 21

description:
Library name: FF_Day21_CITE
10x Genomics Single Cell 5' gene expression library


title: 8044_Pleg_low_16


title: NR3_clone54.1

description: Library name: NR3_clone54.1

value: human skin fibroblasts


title: Patient 2, Blast Reduction, Day 28

city: Aurora

first: Austin

middle: E

last: Gillen

state: CO

address: 12801 East 17th Avenue

institute: University of Colorado Anschutz Medical Campus

description:
Library name: Sample 6
10X Genomics FLEX

data_processing:
QC, alignment, demultiplexing, barcode correction, and gene counting were perfomed using 10X Genomics Cell Ranger v10.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest).
Per-sample Cell Ranger BAMs were converted back into demultiplexed FASTQs using 10X Genomics' bamtofastq tool (https://www.10xgenomics.com/support/software/cell-ranger/latest/miscellaneous/cr-bamtofastq).
Assembly: GRCh38
Supplementary files format and content: Cell Ranger Filtered Feature Barcode Matrices (HDF5 Format)

source_name: bone marrow mononuclear cells

extract_protocol:
A mononuclear cell layer was isolated from bone marrow aspirates via ficoll and washed with sterile PBS.
Single-cell capture and library construction was performed according to manufacturers instructions (10X Genomics GEM-X Flex Gene Expression v1).

treatment_protocol: Bone marrow samples from AML patients treated with venetoclax (28 days) and oral azacitidine (14 days). Samples are at baseline (prior to treatment), after 4 days of treatment (Day 4) and after 28 days of treatment (Day 28)

value: bone marrow mononuclear cells

tag: patient

value: Patient 2

tag: response

value: Blast Reduction

value: Day 28


title: scRNA-seq library of Feeder-free iPS-T cells Day 21

description:
Library name: FF_Day21_GEX
10x Genomics Single Cell 5' gene expression library


title: 8044_Pleg_low_8


title: 8044_Pleg_low_3


title: Patient 2, Blast Reduction, Day 4

description:
Library name: Sample 5
10X Genomics FLEX

value: Day 4


title: Patient 2, Blast Reduction, Baseline

description:
Library name: Sample 4
10X Genomics FLEX

value: Baseline


title: 8044_Pleg_low_0


title: Patient 1, No Response,Day 28

description:
Library name: Sample 3
10X Genomics FLEX

value: Patient 1

value: No Response


title: 8037_Avonex_low_144


title: scRNA-seq library of ATO iPS-T cells Day 21

description:
Library name: ATO_Day21_GEX
10x Genomics Single Cell 5' gene expression library


title: 8037_Avonex_low_120


title: Patient 1, No Response, Day 4

description:
Library name: Sample 2
10X Genomics FLEX


title: 8037_Avonex_low_96