title: NpatKI, dTAG, 0hr, rep2


title: NE-4C, H3f3a knockout, stably expressed H3F3A-HA,repeated

status: Public on Apr 22 2026

type: SRA

city: Shanghai

first: Rui

last: Guo

address: 131 DongAn Road

country: China

institute: Institutes of Biomedical Sciences, Fudan University

library_source: transcriptomic

data_processing:
Performed by GENEWIZ, Inc.
Sequence reads were trimmed by trim_galore.
Trimmed sequence reads were aligned to the reference genome using Hisat2, followed by transcript assembly and quantification using StringTie. Differential expression analysis was condected with Ballgown and Deseq.
Assembly: GRCm38
Supplementary files format and content: text file includes FPKM values for each Sample

molecule: total RNA

organism: Mus musculus

source_name: Brain

growth_protocol: Minimum essential medium (Eagle) with non-essential amino acids and 4 mM L-glutamine, 90%; fetal bovine serum, 10%.

extract_protocol:
The RNA extraction was carried out by GENEWIZ, Inc.. RNA was extracted using Trizol reagent according to the manufacturer’s protocols.1 μg of total RNA was used for the subsequent library preparation.
The process was conducted by GENEWIZ, Inc.The isolation of poly(A) mRNA was conducted using Oligo(dT) beads. The mRNA fragmentation was achieved using divalent cations and high temperature. Priming was executed using Random Primers. First strand cDNA and  second-strand cDNA were synthesized. The purified double-stranded cDNA was subsequently treated to repair both ends and add a dA-tailing in a single reaction, followed by a T-A ligation to attach adaptors to both ends. Size selection of Adaptor-ligated DNA was performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers, and the PCR products were validated.

tag: tissue

value: Brain

tag: cell line

tag: cell type

value: neural stem cell

tag: genotype


title: Heat, GC_1, riboseq

city: Toyama

first: Jun-Dal

last: Kim

state: Toyama

address: 2630 Sugitani

department: Department of Complex Biosystem Research (CBR), Institute of National Medicine (INM)

country: Japan

institute: University of Toyama

description: Library name: Sample 1

data_processing:
Reads were mapped on GRCm38/mm10 mouse reference genome and quantified using CLC Genomics Workbench version 12.0 (Qiagen).
Read counts were normalized by calculating number of reads per kilobase per million (RPKM) for each transcript in individual samples using the CLC Genomic Workbench software version 12.0 (Qiagen).
Filtering characteristics of fold-change and false discovery rate (FDR) were used to identify the DEGs.
Assembly: GRCm38/mm10
Supplementary files format and content: Excel file includes raw read counts and RPKM normalized values for all genes from each sample.

source_name: Heart

growth_protocol: For the lunar gravity (0.167 g) experiment, male mice were purchased from the Charles River Laboratories Japan, Inc. (Kanagawa, Japan). The lunar gravity group was maintained in an artificial gravity environment at 0.167 g on the bottom floor of the habitat cage units (HCU) via centrifugation at 31 rpm in MARS-S (15 cm radius). The GC group comprised six age-matched male C57BL/6 J mice per mission, maintained under the same conditions as those aboard the ISS.

extract_protocol:
The heart of mice was removed and flash frozen by liquid nitrogen. After suspending in lysis buffer, nuclear fraction, insoluble debris and mitochondria were removed by centrifugation. Extracts were digested with RNase I (Ambion). Then, monosomes were purified by ultra-centrifugation (Beckman coulter, Optima MAX-TL Ultracentrifuge) through 50% sucrose. Next, ribosome pellets were digested with Proteinase K. Finally, the ribosome protected fragments (RPFs) were size-selected (25-35 nt) by polyacrylamide gel electrophoresis, and converted to Illumina sequencing library using NEBNext Small RNA Library Prep Set for Illumina (New England Biolabs).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Heart

tag: Sex

value: Male

tag: time

value: 8- or 9-week-old

tag: treatment

value: Ground control (1 g)


title: NE-4C, H3f3a knockout, stably expressed H3F3A-HA


title: NpatKI, dTAG, 0hr, rep1

city: Fukuoka

first: Yuichiro

last: Semba

address: 3-1-1 Maidashi

institute: Kyushu University

library_source: genomic

data_processing:
Data processing employed the nf-core atacseq pipeline. Read mapping to mitochondrial and nuclear DNA was performed using SAMtools (v1.10), with fragment sizes calculated via Picard (v2.23.1).
Assembly: mm10
Supplementary files format and content: bigWig

molecule: genomic DNA

source_name: Bone marrow

growth_protocol: Mouse AML cells were cultured in Iscove's Modified Dulbecco's Media (IMDM) (Life Technologies) supplemented with 20% Fetal Bovine Serum (FBS) (Omega Scientific), 1% penicillin streptomycin (Life Technologies), and mouse SCF (20 ng/ml), mouse IL-3 (10 ng/ml) and mouse IL-6 (10 ng/ml) (all purchased from PeproTech).

extract_protocol:
5 x 104 mouse AML cells were lysed in ice-cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630).
Transposition was then carried out using Tn5 Transposase (Tagment DNA TDE1 Enzyme, Illumina). Transposed DNA fragments were purified using a MinElute Kit (Qiagen), followed by PCR amplification with specific PCR primers. Amplified libraries were further purified with the MinElute Kit.

treatment_protocol: dTAGV-1 was added to culture media at a final concentration of 500 nM.

value: Bone marrow

value: MLL::AF9 mAML

value: AML

value: NpatKI


title: Case 062

type: genomic

city: Montreal

first: Alain

last: Moreau

state: QC

address: 3175 Côte-Ste-Catherine

country: Canada

institute: Azrieli Research Center of CHU Sainte-Justine

hyb_protocol: Standard Illumina protocol

scan_protocol: Standard Illumina protocol

data_processing:
ChAMP package (Version 2.28.0)
[processed value definition] Beta value

label: Cy3 and Cy5

organism: Homo sapiens

source_name: Saliva

label_protocol: Standard Illumina protocol

extract_protocol: Genomic DNA was extracted from saliva using the PureLink Genomic DNA Mini Kit (Thermo Fisher Scientific) according to the manufacturer's protocol.

value: Saliva

value: F

tag: bmi

tag: age at time of test

tag: age of disease onset

tag: subject group

value: EM


title: Pv neurons nuclei ThraAMI4

city: Lyon

first: Frédéric

last: Flamant

state: France

address: 46 allée d'Italie

department: IGFL

country: France

institute: ENSL

description: Library name: Lib15

data_processing:
The NextSeq System Suite was used for base calling.
Mapping of mouse genome mm10 version  with Bowtie2   (Galaxy Version 2.5.3+galaxy1). 20 nt 5' nucleotides were trimmed.
Htseq-count was used to produce the count tables (=processed files)
Assembly: Mus_musculus.GRCm38.dna_rm.primary_assembly.fa
Supplementary files format and content: Count tables.
Supplementary files format and content: Tabular. Genes column 1, count column 2

molecule: nuclear RNA

source_name: Cortex

growth_protocol: Not relevant

extract_protocol:
Nuclei were isolated from individual cortex frozen in liquid nitrogen and nuclei were isolated with a cell sorter. RNA were extracted from sorted nuclei (RNeasy Micro Kit, Qiagen ref 74004) and quantified using Tapestation4150 (Agilent).
cDNA preparation: Smaartseq v4 Takara (ultralow input); cDNA libraries preparation: NexteraXT. Run on Mid output flowcell Nextseq500 Illumina 1x75bp

treatment_protocol: PTU is given in food pellet. TH treatment is intraperitoneal

value: Cortex

value: Parvalbumin neurons

value: PvCre ROSA-tomato-lox ThraAMI/+


title: Heat, GC_2, riboseq

description: Library name: Sample 2


title: Patient15,PBMC,con(ChIP)

city: jinan

first: yuanyuan

last: Zhang

address: jinan

institute: Shandong Second Medical University

description: Library name: ChIP-Con

data_processing:
RNA-seq:Raw reads were subjected to quality control using FastQC.Clean reads were aligned to the human reference genome using HISAT2.Gene expression levels were quantified using featureCounts.Differential expression analysis was performed using DESeq2.
ChIP-seq:Raw reads were quality-checked using FastQC.Reads were aligned to the human genome using Bowtie2.Peak calling was performed using MACS2.Peaks were annotated using HOMER.
Assembly: hg38 and mm10
Supplementary files format and content: fastq,bdg

source_name: peripheral blood

growth_protocol: Human peripheral blood mononuclear cells (PBMCs) were isolated from healthy donors and cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum and 1% penicillin–streptomycin at 37°C in a 5% CO₂ incubator.

extract_protocol:
RNA-seq:Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. RNA quality and integrity were assessed using an Agilent 2100 Bioanalyzer. ChIP-seq:Cells were crosslinked with 1% formaldehyde for 10 min and quenched with 125 mM glycine. Chromatin was isolated, lysed, and sonicated to generate DNA fragments of 200–500 bp.
RNA-seq:RNA-seq libraries were prepared using a poly(A) selection method with the Illumina TruSeq RNA Library Preparation Kit according to the manufacturer’s instructions. ChIP-seq:Immunoprecipitated DNA was collected using magnetic beads and used for library construction with the NEBNext Ultra II DNA Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Cells were treated with lactate (LAC, 10 mM) for 8 hours. Control cells were treated with PBS.

value: peripheral blood

value: primary cells

value: peripheral blood mononuclear cells


title: Case 059


title: ME_3 [leukemia-RNA-seq]

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

data_processing:
The FASTQ-sequenced reads were mapped to the mm10 genome using Hisat2.
Gene counts calculated by FeatureCounts were normalized and differentially expressed genes were identified with Adjusted p value < 0.05 by DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.

molecule: polyA RNA

extract_protocol:
FACS sorted cells were proceeded to RNA extraction using RNeasy columns (Qiagen).
RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit.

tag: strain

value: CD45.2+ bone marrow cells

value: CD45.2(+) MLL-ENL


title: Patient15,PBMC,lac(ChIP)

description: Library name: ChIP-LAC


title: ME_1 [leukemia-RNA-seq]


title: ME_2 [leukemia-RNA-seq]


title: Case 054

value: M


title: Case 046


title: Pv neurons nuclei ThraAMI2

description: Library name: Lib13


title: MA9_3 [leukemia-RNA-seq]


title: MA9_2 [leukemia-RNA-seq]


title: GFP-ChIP in eGFP-PDS5-A

city: Vienna

first: Roman

middle: R

last: Stocsits

address: Campus-Vienna-Biocenter 1

country: Austria

institute: IMP - Research Institute of Molecular Pathology

description: Library name: GFP_ChIP_in_eGFP-PDS5-A

data_processing:
Basecalling software: Illumina RTA
Aligment against hg19 reference assembly: bowtie version 1.2.2 , reads are trimmed and mapped uniquely to genome with 0 to 2 errors
ChIP-Seq  peak calling using MACS2  version 2.2.5
pile-up and heat map generation and plotting with deeptools version 3.5.4
Assembly: hg19
Supplementary files format and content: bigWig files for ChIP-Seq signal distributions represent genomic distribution of the factors as described in the paper, they can be used for visualization in IGV and Juicebox browsers

source_name: HeLa Kyoto

growth_protocol: HeLa Kyoto (RRID:CVCL_1922) were got from Narumiya S (Kyoto University; Kyoto; Japan). MEFs were generated in the lab by 3T3 methods.

extract_protocol:
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with respective antibody; Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step.
Libraries were prepared for sequencing using standard Illumina protocols.

value: HeLa Kyoto

value: human cervical cancer cells


title: Pv neurons nuclei  Ctrl 4

description: Library name: Lib11

value: PvCre ROSA-tomato-lox Thra+/+


title: Pv neurons nuclei ThraAMI1

description: Library name: Lib12


title: Pv neurons nuclei ThraAMI3

description: Library name: Lib14


title: Case 057


title: Case 043


title: Case 040


title: Pv neurons nuclei  Ctrl 3

description: Library name: Lib10


title: MA9_1 [leukemia-RNA-seq]

value: Bone marrow


title: Pv neurons nuclei  Ctrl 2

description: Library name: Lib9


title: SC injection 5

first: Yanshuang

address: No. 2005 Songhu Road

institute: Fudan university

description: Library name: SC5

data_processing:
Raw reads were evaluated using FastQC v0.11.2. Trimmomatic v0.36 was used to remove adapter sequences, trim low-quality bases (Phred score <20), and exclude reads shorter than 35 nucleotides. Clean reads were aligned to rat reference genome using StringTie v1.3.3b. Differential expression analysis was performed with DESeq2 v1.12.4, applying Benjamini-Hochberg procedure for FDR control. Significantly DEGs were defined as adjusted P < 0.001 and |log2FC| > 1.
Assembly: Rattus norvegicus Rnor_6.0 (GCA_000001895.4)
Supplementary files format and content: Excel file includes raw counts for each Sample

organism: Rattus norvegicus

source_name: Skin

extract_protocol:
Total RNA was isolated from dorsal skin tissues using Trizol reagent following manufacturer's instructions. RNA samples were treated with RNase-free DNase I to eliminate genomic DNA contamination. RNA integrity and concentration were assessed using Qubit RNA Assay Kit on a Qubit 2.0 Fluorometer.
Stranded mRNA sequencing libraries were constructed using Hieff NGS MaxUp Dual-mode mRNA Library Prep Kit for Illumina (YEASEN, 12301ES96). PCR products were purified with AMPure XP beads and library quality was verified on Agilent Bioanalyzer 2100.

value: Skin

value: Sprague-Dawley

value: SC injection


title: BN1_3 [leukemia-RNA-seq]


title: Case 039

value: Saliva

value: EM


title: BN1_2 [leukemia-RNA-seq]


title: Pv neurons nuclei. Ctrl 1

description: Library name: Lib8

value: Cortex

value: Parvalbumin neurons


title: SC injection 3

description: Library name: SC3


title: Case 038

value: F


title: BN1_1 [leukemia-RNA-seq]


title: Case 037


title: SC injection 4

description: Library name: SC4


title: Pv neurons nuclei. PTU mice 7

description: Library name: Lib7


title: Pv neurons nuclei. PTU mice 6

description: Library name: Lib6


title: SC injection 2

description: Library name: SC2


title: Case 031


title: Pv neurons nuclei. PTU mice 5

description: Library name: Lib5


title: B6_WT_2 [leukemia-RNA-seq]


title: Case 026


title: B6_WT_1 [leukemia-RNA-seq]


title: Pv neurons nuclei. PTU+TH mice 4

description: Library name: Lib4


title: ID injection 5

description: Library name: ID5

value: ID injection


title: Pv neurons nuclei. PTU+TH mice 3

description: Library name: Lib3


title: SC injection 1

description: Library name: SC1


title: BN1_1_input

data_processing:
The cleaned FASTQs were aligned using Bowtie2 (2.5.4) to the mouse reference genome mm10.
The duplicated reads were removed using picard (3.2.0) MarkDuplicates.
The bigWig files were generated using bamCoverage (3.5.1).
ChIP-seq peaks for H3K27ac were identified using MACS3 (version 3.0.1) (Ref) with the default parameter setting for narrow peak detection.
Identify enhancers and Ses in each sample by calling the ROSE_main.py program using default parameters.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
FACS-sorted cKit+ BN1 cells were processed by H3K27ac fanChIP ()
ChIP libraries were prepared for sequencing using standard Illumina protocols

value: cKit(+) BRD9-NUTM1


title: ID injection 4

description: Library name: ID4


title: B6_WT_3 [leukemia-RNA-seq]

value: CD45.2+ bone marrow cells


title: Case 017


title: ID injection 3

description: Library name: ID3


title: Pv neurons nuclei. PTU+TH mice 2

description: Library name: Lib2


title: control_1_input

value: cKit(+)


title: ID injection 6

description: Library name: ID6


title: Case 021


title: Case 016


title: ID injection 2

description: Library name: ID2


title: Pv neurons nuclei. PTU+TH mice 1

description: Library name: Lib1


title: dLN Neurl3 OE P14 rep2

city: La Jolla

first: Ananda

middle: W

last: Goldrath

state: CA

address: 9500 Gilman Drive

department: Molecular Biology

country: USA

institute: University of California, San Diego

description: Library name: T.8.P14.Neurl3.d12.LN#2

data_processing:
Trimmomatic was used to remove adapters and trim low-quality reads (NexteraPE-PE.fa:2:30:10:1:TRUE LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25). Trimmed reads were then aligned to the gencode M25 annotation of the mm10 genome using STAR with the default conditions. Aligned reads were then quantified with featureCounts101 (-t exon -g gene_id -p -B)
Assembly: mm10
Supplementary files format and content: CSV of raw count values of each gene in each sample.

source_name: draining lymph node

extract_protocol:
1×10^3 were then resorted into 1× TCL lysis buffer+1% 2-mercaptoethanol.
Library preparation for ultra-low-input RNA-seq was performed as described online (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf).

value: draining lymph node

value: P14 CD8 T cells

value: Neurl3 OE

value: MC38 tumor


title: Control ChIP_1

value: Bone marrow


title: BN1 ChIP_1


title: ME_3

data_processing:
The adapter sequences were removed from the FASTQs using Ngmerge.
The cleaned FASTQs were aligned using Bowtie2 (2.5.4) to the mouse reference genome mm10.
The duplicated reads were removed using picard (3.2.0) MarkDuplicates.
The bigWig files were generated using bamCoverage (3.5.1).
Peaks were called using Genrich ATAC mode with the removal of mitochondrial reads and PCR duplicates.
Assembly: GRCm38/mm10
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
FACS-sorted cells (150,000 cells per sample) were processed by a transposition reaction and purification followed the manual of ATAC-seq kit from Active motif (#13150)
ATAC libraries were prepared for sequencing using standard Illumina protocols

value: CD45.2(+) MLL-ENL


title: SC injection of saline control 6

description: Library name: C2_6

value: Skin

value: Sprague-Dawley

value: SC injection of saline control


title: Case 015

value: Saliva

value: EM


title: dLN Neurl3 OE P14 rep1

description: Library name: T.8.P14.Neurl3.d12.LN#1


title: SC injection of saline control 5

description: Library name: C2_5


title: ID injection 1

description: Library name: ID1


title: ME_2


title: dLN EV P14 rep2

description: Library name: T.8.P14.EV.d12.LN#2

value: EV


title: GFP-ChIP in eGFP-PDS5-B

description: Library name: GFP_ChIP_in_eGFP-PDS5-B

value: HeLa Kyoto

value: human cervical cancer cells


title: Case 014

value: F


title: ME_1

value: CD45.2+ bone marrow cells


title: MA9_3


title: Case 012


title: SC injection of saline control 4

description: Library name: C2_4


title: tumor Neurl3 OE P14 rep2

description: Library name: T.8.P14.Neurl3.d12.Ti#2

source_name: MC38 tumor


title: SC injection of saline control 3

description: Library name: C2_3


title: W24h, input, rep1

city: Yokohama

first: Duncan

middle: Peter

last: Coleman

state: Kanagawa

address: 1-7-22 Suehiro-cho, Tsurumi-ku

department: CSRS

institute: Riken

description:
concatenated fastq files
W24h_input.bw
W24h_peaks_annotated.bed

data_processing:
Reads were mapped to the TAIR10 Arabidopsis genome using Bowtie2 (Langmead & Salzberg, 2012)
SAM files were converted to BAM format using SAMTOOLS (Li et al, 2009).
Mapped BAM files were subject to peak calling using MACS2 (Zhang et al, 2008) with a p-value cutoff of 0.05, m-fold of 5 50 and using the input sample as a control.
Peaks were annotated to genes or their promoter (3 kb upstream of the TSS) using a custom bash script.
Assembly: TAIR10
Supplementary files format and content: Bigwig files
Supplementary files format and content: List of peaks and associated genes

organism: Arabidopsis thaliana

source_name: Whole seedling

growth_protocol: Approximately 60 2-week-old seedlings grown at 22°C at constant light

extract_protocol:
Plants were then frozen in liquid Nitrogen and ground using a bead shocker (MB1200 Yasui Kikai) in 50 ml tubes and the nuclear fraction was isolated after cross-linking for 10 min using 1% formaldehyde (Sigma) under vacuum. Chromatin was sheared at 4–6 °C for 15 min with a focused ultrasonicator (Covaris) with the following settings: duty cycle 5%, intensity 4, and cycles per burst 200. Sheared chromatin was immunoprecipitated using antibodies against GFP (ab290, Abcam) and input DNA was kept as a control. The isolated DNA was quantified with the Qubit dsDNA High Sensitivity Assay kit (Thermo Fisher Scientific), and 1–5 ng of DNA was used to make each ChIP-seq library.
Libraries were prepared using the KAPA Hyper Prep Kit for Illumina (KK8502, KAPA Biosystems) and Illumina compatible adaptors (E7335, E7500, E7710, E7730, NEB). The 300–500 bp DNA fragments were enriched using Agencourt AMPure XP (Beckman Coulter). Libraries were pooled and 50-bp, single-read sequences were obtained with Illumina NextSeq500 sequencer at a depth of at least 10 million mapped reads.

treatment_protocol: For heat-stress treatment, three biological replicates of approximately 60 2-week-old seedlings grown at 22°C were subject to heat stress by transferring the plates to a 37°C incubator for 30 minutes. For wounding treatement, one biological replicate of approximately 60 2-week-old seedlings grown at 22°C were cut multiple times with a razor blade and incubated on MS for 10 minutes, 3 hours or 24 hours.

value: Whole seedling

tag: ecotype

value: mixed Columbia-0 (Col-0) and Wassilewskija (Ws)

tag: age

value: 2 weeks

tag: time point

value: 24 hours

value: Wounding


title: W24h, CHIP, rep1

description:
concatenated fastq files
W24h_CHIP.bw
W24h_peaks_annotated.bed


title: SC injection of saline control 2

description: Library name: C2_2


title: W3h, CHIP, rep1

description:
concatenated fastq files
W3h_CHIP.bw
W3h_peaks_annotated.bed

value: 3 hours


title: Case 009


title: dLN EV P14 rep1

description: Library name: T.8.P14.EV.d12.LN#1

value: draining lymph node

value: P14 CD8 T cells

value: MC38 tumor


title: MA9_1

value: Bone marrow


title: tumor EV P14 rep2

description: Library name: T.8.P14.EV.d12.Ti#2


title: MA9_2


title: W3h, input, rep1

description:
concatenated fastq files
W3h_input.bw
W3h_peaks_annotated.bed


title: tumor Neurl3 OE P14 rep1

description: Library name: T.8.P14.Neurl3.d12.Ti#1

value: Neurl3 OE


title: SC injection of saline control 1

description: Library name: C2_1

value: Skin

value: Sprague-Dawley

value: SC injection of saline control


title: BN1_3


title: BN1_2


title: tumor EV P14 rep1

description: Library name: T.8.P14.EV.d12.Ti#1

value: EV


title: W10min, CHIP, rep1

description:
concatenated fastq files
W10min_CHIP.bw
W10min_peaks_annotated.bed

value: 10 minutes


title: ID injection of saline control 6

description: Library name: C1_6

value: ID injection of saline control


title: ID injection of saline control 5

description: Library name: C1_5


title: Gabaergic neurons nuclei. Mice with Thra mutation 10

description:
Library name: Lib10
Lib10

data_processing:
The NextSeq System Suite was used for base calling.
Mapping of mouse genome mm10 version  with Bowtie2   (Galaxy Version 2.5.3+galaxy1). 20 nt 5' nucleotides were trimmed.
Assembly: Mus_musculus.GRCm38.dna_rm.primary_assembly.fa
Supplementary files format and content: txt file with counts

extract_protocol:
Nuclei were isolated from individual cortex frozen in liquid nitrogen and nuclear RNA was extracted as previously described (21) . Nuclear RNA was extracted Nuclei were isolated with a cell sorter. RNA were extracted from sorted nuclei (RNeasy Micro Kit, Qiagen ref 74004) and quantified using Tapestation4150 (Agilent).
cDNA preparation: Smaartseq v4 Takara ; cDNA libraries preparation: NexteraXT. Run on Mid output flowcell Nextseq500 Illumina 2x75bp

value: Cortex

value: GABAergic neurons

value: Thra+/AMI


title: BN1_1

value: CD45.2+ bone marrow cells


title: Gabaergic neurons nuclei. Mice with Thra mutation 8

description:
Library name: Lib8
Lib8


title: ID injection of saline control 4

description: Library name: C1_4


title: Gabaergic neurons nuclei. Mice with Thra mutation 6

description:
Library name: Lib6
Lib6


title: WT0, input, rep1

description:
concatenated fastq files
WT0_input.bw
WT0__peaks_annotated.bed

value: Whole seedling

value: mixed Columbia-0 (Col-0) and Wassilewskija (Ws)

value: 2 weeks

value: 0 minutes

value: Wounding


title: Gabaergic neurons nuclei. Mice with Thra mutation 7

description:
Library name: Lib7
Lib7


title: Control_3

value: Bone marrow


title: W10min, input, rep1

description:
concatenated fastq files
W10min_input.bw
W10min_peaks_annotated.bed


title: ID injection of saline control 1

description: Library name: C1_1


title: Gabaergic neurons nuclei. Control mice 4

description:
Library name: Lib5
Lib5

value: Thra+/+


title: ID injection of saline control 3

description: Library name: C1_3

value: Skin


title: ID injection of saline control 2

description: Library name: C1_2

value: Sprague-Dawley


title: HS, input, rep2

description:
concatenated fastq files
HS_input.bw
HS_peaks_annotated.bed

value: 30 minutes

value: Heat stress (37 degrees)


title: SC injection 6

description: Library name: SC6

value: SC injection


title: WT0, CHIP, rep1

description:
concatenated fastq files
WT0_CHIP.bw
WT0__peaks_annotated.bed


title: Gabaergic neurons nuclei. Control mice 3

description:
Library name: Lib3
Lib3


title: HS, input, rep3


title: HS, input, rep1


title: Gabaergic neurons nuclei. Control mice 2

description:
Library name: Lib2
Lib2


title: Tumor, shNC,rep5

city: Beijing

first: Mingxuan

last: Zhou

state: China

address: No. 2 Nanwei Road, Tianqiao Street

institute: Institute of Materia Medica, Chinese Academy of Medical Sciences

data_processing:
Raw data was filtered with Trimmomatic and aligned to the reference genome by STAR.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample

source_name: Tumor

growth_protocol: For implanted subcutaneous tumor model, 100μl SL4 cells (106 cells) were injected into the left hind leg of C57 mice (n = 9 per group). Mice were sacrificed on day 14 after injection, tumors were dissected and weighed.

extract_protocol:
Total mRNA was enriched with magnetic beads with Oligo(dT) and fragmented by fragmentation buffer.
Then mRNA was reverse transcribed using random primers. Following purification, cDNA was repaired, tailed with dA and ligated with sequence adaptors, then cDNA size distribution pattern was screened by AMPure XP Beads. Filtered cDNA was amplified by PCR to construct the library.

treatment_protocol: Lentiviral vectors were transducted to SL4 cells at a multiplicity of infection of 10 to achieve ideal knockdown efficiency, target cells were harvested after 48 h and resuspended to 107 cells/ml in saline.

value: Tumor

value: Mouse Colon Carcinoma Cells

value: WT


title: Tumor, shNC,rep4


title: 4wpf mutant

city: Onna-son, Kunigami-gun

first: Ichiro

last: Masai

state: Okinawa

address: 1919-1 Tancha

institute: Okinawa Institute of Science and Technology

description:
Library name: 4wpf_mutant
10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3

library_source: transcriptomic single cell

data_processing:
The Cell Ranger pipeline from 10x Genomics was used to perform alignment, filtering, barcode counting, and UMI counting, using the zebrafish reference genome GRCz11.
Assembly: GRCz11
Supplementary files format and content: Filtered feature barcode matrices as .tar files, output of Cell Ranger pipeline from 10x Genomics.

organism: Danio rerio

source_name: Eye

extract_protocol:
Extraction was performed as described by Mazzolini et al, 2018, with modifications. Eyecups were dissected and mashed in a dounce homogenizer containing 15 mM HEPES and 25 mM D-Glucose in 1x HBSS (media A). The samples were washed, strained and resuspended in 22% density gradient medium (100% is prepared as 9:1 Percoll density gradient medium : 10x HBSS) overlaid with 1x DPBS. Then they were centrifuged, washed in media A + 2% normal goat serum, and finally resuspended in 1x DPBS + 2% normal goat serum. Once resuspended, Sytox blue dead cell stain (#S34857) was added at a dilution of 1:1000. Cell sorting was performed immediately on the BD FACSAria II and FACSAria III. Sorting parameters were standardized using fish bearing no fluorescence-expressing transgene as a control, and mfap4:tdTomato-CAAX fish as the test sample at the relevant ages (5 days or 4 weeks post fertilization). Microglia/macrophages were sorted by gating on FSC/SSC scatter, Sytox blue dead stain, and tdTomato intensity.
FACS-isolated cells were loaded onto Chromium Next GEM Chips (10x Genomics). Libraries for sequencing were then prepared using the Chromium Next GEM Single Cell 3’ Reagent Kits v3 or Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) (10x Genomics), following the manufacturer’s protocols. 12 cycles were used for the cDNA amplification PCR and 14 cycles were used for the indexing PCR.

value: Eye

value: microglia/macrophage

value: pde6c -/-

value: 4 wpf


title: HS, CHIP, rep3

description:
concatenated fastq files
HS_CHIP.bw
HS_peaks_annotated.bed

value: Whole seedling

value: mixed Columbia-0 (Col-0) and Wassilewskija (Ws)

value: 2 weeks


title: Gabaergic neurons nuclei. Control mice 1

description:
Library name: Lib1
Lib1

value: Cortex

value: GABAergic neurons


title: Tumor, shNC,rep3


title: Control_1

value: Bone marrow

value: CD45.2+ bone marrow cells


title: Gabaergic neurons nuclei. PTU+TH mice 16

description: Library name: Lib16

data_processing:
The NextSeq System Suite was used for base calling.
Mapping of mouse genome mm10 version  with Bowtie2   (Galaxy Version 2.5.3+galaxy1). 20 nt 5' nucleotides were trimmed.
Assembly: Mus_musculus.GRCm38.dna_rm.primary_assembly.fa
Supplementary files format and content: .bam files contain the aligned reads.

extract_protocol:
Nuclei were isolated from individual cortex frozen in liquid nitrogen and nuclear RNA was extracted as previously described (21) . Nuclear RNA was extracted Nuclei were isolated with a cell sorter. RNA were extracted from sorted nuclei (RNeasy Micro Kit, Qiagen ref 74004) and quantified using Tapestation4150 (Agilent).
cDNA preparation: Smaartseq v4 Takara ; cDNA libraries preparation: NexteraXT. Run on Mid output flowcell Nextseq500 Illumina single end

value: PTU+TH


title: HS, CHIP, rep2

value: 30 minutes

value: Heat stress (37 degrees)


title: 5dpf mutant

description:
Library name: 5dpf_eye_mutant
10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1

value: 5 dpf


title: 4wpf sibling

description:
Library name: 4wpf_sibling
10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3

value: sibling


title: 5dpf sibling

description:
Library name: 5dpf_eye_sibling
10x Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1


title: HS, CHIP, rep1


title: Gabaergic neurons nuclei. PTU+TH mice 15

description: Library name: Lib15


title: Tumor, shNC,rep2

value: Tumor

value: Mouse Colon Carcinoma Cells

value: WT


title: Tumor, shNC,rep1


title: Tumor, shPLXNC1,rep5


title: Gabaergic neurons nuclei. PTU+TH mice 14

description: Library name: Lib14


title: Gabaergic neurons nuclei. PTU+TH mice 13

description: Library name: Lib13


title: HT0, input, rep3

description:
concatenated fastq files
HT0_input.bw
HT0_peaks_annotated.bed

value: 0 minutes


title: zebrafish testis, ZT13, scRNA-seq

city: suzhou

first: Taole

last: LIU

state: JIANGSU

address: Renai Road 199

department: center for circadian clock

institute: Soochow University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0
Assembly: GRCz11
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: testis

extract_protocol:
The testes from WT males at age of 3 months with approximately 0.3-g body weight were collected and minced in the medium RPMI1640 in the presence of digested enzyme. After 30 min of digestion, the cell was centrifuged and resuspended in RPMI1640.
Library was performed according to the manufacter’s instructions (single cell 3' v3, 10x Genomics). Briefly, cells were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs and a sample index were added.

value: testis

value: somatic and germ cells

value: AB strain

value: 3 months old


title: HT0, input, rep1

value: Whole seedling

value: mixed Columbia-0 (Col-0) and Wassilewskija (Ws)

value: 2 weeks


title: zebrafish testis, ZT19, scRNA-seq

description: 10x Genomics


title: Tumor, shPLXNC1,rep3


title: Tumor, shPLXNC1,rep4


title: Tumor, shPLXNC1,rep2


title: zebrafish testis, ZT1, scRNA-seq

description: 10x Genomics


title: Gabaergic neurons nuclei. PTU mice 11

description: Library name: Lib11

value: Cortex

value: GABAergic neurons

value: PTU


title: zebrafish testis, ZT7, scRNA-seq

description: 10x Genomics


title: HT0, input, rep2

value: Heat stress (37 degrees)


title: HT0, CHIP, rep2

description:
concatenated fastq files
HT0_CHIP.bw
HT0_peaks_annotated.bed


title: Ccl19-Cre_Notch2^fl/fl_R26R-EYFP_N2KO_Batch1

city: Epalinges

first: Nagham

last: Alouche

address: Chemin des Boveresses 155

department: Immunobiology

country: Switzerland

institute: University of Lausanne

description:
Library name: N2FRC_RNA
10X Genomics

data_processing:
To generate single cell feature counts, Cellranger (v5.0.1 and v7.1.0) was run to align FASTQ files to the mm10 genome version.
Assembly: mm10
Supplementary files format and content: Tab-separated values file and matrix files

source_name: Lymph node (pooled from 6 mice)

extract_protocol:
For each sample, peripheral lymph nodes (axillary, brachial, and inguinal) were cut into small pieces and digested for 30 min at 37°C with gentle stirring in 1.5 mL RPMI 1640 medium (Gibco) containing 0.3 mg/ml Collagenase P (Roche) and 0.8 mg/ml Dispase II (Sigma Aldrich), and 0.1 mg/ml DNase I and 2% (vol/vol) Fetal Calf Serum (FCS). The small LN pieces were digested for 20 min at 37°C with gentle stirring in 2 mL digestion mix. After incubation, fragments were gently dissociated using a 1 mL pipette equipped with a wide-bore tip and allowed to settle for 30 seconds. The supernatant was transferred to a collection tube containing cold PBS supplemented with 2% FCS and 5 mM ethylenediaminetetraacetic acid (EDTA). 1 mL of fresh digestion media was added to the remaining fragments, which were incubated for an additional 10 minutes at 37°C under stirring. Following this, the single-cell suspension was added to the collection tube containing the first supernatant. Cells were then washed and resuspended in RPMI-2% FCS.  Cell suspensions were depleted of CD45⁺ cells using magnetic-activated cell sorting (MACS, Miltenyi Biotec) according to the manufacturer’s instructions. Live propidium iodide⁻ Hoechst⁺ CD45⁻ CD31⁻ stromal cells were then sorted using a MoFlo Astrios EQ cell sorter (Beckman Coulter).
Single-cell RNA sequencing libraries were prepared using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 with Dual Index (10x Genomics), following the manufacturer's protocol.

value: Lymph node (pooled from 6 mice)

value: Female

value: Fibroblasts

value: Ccl19-Cre x Notch2^fl/fl x R26R-EYFP

value: 12 weeks

tag: batch


title: Tumor, shPLXNC1,rep1

value: Tumor

value: Mouse Colon Carcinoma Cells

value: WT


title: HT0, CHIP, rep3

value: 0 minutes


title: Gabaergic neurons nuclei. PTU mice 12

description: Library name: Lib12


title: Gabaergic neurons nuclei. PTU mice 10

description: Library name: Lib10


title: Ccl19-Cre_R26R-EYFP_WT_Batch1

description:
Library name: WTFRC_RNA
10X Genomics

value: Ccl19-Cre x R26R-EYFP


title: B50-2

status: Public on Apr 21 2026

city: Fuzhou

first: Peichun

last: Ye

address: No.1 Xuefu North Road, Fuzhou, Fujian, China

institute: Fujian Medical University

data_processing:
The raw MeRIP-seq data were aligned to genome reference sequences by Hisat2. The aligned reads were used for m6A-modification peak calling and the significant methylation was identified by exomepeak2 , and the m6A peak calling can be visualized by IGV software.
The MetaTX was used to examine the distribution pattern of epitranscriptome profiles. The STREME  was used to determine if the m6A peaks contained the consensus of m6A motif sequences.
For mRNA-seq, the mRNA expression level was analyzed by StringTie, and differentially expressed mRNAs were calculated by DEseq.
The substrates of m6A regulators were obtained from starBase v2.0.
The statistical enrichment analysis of Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway for differentially expressed genes (DEGs) and differentially methylated mRNAs were applied by DAVID.
Assembly: mm10
Supplementary files format and content: The processed data files is in CSV format, containing the expression levels and m6A methylation status changes for each gene.

organism: Caenorhabditis elegans

extract_protocol:
Total RNA was extracted according to manufacturer’s instruction.
The stranded RNA sequencing library was constructed by KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched

value: Wild type

value: treat with gelsenicine


title: B50-1


title: Gabaergic neurons nuclei. PTU mice 9

description: Library name: Lib9


title: HT0, CHIP, rep1

value: Whole seedling

value: mixed Columbia-0 (Col-0) and Wassilewskija (Ws)

value: 2 weeks


title: B0-3

value: Control


title: MOE_MERFISH_region_1

type: RNA

city: Boston

first: David

last: Brann

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

description: Region 1

hyb_protocol: Cell boundary staining, gel embedding, clearing, and probe hybridization steps were performed according to the fresh-frozen sample preparation guide, using the 300-plex gene panel.

scan_protocol: Samples were imaged on the MERSCOPE instrument using the 300-plex imaging kit

data_processing:
Transcripts were decoded using the MERLIN pipeline provided by Vizgen
*detected_transcripts.csv.gz: Position of each decoded transcript
codebook.csv.gz: bit code for gene panel

label: Gene targeting probes

source_name: whole olfactory mucosa

label_protocol: Tissue fixation, permeabilization, and autofluorescence quenching were performed used the guidelines for fresh frozen tissue. However, the RNA anchoring steps from the formalin-fixed, paraffin-embedded (FFPE) tissue sample preparation guide were added to help the thin MOE tissue adhere to the MERSCOPE slides.

extract_protocol: MOE was extracted from young C57 mice and flash-frozen in OCT. 10 µm sections were cut on the cryostat and mounted onto MERSCOPE beaded coverslips.

value: Male


title: MOE_MERFISH_region_0

description: Region 0


title: B0-1


title: MOE_MERFISH_region_2

description: Region 2


title: B50-3


title: MOE_MERFISH_region_3

description: Region 3


title: AFT8_3

city: Guangzhou, Guangdong Provice

first: ruoxi

last: chen

address: 613 West Huangpu Avenue, Tianhe District

institute: Department of Plastic Surgery of the First Affiliated Hospital of Jinan University

description:
Library name: sample 9
8h group_replicate_3

data_processing:
Differentially expressed genes (DEGs) were analyzed using the BGISEQ-500 platform (Beijing Genomics Institute, China) with the setting as follows: False discovery rate (FDR) = 1%; P-value < 0.05 and fold change ≥ 2.0. The DEGs between the indicated groups were classified with the pathway of Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Enrichment Analysis. The gene expression of the signaling pathways of interest was clustered by using an R-package of pheatmap with z-score parameter. The Gene Set Enrichment Analysis was applied to determine the change of the biological process and molecular function of transcriptomic profiles between indicated groups.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes gene counts for each sample

source_name: fat

extract_protocol:
Total RNA was extracted from the tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction. About 60 mg of tissues were ground into powder by liquid nitrogen in a 2  mL tube, followed by being homogenized for 2 minutes and rested horizontally for 5 minutes. The  mix was centrifuged for 5 minutes at 12,000×g at 4°C, then the supernatant was transferred into a  new EP tube with 0.3 mL chloroform/isoamyl alcohol (24:1). The mix was shacked vigorously for 15s, and then centrifuged at 12,000×g for 10 minutes at 4°C. After centrifugation, the upper aqueous phase where RNA remained was transferred into a new tube with equal volume of supernatant of isopropyl alcohol, then centrifuged at 13,600 rpm for 20 minutes at 4°C. After deserting the supernatant, the RNA pellet was washed twice with 1 mL 75% ethanol, then the mix was centrifuged at 13,600 rpm for 3 minutes at 4°C to collect residual ethanol, followed by the pellet air dry for 5-10 minutes in the biosafety cabinet. Finally, 25µL~100µL of DEPC-treated water was added to dissolve the RNA. Subsequently, total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single-pair end 50 bases reads were generated on BGISEQ-500 platform (Beijing Genomics Institute, China).

value: fat


title: Con2

description:
Library name: sample 11
0h group_replicate_2


title: Con3

description:
Library name: sample 12
0h group_replicate_3


title: Con1

description:
Library name: sample 10
0h group_replicate_1


title: Control_2

value: Bone marrow

value: CD45.2+ bone marrow cells


title: B0-2


title: AFT4_2

description:
Library name: sample 5
4h group_replicate_2


title: AFT4_3

description:
Library name: sample 6
4h group_replicate_3


title: AFT2_2

description:
Library name: sample 2
2h group_replicate_2


title: AFT4_1

description:
Library name: sample 4
4h group_replicate_1


title: AFT2_1

description:
Library name: sample 1
2h group_replicate_1


title: AFT2_3

description:
Library name: sample 3
2h group_replicate_3


title: IkB-/cRel- B-cell progenitors

city: Los Angeles

first: Apeksha

last: Singh

address: 570 Boyer Hall

institute: University of California, Los Angeles

description:
Library name: Sample 3
column name in gene_counts.tsv or norm_counts.tsv: "BM3_S43_L004_Aligned.filter.bam"

data_processing:
Raw data were filtered for adaptor sequences with cutadapt 4.1 69 with Python 3.10.8.
Reads were processed by first concatenating the murine GRCm39 and yeast R64 genomes and annotations, and then aligning with STAR 2.7.1a. Default parameters were used except outFilterType BySJout, outFilterMultimapNmax 20, alignSJoverhangMin 8, alignSJDBoverhangMin 1, and seedSearchStartLmax 30.
Aligned reads were filtered based on mapping score (MAPQ≥30) by Samtools 1.9 and transcript counts were quantified using featureCounts v1.6.5.
Data were then normalized by dividing counts for each mouse gene by the total number of yeast transcripts and scaling by 1e6.
Assembly: murine GRCm39 and yeast R64
Supplementary files format and content: gene_counts.tsv is a tab delimited file containing raw counts for murine and yeast genes in each sample
Supplementary files format and content: norm_counts.tsv is a tab delimited file containing the normalized counts for murine genes in each sample calculated by taking the raw counts and dividing by the total counts of yeast genes per sample

source_name: Hardy Fraction A-B cells

extract_protocol:
Bone marrow from a C57BL/6J and an IκB – mouse was isolated and lymphoid progenitors were magnetically enriched as previously described using the biotinylated antibodies at a concentration of 1:50 in staining panel 12. Following enrichment of the lymphoid progenitors, the cells were surface marker-stained using staining panel 9 as previously described. The cells were then sorted with the BD FACSAriaIII sorter in UCLA Janis V. Flow Cytometry Core Laboratory with adequate compensation setup by using UltraComp eBeads™ Compensation Beads and live cells with staining antibodies prior to actual sample sorting. We sorted approximately 204,000 WT and IκB – fraction A-B cells and added 10ng of yeast RNA (strain BY7473, generous gift from T.L. Johnson lab) per 100,000 cells as an internal control.
The RNA samples were then submitted to UCLA Technology Center for Genomics & Bioinformatics for library preparation and were sequenced using Novaseq X Plus 10B (1250M/lane).

value: Hardy Fraction A-B cells

value: IkB-/cRel-


title: AFT8_2

description:
Library name: sample 8
8h group_replicate_2


title: IkB- B-cell progenitors

description:
Library name: Sample 2
column name in gene_counts.tsv or norm_counts.tsv: "BM2_S42_L004_Aligned.filter.bam"

value: IkB-


title: Wildtype B-cell progenitors

description:
Library name: Sample 1
column name in gene_counts.tsv or norm_counts.tsv: "BM1_S41_L004_Aligned.filter.bam"


title: RARi_RAR_2

description: Library name: RARi_RAR_2

data_processing:
Demultiplexed fastq files were uniformly processed via a custom nextflow pipeline that ran cell ranger (v9, with include-introns=False), as well as custom post-processing to remove multi-mapping reads (see Tsukahara et al. 2021 PMID: 34879231). Samples were integrated together to extract (mature) olfactory sensory neurons for downstream analyses.
Assembly: Ensembl GRCm39 version 105 genome, including ectopic genes like GFP and modified GTF file to extend the 3' UTRs for TAAR genes
Supplementary files format and content: <sample_name>__filtered_feature_bc_matrix.h5: Raw cell x gene matrix from cell ranger for each sample

extract_protocol:
The main olfactory epithelium was dissected and cleaned up in the Earle’s Balanced Salt Solution (EBSS, pre-treated with carbogen for at least 5 minutes before each use, Worthington), then transferred to a round-bottomed glass dish containing 750 µL of papain solution (one vial of Papain, (Worthington) dissolved in 5 mL of EBSS and then equilibrated 10 minutes at 37 °C) and 100 µL of DNase solution (one vial of DNase-I (Worthington) dissolved in 500 µL of EBSS). Bone was removed from the epithelium under a dissecting microscope and the resultant tissue was placed in a 5 mL tube (Becton Dickinson) with an additional 1.75 mL of Papain solution and 200 µL of DNase-I solution and rocked gently for ~60 minutes at 37 °C. The tissue was then gently triturated with a 5 mL pipette 10-15 times, passed through a 40 µm cell strainer (Becton Dickinson), and washed with 1 mL of Hibernate-A medium containing 10 % Fetal Bovine Serum (FBS, GIBCO). Filtered cells were transferred to a new 5 mL tube and centrifuged 5 minutes at 300 x g. The supernatant was decanted, the cells were washed once with 4 mL Hibernate-A containing 10 % FBS and resuspended in 1 mL Hibernate-A containing 0.2 % FBS. Each of the solutions above contained transcriptional inhibitors (5 µg/mL of Actinomycin D, 10 µg/mL of Anisomycin and 10 µM of Triptolide, all obtained from Sigma) for all experiments. Dissociated cells were stained with propidium iodide (final concentration 1.65 µg/mL), and subject to FACS to remove dead cells and obvious doublets. Cells were sorted into Hibernate-A containing 5 % FBS (also include 0.1x of transcriptional inhibitors), centrifuged for 5 minutes at 300 g, and resuspended with PBS. Prepared single cell suspensions were used to prepare single cell RNA-seq library with the chromium single cell gene expression system (chromium single cell 3’ reagents and GEM-X v4 dual index, 10X genomics), using the default protocols provided by 10X genomics. Each of the replicates was loaded to get ~20,000 cells.
Chromium GEM-X Single Cell 3 v4: Dual Index. Quantified via Kapa qPCR kit and sequenced via Illumina platform (NovaSeq X Plus)

treatment_protocol: Manipulations of retinoic acid signaling were performed in adult mice that received a single dose of methimazole (50 mg/kg). Starting 72 hours after methimazole injection, mice received either the RA receptor inverse agonist BMS493 (10 mg/kg, dissolved in 5 % DMSO in corn oil) or vehicle, and drugs were delivered subcutaneously. Littermates within each cohort received either drug or vehicle daily for 3–4 weeks after methimazole-induced regeneration, and scRNA-seq was performed after 4–5 weeks; animals receiving each drug or vehicle control were dissociated and sequenced or processed for in situs in parallel.

value: whole olfactory mucosa

value: BMS493, a pan-retinoic acid receptor (RAR) inverse agonist


title: RARi_DMSO_1

description: Library name: RARi_DMSO_1

value: DMSO


title: AFT8_1

description:
Library name: sample 7
8h group_replicate_1


title: Batch 2 of samples, multiplexed by DNA-barcoded antibodies - ADT

city: Salt Lake City

first: Jaroslav

last: Zak

state: UT

address: 1950 Circle of Hope Dr

department: Department of Radiation Oncology, Huntsman Cancer Institute

institute: University of Utah

description: Library name: Library 2 (ADT)

data_processing:
The libraries were sequenced on the Element AVITI and Illumina NovaSeq X Plus instruments. The de-multiplexed FASTQ files were subjected to alignment, barcode identification, filtering and gene counting using 10X Genomics cellranger-8.0.0 and the GRCm39-2024-A transcriptome reference.
Assembly: GRCm39
Supplementary files format and content: Filtered cell-gene count matrix generated by cellranger-8.0.0

source_name: spleen

extract_protocol:
Mice splenocytes were isolated and subjected to cell straining to obtain a splenocyte suspension, stained for CD45, CD3, CD19, CD11b using fluorophore-conjugated antibodies and live/dead dye. Mouse T cells (CD45+ CD3+ CD19- CD11b- dead dye-) were sorted using flow cytometric sorting. The cells were then stained with DNA-barcoded hashtag antibodies (Biolegend TotalSeq-B) according to the manufacturer's instructions and pooled into 2 sets of 10 barcoded samples.
The 2 pooled cell suspensions were subjected to 3' single-cell transcriptomic library preparation using the 10X Genomics kit according to the manufacturer's instructions (Single Cell 3' v3). The resulting libraries comprise gene expression (GEX) and antibody-dependent tag (ADT) libraries.

treatment_protocol: Mice were infected with LCMV Clone 13 and treated with mouse SAR'877 (1 mg/kg), anti-PD1 (1mg/kg), mouse IL-15 mutein (1 mgk/kg), anti-PD1+mouse IL-15 mutein (1 mg/kg each) or isotype control (1 mkg/kg). Splenic T cells were isolated from these mice at day 30 post infection.

value: spleen

value: T cells

value: wild type

value: see barcode description

value: batch 2


title: Batch 2 of samples, multiplexed by DNA-barcoded antibodies - GEX

description: Library name: Library 2 (GEX)


title: RARi_RAR_1

description: Library name: RARi_RAR_1


title: RARi_DMSO_2

description: Library name: RARi_DMSO_2


title: Batch 1 of samples, multiplexed by DNA-barcoded antibodies - ADT

description: Library name: Library 1 (ADT)

value: batch 1


title: GallicAcid_5

city: Columbus

first: Steve

last: Oghumu

address: 1841 Neil Ave

institute: Ohio State University

description: Library name: Sample_11

data_processing:
Raw RNA sequencing reads were aligned to the Mus musculus reference genome (version mm10) using splice-aware aligner HISAT2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Tongue

extract_protocol:
RNA was harvested using RNeasy Plus Mini Kit (Qiagen, USA).
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: Tongue

value: tumor and tumor-associated

value: Gallic acid


title: GallicAcid_4

description: Library name: Sample_10


title: GallicAcid_1

description: Library name: Sample_7


title: Vehicle_6

description: Library name: Sample_6

value: Vehicle


title: GallicAcid_6

description: Library name: Sample_12


title: Vehicle_5

description: Library name: Sample_5


title: Vehicle_4

description: Library name: Sample_4


title: GallicAcid_2

description: Library name: Sample_8


title: GallicAcid_3

description: Library name: Sample_9


title: Vehicle_3

description: Library name: Sample_3


title: Vehicle_2

description: Library name: Sample_2


title: Batch 1 of samples, multiplexed by DNA-barcoded antibodies - GEX

description: Library name: Library 1 (GEX)


title: Vehicle_1

description: Library name: Sample_1


title: articular chondrocytes, GW3965_4

city: Xi'an

first: Huanbo

last: Wang

address: No. 127, Changle West Road

institute: Xijing Hospital, Fourth Military Medical University

description: Library name: Sample 19

data_processing:
Illumina Casava 1.8 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mouse whole genome using hisat2 v2.0.5 with parameters hisat2 [options]* -x <hisat2-idx> {-1 <m1> -2 <m2> | -U <r> | --sra-acc <SRA accession number>} [-S <hit>]
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Bray N, Pimentel H, Melsted P, et al., Near-optimal RNA-Seq quantification, 2015. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Mus_musculus_Ensemble_94
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

source_name: Chondrocytes

extract_protocol:
RNA was harvested using Trizol reagent.
RNA libraries were prepared for sequencing using Fast RNA-seq Lib Prep Kit V2 (Cat. No. RK20306).

value: Chondrocytes


title: articular chondrocytes, GW3965_5

description: Library name: Sample 20


title: CAST_C57_F1_M2_A

description: Library name: CAST_C57_F1_M2_A

data_processing:
Demultiplexed fastq files were uniformly processed via a custom nextflow pipeline that ran cell ranger (v6), as well as custom post-processing to remove multi-mapping reads (see Tsukahara et al. 2021 PMID: 34879231). All samples (including those in GSE173947) were integrated together to extract (mature) olfactory sensory neurons for downstream analyses.
Assembly: Ensembl GRCm39 version 105 genome, including ectopic genes like GFP and modified GTF file to extend the 3' UTRs for TAAR genes
Supplementary files format and content: All_samples_GEP_usage.csv.gz: usage for each of the gene expression programs described in Tsukahara et al. 2021 (PMID: 34879231) for each cell, for the set of 2.3M mature OSNs identified across all samples, as well as the singularly-expressed olfactory receptor (OR) that was chosen in each mOSN.
Supplementary files format and content: OSN_subtype_hvg_mean.csv.gz: The mean expression of each of the the ~1350 OSN highly-variable genes for each OSN subtype (the set of OSNs singularly expressing a given OR), for the 1100 subtypes detected in our 2.3M integrated OSN dataset
Supplementary files format and content: <sample_name>__filtered_feature_bc_matrix.h5: Raw cell x gene matrix from cell ranger for each sample

extract_protocol:
The main olfactory epithelium was dissected and cleaned up in the Earle’s Balanced Salt Solution (EBSS, pre-treated with carbogen for at least 5 minutes before each use, Worthington), then transferred to a round-bottomed glass dish containing 750 µL of papain solution (one vial of Papain, (Worthington) dissolved in 5 mL of EBSS and then equilibrated 10 minutes at 37 °C) and 100 µL of DNase solution (one vial of DNase-I (Worthington) dissolved in 500 µL of EBSS). Bone was removed from the epithelium under a dissecting microscope and the resultant tissue was placed in a 5 mL tube (Becton Dickinson) with an additional 1.75 mL of Papain solution and 200 µL of DNase-I solution and rocked gently for ~60 minutes at 37 °C. The tissue was then gently triturated with a 5 mL pipette 10-15 times, passed through a 40 µm cell strainer (Becton Dickinson), and washed with 1 mL of Hibernate-A medium containing 10 % Fetal Bovine Serum (FBS, GIBCO). Filtered cells were transferred to a new 5 mL tube and centrifuged 5 minutes at 300 x g. The supernatant was decanted, the cells were washed once with 4 mL Hibernate-A containing 10 % FBS and resuspended in 1 mL Hibernate-A containing 0.2 % FBS. Each of the solutions above contained transcriptional inhibitors (5 µg/mL of Actinomycin D, 10 µg/mL of Anisomycin and 10 µM of Triptolide, all obtained from Sigma) for all experiments. Dissociated cells were stained with propidium iodide (final concentration 1.65 µg/mL), and subject to FACS to remove dead cells and obvious doublets. For GFP-expressing mouse lines , GFP positive and negative cells were sorted separately using a FITC filter. Cells were sorted into Hibernate-A containing 5 % FBS (also include 0.1x of transcriptional inhibitors), centrifuged for 5 minutes at 300 g, and resuspended with PBS. Prepared single cell suspensions were used to prepare single cell RNA-seq library with the chromium single cell gene expression system (chromium single cell 3’ reagents and GEM v3.1 dual index, 10x genomics), using the default protocols provided by 10x genomics. Each of the replicates other than GFP-positive ones was aimed to have 10,000 cells. The expected multiplet rate is ~8.0 %.
Chromium Next GEM Single Cell 3 v3.1: Dual Index. Quantified via Kapa qPCR kit and sequenced via Illumina platform (NovaSeq 6000 or X Plus)

value: C57BL/6J;CAST/EiJ F1 hybrid

value: male


title: CAST_C57_F1_F2_B

description: Library name: CAST_C57_F1_F2_B

value: female


title: CAST_C57_F1_M2_B

description: Library name: CAST_C57_F1_M2_B

value: whole olfactory mucosa


title: CAST_C57_F1_M1_B

description: Library name: CAST_C57_F1_M1_B


title: articular chondrocytes, GW3965_3

description: Library name: Sample 18


title: CAST_C57_F1_F1_A

description: Library name: CAST_C57_F1_F1_A


title: articular chondrocytes, 25HC3S_5

description: Library name: Sample 15


title: CAST_C57_F1_F2_A

description: Library name: CAST_C57_F1_F2_A


title: articular chondrocytes, GW3965_2

description: Library name: Sample 17


title: articular chondrocytes, 25HC3S_1

description: Library name: Sample 11


title: articular chondrocytes, GW3965_1

description: Library name: Sample 16


title: articular chondrocytes, 25HC_5

description: Library name: Sample 10


title: articular chondrocytes, 25HC3S_4

description: Library name: Sample 14


title: CAST_C57_F1_F1_B

description: Library name: CAST_C57_F1_F1_B


title: articular chondrocytes, 25HC3S_2

description: Library name: Sample 12


title: articular chondrocytes, 25HC_2

description: Library name: Sample 7


title: articular chondrocytes, 25HC_4

description: Library name: Sample 9


title: articular chondrocytes, 25HC_1

description: Library name: Sample 6


title: articular chondrocytes, Control_5

description: Library name: Sample 5


title: articular chondrocytes, 25HC_3

description: Library name: Sample 8


title: articular chondrocytes, Control_4

description: Library name: Sample 4


title: articular chondrocytes, 25HC3S_3

description: Library name: Sample 13


title: articular chondrocytes, Control_2

description: Library name: Sample 2


title: articular chondrocytes, Control_1

description: Library name: Sample 1


title: articular chondrocytes, Control_3

description: Library name: Sample 3


title: CAST_C57_F1_M1_A

description: Library name: CAST_C57_F1_M1_A


title: Ostreococcus_16_10uE_3

city: Valencia

first: Javier

last: Forment

address: Ingeniero Fausto Elio, s/n

country: Spain

institute: Instituto de Biología Molecular y Celular de Plantas, IBMCP (Universitat Politècnica de València-CSIC)

description: Library name: sample111

data_processing:
Raw data quality was assessed by FastQC v.0.11.5 with the default parameters.
The genome indexes were made by HISAT2 v 2.1.0 using the function hisat2-build with the default paraments.
The mapping of short reads in the indexes of the four reference genomes was done with the same software using the function hisat2 with the parameter --dta.
Assembly: The reference genomes and the annotations used for the mapping of the reads were GCF_000001735.4, GCA_009936355.2, GCA_009602735.1 and GCA_000214015.2 for Arabidopsis thaliana, Marchantia polymorpha, Mesotaenium endlicherianum and Ostreococcus tauri, respectively.
Supplementary files format and content: Tab-delimted files include raw counts for each sample.

organism: Ostreococcus tauri

source_name: Cells grown for 7d

extract_protocol:
Total RNA extraction from A. thaliana, M. polymorpha and M. endlicherianum were performed with the RNA extraction kit NucleoSpinTM RNA Plant Kit Macherey-Nagel according to the manufacturer's instructions.
Library preparation and sequencing of 100bp pair-end were performed by the company BGI Genomics, Hong Kong. The sequencing platform used was DNBseqTM and the coverage was higher than 50 million reads per sample.

value: Cells grown for 7d

value: WT

value: 16˚C and 10 µmol m-2 s-1 of continuous white light


title: Ostreococcus_24_100uE_1

description: Library name: sample118

value: 24˚C and 100 µmol m-2 s-1 of continuous white light


title: Ostreococcus_24_10uE_2

description: Library name: sample116

value: 24˚C and 10 µmol m-2 s-1 of continuous white light


title: Ostreococcus_24_100uE_2

description: Library name: sample119


title: Ostreococcus_24_10uE_3

description: Library name: sample117


title: Mesotaenium_24_100uE_2

description: Library name: sample107

organism: Mesotaenium endlicherianum

source_name: Cells grown for 10d

value: Cells grown for 10d


title: Ostreococcus_24_100uE_3

description: Library name: sample120


title: Ostreococcus_24_10uE_1

description: Library name: sample115


title: Mesotaenium_24_100uE_1

description: Library name: sample106


title: Mesotaenium_24_10uE_3

description: Library name: sample105


title: Mesotaenium_16_100uE_2

description: Library name: sample101

value: 16˚C and 100 µmol m-2 s-1 of continuous white light


title: Ostreococcus_16_100uE_3

description: Library name: sample114


title: Mesotaenium_16_10uE_2

description: Library name: sample98


title: Ostreococcus_16_10uE_1

description: Library name: sample109


title: Mesotaenium_24_10uE_1

description: Library name: sample103


title: Mesotaenium_16_100uE_3

description: Library name: sample102


title: Ostreococcus_16_100uE_2

description: Library name: sample113


title: Mesotaenium_16_10uE_1

description: Library name: sample97


title: Ostreococcus_16_10uE_2

description: Library name: sample110


title: Mesotaenium_24_10uE_2

description: Library name: sample104


title: Mesotaenium_24_100uE_3

description: Library name: sample108


title: Mesotaenium_16_100uE_1

description: Library name: sample100


title: planarian run2

city: Kansas City

first: Alejandro

last: Sánchez Alvarado

institute: Stowers Institute for Medical Research

description: Library name: planarian run2

data_processing:
Syrah pipeline
Assembly: smed31
Supplementary files format and content: beadl UMI expression count table
Library strategy: Spatial Transcriptomics

organism: Schmidtea mediterranea

source_name: worm fragments

extract_protocol:
Tissue was OCT embedded and cut with cryostat.
Spatial transcriptomic sequencing libraries were generated using Slid-seqV2 pucks per the Slide-seqV2 protocol.

value: worm fragments


title: Mesotaenium_16_10uE_3

description: Library name: sample99


title: Ostreococcus_16_100uE_1

description: Library name: sample112


title: CT26 NP1867 antiPD1 #67

city: Altrincham

first: Maria T.

last: Rodriguez Plata

state: Cheshire

address: 3rd Floor, 1 Ashley Road

country: United Kingdom

institute: NeoPhore Ltd.

hyb_protocol: 100 ng of RNA were used for hybridisation with NanoString’s PanCancer Immune Profiling Panel Codeset. Hybridisation was performed overnight for 16 hours at 65°C with the CodeSet probes according to NanoString protocols. Once hybridised, samples were loaded into the nCounter Prep Station, which performed the loading of the cartridge according to standard NanoString protocols.

scan_protocol: Once the cartridge was prepared, it was then loaded onto the nCounter Digital Analyzer and scanned.

data_processing: Resulting RCC files were imported into nSolver for QC assessment and reviewed for QC flags using NanoString’s default settings. nSolver QC was considered FAIL if a flag for any of the following parameters was present: Imaging QC, Binding Density QC, Positive Control Linearity, Positive Control Limit of Detection QC. If an Imaging QC flag was present, the cartridge lane affected was rescanned.  If a flag is returned on Normalisation parameters, these were considered a PASS as these can be evaluated at time of in silico data analysis for effects on results. Data analysis was performed using the Advanced Analysis module in nSolver.

label: Nanostring nCounter Mouse PanCancer Immune Profiling Panel

source_name: CT26 tumour

label_protocol: Where possible, and using the concentrations calculated by the Bioanalyzer, RNA quantities were normalised to 20 ng/uL across samples to use the same RNA quantity for analysis.  100 ng of RNA were used for hybridisation with NanoString’s PanCancer Immune Profiling Panel Codeset.

growth_protocol: CT26 cells were chronically treated in vitro with DMSO or PMS2 inhibitor NP1867 (0.5uM) for 40 weeks, and then inoculated subcutaneously into syngeneic BALB/c mice.

extract_protocol: RNA was extracted from 3x 10μm FFPE curls from each sample using the RNeasy DSP FFPE kit (Catalogue # 73064, Qiagen) according to the manufacturer’s instructions aligned with guidelines from NanoString. Following RNA isolation, samples were assessed for both quantity and quality on the Nanodrop (Thermo Scientific) and Bioanalyzer 2100 (Agilent Technologies). Nanodrop assessment was used to produce an initial approximate concentration as well as information on sample purity as A260/280 and A260/230 ratios. The Bioanalyzer 2100 was used to determine sample concentration and RNA fragmentation using the RNA 6000 Nano Assay.

treatment_protocol: DMSO or NP1867- CT26-tumour bearing mice were treated with anti-PD-1 or isotype control (5mg/kg) for 4 doses. Tumours were sampled  24 hours after the last dose, and FFPE processed.

value: CT26 tumour

tag: in vitro treatment

tag: in vivo treatment


title: CT26 NP1867 antiPD1 #50

tag: tissue


title: CT26 NP1867 antiPD1 #48


title: planarian run1

description: Library name: planarian run1


title: CT26 NP1867 antiPD1 #78


title: CT26 NP1867 Isotype #74

value: Isotype Control


title: CT26 NP1867 antiPD1 #30


title: CT26 NP1867 Isotype #49


title: CT26 NP1867 Isotype #26


title: CT26 NP1867 antiPD1 #45


title: CT26 DMSO antiPD1 #13

value: DMSO


title: Liver, 18months, sample2

city: Wuhan

first: Jie

last: Cheng

state: Hubei

address: 13 Hangkong Road, Qiaokou District

department: School of Basic Medicine

institute: Huazhong University of Science and Technology

description:
Library name: O2
Male, Stereo-seq

data_processing:
Sequencing data acquisition was performed on the MGI DNBSEQ-Tx platform, generating paired-end reads with embedded spatial identifiers. Read 1 contained dual oligonucleotide barcodes (CID: positions 1-25; MID: positions 26-35), while Read 2 carried cDNA sequences. Primary processing involved cross-referencing CID sequences against predefined spatial coordinates derived from initial sequencing rounds, permitting single nucleotide mismatches to compensate for technical artifacts. Quality filtration excluded reads containing ambiguous bases (N) in MID regions or those exceeding two positions with Phred scores below 10. Validated CID-MID combinations were integrated into FASTQ headers as metadata tags. Sequence alignment was executed through the STAR52 aligner against the reference genome mm10, retaining only uniquely mapped reads with mapping quality scores (MAPQ) exceeding 10 for gene annotation. Molecular deduplication consolidated UMIs sharing identical CID-spatial coordinates and gene loci, incorporating single-nucleotide tolerance to mitigate amplification biases.
Assembly: mm10 reference genome
Supplementary files format and content: Cell bin, Bin1 and figure
Library strategy: Spatial Transcriptomics

source_name: Liver

extract_protocol:
Fresh mouse liver tissue specimens were adhered to BGI-manufactured Stereo-seq spatial transcriptomics chips through brief thermal conditioning at 37 °C for 3 min. Subsequent fixation involved immersion in chilled absolute methanol (-20 °C) for 40 min prior to initiating library construction workflows. For morphological validation, select sections underwent nuclear counterstaining with nucleic acid dye (Thermo Fisher Scientific, Q10212), with fluorescent micrographs captured using a Motic Custom PA53 FS6 microscope system. These quality-controlled specimens were subsequently processed through FITC-channel spatial barcoding workflows for transcriptome capture.
The tissue sections were initially treated with a buffer solution containing 0.1× SSC (Thermo, AM9770) and 0.05 U/mL RNase inhibitor (NEB, M0314L) to prepare them for subsequent steps. Permeabilization was achieved by immersing the sections in a solution containing 0.1% pepsin (Sigma, P7000) in 0.01 M HCl, followed by incubation at 37 °C for 5 min. After this step, the sections were again washed with the same buffer containing RNase inhibitor. The RNA released from the permeabilized tissue was captured by DNA nanoballs (DNBs) and subjected to reverse transcription. This process utilized SuperScript II Reverse Transcriptase (Invitrogen, 18064-014) in a reaction mixture containing 10 U/mL reverse transcriptase, 1 mM dNTPs, 1 M betaine, 7.5 mM MgCl₂, 5 mM DTT, 2 U/mL RNase inhibitor, 2.5 mM Stereo-seq TSO, and 1× First-Strand buffer. The reverse transcription was carried out overnight at 42 °C. Following this, the tissue sections underwent two washes with 0.1× SSC buffer and were then treated with Tissue Removal buffer (comprising 10 mM Tris-HCl, 25 mM EDTA, 100 mM NaCl, and 0.5% SDS) at 55 °C for 10 min to facilitate tissue digestion. The cDNA-containing chips were subsequently treated with a cDNA Release Mix (comprising cDNA Release Enzyme and buffer) overnight at 55 °C. Finally, the cDNA was purified using VAHTSTM DNA Clean Beads at a 0.8× ratio to ensure high-quality cDNA recovery. cDNA amplification was performed using KAPA HiFi HotStart DNA Polymerase Master Mix (Roche, KK2602) supplemented with 0.8 μM cDNA-specific amplification primers. Thermal cycling parameters were configured with the following profile: initial denaturation at 95 °C for 5 min; 15 amplification cycles consisting of denaturation at 98 °C for 20 sec, primer annealing at 58 °C for 20 sec, and strand extension at 72 °C for 3 min per cycle; concluding with a terminal extension phase at 72 °C for 5 min to ensure complete product elongation. DNA quantification of PCR products was performed using the QubitTM dsDNA Assay Kit (Thermo, Q32854). For library preparation, 20 ng of purified DNA underwent fragmentation via incubation with custom-formulated Tn5 transposase at 55 °C for 10 min, with enzymatic activity terminated through the addition of 0.02% SDS solution followed by gentle mixing at 37 °C for 5 min. Amplification reactions were conducted in 100 μL volumes containing 25 μL of fragmented DNA, 1× concentration of KAPA HiFi HotStart Ready Mix, 0.3 μM Stereo-seq-Library-F primer, 0.3 μM Stereo-seq-Library-R primer, and nuclease-free water to reach the final volume. Thermal cycling conditions comprised an initial denaturation at 95 °C for 5 min, followed by 13 cycles of 98 °C for 20 sec, 58 °C for 20 sec and 72 °C for 30 sec, concluding with a final extension at 72 °C for 5 min. Amplified libraries underwent sequential purification using AMPure XP magnetic beads with size selection ratios of 0.63 and 0.153, followed by DNB generation through standard protocols. Final sequencing was executed on the MGI DNBSEQ-Tx platform utilizing a paired-end 150 bp configuration.

value: Liver

tag: cell type

value: All liver cell


title: CT26 DMSO antiPD1 #37


title: CT26 DMSO Isotype #64


title: CT26 DMSO antiPD1 #11


title: Liver, 2months, sample4

description:
Library name: Y2
Male, Stereo-seq

tag: genotype


title: CT26 DMSO Isotype #6


title: CT26 NP1867 Isotype #57


title: CT26 DMSO antiPD1 #43


title: Liver, 2months, sample3

description:
Library name: Y1
Male, Stereo-seq


title: CT26 DMSO Isotype #23


title: CT26 DMSO Isotype #55


title: CT26 DMSO antiPD1 #74


title: CT26 DMSO antiPD1 #7


title: CT26 DMSO Isotype #47


title: CT26 NP1867 Isotype #47


title: Liver, 18months, sample1

description:
Library name: O1
Male, Stereo-seq


title: IDG-SW3 treated with Nutlin-3a [10 μM] for 4 hours, rep 3

city: Shanghai

first: Kai

last: Yang

address: 197 Ruijin 2nd Road, Shanghai, 200025, China

department: Shanghai Institute of Traumatology and Orthopedics

institute: Shanghai Jiao Tong University School of Medicine

description: Library name: p53rep3

data_processing:
[scRNA-seq] Raw sequencing data were processed using the Cell Ranger count pipeline (10x Genomics). Reads were aligned to the mm10 reference genome to generate feature-barcode matrices.
[Cuttag] Trimmed reads were aligned to the mouse reference genome (mm10) using Bowtie2, and analyzed with MACS2, HOMER and deeptools.
Assembly: mouse mm10
Supplementary files format and content: [scRNA-seq] Table-seperated values files and matrix files
Supplementary files format and content: [Cuttag] bigwig
Library strategy: CUT&Tag

growth_protocol: IDG-SW3 osteolineage cells were cultured and differentiated in osteogenic induction medium at 37°C with 5% CO2 according to standard protocols.

extract_protocol:
For scRNA-seq, the single-cell suspension was immediately loaded onto the Chromium Controller (10x Genomics) for droplet generation, cell barcoding, and reverse transcription.
For scRNA-seq, libraries were constructed using the Chromium Single Cell 5' Reagent Kit (10x Genomics) following the manufacturer's protocol. For CUT&Tag, libraries were constructed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) following the manufacturer's instructions.

treatment_protocol: [Cuttag] Differentiating IDG-SW3 cells were treated with Nutlin-3a [10 μM] for 4 hours to induce intracellular p53 stabilization.

tag: cell line

value: osteaoblast-to-osteocyte

tag: cut&tag antibody

value: Nutlin-3a [10 μM] treatment for 4 hours


title: IDG-SW3 treated with Nutlin-3a [10 μM] for 4 hours, rep 2

description: Library name: p53rep2

tag: treatment


title: IDG-SW3 treated with Nutlin-3a [10 μM] for 4 hours, rep 1

description: Library name: p53rep1


title: bone, 8M, scRNA-seq

description: Library name: Bone8M

data_processing:
[scRNA-seq] Raw sequencing data were processed using the Cell Ranger count pipeline (10x Genomics). Reads were aligned to the mm10 reference genome to generate feature-barcode matrices.
[Cuttag] Trimmed reads were aligned to the mouse reference genome (mm10) using Bowtie2, and analyzed with MACS2, HOMER and deeptools.
Assembly: mouse mm10
Supplementary files format and content: [scRNA-seq] Table-seperated values files and matrix files
Supplementary files format and content: [Cuttag] bigwig

source_name: Endosteal/Cortical bone

value: Endosteal/Cortical bone

value: osteaoblast/osteocyte

tag: Sex

value: Male

tag: developmental stage

value: 8 months

value: No treatment


title: tpMSC_1

city: Chongqing

first: Yuantong

last: Qi

address: 30 Gaotanyan Main Street

institute: Third Military Medical University

description: Library name: Sample 10

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of pval below 0.05 and absolute fold change ≥ 1.5 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: Mus_musculus.GRCm38 v101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Lung

extract_protocol:
Total RNA was extracted using Trizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: Lung

value: Wildtype

tag: group

value: tpMSC


title: tpMSC_3

description: Library name: Sample 12


title: tpMSC_2

description: Library name: Sample 11


title: MSC_3

description: Library name: Sample 9

value: MSC


title: MSC_2

description: Library name: Sample 8


title: CT26 NP1867 Isotype #10


title: MSC_1

description: Library name: Sample 7


title: ALI_3

description: Library name: Sample 6

value: ALI


title: Control_3

description: Library name: Sample 3

value: Control


title: ALI_2

description: Library name: Sample 5


title: Control_2

description: Library name: Sample 2


title: CT26 DMSO Isotype #59

value: CT26 tumour

value: Isotype Control


title: Control_1

description: Library name: Sample 1


title: 4h STm-Infected 0RANKL rep_2

city: Nashville

first: James

last: Cassat

state: TN

address: 1161 21st Ave S

institute: Vanderbilt University Medical Center

description:
Library name: CP-14
"CP.14.Aligned.sortedByCoord.out.bam" in counts_all.txt

data_processing:
Raw paired-end reads were trimmed and quality-filtered using fastp v0.23.42 with flags --detect_adapter_for_pe, --correction, --trim_poly_x, and --compression [6].
Reads were mapped to the M. musculus reference genome GRCm39 using STAR v2.73. The STAR index was prepared with flag --sjdbOverhang 149. Reads were mapped in STAR using --twopassModeBasic. To decrease the likelihood of false positive splice junction calls, the minimum overlaps for annotated and unannotated splice junctions in STAR were increased from defaults of 3 and 5 nucleotides to 4 and 8 nucleotides, respectively. These flags were --alignSJDBoverhangMin 4 and --alignSJoverhangMin 8. Finally, the output was a sorted .bam file using flag --outSAMtype BAM SortedByCoordinate.
Counts data were generated using featureCounts in the Rsubread (v2.20.0) package of R (v4.4.1) with flags isPairedEnd=TRUE and minFragLength=50 for features of the GRCm39 reference genome.
Assembly: GRCm39
Supplementary files format and content: all_counts.txt is a tab-delimited file containing RAW counts data for each sample

source_name: murine bone marrow derived macrophages (BMDM)

growth_protocol: Differentiated murine bone marrow derived macrophages (BMDMs) from C57BL/6J mice were plated at a density of 2 x 10^6 cells/well in 6-well plates and cultured in complete MEM-alpha containing 5% CMG 14-12 supernatant (source of mCSF)

extract_protocol:
Total RNA was harvested using the RNeasy Plus Mini Kit (Qiagen). Concentration was assessed using the Qubit fluorometric assay, and quality was assessed using the Agilent BioAnalyzer.
Vanderbilt Technologies for Advanced Genomics (VANTAGE) performed mRNA enrichment and cDNA library preparation using a stranded mRNA (polyA-selected) library preparation kit.

treatment_protocol: Cells were treated with or without 100ng/mL RANKL for 2 days. Afterwards, cells were infected with STm at a multiplicity of infection of 1 or mock infected for either 4h or 24h.

tag: infection

value: STm

tag: rankl treatment_(ng/ml)

tag: time


title: 24h STm-Infected 0RANKL rep_3

description:
Library name: CP-21
"CP.21.Aligned.sortedByCoord.out.bam" in counts_all.txt

value: murine bone marrow derived macrophages (BMDM)


title: 4h STm-Infected 0RANKL rep_1

description:
Library name: CP-13
"CP.13.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 24h STm-Infected 100RANKL rep_1

description:
Library name: CP-22
"CP.22.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 24h STm-Infected 100RANKL rep_2

description:
Library name: CP-23
"CP.23.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 24h STm-Infected 0RANKL rep_2

description:
Library name: CP-20
"CP.20.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 4h STm-Infected 100RANKL rep_3

description:
Library name: CP-18
"CP.18.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 24h STm-Infected 100RANKL rep_3

description:
Library name: CP-24
"CP.24.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 4h STm-Infected 100RANKL rep_1

description:
Library name: CP-16
"CP.16.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: ALI_1

description: Library name: Sample 4


title: 24h STm-Infected 0RANKL rep_1

description:
Library name: CP-19
"CP.19.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 24h Mock-Infected 100RANKL rep_3

description:
Library name: CP-12
"CP.12.Aligned.sortedByCoord.out.bam" in counts_all.txt

value: mock


title: 4h STm-Infected 100RANKL rep_2

description:
Library name: CP-17
"CP.17.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 24h Mock-Infected 100RANKL rep_2

description:
Library name: CP-11
"CP.11.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 4h STm-Infected 0RANKL rep_3

description:
Library name: CP-15
"CP.15.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 24h Mock-Infected 100RANKL rep_1

description:
Library name: CP-10
"CP.10.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 24h Mock-Infected 0RANKL rep_2

description:
Library name: CP-8
"CP.8.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 24h Mock-Infected 0RANKL rep_3

description:
Library name: CP-9
"CP.9.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 4h Mock-Infected 100RANKL rep_1

description:
Library name: CP-4
"CP.4.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 4h Mock-Infected 100RANKL rep_2

description:
Library name: CP-5
"CP.5.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 4h Mock-Infected 100RANKL rep_3

description:
Library name: CP-6
"CP.6.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 4h Mock-Infected 0RANKL rep_3

description:
Library name: CP-3
"CP.3.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: 4h Mock-Infected 0RANKL rep_2

description:
Library name: CP-2
"CP.2.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: Post MI Week 4

first: Mahmood

last: Khan

state: Ohio

address: 2255 Kenny Rd

department: Emergency Medicine

institute: The Ohio State  University

description:
Library name: Post_MI_Wk-4
10X Genomics

data_processing:
The sequencing reads were analyzed with the mouse reference genome mm10 using Cell Ranger v7.1.0 [1]. Introns were included in the analysis.
Assembly: Mouse mm10
Supplementary files format and content: gene-barcode matrices in h5 format

source_name: Heart

extract_protocol:
According to Singulomics Corporation protocol.
We isolated nuclei from frozen mouse heart tissue samples and constructed 3’ single-cell gene expression libraries (Next GEM v3.1) using the 10x Genomics Chromium system. The libraries were sequenced with ~200 million PE150 reads per sample on Illumina NovaSeq. ( Singulomics Corporation protocol).

value: Heart

value: Left Ventricle


title: 4h Mock-Infected 0RANKL rep_1

description:
Library name: CP-1
"CP.1.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: HNF1Bflox_3_1611

city: Paris

first: Pierre

last: Isnard

address: 156-160, rue de Vaugirard

institute: INEM

description:
Library name: 3_1611
3_1611

data_processing:
RNA-seq reads were aligned to the Ensembl release 98 GRCm38.p6 genome assembly using  HISAT2
Reads counts per genes were computed with htseq-count (version 0.13.5)
A raw matrix contain the counts with the Ensembl mouse gene names (Gencode M23)
Assembly: Ensembl release 98 GRCm38.p6
Supplementary files format and content: A tab-delimited matrix that include counts values for each sample

source_name: Kidney

growth_protocol: Experiments were performed on 60-day-old male Hnf1bf/f mice with 4 Cre-positive (Ksp/CreERT2) and 4 Cre-negative. Animals were fed ad libitum and housed in a room with constant ambient temperature and a 12-hour light/12-hour dark cycle.

extract_protocol:
RNA was extracted from nitrogen-frozen kidneys using the miRNeasy Kit (QIAGEN) according to the manufacturer’s instructions.
RNA libraries were prepared using “Ovation Universal RNA-Seq System” (Nugen, Tecan) following manufacturer's protocols.
RNA-seq libraries were sequenced on Illumina NovaSeq6000 (100 base paired-end reads) and 50 million paired-end reads per library were produced.

treatment_protocol: Tamoxifen at 50mg/ml for 2 consecutive days at 60 days of age

value: Kidney

value: HNF1b flox


title: Post MI Week 1

description:
Library name: Post_MI_Wk-1
10X Genomics


title: UUO_kidney_FB_27_S93

description:
Library name: FB_27_S93
7_1602

data_processing:
RNA-seq reads were aligned to the Ensembl release 98 GRCm38.p6 genome assembly using  HISAT2
Reads counts per genes were computed with htseq-count
Reads counts per genes were normalized with DESeq2
Assembly: Ensembl release 98 GRCm38.p6
Supplementary files format and content: A tab-delimited matrix that include normalized counts values for each sample

growth_protocol: Experiments were performed on four 60-day-old male wild-type mice (C57BL/6). Animals were fed ad libitum and housed in a room with constant ambient temperature and a 12-hour light/12-hour dark cycle.

treatment_protocol: Unilateral ureteral obstruction (UUO) was performed on the left kidney, while the right, unobstructed kidney served as the control.


title: CTRL_Kidney_FB_6_S81

description:
Library name: FB_6_S81
8_1619


title: 24h Mock-Infected 0RANKL rep_1

description:
Library name: CP-7
"CP.7.Aligned.sortedByCoord.out.bam" in counts_all.txt


title: UUO_kidney_FB_25_S92

description:
Library name: FB_25_S92
6_1601


title: UUO_kidney_FB_23_S91

description:
Library name: FB_23_S91
3_1611


title: CTRL_Kidney_FB_2_S79

description:
Library name: FB_2_S79
12_1604


title: CTRL_Kidney_FB_4_S80

description:
Library name: FB_4_S80
14_1626


title: HNF1Bflox/KSPcreERT2_14_1626

description:
Library name: 14_1626
14_1626

value: HNF1b flox/KSPcre ERT2

value: Tamoxifen at 50mg/ml for 2 consecutive days


title: HNF1Bflox_6_1601

description:
Library name: 6_1601
6_1601


title: CTRL_Kidney_FB_1_S78

description:
Library name: FB_1_S78
10_1613


title: HNF1Bflox_2_1610

description:
Library name: 2_1610
2_1610


title: UUO_kidney_FB_22_S90

description:
Library name: FB_22_S90
2_1610


title: Control Heart

description:
Library name: Control
10X Genomics


title: HNF1Bflox_7_1602

description:
Library name: 7_1602
7_1602


title: HNF1Bflox/KSPcreERT2_8_1619

description:
Library name: 8_1619
8_1619


title: HNF1Bflox/KSPcreERT2_10_1613

description:
Library name: 10_1613
10_1613


title: wPlug-3L

description: Library name: wPlug-3L

value: whole olfactory mucosa

tag: strain

value: male


title: wPlug-3R

description: Library name: wPlug-3R


title: HNF1Bflox/KSPcreERT2_12_1604

description:
Library name: 12_1604
12_1604


title: tta-GCaMP_cage-2

description: Library name: tta-GCaMP_cage-2

value: OMP-IRES-tTA;TRE-GCaMP


title: tta-GCaMP_ACE-2

description: Library name: tta-GCaMP_ACE-2


title: propyl_acetate-4

description: Library name: propyl_acetate-4


title: tta-GCaMP_ACE-1

description: Library name: tta-GCaMP_ACE-1


title: tta-GCaMP_cage-1

description: Library name: tta-GCaMP_cage-1


title: propanoic_acid-4

description: Library name: propanoic_acid-4


title: propinoic_acid_6

description: Library name: propinoic_acid_6


title: propyl_acetate-2

description: Library name: propyl_acetate-2


title: propanal-9

description: Library name: propanal-9


title: propanoic_acid-2

description: Library name: propanoic_acid-2


title: propyl_acetate-1

description: Library name: propyl_acetate-1


title: propanoic_acid-3

description: Library name: propanoic_acid-3


title: propanal-10

description: Library name: propanal-10


title: propanal-6

description: Library name: propanal-6


title: propyl_acetate-3

description: Library name: propyl_acetate-3


title: propanal-2

description: Library name: propanal-2


title: propanal-8

description: Library name: propanal-8


title: propinoic_acid_5

description: Library name: propinoic_acid_5


title: pentanone-1

description: Library name: pentanone-1


title: pentanone-2

description: Library name: pentanone-2


title: propanal-1

description: Library name: propanal-1


title: propanal-7

description: Library name: propanal-7


title: pentyl_acetate-1

description: Library name: pentyl_acetate-1


title: propanal-5

description: Library name: propanal-5


title: propanoic_acid-1

description: Library name: propanoic_acid-1


title: propanal-4

description: Library name: propanal-4


title: pentanoic_acid-1

description: Library name: pentanoic_acid-1


title: propanal-3

description: Library name: propanal-3


title: pentanoic_acid-2

description: Library name: pentanoic_acid-2


title: octanone-4

description: Library name: octanone-4


title: pentanal-1

description: Library name: pentanal-1


title: pentyl_acetate-2

description: Library name: pentyl_acetate-2


title: octanone-1

description: Library name: octanone-1


title: pentanal-2

description: Library name: pentanal-2


title: octanone-3

description: Library name: octanone-3


title: octanoic_acid-1

description: Library name: octanoic_acid-1


title: octanal-7

description: Library name: octanal-7


title: octanal-5

description: Library name: octanal-5


title: octanal-4

description: Library name: octanal-4


title: octanal-6

description: Library name: octanal-6


title: octanoic_acid-4

description: Library name: octanoic_acid-4


title: octanoic_acid-3

description: Library name: octanoic_acid-3


title: nonanoic_acid_2

description: Library name: nonanoic_acid_2


title: octanone-2

description: Library name: octanone-2


title: octanoic_acid-2

description: Library name: octanoic_acid-2


title: Athy5_24_100uE_3

description: Library name: sample48

source_name: 7d seedlings

value: 7d seedlings

value: 2d under 20˚C and 100 µmol m-2 s-1 of continuous white light followed by 5d under 24˚C and 100 µmol m-2 s-1 of continuous white light


title: octanal-1

description: Library name: octanal-1

source_name: whole olfactory mucosa


title: octanal-3

description: Library name: octanal-3


title: Athy5_24_100uE_1

description: Library name: sample46


title: nonanoic_acid_1

description: Library name: nonanoic_acid_1


title: Athy5_24_100uE_2

description: Library name: sample47


title: nonanoic_acid-1

description: Library name: nonanoic_acid-1


title: octanal-2

description: Library name: octanal-2


title: Athy5_24_10uE_3

description: Library name: sample45

value: 2d under 20˚C and 100 µmol m-2 s-1 of continuous white light followed by 5d under 24˚C and 10 µmol m-2 s-1 of continuous white light


title: Athy5_24_10uE_2

description: Library name: sample44


title: nonanoic_acid-2

description: Library name: nonanoic_acid-2


title: methyl_propionate-2

description: Library name: methyl_propionate-2


title: octanal-8

description: Library name: octanal-8


title: methyl_propionate-1

description: Library name: methyl_propionate-1


title: hexyl_acetate-8

description: Library name: hexyl_acetate-8


title: Athy5_24_10uE_1

description: Library name: sample43


title: hexyl_acetate-7

description: Library name: hexyl_acetate-7


title: hexyl_acetate-6

description: Library name: hexyl_acetate-6


title: Atphyb_24_100uE_2

description: Library name: sample41


title: Atphyb_24_100uE_3

description: Library name: sample42


title: hexyl_acetate-5

description: Library name: hexyl_acetate-5


title: Atphyb_24_100uE_1

description: Library name: sample40


title: hexyl_acetate-4

description: Library name: hexyl_acetate-4


title: Atphyb_24_10uE_3

description: Library name: sample39


title: Atphyb_24_10uE_1

description: Library name: sample37


title: Atphyb_24_10uE_2

description: Library name: sample38


title: hexanone-4

description: Library name: hexanone-4


title: hexyl_acetate-3

description: Library name: hexyl_acetate-3


title: Homo_clone1

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

institute: Van Andel Institute

description: Library name: Sample 5

data_processing:
Convert the AVITI raw basecall output into FASTQ and demultiplex the reads using Bases2Fastq.
Fastq files were mapped to hg38 human genome by cellranger count with default parameter.
Assembly: hg38
Supplementary files format and content: Processed data files include features.tsv.gz containing gene IDs and gene symbols, barcodes.tsv.gz containing cell barcode sequences, and matrix.mtx.gz containing the sparse gene-by-cell UMI count matrix, all generated by 10x Genomics Cell Ranger.

growth_protocol: Cortical organoids were maintained in neurobasal media with 1% L-Glutamine, 1% NEAA, 1% penicillin-streptomycin, 1% N2 and 1% B27-VA, 10ng/ml BDNF and GDNF, 200µM Vitamin C and db-cAMP.

extract_protocol:
Organoids were washed with PBS twice, then incubated with dissociation buffer (HBSS with 30U/ml papain and 25U/ml TURBO DNase) at 37° for 20min. Cell were washed and resuspended in DPBS with 0.04% BSA.
Libraries using the Chromium Single Cell 3′ Reagent Kits (v.3.1) were prepared following the 10× user guide.

value: cultured organoid

value: CBP Homozygous mutant


title: hexyl_acetate-1

description: Library name: hexyl_acetate-1


title: hexanone-2

description: Library name: hexanone-2


title: Het_clone1

description: Library name: Sample 3

value: CBP heterozygou mutant


title: hexyl_acetate-2

description: Library name: hexyl_acetate-2