title: Mphy5_3hUV_1

city: Geneva

first: Roman

last: Ulm

address: 30 Quai E. Ansermet

institute: University of Geneva

description:
Library name: Mphy5_3hUV_1
Column name in norm_counts_All_samples.txt: Mphy5_3h_1

data_processing:
Raw reads were mapped to the MpTak.v7.1 genome reference using STAR v.2.7.4.
Assembly: MpTak.v7.1
Supplementary files format and content: tab-delimited text file includes normolized reads counts for each sample

organism: Marchantia polymorpha

source_name: 7-day-old gemmaling

growth_protocol: Wild type Tak-1 and Mphy5 mutants gemmalings were grown for 7 days in 50 μmol m-2 s-1 white light.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini kit (Qiagen).
Illumina Tru-Seq libraries were generated from cDNA and sequenced using Illumina NovaSeq 100-bp single-end at the iGE3 genomics platform of the University of Geneva.

treatment_protocol: Exposed or not to supplemental UV-B (1.5 μmol m-2 s-1) for 3h

value: 7-day-old gemmaling


title: Mphy5_3hUV_3

status: Public on Apr 21 2026

type: SRA

country: Switzerland

description:
Library name: Mphy5_3hUV_3
Column name in norm_counts_All_samples.txt: Mphy5_3h_3

library_source: transcriptomic

molecule: total RNA

tag: tissue

tag: cell line

value: male

tag: cell type

tag: genotype

tag: treatment


title: Het_clone2

city: Grand Rapids

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

country: USA

institute: Van Andel Institute

description: Library name: Sample 4

library_source: transcriptomic single cell

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.

molecule: polyA RNA

organism: Homo sapiens

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 heterozygou mutant


title: Mphy5_3hUV_2

description:
Library name: Mphy5_3hUV_2
Column name in norm_counts_All_samples.txt: Mphy5_3h_2


title: Mphy5_0hUV_1

description:
Library name: Mphy5_0hUV_1
Column name in norm_counts_All_samples.txt: Mphy5_0h_1


title: WT

description: Library name: Sample 2

value: CBP WT


title: Mphy5_0hUV_2

description:
Library name: Mphy5_0hUV_2
Column name in norm_counts_All_samples.txt: Mphy5_0h_2


title: Mphy5_0hUV_3

description:
Library name: Mphy5_0hUV_3
Column name in norm_counts_All_samples.txt: Mphy5_0h_3


title: Homo_clone2

description: Library name: Sample 6

value: CBP Homozygous mutant


title: hexanone-3

city: Boston

first: David

last: Brann

state: MA

address: 220 Longwood Ave

department: Neurobiology

institute: Harvard Medical School

description: Library name: hexanone-3

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

organism: Mus musculus

source_name: whole olfactory mucosa

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: whole olfactory mucosa

tag: strain

tag: Sex


title: heptanone-4

description: Library name: heptanone-4


title: Parental

description: Library name: Sample 1

value: Parental cells


title: hexanone-1

description: Library name: hexanone-1


title: heptanone-3

description: Library name: heptanone-3


title: Homo_clone2_day30

description: Library name: Sample 28

data_processing:
Element AVITI uses onboard AVITI Control Software with integrated primary analysis/basecalling to convert raw electrical sequencing signals into base calls and Phred quality scores
Fastq files were mapped to hg38 human genome by HISAT2
Gene reads count tables were generated by HTSeq
Assembly: hg38
Supplementary files format and content: raw reads count

extract_protocol:
Total RNA was extracted using the QIAGEN RNeasy Plus Mini Kit according to the manufacturer’s instructions.
KAPA Stranded mRNA-Seq Kit

tag: time point


title: hexanoic_acid-1

description: Library name: hexanoic_acid-1


title: Homo_clone2_day18

description: Library name: Sample 27


title: hexanoic_acid-2

description: Library name: hexanoic_acid-2


title: Tak-1_3hUV_2

description:
Library name: Tak-1_3hUV_2
Column name in norm_counts_All_samples.txt: Tak-1_3h_2


title: Homo_clone2_day12

description: Library name: Sample 26


title: Tak-1_0hUV_2

description:
Library name: Tak-1_0hUV_2
Column name in norm_counts_All_samples.txt: Tak-1_0h_2


title: Tak-1_3hUV_1

description:
Library name: Tak-1_3hUV_1
Column name in norm_counts_All_samples.txt: Tak-1_3h_1


title: Tak-1_0hUV_3

description:
Library name: Tak-1_0hUV_3
Column name in norm_counts_All_samples.txt: Tak-1_0h_3


title: Homo_clone2_day6

description: Library name: Sample 25


title: heptanone-2

description: Library name: heptanone-2


title: heptanone-1

description: Library name: heptanone-1


title: Homo_clone1_day30

description: Library name: Sample 24


title: Mpspa_3h_3

description:
Library name: Mpspa_3h_3
Column name in norm_counts_All_samples.txt: Mpspa_3h_3

growth_protocol: Wild type Tak-1, Mpuvr8, Mprup, Mpcop1 and Mpspa mutants gemmalings were grown for 7 days in 50 μmol m-2 s-1 white light.


title: Tak-1_0hUV_1

description:
Library name: Tak-1_0hUV_1
Column name in norm_counts_All_samples.txt: Tak-1_0h_1


title: Mpspa_3h_2

description:
Library name: Mpspa_3h_2
Column name in norm_counts_All_samples.txt: Mpspa_3h_2


title: heptanoic_acid-1

description: Library name: heptanoic_acid-1


title: Homo_clone1_day18

description: Library name: Sample 23


title: Homo_clone1_day6

description: Library name: Sample 21


title: Mpspa_3h_1

description:
Library name: Mpspa_3h_1
Column name in norm_counts_All_samples.txt: Mpspa_3h_1


title: Homo_clone1_day12

description: Library name: Sample 22


title: Mpspa_0h_3

description:
Library name: Mpspa_0h_3
Column name in norm_counts_All_samples.txt: Mpspa_0h_3


title: Mpspa_0h_1

description:
Library name: Mpspa_0h_1
Column name in norm_counts_All_samples.txt: Mpspa_0h_1


title: heptanal-2

description: Library name: heptanal-2


title: Mpspa_0h_2

description:
Library name: Mpspa_0h_2
Column name in norm_counts_All_samples.txt: Mpspa_0h_2


title: heptanal-1

description: Library name: heptanal-1


title: heptanoic_acid-2

description: Library name: heptanoic_acid-2


title: Mpcop1_3h_2

description:
Library name: Mpcop1_3h_2
Column name in norm_counts_All_samples.txt: Mpcop1_3h_2


title: Mpcop1_3h_3

description:
Library name: Mpcop1_3h_3
Column name in norm_counts_All_samples.txt: Mpcop1_3h_3


title: Mpcop1_3h_1

description:
Library name: Mpcop1_3h_1
Column name in norm_counts_All_samples.txt: Mpcop1_3h_1


title: Het_clone3_day30

description: Library name: Sample 20


title: Mpcop1_0h_3

description:
Library name: Mpcop1_0h_3
Column name in norm_counts_All_samples.txt: Mpcop1_0h_3


title: ethyl_tiglate_6

description: Library name: ethyl_tiglate_6


title: Het_clone3_day12

description: Library name: Sample 18


title: Het_clone3_day18

description: Library name: Sample 19


title: ethyl_tiglate_5

description: Library name: ethyl_tiglate_5


title: Mprup_3h_3

description:
Library name: Mprup_3h_3
Column name in norm_counts_All_samples.txt: Mprup_3h_3


title: Het_clone3_day6

description: Library name: Sample 17


title: Mprup_3h_1

description:
Library name: Mprup_3h_1
Column name in norm_counts_All_samples.txt: Mprup_3h_1


title: Mprup_3h_2

description:
Library name: Mprup_3h_2
Column name in norm_counts_All_samples.txt: Mprup_3h_2


title: Tak-1_3hUV_3

description:
Library name: Tak-1_3hUV_3
Column name in norm_counts_All_samples.txt: Tak-1_3h_3


title: ethyl_tiglate_2

description: Library name: ethyl_tiglate_2


title: Het_clone2_day18

description: Library name: Sample 15


title: Mprup_0h_2

description:
Library name: Mprup_0h_2
Column name in norm_counts_All_samples.txt: Mprup_0h_2


title: Mprup_0h_3

description:
Library name: Mprup_0h_3
Column name in norm_counts_All_samples.txt: Mprup_0h_3


title: ethyl_tiglate_3

description: Library name: ethyl_tiglate_3


title: Mpcop1_0h_1

description:
Library name: Mpcop1_0h_1
Column name in norm_counts_All_samples.txt: Mpcop1_0h_1


title: ethyl_tiglate_1

description: Library name: ethyl_tiglate_1


title: Het_clone2_day12

description: Library name: Sample 14


title: ethyl_tiglate_4

description: Library name: ethyl_tiglate_4


title: Mprup_0h_1

description:
Library name: Mprup_0h_1
Column name in norm_counts_All_samples.txt: Mprup_0h_1


title: ethyl_butyrate_6

description: Library name: ethyl_butyrate_6


title: Mpuvr8_3h_3

description:
Library name: Mpuvr8_3h_3
Column name in norm_counts_All_samples.txt: Mpuvr8_3h_3


title: Mpuvr8_0h_3

description:
Library name: Mpuvr8_0h_3
Column name in norm_counts_All_samples.txt: Mpuvr8_0h_3


title: Mpcop1_0h_2

description:
Library name: Mpcop1_0h_2
Column name in norm_counts_All_samples.txt: Mpcop1_0h_2


title: Mpuvr8_3h_2

description:
Library name: Mpuvr8_3h_2
Column name in norm_counts_All_samples.txt: Mpuvr8_3h_2


title: Het_clone2_day30

description: Library name: Sample 16


title: Mpuvr8_0h_2

description:
Library name: Mpuvr8_0h_2
Column name in norm_counts_All_samples.txt: Mpuvr8_0h_2


title: Het_clone1_day30

description: Library name: Sample 12


title: Mpuvr8_0h_1

description:
Library name: Mpuvr8_0h_1
Column name in norm_counts_All_samples.txt: Mpuvr8_0h_1


title: Mpuvr8_3h_1

description:
Library name: Mpuvr8_3h_1
Column name in norm_counts_All_samples.txt: Mpuvr8_3h_1


title: Tak-1_3h_3

description:
Library name: Tak-1_3h_3
Column name in norm_counts_All_samples.txt: Tak-1_3h_3


title: Het_clone2_day6

description: Library name: Sample 13


title: ethyl_butyrate_4

description: Library name: ethyl_butyrate_4


title: ethyl_butyrate_5

description: Library name: ethyl_butyrate_5


title: Tak-1_3h_1

description:
Library name: Tak-1_3h_1
Column name in norm_counts_All_samples.txt: Tak-1_3h_1


title: Tak-1_3h_2

description:
Library name: Tak-1_3h_2
Column name in norm_counts_All_samples.txt: Tak-1_3h_2


title: Het_clone1_day18

description: Library name: Sample 11


title: Tak-1_0h_3

description:
Library name: Tak-1_0h_3
Column name in norm_counts_All_samples.txt: Tak-1_0h_3


title: Het_clone1_day12

description: Library name: Sample 10


title: ethyl_butyrate_3

description: Library name: ethyl_butyrate_3


title: Tak-1_0h_1

description:
Library name: Tak-1_0h_1
Column name in norm_counts_All_samples.txt: Tak-1_0h_1


title: Tak-1_0h_2

description:
Library name: Tak-1_0h_2
Column name in norm_counts_All_samples.txt: Tak-1_0h_2


title: ethyl_butyrate_2

description: Library name: ethyl_butyrate_2


title: WT_day30

description: Library name: Sample 8


title: ethyl_butyrate_1

description: Library name: ethyl_butyrate_1


title: Het_clone1_day6

description: Library name: Sample 9


title: delta ORF8 mutant_replicate 2

first: Stephen

middle: Joseph

last: Ross

state: Massachusetts

address: 72 E Concord St

institute: Boston University School of Medicine

description: Library name: Sample 12

data_processing:
FASTQ files obtained from BU, YCGA, or Sequence Read Archive (SRA) available datasets (see table below) were trimmed for Illumina adaptor content using Cutadapt. Trimmed FASTQ files were mapped to the MHV-GP33-GFP [15] or SARS-CoV-2 genome (MN985325) using Hisat2 v2.2.1. Once mapped, .sam and .bam files were processed using samtools. Junction reads were quantified using regtools (-junctions extract) with sorted and indexed .bam files. The resulting .bed files were used to obtain raw chimeric read counts. Reads were normalized by total chimeric reads. Statistical analyses were performed using GraphPad Prism v10.
Assembly: MN985325.1

organism: Chlorocebus aethiops

source_name: Cell line

growth_protocol: L929 cells (mouse connective tissue; ATCC CCL-1) and 17CL-1 cells (mouse fibroblasts; kindly provided by Dr. V. Thiel, Institution of Virology and Immunology, Bern, Switzerland) were maintained in Eagle’s Minimum Essential Medium (EMEM; Corning, NY, USA) supplemented with 10% fetal bovine serum (FBS; R&D Systems, Minneapolis, MN, USA), 2 mM L-glutamine (Thermo Fisher Scientific, Waltham, MA, USA), and either 100 U/mL penicillin-streptomycin (Thermo Fisher Scientific, Waltham, MA, USA) or 100 μg/mL Primocin (Invivogen, San Diego, CA, USA). African green monkey kidney epithelial cells (Vero E6, ATCC CRL-1586) were maintained in Dulbecco’s modified Eagle medium (DMEM, Corning, NY, USA) supplemented with 5% FBS (VWR) and 1% Penicillin-Streptomycin-Glutamine (PSG, Corning, NY, USA). Cells were grown at 37°C and 5% CO2.

extract_protocol:
Total cellular RNA was extracted via TRIzol purification for analysis (SARS-CoV-2).
300 ng to 1 µg of total cellular RNA from rMHV-infected L929 cells or Vero E6 cells infected with rSARS-CoV-2 WT, rSARS-CoV-2 DORF8, rSARS-CoV-2 DORF7a, or rSARS-CoV-2 ORF8 DG was used as a template for reverse transcription and (-) sgRNA library generation using the QuantSeq-Flex kit (Lexogen Inc., Greenland, NH, USA). Libraries were created according to the manufacturer’s instructions. Briefly, primers (see below) which bind to nucleotides 26 to 48 of the SARS-CoV-2 or nucleotides 35 to 54 of the rMHV (-) sgRNA 3′ end leader regions, respectively, were used for first strand synthesis. The template RNA was degraded prior to second strand synthesis using reagents provided in the kit. Libraries were amplified via PCR using QuantSeq-Flex kit reagents. Libraries at a final concentration of 1-2 ng DNA/μL were sent to the Yale Center for Genomic Analysis (YCGA) for sequencing (SARS-CoV-2). 10 μg of total RNA isolated from rMHV-infected cells was treated with DNase I (NEB, Ipswich, MA) according to the manufacturer’s instructions. Total RNA was isolated from the DNase I reaction via acid phenol:chloroform extraction and isopropanol precipitation. Briefly, equal parts of acid phenol and chloroform were added to the DNase I reaction. Tubes were placed on ice and centrifuged at ~12,000 x g at 4°C in a table-top centrifuge. The aqueous phase was transferred to a new tube and precipitated with 40 μL 3 M sodium acetate, 12 μL glycerol, and 1 mL of 100% isopropanol for 1 hour at -20°C. Tubes were centrifuged for 10 minutes at ~20,000 x g. The pellets were washed with 70% ethanol and resuspended in 20 μL of nuclease free H2O. RNA was incubated at 55°C for 15 minutes for homogenization. 1 µg of DNase I treated RNA was spiked with 50 ng of yeast RNA. Samples were submitted to Boston University (BU) Sequencing Core for poly(A) selection, library preparation, and sequencing (MHV).

treatment_protocol: The rSARS-CoV-2 WT and mutant viruses used in this study were generated using the bacterial artificial chromosome (BAC)-based reverse genetic system [16]. The rSARS-CoV-2 WT sequence is based on the SARS-CoV-2 Washington strain (WA1, GenBank: MN985325.1). For the mutant rSARS-CoV-2, mutations were introduced into the intermediate plasmid (pUC57-F1) using site-directed mutagenesis (SDM). The modified F1 fragment was then excised via BsmBI digestion and used to replace the corresponding region in the BAC backbone, following the previously described protocol [17]. The mutant rSARS-CoV-2 was recovered by transfection of Vero E6 cells with the resultant BAC as described previously [17].

value: Epithelial

value: ORF8 deletion


title: WT_day18

description: Library name: Sample 7


title: WT_day12

description: Library name: Sample 6


title: ethyl_acetate-8

description: Library name: ethyl_acetate-8


title: ethyl_acetate-6

description: Library name: ethyl_acetate-6


title: delta ORF8 mutant_replicate 1

description: Library name: Sample 11


title: Bactrocera oleae, Bulbs, sample B2

city: Heraklion

first: John

last: Vontas

address: Nik. Plastira 100

country: Greece

institute: IMBB-FORTH

description: Library name: EB2

data_processing:
Sequence reads were trimmed for adapter sequences/low- quality sequences using fastp
Removed rRNA fragments from the transcriptomic data using SortMeRNA
Sequence reads were mapped to GCF_042242935.1 B. oleae genome using HISAT2 (default parameters except for a modified alignment score cutoff : --score-min L,0,-0.5)
Read count was performed using HTSeq-count using the default settings
Assembly: GCF_042242935.1
Supplementary files format and content: Each count file contains gene name in the first column and counts in the second column. Count files are tab-delimited.

organism: Bactrocera oleae

source_name: Esophageal bulb

extract_protocol:
RNA was extracted using TRIzol™ Reagent( Invitrogen™ ), according to manufacturer's instructions
Libraries were prepared using the TruSeq Stranded Total RNA Ribo-Zero Plus kit.

value: Esophageal bulb

value: female

value: WT

value: untreated

tag: batch


title: Bactrocera oleae, Bulbs, sample B3

description: Library name: EB3


title: Muscle, HSV-1 infection with vehicle control, rep3

city: Guangzhou

first: Shen

last: Weishan

state: Guangdong

address: 58 Zhongshan 2nd Road

department: cirtical care medicine

country: China

institute: The First Affiliated Hospital, Sun Yat-sen University (FAH-SYSU)

description: Library name: HSV1-infection-DMSO_group-3

data_processing:
scRNA-seq data analysis was performed by NovelBio Co.,Ltd. with NovelBrain Cloud Analysis Platform. We applied fastp with default parameter filtering the adaptor sequence and removed the low-quality reads to achieve the clean data. To quantify the gene expression of the single-cell data, we used STARsolo (version 2.7.11b) along with mouse genome mm10 (ensembl annotation version 100).
Assembly: mm10
Supplementary files format and content: 10x Genomics Cell Ranger standard output (Matrix Market format). Content: The dataset includes compressed sparse matrices (matrix.mtx.gz) , feature annotation (features.tsv.gz) and cell barcode lists (barcodes.tsv.gz).

source_name: brain

extract_protocol:
Single-cell RNA-seq experiment was performed by experimental personnel in the laboratory of NovelBio Co.,Ltd. The tissues were surgically removed and kept in MACS Tissue Storage Solution (Miltenyi Biotec) until processing. The tissue samples were processed as described below. Briefly, samples were first washed with phosphate-buffered saline (PBS) containing 0.5% bovine serum albumin (BSA), minced into small pieces (approximately 1mm3) on ice and enzymatically digested with 20 U/mL papain (Worthington) and 30 U/mL DNase I (Worthington) for 10 min at 37 ℃, with agitation (100 r/min). After digestion, samples were sieved through a 70 µm cell strainer, and centrifuged at 300g for 5 min. After the supernatant was removed, the pelleted cells were suspended in red blood cell lysis buffer (Miltenyi Biotec) to lyse red blood cells. After washing with PBS containing 0.5% BSA, the cell pellets were re-suspended in PBS containing 0.5% BSA and re-filtered through a 40 µm cell strainer. Dissociated single cells were then stained for viability assessment using Calcein-AM (Thermo Fisher Scientific) and Draq7 (BD Biosciences).
The NovelCyto Single-Cell Analysis System (NovelBio Co., Ltd, China) was employed to capture transcriptome data by first distributing a single-cell suspension randomly across over 100,000 microwells through a limited dilution method, followed by the addition of oligonucleotide barcoded beads until saturation was achieved, ensuring that each bead paired with a cell in a microwell. After cells were lyzed in the microwells, mRNA molecules hybridized with the barcoded capture oligos on the beads. These beads were then gathered into a single tube for reverse transcription and ExoI digestion. During cDNA synthesis, each cDNA molecule was tagged at the 5’ end (corresponding to the 3’ end of the mRNA transcript) with a unique molecular identifier (UMI) and a cell barcode, which was used as cell origin. The whole transcriptome library was constructed with the NovelCyto single-cell whole-transcriptome amplification (WTA) workflow, including random priming and extension, amplification PCR, and WTA library index PCR. The libraries were quantified with a High Sensitivity DNA chip (Agilent) on a Bioanalyzer 4200 and a Qubit High Sensitivity DNA assay (Thermo Fisher Scientific). All libraries were sequenced by DNBSEQ-T7 Sequencer (MGI, Shenzhen, China) on a 150 bp paired-end run.

value: brain

value: wild-type

value: HSV-1 infection with vehicle control


title: ethyl_acetate-7

description: Library name: ethyl_acetate-7


title: WT_day6

description: Library name: Sample 5


title: Spatial_transcriptomics_day21_spleen2

city: Melbourne

first: Oliver

middle: Philip

last: Skinner

state: VIC

address: 792 Elizabeth Street

department: Microbiology and Immunology

country: Australia

institute: Peter Doherty Institute, University of Melbourne

description:
Library name: ST_Day21_Spleen2
STOmics (BGI)

data_processing:
For experiment 3, the transcriptome of splenic B cells was aligned using Cell Ranger 9.1.0 (10X Genomics) against mouse genome GRCm39-2024-A (10X Genomics). Hashtag demultiplexing and pre-processing of the data was performed using R version 4.3.1 and Seurat version 4. For spatial transcriptomics, sequenced data was processed following STOmics Stereo-seq Analysis Workflow (SAW pipeline).
Assembly: mm10
Supplementary files format and content: experiment3_contig_annotations.csv file of BCR contig annotations for Experiment 3. experiment3.RDS is Seurat object of demultiplexed data for experiment 3 and Spleen_stomics1.rds and Spleen_stomics2.RDS are Seurat objects of bin20 spatial transcriptomics datasets. experiment3_feature_hto.csv file of Experiment 3 detailing HTO's in each sample. C04278C6.barcodeToPos.h5 provides info on spatial barcodes for Spleen 1. C04278A3.barcodeToPos.h5 provides info on spatial barcodes for Spleen 2. exp1_activatedBcells.RDS is the activated B cell reclustered Seurat object from Experiment 1. exp2_ASCs.RDS is the ASC reclustered Seurat object from Experiment 2. exp2_GC_Bcells.RDS is the GC B cell reclustered Seurat object from Experiment 2.
Library strategy: Spatial Transcriptomics

source_name: Spleen

extract_protocol:
For Experiment 3, spleens were harvested from mice and homogenised through 70µM cell strainers. RBCs were lysed using Pharm Lyse (BD) for 3 minutes at room temperature and then single cell suspensions washed twice in 1x PBS. Samples were then incubated with Fc receptor-blocking antibodies (BD) for 20 minutes on ice, followed by incubation with titrated monoclonal fluorescently conjugated antibodies. A single representative mouse spleen was chosen for sorting and sequencing. For superloading purposes, a single mouse spleen was split into 6 wells and incubated with separate TotalSeq-C (BioLegend) mouse hashtags for 20 minutes on ice. Cells were washed twice and resuspended with propidium iodide (1:500 dilution) in PBS 2% BSA. Hashtagged samples were pooled together. Live, CD19+, B220int-hi were sorted into either CD138+ IgD- ASCs or CD38- Fas+ GC B cells using a FACS Aria III (BD) at a 1:1 ratio. A small number of IgDhi naive cells were spiked in. For stereo-seqv.12 spatial transcriptomics, PcAS infected spleens were isolated from 21 dpi mice and fresh frozen in liquid nitrogen, embedded in Tissue-Tek® O.C.T Compound (Sakura) and stored at -80ºC. Stereo-seqv1.2 (BGI) was performed as per manufacturer’s instructions and two independent mouse spleens. Briefly, once appropriate red and white pulp regions were located within the spleen, a 10µM cryosection was mounted onto a spatially barcoded 1x1cm chip. A serial cryosection was collected to confirm spleen morphology via H&E staining. Spleen sections on chips were fixed with 4% PFA (BioScientific) followed by DAPI (Thermo Fisher Scientific) staining for 2 minutes. Chips were imaged using an Axioscan 7 microscope (Zeiss). Following imaging, tissue permeabilisation was conducted for 8 minutes as determined by preliminary permeabilisation tests.
For Experiment 3 - After sorting, cells were loaded onto the chromium controller and using the Chromium GEM-X Single Cell 5' Kits v3 (Catalogue #1000695;10X Genomics), cDNA-sequencing libraries were prepared as per manufacturer's instructions. For spatial transcriptomics, libraries were prepped using the Stereoseqv1.2 workflow.

treatment_protocol: Plasmodium infection with 1x10^5 infected RBCs (Plasmodium chabaudi chabaudi AS strain - PcAS)

value: Spleen

tag: age

value: 6-12 weeks

value: Plasmodium infection


title: Muscle, no HSV-1 infection as healthy control

description: Library name: Noninfection-control

value: no HSV-1 infection as healthy control


title: ethyl_acetate-5

description: Library name: ethyl_acetate-5

value: male


title: Muscle, HSV-1 infection with vehicle control, rep2

description: Library name: HSV1-infection-DMSO_group-2


title: Parental_day30

description: Library name: Sample 4

value: cultured organoid


title: Spatial_transcriptomics_day21_spleen1

description:
Library name: ST_Day21_Spleen1
STOmics (BGI)


title: ethyl_acetate-4

description: Library name: ethyl_acetate-4

value: whole olfactory mucosa


title: delta ORF7a mutant_replicate 2

description: Library name: Sample 10

value: ORF7a deletion


title: Muscle, HSV-1 infection with vehicle control, rep1

description: Library name: HSV1-infection-DMSO_group-1


title: Muscle, HSV-1 infection with CFZ treatment, rep3

description: Library name: HSV1-infection-CFZ_group-3

value: HSV-1 infection with CFZ treatment


title: Parental_day12

description: Library name: Sample 2

value: Parental cells


title: ethyl_acetate-2

description: Library name: ethyl_acetate-2


title: delta ORF7a mutant_replicate 1

description: Library name: Sample 9

value: Epithelial


title: Parental_day18

description: Library name: Sample 3


title: SARS-CoV-2 Wiltype replicate 7

description: Library name: Sample 7


title: Muscle, HSV-1 infection with CFZ treatment, rep2

description: Library name: HSV1-infection-CFZ_group-2


title: SARS-CoV-2 Wiltype replicate 8

description: Library name: Sample 8


title: Muscle, HSV-1 infection with CFZ treatment, rep1

description: Library name: HSV1-infection-CFZ_group-1


title: ethyl_acetate-3

description: Library name: ethyl_acetate-3


title: SARS-CoV-2 Wiltype replicate 6

description: Library name: Sample 6


title: ethyl_acetate-1

description: Library name: ethyl_acetate-1


title: envB-2w-2

description: Library name: envB-2w-2


title: Parental_day6

description: Library name: Sample 1


title: C06128C3

description: Library name: C06128C3

data_processing:
Two samples were pooled per sequencing run, and the resulting libraries were sequenced on DNBSEQ-T7 flowcells in the PE75 (50+100) configuration. Demultiplexed fastq files were aligned to the transcriptome via the SAW pipeline (SAW count and SAW realign), and the resulting gene counts and decoded positions were used 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, processed with SAW makeRef
Supplementary files format and content: <sample_name>.tissue.gef Stereo-seq tissue gene expression file (GEF) in hdf5 format, which summarizes the gene expression information of the tissue coverage region, binned at various spatial resolutions (bin1, bin10, bin100, etc).
Library strategy: Spatial Transcriptomics

extract_protocol:
10 μm coronal sections from fresh frozen MOE samples (from young 4-5 week mice) were sectioned onto 1 mm2 Stereo-seq Chip T Slides, dried at 37°C for 5 minutes and methanol-fixed for 30 minutes at -20°C. The cells were stained with Qubit ssDNA reagent, and the slide was then rapidly imaged on an Olympus VS200 slide scanner with a 10x objective.
Stereo-seq was performed using the STOmics Stereo-seq Transcriptomics T v1.3 kits following the manufacturer’s user guide (STUM-TT001). Following imaging, slides were permeabilized at 37°C for 12– 15 minutes, and the captured RNA was reverse transcribed for 2 hours at 45°C. The resulting cDNA was released at 55°C for 10 minutes and then amplified via PCR and size-selected with SPRIselect beads. 100ng cDNA was used for each sample and sequencing libraries were prepared according to the manufacturer’s user guide (STUM-LP002), using an equimolar mix of 4 index barcodes per sample.


title: Atpif4_24_100uE_2

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: sample35

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: Arabidopsis thaliana

source_name: 7d seedlings

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: 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: Atpif4_24_100uE_1

description: Library name: sample34


title: envB-2w-1

description: Library name: envB-2w-1


title: INO6A

city: WuHan

first: XiaoTing

last: Wu

address: Luojiashan Street

institute: Wuhan University

library_source: genomic

data_processing:
1. Filter adapter: if the sequencing read matches 25.0% or more of the adapter sequence (maximum 2 base mismatches are allowed), remove the entire read; 2. Filter read length: if the length of the sequencing read is less than 150 bp, discard the entire read; 3. Remove N: if the N content in the sequencing read accounts for 0.1% or more of the entire read, discard the entire read; 4. Remove polyX: if the length of polyX (X can be A, T, G or C) in the sequencing read exceeds 50bp, discard the entire read; 5. Filter low-quality data: if the bases with a quality value of less than 10 in the sequencing read account for 50.0% or more of the entire read, discard the entire read; 6. Obtain Clean reads: the output read quality value system is set to Phred+33.
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: CT3.RPKM.bw INO3.RPKM.bw

molecule: genomic DNA

source_name: liver

extract_protocol:
mice liver tissue suspended 1.0 mL lysis buffer、100 μL protease K（20mg/mL）、100 μL SDS（20%）to 2.0mL centrifuge tube，incubate at 56℃. Transfer 50-100 mg tissue with scalpel blade to the prewarmed centrifuge tube. Incubate at 56℃ for 1-2 h，centrifuge at 12,000×g for 10min in room temperature. Transfer the supernatant toa new 2.0 mL centrifuge tube, add equal volume of Phenol/chloroform/isoamyl alcohol (25:24:1), mix thoroughly by inverting vigorously. Centrifuge at 12,000×g for 10 min in room temperature. Transfer the supernatant to a new 1.5 mL centrifuge tube, taking care not to transfer the intermediate protein layer, add 2/3 of the supernatant volume of isopropanol and 100 μl of sodium acetate, mix well by gently inverting. Transfer to -20°C for 2 hours. Centrifuge at 18213×g for 15 minutes at room temperature and remove the supernatant. Add 1 mL 75% ethanol and wash the precipitation by pipetting. Centrifuge at 18213×g for 3 minutes in room temperature and remove the supernatant. Air dry the precipitation for 3-5 min. Add 20-200 μl TE buffer to resolve. After sample QC, genomic DNA fragment, fragments selection, end Repair, add A and adaptor ligation, PCR, library QC, Circularization, single-stranded circle DNA molecules are replicated via rolling cycle amplification, and a DNA nanoball (DNB) which contain multiple copies of DNA is generated. Sufficient quality DNBs are then loaded into patterned nanoarrays using high-intensity DNA nanochip technique and sequenced through combinatorial Probe-Anchor Synthesis (cPAS).
1. DNA fragmentation 2. Size selection 3. End repair and "A" tailing 4. Adapter ligation 5. Product size selection 6. PCR reaction 7. Library QC
Raw data with adapter sequences or low-quality sequences was filtered. We first went through a series of data processing to remove contamination and obtain valid data. This step was completed by SOAPnuke software developed by BGI.

value: liver


title: Atpif4_24_100uE_3

description: Library name: sample36


title: env2-DPG30m-2

description: Library name: env2-DPG30m-2


title: Atpif4_24_10uE_3

description: Library name: sample33

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: SARS-CoV-2 Wiltype replicate 5

description: Library name: Sample 5

value: WT


title: SARS-CoV-2 Wiltype replicate 4

description: Library name: Sample 4


title: CT6A


title: C06112G5

description: Library name: C06112G5


title: SARS-CoV-2 Wiltype replicate 3

description: Library name: Sample 3


title: env2-DPG30m-1

description: Library name: env2-DPG30m-1


title: SARS-CoV-2 Wiltype replicate 2

description: Library name: Sample 2


title: Atpif4_24_10uE_2

description: Library name: sample32


title: env2-ACE10p-2

description: Library name: env2-ACE10p-2


title: Ino-3

data_processing:
Bowtie2
RSEM
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: xlsx

extract_protocol:
Trizol extract total tissue RNA
total RNA used to sequencing, after data filtering and quantaty analysis, library was constructed.

value: inosine intraperitoneal injection


title: Ino-2


title: SARS-CoV-2 Wiltype replicate 1

description: Library name: Sample 1


title: Mouse 19, Tumor 2, Time separated

city: Odense M

first: Sofie

last: Traynor

address: Fioniavej 36

country: Denmark

institute: University of Southern Denmark

description: Library name: Mouse 19, Tumor 2, Time separated

data_processing:
TCR reads were pre-processed using the Cogent NGS Immune Profiler Software v2.0 (Takara) where data pre-processing, UMI based analysis and clonotype calling were performed, following manufacturer's instructions.
Assembly: Curated mouse V(D)J germline reference (Ig/TCR loci) prepackaged inside Cogent NGS Immune Profiler v2.0
Supplementary files format and content: CSV files containing organism_id,sample_processing_id,read_count,fraction,clonal_sequence,clonal_sequence_quality,cdr3_min_quality,cdr3_sequence,cdr3_amino_acid_sequence,clonal_type,frame_shift,stop_codon,junction_length_aa,v_segment,all_v_hits,d_segment,all_d_hits,j_segment,all_j_hits,c_segment,all_c_hits
Library strategy: TCR-Seq

source_name: Colon cancer

growth_protocol: CT26 cells were maintained in RPMI 1640 medium  supple- mented with 10% FBS, 4.5 g/L Glucose Solution, 1 nM Sodium Pyruvate, 10 nM HEPES Buffer Solution, 0.1 nM non-essential amino-acids and 0.5 mg/mL G418 Sulfate (Corning). The cellswere kept in humidified atmosphere with 5% CO2 at 37 °C.

extract_protocol:
Total RNA was purified from whole tumors using TriReagent and EconoSpin Columns. Tumors were homogenized by adding 2.8 mm Zirconium beads to the tissue, and homogenization was carried out using a Precellus Homogenizer run at 3 x 15 seconds at 6500 rpm.
TCRa and TCRb receptor libraries covering the complemen-tarity determining region 3 (CDR3) were prepared using SMART-Seq Mouse TCR (with UMIs) (Takara, 634815) and SMARTer RNA Unique Dual Index Kit (Takara, 634451) following manufacturer’s instructions.

treatment_protocol: Female babl/c mice wre incolulated with 0.5*10^6 CT26 cells subcutanously in both flanks in ECM gel and bilateral tumors were formed. The protocols are described below for the different groups:                                                                                Time-matched group: Mice were inoculated as described. After bilateral tumors had formed, both tumors were simultaneously harvested after euthanasia 13 days after inoculation. Tumors were snap-frozen in liquid nitrogen and stored at -80 °C before further processing. Time-separated group: Mice were inoculated as described. When bilateral tumors had reached a size of approximately 4–5 mm in diameter , mice were anesthetized, and one tumor was surgically excised (referred to as the“early tumor”). Wounds were closed with sterilized clips, and analgesic treatment were administered. The remaining tumor was left to grow and was harvested 11 days after the surgery after euthanasia (referred to as the“late tumor”). Tumors were snap-frozen in liquid nitrogen and stored at -80 °C before further processing. Three mice were included in this group. Decitabine treatment groups: Mice were inoculated and one tumor surgically removed as previously described (referred to as the“early tumor”). Three days after removal of one of the tumors, mice were randomized into two treatment groups, that were treated with 0.5 mg/kg or 2 mg/kg decitabine (DAC) administrered intraperitoneally for five consecutive days. Four days after the last treatment, the remaining tumor was harvested after euthanasia (referred to as the“late tumor”). Tumors were snap-frozen in liquid nitrogen and stored at -80 °C before further processing.

value: Colon cancer

value: Colon cancer cells


title: Atpif4_24_10uE_1

description: Library name: sample31


title: Atcol0_24_100uE_3

description: Library name: sample30


title: Ino-1


title: env2-ACE0_1p-2

description: Library name: env2-ACE0_1p-2


title: Mouse 19, Tumor 1, Time separated

description: Library name: Mouse 19, Tumor 1, Time separated


title: Atcol0_24_100uE_2

description: Library name: sample29


title: Atcol0_24_100uE_1

description: Library name: sample28


title: Atcol0_24_10uE_3

description: Library name: sample27


title: env2-ACE10p-1

description: Library name: env2-ACE10p-1


title: Mouse 17, Tumor 2, Time separated

description: Library name: Mouse 17, Tumor 2, Time separated


title: Ctrl-1

value: control


title: env2-ACE0_1p-1

description: Library name: env2-ACE0_1p-1


title: Atcol0_24_10uE_2

description: Library name: sample26


title: Ctrl-2


title: Mouse 17, Tumor 1, Time separated

description: Library name: Mouse 17, Tumor 1, Time separated


title: env1-DPG30m-1

description: Library name: env1-DPG30m-1


title: env1-DPG30m-2

description: Library name: env1-DPG30m-2


title: Ctrl-3


title: Atcol0_24_10uE_1

description: Library name: sample25


title: Mphy5_24_100uE_3

description: Library name: sample96

source_name: thallus 10d after germination

value: thallus 10d after germination

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


title: env1-ACE10p-2

description: Library name: env1-ACE10p-2

value: male


title: env1-ACE10p-1

description: Library name: env1-ACE10p-1

value: whole olfactory mucosa


title: Mouse 4, Tumor 2, Time separated

description: Library name: Mouse 4, Tumor 2, Time separated


title: Mouse 14, Tumor 2, Time matched

description: Library name: Mouse 14, Tumor 2, Time matched


title: Mphy5_24_100uE_2

description: Library name: sample95


title: Mphy5_24_100uE_1

description: Library name: sample94


title: Mouse 4, Tumor 1, Time separated

description: Library name: Mouse 4, Tumor 1, Time separated


title: Athy5_16_100uE_3

description: Library name: sample24

value: 2d under 20˚C and 100 µmol m-2 s-1 of continuous white light followed by 5d under 16˚C and 100 µmol m-2 s-1 of continuous white light


title: Mouse 14, Tumor 1, Time matched

description: Library name: Mouse 14, Tumor 1, Time matched


title: Athy5_16_100uE_2

description: Library name: sample23


title: Mphy5_24_10uE_3

description: Library name: sample93

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


title: Mphy5_24_10uE_2

description: Library name: sample92


title: Mouse 12, Tumor 2, Time matched

description: Library name: Mouse 12, Tumor 2, Time matched


title: Athy5_16_100uE_1

description: Library name: sample22


title: Athy5_16_10uE_3

description: Library name: sample21

value: 2d under 20˚C and 100 µmol m-2 s-1 of continuous white light followed by 5d under 16˚C and 10 µmol m-2 s-1 of continuous white light


title: cre-2

description: Library name: cre-2

value: female


title: Mouse 12, Tumor 1, Time matched

description: Library name: Mouse 12, Tumor 1, Time matched


title: env1-ACE0_1p-1

description: Library name: env1-ACE0_1p-1


title: cre-1

description: Library name: cre-1


title: Mpphy_24_100uE_3

description: Library name: sample90


title: env1-ACE0_1p-2

description: Library name: env1-ACE0_1p-2


title: Athy5_16_10uE_2

description: Library name: sample20

value: 7d seedlings


title: Athy5_16_10uE_1

description: Library name: sample19


title: cellecta_round7_GFPpos

description: Library name: cellecta_round7_GFPpos


title: Mpphy_24_100uE_2

description: Library name: sample89


title: Mouse 6, Tumor 1, Time matched

description: Library name: Mouse 6, Tumor 1, Time matched


title: Mphy5_24_10uE_1

description: Library name: sample91


title: cellecta_round7_GFPneg

description: Library name: cellecta_round7_GFPneg


title: Mouse 6, Tumor 2, Time matched

description: Library name: Mouse 6, Tumor 2, Time matched


title: Mouse 20, Tumor 1, low dose DAC

description: Library name: Mouse 20, Tumor 1, low dose DAC

value: 0.5 mg/kg decitabine


title: Mpphy_24_10uE_3

description: Library name: sample87


title: Atphyb_16_100uE_3

description: Library name: sample18


title: Mouse 11, Tumor 2, low dose DAC

description: Library name: Mouse 11, Tumor 2, low dose DAC


title: cellecta_round6_GFPneg

description: Library name: cellecta_round6_GFPneg


title: cellecta_round6_GFPpos

description: Library name: cellecta_round6_GFPpos


title: Mpphy_24_100uE_1

description: Library name: sample88


title: Atphyb_16_100uE_2

description: Library name: sample17


title: Mpphy_24_10uE_2

description: Library name: sample86


title: cellecta_round5_GFPpos

description: Library name: cellecta_round5_GFPpos


title: cellecta_round5_GFPneg

description: Library name: cellecta_round5_GFPneg


title: Atphyb_16_100uE_1

description: Library name: sample16


title: Mouse 11, Tumor 1, low dose DAC

description: Library name: Mouse 11, Tumor 1, low dose DAC


title: Atphyb_16_10uE_3

description: Library name: sample15


title: cellecta_round4_GFPpos

description: Library name: cellecta_round4_GFPpos


title: Mpphy_24_10uE_1

description: Library name: sample85


title: Atphyb_16_10uE_2

description: Library name: sample14


title: Atphyb_16_10uE_1

description: Library name: sample13


title: Mouse 3, Tumor 2, low dose DAC

description: Library name: Mouse 3, Tumor 2, low dose DAC


title: Mouse 3, Tumor 1, low dose DAC

description: Library name: Mouse 3, Tumor 1, low dose DAC


title: Mppif_24_100uE_2

description: Library name: sample83


title: cellecta_round4_GFPneg

description: Library name: cellecta_round4_GFPneg


title: Mouse 16, Tumor 2, high dose DAC

description: Library name: Mouse 16, Tumor 2, high dose DAC

value: 2 mg/kg decitabine


title: Mppif_24_100uE_1

description: Library name: sample82


title: Atpif4_16_100uE_3

description: Library name: sample12


title: cellecta_round3_GFPneg

description: Library name: cellecta_round3_GFPneg


title: Mppif_24_10uE_3

description: Library name: sample81


title: Mppif_24_100uE_3

description: Library name: sample84


title: cellecta_round3_GFPpos

description: Library name: cellecta_round3_GFPpos


title: Atpif4_16_100uE_2

description: Library name: sample11


title: Mouse 10, Tumor 1, high dose DAC

description: Library name: Mouse 10, Tumor 1, high dose DAC


title: cellecta-round2-GFPpos

description: Library name: cellecta-round2-GFPpos


title: Atpif4_16_10uE_3

description: Library name: sample9


title: Mouse 10, Tumor 2, high dose DAC

description: Library name: Mouse 10, Tumor 2, high dose DAC


title: Atpif4_16_100uE_1

description: Library name: sample10


title: Mppif_24_10uE_2

description: Library name: sample80


title: cellecta-round2-GFPneg

description: Library name: cellecta-round2-GFPneg


title: Mppif_24_10uE_1

description: Library name: sample79


title: Atpif4_16_10uE_2

description: Library name: sample8


title: Mptak1_24_100uE_3

description: Library name: sample78


title: butyl_acetate-2

description: Library name: butyl_acetate-2


title: Mouse 7, Tumor 2, high dose DAC

description: Library name: Mouse 7, Tumor 2, high dose DAC


title: Mouse 7, Tumor 1, high dose DAC

description: Library name: Mouse 7, Tumor 1, high dose DAC


title: Mouse 16, Tumor 1, high dose DAC

description: Library name: Mouse 16, Tumor 1, high dose DAC


title: Mouse 20, Tumor 2, low dose DAC

description: Library name: Mouse 20, Tumor 2, low dose DAC


title: Atcol0_16_100uE_3

description: Library name: sample6


title: butyl_acetate-1

description: Library name: butyl_acetate-1


title: Exp3, Splenic B cells, Day14, scRNAseq, HTO

description:
Library name: Experiment3_Day14_HTO
10x Genomics

data_processing:
For experiment 3, the transcriptome of splenic B cells was aligned using Cell Ranger 9.1.0 (10X Genomics) against mouse genome GRCm39-2024-A (10X Genomics). Hashtag demultiplexing and pre-processing of the data was performed using R version 4.3.1 and Seurat version 4. For spatial transcriptomics, sequenced data was processed following STOmics Stereo-seq Analysis Workflow (SAW pipeline).
Assembly: mm10
Supplementary files format and content: experiment3_contig_annotations.csv file of BCR contig annotations for Experiment 3. experiment3.RDS is Seurat object of demultiplexed data for experiment 3 and Spleen_stomics1.rds and Spleen_stomics2.RDS are Seurat objects of bin20 spatial transcriptomics datasets. experiment3_feature_hto.csv file of Experiment 3 detailing HTO's in each sample. C04278C6.barcodeToPos.h5 provides info on spatial barcodes for Spleen 1. C04278A3.barcodeToPos.h5 provides info on spatial barcodes for Spleen 2. exp1_activatedBcells.RDS is the activated B cell reclustered Seurat object from Experiment 1. exp2_ASCs.RDS is the ASC reclustered Seurat object from Experiment 2. exp2_GC_Bcells.RDS is the GC B cell reclustered Seurat object from Experiment 2.

value: Spleen

value: 6-12 weeks

value: B cells

value: Plasmodium infection


title: Mptak1_24_100uE_2

description: Library name: sample77


title: Exp3, Splenic B cells, Day14, scRNAseq, BCR

description:
Library name: Experiment3_Day14_VDJ
10x Genomics


title: Mptak1_24_100uE_1

description: Library name: sample76


title: Atcol0_16_100uE_2

description: Library name: sample5


title: Exp3, Splenic B cells, Day14, scRNAseq, mRNA

description:
Library name: Experiment3_Day14_GEX
10x Genomics


title: butanone-4

description: Library name: butanone-4


title: Mptak1_24_10uE_3

description: Library name: sample75


title: butanone-2

description: Library name: butanone-2


title: butanone-3

description: Library name: butanone-3


title: Mptak1_24_10uE_1

description: Library name: sample73


title: Mptak1_24_10uE_2

description: Library name: sample74


title: Atcol0_16_100uE_1

description: Library name: sample4


title: P1Sham(nPAB)7dpsRV13

city: Bonn

first: Mona

last: Malek Mohammadi

address: Venusberg-Campus 1

country: Germany

institute: University Hospital Bonn

description:
Library name: sample 22
Column name in RV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "Sham5"

data_processing:
Data was uploaded into Galaxy Europe
Sequnce reads were trimmed for adapter sequences using "cutadapt" (minimum overlap length: 3)
RNA sequences were mapped to th reference genome using "RNAStar" (parameters: length:60, MAPQ value for unique mappers: 60)
Mapping was quantified using "featureCounts" (parameters: exclude chimeric alignments)
differential expression between "Sham" and "nPAB" groups was analyzed using DeSeq2
Assembly: mm10
Supplementary files format and content: files: LV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular, RV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular content: normalized counts using DeSeq2
Supplementary files format and content: files: LV_nPAB_Sham_7dps_DeSeq2_results.tabular, RV_nPAB_Sham_7dps_DeSeq2_results.tabular content: differential expression of individual genes nPAB vs. Sham groups

source_name: Heart

extract_protocol:
RNA was isolated using the Qiagen Rneasy plus Mini Kit
The library was prepared using the Revelo™ RNA-Seq High Sensitivity library preparation kit following manufacturer's instructions

treatment_protocol: nPAB using 30G needle or sham were performed at P1 and the hearts were harvested 7days after operation

value: Heart

tag: tissue type

value: RV

value: bulk

value: Sham


title: butanone-1

description: Library name: butanone-1

value: male


title: Atcol0_16_10uE_3

description: Library name: sample3


title: P1Sham(nPAB)7dpsLV13

description:
Library name: sample 21
Column name in LV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "Sham5"

value: LV


title: butanoic_acid-4

description: Library name: butanoic_acid-4

value: whole olfactory mucosa


title: P1Sham(nPAB)7dpsRV12

description:
Library name: sample 20
Column name in RV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "Sham4"


title: Mphy5_16_100uE_2

description: Library name: sample71

value: thallus 10d after germination

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


title: butanoic_acid-3

description: Library name: butanoic_acid-3


title: Atcol0_16_10uE_1

description: Library name: sample1

value: 2d under 20˚C and 100 µmol m-2 s-1 of continuous white light followed by 5d under 16˚C and 10 µmol m-2 s-1 of continuous white light


title: butanoic_acid-2

description: Library name: butanoic_acid-2


title: P1Sham(nPAB)7dpsLV12

description:
Library name: sample 19
Column name in LV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "Sham4"


title: Flavo 6d-3

city: Leiden

first: Salma

last: Balazadeh

address: Sylviusweg 72

department: Plant Cluster

country: Netherlands

institute: Leiden University

data_processing:
Reads were trimmed using trimmomatic 0.39 PE with these arguments HEADCROP:11 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were aligned against the reference genome GCF_000001735 using hisat 2 2.2.1
Samtools 1.11 were used to process the alignment sam files into ordered bam files
featureCounts from subread 2.0.1 was used to extract the counts for each sample (arguments:  -t transcript -g gene_id)
Assembly: GCF_000001735
Supplementary files format and content: txt-file DEseq2 normalized counts

source_name: Root

growth_protocol: Arabidopsis seedlings were grown on 1/2 MS plates and grown vertically. Seven days old seedlings were inoculated with Flavobacterium (2µl OD=1) or Mock (100mM MgSO4) at the root tips and roots were harvested at different time points after inoculations.

extract_protocol:
total RNA was extracted via QIAGEN the RNeasy® PlantMini Kit. mRNA molecules were purified from total RNA using oligo(dT)-attached magnetic beads. mRNA molecules were fragmented into small pieces using fragmentation reagent after reactiona certain period in proper temperature
First Strand cDNA Synthesis: Add an appropriate amount of primers to the interrupted sample, mix well, and react at asuitable temperature on a thermal cycler for a certain period of time to open the secondary structureand combine with the primers. Then add the first-strand synthesis reaction system Mix prepared inadvance. Synthesize first-strand cDNA according to the corresponding procedure on the instrument.Second Strand cDNA Synthesis: Prepare a second-strand synthesis reaction system (using dUTP instead of dTTP). React onThermomixer at an appropriate temperature for a certain time to synthesize second-strand cDNA.The reaction product was purified by magnetic beads.End repair & Add ‘A’: Prepare the end repair & add "A" reaction system, react on a thermal cycler for a certain time,under the action of enzymes, repair the sticky ends of the cDNA double-stranded by reverse Adaptor Ligation:  Prepare the linker connection reaction system. React on a thermal cycler at a suitabletemperature for a certain time. Under the action of the enzyme, connect the linker to the A base. The reaction product was purified by magnetic beads.PCR: Prepare the PCR reaction system, digest the U-labeled second-strand template with UDG enzyme and perform PCR amplification. PCR products were purified with XP Beads, and dissolvedin EB solution.Library was validated on the Agilent Technologies 2100 bioanalyzer.
Library was validated on the AgilentTechnologies 2100 bioanalyzer

value: Root

tag: time

value: Flavobacterium


title: Mphy5_16_100uE_3

description: Library name: sample72


title: Atcol0_16_10uE_2

description: Library name: sample2

value: 7d seedlings


title: Mphy5_16_10uE_3

description: Library name: sample69

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


title: P1Sham(nPAB)7dpsRV11

description:
Library name: sample 18
Column name in RV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "Sham3"


title: butanoic_acid-1

description: Library name: butanoic_acid-1


title: P1Sham(nPAB)7dpsLV11

description:
Library name: sample 17
Column name in LV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "Sham3"


title: Mphy5_16_10uE_2

description: Library name: sample68


title: Mphy5_16_100uE_1

description: Library name: sample70


title: Flavo 6d-1

treatment_protocol: Seven days old seedlings were inoculated with Flavobacterium (2µl OD=1) or Mock (100mM MgSO4) at the root tips and roots were harvested at different time points after inoculations.


title: butanal-4

description: Library name: butanal-4


title: Mock 6d-3

value: Mock (MgSO4)


title: butanal-3

description: Library name: butanal-3


title: P1Sham(nPAB)7dpsRV10

description:
Library name: sample 16
Column name in RV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "Sham2"


title: P1Sham(nPAB)7dpsLV10

description:
Library name: sample 15
Column name in LV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "Sham2"


title: Flavo 6d-2


title: Mock 6d-2


title: Mpphy_16_100uE_3

description: Library name: sample66


title: P1Sham(nPAB)7dpsRV9

description:
Library name: sample 14
Column name in RV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "Sham1"


title: Mock 6d-1


title: Mphy5_16_10uE_1

description: Library name: sample67


title: Mpphy_16_100uE_2

description: Library name: sample65


title: butanal-1

description: Library name: butanal-1


title: Flavo 72h-2


title: Flavo 72h-3


title: butanal-2

description: Library name: butanal-2


title: Mpphy_16_100uE_1

description: Library name: sample64


title: P1nPAB30G7dpsRV11

description:
Library name: sample 12
Column name in RV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "nPAB6"

value: nPAB


title: baseline-female-2

description: Library name: baseline-female-2

value: female


title: Mpphy_16_10uE_3

description: Library name: sample63


title: baseline-female-1

description: Library name: baseline-female-1


title: Flavo 72h-1


title: P1nPAB30G7dpsRV10

description:
Library name: sample 10
Column name in RV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "nPAB5"

value: Heart


title: baseline-6

description: Library name: baseline-6


title: Mpphy_16_10uE_1

description: Library name: sample61


title: Mock 72h-3


title: Mpphy_16_10uE_2

description: Library name: sample62


title: baseline-5

description: Library name: baseline-5


title: Mppif_16_100uE_3

description: Library name: sample60


title: P1nPAB30G7dpsLV10

description:
Library name: sample 9
Column name in LV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "nPAB5"


title: P1nPAB30G7dpsLV11

description:
Library name: sample 11
Column name in LV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "nPAB6"


title: Mppif_16_100uE_2

description: Library name: sample59


title: P1nPAB30G7dpsRV8

description:
Library name: sample 8
Column name in RV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "nPAB4"

value: RV


title: Mock 72h-2


title: acetone-4

description: Library name: acetone-4


title: Flavo 48h-3


title: Mock 72h-1


title: Flavo 48h-2


title: Mppif_16_100uE_1

description: Library name: sample58


title: acetone-3

description: Library name: acetone-3


title: P1nPAB30G7dpsRV7

description:
Library name: sample 6
Column name in RV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "nPAB3"

value: bulk


title: Mppif_16_10uE_2

description: Library name: sample56


title: P1nPAB30G7dpsLV7

description:
Library name: sample 5
Column name in LV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "nPAB3"


title: acetone-1

description: Library name: acetone-1


title: Mppif_16_10uE_3

description: Library name: sample57


title: P1nPAB30G7dpsLV8

description:
Library name: sample 7
Column name in LV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "nPAB4"


title: acetic_acid_4

description: Library name: acetic_acid_4


title: P1nPAB30G7dpsRV6

description:
Library name: sample 4
Column name in RV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "nPAB2"


title: Flavo 48h-1


title: Mock 48h-2


title: P1nPAB30G7dpsLV6

description:
Library name: sample 3
Column name in LV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "nPAB2"


title: Mptak1_16_100uE_3

description: Library name: sample54


title: acetic_acid_3

description: Library name: acetic_acid_3


title: acetic_acid_2

description: Library name: acetic_acid_2


title: Mock 48h-3


title: Mppif_16_10uE_1

description: Library name: sample55


title: acetone-2

description: Library name: acetone-2


title: P1nPAB30G7dpsRV5

description:
Library name: sample 2
Column name in RV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "nPAB1"


title: Mock 48h-1


title: Mptak1_16_100uE_2

description: Library name: sample53


title: P1nPAB30G7dpsLV5

description:
Library name: sample 1
Column name in LV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "nPAB1"


title: Flavo 12h-3


title: Flavo 12h-2


title: repression of all three Pcx, Me1 and Me2 (3xKD) in EpiLCs day 2 replicate 3

city: Copenhagen

first: Jan

middle: Jakub

last: Żylicz

address: Blegdamsvej 3B

department: Novo Nordisk Foundation Center for Stem Cell Medicine, reNEW

institute: University of Copenhagen

description: Library name: D2_3KD_wtD_R3

data_processing:
Raw sequencing data were demultiplexed and converted into FASTQ files using Illumina bcl2fastq Conversion Software (v2.20.0.422).
FASTQ files were processed using nf-core/rnaseq v3.14.0 (doi: https://doi.org/10.5281/zenodo.1400710).
In brief, adapters and low-quality reads were removed using Trim Galore (v0.6.7), trimmed reads were mapped to the mouse reference genome (GRCm39, Ensembl release 111) using STAR (v2.7.9a) and transcript expression was quantified with Salmon (v1.10.1).
Transcript-level abundance estimates were imported into R and summarized to gene level using tximport (reading Salmon quant.sf files and tx2gene table, as provided as Supplementary files).
Assembly: GRCm39
Supplementary files format and content: *.quant.sf.tsv: Transcript quantification output file from Salmon, as tab-delimited text file with a single header line.
Supplementary files format and content: tx2gene.tsv: provides the mapping of transcript IDs to gene IDs and symbols

source_name: embryonic

extract_protocol:
RNA was purified using the RNeasy Mini Kit (Qiagen) with a 15min treatment of RNase-Free DNase (Qiagen) at RT.
500 ng of RNA per sample was used for library preparation with the NEBNext rRNA Depletion Kit v2 (New England Biolabs), NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs) and NEBNext Multiplex Oligos for Illumina Dual Index Primers Set 2 (New England Biolabs).

value: embryonic

value: Mouse:ESC E14-dox-CRISPRi Pcx-Me1-Me2 3xKD

value: mouse embryonic epiblast-like cells (EpiLCs day 2 of induction)


title: Mptak1_16_100uE_1

description: Library name: sample52


title: acetic_acid-2

description: Library name: acetic_acid-2

value: whole olfactory mucosa

value: male


title: Mptak1_16_10uE_3

description: Library name: sample51

value: thallus 10d after germination


title: acetic_acid-1

description: Library name: acetic_acid-1


title: Flavo 12h-1


title: Mptak1_16_10uE_2

description: Library name: sample50


title: Tmem63b-flox-2

description: Library name: Tmem63b-flox-2


title: repression of all three Pcx, Me1 and Me2 (3xKD) in EpiLCs day 2 replicate 1

description: Library name: D2_3KD_wtD_R1


title: acetic_acid_1

description: Library name: acetic_acid_1


title: Mptak1_16_10uE_1

description: Library name: sample49


title: mouse HSPCs with Kdm6a WT rep3, batch3

city: Chengdu

first: Yiman

last: Peng

state: Sichuan

address: No.1, Keyuan 4th Road, Gaopeng Avenue, Chengdu, Sichuan, China

department: State Key Laboratory of Biotherapy, West China Hospital, Sihcuan University

institute: Sichuan University

description:
Library name: 3_RNAseq_Kdm6a_WT_rep3
batch3_RNASeq_raw_counts.csv

data_processing:
For RNA-Seq, after removing the adapters, ploy-N, and low-quality reads, clean data were aligned against the reference mouse genome (mm10) using STAR_2.7.10b. Following this, raw counts were normalized and significance scores as well as log2-fold change values were calculated using the DESeq2 (v1.26.0).
Assembly: mm10
Supplementary files format and content: csv files include raw counts and DESeq2 normalized data of RNAseq.

source_name: Bonemarrow

growth_protocol: For Utx KO/WT samples, WBM cells were freshly isolated from Utxf/f and Utxf/f; Mx1-Cre mice, and then HSPCs were sorted with mouse CD117 magnetic microbeads. Primary mouse cells were cultured in BCM medium (50% IMDM+50% DMEM+10% FBS+5% PS+0.34% BME) with 10% Stem Cell Medium (SCM) including 10% FBS, IL3 (10ng/mL; 1:1000), IL6 (10ng/mL; 1:500), and SCF (50ng/mL; 1:1000). For other RNA-Seq samples, mouse cKit+ HSPCs and AML cells were cultured at 37 °C with 7.5% CO2 in BCM medium [45% IMDM + 45% DMEM + 10% FBS + 50 × 10-6 M β-mercaptoethanol + penicillin (100 U mL-1)/streptomycin (0.1 mg mL-1)] supplemented with 10% stem cell medium (SCM) including mIL-3 (10 ng mL-1, Cat# 403-ML; R&D Systems), mIL-6 (10 ng mL-1, Cat# 406-ML; R&D Systems), and mSCF (50 ng mL-1, Cat# 455-MC; R&D Systems)

extract_protocol:
RNA-seq libraries were constructed using an Illumina stranded mRNA sample preparation kits (NEB, E7770) according to the manufacturer's protocol.
RNA-seq libraries were constructed using an Illumina stranded mRNA sample preparation kits (NEB, E7770) according to the manufacturer's protocol.

value: Bonemarrow

value: HSPC

value: Kdm6a WT


title: control (negative/scramble) EpiLCs day 2 replicate 3

description: Library name: D2_Neg_wtD_R3

value: Mouse:ESC E14-dox-CRISPRi Neg

value: mouse embryonic stem cells (ESCs)

value: control (negative/scramble)


title: Tmem63b-flox-1

description: Library name: Tmem63b-flox-1


title: Tmem63b-cKO-2

description: Library name: Tmem63b-cKO-2


title: repression of all three Pcx, Me1 and Me2 (3xKD) in EpiLCs day 2 replicate 2

description: Library name: D2_3KD_wtD_R2


title: Mock 12h-2

value: Root

value: Mock (MgSO4)


title: Mock 12h-1


title: control (negative/scramble) EpiLCs day 2 replicate 2

description: Library name: D2_Neg_wtD_R2


title: P1Sham(nPAB)7dpsLV9

description:
Library name: sample 13
Column name in LV_nPAB_Sham_7dps_DeSeq2_normalizedcounts.tabular: "Sham1"

value: Heart

value: LV

value: Sham


title: mouse HSPCs with Kdm6a WT rep2, batch3

description:
Library name: 3_RNAseq_Kdm6a_WT_rep2
batch3_RNASeq_raw_counts.csv


title: Tmem63b-cKO-1

description: Library name: Tmem63b-cKO-1

value: female


title: mouse HSPCs with Kdm6a WT rep1, batch3

description:
Library name: 3_RNAseq_Kdm6a_WT_rep1
batch3_RNASeq_raw_counts.csv


title: ERF115-SRDX-2

data_processing:
Reads were trimmed using trimmomatic 0.39 PE with these arguments HEADCROP:11 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
Trimmed reads were aligned against the reference genome GCF_000001735 using hisat 2 2.2.1
Samtools 1.11 were used to process the alignment sam files into ordered bam files
featureCounts from subread 2.0.1 was used to extract the counts for each sample (arguments:  -t transcript -g gene_id)
Assembly: GCF_000001735
Supplementary files format and content: Excel file: DEseq2 normalized counts

growth_protocol: Arabidopsis seedlings were grown on 1/2 MS plates. Roots of four days old seedlings were harvested.

value: 35S:ERF115-SRDX (ERF115-SRDX)

value: 4 day old


title: S50G-2

description: Library name: S50G-2

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

value: whole olfactory mucosa


title: Mock 12h-3


title: repression of all three Pcx, Me1 and Me2 (3xKD) in ESCs replicate 3

description: Library name: D0_3KD_wtD_R3

value: embryonic

value: Mouse:ESC E14-dox-CRISPRi Pcx-Me1-Me2 3xKD

value: mouse embryonic epiblast-like cells (EpiLCs day 2 of induction)


title: repression of all three Pcx, Me1 and Me2 (3xKD) in ESCs replicate 2

description: Library name: D0_3KD_wtD_R2


title: ERF115-SRDX-3


title: S50G-1

description: Library name: S50G-1

value: male


title: mouse HSPCs with Kdm6a KO rep3, batch3

description:
Library name: 3_RNAseq_Kdm6a_KO_rep3
batch3_RNASeq_raw_counts.csv

value: Bonemarrow

value: HSPC

value: Kdm6a KO


title: ERF114-OX-3


title: mouse HSPCs with Kdm6a KO rep2, batch3

description:
Library name: 3_RNAseq_Kdm6a_KO_rep2
batch3_RNASeq_raw_counts.csv


title: control (negative/scramble) EpiLCs day 2 replicate 1

description: Library name: D2_Neg_wtD_R1

value: Mouse:ESC E14-dox-CRISPRi Neg

value: mouse embryonic stem cells (ESCs)

value: control (negative/scramble)


title: repression of all three Pcx, Me1 and Me2 (3xKD) in ESCs replicate 1

description: Library name: D0_3KD_wtD_R1


title: mouse HSPCs with Kdm6a KO rep1, batch3

description:
Library name: 3_RNAseq_Kdm6a_KO_rep1
batch3_RNASeq_raw_counts.csv


title: RevOccl-DPG-2L

description: Library name: RevOccl-DPG-2L


title: ERF114-OX-2

value: Root


title: control (negative/scramble) ESCs replicate 3

description: Library name: D0_Neg_wtD_R3


title: control (negative/scramble) ESCs replicate 2

description: Library name: D0_Neg_wtD_R2


title: BCR-Seq, Spleen, MRV-infected, Untreated

city: St. Louis

first: Tarin

last: Bigley

state: MO

address: 1 Children's Pl

department: Pediatrics

institute: Washington University in St. Louis

description:
Library name: MRV_Control_BCR
10x Genomics

data_processing:
Sequences were aligned using CellRanger to the murine and MRV genome. Raw RNAseq and vdj files were processed and utilized to create and rds file. scRNA-Seq data from the 4 different samples were processed, cell cycle corrected, and analyzed in R (v4.4.1) using Seurat (v5.2.1) package. The data was initially normalized using SCTransform followed by quality control which had thresholds set to nFeature_RNA > 500, nCount_RNA > 1000 and percent.mt < 5. Following this, Harmony (v1.2.3) was used to eliminate batch effects followed by dimensionality reduction and unbiased clustering. Cluster annotations were made based on canonical marker gene expressions. Cell-level heatmaps and hierarchical heatmaps were generated using DoHeatmap and pheatmap respectively to confirm the marker gene expression. Cell types of interest were subset followed by dimensionality reduction. scRepertoire (v2.6.2) was primarily used to analyze TCR-Seq data of all 4 samples. The contig data from all the samples were combined and processed into clonal information which was subsequently added to the single-cell data. The integrated clonal data was used for used for downstream analyses.
Assembly: mm10, MRV
Supplementary files format and content: filtered H5, MTX, and TSV ( matrix files and tab separated files)
Library strategy: BCR-Seq

growth_protocol: C57BL/6 mice were maintained under SPF conditions.

extract_protocol:
Spleens were isolated and minced to obtain single cell suspension. Samples were treated with RBC lysis buffer then filterd though a 70um filter. The spleen cells from three separate mice were combined into one sample then counts and analyzed for cell death.
Single-cell 5’ cDNA gene expression libraries were generated using the 10X Genomic Chromium Single-Cell 5’ Library and Gel Bead Kit v1 and 10x Chromium Controller (10x Genomics, Pleasanton, CA) platform for microdroplet-based, single-cell barcoding. Sequencing ws performed on the NovaSeq Sequencing System.

treatment_protocol: Mice were mock or MRV infected on day-of-life 0, then from weeks 8-13 treated with vehicle control or R848.

value: Spleen


title: ERF114-OX-1


title: control (negative/scramble) ESCs replicate 1

description: Library name: D0_Neg_wtD_R1


title: BCR-Seq, Spleen, MRV-infected, R848-Treated

description:
Library name: MRV_R848_BCR
10x Genomics


title: ERF115-OX-3


title: RevOccl-ACE-4L

description: Library name: RevOccl-ACE-4L


title: BCR-Seq, Spleen, Uninfected, R848-Treated

description:
Library name: Mock_R848_BCR
10x Genomics


title: RevOccl-ACE-4R

description: Library name: RevOccl-ACE-4R


title: BCR-Seq, Spleen, Uninfected, Untreated

description:
Library name: Mock_Control_BCR
10x Genomics


title: ERF115-SRDX-1


title: RevOccl-ACE-3L

description: Library name: RevOccl-ACE-3L


title: RevOccl-DPG-2R

description: Library name: RevOccl-DPG-2R


title: ERF115-OX-2


title: Closed sundew traps induced by living fruit flies (rep 2)

city: Beijing

first: daoxin

last: Xie

address: Tsinghua University Haidian District

institute: Tsinghua University

data_processing:
Low-quality reads were removed from the raw reads using Cutadapt and Trimmomatic software to get clean reads.
The filtered reads were then de novo assembled by Trinity (v2.15.1).
Transdecoder (https://github.com/TransDecoder/TransDecoder) was performed to identify the coding region of the transcripts.
Annotations of the consensus assembly were performed against the nr database from InterProScan (https://interproscan-docs.readthedocs.io/en/latest/), and from the Swissprot databases from UniProt.
Clean reads were mapped to the corresponding reference genome using RSEM pipeline. The R package DEseq2 (v1.16.1) was used to identify the differentially expressed genes based on the following criteria: padj < 0.05 & log2FoldChange > 2.
Assembly: Reference genome is not available for Drosera capensis. Trinity is used to assembe the transcripts with RNA-seq data.
Supplementary files format and content: text file includes raw counts for each sample

organism: Drosera capensis

source_name: leaf

extract_protocol:
RNA isolation for Cape sundew was performed according to previous study (Bekesiova et al., 1999).
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: leaf

tag: agent

value: induced by GSH treatment

value: Closed sundew traps


title: ERF115-OX-1

value: 4 day old


title: TCR-Seq, Spleen, MRV-infected, R848-Treated

description:
Library name: MRV_R848_TCR
10x Genomics

data_processing:
Sequences were aligned using CellRanger to the murine and MRV genome. Raw RNAseq and vdj files were processed and utilized to create and rds file. scRNA-Seq data from the 4 different samples were processed, cell cycle corrected, and analyzed in R (v4.4.1) using Seurat (v5.2.1) package. The data was initially normalized using SCTransform followed by quality control which had thresholds set to nFeature_RNA > 500, nCount_RNA > 1000 and percent.mt < 5. Following this, Harmony (v1.2.3) was used to eliminate batch effects followed by dimensionality reduction and unbiased clustering. Cluster annotations were made based on canonical marker gene expressions. Cell-level heatmaps and hierarchical heatmaps were generated using DoHeatmap and pheatmap respectively to confirm the marker gene expression. Cell types of interest were subset followed by dimensionality reduction. scRepertoire (v2.6.2) was primarily used to analyze TCR-Seq data of all 4 samples. The contig data from all the samples were combined and processed into clonal information which was subsequently added to the single-cell data. The integrated clonal data was used for used for downstream analyses.
Assembly: mm10, MRV
Supplementary files format and content: filtered H5, MTX, and TSV ( matrix files and tab separated files)
Library strategy: TCR-Seq


title: Closed sundew traps induced by living fruit flies (rep 1)


title: Closed sundew traps induced by living fruit flies (rep 3)


title: WT-3


title: TCR-Seq, Spleen, Uninfected, R848-Treated

description:
Library name: Mock_R848_TCR
10x Genomics


title: RA_inh_new_2

description: Library name: RA_inh_new_2

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: whole olfactory mucosa


title: RA_inh_old_2

description: Library name: RA_inh_old_2


title: TCR-Seq, Spleen, MRV-infected, Untreated

description:
Library name: MRV_Control_TCR
10x Genomics


title: WT-1


title: None-stimulated normal sundew traps (rep 3)

description:
The mock control of living fruit fly treatment
0min-5

value: Sundew traps


title: RA_inh_old_1

description: Library name: RA_inh_old_1


title: WT-2


title: None-stimulated normal sundew traps (rep 2)

description:
The mock control of living fruit fly treatment
0min-3


title: M48_13_x

city: Yinchuan

first: Ye

last: Li

address: School of Public Health and Management, Ningxia Medical University, Yinchuan 750004, China

institute: Ningxia Medical University

data_processing:
Trimmomatic software was first used for adpter removing, and then low-quality bases and N-bases or low-quality reads were filtered out.
HISAT2 was used to align clean reads to the reference genome of the experimental species, and RSeQC suite was used to calculate the proportion of various alignment types and evaluate the alignment results.
Stringtie software was used to assemble the reads aligned to genes, and the Single Transcripts of each sample were fused into a Merged Transcripts.
The Merged Transcripts were compared with the known reference gene models by Cuffcompare software
After alignment of clean reads to the transcription template (mRNA+novel lncRNA+known lncRNA or mRNA+candidate lncRNA) by Bowtie2 software, eXpress software was used for transcript quantification to obtain FPKM values and counts of mRNA and lncRNA 200 bp or more apart from the existing annotation gene;   and not less than 180 bp in length.
Assembly: Rnor_6.0
Supplementary files format and content: RPKM values for each Sample

organism: Rattus norvegicus

source_name: Splenic tissue

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer’s protocol.1.3 ug of tota RNA was used for the construction of sequencing libraries
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

value: Splenic tissue

value: Sprague Dawley

value: Achronic mild stress stimulation model (CUMS)

value: M group


title: RA_dmso_old_2

description: Library name: RA_dmso_old_2

value: male


title: scRNA-seq, Spleen, MRV-infected, R848-Treated

description:
Library name: MRV_R848_GEX
10x Genomics

data_processing:
Sequences were aligned using CellRanger to the murine and MRV genome. Raw RNAseq and vdj files were processed and utilized to create and rds file. scRNA-Seq data from the 4 different samples were processed, cell cycle corrected, and analyzed in R (v4.4.1) using Seurat (v5.2.1) package. The data was initially normalized using SCTransform followed by quality control which had thresholds set to nFeature_RNA > 500, nCount_RNA > 1000 and percent.mt < 5. Following this, Harmony (v1.2.3) was used to eliminate batch effects followed by dimensionality reduction and unbiased clustering. Cluster annotations were made based on canonical marker gene expressions. Cell-level heatmaps and hierarchical heatmaps were generated using DoHeatmap and pheatmap respectively to confirm the marker gene expression. Cell types of interest were subset followed by dimensionality reduction. scRepertoire (v2.6.2) was primarily used to analyze TCR-Seq data of all 4 samples. The contig data from all the samples were combined and processed into clonal information which was subsequently added to the single-cell data. The integrated clonal data was used for used for downstream analyses.
Assembly: mm10, MRV
Supplementary files format and content: filtered H5, MTX, and TSV ( matrix files and tab separated files)


title: TCR-Seq, Spleen, Uninfected, Untreated

description:
Library name: Mock_Control_TCR
10x Genomics


title: M9_12


title: RA_dmso_old_1

description: Library name: RA_dmso_old_1


title: M24_3


title: scRNA-seq, Spleen, MRV-infected, Untreated

description:
Library name: MRV_Control_GEX
10x Genomics


title: Closed sundew traps induced by GSH treatment (rep 3)


title: Closed sundew traps induced by GSH treatment (rep 2)


title: RA_inh_new_1

description: Library name: RA_inh_new_1


title: scRNA-seq, Spleen, Uninfected, R848-Treated

description:
Library name: Mock_R848_GEX
10x Genomics


title: M9_2


title: RA_dmso_new_2

description: Library name: RA_dmso_new_2


title: scRNA-seq, Spleen, Uninfected, Untreated

description:
Library name: Mock_Control_GEX
10x Genomics


title: Sundew traps without small molecule treatment (rep3)

description:
The mock control of GSH treatment
w0-4


title: M9_5


title: RA_dmso_new_1

description: Library name: RA_dmso_new_1


title: CNP_NP_20

city: Aarhus

first: Lin

last: Lin

address: Høegh-Guldbergs Gade 10

department: Department of Biomedicine

institute: Aarhus University

description: Library name: NP_20

data_processing:
Raw FASTQ files were aligned to the Mus musculus reference genome (GRCm39, Ensembl 112) using STAR. Reads were mapped with unique-mapping enabled, unmapped reads retained. Gene-level counts were generated using STAR’s GeneCounts/STARsolo module. UMI sequences were extracted and deduplicated. Alignment statistics and count matrices were produced directly by STAR.
Assembly: GRCm39, Ensembl 112
Supplementary files format and content: Count matrix file

source_name: Retina

extract_protocol:
Tissue was homogenized using a mini hand-held homogenizer (LX140MHH, Labdex) and  RNA was harvested using the RNeasy mini plus kit (Qiagen)
Polyadenylated mRNAs were reverse transcribed using barcoded primers with UMI and template switching to generate full-length cDNA, which was subsequently amplified. For library construction, amplified cDNA was processed using the Illumina-compatible library preparation workflow with library construction kit (10X Genomics). Final libraries were quality-checked and sequenced on an Illumina NovaSeqX Plus platform.

treatment_protocol: Intravitreal injection in C57BL6/JRj female mice of 1 µL of a 1 mg/mL hg-C3N4 solution diluted in PBS (CNP group) or PBS using a Hamilton 34G blunt needle. Mice were sacrificed 14 days post injection and neuroretinas were isolated and snapfrozen.

value: Retina

value: CNP


title: Sundew traps without small molecule treatment (rep2)

description:
The mock control of GSH treatment
w0-3


title: M48_13_c


title: PBS_NP_18

description: Library name: NP_18

value: PBS


title: Closed sundew traps induced by GSH treatment (rep 1)


title: Sundew traps without small molecule treatment (rep1)

description:
The mock control of GSH treatment
w0-1


title: RA_dmso_OE_3

description: Library name: RA_dmso_OE_3


title: M9_7


title: CNP_NP_16

description: Library name: NP_16


title: RA_dmso_OE_4

description: Library name: RA_dmso_OE_4


title: M24_2


title: RA_OE_2

description: Library name: RA_OE_2


title: C25_6

value: C group


title: RevOccl-ACE-3R

description: Library name: RevOccl-ACE-3R


title: HCD3

city: San Diego

first: Emmie

last: Yao

state: California

address: 9500 Gilman Drive, SME 218

institute: UC San Diego

description: Library name: Sample 5

data_processing:
RNA Galaxy
Quality control using FASTQC, trimmed by Trimmomatic, aligned with HISTAT2, and differential gene expression was analyzed using DESeq2.
Assembly: hg38
Supplementary files format and content: tab deliminated text file includes raw counts

source_name: 3D bioprint with gelatin methacrylate

extract_protocol:
RNA was harvested using Zymo's RNA extraction kit
RNA libraries were created using polyA enrichment library preparation

value: 3D bioprint with gelatin methacrylate

value: glioma stem cell

tag: sample group

value: HCD


title: PBS_NP_14

description: Library name: NP_14


title: HCD2

description: Library name: Sample 4


title: CNP_NP_12

description: Library name: NP_12


title: C1_1


title: HCD1

description: Library name: Sample 3


title: Pentanal2h-2

first: David

last: Brann

address: 220 Longwood Ave

institute: Harvard Medical School

description: Library name: Pentanal2h-2

source_name: whole olfactory mucosa


title: BASE3

description: Library name: Sample 2

value: BASE


title: CNP_NP_8

description: Library name: NP_8


title: PBS_NP_10

description: Library name: NP_10


title: RA_OE_1

description: Library name: RA_OE_1


title: C_25_4


title: None-stimulated normal sundew traps (rep 1)

description:
The mock control of living fruit fly treatment
0min-1

value: leaf


title: PEA2

description: Library name: PEA2


title: C17_23


title: Pentanal2h-1

description: Library name: Pentanal2h-1


title: PBS_NP_6

description: Library name: NP_6


title: C17_20


title: PEA1

description: Library name: PEA1


title: BASE2

description: Library name: Sample 1


title: OMPitTA_cage-1

description: Library name: OMPitTA_cage-1

value: OMP-IRES-tTA

value: female


title: C1_2


title: C25_9


title: OMPitTA_cage-2

description: Library name: OMPitTA_cage-2

value: whole olfactory mucosa


title: A549 SA 5F_3

city: León

first: Blanca

last: Lorente Torres

address: Cjón. Campus de Vegazana s/n

institute: Universidad de León

description: Library name: A549_SA_5F_3

data_processing:
Raw RNA-seq reads were aligned to the Homo sapiens reference genome using STAR. Gene-level count matrices were generated with featureCounts. Normalization and differential gene expression analyses were performed in R using DESeq2, and variance-stabilized counts were obtained using the variance-stabilizing transformation (VST). Functional enrichment analyses were carried out using Gene Ontology and Reactome databases, and weighted gene co-expression network analysis (WGCNA) was performed to identify gene modules associated with experimental conditions.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text files includes raw counts for each sample

source_name: Pulmonary epithelium

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions. RNA concentration and purity were assessed using a NanoDrop One/OneC spectrophotometer (Thermo Fisher Scientific) prior to RNA sequencing.
Messenger RNA (mRNA) was isolated from total RNA using oligo(dT)-conjugated magnetic beads. Following fragmentation, first-strand cDNA synthesis was performed using random hexamer primers. Second-strand synthesis incorporated dUTP to generate strand-specific (directional) libraries. Libraries were prepared through end repair, A-tailing, adapter ligation, size selection, PCR amplification, and purification, including a USER enzyme digestion step prior to amplification for strand specificity. Library concentration was measured using a Qubit fluorometer, and library quality and fragment size distribution were assessed using a Bioanalyzer. Libraries were pooled equimolarly and sequenced on an Illumina platform

value: Pulmonary epithelium


title: AML mouse BM cells with Tazemetostat rep3, batch5

description:
Library name: 5_Tazemetostat_3
batch5_RNASeq_raw_counts.csv

source_name: Bone marrow

extract_protocol: RNA-seq libraries were constructed using an Illumina stranded mRNA sample preparation kits (NEB, E7770) according to the manufacturer's protocol.

value: Bone marrow

value: AML BM celline

value: Tazemetostat


title: A549 SA 5F_1

description: Library name: A549_SA_5F_1


title: A549 SA_3

description: Library name: A549_SA_3

value: No treatment


title: OMP-P2_cage-2

city: Boston

description: Library name: OMP-P2_cage-2


title: CNP_NP_4

description: Library name: NP_4

value: Retina


title: OMP-P2_cage-1

description: Library name: OMP-P2_cage-1

value: male


title: A549 SA 5F_2

description: Library name: A549_SA_5F_2


title: A549 SA_2

description: Library name: A549_SA_2


title: C7_6

value: Splenic tissue

value: Sprague Dawley

value: Achronic mild stress stimulation model (CUMS)


title: OMP-P2_UD-2

description: Library name: OMP-P2_UD-2


title: ICSI-F2_64G1

city: Kyoto

first: mito

last: shinohara

state: Kyoto

address: Sakyo-ku, Yoshida Konoe

department: Medicine

country: Japan

institute: Kyoto University

description: Library name: ICSI-F2_64G1

data_processing:
RNAseq
Illumina RTA version 3.10.30 and  bcl2fastq version 2.20 were used for basecalling and fastq generation, respectively.
The sequenced reads were mapped to the mm10 mouse reference genome using HISAT2 (version 2.2.1), with the GENCODE M23 annotation gtf file after trimming adaptor sequences and low-quality bases by cutadapt-3.4.
The gene expression count matrix was generated using HTSeq (version 2.0.2) with GENCODE M23 annotation gtf file.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RawCounts values for each Sample

source_name: brain

growth_protocol: Neonatal brain tissue were prepared from male F2 offspring of C57BL/6 strain produced by natural mating from male ICSI-F1 offspring. Control brain samples were prepared from neonate born by natural mating from wild-type C57BL/6 parents .

extract_protocol:
Neonatal brain tissue were homogenized. Total RNA samples were extracted with miRNeasy mini kit (Quiagen  217084) with treatment with RNase-Free DNase (Quiagen 79254).
The library preparation was performed using a Illumina Stranded mRNA Prep Ligation Kit (Illumina), according to the manufacturer’s instructions.

value: brain


title: VAT63

city: Los Angeles

first: Kyla

last: Gelev

email: kylagelev@gmail.com, kzg@g.ucla.edu

address: 695 Charles E. Young Drive South

institute: University of California, Los Angeles

description:
Library name: VAT63
10x Genomics

data_processing:
Alignment was performed against the GRCh38 human genome reference with GENCODE v42 gene annotations using STAR v2.7.10a, with parameter ‘--soloFeatures Gene GeneFull SJ Velocyto’ to accommodate snRNA-seq data.
We used demuxlet v2 via popscle to demultiplex the samples within the batches.
Afterwards, we used DIEM v2.4.1 and DecontX (celda v1.16.1) to remove empty droplets and contaminated reads.
DoubletFinder v2.0.3 was used to remove heterotypic doublets.
Assembly: GRCh38
Supplementary files format and content: Gene counts are found in matrix market file format.
Supplementary files format and content: Barcodes, gene names, and meta data are in tab-separated value formats.

source_name: visceral adipose tissue

extract_protocol:
Frozen visceral adipose tissue biopsies were incubated in ice cold lysis buffer (1mL per 100mg), consisting of 10mM Tris-HCl, 10nM NaCl, 3mM MgCl2, 0.1% of IGEPAL, and 0.2 U/μL of RNase inhibitor (Sigma #3335402001). The lysate was immediately run on the gentleMACS dissociator gentleMACS Program 4C_nuclei_1a followed by the gentleMACS Program 4C_nuclei_1b (5 min total). The lysate was then incubated for an additional 10 minutes. The lysate was filtered through MACS 30μm strainer (Miltenyi Biotec #130-110-915) and then centrifuged at 500 x g for 5 minutes at 4°C.  The pellet was re-suspended in 1mL wash buffer consisting of 2.0% BSA, 1X PBS, and 0.2 U/μL of RNase inhibitor (Sigma #3335402001). Following this, the lysate was filtered through another MACS 30μm strainer (Miltenyi Biotec #130-110-915) and centrifuged again at 500 x g for 5 minutes at 4°C. Re-suspension of the pellet was done in 70 uL wash buffer in preparation of library construction.
Libraries were prepared using the 10x Chromium Single Cell 3' Reagent kit v3.1.

value: visceral adipose tissue

tag: cohort

value: Molecular Architecture of FAtty Liver Disease in individuals with obesity undergoing bAriatric surgery (MAFALDA)


title: ICSI-F2_64G4

description: Library name: ICSI-F2_64G4


title: AML mouse BM cells with DMSO rep2, batch5

description:
Library name: 5_DMSO_2
batch5_RNASeq_raw_counts.csv

value: DMSO


title: AML mouse BM cells with Tazemetostat rep1, batch5

description:
Library name: 5_Tazemetostat_1
batch5_RNASeq_raw_counts.csv


title: ICSI-F2_64F3

description: Library name: ICSI-F2_64F3


title: PBS_NP_2

description: Library name: NP_2

value: PBS


title: VAT61

description:
Library name: VAT61
10x Genomics


title: AML mouse BM cells with DMSO rep1, batch5

description:
Library name: 5_DMSO_1
batch5_RNASeq_raw_counts.csv


title: OMP-P2_ACE-2

description: Library name: OMP-P2_ACE-2


title: OMP-P2_UD-1

description: Library name: OMP-P2_UD-1

value: female


title: AML mouse BM cells with Tazemetostat rep2, batch5

description:
Library name: 5_Tazemetostat_2
batch5_RNASeq_raw_counts.csv


title: AML mouse BM cells with DMSO rep3, batch5

description:
Library name: 5_DMSO_3
batch5_RNASeq_raw_counts.csv


title: A549 SA_1

description: Library name: A549_SA_1


title: VAT62

description:
Library name: VAT62
10x Genomics


title: OMP-P2_ACE-1

description: Library name: OMP-P2_ACE-1

value: whole olfactory mucosa


title: VAT60

description:
Library name: VAT60
10x Genomics


title: VAT59

description:
Library name: VAT59
10x Genomics


title: ICSI-F2-pl-63D2

description: Library name: ICSI-F2-pl-63D2

data_processing:
Adapter sequences were trimmed from the raw reads using Clip adapter (Galaxy Version 2.5.1). Small RNA analyses were performed using sRNAtoolbox and Galaxy mississippi [2].
Assembly: mm39
Supplementary files format and content: Excel file include raw counts data.

source_name: E13.5 placenta

growth_protocol: C57BL/6 wt females were mated with male ICSI-F1 offspring. Placenta were recovered from pregnant females at E13.5. Control placenta samples were prepared from C57BL/6 wt pregnant females at

extract_protocol:
Placenta tissue were homogenized. Total RNA samples were extracted with miRNeasy mini kit (Quiagen  217084) with treatment with RNase-Free DNase (Quiagen 79254).
RNA integrity was assessed with Bioanalyzer (Agilent Technologies). The library preparation was performed using a NEB Next Multiplex Small RNA Library Prep Set for Illumina (Cat No. E7300) according to the manufacturer’s instructions. Sequencing was performed on an Illumina NovaSeq X plus (51bp single-end).

value: E13.5 placenta


title: control_64D6

description: Library name: control_64D6

value: control


title: OMP-Ai95-2

description: Library name: OMP-Ai95-2


title: control_64D7

description: Library name: control_64D7


title: control_64A6

description: Library name: control_64A6


title: ICSI-F2-pl-63B2

description: Library name: ICSI-F2-pl-63B2