title: Mini-bulk samples indexed with RPI-41

city: Parkville

first: Peter

last: Hickey

address: 1G Royal Parade

country: Australia

institute: WEHI

description: Library name: RPI-41

data_processing:
gene count matrix generated using scPipe v1.14.0
reads were aligned using Rsubread v2.6.1
Assembly: PlasmoDB-51_Pfalciparum3D7
Supplementary files format and content: CSV, gene count matrix, rows represent genes and each column is a well, values corresponding to read counts
Supplementary files format and content: CSV, sample sheet, rows represent a sample and columns contain metadata on the sample in the well

organism: Plasmodium falciparum

source_name: Infected erythrocyte

growth_protocol: Wild-type P. falciparum 3D7 asexual blood stage parasites were cultured in Group O RhD+ red blood cells from healthy donors in RPMI-HEPES supplemented with 50mg/ml hypoxanthine, 25 mg/ml gentamicin, 2.1g/L NaHCO3, and 5g/L AlbumaxII™ (GIBCO) (RPMI-HEPES Complete media).

extract_protocol:
At 30 hours, cultures with and without DFO were treated with saponin to obtain parasite pellets. Pellets from each treatment condition were resuspended in 50uL of RNAlater and stored at -20°C for RNA extraction and sequencing. Four biological replicates were performed at least one week apart, and all samples from the replicates were subsequently processed together. RNA was extracted using the Isolate II RNA mini kit (Bioline) and performed as per the protocol and eluted in 35uL of water. RNA was quantified using the Qubit 2.0 HS RNA assay (Thermo Fisher) and the quality of a subset assessed using the 2200 TapeStation System High Sensitivity RNA Screen Tape (Agilent). Samples were normalised to RNA concentrations of 10ng/mL.
Sequencing was performed using WEHI’s Cellular Genomics Projects Team’s mini bulk sequencing protocol. In short, single cell transcriptome libraries were generated by adapting the CelsSeq2 protocol as follows: samples were pooled after first strand cDNA synthesis, treated with Exonuclease 1 for 30 minutes, followed by a 1.2X bead clean-up. Second strand synthesis was performed using NEBNext Second Strand Synthesis module (NEB) in a final reaction volume of 20 µL and NucleoMag NGS Clean-up and Size select magnetic beads (Macherey-Nagel) were used for all DNA purification and size selection steps. Sequencing was performed on the Illumina NextSeq2000 instrument (San Diego, USA), using a 100 cycle kit.

treatment_protocol: Parasite cultures were synchronised using a combination of serial sorbitol treatments and heparin exposure (Supplementary Figure X) prior to being set up at 1% parasitaemia, 1% HCT and total volume of 10ml with concentrations of 0 and 12.5µM of DFO. Cultures were incubated at 37°C in an atmosphere of 1% O2, 5% CO2, 94% N2 for 30 hours.

value: Infected erythrocyte


title: Mini-bulk samples indexed with RPI-44

status: Public on Jan 04 2026

type: SRA

description: Library name: RPI-44

library_source: transcriptomic

molecule: polyA RNA

tag: cell type


title: UBC-Mn-3

city: Haikou

first: Zhijian

last: Chen

email: jchen@scau.edu.cn, zjchen@catas.cn

address: Xueyuanlu 4

country: China

institute: Institute of Tropical Crop Genetic Resources, Chinese Academy of Tropical Agricultural Sciences

description: Library name: Sample 6

data_processing:
Oligo (dT) magnetic beads are used to select mRNA with polyA tail.
Sequencing libraries were generated using the NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, Ipswich, USA)
The cDNA libraries of the three biological replicates were sequenced using an Illumina HiseqTM platform (Illumina, San Diego, USA) and paired-end, 150 nucleotide reads were generated
Remove contaminated Reads (the number of bases contaminated with Reads is greater than 5 bp. For double-stranded sequencing, if one end is affected Connector contamination, then remove both ends of the Reads). Remove low-quality Reads (Quality Q ≤ 19 bases in Reads account for more than 50% of total bases. For double-stranded sequencing, If one end has low quality Reads, both ends will be removed). Remove Reads containing more than 5% of N (for double-ended sequencing, if the ratio of N at one end is greater than 5%, both ends will be removed Reads)
As the genome sequence for stylo remains unavailable, a de novo assembly approach was conducted. The obtained clean reads were assembled into unigenes using the Trinity software with default parameters. The clean reads were mapped back to the assembled contigs by Bowtie2 v.2.2.3
Assembly: All unigene sequences were aligned by BLAST search (E-value<1e-5) against the databases of the NCBI non-redundant protein sequences (Nr), the NCBI non-redundant nucleotide sequences (Nt), the Universal Protein (UniProt), the Gene Ontology (GO), the Clusters of Orthologous Groups of protein database (COG), the Functional Annotation (eggNOG), the Kyoto Encyclopedia of Genes and Genomes (KEGG) database and the Protein Family (Pfam).
Supplementary files format and content: tab-delimited text files include RPKM values for each sample.

molecule: total RNA

organism: Stylosanthes guianensis

source_name: Root

extract_protocol:
Total RNA from roots of stylo were extracted using TRIzol Reagent (Invitrogen, Carlsbad, USA) according to the manufacturer’s protocol. RNA integrity and concentration were determined using an Agilent 2100 RNA Nano 6000 Assay Kit (Agilent Technologies, California, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: Root

tag: cell line

value: Root cells

tag: genotype


title: Mini-bulk samples indexed with RPI-25

description: Library name: RPI-25


title: L4435

city: Leiden

first: Debora

last: Meijer

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

description: Library name: 104320-001-032

data_processing:
Raw RNA-seq data was processed by the RNA-seq BioWDL pipeline using default settings, developed by the SASC (https://biowdl.github.io/, LUMC, Leiden, the Netherlands)
Assembly: hg38
Supplementary files format and content: Tab-delimited tsv file with raw counts for each sample

organism: Homo sapiens

source_name: tumor

extract_protocol:
RNA was isolated from tissue sections (thickness = 20 µm) in TRIzol (15596018, Ambion) according to manufacturer’s instructions. RNA purification was performed using RNaesy mini kit (74104, Qaigen) and included DNAse treatment according to manufacturer’s instructions
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the samples.

tag: disease

value: Con. Central CS

tag: grade

value: tumor


title: BV2 microglial cells, overexpress GFP, rep3

city: Shanghai

first: Shenrui

last: Guo

address: Kongjiang Road 1665, Yangpu District

institute: Xinhua Hospital, Shanghai Jiao Tong University School of Medicine

description: Library name: GFP3

data_processing:
ZTRON(Version:22.0.5)
Data filtering: removal of adapter-contaminated reads, removal of low-quality reads, and removal of reads containing an excessive proportion of undetermined bases (N).
Bowtie2 v2.2.3 was used for building the genome index, and Clean Data was then aligned to the reference genome using HISAT2 v2.1.0.
Reads Count for each gene in each sample was counted by HTSeq v0.6.0, and FPKM (Fragments Per Kilobase Millon Mapped Reads) was then calculated to estimate the expression level of genes in each sample.
Assembly: Mus_Musculus.GRCm39.chr
Supplementary files format and content: txt files include FPKM values for each sample
Supplementary files format and content: txt files include raws counts for each sample

organism: Mus musculus

source_name: BV2 microglial cells

growth_protocol: BV2 microglial cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum and 100 U/ml penicillin and 100 mg/ml streptomycin. All cells were cultured at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
Total RNA was extracted using Trizol reagent. A total of 2 µg RNA per sample was used as the input material for library preparation.
Sequencing libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (#E7530L, NEB, USA) following the manufacturer’s instructions, and unique index codes were added to each sample for multiplexing. Briefly, mRNA was isolated from total RNA using poly-T oligonucleotide-attached magnetic beads. The mRNA was fragmented in NEBNext First Strand Synthesis Reaction Buffer (5X) at elevated temperature in the presence of divalent cations. First-strand cDNA was synthesized using random hexamer primers and reverse transcriptase, followed by second-strand cDNA synthesis with DNA polymerase I, dNTPs, and RNase H. The cDNA fragments were purified using QiaQuick PCR purification kits and eluted in EB buffer. The purified products were subsequently subjected to end repair, A-tailing, and adapter ligation. Finally, target-sized fragments were selected and PCR-amplified to complete the library construction.

value: BV2 microglial cells

value: overexpress GFP


title: Mini-bulk samples indexed with RPI-48

description: Library name: RPI-48


title: L4066

description: Library name: 105372-001-010


title: HU25_NEUN

city: JERUSALEM

first: Serafima

last: Dubnov

address: The Edmond J. Safra Campus, Givat Ram

country: Israel

institute: The Hebrew University of Jerusalem

description: Library name: Sample 55

data_processing:
Quality control was re-assessed using FastQC version 0.11.8, with Cutadapt for removing the adaptor sequences.
Assembly: Alignment to tRFs was done using MINTmap to MINTbase v2.0 and to microRNA using miRDeep2 to miRbase 22.1.
Supplementary files format and content: Tab-limited csv files with microRNA, tRNA fragments and tRNA fragment family raw counts for each sample.

source_name: Cerebral Cortex

extract_protocol:
Neurosurgery-obtained fresh human brain specimens were lightly fixed with formalin and broken down to single nuclei with cytoplasmatic fractions. The cell suspensions were next stained cell-type-specific antibodies (NeuN for neurons, Iba1 for microglia, Gfap for astrocytes, Olig2 for oligodendrocytes) and FACS-sorted to distinct cell type populations. RNA from FACS-sorted cell populations was extracted using the RNeasy FFPE kit (Qiagen, 73504), according to the manufacturer’s instructions.
Libraries were constructed using the D-Plex Small RNA-seq Kit from Illumina (Diagenode, C05030001), using 500 and 1000 pg/sample in Batch 1 and Batch 2, respectively.

value: Cerebral Cortex

value: Neurons

tag: treatment

value: FACS-sorted with NEUN antibody

tag: batch

value: Batch 1

tag: Sex

value: F

tag: age

tag: hemisphere and_lobe

value: Right frontal


title: BV2 microglial cells, overexpress GFP, rep1

description: Library name: GFP1


title: UBC-Mn-1

description: Library name: Sample 4


title: HU11_NEUN

description: Library name: Sample 52

value: M

value: Right temporal


title: L4165

description: Library name: 105372-001-011

value: ACT


title: BV2 microglial cells, overexpress GFP, rep2

description: Library name: GFP2


title: UBC-Mn-2

description: Library name: Sample 5


title: HU75_NEUN

description: Library name: Sample 50

value: Batch 2

value: Left parietal


title: Mini-bulk samples indexed with RPI-16

description: Library name: RPI-16

value: Infected erythrocyte


title: HU73_NEUN

description: Library name: Sample 48

value: Left frontal


title: EV-Mn-3

description: Library name: Sample 3

value: Root

value: Root cells


title: L3808

description: Library name: 105372-001-007

value: Con. Central CS

value: tumor


title: Mini-bulk samples indexed with RPI-22

description: Library name: RPI-22


title: Mini-bulk samples indexed with RPI-19

description: Library name: RPI-19


title: HU12_NEUN

description: Library name: Sample 51

value: Cerebral Cortex


title: liver_selo_KO3

city: Tian Jin

first: Xiaofan

last: Jia

address: No.22, Qixiang Tai Road, Heping District, Tianjin

department: School of basic medical sciences

institute: Tianjin Medical University

data_processing:
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
The clean reads were mapped to the reference genome using HISAT2. After that, Ericscript (v0.5.5) and rMATS (V3.2.5) were used to detect fusion genes and differential splicing genes (DSGs), respectively
Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included. Expression level of gene was calculated by RSEM (v1.3.1)
Assembly: GRCm38
Supplementary files format and content: tab-delimited text file including read count and RPKM for each sample

source_name: liver

extract_protocol:
Liver samples were ground into a powder using liquid nitrogen and incubated with TRIzol. After centrifugation, the upper aqueous layer containing RNA was further purified through extraction with chloroform/isoamyl alcohol (24:1). RNA was then precipitated with isopropyl alcohol and washed twice with 75% ethanol. Finally, the RNA was redissolved in DEPC-treated water.
mRNA was enriched using oligo(dT)-attached magnetic beads. The RNA was fragmented, and cDNA synthesis was initiated using random hexamers as primers. The resulting double-stranded cDNA underwent an end-repair reaction, followed by adaptor ligation. Finally, the library products were amplified by PCR and subjected to quality control.

value: liver

value: Selofl/fl Alb-Cre

value: knockout


title: liver_selo_KO2


title: HU10_NEUN

description: Library name: Sample 49

value: Neurons

value: FACS-sorted with NEUN antibody

value: Batch 1

value: F


title: L2375

description: Library name: 105372-001-001


title: L2788

description: Library name: 105372-001-002


title: Mini-bulk samples indexed with RPI-15

description: Library name: RPI-15


title: L3522

description: Library name: 104320-001-030


title: HU71_NEUN

description: Library name: Sample 47

value: M

value: Right occipital


title: liver_cont3

value: Selofl/fl


title: EV-Mn-2

description: Library name: Sample 2


title: HU67_NEUN

description: Library name: Sample 45

value: Batch 2

value: Right frontal


title: L2814

description: Library name: 105372-001-003


title: HU13_NEUN

description: Library name: Sample 44

value: Left temporal


title: MI2

type: RNA

city: Harbin

first: Feiyong

last: Xu

state: Heilongjiang Province

address: 157 Baojian Road, Nangang District, Harbin City, Heilongjiang Province

department: College of Pharmacy

institute: Harbin Medical University

description: Sample = 5

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Mouse circRNA Arrays V2（8X15K，Arraystar）,and incubated for 17 hours at 65℃ in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: Mouse with MI treated for 4 hweeks

label_protocol: Total RNA from each sample was treated with Rnase R to enrich circular RNA.The enriched circular RNA was then amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol.

extract_protocol: Total RNA was extracted with Trizol

treatment_protocol: Wild-type male mice (10 weeks old) had their left anterior descending coronary artery (LDA) ligated for 1 Day.

value: Heart

tag: gender

value: Male


title: L0795

description: Library name: 104320-001-089

value: Con. Central CS

value: tumor


title: liver_cont1

value: liver


title: MI1

description: Sample = 4


title: T84 IFNLR KO cells, replicate 3

city: Gainesville

first: Yagmur

last: Keser

state: Florida

address: 1200 Newell Dr.

department: Molecular Genetics and Microbiology (MGM)

country: USA

institute: University of Florida

description:
Library name: sample 12
dLR_high_3

data_processing:
Novogene Illumina PE150 sequencing was used.
Assembly: GRCh38 - hg38
Supplementary files format and content: tap deliminated 'gene_count.txt' file includes raw counts for each sample

growth_protocol: Wild type (WT) T84 as well as T84 reporter and knock-out (KO) cells were cultured in a 50:50 mixture of Dulbecco’s Modified Eagle’s Medium (DMEM) and F12 supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin and 100 μg/mL streptomycin. All cells were cultured on collagen coated surfaces, and were kept in a constant humid atmosphere at 37°C, 5% CO2 and 21% oxygen.

extract_protocol:
RNA was isolated using the RNAeasy RNA extraction kit. ≥ 200 ng of total RNA was used to generate sequencing library.
RNA libraries were prepared for RNA-sequencing by Novogene.

treatment_protocol: For high cell density, 2.2x10^5 cells/cm2 were seeded. One-day post-seeding, medium was exchanged with fresh medium, and two days post-seeding, cells were harvested for sequencing.

value: intestinal epithelial cells

value: IFNLR KO

value: mock


title: L0903

description: Library name: 104320-001-024


title: EV-Mn-1

description: Library name: Sample 1

value: Root

value: Root cells


title: HU17_IBA1

description: Library name: Sample 42

value: Cerebral Cortex

value: Microglia

value: FACS-sorted with IBA1 antibody

value: Batch 1

value: Left occipital


title: liver_selo_KO1

value: Selofl/fl Alb-Cre

value: knockout


title: T84 IFNLR KO cells, replicate 2

description:
Library name: sample 11
dLR_high_2


title: MI3

description: Sample = 6

value: Heart


title: T84 IFNLR KO cells, replicate 1

description:
Library name: sample 10
dLR_high_1


title: Sham1

description: Sample = 1

source_name: Mouse with sham surgery

value: Male


title: BMDM_PLG_5

city: Nashville

first: Danielle

middle: L

last: Michell

state: TN

address: 2220 Pierece Ave

department: Department of Medicine

institute: Vanderbilt Univ. Medical Center

description: Library name: BMDM_PLG_5

data_processing:
Reads were trimmed to remove adapter sequences using Cutadapt (v2.10)
Quality control on both raw reads and adaptor-trimmed reads was performed using FastQC (v0.11.9)(www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned to the Gencode GRCm38.p6 genome using STAR (v2.7.3a). Gencode vM24 gene annotations were provided to STAR to improve the accuracy of mapping. featureCounts (v2.0.0) was used to count the number of mapped reads to each gene. Only protein coding genes were used in the down-stream analysis.
Significantly differential expressed genes with absolute fold change >= 2 and FDR adjusted p value <= 0.05 were detected by DESeq2 (v1.24.0). For each differential expression comparison, low expressed genes with less than 5 median read count in both conditions were excluded.
Assembly: GRCm38.p6
Supplementary files format and content: csv file containing fpkm reads

source_name: bone marrow

growth_protocol: Bone marrow-derived macrophages were differentiated for 7days with GM-CSF (50ng/mL)

extract_protocol:
Total RNA was isolated using the Total RNA Purification kits (Norgen Biotek).
Libraries were prepared using the Universal RNA-seq with NuQuant (NuGen).

treatment_protocol: Macrophages were untreated or treated with PLG for 24h

value: bone marrow

value: bone marrow-derived macrophages

value: PLG


title: MI Thoracic DRG Poly RNAseq Data in rat 5

city: Omaha

first: Hanjun

last: Wang

state: Nebraska

address: 984455 University of Nebraska Medical Center 985850 University of Nebraska Medic

department: Anesthesiology

institute: University of Nebraska Medical Center

description:
Library name: MI 5
HW-CR-9_S9

data_processing:
Demultiplexing used bcl2fastq v2.16.0.10.
Assembly: RAT RN6 genome
Supplementary files format and content: Wang_NS162_edgeR

organism: Rattus

source_name: Dorsal root ganglia

growth_protocol: No cell cutlture condition

extract_protocol:
Qiagen miRNeasy Mini Kit used for RNA extraction
Illumina NextSeq,

treatment_protocol: Sham or coronary ligation was done in rats.

value: Dorsal root ganglia

value: SD rat

value: MI


title: BMDM_PLG_4

description: Library name: BMDM_PLG_4


title: liver_cont2

value: liver

value: Selofl/fl


title: Sham3

description: Sample = 3


title: HU27_NEUN

description: Library name: Sample 46

value: Cerebral Cortex

value: Neurons

value: FACS-sorted with NEUN antibody

value: M

value: Right superior temporal


title: HU26_NEUN

description: Library name: Sample 43

value: Batch 1

value: F

value: Right temporo-parietal


title: T84 IFNL2/3 KO cells, replicate 3

description:
Library name: sample 9
dL23_high_3

value: intestinal epithelial cells

value: IFNL2/3 KO

value: mock


title: HU19_IBA1

description: Library name: Sample 40

value: Microglia

value: FACS-sorted with IBA1 antibody

value: Right frontal suprasylvian


title: MI Thoracic DRG Poly RNAseq Data in rat 4

description:
Library name: MI 4
HW-CR-8_S8

value: Dorsal root ganglia

value: SD rat

value: MI


title: Sham2

description: Sample = 2

value: Heart

value: Male


title: MI Thoracic DRG Poly RNAseq Data in rat 2

description:
Library name: MI2
HW-CR-6_S6


title: T84 IFNL2/3 KO cells, replicate 2

description:
Library name: sample 8
dL23_high_2


title: BMDM_PLG_2

description: Library name: BMDM_PLG_2

value: bone marrow

value: bone marrow-derived macrophages

value: PLG


title: BMDM_PLG_1

description: Library name: BMDM_PLG_1


title: MI Thoracic DRG Poly RNAseq Data in rat 3

description:
Library name: MI 3
HW-CR-7_S7


title: T84 IFNL2/3 KO cell, replicate 1

description:
Library name: sample 7
dL23_high_1


title: MI Thoracic DRG Poly RNAseq Data in rat 1

description:
Library name: MI 1
HW-CR-5_S5


title: BMDM_untreated_4

description: Library name: BMDM_untreated_4

value: untreated


title: Sham Thoracic DRG Poly RNAseq Data in rat 3

description:
Library name: Sham 3
HW-CR-3_S3

value: Sham


title: Sham Thoracic DRG Poly RNAseq Data in rat 4

description:
Library name: Sham 4
HW-CR-4_S4


title: HU13_IBA1

description: Library name: Sample 41

value: Cerebral Cortex

value: Batch 1

value: M

value: Left temporal


title: HU22_IBA1

description: Library name: Sample 36

value: Microglia

value: Right frontal pericentral


title: HU15_IBA1

description: Library name: Sample 38

value: FACS-sorted with IBA1 antibody

value: Left frontal


title: T84 IFNL1 KO cells, replicate 2

description:
Library name: sample 5
dL1_high_2

value: intestinal epithelial cells

value: IFNL1 KO

value: mock


title: T84 IFNL1 KO cells, replicate 1

description:
Library name: sample 4
dL1_high_1


title: BMDM_untreated_5

description: Library name: BMDM_untreated_5


title: HU12_IBA1

description: Library name: Sample 39

value: F

value: Right frontal


title: T84 IFNL1 KO cells, replicate 3

description:
Library name: sample 6
dL1_high_3


title: HU16_IBA1

description: Library name: Sample 35

value: Right occipital


title: HU20_IBA1

description: Library name: Sample 37

value: Left frontal tip


title: Sham Thoracic DRG Poly RNAseq Data in rat 2

description:
Library name: Sham 2
HW-CR-2_S2

value: Dorsal root ganglia

value: SD rat


title: BMDM_PLG_3

description: Library name: BMDM_PLG_3

value: bone marrow

value: bone marrow-derived macrophages

value: PLG


title: HU11_IBA1

description: Library name: Sample 33

value: Cerebral Cortex

value: Batch 1

value: M

value: Right temporal


title: BMDM_untreated_3

description: Library name: BMDM_untreated_3

value: untreated


title: HU23_IBA1

description: Library name: Sample 34

value: Microglia

value: FACS-sorted with IBA1 antibody

value: Left frontal


title: T84 WT cells, replicate 3

description:
Library name: sample 3
WT_high_3

value: intestinal epithelial cells

value: WT

value: mock


title: Sham Thoracic DRG Poly RNAseq Data in rat 1

description:
Library name: Sham 1
HW-CR-1_S1

value: Sham


title: HU25_IBA1

description: Library name: Sample 32

value: F

value: Right frontal


title: BMDM_untreated_2

description: Library name: BMDM_untreated_2

value: bone marrow


title: T84 WT cells, replicate 2

description:
Library name: sample 2
WT_high_2


title: BMDM_untreated_1

description: Library name: BMDM_untreated_1

value: bone marrow-derived macrophages


title: T84 WT cells, replicate 1

description:
Library name: sample 1
WT_high_1


title: RNA-Seq of nothobranchius furzeri: FACS-sorted head kidney - myeloid 88 days old

city: Stanford

first: Jingxun

state: CA

address: 290 Jane Stanford Way, Room E365

department: Genetics

institute: Stanford University - Stanford, CA

description:
Library name: 215_01_myeloid_middle
cDNA libraries were prepared using a SmartSeq-based in-house protocol.

data_processing:
Raw sequencing data (FASTQ files) were checked for quality using Trim-galore v0.5.0.
The processed reads were aligned to the African turquoise killifish reference genome downloaded from NCBI (Nfu_20140520, GCF_001465895.1) using STAR v2.7.10b83 with the default parameters. Samtools v1.16.184, with the parameters of MAPQ < 255 (‘samtools view -q255 -b’), was used to remove the reads mapped to multiple genomic regions. Next, we input the uniquely mapped reads into the ‘featureCounts’ program (with the default parameters) from subread v2.0.685 to generate the read counts for each gene.
RNA-seq analysis (quality control, mapping, count generation, DESeq2 analysis) and plotting were also performed as in the atlas dataset, except using a different expression cutoff from the atlas: in this case, genes with at least one count in at least one sample were retained (rather than requiring at least 80% samples having at least one count). The Principal Component Analysis plot was generated using the ‘plotPCA’ function in the DESeq2 (v.1.34.0), and the heatmap by ‘pheatmap’ (v.1.0.12) with the parameters: rows and columns clustered, Z-scale for each gene, and capping z-scale at -2 and 2 (any value below -2 or above 2 was assigned as the lowest color or the highest color, respectively).
Assembly: NCBI African turquoise killifish reference genome (Nfu_20140520, GCF_001465895.1).
Supplementary files format and content: Comma-separated text files include the DESeq2 normalized counts for all files in a matrix.

organism: Nothobranchius furzeri

source_name: kidney

growth_protocol: All experiments used the GRZ strain of the African turquoise killifish species Nothobranchius furzeri. Fish were housed in a 26°C circulating water system kept at a conductivity between 3500 and 4500 μS/cm and a pH between 6.5 and 7.5, with a daily water exchange of 10% with reverse-osmosis-treated water. All animals were kept on a 12 h/12 h day/night cycle. The detailed protocol for embryo collection and husbandry of juvenile fish before sexual maturity can be found in the associated publication.

extract_protocol:
Five males of various ages (67, 88, and 201 days) were used to test the gating strategies for sorting different populations of kidney-dissociated cells by FACS. The number of cells collected per sample is listed in Supplemental File 20 of the associated publication. Cells were sorted into 350 µL Buffer RLT Plus (reagent from the QIAGEN RNeasy Plus Micro Kit [QIAGEN, 74034]) containing β-mercaptoethanol (10 µL β-ME per 1 mL Buffer RLT Plus), briefly vortexed for 30 sec, and then frozen immediately on dry ice. For sorted volumes exceeding 500 µL, additional Buffer RLT Plus was added to the sorted cells before vortexing and freezing at a ratio of 350 µL Buffer RLT Plus for each additional 100 µL of cytometer sheath fluid. Frozen homogenates were stored at -80°C until RNA extraction. Bulk total RNA extraction of the sorted cell populations from flow cytometry was performed using the QIAGEN RNeasy Plus Micro Kit (QIAGEN, 74034) according to the manufacturer's instructions. The frozen homogenates of sorted cells were thawed on ice for 30 min. Once completely thawed, homogenates were briefly centrifuged, then applied to a gDNA Eliminator spin column and centrifuged at 10,000 x g for 30 sec. The flow-through was then added to a DNA LoBind tube (Sigma-Aldrich, 022431021) containing an equal volume of 70% ethanol. This process was repeated until all the remaining volume of homogenate was passed through a gDNA Eliminator spin column and mixed with an equal volume of 70% ethanol. Then, samples were pipette mixed, transferred to a RNeasy MinElute Spin Column, and centrifuged at 10,000 x g for 15 sec, discarding the flow-through. This step was repeated until the entire ethanol-homogenate mixture was applied to the RNeasy MinElute Spin Column. The column was then washed twice, first with 700 µL of Buffer RW1 and then 500 µL of Buffer RPE, centrifuging at 10,000 x g for 15 sec and discarding the flow-through each time. A final, longer wash was performed with 80% ethanol, after which the spin column was centrifuged for 2 min at 10,000 x g. Then, the spin column was transferred to a new collection tube and dried by centrifuging at 12,000 x g for 5 min. Finally, the column was transferred to a new 1.5 mL collection tube, and 14 µL of RNAse-free water was applied to the membrane. The column was then centrifuged for 1 min at 12,000 x g to elute the RNA.  RNA was quantified using the Quant-iT RNA BR kit (Thermo Fisher, Q10213) on a Varioskan LUX multimode microplate reader, aliquoted, and stored at -80°C.
cDNA libraries were prepared using a modified in-house SmartSeq2–based protocol. RNA samples were thawed on ice, and concentrations were measured using the Quant-iT RNA BR Kit (Thermo Fisher Scientific, Q10213) on a Varioskan LUX multimode microplate reader (Thermo Fisher Scientific, VL0000D0). For first-stand cDNA synthesis, 2 µL of each RNA sample was used as input for first-strand cDNA synthesis (maximum input of 50 ng). Full-length cDNA libraries were amplified using 16 PCR cycles. A 6 µL aliquot of each amplified cDNA library was purified using Agencourt AMPure XP beads (Beckman Coulter, A63881) at a 0.7× bead-to-sample ratio following the manufacturer’s instructions, including two washes with 10.7 µL of freshly prepared 80% ethanol (200 proof ethanol, Gold Shield Distributors, 412804; diluted in nuclease-free water). Purified cDNA was eluted in 4.5 µL of nuclease-free water (Invitrogen, 10977023). cDNA concentrations were quantified using the Quant-iT dsDNA High Sensitivity Kit (Thermo Fisher Scientific, 33120), and a subset of libraries was assessed for size distribution using an Agilent TapeStation 4200 with High Sensitivity D5000 ScreenTape (Agilent, 5067-5592). Sequencing libraries were generated using a SmartSeq2–based tagmentation protocol with custom Illumina-compatible IDT dual indices. For tagmentation, 0.6 µL of cDNA (maximum input of 0.16 ng) was combined with a master mix containing 0.1 µL Illumina Tn5 transposase (Illumina, 20034198), 0.64 µL of 2.5× TAPS-PEG crowding agent, and 0.26 µL of nuclease-free water. Reactions were incubated at 55 °C for 10 min and then cooled to 10 °C. The 2.5× TAPS-PEG crowding agent was prepared by mixing filtered 40% (w/w) PEG-8000 (Promega, V3011) 1:1 (v/v) with 5× TAPS-MgCl₂ buffer, consisting of 0.5 M TAPS-NaOH (pH 8.5; Boston BioProducts, BB2375) and 1 M MgCl₂ (Sigma-Aldrich, M1028) diluted in nuclease-free water and adjusted to pH 8.4. Tagmentation reactions were terminated by addition of 0.4 µL of 0.1% SDS, followed by thorough mixing and incubation on ice for 10 min. Indexed amplification was performed by adding 0.8 µL of dual indices and a PCR master mix containing 0.08 µL KAPA HiFi DNA polymerase (KAPA HiFi PCR Kit, Roche, KK2102), 0.80 µL of 5× buffer, 0.12 µL of 10 mM dNTPs, and 0.20 µL of nuclease-free water. Libraries were amplified for 12 PCR cycles. The resulting PCR products were pooled across samples and were purified AMPure XP beads at a 0.8× bead-to-sample ratio. Most low-volume liquid handling steps were performed using Dragonfly or Mosquito HV robotic liquid handlers (SPT Labtech) to improve throughput and pipetting precision. All thermocycling steps were carried out using a 384-well thermocycler (Bio-Rad). Final library concentration and size distribution were assessed using an Agilent TapeStation 4200 with High Sensitivity D5000 ScreenTape (Agilent, 5067-5592).

treatment_protocol: Fish were anesthetized in a solution of tricaine made using system water. Once operculum movement slowed, and the fish was no longer responsive to touch, the animal was dissected and transcardially perfused with 10 mL of ice-cold 0.25 M EDTA solution (Fisher Scientific, AAJ15694AP) in 1x PBS (Thermo Fisher, 10010049) as described above. Following perfusion, head kidney tissue was carefully dissected from the body wall and placed in 5 mL of ice-cold fetal bovine serum (FBS) (Fisher, 50-152-7067) in a well of a 12-well culture plate (Celltreat, 229111). This process was repeated until all animals in the batch were perfused and dissected.  Single-cell suspensions from head kidney tissue were prepared for flow cytometry using a non-enzymatic dissociation protocol adapted from zebrafish. Kidney marrow in FBS was pipetted 50 times with a 5 mL serological pipette to dissociate the tissue mechanically. The digestion mixture was then applied to a 100 µm Cell Strainer (Fisher Scientific, 07-201-432) sitting atop a 50 mL conical tube (Fisher Scientific, 1443222). Tissue clumps remaining on the mesh were gently triturated using the plunger of a 1 mL syringe (Fisher Scientific, 14-826-88), and then 5 mL of SM Buffer (5% FBS in 1x PBS) was used to wash the well of the 12-well plate and the 100 µm strainer mesh. Filtered cells were then pelleted (400 x g, 4 min, 4C), and the supernatant was removed using a 10 mL serological pipette until about 200 µL remained. The pellet was then resuspended in 5 mL of SM buffer by pipette 5 times and then was applied to a 40 µm Cell Strainer (Sigma-Aldrich, CLS431750-50EA) on top of a 50 mL tube. The strainer was then washed with 2 mL of SM buffer, and cells were pelleted once more under the same conditions. The supernatant was again removed (leaving about 100 µL of SM Buffer), and pellets were resuspended using 500 µL of additional SM Buffer. The cell suspension was moved to a 1.5 mL Low-Adhesion Tube (USA Scientific, 1415-2600) and centrifuged at 400 x g for 2 min at 4C. Finally, the supernatant was removed until 200 µL remained. Cells were resuspended, and about 5-10 min before the sample loading onto the cytometer, 15 µL of the live/dead stain 7-AAD (BD Biosciences, 559925) was added. Right before loading onto the cytometer, the cell suspension was passed through the 35 µm strainer mesh cap of a 5 mL round-bottom FACS tube (Corning, 352235) followed by gentle vortex. Then, the sample was loaded for analysis and/or sorting on a Sony MA900 Cell Sorter (nozzle size: 100 µm, flow rate: 4).  Gates were drawn to exclude debris and to capture live, single cells. Then, gross populations of immune cells (erythroid, myeloid, lymphoid, progenitor, all leukocytes) were identified by side-scatter and forward-scatter based on a protocol developed for zebrafish.

value: kidney

value: myeloid

value: GRZ wild type

value: male

tag: age days

tag: library id


title: HU14_IBA1

description: Library name: Sample 30

value: Cerebral Cortex

value: Batch 1


title: MNNG/HOS-3

city: Guangzhou

first: Zehao

state: Guangdong

address: zhongshan 2 road

institute: The First Affiliated Hospital, Sun Yat-sen University

description:
Library name: Sample 6
B_5

data_processing:
Raw sequencing reads were first assessed for quality using FastQC.
Adapter sequences and low-quality bases were trimmed with Trimmomatic.
Clean reads were then aligned to the mouse reference genome (GRCm39/mm39) using HISAT2.
Gene-level read counts were quantified with featureCounts.
Differential expression analysis between treatment groups was performed using DESeq2 in R.
Assembly: mouse reference genome (GRCm39/mm39)
Supplementary files format and content: Read count matrix in .xlsx format, where rows represent genes and columns represent samples.

source_name: lung

growth_protocol: HFL-1 human lung fibroblast cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin at 37°C in a humidified atmosphere containing 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent following the manufacturer’s protocol. RNA quantity and integrity were assessed using an Agilent 2100 Bioanalyzer with the RNA 6000 Nano Kit.
RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Nude mice were injected with 143B-derived EVs or MNNG/HOS-derived EVs via the tail vein.

value: lung

value: MNNG/HOS-derived EVs


title: HU26_IBA1

description: Library name: Sample 31

value: Microglia

value: FACS-sorted with IBA1 antibody

value: Right temporo-parietal


title: PBMC 2, HTO-ADT

city: Seoul

first: Byungjin

last: Hwang

address: 50-1, Yonsei-ro, Seodaemun-gu

country: South Korea

institute: Yonsei University

description:
Library name: HTO-ADT_PBMC2
count matrix for all samples included

library_source: other

data_processing:
Raw data was processed using Cell Ranger v7.1.0 multi pipeline with 10x Genomics reference (Chromium Human Transcriptome Probe Set v1.0.1 GRCh38-2020-A)
Sample demultiplexing
Genes and cells were filtered by QC criteria (total count, n_gene per cells, mitochondrial content, hemoglobin content)
Doublets removed
Assembly: GRCh38
Supplementary files format and content: The PBMC 1 GEX h5ad file contains RNA count matrix, quality metrics, and cell annotations for all cells passing quality control filters. The PBMC 1 ADT h5ad file contains protein count matrix for all cells passing quality control filters. The feature reference file provides information for ADT counts in Cell Ranger.
Supplementary files format and content: The PBMC 2 RDS file contains RNA, protein count matrix and cell annotations for all cells passing quality control. The PBMC 2 csv file contains HTO associated metadata for pre-filtering cells. The feature reference file provides required information for processing ADT/HTO counts in Cell Ranger.
Library strategy: SCITO-seq2

molecule: protein

source_name: Blood

extract_protocol:
Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using a Histopaque gradient.
For cell hashing, samples were labeled with unique TotalSeq-B hashing antibodies. Cells were loaded onto a Chromium Next GEM Chip Q for GEM generation using the Chromium X system. Libraries were constructed following the 10x Genomics fixed RNA profiling protocol. During pre-amplification, TotalSeq C-additive primer was spiked in to amplify reads containing the Read 2 Nextera sequence.
SCITO-seq2; Single-cell fixed RNA, protein, and hashtag oligo (HTO) sequencing

value: Blood

value: PBMC

value: Mixed (Normal, cSLE, CHAI)


title: RNA-Seq of nothobranchius furzeri: FACS-sorted head kidney - myeloid 201 days old

description:
Library name: 1025_08_myeloid_old
cDNA libraries were prepared using a SmartSeq-based in-house protocol.


title: MNNG/HOS-2

description:
Library name: Sample 5
B_4


title: MNNG/HOS-1

description:
Library name: Sample 4
B_3


title: HU10_IBA1

description: Library name: Sample 29

value: F

value: Left frontal


title: RNA-Seq of nothobranchius furzeri: FACS-sorted head kidney -  lymphoid 88 days old

description:
Library name: 215_04_lymphoid_middle
cDNA libraries were prepared using a SmartSeq-based in-house protocol.

value: lymphoid


title: 143B-2

description:
Library name: Sample 2
C_4

value: 143B-derived EVs


title: RNA-Seq of nothobranchius furzeri: FACS-sorted head kidney - lymphoid 88 days old

description:
Library name: 215_03_lymphoid_middle
cDNA libraries were prepared using a SmartSeq-based in-house protocol.

value: kidney


title: PBMC 1, ADT

description:
Library name: ADT_PBMC1
count matrix for all samples included

value: Normal


title: HU27_IBA1

description: Library name: Sample 28

value: M

value: Right superior temporal


title: HU44_IBA1

description: Library name: Sample 27

value: Cerebral Cortex

value: Batch 2

value: Right frontal


title: 143B-1

description:
Library name: Sample 1
C_3

value: lung


title: Col0, leaf, LD, biorep3, RNAseq

city: Neuherberg

first: Martin

last: Groth

address: Ingolstädter Landstr. 1

department: Institute of Functional Epigenetics

country: Germany

institute: Helmholtz Munich

description:
Library name: RNAseq_wt_rep3
wt_4_LD

data_processing:
BS-seq: Raw reads were pre-processed with trimmomatic using the parameters ILLUMINACLIP:TruSeq3-PE-2.fa:1:30:12:3:true CROP:150 HEADCROP:3 (for standard)/12 (for PBAT libraries) LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20 for PE150 reads and ILLUMINACLIP:TruSeq3-SE.fa:1:30:10 CROP:50 HEADCROP:2 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:20 for SE50 reads. Pre-processed reads were mapped to TAIR10 using Bismark (v0.23.1) with parameters N set to 1 (allowing 1 mismatch in seed alignments) and X (maximum insert size for valid paired-end alignments) set to 700. Duplicated reads and reads flagged as unconverted due to three or more consecutive methylated CHH sites were discarded. Methylation ratios were calculated separately for CG, CHG, and CHH sites as #C/(#C+#T). Non-conversion ratios were calculated from chloroplast cytosine methylation ratios. Genome browser tracks showing CG, CHG, and CHH methylation ratios at single cytosine resolution were generated from Bismark genome-wide cytosine methylation output files for cytosine sites with at least 4 reads.
mRNA-seq: mRNA-seq reads were processed using the nf-core/rnaseq pipeline (v3.10.1) in Nextflow  (v22.10.6) executed using singularity containers on the high-performance computing cluster at Helmholtz Munich. Default parameters were used for read trimming/filtering, alignment, and quantification with Trim Galore!, STAR, and Salmon, respectively, except as stated below. TEs and genes were analyzed separately. For TEs, reads were aligned to the TAIR10 reference genome using a transcript-based TE annotation and extra STAR alignment arguments “--outMultimapperOrder Random --outFilterMultimapNmax 50 --alignIntronMax 10000 --alignSJoverhangMin 3”, whereas Araport11 gene models and extra STAR alignment arguments “--outFilterMultimapNmax 50 --alignIntronMax 10000 --alignSJoverhangMin 3” were used for genes. Transcript abundance estimates from Salmon were used to generate TE/gene-level count matrices for visualization and differential expression analysis with DESeq2 (v1.38.3). TEs/genes with less than 6 counts across all samples were removed.
Assembly: TAIR10/Araport11
Supplementary files format and content: BS-seq: wig or bigWig files showing single cytosine methylation ratios for each sequence context.
Supplementary files format and content: mRNA-seq: tab-separated text file containing TPM per gene/TE for all samples of the experiment.

organism: Arabidopsis thaliana

source_name: leaf

growth_protocol: Plants were cultivated in growth chambers (Weiss Technik & Vötsch) at 23/20 °C (day/night), 65 % relative humidity and 100 μmol m-2 s-1 photosynthetically active radiation (PAR, 400–700 nm) under long day (LD), i.e. 16h light, and short day (SD), i.e. 10h light, 24h cycles. Plants were germinated and grown on soil consisting of 4 parts multiplication substrate (Floragard) and 1 part quartz sand.

extract_protocol:
Samples consisted of rosette leave tissue that was harvested 21 and 28 days after germination for LD and SD conditions, respectively. Genomic DNA was isolated from 100 mg (fresh weight) of rosette leave tissue pooled from 3-4 plants per sample using DNeasy Plant Mini Kit (Qiagen), except for comparison of DNA methylation under SD and LD conditions, where 14 days old seedlings grown on Phyto agar (RPI Corp.) with half-strength Murashige and Skoog (MS) basal salt mixture (MP Biomedicals) were used. Total RNA was isolated from 100 mg (fresh weight) of rosette leave tissue pooled from 3-4 plants per sample using RNeasy Plant Mini Kit (Qiagen) followed by DNA digestion with amplification grade DNase I (Thermo Fisher Scientific).
BS-seq: The isolated DNA was sheared into 200-400bp fragments by ultrasonication (Covaris S2/S220/E220). WGBS of wild type, mthfd1, thfs single and mt double mutants was performed by BGI TECH Solutions (Hong Kong), proceeding with end repair of the sheared DNA, deoxyadenylation, and ligation of methylated sequencing adaptors, followed by bisulfite conversion using EZ DNA Methylation-Gold kit (ZYMO Research), size selection, PCR amplification and final size selection of libraries. Libraries for WGBS of seedlings grown under SD and LD conditions and CRISPR-Cas9 lines were prepared the same way, except using KAPA HyperPrep Kit (Roche), TruSeq DNA LT (Illumina)/NEBNext Multiplex Oligos (New England Biolabs) methylated adaptors, and EpiTect Bisulfite Kit (Qiagen), and sequenced at Novogene. WGBS of wild type and mthfd1 plants grown under cCO2 and hCO2 was performed by Novogene using post-bisulfite adaptor tagging (PBAT) with Accel-NGS Methyl-Seq DNA Library Kit for Illumina (Swift Biosciences).
mRNA-seq: Library construction and sequencing was performed by Novogene. For preparation of non-directional libraries, messenger RNA (mRNA) was purified from total RNA using oligo-dT-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers, followed by the second strand cDNA synthesis, end repair, A-tailing, adapter ligation, size selection, amplification, and purification.

treatment_protocol: For analysis of methylome and transcriptome changes upon suppression of photorespiration, plants were grown in a sun simulator climate chamber at the Research Unit for Environmental Simulation, Helmholtz Munich. Growth conditions were controlled with light intensity of 130 µmol m⁻² s⁻¹ (PAR) at plant height, day/night temperature cycle of 23°C (16 h) and 21°C (8 h), and relative humidity of 65%. Plants were grown in two Plexiglas cuvettes of dimensions 55 × 28 × 110 cm (W × D × H). One cuvette was flushed with 60 m³ h⁻¹ of air containing ambient CO₂ concentrations (cCO2), while the other was flushed with air and continuously fumigated with CO₂ (Air Liquide) at ~3000 ppm final concentration (hCO2). Airflows were controlled using a 1L mass flow controller (MKS Instruments GmbH), calibrated with a mass flow meter (ADM 3000, Agilent).

value: leaf

value: wild type

value: long day


title: PBMC 1, GEX

description:
Library name: GEX_PBMC1
count matrix for all samples included

value: Blood

value: PBMC


title: RNA-Seq of nothobranchius furzeri: FACS-sorted head kidney - myeloid 67 days old

description:
Library name: 308_03_myeloid_young
cDNA libraries were prepared using a SmartSeq-based in-house protocol.

value: myeloid

value: GRZ wild type

value: male


title: 143B-3

description:
Library name: Sample 3
C_5

value: 143B-derived EVs


title: HU75_IBA1

description: Library name: Sample 26

value: Microglia

value: FACS-sorted with IBA1 antibody

value: Left parietal


title: Col0, leaf, LD, biorep2, RNAseq

description:
Library name: RNAseq_wt_rep2
wt_3_LD


title: PBMC 2, GEX

description:
Library name: GEX_PBMC2
count matrix for all samples included

value: Mixed (Normal, cSLE, CHAI)


title: U87_nox_3

city: Lund

first: Mattias

last: Belting

address: Barngatan 4

department: Department of Clinical Sciences, Division of Oncology

country: Sweden

institute: Lund University

description:
Replicate 3
200118400033_G

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Illumina BeadChip data was processed using the R statistical language (v4.4.2) within Rstudio. Using limma (v3.62.1) package, probe profiles were imported (limma::read.ilmn), then normalized using limma's background correction method for Illumina BeadChips (limma::nqec). Probe IDs wer annotated against the HumanHt12v4 annotation using illuminaHumanv4.db (v1.26.0), then reannotated against org.Hs.eg.db (v3.20.0) to reduce the number of unannotated probes and deprecated identifiers. Probes with no annotation and below-threshold detection (p < 0.05 in at least three arrays) were excluded from downstream analysis. Analysis of differentially expressed genes was performed with limma (v3.62.1) package in R according to best practices, such as design matrix was built (stats::model.matrix), a linear model was fitted (limma::lmFit), a contrast matrix was constructed (limma::makeContrast), coefficients and errors were estimated (limma::contrast.fit), empirical Bayes statistics moderation was applied (limma::eBayes), and finally DEGs were extracted using limma::topTable.

label: Biotin

source_name: U87MG glioblastoma cell line, normoxia

label_protocol: Biotinylated cRNA were prepared with the Illumina® TotalPrep™ RNA Amplification Kit.

growth_protocol: Cells were routinely cultured in high-glucose DMEM supplemented with 10% FBS, 2 mM L-glutamine, 100 U/mL penicillin and 100 µg/mL streptomycin in a humidified atmosphere of 5% CO2 at 37°C. To investigate the effects of acidosis, cells were cultured for indicated timepoints in pH 6.4 medium (or pH 7.4 = Ctrl) supplemented with HEPES (20 mM), MES sodium salt (20 mM) and MOPS (20 mM). Medium pH was adjusted using 1 M HCl and/or 1 M NaOH, and sterile filtered prior to usage. For hypoxia experiments, cells were incubated in a humidified Sci-tive NN Hypoxia workstation set at 5 % CO2, 94 % N2, 1 % O2, and 37°C.

extract_protocol: All samples were dissolved in 250 μl lysis solution provided by the RNAeasy mini kit (Qiagen) for RNA isolation according to the manufacturer’s instructions. Quality control was performed with Agilent Bioanalyser.

treatment_protocol: For acidosis-adapted cells were chronically cultured at pH 6.4 for 10 weeks. Control, non-adapted cells were grown under the same conditions but at physiological pH 7.4. For short-term acidosis treatment cells grown at pH 6.4 or 7.4 (pH control) for 48 h. For short-term hypoxia cells were grown at hypoxic (1% oxygen) or normoxic (21% oxygen) conditions for 48 h.

value: Brain

value: Normoxia (21 % O2) 48 h


title: Group23

city: Jinan

first: Huirui

state: -- None selected --

address: 44 Wenhuaxi Road

institute: Shandong University

description:
Library name: Group23
Group2_3

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using hisat2 v2.0.5。
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Trapnell,Cole et al., Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol, 2010. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: mmp10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Lung tissues were lysed in TRIzol reagent, and total RNA was extracted by using a Rapid RNA Extraction Kit per the manufacturer’s protocol. The integrity of the RNA was verified via agarose gel electrophoresis, and the RNA concentrations were quantified with a NanoDrop spectrophotometer.
RNA-Seq libraries were prepared and sequenced on an Illumina NovaSeq 6000. The index of the reference genome was built by using HISAT2 (v2.0.5), and paired-end clean reads were aligned to the reference genome.

value: aged


title: Col0, leaf, LD, biorep1, RNAseq

description:
Library name: RNAseq_wt_rep1
wt_2_LD


title: HU71_IBA1

description: Library name: Sample 25

value: Cerebral Cortex

value: Batch 2

value: M

value: Right occipital


title: Group22

description:
Library name: Group22
Group2_2

value: lung


title: HU29_IBA1

description: Library name: Sample 24

value: F

value: Left frontal


title: thfs, leaf, LD, biorep2, RNAseq

description:
Library name: RNAseq_t_rep2
t_3_LD

value: leaf

value: thfs

value: long day


title: HU8_IBA1

description: Library name: Sample 23

value: Microglia

value: Batch 1


title: U87_nox_1

description:
Replicate 1
200118400033_H


title: HU46_IBA1

description: Library name: Sample 22

value: FACS-sorted with IBA1 antibody


title: HU54_IBA1

description: Library name: Sample 21

value: Right parietal


title: Group21

description:
Library name: Group21
Group2_1


title: mt, leaf, LD, biorep3, RNAseq

description:
Library name: RNAseq_mt_rep3
mt_4_LD

value: mt


title: thfs, leaf, LD, biorep3, RNAseq

description:
Library name: RNAseq_t_rep3
t_4_LD


title: U87_hox_3

description:
Replicate 3
200118400035_E

source_name: U87MG glioblastoma cell line, short-term hypoxia

value: Brain

value: Hypoxia (1 % O2) 48 h


title: U87_hox_2

description:
Replicate 2
200118400035_H


title: U87_nox_2

description:
Replicate 2
200118400035_L

value: Normoxia (21 % O2) 48 h


title: Group11

description:
Library name: Group11
Group1_1

value: young


title: mt, leaf, LD, biorep2, RNAseq

description:
Library name: RNAseq_mt_rep2
mt_3_LD


title: thfs, leaf, LD, biorep1, RNAseq

description:
Library name: RNAseq_t_rep1
t_2_LD


title: U87_aactrl74_2

description:
Replicate 2
200118400068_D

source_name: U87MG glioblastoma cell line, pH control

value: Neutral pH (pH 7.4) 48 h


title: HU31_IBA1

description: Library name: Sample 20

value: Cerebral Cortex

value: Batch 2

value: M


title: mthfd1-1, leaf, LD, biorep2, RNAseq

description:
Library name: RNAseq_m_rep2
m_3_LD


title: mt, leaf, LD, biorep1, RNAseq

description:
Library name: RNAseq_mt_rep1
mt_2_LD


title: mthfd1-1, leaf, LD, biorep3, RNAseq

description:
Library name: RNAseq_m_rep3
m_4_LD


title: Group13

description:
Library name: Group13
Group1_3

value: lung


title: heart tissue 8,Terf2(f,+)

city: shanghai

first: Jing

last: Ye

address: Ruijin 2nd Road

institute: Shanghai Jiao Tong University Medical School Affiliated Ruijin Hospital: Shanghai, CN

description:
Library name: Sample 8
10x Genomics

library_source: transcriptomic single cell

data_processing:
The preprocessing procedures were carried out using CellRanger software (version 7.0.1). Filtering was done for cells with fewer than 200 genes, UMIs under 1000, and log10GenesPerUMI below 0.7. Additionally, low-quality cells were eliminated if mitochondrial genes accounted for more than 15% of the counts and haemoglobin genes for more than 5%. To find possible doublets, DoubletFinder (version 2.0.3) was also used. The postprocessing procedures were carried out using Seurat (version 4.0.0). The FindVariableGenes function was used to find the genes with the highest variability. Using the FindClusters function, graph-based clustering was employed to cluster cells based on their gene expression profile. Using the RunUMAP function and the 2-dimensional uniform manifold approximation and projection (UMAP) technique, the cells were visualised. Each cluster's marker genes were found using the FindAllMarkers tool. SingleR was used to help with cell-type annotations (version 1.4.1). The FindMarkers feature was used to identify differentially expressed genes (DEGs). Significant differential expression was defined as | fold change | >1.5 and a Benjamin false discovery rate (FDR)-corrected p-value <0.05. Sequencing and bioinformatics analysis were performed by OE Biotech Co., Ltd. (Shanghai, China). The Protein-Protein Interaction Networks (PPI), GO and KEGG pathway enrichment analysis of DEGs was performed on STRING database (https://string-db.org/).
Assembly: Mouse mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell nuclei

molecule: nuclear RNA

source_name: heart tissue

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Then Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed,  and index adaptor ligated and library amplification.
After a sequence of procedures, including lysis, centrifugation, and filtration, produced single-nucleus suspensions. The 10× Genomics platform (version 3.1) was used to load isolated nuclei. Following the manufacturer's instructions, subsequent barcoding, cDNA synthesis, and library creation were carried out.

value: heart tissue

value: Goblet cells


title: heart tissue 9,Terf2(f,+)

description:
Library name: Sample 9
10x Genomics


title: U87_aactrl74_3

description:
Replicate 3
200118400068_A


title: HU39_IBA1

description: Library name: Sample 19

value: Left frontal


title: Group12

description:
Library name: Group12
Group1_2


title: HU44_GFAP

description: Library name: Sample 18

value: Astrocytes

value: FACS-sorted with GFAP antibody

value: F

value: Right frontal


title: mthfd1-1, leaf, highCO2, biorep2, BSseq

description: Library name: BSseq_m_h_rep2

library_source: genomic

molecule: genomic DNA

value: leaf


title: heart tissue 7,Terf2(f,+)

description:
Library name: Sample 7
10x Genomics


title: U87_hox_1

description:
Replicate 1
200118400033_I

value: Brain


title: U87_aapH64_3

description:
Replicate 3
200118400035_B

source_name: U87MG glioblastoma cell line, short-term acidosis

value: Acidosis (pH 6.4) 48 h


title: heart tissue 6,Terf2(f,f)

description:
Library name: Sample 6
10x Genomics


title: mthfd1-1, leaf, LD, biorep1, RNAseq

description:
Library name: RNAseq_m_rep1
m_2_LD

value: long day


title: mthfd1-1, leaf, highCO2, biorep1, BSseq

description: Library name: BSseq_m_h_rep1


title: U87_selctrlpH74_3

description:
Replicate 3
200118400035_D

source_name: U87MG glioblastoma cell line, non-adapted

value: Neutral pH (pH 7.4) 10 weeks


title: HU64_GFAP

description: Library name: Sample 17

value: Biilateral parietal


title: HU75_GFAP

description: Library name: Sample 16

value: Cerebral Cortex

value: Left parietal


title: U87_aapH64_1

description:
Replicate 1
200118400033_B


title: Col0, leaf, highCO2, biorep2, BSseq

description: Library name: BSseq_wt_h_rep2

value: wild type


title: heart tissue 3,Terf2(+,+)

description:
Library name: Sample 3
10x Genomics


title: HU71_GFAP

description: Library name: Sample 14

value: Batch 2

value: M

value: Right occipital


title: heart tissue 2,Terf2(+,+)

description:
Library name: Sample 2
10x Genomics

value: heart tissue

value: Goblet cells


title: heart tissue 5,Terf2(f,f)

description:
Library name: Sample 5
10x Genomics


title: heart tissue 4,Terf2(f,f)

description:
Library name: Sample 4
10x Genomics


title: HU34_GFAP

description: Library name: Sample 15

value: Astrocytes

value: FACS-sorted with GFAP antibody


title: U87_aactrl74_1

description:
Replicate 1
200118400068_K

value: Neutral pH (pH 7.4) 48 h


title: mthfd1-1, leaf, controlCO2, biorep1, BSseq

description: Library name: BSseq_m_c_rep1

value: leaf


title: Col0, leaf, highCO2, biorep1, BSseq

description: Library name: BSseq_wt_h_rep1


title: U87_selpH647_2

description:
Replicate 2
200118400035_G

source_name: U87MG glioblastoma cell line, acidosis adapted

value: Brain

value: Acidosis (pH 6.4) 10 weeks


title: U87_aapH64_2

description:
Replicate 2
200118400068_B

value: Acidosis (pH 6.4) 48 h


title: Fe R_2

city: Nanjing, Jiangsu

first: xuan

last: zhao

address: 300 Guangzhou Road

department: Orthopedics

institute: The First Affiliated Hospital of Nanjing Medical University

data_processing:
fastp version 0.17.1
HISAT2 version 2.1.0
String Tie v1.3.4d
DESEQ2 v1.18.1
R version 3.4.3
Assembly: gencode v27
Supplementary files format and content: xls files include RPKM values for each Sample

source_name: microglia

extract_protocol:
Total RNA was extracted using TAKARA RNAiso Plus#9109 following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US). RNA degradation and contamination was monitored on 1% agarose gels. RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) .  RNA concentration was measured using Qubit® RNA Assay Kit in Qubit®2.0 Flurometer (Life Technologies, CA, USA).
Quality RNA samples were converted into cDNA libraries using VAHTSTM mRNA-seq V2 Library Prep Kit for Illumina® (NR601, Vazyme, NanJing, China). VAHTSTM DNA Clean Beads (Vazyme #N411) in this study was used to purify the fragments during the process of library constructing. The purified products were enriched with 12-15 cycles of PCR to create the final cDNA library. Finally, libraries were sequenced on the Illumina NovaSeq 6000 according the manufacturer's protocols.

treatment_protocol: Microglia  were treated with culture medium from ferroptotic BMDMs and normal BMDMs.

value: microglia

value: WT

value: FeM CM-treated


title: HU70_GFAP

description: Library name: Sample 13

source_name: Cerebral Cortex

value: Cerebral Cortex

value: F

value: Left temporal


title: U87_selpH647_3

description:
Replicate 3
200118400035_F


title: U87_selpH647_1

description:
Replicate 1
200118400035_K


title: Fe R_1


title: miRNA_Active CD4 T

city: Beijing

first: Dong

last: Zhang

address: #95 Yongan Street

institute: Beijing Friendship Hospital

description:
miRNA
ACD

data_processing:
Illumina Casava1.8 software used for basecalling.
Indexes of the reference genome were built using Bowtie v2.0.6 and paired-end clean reads were aligned to the reference genome using TopHat v2.0.9.
HTSeq v0.6.1 was used to count the read numbers mapped of each gene. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
miRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010): Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Genome_build: mm8
Supplementary_files_format_and_content: txt files include RPKM values or TPM for each Sample.

source_name: spleen and lymph node

growth_protocol: Spleen and lymph node CD4+CD25- T cells were separated according to CD8/NK1.1/CD25/Ter119/CD19/TCRgd-negative selection with LS columns.

extract_protocol:
CD3+CD4+CD25- naïve CD4 T cells, CD3+CD4−CD8−NK1.1− DNT cells and CD3+CD4+CD8−NK1.1− activated CD4 T cells were sorted using a FACSAriaII sorter
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: CD4+CD25- T cells were incubated with mDCs at the ratio of 4:1 with the stimulation of 50 ng/mL rmIL-2 for 7 days

tag: strain

tag: cell markers

value: T cell

value: spleen and lymph node


title: miRNA_Naive CD4 T

description:
miRNA
NCD


title: mt, leaf, LD, biorep2, BSseq

description: Library name: BSseq_mt_rep2

value: mt

value: long day


title: HU67_GFAP

description: Library name: Sample 11

value: Astrocytes

value: Batch 2

value: M

value: Right frontal


title: HU69_GFAP

description: Library name: Sample 12

value: FACS-sorted with GFAP antibody

value: Right temporal


title: mthfd1-1, leaf, controlCO2, biorep2, BSseq

description: Library name: BSseq_m_c_rep2

value: leaf


title: U87_selctrlpH74_1

description:
Replicate 1
200118400068_I

value: Brain

value: Neutral pH (pH 7.4) 10 weeks


title: miRNA_DNT

description:
miRNA
LCD


title: HU43_GFAP

description: Library name: Sample 9

value: Right parietal


title: Col0, leaf, controlCO2, biorep1, BSseq

description: Library name: BSseq_wt_c_rep1

value: wild type


title: heart tissue 1,Terf2(+,+)

description:
Library name: Sample 1
10x Genomics

value: heart tissue

value: Goblet cells


title: HU60_GFAP

description: Library name: Sample 8

value: Cerebral Cortex

value: F


title: U87_selctrlpH74_2

description:
Replicate 2
200118400035_I


title: HU62_GFAP

description: Library name: Sample 10

value: Bilateral frontal


title: Col0, leaf, controlCO2, biorep2, BSseq

description: Library name: BSseq_wt_c_rep2


title: HU58_GFAP

description: Library name: Sample 7


title: NC R_2

value: microglia

value: WT

value: C CM-treated


title: Fe R_3

value: FeM CM-treated


title: HU52_GFAP

description: Library name: Sample 4

value: Astrocytes

value: Batch 2

value: Left parietal


title: mthfd1-1, leaf, LD, biorep2, BSseq

description: Library name: BSseq_m_rep2

value: leaf

value: long day


title: U2OS

description:
Library name: Sample 4
U2OS

data_processing:
Raw sequencing reads were assessed for quality using FastQC.
Adapter sequences and low-quality bases were trimmed with Trimmomatic (v0.36) using parameters TRAILING:20, MINLEN:25, and CROP:235.
Clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2.
Gene-level read counts were obtained with HTSeq.
Assembly: Homo sapiens reference genome GRCh38 (hg38).
Supplementary files format and content: Read count matrix in .xlsx format, where rows represent genes and columns represent samples.

extract_protocol:
Total RNA was extracted from EVs using TRIzol reagent according to the manufacturer’s protocol. RNA quantity and integrity were assessed using the Agilent 2200 TapeStation and Qubit® 2.0 Fluorometer.
RNA-seq libraries were constructed using the NEBNext® Ultra™ RNA Library Prep Kit for Illumina (NEB, USA) following the manufacturer’s instructions


title: mRNA_Naive CD4 T_2

description:
mRNA
NCD_2

value: T cell

value: spleen and lymph node


title: NC R_1


title: SJSA1

description:
Library name: Sample 3
SJSA1


title: thfs, leaf, LD, biorep1, BSseq

description: Library name: BSseq_t_rep1

value: thfs


title: mthfd1-1, leaf, LD, biorep1, BSseq

description: Library name: BSseq_m_rep1


title: mRNA_Active CD4 T_1

description:
mRNA
ACD_1


title: HU56_GFAP

description: Library name: Sample 6

value: FACS-sorted with GFAP antibody

value: Right occipital


title: thfs, leaf, LD, biorep2, BSseq

description: Library name: BSseq_t_rep2


title: NC R_3


title: HU54_GFAP

description: Library name: Sample 5

value: Cerebral Cortex

value: Right parietal


title: mt, leaf, LD, biorep1, BSseq

description: Library name: BSseq_mt_rep1

value: mt


title: mRNA_Naive CD4 T_1

description:
mRNA
NCD_1


title: MNNGHOS

description:
Library name: Sample 2
MNNGHOS

source_name: MNNG/HOS

value: MNNG/HOS


title: HU51_GFAP

description: Library name: Sample 3

value: M

value: Left frontal


title: mRNA_Active CD4 T_2

description:
mRNA
ACD_2


title: HU50_GFAP

description: Library name: Sample 2


title: mRNA_DNT_2

description:
mRNA
LCD_2


title: MOPS-1Cu-A

status: Public on Jan 03 2026

city: Ann Arbor

first: Peng

last: Peng

state: MI

address: 1351 Beal Avenue

institute: University of Michigan

description:
Library name: SAMPLES12
MOPS-1CuA

data_processing:
Read quality was assessed with FastQC and the adapter sequence was removed using Cutadapt
Reads were mapped against the reference genome of Msn. trichosporium OB3b using STAR
Counting of the reads was performed using featureCounts
Analysis of the differential gene expression based on the reads counting was performed with DESeq2
Assembly: RNA reads were mapped against the reference genome of Msn. trichosporium OB3b using STAR
Supplementary files format and content: csv files including comparison of differential gene expression under tested conditions

organism: Methylosinus trichosporium OB3b

source_name: Bacterial cell

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen, Hilden, Germany)
RNA library was prepared following a standard procedure of Ribo-depletion method

value: Bacterial cell

value: WT

value: methanol+copper+MOPS


title: HU47_GFAP

description: Library name: Sample 1

data_processing:
Quality control was re-assessed using FastQC version 0.11.8, with Cutadapt for removing the adaptor sequences.
Assembly: Alignment to tRFs was done using MINTmap to MINTbase v2.0 and to microRNA using miRDeep2 to miRbase 22.1.
Supplementary files format and content: Tab-limited csv files with microRNA, tRNA fragments and tRNA fragment family raw counts for each sample.

extract_protocol:
Neurosurgery-obtained fresh human brain specimens were lightly fixed with formalin and broken down to single nuclei with cytoplasmatic fractions. The cell suspensions were next stained cell-type-specific antibodies (NeuN for neurons, Iba1 for microglia, Gfap for astrocytes, Olig2 for oligodendrocytes) and FACS-sorted to distinct cell type populations. RNA from FACS-sorted cell populations was extracted using the RNeasy FFPE kit (Qiagen, 73504), according to the manufacturer’s instructions.
Libraries were constructed using the D-Plex Small RNA-seq Kit from Illumina (Diagenode, C05030001), using 500 and 1000 pg/sample in Batch 1 and Batch 2, respectively.

value: Astrocytes

value: Batch 2


title: MeOH-1Cu-B

description:
Library name: SAMPLES10
MeOH-1CuB

value: methanol+copper


title: MOPS-1Cu-B

description:
Library name: SAMPLES13
MOPS-1CuB


title: 143B

description:
Library name: Sample 1
143B


title: CH4-0Cu-C

description:
Library name: SAMPLES3
CH4-0CuC

value: methane


title: MeOH-1Cu-C

description:
Library name: SAMPLES11
MeOH-1CuC


title: CH4-0Cu-A

description:
Library name: SAMPLES1
CH4-0CuA


title: EOP+EP-19

city: Xiamen

first: Xing

address: 422, Siming South Road

institute: Xiamen University

description:
Library name: EOP+EP-19
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

data_processing:
The source code for the analysis of scBiopsy-seq is available on github (https://github.com/linl-linl/scBiopsy-seq).
Assembly: GRCh38,GRCh38.105, GRCm38 and GRCm38.102
Supplementary files format and content: matrix files

source_name: Ascites

extract_protocol:
The capillary tip was filled with 1.5 μL of mixed solution (2.5 μM biotinylated-oligo-dT primer, 2.5 mM dNTP (AD101–12, TransGen Biotech, Beijing, China), 0.4 U·μL−1 Murine RNase Inhibitor (GMP4102PA-01, Vazyme Biotech Co., Ltd., Nanjing, China)), and then connected to the work electrode of the ultra-micro extraction instrument (Rayme Biotechnology Co., Ltd., Jiangsu, China). The counter electrode and the reference electrode were immersed in the culture medium within the confocal dish. The cells to be extracted were visualized by microscope and the preloaded capillary was gradually moved downward until it touched the cytoplasm of the selected cell. The tip of the capillary was then inserted into the cytoplasm, with a deformation observed in the selected cell. By setting the applied voltages and the duration of current application, a precisely controlled volume was extracted from the cell. After that, the capillary was retracted out of the cell, taken out of the extraction instrument and placed at -80°C for RNA storage.
Once it was required to undergo the RNA library construction, the capillary was connected to the work electrode again. The cellular contents within the capillary were injected into the top plate of the DMF device, enabling the subsequent RNA library processing on the DMF system. The lysis buffer (2.5 μM biotinylated-oligo-dT primer, 2.5 mM dNTP, 0.4 U·μL−1 Murine RNase Inhibitor and 0.2% Triton-X-100(A110694, Sangon Biotech, Shanghai, China) was introduced and mixed with the cellular contents at 72°C for 3 minutes for complete RNA release. Then the reverse transcription (RT) mix (1.7 μM biotinylated-TSO oligo, 5 × HiScript II RT buffer (Vazyme Biotech Co., Ltd., Nanjing, China), 1.7 U·μL−1 Murine RNase Inhibitor, 19 U·μL−1 HiScript II Reverse Transcriptase (R201, Vazyme Biotech Co., Ltd., Nanjing, China) and 0.05% Pluronic F68 (24040032, ThermoFisher, America)) was introduced to initiate the RT reaction at 42°C for 90 minutes, which was stopped by heat at 70°C for 15 min. After that, the PCR mix (2 × KAPA HiFi HotStart ReadyMix (KK2602, KAPA, America), 0.06 μM Biotinylated-ISPCR oligo and 0.05% Pluronic F68) was introduced to amplify the cDNAs (95°C 3 minutes, 25 cycles of 98°C 30 s, 65°C 45 s and 72°C 6 minutes, followed by a final step at 72˚C for 5 min). The products were recovered from the DMF device into a 200-μL eppendorf tube, purified with 0.6 × DNA clean beads (Vazyme Biotech Co., Ltd., Nanjing, China) and quantified by qubit 3.0. Then 1 ng of the products were utilized and processed by sequencing-ready library construction kits (TD503, Vazyme). The library was purified twice with 0.6 × DNA clean beads (N411, Vazyme Biotech Co., Ltd., Nanjing, China) and sequenced by Novaseq500 according to the manufacturer’s instructions.

treatment_protocol: The cellular contents of SW480 cells were extracted initially prior to the ARV771 treatment, designated as the sample at 0 h. Immediately thereafter 250 nM ARV771 was added to the culture medium, and the cells were extracted at 1 h and 4 h.

value: Ascites

value: Macrophage


title: MeOH-0Cu-B

description:
Library name: SAMPLES8
MeOH-0CuB

value: methanol


title: F22_KD

city: Suita

first: Daisuke

last: Motooka

state: Osaka

address: 3-1, Yamadaoka

country: Japan

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

description: Library name: GA43710

data_processing:
Sequencing was performed on NovaSeq 6000 platform in a 101-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Generated reads were mapped to the dog (ROS_Cfam_1.0) reference genome using Hisat2 v2.1.0.
Fragments per kilobase of exon per million mapped fragments (FPKMs) were calculated using cuffdiff of Cufflinks 2.2.1 with parameter -max-bundle-frags 50000000.
Assembly: ROS_Cfam_1.0 (GCF_014441545.1)
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

organism: Canis lupus familiaris

source_name: MDCK

extract_protocol:
The cells (3 × 10^4) were seeded on 36-mm dishes and subjected to siRNA transfection. Eighteen hours after the second transfection, RNA was extracted from the cells using the miRNeasy Mini Kit (QIAGEN, 217004), according to the manufacturer’s instructions.
The cDNA libraries were constructed according to the manufacturer's instructions using the TruSeq Stranded mRNA Library Prep (Illumina, Inc., San Diego, CA).

value: MDCK

value: Canine kidney epithelial

value: PRL2-/-; PRL1+/- clone #2


title: mRNA_DNT_1

description:
mRNA
LCD_1

value: T cell

value: spleen and lymph node


title: MeOH-0Cu-A

description:
Library name: SAMPLES7
MeOH-0CuA


title: Col0, leaf, LD, biorep1, BSseq

description: Library name: BSseq_WT_rep1

value: leaf

value: wild type

value: long day


title: EOP+EP-18

description:
Library name: EOP+EP-18
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

value: WT


title: F22_ctrl

description: Library name: GA43709

value: control siRNA


title: CH4-1Cu-C

description:
Library name: SAMPLES6
CH4-1CuC

value: Bacterial cell

value: methane+copper


title: EOP+EP-17

description:
Library name: EOP+EP-17
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: EOP+EP-16

description:
Library name: EOP+EP-16
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: D7_KD

description: Library name: GA43708

value: PRL2-/-; PRL1+/- clone #1


title: CH4-0Cu-B

description:
Library name: SAMPLES2
CH4-0CuB

value: methane


title: EOP+EP-12

description:
Library name: EOP+EP-12
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

value: Ascites


title: EOP+EP-14

description:
Library name: EOP+EP-14
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

value: Macrophage


title: EOP+EP-15

description:
Library name: EOP+EP-15
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: wt_ctrl

description: Library name: GA43705


title: EOP+EP-8

description:
Library name: EOP+EP-8
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: CH4-1Cu-A

description:
Library name: SAMPLES4
CH4-1CuA


title: MeOH-1Cu-A

description:
Library name: SAMPLES9
MeOH-1CuA

value: methanol+copper


title: CH4-1Cu-B

description:
Library name: SAMPLES5
CH4-1CuB


title: EOP+EP-10

description:
Library name: EOP+EP-10
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: wt_KD

description: Library name: GA43706

value: MDCK


title: EOP+EP-11

description:
Library name: EOP+EP-11
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: VIPKO Hypoxia 2

city: Hempstead

first: Anthony

last: Szema

state: New York

address: 500 Hofstra Blvd,

department: Department of Occupational Medicine, Epidemiology and Prevention,

institute: Donald and Barbara Zucker School of Medicine

description:
Library name: A4_12_408
Normalized_Gene_counts_all_samples.cvs : A4_12_408

data_processing:
Partek Flow genomic suite is used for data processing steps genome assembly and differential gene expression are derived after alignment to mm10.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partekflow genomic suite (parameter- Quality limit: 0.05)
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Whole Lung

extract_protocol:
RNA was harvested using the RNeasy Mini Plus kit (Qiagen). 1 μg of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ II Directional RNA Library Prep with Sample Purification Beads following manufacturer's protocols.

value: Whole Lung

value: VIP Knockdown

value: chronic hypoxia (10% O2 ),4 weeks

value: Batch 1


title: EOP-EP-14

description:
Library name: EOP-EP-14
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: D7_ctrl

description: Library name: GA43707

value: Canine kidney epithelial


title: VIPKO Hypoxia 1

description:
Library name: A4_11_401
Normalized_Gene_counts_all_samples.cvs : A4_11_401


title: Col0, leaf, LD, biorep2, BSseq

description: Library name: BSseq_WT_rep2

value: leaf

value: wild type


title: VIPKO Hypoxia 3

description:
Library name: A4_13_412
Normalized_Gene_counts_all_samples.cvs : A4_13_412


title: EOP-EP-12

description:
Library name: EOP-EP-12
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

value: WT


title: EOP-EP-13

description:
Library name: EOP-EP-13
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: VIPKO Hypoxia 4

description:
Library name: A4_14_413
Normalized_Gene_counts_all_samples.cvs : A4_14_413


title: EOP-EP-10

description:
Library name: EOP-EP-10
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: VIPKO Hypoxia 5

description:
Library name: A4_15_421
Normalized_Gene_counts_all_samples.cvs : A4_15_421


title: VIPKO Normoxia4

description:
Library name: A3_21_423
Normalized_Gene_counts_all_samples.cvs : A3_21_423

value: Normoxia (21% O2),4 weeks


title: EOP+EP-13

description:
Library name: EOP+EP-13
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: WT Normoxia 4

description:
Library name: A2_7_69
Normalized_Gene_counts_all_samples.cvs : A2_7_69

value: Wild Type


title: WT Normoxia 6

description:
Library name: A2_9_82
Normalized_Gene_counts_all_samples.cvs : A2_9_82


title: VIPKO Normoxia2

description:
Library name: A3_19_425
Normalized_Gene_counts_all_samples.cvs : A3_19_425


title: WT Normoxia 5

description:
Library name: A2_8_77
Normalized_Gene_counts_all_samples.cvs : A2_8_77


title: EOP-EP-8

description:
Library name: EOP-EP-8
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: EOF+EP+DMF-17

description:
Library name: EOF+EP+DMF-17
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: EOF+EP+DMF-18

description:
Library name: EOF+EP+DMF-18
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: VIPKO Normoxia3

description:
Library name: A3_20_411
Normalized_Gene_counts_all_samples.cvs : A3_20_411


title: EOP-EP-11

description:
Library name: EOP-EP-11
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: EOF+EP+DMF-16

description:
Library name: EOF+EP+DMF-16
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: WT Normoxia 3

description:
Library name: A2_6_68
Normalized_Gene_counts_all_samples.cvs : A2_6_68


title: WT Normoxia 2

description:
Library name: A2_24_67
Normalized_Gene_counts_all_samples.cvs : A2_24_67


title: EOF+EP+DMF-19

description:
Library name: EOF+EP+DMF-19
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: EOF+EP+DMF-15

description:
Library name: EOF+EP+DMF-15
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: EOF+EP+DMF-12

description:
Library name: EOF+EP+DMF-12
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: WT Normoxia 1

description:
Library name: A2_10_81
Normalized_Gene_counts_all_samples.cvs : A2_10_81


title: EOF+EP+DMF-10

description:
Library name: EOF+EP+DMF-10
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: EOP-EP-9

description:
Library name: EOP-EP-9
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: EOF+EP+DMF-13

description:
Library name: EOF+EP+DMF-13
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: VIPKO Normoxia1

description:
Library name: A3_18_424
Normalized_Gene_counts_all_samples.cvs : A3_18_424


title: WT  Hypoxa 2

description:
Library name: A1_2_62
Normalized_Gene_counts_all_samples.cvs : A1_2_62

value: chronic hypoxia (10% O2),4 weeks


title: WT Hypoxia 4

description:
Library name: A1_4_74
Normalized_Gene_counts_all_samples.cvs : A1_4_74


title: 38

city: Cambridge

first: Samuel

last: Wright

state: MA

address: 415 Main St.

institute: Broad Institute of MIT and Harvard

description:
Library name: Sample 13
10x Genomics

data_processing:
CellRanger v7.0.0 was used to align sequencing reads to the GRCh38 human genome reference. Cell barcodes were filtered out if they met any of the following criteria: (1) fewer than 100 detected genes, (2) more than 6,000 detected genes, or (3) over 40% of unique molecular identifiers (UMIs) mapping to the mitochondrial genome.
Assembly: Human GRCh38
Supplementary files format and content: Hierarchical data format (h5) files

source_name: Primary melanoma tumor

extract_protocol:
Tissue was collected fresh in phosphate-buffered saline. For single-cell RNA-sequencing, fresh melanoma tumors were dissociated and scRNA-seq libraries were prepared using the 10x Genomics chromium controller and reagent kits as described below.
Tumor samples were processed using the Human Tumor Dissociation Kit (Miltenyi Biotec, Cat#130-095-929) following established protocols. Initially, tumor biopsies were minced in 1.5 mL Eppendorf tubes containing a mixture of enzymes H, R, and A (provided with the kit) and RPMI medium, and tubes were incubated in an Eppendorf thermomixer at 37°C with continuous shaking at 400 rpm for 15 minutes. Post-incubation, the dissociated cell suspension was filtered through a 50 μm filter (Sysmex, Cat#04-004-2327), followed by a wash with 5 mL of RPMI supplemented with 10% heat-inactivated fetal calf serum (FCS). The filtrate was centrifuged at 1500 rpm for 5 minutes at 4°C. After discarding the supernatant, ACK lysis buffer (Gibco, Cat#A1049201) was added to the cell pellet, gently mixed, and centrifuged under the same conditions. The ACK buffer was removed, and the cells were resuspended in RPMI with 10% heat-inactivated FCS. Cell concentration and viability were assessed using trypan blue with a Bright-Line hemocytometer (Cat#1492). For samples with viability below 70%, viable cells were enriched using a modified EasySep Dead Cell Removal (Annexin V) kit protocol (STEMCELL, Cat#17899) as described by Fang et al. (2024). After this step, cell counts and viability were reassessed, and samples were immediately prepared for single-cell RNA sequencing (scRNA-seq). Gene expression (GEX) libraries were constructed using the 10x Genomics Chromium NextGEM Single Cell V(D)J Reagents Kits v1.1 (PN-1000165, PN-1000120, PN-1000213) and the Chromium NextGEM Single Cell 5’ Reagent Kits v2 (PN-1000263, PN-1000286, PN-1000215) according to the manufacturer's guidelines. Quality control of amplified cDNA and generated libraries included quantification using the Qubit dsDNA High Sensitivity Kit (Invitrogen, Cat#Q32854) and size distribution analysis with the Agilent High Sensitivity Bioanalyzer DNA Kit (Cat#5067-4626). Sequencing was performed on an Illumina NextSeq 500 sequencer using the 75-cycle kit (Cat#20024906). The read configurations were as follows: 1. NextGEM v1.1: Read 1 - 26 cycles; Read 2 - 55 cycles; 2. NextGEM v2: Read 1 - 26 cycles; Read 2 - 46 cycles.

value: Primary melanoma tumor


title: Old Mice, Control, 10 days, ATAC

city: Baltimore

first: Yang

last: Jin

state: MD

address: 620 Boulton St. Bel Air

institute: Johns Hopkins University

description:
Library name: Old_Con_10d_ATAC
Old mice, DMSO treatment 10 days, snATACseq

library_source: genomic single cell

data_processing:
snRNA-seq samples were analyzed using R package Seurat v4.1.4108.All snATAC-seq samples were analyzed using Seurat v4.1.4108 and Signac v1.10.0111 packages follow the standard pipeline.
Assembly: GRCm38
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: Eye

growth_protocol: Experiments were in accordance with NIH guidelines and approved by the Johns Hopkins Animal Care and Use Committee. C56BL/6J mice that were free of the Rd8 mutation (Jackson Labs, Bar Harbor, ME) were given water ad libitum and kept in a 12-hr light–12-hr dark cycle.

extract_protocol:
At 3, 6, and 10 days following the first injection, mice were sacrificed, and their eyes are enucleated. RPE/choroidal cells were scraped from the posterior eye cup and placed in cold 1ml 1X Dulbecco’s PBS. The nuclei from RPE/choroid (3 eyes from male and 3 eyes from female mice per condition) was prepared using the 10X Genomics “Nuclei Isolation Singh et al. 18 from Complex Tissues for Single Cell Multiome ATAC + Gene Expression Sequencing” (10X Genomics, Inc., Pleasanton, CA) protocol. The RPE/choroid was centrifuged for 5 min with 500g at 40C. The pellet was resuspended in 500ml of 0.1X Lysis buffer (10 mM Tris-HCl, pH 7.4,10 mM NaCl, 3 mM MgCl2, 0.1% Tween 20,0.1 % Nonidet P40,0.01 % Digitonin,1% BSA,1 mM DTT, RNase inhibitor 1 U/ml) and incubated for 5 min on ice, washed, and passed through a 70 μm Flowmi Cell Strainer followed by 40 μm Flowmi Cell Strainer, and centrifuged at 500 g for 5 min at 40C. The resulting pellet was washed and resuspended in 0.1X Nuclei buffer containing trypan blue, and nuclei were counted with a Neubauer chamber. The obtained nuclei number were in the range of ~2700 to 10000 nuclei/ml.
SnRNA-seq and snATAC-seq libraries were generated using the Chromium Next GEM single Multiome ATAC+Gene Expression kit protocol (10X Genomics, Inc.). Nuclei resuspended (10-15k) in 0.1X Nuclei Buffer were incubated with a transposition mix containing transposase. Gel Beads in Emulsion (GEMs) were generated by mixing transposed nuclei, barcoded Gel Beads, and partitioning oil on a chromium NEXT GEM Chip controller. After GEM generation, oligonucleotides included Illumina® P5 sequence barcodes for ATAC library and cDNA included an Illumina® TruSeq Read 1 (read 1 sequencing primer), 16 nt 10x Barcode (for GEX), 12 nt unique molecular identifier (UMI) and a 30 nt poly(dT) sequence. Magnetic beads (SILANE) were used to clean up barcoded products from the obtained GEM-RT reaction mixture. ATAC libraries were amplified with 10 PCR cycles and were sequenced on Illumina NovaSeq with 25,000 read pairs per nucleus. RNA libraries were amplified from cDNA with 14 PCR cycles and were sequenced on Illumina NovaSeq with 50,000 reads per nucleus.

treatment_protocol: For experiments, an equal number of male and female mice aged either 3- or 12-months old were given an IVT injection of 250 μg/ml CSC in 1 μl (Murty Pharmaceuticals, Inc. Lexington, KY) or an equal volume (1 μl) of vehicle (DMSO) in both eyes using a microinjection pump (Harvard Apparatus, Holliston, MA, USA) on day 1 and day 3.

value: Eye

value: RPE

value: Old Mice, Control, 10 days

value: DMSO

tag: library type

value: ATAC


title: EOF+EP+DMF-8

description:
Library name: EOF+EP+DMF-8
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

value: Ascites

tag: cell type

value: Macrophage


title: EOF+EP+DMF-11

description:
Library name: EOF+EP+DMF-11
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

tag: tissue


title: WT Hypoxia 1

description:
Library name: A1_1_61
Normalized_Gene_counts_all_samples.cvs : A1_1_61

value: Whole Lung


title: EOF+EP+DMF-20

description:
Library name: EOF+EP+DMF-20
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

tag: cell line


title: EOF+EP+DMF-14

description:
Library name: EOF+EP+DMF-14
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

tag: genotype


title: WT Hypoxia 3

description:
Library name: A1_3_73
Normalized_Gene_counts_all_samples.cvs : A1_3_73

value: Batch 1


title: Old Mice, CSC treatment, 10 days, ATAC

description:
Library name: Old_CSC_10d_ATAC
Old mice, CSC treatment 10 days, snATACseq

value: Old Mice, CSC treatment, 10 days

value: CSC


title: Young Mice, CSC treatment, 10 days, ATAC

description:
Library name: Young_CSC_10d_ATAC
Young mice, CSC treatment 10 days, snATACseq

value: Young Mice, CSC treatment, 10 days


title: Old Mice, Control, 10 days, GEX

description:
Library name: Old_Con_10d_GEX
Old mice, DMSO treatment 10 days, snRNAseq

value: mRNA


title: 592

description:
Library name: Sample 10
10x Genomics


title: WT Hypoxia 5

description:
Library name: A1_5_76
Normalized_Gene_counts_all_samples.cvs : A1_5_76


title: ZE8-4

description:
Library name: ZE8-4
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

organism: Danio rerio

source_name: Cleavage stage

value: Cleavage stage

value: Zebrafish blastomeres

value: Cleavage

value: WT


title: 507

description:
Library name: Sample 11
10x Genomics

value: Primary melanoma tumor


title: 896

description:
Library name: Sample 6
10x Genomics


title: 57

description:
Library name: Sample 12
10x Genomics


title: 627

description:
Library name: Sample 8
10x Genomics


title: Young Mice, Control, 10 days, ATAC

description:
Library name: Young_Con_10d_ATAC
Young mice, DMSO treatment 10 days, snATACseq

value: Eye

value: RPE

value: Young Mice, Control, 10 days


title: Young Mice, CSC treatment, 10 days, GEX

description:
Library name: Young_CSC_10d_GEX
Young mice, CSC treatment 10 days, snRNAseq


title: Old Mice, CSC treatment, 10 days, GEX

description:
Library name: Old_CSC_10d_GEX
Old mice, CSC treatment 10 days, snRNAseq


title: Young Mice, Control, 10 days, GEX

description:
Library name: Young_Con_10d_GEX
Young mice, DMSO treatment 10 days, snRNAseq

value: DMSO


title: EOF+EP+DMF-9

description:
Library name: EOF+EP+DMF-9
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

value: Ascites


title: Young Mice, Control, 6 days, ATAC

description:
Library name: Young_Con_6d_ATAC
Young mice, DMSO treatment 6 days, snATACseq

value: Young Mice, Control, 6 days

value: ATAC


title: 603

description:
Library name: Sample 9
10x Genomics


title: Young Mice, Control, 6 days, GEX

description:
Library name: Young_Con_6d_GEX
Young mice, DMSO treatment 6 days, snRNAseq


title: ZE8-3

description:
Library name: ZE8-3
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: Young Mice, CSC treatment, 6 days, ATAC

description:
Library name: Young_CSC_6d_ATAC
Young mice, CSC treatment 6 days, snATACseq

value: Young Mice, CSC treatment, 6 days


title: 1146

description:
Library name: Sample 5
10x Genomics


title: 1149

description:
Library name: Sample 4
10x Genomics


title: Young Mice, CSC treatment, 6 days, GEX

description:
Library name: Young_CSC_6d_GEX
Young mice, CSC treatment 6 days, snRNAseq


title: ZE8-1

description:
Library name: ZE8-1
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: ZE8-2

description:
Library name: ZE8-2
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.


title: 713

description:
Library name: Sample 7
10x Genomics


title: 1232

description:
Library name: Sample 3
10x Genomics


title: WT_MG_3

first: jianhua

last: zhang

address: gongyebei street No. 23788

institute: Shandong Academy of Agricultural Sciences

description: Library name: WT_MG_3

data_processing:
Raw reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.
Assembly: ASM333518v2
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

organism: Laodelphax striatellus

source_name: midgut

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Approximately 5 µg of total RNA were used to prepare small RNA libraries according to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol.

value: midgut

value: RBSDV-free


title: Young Mice, CSC treatment, 3 days, ATAC

description:
Library name: Young_CSC_3d_ATAC
Young mice, CSC treatment 3 days, snATACseq

value: Young Mice, CSC treatment, 3 days

value: CSC


title: Young Mice, CSC treatment, 3 days, GEX

description:
Library name: Young_CSC_3d_GEX
Young mice, CSC treatment 3 days, snRNAseq

value: mRNA


title: Young Mice, Control, 3 days, GEX

description:
Library name: Young_Con_3d_GEX
Young mice, DMSO treatment 3 days, snRNAseq

value: Young Mice, Control, 3 days


title: Young Mice, Control, 3 days, ATAC

description:
Library name: Young_Con_3d_ATAC
Young mice, DMSO treatment 3 days, snATACseq


title: ZE4-3

description:
Library name: ZE4-3
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.

value: Cleavage stage

value: Zebrafish blastomeres

value: Cleavage


title: WT_MG_1

description: Library name: WT_MG_1


title: 1340

description:
Library name: Sample 2
10x Genomics

value: Primary melanoma tumor


title: WT_MG_2

description: Library name: WT_MG_2


title: WPS3

description:
Library name: WPS3
expression matrix (txt) and original file (fastq)
Each human sample represents a pool of single cells.

source_name: colon

value: colon

value: colon cancer cell line

value: WT


title: 1683

description:
Library name: Sample 1
10x Genomics


title: RB_MG_3

description: Library name: RB_MG_3

value: RBSDV infection


title: ZE4-4

description:
Library name: ZE4-4
expression matrix (txt) and original file (fastq)
Each mouse or zebrafish sample represents data from a single cell.