title: Liver, 500nm, Sample 2

city: Bonn

first: Lisa

middle: Maria

last: Steinheuer

state: NRW

address: Venusberg Campus 1

department: Institute of Experimental Oncology

country: Germany

institute: University Hospital Bonn

description:
Library name: Sample 6 500nm
10X Genomics

data_processing:
The raw sequencing data was  processed with the ‘count’ command of the Cell Ranger software (v7.1.0) provided by 10X Genomics using the refdata-gex-mm10-2020-A reference genome.  All other options were used as per default.
Assembly: refdata-gex-mm10-2020-A
Supplementary files format and content: Tab-delimited text files include cell-barcode names (barcodes.tsv) as well as gene names (features.tsv) corresponding to the count data in matrix.mtx.

molecule: nuclear RNA

extract_protocol:
Nuclei were isolated from approximately 100 mg of fresh-frozen adult liver tissue. Liver tissue was minced, and then immediately transferred into a homogenizer containing 1 ml of ice-cold homogenization buffer (320mM Sucrose, 5mM CaCl2, 3mM Magnesium Acetate, 10mM Tris, 0.1mM EDTA, 0.1% IGEPAL CA-630 (Cat# I8896, Merck), 0.1mM PMSF (Cat# 10837091001, Roche), 1µM flavopiridol, 1mM β-mercaptoethanol and 0.2U/µl RNAse inhibitor in Ultrapure H20). Tissues were homogenized using a glass douncer with five strokes of pestle A and ten strokes of pestle B. The homogenate was passed through a 70 µm cell strainer into a 50 ml falcon tube, and the strainer was washed with 1.65 ml homogenization buffer to achieve a final volume of 2.65 ml. Subsequently, 2.65 ml of gradient medium (50% Optiprep (Cat# D1556, Merck) with 5mM CaCl2, 3mM Magnesium Acetate, 10mM Tris, 0.1mM PMSF and 1mM β-mercaptoethanol in UltraPure H2O) was added to the sample to reach a total volume of 5.3 ml. A 4 ml layer of 29% cushion (29% Optiprep with 150 mM KCl, 30 mM MgCl2, 60mM Tris and 250mM Sucrose in UltraPure H2O) was prepared in ultracentrifuge tubes. The homogenized sample was carefully layered on top of the cushion using a low retention P1000 pipette to avoid disturbing the interface. Centrifugation was performed using an JS13.1 rotor in Avanti high-speed centrifuge (Beckman Coulter) at 10,000 xg, with low acceleration and maximum deceleration at 4°C for 30 minutes. Following centrifugation, supernatants were gently removed, the nuclei were resuspended in 400 µL of resuspension buffer and passed through a 0.35 µm filter. Nuclei were stained with 1 µg/ml DAPI, and mononuclei were sorted using Aria III cell sorter (BD Biosciences) into 200 µl of 10X resuspension buffer (1% BSA with 0.2 U/µL RNase inhibitor and 1 µM flavopiridol in PBS). After sorting, the volume of each sample was diluted accordingly to obtain 1X resuspension buffer. Next, the nuclei were centrifuged at 400 ×g for 3 minutes, followed by 600 ×g for 5 minutes at 4°C. The pellet was resuspended in 100 µl of resuspension buffer for counting, and samples were subsequently diluted to 1100 nuclei/µl.
16,000 nuclei per sample were loaded and used for analysis with the Chromium Single Cell 3' Gene Expression v3.1 Dual Index Kit (Cat# PN-1000269, 10x Genomics) and Gel Beads in Emulsion (GEMs) using the Chromium Next GEM Chip G Single Cell Kit (Cat# PN-1000127, 10x Genomics). After GEM-RT cleanup, pre-amplification of the sample was performed, producing material for cDNA amplification for gene expression library construction. During the reverse transcription (RT) reaction, cDNA tagging was achieved with 16-nucleotide barcodes and 10-nucleotide molecular identifiers followed by using 35 μl for further cDNA amplification. For snRNA-seq library preparation, 25 % of the total cDNA was used to generate gene expression (GEX) libraries. Libraries were prepared and sequenced according to the manufacturer’s protocol using the Dual Index TT Set A (Cat# PN-1000215, 10x Genomics). Final library quality was assessed using a High Sensitivity D5000 assay on a Tape station 4200 (Agilent Technologies) and quantified using the Qubit high-sensitivity dsDNA assay (Invitrogen). Pooled and barcoded libraries were sequenced on an Illumina NextSeq 2000 system with P4 flow cells, achieving an average depth of 30,000 reads per nucleus.

treatment_protocol: Mice were treated weekly with 100mg/kg of 50nm PS, 500nm PS or PBS as a control, for 12 weeks.

value: Liver

value: 20-22 weeks old

value: 500nm polysterene particles


title: mRNA_RIPseq_lin-28(xe197)_input_rep2

status: Public on Jun 09 2026

type: SRA

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: Sample 5

library_source: transcriptomic

data_processing:
RNA-seq data was mapped to the C. elegans genome (ce11) using the Align (qAlign) function from the QuasR (v1.41.2) package in R with splicedAlignement = TRUE, using the aligner HISAT2 (v1.20.0) including an exon-exon junction database (WS270). Gene expression levels were quantified using the qCount() function, counting the reads on the opposite strand of annotated transcripts. For paired-end samples, the first read was considered for counting. For annotations, coding transcript information from WormBase WS270 was used. We further compensated for differences in library sizes by scaling each library to the average library size. Finally, we log2 transformed the data using a pseudo count of 8 (log2(x+8)).
Assembly: ce11
Supplementary files format and content: tab-delimited text file with raw gene expression read counts
Supplementary files format and content: tab-delimited text file with normalized gene expression read counts

molecule: polyA RNA

organism: Caenorhabditis elegans

source_name: whole organism

growth_protocol: Approximately 4.5 millions of synchronized L1s of each genotype were plated on peptone-enriched 2% NGM agar XL plates seeded with E. coli OP50 bacteria (~ 500,000 L1s per plate) and grown for 6 hours at 25°C.

extract_protocol:
At the time of sample collection, animals were harvested, washed three times with M9 buffer, once with 0.1 M KCl and dry pellets were snap frozen in liquid nitrogen. Upon thawing, the pellets were lysed in extraction buffer (50 mM HEPES/KOH (pH 7.4 at 4°C), 150 mM KCl, 5 mM MgCl2, 0.1% (v/v) Triton X-100, 10% (w/v) glycerol, 1 mM PMSF, 1 tablet/10 ml cOmplete Mini Protease Inhibitor Tablets (EDTA-free; Roche, 11836170001), 200 U/ml RNaseOUT Recombinant Ribonuclease Inhibitor (Thermo Fisher Scientific, 10777019)), with mortar and pestle in the presence of liquid nitrogen. Anti-GFP IPs were performed by incubating 3 mg total protein with 50 µl of Dynabeads Protein G (Thermo Fisher Scientific, 10003D) bound to anti-GFP antibody (5 µg/IP; Abcam, ab290). The immunoprecipitated RNA was extracted by directly adding TRI Reagent (MRC, TR-118) to the beads and snap-freezing in liquid nitrogen. For each condition (N2 and HW2805), three IPs were performed in parallel as technical replicates. Three aliquots of input lysate each corresponding to 100 µg total protein were snap-frozen in liquid nitrogen upon addition of TRI Reagent for extraction of the input RNA. RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research; R2062) according to the manufacturer’s protocol including the on column DNase digestion. RNA was eluted in nuclease-free water (Thermo Fisher Scientific, Ambion, AM9937).
Illumina Stranded mRNA-seq

tag: strain

tag: tissue

value: whole organism

tag: genotype

tag: time (h)


title: smallRNA_TC2_WT_36h

description: Library name: Sample 13

data_processing:
The small RNA-seq fastq files were adapter trimmed (TGGAATTCTCGGGTGCCAAGG) at the 3' end using the function preprocessReads() from the R packege QuasR (version 1.26)  and mapped to the C.elegans genome (ce10) with the R package QuasR (version 1.26) using the alignment algorithm Bowtie. The command used to perform the alignments was "proj <- qAlign("samples.txt","BSgenome.Celegans.UCSC.ce10",maxHits=100)". For miRNA quantification, gene annotation from miRBase v22 was used and lifted over to ce10. We extended the genomic coordinates of the 5' end of each miRNA by 3bp on both sides and counted all the reads that started within those regions using the following command: "qCount(proj,matureMirsExt,orientation="same"). To normalize for sequencing depth, each sample was divided by the total number of reads and multiplied by the average library size. Finally the count table was log2 transformed after the addition of a pseudocount of 8 in order to minimize large changes in expression caused by low count numbers.
Assembly: ce10
Supplementary files format and content: tab-delimited text file with raw counts for each sample
Supplementary files format and content: tab-delimited text file with normalized counts for each sample

molecule: total RNA

growth_protocol: Synchronized L1 animals were grown in liquid culture (S-Basal supplemented with OP50; OD600 = 2.7; 1000 animals/ml) at 25°C shaking at 180 rpm.

extract_protocol:
At the time of sample collection, animals were washed off the plates with M9 buffer, washed twice with M9 buffer, resuspended in TRI Reagent (MRC, TR-118) and snap-frozen in liquid nitrogen. Prior to RNA extraction, animals were lysed by five cycles of thawing (42°C) and snap-freezing in liquid nitrogen. RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research; R2062; DNase treatment included) according to the manufacturer’s protocol. RNA was eluted in nuclease-free water (Thermo Fisher Scientific, Ambion, AM9937).
Illumina TruSeq Small RNA Library Prep Kit


title: cardiac organoid; loxapine + adrenaline; well C2

city: Trondheim

first: Aleksandr

last: Ianevski

address: Høgskoleringen 1

country: Norway

institute: NTNU

description:
Library name: C2_Loxaipne_Adrenaline
iPSC-derived cardiac organoid, plate well C2; demultiplexed by 12 bp cell barcode TAGCTGCACCAA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

data_processing:
Reads filtered for low-quality and adapter contamination.
Raw FASTQs demultiplexed per well by exact match of the 12 bp cell barcode (read 1, bases 1-12); reads merged across lanes and the two sequencing runs per sample.
Cell barcode (XC) and UMI (XM) tagged; SMART adapter and polyA trimmed (Drop-seq tools).
Aligned to GRCh38 with STAR v2.7.11b; gene tagging with refFlat annotation.
Per-well UMI-collapsed digital gene expression via Drop-seq DigitalExpression; edgeR v3.42 quasi-likelihood for differential expression (downstream).
Assembly: GRCh38
Supplementary files format and content: Expression_counts.txt: tab-delimited gene x 96-sample UMI count matrix; first column Gene_ID; column headers match sample library names.
Supplementary files format and content: DGE_final_Pool1.txt (cardiac) and DGE_final_Pool2.txt (retinal): per-pool DigitalExpression matrices.

organism: Homo sapiens

source_name: iPSC-derived cardiac organoid

growth_protocol: Cardiac and retinal organoids generated from human iPSCs using modified published cardiac (Hofbauer 2021) and retinal (Nakano 2012) protocols. iPSCs reprogrammed from human dermal fibroblasts (CytoTune-iPS 2.0 Sendai kit), maintained in Essential 8, passaged with 0.5 mM EDTA, orbital shaking throughout differentiation. Retinal and cardiac organoids collected on days 20 and 53 post-induction; one organoid per well of an ultralow-attachment 96-well plate in 100 ul medium.

extract_protocol:
Total RNA isolated with the NAxtra kit; mRNA enriched with oligo-dT beads, fragmented, reverse-transcribed.
3'-barcoded bulk RNA-seq (Drop-seq-style DGE): read 1 = 12 bp per-well cell barcode (bases 1-12) + 8 bp UMI (bases 13-20); read 2 = cDNA. Libraries adaptor-ligated, PCR-amplified, pooled per organoid. NOTE: manuscript states DNBSEQ but the delivered runs are Element AVITI.

treatment_protocol: Treated 24 h at 5 uM (submaximal) with the indicated psychotropic drug and/or neurotransmitter/co-treatment; vehicle/chemical-control wells received the indicated control agent.

value: iPSC-derived cardiac organoid

tag: cell line

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

tag: cell type

value: cardiac organoid

tag: treatment

value: loxapine 5 uM, 24 h; adrenaline

tag: batch


title: Liver, 500nm, Sample 1

description:
Library name: Sample 5 500nm
10X Genomics

library_source: transcriptomic single cell

organism: Mus musculus

source_name: Liver

tag: age


title: mRNA_RIPseq_lin-28(xe197)_input_rep1

description: Library name: Sample 4


title: smallRNA_TC2_WT_35h

description: Library name: Sample 12


title: cardiac organoid; aripiprazole + adrenaline; well B2

description:
Library name: B2_Aripiprazole_Adrenaline
iPSC-derived cardiac organoid, plate well B2; demultiplexed by 12 bp cell barcode ACTGATCGTTGG (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: aripiprazole 5 uM, 24 h; adrenaline


title: mRNA_RIPseq_N2_input_rep3

description: Library name: Sample 3

value: WT


title: Liver, 50nm, Sample 2

description:
Library name: Sample 4 50nm
10X Genomics

value: 50nm polysterene particles


title: E3d_rep3

status: Public on Jun 10 2026

city: Yokohama

first: motoaki

last: seki

state: Kanagawa

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

department: CSRS

country: Japan

institute: RIKEN

description:
Library name: Sample 15
g115

data_processing:
base-calling:RTA and bcl2fastq
adapter trim: trimmomatic
alignment: HISAT2
aligned reads count: featureCounts
normalize: DESeq2
Assembly: TAIR10
Supplementary files format and content: rawCounts

organism: Beta vulgaris subsp. vulgaris

source_name: shoot

growth_protocol: Arabidopsis seedlings were grown in pots containing horticultural cray granule soil at 22 °C with a 16 h light (110 to 140 µmol m-2 s-1 photon flux density) / 8 h dark cycle.

extract_protocol:
Total RNAs were extracted using purelink Plant RNA Reagent (Thermo Fisher Scientifc Inc., Waltham, MA, USA).
The sequencing library was prepared using the Lasy-Seq method (Kamitani et al. 2019). Specifically, 200 ng of total RNA was used per sample.

treatment_protocol: Fourteen-day-old plants grown in pots were used for ethanol pretreatment. The bottoms of the pots were dipped into 20 mM ethanol solution and kept for 6 days. After ethanol pretreatment, the pots were subjected to freezing temperature treatment at -4.0 °C onvernight by a low-temperature incubator. During the freezing temperature stress treatment, the pots were electrically rotated in the incubator to avoid the local effect. After the treatment, the pots were returned to the growth room and maintained for the indicated time periods.

value: shoot


title: cardiac organoid; No_drug + adrenaline; well A2

description:
Library name: A2_No_drug_Adrenaline
iPSC-derived cardiac organoid, plate well A2; demultiplexed by 12 bp cell barcode GTCTTAGGAAGG (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: No_drug 5 uM, 24 h; adrenaline


title: mRNA_RIPseq_N2_input_rep2

description: Library name: Sample 2


title: Liver, 50nm, Sample 1

description:
Library name: Sample 3 50nm
10X Genomics


title: smallRNA_TC2_WT_33h

description: Library name: Sample 10


title: CBO, EB60, Rep 2

city: Gyeongsan

first: Byoung-San

last: Moon

state: Gyeongbuk

address: 280 Deahak-ro

department: Medical Biotechnology

country: South Korea

institute: Yeungnam University

description:
Library name: EB60_2
10x Genomics

data_processing:
Raw BCL files were demultiplexed to FASTQ files using Cell Ranger (v3.1.0) and aligned to the GRCh38 human reference transcriptome.
Filtered feature-barcode matrices were generated following barcode and UMI counting.
Low-quality cells were excluded based on the following thresholds: fewer than 500 UMIs, fewer than 250 detected genes, or mitochondrial transcript proportion exceeding 20%.
Each sample was normalized and scaled using SCTransform while regressing out mitochondrial transcript proportion (Seurat v4.1.1).
Samples within the same timepoint (EB60 or EB120) were integrated using canonical correlation analysis on 5,000 highly variable genes.
Assembly: GRCh38
Supplementary files format and content: Seurat object (.rds file)
Supplementary files format and content: Feature bc matrix (.h5 files)

source_name: Brain organoid

growth_protocol: CBOs were generated from hiPSCs following Pasca’s protocol with minor modifications (Paşca et al., 2015). hiPSC colonies at 60-70% confluence in Primaria dishes (Corning 100 mm ULA dish, Cat. 4615) were detached using 10% Dispase (STEMCELL Technologies Inc.) and transferred to ultra-low attachment plates to form embryoid bodies in mTeSR medium supplemented with 10 μM SB431542, 5 μM dorsomorphin, and 10 μM Y27632, with daily medium changes. On day 6, neuroectoderm induction was initiated in Neurobasal-A medium containing 1X B27 supplement without vitamin A, 1X penicillin/streptomycin, 1X GlutaMAX, 20 ng/ml bFGF, and 20 ng/ml EGF, with daily medium replenishment. From days 26 to 43, neural differentiation was promoted by supplementing the medium with 20 ng/ml NT3 or 20 ng/ml BDNF, with medium changes every other day. From day 44 onward, organoids were matured in Neurobasal-A medium supplemented with 1X B27, 1X penicillin/streptomycin, and 1X GlutaMAX, with medium replacement every other day.

extract_protocol:
CBOs at EB60 and EB120 were dissociated using papain/DNase I at 37°C for 30 min and triturated into single-cell suspensions. Cells were pelleted and lysed for 3 min in cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 0.1% Igepal CA-630, 0.01% digitonin, 1% BSA), then washed with chilled wash buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween-20, 1% BSA), and nuclei were pelleted at 500 rcf for 5 min at 4°C
Single-cell libraries were constructed using the Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics), targeting 10,000 cells per sample. GEM-based barcoding was followed by reverse transcription to generate 10X barcoded cDNA.

value: Brain organoid

value: brain cells

tag: developmental timepoint

value: embryoid body day 60 (EB60, immature)


title: Control (maintained under well-watered ) and sampling after the third drought stress , Root, rep 3

city: Beaucouze

first: Sandrine

last: Balzergue

address: 42 rue G. Morel

country: France

institute: INRAE

description: Library name: C3_S3_RO

data_processing:
Raw data quality was checked using FastQC (Andrews, 2010) and the estimation of transcript-level abundance was performed by Salmon tool (Patro et al., 2017) using default parameters. The reads were aligned against the Malus domestica GDDH13 genome v1.1 (Daccord et al., 2017).
The differential gene analysis was performed by the R package DESeq (Anders and Huber, 2010). The genes presenting a p-value lower than 0.05 were considered as differentially expressed in this study.
Assembly: Malus domestica GDDH13 genome v1.1 (Daccord et al., 2017).
Supplementary files format and content: for each comparison, txt file with at list logCPM_Ttmt_Drought, logCPM_Ctrl_Control, logFC,pval_DESeq2and BH_DESeq2

organism: Malus domestica

source_name: Root

growth_protocol: Apple seedlings were grown in the greenhouses of France's National Research Institute for Agriculture, Food and Environment (INRAe) in Angers, France (47° 28' 36.804'' N 0° 36' 41.4'' W). The seeds from ‘Golden Delicious’ double haploid 18 (GDDH18; Daccord et al., 2017) were stratified for 3 months in a 1:1 mixture of sand and vermiculite (humidity of 70%) and kept at 3 °C for 90 days. After the period of stratification, the seeds were sown in a soil mixture containing 50% peat moss, 40% perlite, 10% coco fibers, 7.5kg/ea carbonates and N-P-K mix 14-16-18. The sowing was performed in three blocks, interspersed by one week each, representing three biological replicates. The germination was carried out in a greenhouse (ambient light; 21 °C ± 5 °C; relative humidity 60 % ± 20). Four weeks after germination, the seedlings were transplanted into 0.4 L plastic pots using the same soil mixture and maintained under the same environmental conditions. At eight weeks of age, the seedlings were transferred to final 1 L pots and grown for an additional four weeks before the initiation of drought stress (DS) cycles.

extract_protocol:
For each tissue and condition, approximately 50 mg (fresh weight) were used for total RNA extraction using the NucleoSpin® RNA Plus kit (Macherey Nagel, Germany).
libraries were built using the NEB® mRNA stranded library preparation kit (New England Biolabs, USA). Sequencing was performed using Illumina NovaSeq S4 in a paired-end (PE) mode with read length 100 bp. A minimum of 25 million PE reads per sample were generated

treatment_protocol: Irrigation management was conducted by monitoring the soil water content (SWC) of all plants every two days using pot weighing. During well-watered (WW) periods, plants were maintained near field capacity (FC; 80% SWC), whereas during drought stress (DS) periods, irrigation was adjusted to maintain SWC at 45% of FC. The SWC corresponding to 100% FC was determined for the previously described soil mix by saturating pots with water and allowing free drainage for 24 hours. Two distinct irrigation regimes were established : (I) Control group (64 plants): maintained under WW conditions throughout the entire experiment. (II) Multiple-DS group (61 plants): subjected to three consecutive drought cycles, each consisting of three weeks under DS conditions followed by three weeks of recovery (as WW condition). To investigate long-term transcriptomic and epigenetic memory responses, in year n+1, roots and leaves from Control and Multiple-DS plants were also sampled prior to the application of a new stress (Before Stress – BS), after completing one winter cycle. For root samples only,  two biological replicates was performed due to the limited availability of root for this treatment.

value: Root

value: Golden Delicious double haploid 18 (GDDH18)

value: Control

value: replicate 3


title: mRNA_RIPseq_N2_input_rep1

description: Library name: Sample 1

value: whole organism


title: Liver, PBS,  Sample 2

description:
Library name: Sample 2 PBS
10X Genomics

value: Liver

value: 20-22 weeks old

value: PBS treatment


title: cardiac organoid; control No drug; well H1

description:
Library name: H1_No_drug
iPSC-derived cardiac organoid, plate well H1; demultiplexed by 12 bp cell barcode CGCTCAGTGGAA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: iPSC-derived cardiac organoid

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: cardiac organoid

value: vehicle/chemical control:No drug


title: cardiac organoid; control No drug; well G1

description:
Library name: G1_No_drug
iPSC-derived cardiac organoid, plate well G1; demultiplexed by 12 bp cell barcode GAGCGCTACCTT (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt


title: smallRNA_TC2_WT_32h

description: Library name: Sample 9


title: Liver, PBS,  Sample 1

description:
Library name: Sample 1 PBS
10X Genomics


title: smallRNA_TC2_WT_31h

description: Library name: Sample 8


title: cardiac organoid; xanomeline; well F1

description:
Library name: F1_Xanomeline_No_drug
iPSC-derived cardiac organoid, plate well F1; demultiplexed by 12 bp cell barcode CTGCGCATTTCC (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: xanomeline 5 uM, 24 h


title: Cdo1KKO/Sed mouse kidney, biological rep 3

city: Shanghai

first: Linjing

last: Yan

address: No. 650 Hengren Road, Yangpu District, Shanghai, China

country: China

institute: Shanghai University of Sports

description: Library name: KO_3

data_processing:
Raw reads were subjected to quality control using fastp (v0.23.4).
Assembly: GRCm38/mm10
Supplementary files format and content: Tab-delimited text file including raw gene counts and TPM values for each sample

source_name: kidney

extract_protocol:
Total RNA was extracted from mouse kidney tissue. RNA purity was assessed using Nanodrop (OD260/280 and OD260/230 ratios), and integrity was evaluated using Agilent 2100/4150.
mRNA was enriched using oligo(dT) magnetic beads, followed by library preparation with the VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina (Vazyme, NR605).

treatment_protocol: Type 1 diabetes was induced by streptozotocin (STZ) injection. Mice were divided into WT/Sed and Cdo1KKO/Sed groups.

value: kidney

value: KO


title: Populus davidiana, 120h, replicate 3

city: Kunming

first: Xiaolin

last: Zhang

address: qingyun street

institute: southwest forestry university

description: Library name: S120-3

data_processing:
Waiting for submitter
Assembly: Populus trichocarpa GCA_000002775.4
Supplementary files format and content: All_gene_fpkm.list

organism: Populus davidiana

source_name: stem

extract_protocol:
Cultivation of two poplars under different growth stage
The mRNA was collected from the stem of cuttings under different growth stage, respectively.
Based on sequencing-by-synthesis (Sequencing By Synthesis, SBS) technology, cDNA libraries were sequenced on Illumina high-throughput platform.

value: stem

tag: Stage

value: growth stage

value: cutting

tag: time


title: Cdo1KKO/Sed mouse kidney, biological rep 2

description: Library name: KO_2


title: oml 7dpl, biological rep2

type: RNA

city: Frankfurt

first: Jessica

last: Schlaudraff

address: Heinrich-Hoffmann-Straße

institute: Klinische Neuroanatomie

description: gene expression data from tissue of the outer molecular layer 7 days postlesion

hyb_protocol: The Encore Biotin Module Kit (NuGEN) was then used for fragmentation and labeling of cDNA for analysis on Affymetrix Gene Chips. Samples were hybridized on a Mouse Gene 1.0 ST array  (Affymetrix)

scan_protocol: GeneChips were scanned using the GeneChip Scanner 3000 7G (Applied Biosystems)

data_processing: The data were checked with Expression console (Affymetrix) and analyzed with Partek-Software 6.5 (Partek) using default analysis settings.

label: biotin

source_name: 7 days postlesion

label_protocol: Total RNA was transcribed into cDNA and amplified with Single Primer Isothermal Amplification (SPIA) technology including in Ovation® Pico WTA System (NuGEN).

growth_protocol: 12 weeks old adult male Wildtype mice (C57Bl6/J@RJ ) were purchased from Janvier.

extract_protocol: Total RNA was isolated with RNeasy Plus Micro Kit (Qiagen) according to the manufacturer's instructions.

treatment_protocol: Experimental animals with transaction of the perforant path (n = 2-3 each time point) were allowed to survive 1, 3, 7, 14 or 28 days.

value: outer molecular layer


title: smallRNA_TC2_WT_30h

description: Library name: Sample 7


title: cardiac organoid; quetiapine; well E1

description:
Library name: E1_Quetiapine_No_drug
iPSC-derived cardiac organoid, plate well E1; demultiplexed by 12 bp cell barcode GCAGCGTAAACC (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: quetiapine 5 uM, 24 h


title: Populus davidiana, 120h, replicate 2

description: Library name: S120-2


title: Cdo1KKO/Sed mouse kidney, biological rep 1

description: Library name: KO_1


title: cardiac organoid; sertraline; well D1

description:
Library name: D1_Sertaline_No_drug
iPSC-derived cardiac organoid, plate well D1; demultiplexed by 12 bp cell barcode AGGCTCCGGGCC (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: sertraline 5 uM, 24 h


title: smallRNA_TC2_WT_29h

description: Library name: Sample 6

value: whole organism


title: Populus davidiana, 120h, replicate 1

description: Library name: S120-1


title: mRNA_TC1_lin-28(n719)_5h_rep1

description: Library name: Sample 11

growth_protocol: Synchronized L1 animals were plated on 2% NGM plates seeded with OP50 E. coli bacteria and grown at 25°C.

extract_protocol:
At the time of sample collection, animals were washed off the plates with M9 buffer, washed twice with M9 buffer, resuspended in TRI Reagent (MRC, TR-118) and snap-frozen in liquid nitrogen. Prior to RNA extraction, animals were lysed by five cycles of thawing (42°C) and snap-freezing in liquid nitrogen. RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research; R2062; DNase treatment included) according to the manufacturer’s protocol. RNA was eluted in nuclease-free water (Thermo Fisher Scientific, Ambion, AM9937).
Illumina Stranded mRNA-seq


title: smallRNA_TC2_lin-28(xe192)_33h

description: Library name: Sample 31


title: WT/Sed mouse kidney, biological rep 3

description: Library name: WT_3

value: WT


title: smallRNA_TC2_WT_28h

description: Library name: Sample 5


title: smallRNA_TC2_WT_34h

description: Library name: Sample 11


title: cardiac organoid; loxapine + histamine; well C4

description:
Library name: C4_Loxaipne_Histamine
iPSC-derived cardiac organoid, plate well C4; demultiplexed by 12 bp cell barcode TACTCCGGACGC (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: loxapine 5 uM, 24 h; histamine


title: Populus davidiana, 96h, replicate 3

description: Library name: S96-3


title: cardiac organoid; loxapine; well C1

description:
Library name: C1_Loxaipne_No_drug
iPSC-derived cardiac organoid, plate well C1; demultiplexed by 12 bp cell barcode TACTACGCCCGG (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: loxapine 5 uM, 24 h


title: WT/Sed mouse kidney, biological rep 2

description: Library name: WT_2


title: smallRNA_TC2_WT_27h

description: Library name: Sample 4


title: mRNA_TC1_WT_6h_rep2

description: Library name: Sample 8


title: smallRNA_TC2_lin-28(xe192)_30h

description: Library name: Sample 28


title: cardiac organoid; aripiprazole; well B1

description:
Library name: B1_Aripiprazole_No_drug
iPSC-derived cardiac organoid, plate well B1; demultiplexed by 12 bp cell barcode GTAGCTCCTTAA (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: iPSC-derived cardiac organoid

value: aripiprazole 5 uM, 24 h


title: smallRNA_TC2_lin-28(xe192)_29h

description: Library name: Sample 27


title: Populus davidiana, 96h, replicate 2

description: Library name: S96-2


title: WT/Sed mouse kidney, biological rep 1

description: Library name: WT_1


title: smallRNA_TC2_WT_26h

description: Library name: Sample 3


title: cardiac organoid; No_drug; well A1

description:
Library name: A1_No_drug_No_drug
iPSC-derived cardiac organoid, plate well A1; demultiplexed by 12 bp cell barcode TAGCGAGTAATT (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: human iPSC (CytoTune Sendai-reprogrammed dermal fibroblasts)

value: cardiac organoid

value: No_drug 5 uM, 24 h


title: DK - CD40 stimulation

city: Madison

first: Huy

last: Dinh

state: WI

address: 1111 Highland Avenue

country: USA

institute: University of Wisconsin-Madison

description: Library name: DK_CD40

data_processing:
Raw FASTQs were run through PIP-Seeker analysis pipeline v02.00.00 , using the GRCm39 mouse genome for alignment and otherwise default parameters.
Assembly: pipseeker-gex-reference-GRCm39-2022.04
Supplementary files format and content: PIP-Seeker  Feature Barcode Matrices (barcode, feature and matrix)

source_name: Spleen

extract_protocol:
Splenic B cells were isolated from WT and NEMODK mice, either left unstimulated or stimulated with anti-CD40 and IL-4 for three days.  On day three, cells were collected and subjected to density gradient centrifugation using LymphoprepTM (18061, Stemcell Technologies) to remove dead cells and debris.
PIPseq T20 3′ Single Cell RNA Kit (Fluent BioSciences, FBS-SCR-T20-4-V3)

value: Spleen

value: primary

value: B cells


title: Populus davidiana, 96h, replicate 1

description: Library name: S96-1

value: stem

value: growth stage


title: smallRNA_TC2_WT_25h

description: Library name: Sample 2


title: smallRNA_TC2_lin-28(xe192)_27h

description: Library name: Sample 25


title: Populus davidiana, 48h, replicate 3

description: Library name: S48-3

value: cutting


title: Conjunctiva, scar, replicate2

first: Ning

last: Li

address: 160 Pujian Road

department: Department of Ophthalmology, Renji Hospital

institute: Shanghai Jiao Tong University School of Medicine

description:
Library name: Sample4
10x Genomics

data_processing:
scRNA-seq: Results from Illumina sequencing offline were converted to FASTQ format using bcl2fastq software (version 5.0.1). The scRNA-seq sequencing data were compared to reference genome using CellRanger software, and cellular and individual cellular 3' end transcripts were identified and counted in the sequenced samples. (https://support.10xgenomics.com/single-cell-gene expression/software/pipelines/latest/what-is cell-ranger , version 7.0.0) The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering of low quality cells from scRNA-seq data, and the filtered data was downscaled and clustered. Filtering low cell quality thresholds: number of genes expressed per cell >500, mitochondrial genes expressed in <25% of cells. Cells were projected into 2D space using t-SNE or UMAP. These steps include:
1. calculating gene expression values using the LogNormalize method of Seurat's "NormalizeData" function;
2. performing principal component analysis (PCA) using the normalized expression values, using the top 20 PCs for clustering, and Findcluster analysis. 3. analyze the marker genes of each cluster based on Findallmarker, and the marker genes were selected based on the following criteria: expressed in more than 10% of cells in each cluster, P value ≤ 0.01, gene expression ploidy logFC ≥ 0.26;
Hypergeometric testing was used to perform GO and KEGG enrichment analysis on the differential genes of each cluster obtained from Findallmarker analysis relative to other clusters. In human and mouse species, singleR database, scCATCH database and our self-developed LC-Marker were used to identify each cluster cell type, and some cells were re-clustered based on the identification results of SingleR database to find marker genes, cell communication analysis and Pseudotime analysis to provide ideas for further analysis.
Assembly: hg38
Supplementary files format and content: scRNA-seq: Tab-separated values files and matrix files.

source_name: Ocular conjunctival tissue

extract_protocol:
scRNA-seq: The obtained tissues were transferred to a Petri dish (Petri dish was placed on wet ice) pre-spiked with 1×PBS (without RNase and Ca, Mg ions) and washed with 1XPBS to remove blood stains, grease and other adherents from the tissue surface. The tissue was then cut into 0.5 mm2 pieces and washed again with 1×PBS. The washed pieces were added with dissociation solvent (0.35% collagenase IV5, 2 mg/ml papain, 120 Units/ml DNase I) and reacted for 20 min at 37°C in a water bath shaker (100 rpm). PBS (containing 10% fetal bovine serum) was used to terminate the dissociation. The cells were repeatedly puffed 5-10 times with a pipette gun (gentle handling to prevent cell death due to shear force). The cell suspension was filtered through a 70-30um cell sieve and subsequently centrifuged at 300g for 5 min at 4°C. After centrifugation, the cell sediment was collected and the cells were resuspended by adding 100ul of 1× PBS (0.04% BSA) solution. To remove erythrocytes, 1 ml of 1X erythrocyte lysis solution (MACS 130-094-183, 10×) was added and reacted at room temperature or on wet ice for 2-10 min. After lysis, the cells were centrifuged at 300g for 5 min at 4°C, and the cell precipitate was collected after centrifugation. Add 100μl of Dead Cell Removal MicroBeads (MACS 130-090-101), mix well and incubate for 15min at room temperature. At the end of incubation, Binding Buffer was added, after MS Columns (130-042-201) to remove reagents, and dead cells.Cell precipitates were collected by centrifugation at 300g for 5min at 4°C. Subsequently 1×PBS (0.04% BSA) was used to resuspend the cell precipitate and centrifuged at 4°C 300g for 5min (repeated twice). The candidate cells were obtained after tissue dissociation, lysis of erythrocytes and removal of dead cells, and 100 μl of 1×PBS (0.04% BSA) was added to form a cell suspension. The cell activity was detected by trypan blue staining method, and the cell activity was required to be >85%. The number of cells was counted using a hemocytometer or Countess II Automated Cell Counter, and the cell concentration was 700-1200 cells/μl.
scRNA-seq: Single-cell suspension was added to the 10x Chromium chip according to the instructions for the 10X Genomics Chromium Single-Cell 3' kit (V3), with the expectation of capturing 8,000 cells. cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced by LC-Bio Technology (Hangzhou, China) on an Illumina NovaSeq 6000 sequencing system (double-end sequencing, 150 bp) at a minimum depth of 20,000 reads per cell.

value: Ocular conjunctival tissue

value: With scar tissue


title: WT - CD40 stimulation

description: Library name: WT_CD40


title: Conjunctiva, scar, replicate1

description:
Library name: Sample3
10x Genomics


title: Populus davidiana, 48h, replicate 2

description: Library name: S48-2


title: smallRNA_TC2_WT_24h

description: Library name: Sample 1

value: whole organism


title: DK - unstimulated

description: Library name: DK_Unstim


title: mRNA_TC2_lin-28(xe192)_44h

description: Library name: Sample 90

extract_protocol:
At the time of sample collection, animals were washed off the plates with M9 buffer, washed twice with M9 buffer, resuspended in TRI Reagent (MRC, TR-118) and snap-frozen in liquid nitrogen. Prior to RNA extraction, animals were lysed by five cycles of thawing (42°C) and snap-freezing in liquid nitrogen. RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research; R2062; DNase treatment included) according to the manufacturer’s protocol. RNA was eluted in nuclease-free water (Thermo Fisher Scientific, Ambion, AM9937).
TruSeq Illumina mRNA-seq


title: Conjunctiva, control, replicate2

description:
Library name: Sample2
10x Genomics

value: Control without treatment


title: Populus davidiana, 48h, replicate 1

description: Library name: S48-1


title: smallRNA_TC2_lin-28(xe192)_25h

description: Library name: Sample 23


title: cardiac organoid; xanomeline + dopamine; well F3

description:
Library name: F3_Xanomeline_Dopamine
iPSC-derived cardiac organoid, plate well F3; demultiplexed by 12 bp cell barcode TTGGACTGATCG (Pool-1 i7 CGAGGCTG)
DGE_final_Pool1.txt

value: xanomeline 5 uM, 24 h; dopamine


title: WT - unstimulated

description: Library name: WT_Unstim


title: mRNA_TC2_lin-28(xe192)_43h

description: Library name: Sample 89


title: Conjunctiva, control, replicate1

description:
Library name: Sample1
10x Genomics


title: mRNA_TC2_lin-28(xe192)_42h

description: Library name: Sample 88


title: WT, Unstimulated, 2 days, H3K27Ac, rep3

city: Milwaukee

first: Demin

last: Wang

address: 8727 W Watertown Plank Rd

institute: 1Versiti Blood Research Institute

description: Library name: Unstim_27_H3K27Ac

library_source: genomic

data_processing:
For data analysis, reads were aligned to the mm10 mouse genome, and peaks were identified using SEACR v1.3  in stringent mode with IgG controls. Data normalization and differential peak analysis were conducted using DESeq2 v1.32.0
Assembly: mm10
Supplementary files format and content: bigWig files after peakcalling
Library strategy: CUT&Tag

molecule: genomic DNA

source_name: primary cells

extract_protocol:
Splenic B cells were isolated from WT and NEMODK mice, stimulated with anti-CD40 and IL-4 for two days, then washed and resuspended in wash buffer. Cells were bound to ConA-coated beads, incubated overnight with anti-RelA (Cell Signaling, 8242), anti-H3K4me3 (Active Motif, 39159), anti-H3K27ac (Active Motif, 39034), and anti-H3K27me3 (Cell Signaling, 9733) antibodies, followed by secondary incubation with anti-rabbit IgG antibodies (Antibodies Online). After washing, the cells were incubated with the pA-Tn5 adapter complex (Epicypher) at room temperature for 1 hour.
Tagmentation was performed at 37°C, after which DNA was extracted and PCR-amplified to generate sequencing libraries. Libraries were sequenced on an Illumina NovaSeq platform to produce paired-end 150 bp reads.

value: WT

value: medium


title: Populus davidiana, 0h, replicate 3

description: Library name: SCK-3


title: Endothelial cell, overexpress, replicate3

description: Library name: Sample6

data_processing:
RNA-seq: We used HISAT2 (http://daehwankimlab.github.io/hisat2) to map reads to the reference genome homo sapiens (Version: v107). Peak calling and diff peak analysis were performed by R package exomePeak (https://www.bioconductor.org/packages/3.3/bioc/html/exomePeak.html), and peaks were annotated by intersection with gene architecture using R package ANNOVAR (http://www.openbioinformatics.org/annovar/). HOMER (http://homer.ucsd.edu/homer/motif) was used for de novo and known motif finding followed by localization of the motif with respect to peak summit. And StringTie (https://ccb.jhu.edu/software/stringtie) was used to perform expression level for all transcripts and genes from input libraries by calculating FPKM (total exon fragments /mapped reads (millions) × exon length (kB)). The differentially expressed transcripts and genes were selected with log2 (fold change) ≥ 1 or log2 (fold change) ≤ -1 and p value < 0.05 by R package edgeR (https://bioconductor.org/packages/edgeR).
Assembly: hg38
Supplementary files format and content: RNA-seq: bigWig, narrow peak
Library strategy: MeRIP-Seq

source_name: Human umbilical vein endothelial cells

extract_protocol:
RNA-seq: Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA). Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) by two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were incubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. At last, we performed paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 platform(LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.
RNA-seq: fastp software (https://github.com/OpenGene/fastp) was used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. And sequence quality of IP and Input samples were verified using FastQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and RseQC (http://rseqc.sourceforge.net/).

value: Human umbilical vein endothelial cells

value: Overexpress ALKBH5


title: Populus davidiana, 0h, replicate 2

description: Library name: SCK-2


title: NEMODK, Unsimulated, 2 days, H3K27Ac, rep3

description: Library name: Unstim_26_H3K27Ac

value: NEMODK


title: mRNA_TC2_lin-28(xe192)_41h

description: Library name: Sample 87


title: Cd11b_rep2

city: Pieve Emanuele (MI)

first: Bioinformatics

last: Unit

address: Via Rita Levi Montalcini 4

country: Italy

institute: IRCCS Humanitas Research Hospital

description: Library name: Cd11b_rep2

data_processing:
Quality control of raw reads was performed with FastQC (v0.11.9), and sequences were aligned to the Mus musculus reference genome (mm10) using STAR (v2.7.10a). Read quantification was carried out using the featureCounts function of the Rsubread package (v2.12.3) at gene-level using GENCODE annotation retaining only uniquely mapping reads.
Assembly: mm10
Supplementary files format and content: comma separated text file (.csv) of raw counts with all samples.

source_name: lung

extract_protocol:
Total RNA was isolated from FACS-sorted spleen and lung cells of WT and Dpp3−/− mice using QIAzol Lysis Reagent (QIAGEN) according to the manufacturer’s instructions. RNA concentration and purity were assessed prior to downstream applications.
total RNA was subjected to poly(A) mRNA sequencing using SMARTer-Stranded Total RNA Kit (Clontech), according to the manufacturer’s instructions.

value: lung


title: Endothelial cell, overexpress, replicate2

description: Library name: Sample5


title: Populus davidiana, 0h, replicate 1

description: Library name: SCK-1


title: WT, Unstimulated, 2 days, H3K27Ac, rep2

description: Library name: Unstim_25_H3K27Ac

value: Spleen


title: mRNA_TC2_lin-28(xe192)_40h

description: Library name: Sample 86


title: Endothelial cell, overexpress, replicate1

description: Library name: Sample4


title: Populus yunnanensis, 120h, replicate 3

description: Library name: D120-3

organism: Populus yunnanensis


title: WT, Unstimulated, 2 days, H3K27Ac, rep1

description: Library name: Unstim_19_H3K27Ac


title: Populus yunnanensis, 120h, replicate 2

description: Library name: D120-2


title: Endothelial cell, control, replicate3

description: Library name: Sample3


title: NEMODK, Unstimulated, 2 days, H3K27Ac, rep2

description: Library name: Unstim_14_H3K27Ac


title: Populus yunnanensis, 120h, replicate 1

description: Library name: D120-1


title: Endothelial cell, control, replicate2

description: Library name: Sample2


title: mRNA_TC2_lin-28(xe192)_38h

description: Library name: Sample 84


title: NEMODK, Unstimulated, 2 days, H3K27Ac, rep1

description: Library name: Unstim_12_H3K27Ac


title: Populus yunnanensis, 96h, replicate 3

description: Library name: D96-3


title: WT, Stimulated, 2 days, H3K27Ac, rep3

description: Library name: Stim_27_H3K27Ac

value: Anti-CD40 and IL-4


title: Endothelial cell, control, replicate1

description: Library name: Sample1


title: NEMODK, Stimulated, 2 days, H3K27Ac, rep3

description: Library name: Stim_26_H3K27Ac

value: B cells


title: Populus yunnanensis, 96h, replicate 2

description: Library name: D96-2

value: stem


title: S100A8_A9 experiment 3, 24 hrs of S100A8_A9 treatment

city: Ulm

first: Pallab

last: Maity

address: Meyerhofstrasse/James Franck Ring

department: Dermatology

institute: University of Ulm

description: Library name: S100A8_A9_24h_3

data_processing:
Raw reads (fastq) were pseudoaligned and quantified with Kallisto quant with bootostrap set to 100. Transcript abundance counts from kallisto quant for all the samples were merged to a single transcript expression count matrix. This transcript expression count matrix was applied for differential transcript expression analyses using DESeq2. Visualization and representation of the transcriptome data were performed by custom R scripts in R-Studio environment.
Assembly: GRCh38
Supplementary files format and content: tab delimited txt file for count data

source_name: adipose tissue derived mesenchymal stromal cell

growth_protocol: cells were cultured in Mesenchymal Stem Cell Growth Medium 2 at 37C and 5% CO2

extract_protocol:
RNA was isolated from the cells using Rneasy plus kit (Qiagen). 1 µg of total RNA was used for the rRNA depletion and library preparation.
Library was prepared using NEBNext Ultra II Directional RNA Library Preparation kit (NEB)

treatment_protocol: Cells were treated either with vehicle or S100A8_A9 (0.5 µg/ml) for 6, 12 or 24 hrs


title: mRNA_TC2_lin-28(xe192)_35h

description: Library name: Sample 81


title: WT, Stimulated, 2 days, H3K27Ac, rep2

description: Library name: Stim_25_H3K27Ac


title: Populus yunnanensis, 96h, replicate 1

description: Library name: D96-1

value: growth stage


title: mRNA_TC2_lin-28(xe192)_34h

description: Library name: Sample 80


title: S100A8_A9 experiment 1, 24 hrs of S100A8_A9 treatment

description: Library name: S100A8_A9_24h_1

value: adipose tissue derived mesenchymal stromal cell


title: WT, Stimulated, 2 days, H3K27Ac, rep1

description: Library name: Stim_19_H3K27Ac


title: mRNA_TC2_lin-28(xe192)_33h

description: Library name: Sample 79


title: Populus yunnanensis, 48h, replicate 3

description: Library name: D48-3

value: cutting


title: S100A8_A9 experiment 3, 12 hrs of S100A8_A9 treatment

description: Library name: S100A8_A9_12h_3


title: Populus yunnanensis, 48h, replicate 2

description: Library name: D48-2


title: NEMODK, Stimulated, 2 days, H3K27Ac, rep2

description: Library name: Stim_14_H3K27Ac


title: mRNA_TC2_lin-28(xe192)_32h

description: Library name: Sample 78


title: Populus yunnanensis, 48h, replicate 1

description: Library name: D48-1


title: NEMODK, Stimulated, 2 days, H3K27Ac, rep1

description: Library name: Stim_12_H3K27Ac


title: WT, Unstimulated, 2 days, H3K27me3, rep3

description: Library name: Unstim_27_H3K27me3


title: mRNA_TC2_lin-28(xe192)_30h

description: Library name: Sample 76


title: S100A8_A9 experiment 3, 6 hrs of S100A8_A9 treatment

description: Library name: S100A8_A9_6h_3


title: NEMODK, Unsimulated, 2 days, H3K27me3, rep3

description: Library name: Unstim_26_H3K27me3


title: Populus yunnanensis, 0h, replicate 2

description: Library name: DCK-2


title: mRNA_TC2_lin-28(xe192)_29h

description: Library name: Sample 75


title: S100A8_A9 experiment 2, 6 hrs of S100A8_A9 treatment

description: Library name: S100A8_A9_6h_2


title: WT, Unstimulated, 2 days, H3K27me3, rep2

description: Library name: Unstim_25_H3K27me3


title: mRNA_TC2_lin-28(xe192)_28h

description: Library name: Sample 74


title: S100A8_A9 experiment 1, 6 hrs of S100A8_A9 treatment

description: Library name: S100A8_A9_6h_1


title: kc167 cells,roX2 overexpression

first: Yonghao

address: Siping Road No.1239

department: School of Life Sciences and Technology

institute: Tongji University

description: Library name: roX2-OE

data_processing:
Sequencing ﬁles were removed of adapters by fastp with parameter --detect_adapter_for_pe.
Then clean reads mapped to genome dm6 and MG1655 (Escherichia coli strain K12) by bowtie2 with parameters: --local --very-sensitive-local --no-mixed --no-discordant --no-unal --phred33 –X 2000.
Low mapping quality reads were removed by samtools view with -F 0×904 -q 20. Duplications were removed by sambamba markdup –r, and reads mapped to unusual chromosomes (e.g., chrM, chrUn or random) were also removed.
Bam ﬁles mapped to dm6 were transferred to bedgraph and bigwig (20 bp window) by bedtools genomecov and bamCoverage, using scale factors 10,000,000/(reads mapped to MG1655).
Assembly: dm6, MG1655
Supplementary files format and content: bigwig, 20 bp window

organism: Drosophila melanogaster

source_name: cell

growth_protocol: Drosophila Kc cells were cultured in Schneider’s Drosophila Medium (Gibco, 21720024) containing 10% FBS (Gibco, A5256701) and 1% penicillin/streptomycin (HYClone, SV30010) at 27 °C.

extract_protocol:
Nuclei were isolated as follows: cells were harvested and lysed in a cold lysis buffer (10 mM Tris-HCl pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.1% IGEPAL CA-630) for 10 minutes on ice. The nuclei were then pelleted by centrifugation at 500 × g for 10 minutes at 4°C.
The cell pellet was resuspended in a transposase reaction mixture (25 µL of 2× TD buffer, 2.5 µL of Illumina transposase, and 22.5 µL of nuclease-free water) and incubated at 37°C for 30 min. Following transposition, the DNA was purified using a Qiagen MinElute kit. The library fragments were then amplified with 1× NEBnext PCR master mix and 1.25 µM custom Nextera PCR primers using the following thermocycling conditions: 72°C for 5 min; 98°C for 30 s; followed by 12 cycles of 98°C for 10 s, 63°C for 30 s, and 72°C for 1 min.

treatment_protocol: The  plasmid was introduced into the cells through transfection using Cellfectin (Invitrogen, 10362100). Following a 48-hour incubation, the cells were collected to further analysis

value: cell

value: embryonic cells

value: transfection


title: WT, Unstimulated, 2 days, H3K27me3, rep1

description: Library name: Unstim_19_H3K27me3


title: mRNA_TC2_lin-28(xe192)_27h

description: Library name: Sample 73

value: whole organism


title: Control experiment 3, 24 hrs of vehicle treatment

description: Library name: Co_24h_3

value: vehicle


title: NEMODK, Unstimulated, 2 days, H3K27me3, rep2

description: Library name: Unstim_14_H3K27me3

value: medium


title: kc167 cells,GFP overexpression

description: Library name: GFP-OE


title: mRNA_TC2_lin-28(xe192)_26h

description: Library name: Sample 72


title: C. sardiniense with subsequent C. difficile prdB mutant 24 hours post infection Mouse 8

city: Boston

first: Lynn

last: Bry

state: MA

address: 75 Francis St.

department: Pathology

institute: Brigham and Women's Hospital

data_processing:
Bowtie2 was used to align filtered and trimmed reads to a library consisting of C. diffcile, C. saridiniense, and Mus musculus DNA sequences for all reactions to ensure specific alignments to C. difficile gene features.
Reads were assigned to features in alignments using HTSeq. Reads overlapping multiple features were assigned to both to account for polycistronic RNAs.
Reads were also analyzed with Kraken2 to check for contaminants. Note - mouse chow contains RNAs which are present in caecal contents.
A 10 read average cutoff was applied. C. difficile genomic features were analyzed.
DESeq2 was used to normalize read counts and for subsequent differential expression analyses.
Assembly: C. difficile ATCC 43255 https://www.bv-brc.org/view/Genome/1496.5150, M. musculus GRCm39 https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000001635.27/, C. sardiniense DSM 599 https://www.bv-brc.org/view/Genome/29369.14
Supplementary files format and content: HTSeq CDS read counts per gene.

organism:
Clostridioides difficile
Mus musculus
Clostridium sardiniense

source_name: Mouse caecal contents

growth_protocol: 6-7 week-old male and female gnotobiotic (germ-free) mice were pre-colonized by gavage (C. sardiniense) with 10^8 cfu 1 week before inoculation by gavage with10^3 C. difficile ATCC43255 spores.

extract_protocol:
Mice were sacrificed at the indicated timepoint and dissected. Cecal contents were immediately cryogenically stored for RNA extraction.
Purified RNAs were rRNA depleted and eukaryotic (mouse) poly-A mrRNA depleted. Illumina NovaSeq S4-300 with paired-end 150 nucleotide runs were performed.

value: Mouse caecal contents


title: NEMODK, Unstimulated, 2 days, H3K27me3, rep1

description: Library name: Unstim_12_H3K27me3


title: Control experiment 1, 24 hrs of vehicle treatment

description: Library name: Co_24h_1


title: mRNA_TC2_lin-28(xe192)_24h

description: Library name: Sample 70

data_processing:
RNA-seq data was mapped to the C. elegans genome (ce11) using the Align (qAlign) function from the QuasR (v1.41.2) package in R with splicedAlignement = TRUE, using the aligner HISAT2 (v1.20.0) including an exon-exon junction database (WS270). Gene expression levels were quantified using the qCount() function, counting the reads on the opposite strand of annotated transcripts. For paired-end samples, the first read was considered for counting. For annotations, coding transcript information from WormBase WS270 was used. We further compensated for differences in library sizes by scaling each library to the average library size. Finally, we log2 transformed the data using a pseudo count of 8 (log2(x+8)).
Assembly: ce11
Supplementary files format and content: tab-delimited text file with raw gene expression read counts
Supplementary files format and content: tab-delimited text file with normalized gene expression read counts

source_name: whole organism


title: WT, Stimulated, 2 days, H3K27me3, rep3

description: Library name: Stim_27_H3K27me3

value: WT


title: C. sardiniense with subsequent C. difficile prdB mutant 24 hours post infection Mouse 6


title: NEMODK, Stimulated, 2 days, H3K27me3, rep3

description: Library name: Stim_26_H3K27me3

value: NEMODK


title: mRNA_TC2_lin-28(xe192)_23h

description: Library name: Sample 69


title: Control experiment 2, 12 hrs of vehicle treatment

description: Library name: Co_12h_2


title: C. sardiniense with subsequent C. difficile prdB mutant 24 hours post infection Mouse 5


title: WT, Stimulated, 2 days, H3K27me3, rep2

description: Library name: Stim_25_H3K27me3


title: KS05

city: New Haven

first: Jeffrey

last: Ishizuka

state: CT

address: 300 George Street

institute: Yale University

description: Library name: KS05

data_processing:
RNA-seq reads were preprocessed with fastp for adaptor trimming. The trimmed reads were first aligned to the human reference genome (GRCh38.p14) using STAR and the aligned reads were quantified with Salmon. The unmapped reads were then extracted and quantified against the KSHV reference transcriptome derived from NC_009333 using Salmon. Transcript abundance estimates in transcripts per million (TPM) and estimated read counts were generated for both human and KSHV alignments.
Assembly: GRCh38.p14, NC_009333
Supplementary files format and content: Clinical metadata annotations for each samples
Supplementary files format and content: Salmon quantification summarized in csv files for counts and/or TPM for KSHV and human genes

source_name: Tumor

extract_protocol:
RNA was extracted from formalin-fixed paraffin-embedded (FFPE) tissue using the FormaPure XL RNA Kit (Beckman Coulter) according to the manufacturer’s protocol. RNA quantity and purity were assessed by micro-volume spectrophotometry (NanoDrop 2000, Thermo Scientific), and RNA integrity was evaluated using the Agilent 2100 Bioanalyzer.
RNA-seq libraries were prepared using the KAPA RNA HyperPrep Kit with RiboErase (Roche/KAPA Biosystems). Briefly, ribosomal RNA was depleted by hybridization to complementary DNA oligonucleotides followed by RNase H and DNase treatment. The remaining RNA was fragmented using heat and magnesium, followed by first-strand cDNA synthesis using random priming and second-strand synthesis incorporating dUTP to enable strand-specific sequencing. Adapters were ligated, and libraries were PCR-amplified. Library quality and fragment size distribution were assessed using the Agilent Bioanalyzer or LabChip GX, and libraries were quantified by qPCR.

value: Tumor

tag: disease state

value: Kaposi sarcoma (KS)


title: KS11

description: Library name: KS11


title: Control experiment 1, 12 hrs of vehicle treatment

description: Library name: Co_12h_1


title: mRNA_TC2_lin-28(xe192)_22h

description: Library name: Sample 68


title: C. sardiniense with subsequent C. difficile prdB mutant 24 hours post infection Mouse 4


title: mRNA_TC2_lin-28(xe192)_21h

description: Library name: Sample 67


title: mRNA_TC2_lin-28(xe192)_20h

description: Library name: Sample 66


title: C. sardiniense with subsequent C. difficile prdB mutant 24 hours post infection Mouse 3


title: Control experiment 2, 6 hrs of vehicle treatment

description: Library name: Co_6h_2


title: Ovarian cancer cell line with shRNA for RelB, spheroid growth condition, replicate 1

city: San Diego

first: Mikella

last: Robinson

address: 5500 Campanile Drive

institute: San Diego State University

description: Library name: Spheroid1_shRelB

data_processing:
Adapter trimming: Cutadapt
Alignment: STAR
Normalization: RSEM - CPM - TMM
Assembly: Genome_build: hg38 (GRCh38)
Supplementary files format and content: RSEM counts for each sample
Supplementary files format and content: Tab-delimited normalized RSEM-CPM-TMM counts matrix with all samples

source_name: ovarian serous carcinoma

growth_protocol: Adherent OV90 cells were grown in RPMI 1640 medium supplemented with Tetracycline-free Fetal Calf Serum (10%) and 1% penicillin/streptomycin. Spheroids were grown in ultra-low attachment plates or flasks in DMEM-F12 media supplemented with 1% KnockOut serum replacement, 1% penicillin/streptomycin, 0.1% insulin-transferrin-selenium, and 0.4% bovine serum albumin and growth factors EGF 20 ng/mL and FGF 10 ng/mL.

extract_protocol:
Total RNA was collected from cells according to the manufacturer's instructions using the RNeasy Mini Kit (Qiagen 74104).
Libraries were prepared according to the manufacturer's instructions using TruSeq Stranded mRNA library kit (Illumina 20020594).

treatment_protocol: 6 days growth in each condition, fresh medium was supplemented after 72 hours.

value: ovarian serous carcinoma

value: ovarian cancer cell line

value: shRelB

tag: growth condition

value: Spheroid


title: mRNA_TC2_lin-28(xe192)_19h

first: Dimos

address: Maulbeerstrasse 66

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: Sample 65


title: NEMODK, Stimulated, 2 days, H3K27me3, rep1

description: Library name: Stim_12_H3K27me3

value: Spleen

value: B cells

value: Anti-CD40 and IL-4


title: Control experiment 1, 6 hrs of vehicle treatment

description: Library name: Co_6h_1

value: adipose tissue derived mesenchymal stromal cell


title: mESCs, 2i+LIF LP, rep3

city: Bristol

first: Lucia

last: Marucci

state: UK

address: University Walk

department: Engineering Mathematics and School of cellular and molecular biology.

country: United Kingdom

institute: University of Bristol

description: Library name: Sample 6

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq
Trimming and cleaning with bbduk
Alignment was performed with STAR 2.6.0a
The expression levels of genes were determined with HTseq-counts 0.9.1
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts

growth_protocol: Cell lines were maintained in Ndiff227 basal media supplemented with CHIR99021 3uM and PD03259011uM for 1 week and then at each passagge we adopted a regimen of alternating drug administration and withdrawal in the basal medium (NDiff) with CH, PD and LIF

extract_protocol:
RNeasy Plus Mini Kit from Qiagen
Libraries were prepared from 125 ng of total RNA using mRNA-seq research grade sequencing service (Next Generation Diagnostics srl)

value: Mouse embryionic stem cells

value: 2i+LIF LP

value: pluripotency maintainance


title: C. sardiniense with subsequent C. difficile prdB mutant 24 hours post infection Mouse 1


title: WT, Unstimulated, 2 days, H3K4me3, rep3

description: Library name: Unstim_27_H3K4me3

value: medium


title: mRNA_TC2_lin-28(xe192)_18h

last: Gaidatzis

description: Library name: Sample 64

value: whole organism


title: C. sardiniense with subsequent C. difficile prdB mutant 20 hours post infection Mouse 8

value: Mouse caecal contents


title: Placenta, CVS 11-13 weeks gestation, D4831, small RNAseq

city: Melbourne

first: Ellen

last: Menkhorst

state: Victoria

address: Royal Women's Hospital

department: Obstetrics, Gynecology and Newborn Health

country: Australia

institute: The University of Melbourne

description: Library name: CVS D4831 small RNAseq

data_processing:
Primary sequence data generated: Illumina bcl2fastq 2.20.0.422 pipeline
Quality control: small RNA reads were trimmed and length filtered using Trim_Galore! To be between 14 and 38 base pairs long
Reads mapping: Homo sapian genome (Build version GRCh38, GCF_000001405.39)
Map reads to genomic sequences: STAR aligner (v2.5.3a)
Assembly: GRCh38
Supplementary files format and content: CVS mRNA gene counts.xlsx; excel format, first column gene IDs; followed by a column of read counts for each sample. First row shows sample name for each column.
Supplementary files format and content: CVS sRNA gene counts.xlsx; excel format, first column of gene biotypes, second column of gene IDs followed by a column of read counts for each sample. The first row shows a sample name for each column.

source_name: Chorionic villus

extract_protocol:
RNA was extracted from snap-frozen tissue and cells using the RNeasy Mini kit (QIAGEN) according to the manufacturer’s instructions. Genomic DNA was digested using the on column (RNase-free DNase set, #79256, QIAGEN) according to the manufacturer’s instructions. RNA concentration, yield and purity were analyzed by spectrophotometry (Nanodrop Thermo Scientific, Scoresby, Victoria, Australia) at an absorbance ratio of A260/280nm.
Illumina Ribo-zero Gold

value: Chorionic villus

tag: outcome

value: Preterm Preeclampsia


title: NEMODK, Unsimulated, 2 days, H3K4me3, rep3

description: Library name: Unstim_26_H3K4me3

value: NEMODK


title: Placenta, CVS 11-13 weeks gestation, D4596, small RNAseq

description: Library name: CVS D4596 small RNAseq

value: Normotensive control


title: C. sardiniense with subsequent C. difficile prdB mutant 20 hours post infection Mouse 7


title: WT, Unstimulated, 2 days, H3K4me3, rep2

description: Library name: Unstim_25_H3K4me3

value: WT


title: mRNA_TC2_lin-28(xe192)_16h

city: Basel

description: Library name: Sample 62


title: C. sardiniense with subsequent C. difficile prdB mutant 20 hours post infection Mouse 6


title: mRNA_TC2_lin-28(xe192)_15h

description: Library name: Sample 61


title: Placenta, CVS 11-13 weeks gestation, D2607, small RNAseq

description: Library name: CVS D2607 small RNAseq

value: Term Preeclampsia


title: mRNA_TC2_lin-28(xe192)_39h

description: Library name: Sample 85


title: mRNA_TC2_lin-28(xe192)_14h

description: Library name: Sample 60


title: Placenta, CVS 11-13 weeks gestation, D2004, small RNAseq

description: Library name: CVS D2004 small RNAseq


title: Cd3_rep2

description: Library name: Cd3_rep2

value: lung


title: NEMODK, Unstimulated, 2 days, H3K4me3, rep1

description: Library name: Unstim_12_H3K4me3

value: Spleen


title: mRNA_TC2_lin-28(xe192)_17h

description: Library name: Sample 63


title: mRNA_TC2_lin-28(xe192)_13h

description: Library name: Sample 59


title: Placenta, CVS 11-13 weeks gestation, D4008, small RNAseq

description: Library name: CVS D4008 small RNAseq


title: Placenta, CVS 11-13 weeks gestation, D1921, small RNAseq

description: Library name: CVS D1921 small RNAseq


title: C. sardiniense with subsequent C. difficile prdB mutant 20 hours post infection Mouse 3


title: WT, Unstimulated, 2 days, H3K4me3, rep1

description: Library name: Unstim_19_H3K4me3

value: B cells


title: WT, Stimulated, 2 days, H3K4me3, rep3

description: Library name: Stim_27_H3K4me3

value: Anti-CD40 and IL-4


title: mRNA_TC2_lin-28(xe192)_12h

description: Library name: Sample 58


title: Placenta, CVS 11-13 weeks gestation, C9453, small RNAseq

description: Library name: CVS C9453 small RNAseq


title: C. sardiniense with subsequent C. difficile prdB mutant 20 hours post infection Mouse 2


title: C. sardiniense with subsequent C. difficile prdB mutant 20 hours post infection Mouse 5


title: NEMODK, Stimulated, 2 days, H3K4me3, rep3

description: Library name: Stim_26_H3K4me3


title: mRNA_TC2_lin-28(xe192)_11h

description: Library name: Sample 57


title: Placenta, CVS 11-13 weeks gestation, C9186, small RNAseq

description: Library name: CVS C9186 small RNAseq


title: C. sardiniense with subsequent C. difficile prdB mutant 20 hours post infection Mouse 1


title: WT, Stimulated, 2 days, H3K4me3, rep2

description: Library name: Stim_25_H3K4me3


title: BRAC2_OCDC_M58_ROI-088_TMA4B

city: Lausanne

first: Aspram

last: Minasyan

address: Bugnon 25A

institute: Ludwig Institute for Cancer Research / CHUV

description: Library name: TMA4B__088

data_processing:
Raw sequencing data were processed with the bcl2fastq program from Illumina to generate FASTQ files.
FASTQ files were converted into Digital Count Conversion (DCC) format through Nanotring's GeoMx DnD pipeline v2.0.0.16.
QC was performed using the R package GeoMxTools v3.4.0.
Batch effect correction was done by substracting  background and then minimum value was added per batch.
Q3 normalization were performed on the merged corrected experiment.
Assembly: probe-based quantification, Mm_R_NGS_WTA_v1.0.pkc
Supplementary files format and content: DCC files are count files converted from FASTQ files
Supplementary files format and content: data_matrix.csv contains corrected and Q3-normalized read counts from all QC-passed AOIs and filtered genes.
Library strategy: Spatial Transcriptomics

source_name: tumor

extract_protocol:
Tissue microarrays were prepared by extracting 2 mm punches from FFPE blocks to prepare nine slides, each containing up to 30 tumor sections. 5µm FFPE tissue microarrays were baked at 60°C for 1hour, then deparaffinized and underwent antigen retrieval at 100°C for 15 minutes, followed by 1µg/mL proteinase K at 37°C for 15 min. The slides were incubated overnight with the RNA probe mix (Whole Transcriptome Atlas).Tissues were stained with visualization markers panCK-AF647, CD68-AF594 and CD3-AF488 along with the nuclear marker Syto83. Tissue slides were then loaded into the GeoMx DSP instrument for scanning. Probe barcodes from each ROI were UV-photocleaved, collected into a 96-well plate, followed by library preparation and sequencing.
GeoMx DSP Whole Transcriptomic Atlas (WTA) library construction involving probe hybridization, ligation and PCR amplification were done according to Nanostring's protocol (GeoMx DSP NGS readout User Manual Library Preparation & GeoMx NGS Pipeline, MAN-10153-01).

treatment_protocol: Treatment of mice carrying ID8 tumors started 10 days after tumor graft and continued for 3 weeks. Mice were vaccinated intradermally with 1 x 106 OCDC every week. Anti-VEGF (40 µg, together with OCDC, Absolute Antibody) and anti-PD1 (200 µg, every 3 days, BioXcell) were given intraperitoneally (i.p.). Olaparib (PARPi) was administered orally at 40 mg/kg/day. As treatment controls, tumor-bearing mice were treated with PBS or isotype controls.

value: tumor

tag: mouse id

tag: slide id

tag: region of_interest

tag: model

value: OCDC

tag: ck

value: B


title: NEMODK, Unstimulated, 2 days, H3K4me3, rep2

description: Library name: Unstim_14_H3K4me3

tag: tissue

tag: genotype


title: mRNA_TC2_lin-28(xe192)_10h

description: Library name: Sample 56

tag: strain

tag: time (h)


title: Placenta, CVS 11-13 weeks gestation, C6471, small RNAseq

description: Library name: CVS C6471 small RNAseq


title: C. sardiniense with subsequent C. difficile prdB mutant 14 days post infection Mouse 5


title: BRAC2_OCDC_M59_ROI-094_TMA4B

description: Library name: TMA4B__094

tag: treatment

tag: batch


title: WT, Stimulated, 2 days, H3K4me3, rep1

description: Library name: Stim_19_H3K4me3

tag: cell type


title: mRNA_TC2_lin-28(xe192)_9h

description: Library name: Sample 55


title: Placenta, CVS 11-13 weeks gestation, C4318, small RNAseq

description: Library name: CVS C4205 small RNAseq


title: C. sardiniense with subsequent C. difficile prdB mutant 14 days post infection Mouse 4


title: NEMODK, Stimulated, 2 days, H3K4me3, rep2

description: Library name: Stim_14_H3K4me3


title: mRNA_TC2_lin-28(xe192)_8h

description: Library name: Sample 54


title: Placenta, CVS 11-13 weeks gestation, C4205, small RNAseq

description: Library name: CVS C4144 small RNAseq


title: NEMODK, Stimulated, 2 days, H3K4me3, rep1

description: Library name: Stim_12_H3K4me3


title: C. sardiniense with subsequent C. difficile prdB mutant 14 days post infection Mouse 3


title: mRNA_TC2_lin-28(xe192)_7h

description: Library name: Sample 53


title: Placenta, CVS 11-13 weeks gestation, C4144, small RNAseq

description: Library name: CVS C4105 small RNAseq


title: C. sardiniense with subsequent C. difficile prdB mutant 14 days post infection Mouse 2


title: WT, Unstimulated, 2 days, RelA, rep3

description: Library name: Unstim_27_RelA


title: mRNA_TC2_lin-28(xe192)_6h

description: Library name: Sample 52


title: Placenta, CVS 11-13 weeks gestation, C4105, small RNAseq

description: Library name: CVS C3729 small RNAseq


title: C. sardiniense with subsequent C. difficile prdB mutant 14 days post infection Mouse 1


title: NEMODK, Unsimulated, 2 days, RelA, rep3

description: Library name: Unstim_26_RelA


title: mRNA_TC2_lin-28(xe192)_5h

description: Library name: Sample 51


title: Placenta, CVS 11-13 weeks gestation, C3729, small RNAseq

description: Library name: CVS C1966 small RNAseq


title: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 9


title: WT, Unstimulated, 2 days, RelA, rep2

description: Library name: Unstim_25_RelA


title: mRNA_TC2_lin-28(xe192)_4h

description: Library name: Sample 50


title: Placenta, CVS 11-13 weeks gestation, C1966, small RNAseq

description: Library name: CVS C1941 small RNAseq


title: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 7


title: C. sardiniense with subsequent C. difficile prdB mutant 20 hours post infection Mouse 4


title: WT, Unstimulated, 2 days, RelA, rep1

description: Library name: Unstim_19_RelA


title: mRNA_TC2_lin-28(xe192)_3h

description: Library name: Sample 49


title: Placenta, CVS 11-13 weeks gestation, C1941, small RNAseq

description: Library name: CVS C1934 small RNAseq


title: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 6


title: NEMODK, Unstimulated, 2 days, RelA, rep2

description: Library name: Unstim_14_RelA


title: mRNA_TC2_lin-28(xe192)_2h

description: Library name: Sample 48


title: Placenta, CVS 11-13 weeks gestation, C1934, small RNAseq

description: Library name: CVS C1918 small RNAseq


title: NEMODK, Unstimulated, 2 days, RelA, rep1

description: Library name: Unstim_12_RelA


title: mRNA_TC2_lin-28(xe192)_1h

description: Library name: Sample 47


title: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 5


title: Placenta, CVS 11-13 weeks gestation, C1796, small RNAseq

description: Library name: CVS C1796 small RNAseq


title: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 4


title: WT, Stimulated, 2 days, RelA, rep3

description: Library name: Stim_27_RelA


title: mRNA_TC2_lin-28(xe192)_0h

description: Library name: Sample 46


title: Placenta, CVS 11-13 weeks gestation, 112886, small RNAseq

description: Library name: CVS 112886 small RNAseq


title: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 2


title: NEMODK, Stimulated, 2 days, RelA, rep3

description: Library name: Stim_26_RelA


title: mRNA_TC2_WT_44h

description: Library name: Sample 45


title: Placenta, CVS 11-13 weeks gestation, D4831

description: Library name: CVS D4831


title: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 12


title: WT, Stimulated, 2 days, RelA, rep2

description: Library name: Stim_25_RelA


title: mRNA_TC2_WT_43h

description: Library name: Sample 44


title: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 11


title: Placenta, CVS 11-13 weeks gestation, D4596

description: Library name: CVS D4596


title: WT, Stimulated, 2 days, RelA, rep1

description: Library name: Stim_19_RelA


title: Placenta, CVS 11-13 weeks gestation, D4008

description: Library name: CVS D4008


title: mRNA_TC2_WT_42h

description: Library name: Sample 43


title: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 10


title: NEMODK, Stimulated, 2 days, RelA, rep2

description: Library name: Stim_14_RelA


title: S100A8_A9 experiment 2, 12 hrs of S100A8_A9 treatment

description: Library name: S100A8_A9_12h_2

tag: cell line

value: adipose tissue derived mesenchymal stromal cell


title: mRNA_TC2_WT_41h

description: Library name: Sample 42


title: Placenta, CVS 11-13 weeks gestation, D2607

description: Library name: CVS D2607


title: NEMODK, Stimulated, 2 days, RelA, rep1

description: Library name: Stim_12_RelA


title: mRNA_TC2_WT_40h

description: Library name: Sample 41


title: Placenta, CVS 11-13 weeks gestation, D2004

description: Library name: CVS D2004


title: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 9


title: C. sardiniense with subsequent C. difficile 24 hours post infection Mouse 1


title: mRNA_TC2_WT_39h

description: Library name: Sample 40


title: WT, Unstimulated, 2 days, IgG, rep3

description: Library name: Unstim_27_IgG

value: medium


title: Placenta, CVS 11-13 weeks gestation, D1921

description: Library name: CVS D1921


title: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 8


title: NEMODK, Unsimulated, 2 days, IgG, rep3

description: Library name: Unstim_26_IgG


title: mRNA_TC2_WT_38h

description: Library name: Sample 39

value: whole organism


title: Placenta, CVS 11-13 weeks gestation, C9453

description: Library name: CVS C9453


title: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 7

value: Mouse caecal contents


title: WT, Unstimulated, 2 days, IgG, rep2

description: Library name: Unstim_25_IgG


title: mRNA_TC2_WT_37h

description: Library name: Sample 38


title: Placenta, CVS 11-13 weeks gestation, C9186

description: Library name: CVS C9186

value: Chorionic villus


title: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 6


title: WT, Unstimulated, 2 days, IgG, rep1

description: Library name: Unstim_19_IgG


title: mRNA_TC2_WT_36h

description: Library name: Sample 37


title: Placenta, CVS 11-13 weeks gestation, C6471

description: Library name: CVS C6471


title: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 5


title: NEMODK, Unstimulated, 2 days, IgG, rep2

description: Library name: Unstim_14_IgG


title: mRNA_TC2_lin-28(xe192)_25h

description: Library name: Sample 71


title: mRNA_TC2_WT_35h

description: Library name: Sample 36


title: Placenta, CVS 11-13 weeks gestation, C4318

description: Library name: CVS C4318


title: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 3


title: NEMODK, Unstimulated, 2 days, IgG, rep1

description: Library name: Unstim_12_IgG


title: mRNA_TC2_WT_34h

description: Library name: Sample 35


title: Placenta, CVS 11-13 weeks gestation, C4205

description: Library name: CVS C4205


title: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 2


title: WT, Stimulated, 2 days, IgG, rep3

description: Library name: Stim_27_IgG


title: Placenta, CVS 11-13 weeks gestation, C4144

description: Library name: CVS C4144


title: mRNA_TC2_WT_32h

description: Library name: Sample 33


title: NEMODK, Stimulated, 2 days, IgG, rep3

description: Library name: Stim_26_IgG


title: mRNA_TC2_WT_33h

description: Library name: Sample 34


title: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 11


title: Placenta, CVS 11-13 weeks gestation, C4105

description: Library name: CVS C4105


title: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 10


title: WT, Stimulated, 2 days, IgG, rep2

description: Library name: Stim_25_IgG


title: mRNA_TC2_WT_31h

description: Library name: Sample 32


title: Placenta, CVS 11-13 weeks gestation, C3729

description: Library name: CVS C3729


title: C. sardiniense with subsequent C. difficile 20 hours post infection Mouse 1


title: WT, Stimulated, 2 days, IgG, rep1

description: Library name: Stim_19_IgG


title: Placenta, CVS 11-13 weeks gestation, C1966

description: Library name: CVS C1966


title: mRNA_TC2_WT_30h

description: Library name: Sample 31


title: OSC19 cells (oral quaous cell carcinoma cells), treated with Tryp metabolites and CH223191, rep 3

city: State College

first: Gary

middle: H

last: Perdew

state: PA

address: 101 Huck Life Sciences Building, Suite 315

department: Veterinary and Biomedical Sciences

institute: Pennsylvania State University

description: Library name: OSC19 Tryp+CH 3

data_processing:
Raw ATAC-seq data were processed using the nf-core/atacseq pipeline (v2.1.2) (https://nf-co.re/atacseq/2.1.2/). Sequencing quality were assessed using FastQC, adapter trimming was performed using Trim Galore (default settings), which integrates Cutadapt and FastQC to remove adapter sequences and improve read quality. Trimmed paired-end reads were aligned to the reference genome using Bowtie2 or BWA, and SAM outputs were converted to BAM format using SAMtools.
Post-alignment filtering using SAMtools, BEDTools, BAMTools, and Pysam to removed mitochondrial reads, reads mapping to ENCODE blacklisted regions, duplicates, unmapped or non-primary alignments, multimappers, reads with>4 mismatches, soft-clipped reads, pairs with insert size >2 kb, inter-chromosomal pairs, and improperly oriented pairs.
Peak calling – Accessible chromatin regions were identified using MACS2 with standard parameters for narrow peaks and --broad option for broad accessible regions. Filtered BAM files were converted to Counts Per Milllion (CPM)-normalized bigWig files using deepTools for genome-wide accessibility visualization in IGV.
Differential analysis – Differential accessibility analysis was performed using DESeq2 on unnormalized consensus peak count matrices with minimal pre-filtering (≥10 total reads/peak) using its median-of-ratios method. Peaks with an adjusted p-value < 0.05 were classified as significantly differential.
Differential motif analysis - Motif enrichment analysis was performed using HOMER to identify overrepresented transcription factor (TF) binding motifs within differential peak regions. Known motif enrichment was determined by comparing motif frequencies within the target peak set to an appropriate background set of matched peaks, using HOMER (hypergeometric test) statistical test. Dot plots were generated to visualize the percentage of motif-containing peaks for enriched motifs and −log10 p-values.
Assembly: GRCh38
Supplementary files format and content: anotatePeaks, narrowPeaks

source_name: Tounge squamous cell carcinoma

growth_protocol: OSC19 cell lines were maintained in 1:1 Dulbecco’s Modified Eagle Medium/Ham’s F-12 (Gibco), supplemented with 10% fetal bovine serum (FBS; HyClone), 25mM HEPES pH 7.4 (Sigma), 100 U/mL penicillin, and 100 μg/mL streptomycin (Sigma) at 37°C with 5% CO2 and 95% air.

extract_protocol:
Cells were incubated with DNase enzyme (20,000 IU/ml) in 1x HBSS (supplemented with 250 mM MgCl2 and 50 mM CaCl2) for 30 min in 37°C incubator. Cells were washed with 1x PBS, detached using Trypsin-EDTA solution (Sigma), neutralized with FBS-containing media, resuspended in cold 1xPBS, counted, and frozen 150,000 cells per replicate in freezing media (50% FBS, 40% DMEM/F12, 10% DMSO) at -80°C. Triplicate samples per treatment group were submitted to ActiveMotif, Inc (Carlsbad, CA) for ATAC-seq analysis.
Frozen cells were thawed, diluted in RPMI medium, pelleted, washed with cold 1x PBS, and subjected to Tn5-mediated tagmentation as previously described using the Active Motif ATAC-Seq Kit. Tagmented DNA was purified using the MinElute PCR Purification Kit (Qiagen), amplified for 10 PCR cycles, cleaned using Agencourt AMPure SPRI beads (Beckman Coulter), libraries quantified using Qubit (Invitrogen) and TapeStation (Agilent), and sequenced as PE50 reads on an Illumina NovaSeq X Plus platform.

treatment_protocol: OSC19 cells were treated with vehicle, TCDD (2 nM), Tryp pool, or Tryp pool plus CH223191(1 μM) for 72 h in DMEM/F12 media (supplemented with 1% FBS, 25 mM HEPES pH 7.4, 100 U/mL penicillin, and 100 μg/mL streptomycin)

value: Tounge squamous cell carcinoma

value: Human tounge squamous cell carcinoma cells

value: Tryp with CH223193


title: NEMODK, Stimulated, 2 days, IgG, rep2

description: Library name: Stim_14_IgG

value: NEMODK


title: mRNA_TC2_WT_29h

description: Library name: Sample 30


title: OSC19 cells (oral quaous cell carcinoma cells), treated with Tryp metabolites and CH223191, rep 2

description: Library name: OSC19 Tryp+CH 2

value: Tryp with CH223192


title: Placenta, CVS 11-13 weeks gestation, C1941

description: Library name: CVS C1941

value: Normotensive control


title: NEMODK, Stimulated, 2 days, IgG, rep1

description: Library name: Stim_12_IgG

value: Spleen


title: WT, Stimulated, 2 days, H3K27me3, rep1

description: Library name: Stim_19_H3K27me3

value: B cells

value: WT


title: mRNA_TC2_WT_28h

description: Library name: Sample 29


title: Placenta, CVS 11-13 weeks gestation, C1934

description: Library name: CVS C1934

value: Preterm Preeclampsia


title: OSC19 cells (oral quaous cell carcinoma cells), treated with Tryp metabolites and CH223191, rep 1

description: Library name: OSC19 Tryp+CH 1

value: Tryp with CH223191


title: mRNA_TC2_WT_27h

description: Library name: Sample 28


title: WT, Unstimulated, 2 days, rep3

description: Library name: Unstim_27_ATAC

data_processing:
ATAC-Seq data were first pre-processed, aligned and done with peak-calling using nfcore/atacseq pipeline (10.5281/zenodo.2634132).
Assembly: mm10

extract_protocol:
Cells were washed once with cold PBS, lysed in cold lysis buffer, and immediately centrifuged to collect nuclei.
The nuclei pellet was resuspended in a transposition reaction mix (Illumina) and incubated at 37°C for 30 minutes. Following transposition, DNA was purified using the MinElute Kit (Qiagen) and amplified with NEBNext PCR Master Mix (New England Biolabs).


title: Placenta, CVS 11-13 weeks gestation, C1796

description: Library name: CVS C1796


title: OSC19 cells (oral quaous cell carcinoma cells), treated with Tryp metabolites, rep 3

description: Library name: OSC19 Tryp 3

value: Tryptopham metabolites (Tryp)


title: NEMODK, Unsimulated, 2 days, rep3

description: Library name: Unstim_26_ATAC


title: mRNA_TC2_WT_26h

description: Library name: Sample 27


title: Placenta, CVS 11-13 weeks gestation, 112886

description: Library name: CVS 112886


title: OSC19 cells (oral quaous cell carcinoma cells), treated with Tryp metabolites, rep 2

description: Library name: OSC19 Tryp 2


title: WT, Unstimulated, 2 days, rep2

description: Library name: Unstim_25_ATAC


title: mRNA_TC2_WT_25h

description: Library name: Sample 26


title: OSC19 cells (oral quaous cell carcinoma cells), treated with Tryp metabolites, rep 1

description: Library name: OSC19 Tryp 1


title: SCN2A_multiplex_scRNAseq_data

city: Toronto

first: Jarryll

middle: Anthony

last: Uy

state: ON

address: 60 Leonard Ave

department: Laboratory Medicine and Pathobiology

country: Canada

institute: University of Toronto

description:
Library name: SCN2A_multiplex_scRNAseq
Mix of samples: CTRL_1, CTRL_2, CTRL_3, SCN2A_G1744X_1, SCN2A_G1744X_2, SCN2A_G1744X_3, SCN2A_KO_1, SCN2A_KO_2, SCN2A_KO_3.

data_processing:
Generation of feature-barcode matrices were generated using Cell Ranger 7.0.1 (10X Genomics) with the reference genome GRCh38.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Cerebral organoid

extract_protocol:
Cerebral organoids were dissociated into single cell suspension and fixed using the formaldehyde-based Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit.
The samples were processed according to the 10X Genomics protocol. Single cell libraries were prepared using the Human Probe Set (10X Genomics) and sequenced using an Illumina NovaSeq 6000.

value: Cerebral organoid

value: H1 ESC

value: Cortical

value: multiplexed sample:mix of Control, SCN2A+/G1744X, and SCN2A-/-


title: WT, Unstimulated, 2 days, rep1

description: Library name: Unstim_19_ATAC

value: medium


title: mRNA_TC2_WT_24h

description: Library name: Sample 25

value: whole organism


title: DLBCL, Patient 2, Spatial Transcriptomics (Visium)

city: Chicago

first: Arjun

middle: S

last: Raman

state: IL

address: 900 E. 57th Street, KCBD rm. 4126

department: Department of Pathology and Duchossois Family Institute

institute: University of Chicago

description: Library name: DLBCL_P2

data_processing:
FASTQ files were processed using Space Ranger 2.0.0 with GRCh38 reference in the manual alignment mode. Filtered gene-barcode matrices from Space Ranger output were created using default settings and used for downstream analyses.
Assembly: GRCh38
Supplementary files format and content: *_filtered_feature_bc_matrix.tar.gz contains gene expression matrices produced by spaceranger : barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz
Supplementary files format and content: *_spatial.tar.gz contains mainly images : aligned_fiducials, detected_tissue_image, scalefactors_json.json, tissue_hires_image, tissue_lowres_image and tissue_positions_list
Supplementary files format and content: *_filtered_feature_bc_matrix.h5 is a compressed binary format file to access gene expression matrices produced by spaceranger.
Library strategy: Spatial Transcriptomics

source_name: DLBCL tumor

extract_protocol:
Selected formalin-fixed paraffin-embedded (FFPE) tumor samples were identified and used for cutting five-mm µm-thin FFPE sections to be mounted on standard glass slides. Extraction, whole transcriptome probe hybridization, release, and capture were performed according to 10X Genomics Visium protocols CG000520 and CG000495.
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium protocol CG000495.

value: DLBCL tumor

tag: Stage

tag: biopsy site

value: lymph node

tag: treatment regimen

value: RCHOP

tag: treatment response

value: CR


title: OSC19 cells (oral quaous cell carcinoma cells), treated with TCDD, rep 3

description: Library name: OSC19 TCDD 3

value: Tounge squamous cell carcinoma

value: Human tounge squamous cell carcinoma cells

value: TCDD (2 nM)


title: NEMODK, Unstimulated, 2 days, rep2

description: Library name: Unstim_14_ATAC

value: Spleen

value: B cells

value: NEMODK


title: mRNA_TC2_WT_23h

description: Library name: Sample 24


title: DLBCL, Patient 1, Spatial Transcriptomics (Visium)

description: Library name: DLBCL_P1

value: CHOP + RT


title: NEMODK, Unstimulated, 2 days, rep1

description: Library name: Unstim_12_ATAC


title: OSC19 cells (oral quaous cell carcinoma cells), treated with TCDD, rep 2

description: Library name: OSC19 TCDD 2


title: mRNA_TC2_WT_22h

description: Library name: Sample 23


title: OSC19 cells (oral quaous cell carcinoma cells), treated with TCDD, rep 1

description: Library name: OSC19 TCDD 1


title: NCI-H1299 cells, shALDH18A1-3

city: Nanjing

first: Shan

last: Gao

address: No. 2 Sipailou, Xuanwu District

institute: Southeast University

data_processing:
Raw FASTQ files were trimmed by fastp 0.23.2
Trimmed FASTQ files were aligned to hg38 genome by STAR 2.7.10a
BAM files were counted by featureCounts
Riborex was used to perform differential analysis
Assembly: hg38
Supplementary files format and content: DTEG.xlsx, xlsx format, containing the differential translated genes
Library strategy: Ribo-seq

source_name: lung adenocarcinoma

growth_protocol: NCI-H1299 cell lines were maintained in RPMI1640 medium (Gibco) supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidfied atmosphere with 5%CO2 at 37℃.

extract_protocol:
Total RNA isolated using RNAiso Plus (Takara).
Ribo libraries for Ribo-seq were prepared using Tru-seq Library Prep Kit following manufacturer's protocols

value: lung adenocarcinoma

value: Human lung adenocarcinoma cell


title: WT, Stimulated, 2 days, rep3

description: Library name: Stim_27_ATAC

value: WT

value: Anti-CD40 and IL-4


title: NCI-H1299 cells, shALDH18A1-2


title: NEMODK, Stimulated, 2 days, rep3

description: Library name: Stim_26_ATAC


title: mRNA_TC2_WT_21h

description: Library name: Sample 22

extract_protocol:
At the time of sample collection, animals were washed off the plates with M9 buffer, washed twice with M9 buffer, resuspended in TRI Reagent (MRC, TR-118) and snap-frozen in liquid nitrogen. Prior to RNA extraction, animals were lysed by five cycles of thawing (42°C) and snap-freezing in liquid nitrogen. RNA was extracted using Direct-zol RNA Microprep kit (Zymo Research; R2062; DNase treatment included) according to the manufacturer’s protocol. RNA was eluted in nuclease-free water (Thermo Fisher Scientific, Ambion, AM9937).
TruSeq Illumina mRNA-seq


title: mRNA_TC2_WT_20h

description: Library name: Sample 21


title: OSC19 cells (oral quaous cell carcinoma cells), treated with vehicle, rep 3

description: Library name: OSC19 vehicle 4

value: Vehicle (DMSO)


title: NCI-H1299 cells, shALDH18A1-1


title: mRNA_TC2_WT_19h

description: Library name: Sample 20

value: whole organism


title: OSC19 cells (oral quaous cell carcinoma cells), treated with vehicle, rep 2

description: Library name: OSC19 vehicle 3


title: WT, Stimulated, 2 days, rep2

description: Library name: Stim_25_ATAC


title: NCI-H1299 cells, shControl-3


title: OSC19 cells (oral quaous cell carcinoma cells), treated with vehicle, rep 1

description: Library name: OSC19 vehicle 1


title: WT, Stimulated, 2 days, rep1

description: Library name: Stim_19_ATAC


title: mRNA_TC2_WT_18h

description: Library name: Sample 19


title: NCI-H1299 cells, shControl-2


title: NEMODK, Stimulated, 2 days, rep2

description: Library name: Stim_14_ATAC


title: Skin scRNAseq, ulcers and control skin

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

description: Parse Biosciences Evercode WT

data_processing:
Sublibraries were created and sequenced seperately - 2 sublibraries on the Mini kit for VLU1 and 7 sublibraries on the WT kit for all other samples
Each pair of FASTQ files for each sublibrary was processced with split-pipe version 1.1.2 with parameters --mode all --chemistry v2 and a list of sample barcodes as noted in the parse barcode
Subsequently split-pipe was run with parameters --mode comb and a list of previously generated sublibrary directories
Assembly: GRCh38
Supplementary files format and content: all_genes.csv.gz: list of genes assayed (column information for the count matrix)
Supplementary files format and content: VLU1.cell_metadata.csv.gz: list of cells with associated sample information for sample VLU1 only (row information for the count matrix)
Supplementary files format and content: combined.cell_metadata.csv.gz: list of cells with associated sample information for combined samples from WT kit only (row information for the count matrix)
Supplementary files format and content: VLU1.count_matrix.mtx.gz: count matrix per gene per cell in VLU1
Supplementary files format and content: combined.count_matrix.mtx.gz: count matrix per gene per cell in the WT combined file
Supplementary files format and content: sample_info.txt: tab delimited table of sample information

source_name: skin

extract_protocol:
A single-cell suspension from chronic VLU and control skin samples was isolated using the Whole Skin Dissociation Kit, following the manufacturer's instructions (Miltenyi Biotec)
The cells were first fixed using the Fixation Kit (Parse Biosciences) and then subjected to the EvercodeTM Mini (VLU1) or WT kit (all other samples) from Parse Biosciences for library construction according to the manufacturer's protocol.

value: skin


title: mRNA_TC2_WT_17h

description: Library name: Sample 18


title: NCI-H1299 cells, shControl-1


title: Skin ulcer, VLU1

description: Parse Biosciences Evercode Mini


title: NEMODK, Stimulated, 2 days, rep1

description: Library name: Stim_12_ATAC


title: mRNA_TC2_WT_16h

description: Library name: Sample 17


title: NCI-H1299 cells, shALDH18A1-3

data_processing:
Raw FASTQ files were trimmed by fastp 0.23.2
Trimmed FASTQ files were aligned to hg38 genome by STAR 2.7.10a
BAM files were counted by featureCounts
Deseq2 was used to perform differential analysis
Assembly: hg38
Supplementary files format and content: DEG.xlsx, xlsx format, containing the differential expressed genes

extract_protocol:
Total RNA isolated using RNAiso Plus (Takara).
RNA libraries for RIP-seq were prepared using Tru-seq Library Prep Kit following manufacturer's protocols


title: hippocampus, MELANOMA + ICI5

city: IRVINE

first: Devyani

last: swami

state: CA

address: 811 Health Sciences Road

department: Anatomy & Neurobiology

institute: UNIVERSITY OF CALIFORNIA IRVINE

description:
Library name: MEL-ICI-74
Raw counts_MEL ICI-74

data_processing:
Read counts were normalized to adjust for various factors, such as variations of sequencing yield between samples (software package DESeq2 v.1.16.1
Assembly: The trimmed reads were mapped to Mus musculus reference genome available on ENSEMBL using the STAR aligner v.2.5.2b
Supplementary files format and content: TXT files containing Raw count for each sample

source_name: Brain Hippocampus

growth_protocol: For  Bulk RNA seq data, fresh frozen single hippocampi from N=5 brains /groups were excised from the mouse brain and were sent to Azenta Life science

extract_protocol:
Total RNA was extracted from frozen tissue samples using the Qiagen RNeasy Plus Universal Mini kit following the manufacturer’s instructions (Qiagen, Hilden, Germany).
RNA samples were quantified using Qubit 2.0 Fluorometer (Life Technologies, Carlsbad, CA, USA) and RNA integrity was checked using Agilent TapeStation 4200 (Agilent Technologies, Palo Alto, CA, USA).

treatment_protocol: All animals used in this study were housed and cared for in accordance with National Institutes of Health (NIH) guidelines and protocols approved by the Institutional Animal Care and Use Committee (IACUC). Adult male wild-type (WT) mice aged 10–12 weeks were randomly assigned to one of the following experimental groups: (i) WT mice receiving isotype-matched control antibodies (intraperitoneal, i.p.); (ii) WT mice bearing D4M-3A.UV2 tumors and treated with isotype-matched control antibodies (i.p.); (iii) WT mice treated with immune checkpoint inhibitors (ICIs), including anti–CTLA-4 (1 mg per dose, three times weekly, i.p.) and anti–PD-1 (200 µg per dose, twice weekly, i.p.); and (iv) WT mice bearing D4M-3A.UV2 tumors treated with the same combination ICI regimen for three weeks. For tumor induction, mice in the cancer groups received bilateral intradermal injections of 5 × 10⁵ syngeneic D4M-3A.UV2 melanoma cells. Tumors were allowed to engraft for one week prior to initiating ITC or ICI treatments. Following completion of the treatment regimen, mice were euthanized 72 hours after the final injection, and brains were harvested for downstream analyses.

value: Brain Hippocampus

value: MELANOMA + ICI


title: mRNA_TC2_WT_15h

description: Library name: Sample 16


title: NCI-H1299 cells, shALDH18A1-2


title: mRNA_TC2_WT_14h

description: Library name: Sample 15


title: hippocampus, MELANOMA + ICI4

description:
Library name: MEL-ICI-73
Raw counts_MEL ICI-73


title: NCI-H1299 cells, shALDH18A1-1