title: Mouse_p53WT_untreated_1

first: John

last: Parant

description: Library name: Sample 11


title: Rubi g9242 knockout repeat 1

status: Public on Jun 16 2025

type: SRA

city: hangzhou

first: Chao

last: Liu

state: 浙江

address: 浙江省

country: China

institute: 浙江大学

description: Rubi g9242 knockout repeat 1

library_source: transcriptomic

data_processing:
Trimmomatic v0.39   STAR v2.7.6a  featureCounts v1.6.0
Assembly: N.rubi.CDS, N.rubi.gff3
Supplementary files format and content: reads counts

molecule: total RNA

organism: Nigrospora rubi

source_name: hyphae

growth_protocol: PDA growth

extract_protocol:
Flash-freeze fungal tissue in liquid nitrogen and homogenize. Mix with lysis buffer containing RNase inhibitors. Add chaotropic salt, vortex, and perform phenol-chloroform extraction. Centrifuge, collect the aqueous phase, and precipitate RNA with alcohol. Wash the pellet, air-dry, dissolve in RNase-free water, and verify RNA quality.
Start fungal library construction with high-quality RNA extraction and genomic DNA removal. Convert RNA to cDNA using reverse transcription, then fragment the cDNA for sequencing. Attach adapters to the fragments, amplify via PCR, and quantify the library with a bioanalyzer before sequencing.

treatment_protocol: To ascertain which genes were influenced in deletion mutants, we newly generated transcriptome data for deletion mutant vs control for each of three convergent genes (ΔNrURED, ΔNrGMF1, and ΔNrGLA) in N. rubi

tag: tissue

value: hyphae

tag: genotype

value: g9242 knockout


title: BT16 cells, DMSO, replicate 1, RNA-seq

city: AURORA

first: Etienne

last: Danis

state: CO

department: Cancer Center

country: USA

institute: University of Colorado, Denver - Anschutz Medical Campus

data_processing:
FASTQ files were processed using the nf-core-rnaseq pipeline (v3.12.0) (auto strandedness).
Adapter sequences were removed withTrim Galore.
Reads were aligned with STAR to GRCh38 (NCBI, p.14, release 110) and quantified to gene counts using RSEM.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text files includes raw counts for each Sample

molecule: polyA RNA

organism: Homo sapiens

source_name: ATRT

growth_protocol: BT16 ATRT cells were cultured in RPMI medium (Life Technologies, Gibco #11875-093) supplemented with 10% fetal bovine serum (FBS; Atlanta Biologicals, Inc. #S11550) and 1% penicillin/streptomycin (Life Technologies, Gibco #15140-122).  Cells were cultured at 37 °C with 95% air and 5% CO2.

extract_protocol:
Ribonucleic acid was isolated from treated cells using a QIAGEN miRNAeasy kit Cat#217004 (Qiagen, Valencia, CA, USA). 500ng total RNA was used.
Libraries were prepared and sequenced by Genomics and Microarray Core Facility (University of Colorado Denver). Universal Plus™ mRNA-Seq library kit with NuQuant (Tecan) was used. Libraries were sequenced on an Illumina NovaSEQ X. High-quality base calls at Q30R ≥80% were obtained with 40M paired end reads.

treatment_protocol: BT16 ATRTcells were treated with TM with dose 30um for 72 hrs or with DMSO which was used for control.

value: ATRT

tag: cell line

tag: treatment

value: DMSO

tag: condition

value: Vehicle


title: Opaque-5

city: Baoding , China

first: Chun-Hao

last: Han

state: Baoding , China

address: Baoding , China

institute: Hebei Agricultural University

description: Library name: Sample10

data_processing:
After library construction, fastp was used for quality control to filter out low-quality data, generating clean reads. These reads were then aligned to the ribosomal RNA (rRNA) database of Gallus gallus (chicken) using Bowtie2 with zero mismatches allowed, and any reads mapped to rRNA were removed. The remaining unmapped reads were retained for subsequent transcriptomic analysis.Next, HISAT2 was employed to align the clean reads to the reference genome (Gallus gallus). Based on the HISAT2 alignment results, StringTie was used to reconstruct transcripts, and RSEM was applied to quantify gene expression levels in each sample.The expression levels are presented by the original reads count and FPKM. The original reads count represents the number of reads contained in the transcript. FPKM is the value corrected by sequencing depth and gene length. After obtaining the expression levels of all genes, we performed Principal Component Analysis (PCA) using R (http://www.r-project.org/). The gene expression data were analyzed using the DESeq2 software, which consisted of three main steps: (Ⅰ) Normalization of read counts; (Ⅱ) Calculation of p-values based on statistical modeling and hypothesis testing; (Ⅲ) Multiple testing correction to obtain the False Discovery Rate (FDR). Finally, based on the differential expression analysis results, genes with FDR < 0.05 and |log₂FC| > 1 were identified as significantly differentially expressed genes (DEGs).
Assembly: Ensembl_release100
Supplementary files format and content: Columns:  - Row 1: Gene Symbol (official HUGO symbols)  - Row 2: Sample1_Log2Expression, Sample2_Log2Expression, ...  - Normalization: RPKM values log2-transformed.

organism: Gallus gallus

source_name: Isthmus

extract_protocol:
Extract total RNA using the Trizol method
According to the manufacturer's instructions, total RNA was extracted and purified using Trizol reagent (Life Technologies, Carlsbad, California, USA). mRNA was enriched using mRNA Capture Beads, followed by fragmentation at high temperature. The fragmented mRNA served as a template for first-strand cDNA synthesis in a reverse transcription system. Second-strand cDNA synthesis was performed simultaneously with end repair and A-tailing. Subsequently, adapters were ligated, and target fragments were selected and purified using Hieff NGS® DNA Selection Beads. Finally, PCR amplification was conducted to construct the library, which was sequenced on the Illumina Novaseq X Plus platform.

value: Isthmus

value: WT

value: opaque


title: Mouse_p53WT_3hpi_2

city: Birmingham

middle: M

state: AL

address: 1670 University Blvd

institute: University of Alabama at Birmingham

description: Library name: Sample 10

data_processing:
Raw sequencing reads were aligned to Mus musculus GRCm39 genome assemblies using STAR (version 2.7.3a, GCC 6.4.0-2.28) with default setting.
Following alignment, raw read counts were generated using HTSeq (version 0.12.3, foss-2018b, Python-3.6.6). The corresponding gene annotation files used in HTSeq were Mus_musculus.GRCm39.103.chr.gtf for mouse samples.
Differentially expressed genes (DEGs) were identified using DESeq2 (version 1.42.1) in R (version 4.3.3).
Normalized counts were obtained using RSEM (version 1.3.3)
Assembly: mm39 (Mus_musculus.GRCm39)
Supplementary files format and content: tab-delimited text file includes TPM values for each samples

organism: Mus musculus

source_name: E9.5 embryos

extract_protocol:
Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit (QIAGEN, #74134) according to the manufacturer’s instructions. ~500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were generated using the Illumina RNA kit with PolyA selection, followed by sequencing on the Illumina HiSeq platform, producing 2 × 75 bp paired-end reads. Sequencing was conducted by the UAB Heflin Center for Genomic Core.

treatment_protocol: Pregnant mice carrying E9.5-stage embryos were placed at the closest position to the ionizing radiation source in an X-RAD 320 X-ray irradiator, exposing the embryos to 5 Gy/min of radiation for a total dose of 30 Gy.

value: E9.5 embryos

value: ionizing radiation-irradiation


title: inactive_exp2_1

city: Warsaw

first: Andrzej

last: Dziembowski

address: 4 Ks. Trojdena Street

country: Poland

institute: International Institute Of Molecular And Cell Biology In Warsaw

description:
Illumina RNA Sequencing of C. elegans inactive miniSOG strain after illumination, second experiment, biological replicate 1
raw_counts_ablation.xlsx

data_processing:
Illumina RNA-seq were performed in external companies. FastQ files were then mapped to WBCel235 reference genome using STAR aligner (v2.7.10a) and processed with samtools (v1.961). Read counts were obtained with featureCounts from the Subread package (v2.0.665, using options -Q 10 -p -C -B). Differential expression analysis was conducted using DESeq2 Bioconductor package (v1.28) with default settings.
Nanopore Direct RNA Sequencing was performed with the MinION device, followed by basecalling with Guppy 6.0.0 (ONT), mapping to WBCel235 reference (MiniMap v2.17 (25) with options -k 14 -ax map-ont –secondary = no), and processing with samtools v1.9. Lengths of poly(A) tails were estimated with Nanopolish (v0.13.2).
Assembly: WBcel235
Supplementary files format and content: Excel files with raw number of counts for Illumina RNA sequencing and poly(A) tails statistics for Nanopore direct RNA sequencing

organism: Caenorhabditis elegans

source_name: whole worm

growth_protocol: Strains were cultured at 20°C (or 15°C for ablation experiments) on nematode growth medium (NGM) plates seeded with E. coli HB101 (or HT115 expressing corrensponding RNAi vector) as a food source.

extract_protocol:
Populations of worms were collected and washed three times with 50 mM NaCl. Worm pellets were resuspended in 1 ml TRI Reagent (Sigma-Aldrich), vortexed for 15 minutes at room temperature, and stored at -80°C until further processing. RNA extraction was performed according to the manufacturer’s protocol for TRIzol-based isolation, with additional purification using KAPA Pure magnetic beads (RNA to beads ratio: 1:3 v/v). RNA quality and integrity were confirmed using the Agilent TapeStation system.
Total RNA samples for Illumina RNA sequencing were sent to Center for New Technology (Poland) or Genewiz (Germany) and libraries were prepared with the use of internal protocols. Sequencing libraries for Nanopore direct RNA sequencing were prepared using the DRS Kit (Oxford Nanopore Technologies, SQK- RNA002) according to the manufacturer’s protocol. In each library, total RNA isolated from worms (1,5 - 2 μg depending on the amount of isolated RNA) was mixed with 2 ng of in vitro transcribed poly(A) standards.

value: whole worm

value: nspc-10p::inactive miniSOG

tag: strain

value: ADZ74 (this study)

tag: developmental stage

value: young adult

value: grown at 15℃ on NGM plates seeded with E. coli HB101 ; illuminated 5x10min with blue light at L3 stage


title: Rubi g999 knockout repeat 3

description: Rubi g999 knockout repeat 3

value: g999 knockout


title: IFE-1 CLIP Replicate 2 (CLIP)

city: Indianapolis

first: Scott

middle: T

last: Aoki

state: Indiana

address: 635 Barnhill Drive MS-4071

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

description: Library name: IFE-1 Rep 2 CLIP

data_processing:
Fastq raw sequencing files were assessed for quality and filtered to remove adapters by fastp (v0.21.0). Barcodes were subsequently removed and reads deduplicated. Paired reads were merged with Ngmerge (v0.03). Processed reads were mapped to the C. elegans genome using STAR (v2.7.10b). Custom perl scripts were used to identify RNA start sites and read coverage. Targets were identified using the CLIPPER software package.
Assembly: WBcel235
Supplementary files format and content: bam
Supplementary files format and content: bigwig

source_name: Whole organism

growth_protocol: Large synchronized populations of IFE-1::3xFLAG worms were generated by standard bleaching protocol and allowed to develop for 72 hours on NGM plates seeded with HB101 bacteria as a food source.

extract_protocol:
Homogenized samples were treated with 250 U of RNase I (Ambion) at 37°C for 10 minutes with constant shaking at 1200 rpm prior to immunoprecipitation. Briefly, upon RNase I digestion, 2% of 5 mg worm lysate was taken as inputs and the rest of the lysate was incubated with 100 µl of anti-FLAG magnetic beads (Sigma) with a final concentration of 1:5 dilution of wash buffer (20 mM Tris-HCl (pH 7.5), 10 mM MgCl2, 5 mM NaCl, 0.2% Tween-20) for 1 hour. IP samples were washed once with high-salt wash buffer (50 mM Tris-HCl (pH 7.5), 1 M NaCl, 1 mM EDTA, 0.1% SDS, 1% NP-40) and washed twice with the wash buffer. T4 PNK Minus reaction was performed on bead using T4 PNK Minus (NEB) at 37°C for 20 minutes with constant shaking at 1200 rpm, followed by 1x wash with high-salt wash buffer and 3x wash with wash buffer. IP samples were subjected to Fast AP (Thermo Scientific) reaction at 37°C for 10 minutes with constant shaking at 1200 rpm and PNK reaction with T4 PNK (NEB) at 37°C for 20 minutes with constant shaking at 1200 rpm without removing the FastAP reaction mixture. IP samples were washed 1x with high-salt wash buffer and 3x with wash buffer. 3’ RNA adapter (CLASHInvRiL19) was ligated on bead using T4 RNA ligase (high-concentration, NEB) at RT for 75 minutes on a rotator. IP samples were washed 1x with wash buffer, 1x with high-salt wash buffer, and 2x with wash buffer. All input and IP samples were denatured using 4xNuPAGE™ sample buffer (Invitrogen) at 65°C for 10 minutes and resolved in NuPAGE™ 4-12% Bis-Tris gel (Invitrogen) at 150 V for 75 minutes, followed by transfer to nitrocellulose membrane at 30 V for overnight. After confirming the position of IFE-1 protein by western blot using FLAG antibody (Sigma), regions above IFE-1 protein (up to ~250 kDa) were excised for proteinase K (NEB) treatment at 37°C for 40 minutes with constant shaking at 1200 rpm. RNA was isolated from proteinase K treatment reaction using Zymo RNA clean & concentrator kit (Zymo Research). Upon RNA isolation, input samples were also treated with FastAP (Thermo Scientific) for 10 minutes and T4 PNK (NEB) for 20 minutes, both at 37°C with constant shaking at 1200 rpm, followed by clean up using Zymo RNA clean & concentrator kit (Zymo Research).
3’ RNA adapter (CLASHInvRiL19) was ligated to input samples after incubation at 65°C for 2 minutes using T4 RNA ligase (high-concentration, NEB) at RT for 60 minutes with flicking every 15 minutes. Input samples were cleaned up using MyONE Silane beads (Invitrogen). Reverse transcription was performed for both IP and input samples after incubation at 65°C for 2 minutes using an RT primer (InvAR17) and then at 55°C for 20 minutes using Superscript IV (Invitrogen). The reaction was cleaned up using ExoSAP-IT (Applied Biosystems) and MyONE Silane beads (Invitrogen). Then, 5’ DNA adapter (Invrand10_3Tr3) was ligated after incubation at 70°C for 2 minutes and then at RT for overnight using T4 RNA ligase (high-concentration, NEB) and 5’ deadenylase (NEB). Samples were cleaned up using MyONE Silane beads (Invitrogen) and PCR amplified for 8 cycles (Input) and 13 cycles (IP) using Q5 High-Fidelity PCR master mix (NEB) and PCR forward and reverse primers with specific barcodes. Libraries were purified using Ampure XP beads (Beckman Coulter) and quantified using the D1000 high sensitivity screen tape system (Agilent, La Jolla, CA) before pooling. The pooled library was sequenced on NextSeq2000 (Illumina, San Diego, CA) at the center of bioinformatics and genomics (CGB) at Indiana University, Bloomington using paired-end sequencing.

treatment_protocol: Synchronized adults were washed four times in PBS buffer and then exposed to 25 mJ/cm2 UV radiation on 10-cm NGM plates, washed into 15-ml conical tubes, and spun down. Irradiated worms were slowly dripped into a prechilled mortar filled with liquid nitrogen, forming small frozen spheres. Frozen worm spheres were vigorously grinded for 5 minutes using a pre-chilled mortar and pestle. Liquid nitrogen was added periodically to keep samples frozen. Ground samples were collected and stored at -80°C until use.

value: Whole organism


title: Opaque-4

description: Library name: Sample9

growth_protocol: According to the manufacturer's instructions, total RNA was extracted and purified using Trizol reagent (Life Technologies, Carlsbad, California, USA). mRNA was enriched using mRNA Capture Beads, followed by fragmentation at high temperature. The fragmented mRNA served as a template for first-strand cDNA synthesis in a reverse transcription system. Second-strand cDNA synthesis was performed simultaneously with end repair and A-tailing. Subsequently, adapters were ligated, and target fragments were selected and purified using Hieff NGS® DNA Selection Beads. Finally, PCR amplification was conducted to construct the library, which was sequenced on the Illumina Novaseq X Plus platform.


title: Mouse_p53WT_3hpi_1

description: Library name: Sample 9


title: Mouse_p53WT_1hpi_2

description: Library name: Sample 8


title: Rubi g999 knockout repeat 2

description: Rubi g999 knockout repeat 2

value: hyphae


title: Opaque-2

description: Library name: Sample7


title: WT_exp2_2

description:
Illumina RNA Sequencing of C. elegans wild-type strain after illumination, second experiment, biological replicate 2
raw_counts_ablation.xlsx

value: wild type

value: N2 Bristol (CGC)


title: WT_exp2_1

description:
Illumina RNA Sequencing of C. elegans wild-type strain after illumination, second experiment, biological replicate 1
raw_counts_ablation.xlsx


title: Rubi g6379 knockout repeat 3

description: Rubi g6379 knockout repeat 3

value: g6379 knockout


title: Rubi g999 knockout repeat 1

description: Rubi g999 knockout repeat 1


title: Opaque-3

description: Library name: Sample8


title: Mouse_p53KO_untreated_2

description: Library name: Sample 6

value: w/o ionizing radiation-irradiation


title: active_exp1_3

description:
Illumina RNA Sequencing of C. elegans active miniSOG strain after illumination, first experiment, biological replicate 3
raw_counts_ablation.xlsx

value: nspc-10p::active miniSOG

value: ADZ83 (this study)


title: active_exp1_2

description:
Illumina RNA Sequencing of C. elegans active miniSOG strain after illumination, first experiment, biological replicate 2
raw_counts_ablation.xlsx


title: Mouse_p53WT_1hpi_1

description: Library name: Sample 7


title: Translucent-5

description: Library name: Sample5

value: Isthmus

value: WT

value: translucent


title: Rubi g6379 knockout repeat 2

description: Rubi g6379 knockout repeat 2


title: Mouse_p53KO_untreated_1

description: Library name: Sample 5

value: E9.5 embryos


title: active_exp1_1

description:
Illumina RNA Sequencing of C. elegans active miniSOG strain after illumination, first experiment, biological replicate 1
raw_counts_ablation.xlsx

value: whole worm


title: Rubi g6379 knockout repeat 1

description: Rubi g6379 knockout repeat 1


title: Translucent-4

description: Library name: Sample4


title: WT_exp2_3

description:
Illumina RNA Sequencing of C. elegans wild-type strain after illumination, second experiment, biological replicate 3
raw_counts_ablation.xlsx


title: Mouse_p53KO_3hpi_1

description: Library name: Sample 3

value: ionizing radiation-irradiation


title: inactive_exp1_3

description:
Illumina RNA Sequencing of C. elegans inactive miniSOG strain after illumination, first experiment, biological replicate 3
raw_counts_ablation.xlsx

value: nspc-10p::inactive miniSOG

value: ADZ74 (this study)

value: young adult


title: inactive_exp1_2

description:
Illumina RNA Sequencing of C. elegans inactive miniSOG strain after illumination, first experiment, biological replicate 2
raw_counts_ablation.xlsx

value: grown at 15℃ on NGM plates seeded with E. coli HB101 ; illuminated 5x10min with blue light at L3 stage


title: Rubi WT repeat 3

description: Rubi WT repeat 3

value: hyphae


title: Translucent-3

description: Library name: Sample3


title: Rubi WT repeat 2

description: Rubi WT repeat 2

value: wild type


title: Mouse_p53KO_1hpi_2

description: Library name: Sample 2


title: Translucent-2

description: Library name: Sample2


title: Rubi WT repeat 1

description: Rubi WT repeat 1


title: inactive_exp1_1

description:
Illumina RNA Sequencing of C. elegans inactive miniSOG strain after illumination, first experiment, biological replicate 1
raw_counts_ablation.xlsx


title: Translucent-1

description: Library name: Sample1


title: Mouse_p53KO_1hpi_1

description: Library name: Sample 1


title: Opaque-1

description: Library name: Sample6

value: opaque


title: Pasteurella multocida, co-cultured with Actinobacillus pleuropneumoniae, 20 h, AP_1

status: Public on Jun 15 2025

city: jingzhou

first: Huasong

last: Xiao

address: jingmilu

institute: Yangtze university

description: Library name: Sample 4

data_processing:
RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.After library quality control, different libraries were pooled based on the effective concentration and targeted data amount, then subjected to Illumina sequencing.
Raw data (raw reads) of fastq format were firstly processed through fastp software.. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reference genome and gene model annotation files were downloaded from genome website directly. Both building index of reference genome and aligning clean reads to reference genome were used Bowtie2-2.2.3.
Read count extraction and normalization were performed using HTSeq v0.6.1
Differential expression analysis for two conditions/groups was performed using the DESeq2 R package (1.20.0).
Assembly: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/512/395/GCF_000512395.1_ASM51239v1/
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample.

organism: Pasteurella multocida

source_name: strain

growth_protocol: Pasteurella multocida was co-cultured with A. pleuropneumoniae in brain heart infusion (BHI) medium containing 10% fetal bovine serum (FBS) and 10 μg/mL nicotinamide adenine dinucleotide (NAD), while P. multocida was mono-cultured in medium containing 10% FBS without NAD

extract_protocol:
RNA was harvested using RNAprep Pure Cell/Bacterial Total RNA Extraction Kit (Centrifugal Column Type) catalog number: DP430. 0.5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Pasteurella multocida was co-cultured with A. pleuropneumoniae in BHI medium containing 10% FBS and 10 μg/mL NAD.

value: strain

value: treatment (co-cultured with Actinobacillus pleuropneumoniae)


title: Pasteurella multocida, co-cultured with Actinobacillus pleuropneumoniae, 20 h, AP_3

description: Library name: Sample 6


title: Pasteurella multocida, co-cultured with Actinobacillus pleuropneumoniae, 20 h, AP_2

description: Library name: Sample 5


title: Pasteurella multocida, mono-culture, 20h, Pm_1

description: Library name: Sample 1

value: control (mono-culture)


title: Pasteurella multocida, mono-culture, 20h, Pm_2

description: Library name: Sample 2


title: DSS-2

city: Hong Kong

first: Yiqi

last: Xu

address: Room 201-207 of 2/F of Building 15W, Phase Three

country: Hong Kong

institute: Centre for Chinese Herbal Medicine Drug Development Limited

description: Library name: D2

data_processing:
Illumina NovaSeq X Plus
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

source_name: Liver

extract_protocol:
Liver RNA was extracted using RNeasy Plus Micro Kit (Qiagen, Germany). 400 ng RNA was used  for the construction of sequencing libraries.
Libraries (400 ng RNA) were sequenced on a DNBSEQ platform (BGI), aligned to the mouse genome, and analyzed.

value: Liver

value: DSS


title: Indirubin-3

description: Library name: B4

value: DSS+Indirubin


title: DSS-3

description: Library name: D3


title: Indirubin-1

description: Library name: B2


title: Indirubin-2

description: Library name: B3


title: Mouse_p53KO_3hpi_2

description: Library name: Sample 4


title: Control-3

description: Library name: C3

value: water


title: Control-1

description: Library name: C1


title: Control-2

description: Library name: C2


title: HKO+FOXA2_3

city: Harbin

first: Zheng

last: Chen

state: Heilongjiang

address: 92 Xidazhijie  Harbin Institute of Technology

institute: Harbin Institute of Technology

description: Library name: HKO+FOXA2_3

data_processing:
The image data measured by the high-throughput sequencer are converted into sequence data (reads) by CASAVA base recognition. Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 (v2.2.1) and paired-end clean reads were aligned to the mouse reference genome(grcm39) using Hisat2 (v2.2.1). We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
featureCounts (v2.0.6) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.42.0). DESeq2 provide statistical routines for determining differential expression in digital gene expression data using a model based on the negative binomial distribution. The resulting P-values were adjusted using the Benjamini and Hochberg’s approach for controlling the false discovery rate .
Assembly: mouse reference genome(grcm39)
Supplementary files format and content: Processed data files; excel; gene_fpkm.xlsx

source_name: liver

extract_protocol:
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNA was synthesized using random hexamer primers. Then the second strand cDNA was synthesized using dUTP, instead of dTTP. The directional library was ready after end repair, A-tailing, adapter ligation, size selection, USER enzyme digestion, amplification, and purification. The library was checked with Qubit and real-time PCR for quantification and bioanalyzer for size distribution detection.
After the library is qualified, the different libraries are pooling according to the effective concentration and the target amount of data off the machine, then being sequenced by the Illumina  novaseq x plus. The end reading of 150bp pairing is generated. The basic principle of sequencing is to synthesize and sequence at the same time (Sequencing by Synthesis). Four fluorescent labeled dNTP, DNA polymerase and splice primers were added to the sequenced flowcell and amplified. When the sequence cluster extends the complementary chain, each dNTP labeled by fluorescence can release the corresponding fluorescence. The sequencer captures the fluorescence signal and converts the optical signal into the sequencing peak by computer software, so as to obtain the sequence information of the fragment to be tested.

treatment_protocol: Four-week-old male Ythdc1flox/flox mice were injected with AAV8-TBG-βGal (2×10^11 vp/mouse) via tail vein. Four-week-old male Ythdc1-HKO mice were injected with equal amounts of AAV8-TBG-βGal, AAV8-TBG-FOXA1, or AAV8-TBG-FOXA2 via tail vein. Phenotypes were measured, and mice were sacrificed three weeks later.Total RNA was extracted from liver tissues using Tripure Isolation Reagent (Roche, Mannheim, Germany). Three independent biological replicates for each group were used for RNA-seq.

value: liver

value: tail-vein injection of AAV8-TBG-FOXA2


title: HKO+FOXA2_2

description: Library name: HKO+FOXA2_2


title: HKO+FOXA1_3

description: Library name: HKO+FOXA1_3

value: tail-vein injection of AAV8-TBG-FOXA1


title: HKO+FOXA2_1_

description: Library name: HKO+FOXA2_1_


title: HKO+FOXA1_1

description: Library name: HKO+FOXA1_1


title: HKO+bGal_1

description: Library name: HKO+bGal_1

value: tail-vein injection of AAV8-TBG-bGal


title: HKO+bGal_3

description: Library name: HKO+bGal_3


title: ff+bGal_3

description: Library name: ff+bGal_3


title: ff+bGal_2

description: Library name: ff+bGal_2


title: ff+bGal_1

description: Library name: ff+bGal_1


title: Pasteurella multocida, mono-culture, 20h, Pm_3

description: Library name: Sample 3


title: DSS-1

description: Library name: D1


title: Schmidtea mediterranea, whole-body, unperturbed conditions, scATAC-seq, batch 1

city: Exeter

first: Jordi

last: Solana

address: Northcote House

department: Health and Life Sciences

country: United Kingdom

institute: University of Exeter

description: Trypsin dissociation

library_source: genomic single cell

data_processing:
We created a reference index for CellRanger using cellranger mkref and providing the genome fasta and the GTF (see above). We then mapped the scATAC-seq reads using `cellranger-atac` with the reference index and standard parameters to create a region x cell sparse matrix for downstream analysis
Assembly: Genome assembly from (https://doi.org/10.1101/2023.12.22.572568) will be available on planmine (https://planmine.mpibpc.mpg.de/planmine/genome.do)
Supplementary files format and content: Tab-separated values files and .RDS Seurat object files

molecule: genomic DNA

organism: Schmidtea mediterranea

source_name: whole-body

extract_protocol:
Nuclei suspensions for scATAC-seq were obtained frmo trypsin dissociated cells. Nuclei were resuspended in Diluted Nuclei Buffer (10X Genomics) and counted before injection in the 10X Genomics Chromium, following the manufacturer's protocol.
Libraries were amplified using Nextera library prep and sequenced in a NextSeq Illumina sequencer to obtain 75PE reads.

value: whole-body

value: WT


title: p1_nc1

city: Guangzhou

first: Tianhao

last: Huang

state: Guangdong

address: No.106 Zhong Shan Er Road

institute: Southern Medical University

description: Library name: Sample4

data_processing:
Raw reads were quality filtered with fastp v0.23.0; Clean reads were aligned to the human reference genome (hg38) using HISAT2 v2.2.1. Transcript assembly was performed with StringTie v2.2.1, gene expression quantified with HTSeq v0.13.5, and differential expression analyzed using DESeq2 v1.34.0. GO and KEGG enrichment used clusterProfiler.
Assembly: GRCh38 / hg38
Supplementary files format and content: Processed data include normalized gene expression matrix (FPKM), count matrix(HTSeq), differential expression result tables, and annotation files (CSV/TSV format).

growth_protocol: PANC-1 cells were cultured in DMEM supplemented with 10% FBS and 1% penicillin-streptomycin at 37°C in a humidified incubator with 5% CO₂.

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen), following the manufacturer’s instructions. RNA quality was assessed with Agilent 2100 Bioanalyzer and Qubit fluorometer.
RNA libraries were constructed using the mRNA enrichment protocol with poly(A) magnetic beads, fragmentation, cDNA synthesis, end repair, A-tailing, adapter ligation, size selection, and PCR amplification. Libraries were validated with Agilent 2100 Bioanalyzer and sequenced using Illumina platform.

treatment_protocol: For the lactate experiment, PANC-1 cells were treated with 30 mM sodium lactate for 24 h; control cells received an equal volume of ddH₂O. For NSUN2 knockdown, PANC-1 cells were transfected with siRNA targeting NSUN2 (si-NSUN2) or negative control siRNA (si-NC) using Lipofectamine RNAiMAX (Thermo Fisher) for 48 h.

tag: cell type

value: pancreatic cancer cell

value: control

tag: batch


title: p1_nc2

description: Library name: Sample5


title: p1_lac3

description: Library name: Sample3

value: 30 mM lactate


title: p1_si3

description: Library name: Sample12


title: p1-sinc2

description: Library name: Sample8

value: siNC


title: p1_si1

description: Library name: Sample10


title: p1-sinc1

description: Library name: Sample7


title: p1_lac2

description: Library name: Sample2


title: p1_nc3

description: Library name: Sample6


title: p1_si2

description: Library name: Sample11


title: HKO+FOXA1_2

description: Library name: HKO+FOXA1_2


title: p1_lac1

description: Library name: Sample1


title: scRNA-seq_HDM-only

city: Houston

middle: E

last: Evans

state: TX

address: 6565 MD Anderson Blvd, Unit 1059

department: Pulmonary Medicine

institute: University of Texas MD Anderson Cancer Center

description:
Library name: Sample 1
10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cell ranger software v7.10.
Assembly: mm10
Supplementary files format and content: A group of TSV.GZ, MTX.GZ and H5 files containing barcodes, features and matrices per sample.

source_name: Lungs

extract_protocol:
After being dissected in PBS and cut into pieces using forceps, the entire lung was digested in 1 ml Liebovitz media (Gibco, 21083-027) for 30 minutes at 37°C with 0.5 mg/mL of DNase I (Worthington, D, LS002007), 2 mg/mL of collagenase type I (Worthington, CLS-1, LS004197), and 2 mg/mL of elastase (Worthington, ESL, LS002294). By pipetting up and down, a mechanical trituration was performed on the tissue at 15 minutes during the digestion until the piece were small enough to go through pipet tip. Following the addition of 20% fetal bovine serum, 300 µl (FBS, Invitrogen, 10082–139) to stop the enzymatic reaction, the tissue was homogenized by trituration. The samples were put on ice in the cold room, filtered through a 70 μm cell strainer (Falcon, 352350), and spun down for one minute at 5000 rpm. This was followed by the removal of the supernatant, the addition of 1 ml of red blood cell lysis buffer (15 mM NH₄Cl, 12 mM NaHCO₃, 0.1 mM EDTA, pH 8.0), and the samples' incubation on ice for 3 minutes. Cells were pelleted again by centrifugation at 5000 g for 1 min, washed with once Liebovitz + 10% FBS, resuspended with 1 ml Liebovitz + 10% FBS and filtered through 70 μm cell strainer into a 5 ml glass tube. Samples were stained with CD45-PE/Cy7 (BioLegend, 103114), ECAD-PE (BioLegend, 147304), and ICAM2-A647 (Invitrogen, A15452) antibodies (1:250 dilutions for all antibodies) for 30 min on ice. SYTOX Blue (1:1000, Invitrogen, S34857) was added for viability. A BD FACS Aria Fusion Cell Sorter was used to sort the samples. Dead cells and doublets were excluded. For scRNA-seq CD45-positive cells were collected as the immune cell lineage; from the CD45-negative population, ICAM2-positive cells were collected as the endothelial cell lineage; from the ICAM2-negative population, ECAD-positive cells were collected as the epithelial cell lineage; and the remaining triple-negative population was collected as the mesenchymal lineage. Equal amounts of the immune cell lineage (CD45+) and epithelial cell lineage were combined for the preparation of the 10x Genomics library.
The library construction was performed according to the manufacturer's protocol (single cell 3' v3, 10x Genomics). Briefly, lung single cells that were prepared and gel beads containing unique 10X barcodes were loaded onto a Chromium Chip B along with reverse transcription reagents and partitioning oil. An emulsion was created, partitioning cells and beads into nano-droplets (GEMs) within the microfluidic channels that were run in the 10X Genomics Chromium Controller. A single cell and a barcoded gel bead were co-encapsulated in droplets within the emulsion. The released barcoded oligo(dT) primers containing a unique 10X Cell Barcode allowed for reverse transcription of polyA RNA into cDNA. After reverse transcription, the GEMs were broken, and the cDNA was purified and amplified using PCR.

treatment_protocol: A solution of ODN (1 μM) and Pam2CSK4 (4 μM) in 8 ml of endotoxin-free sterile PBS or 8 ml of PBS control was placed in an Aerotech II nebulizer (Biodex Medical Systems, Shirley, NY) driven by 10 L/min of 5% CO2 in air to promote deep breathing. Polyethylene tubing (30 cm × 22 mm) was used to connect the nebulizer to a 10-L polyethylene container that was vented to a biosafety hood. Mice were exposed to the aerosol for ∼ 40 minutes.

value: Lungs

value: Wild type

value: Epithelial and CD45+ cells

value: PBS


title: Acod1-/-  KO3  + PBS

city: Dresden

first: Ismini

middle: Vasileia

last: Alexaki

state: Saxony

address: Fetscherstraße 74

country: Germany

institute: IKL , Carl Gustav Carus Universitätsklinikum, TU Dresden

description: Library name: sample23

data_processing:
Low quality nucleotides were removed Illumina fastq filterer/).
Reads were further subjected adaptor trimming using cutadapt.
Alignment of the reads to the Mouse genome was done using STAR Aligner  using the parameters: “--runMode alignReads --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --readFilesCommand zcat”. Mouse Genome version GRCm38 (release M12 GENC
HTSeq-0.6.1p1  was used to count the reads that map to the genes in the aligned sample files. Read Quantification was performed using the parameters: 'htseq-count -f bam -s reverse -m union -a 20'. The GTF file (gencode.vM12.annotation.gtf) used for read
Assembly: mm10
Supplementary files format and content: Tab-Delimited Gene-Wise Raw read counts text file

source_name: Whole brain

extract_protocol:
RNA was isolated from sorted microglia with the Nucleospin RNA kit (Macherey-Nagel) and used for construction of sequencing libraries.
Strand-specific paired-end sequencing libraries from total RNA were constructed using TruSeq stranded Total RNA kit (Illumina Inc).

value: Whole brain

value: Microglia

value: LPS


title: Acod1-/-  KO5  + PBS

description: Library name: sample25


title: HKO+bGal_2

description: Library name: HKO+bGal_2

value: liver


title: Acod1-/-  KO4  + PBS

description: Library name: sample24


title: Acod1-/-  KO2  + PBS

description: Library name: sample22


title: Acod1-/-  KO1  + PBS

description: Library name: sample21


title: Wt5/LPS

description: Library name: sample19


title: Wt6/LPS

description: Library name: sample20


title: Wt3/LPS

description: Library name: sample17


title: Wt4/LPS

description: Library name: sample18


title: Wt1/PBS

description: Library name: sample15


title: p1-sinc3

description: Library name: Sample9


title: PBS3

description: Library name: sample14


title: PBS2

description: Library name: sample13


title: Acod1-/-  KO6  + PBS

description: Library name: sample26


title: LPS_1

description: Library name: sample9


title: LPS_3

description: Library name: sample11


title: PBS1/Basal1

description: Library name: sample1


title: LPS1

description: Library name: sample5


title: LPS2

description: Library name: sample6


title: scRNA-seq_PAM2ODN-HDM

description:
Library name: Sample 2
10x Genomics


title: PBS2/Basal2

description: Library name: sample2


title: PBS1

description: Library name: sample12


title: LPS4

description: Library name: sample8


title: PBS3/Basal3

description: Library name: sample3


title: scATAC_PAM2ODN-HDM

description:
Library name: Sample 2
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cell ranger software. Raw sequencing data were processed using the cellranger-atac count function in the Cell Ranger ATAC pipeline to generate fragment files and peak-barcode matrices. Downstream analysis was performed in R using the Seurat (version 4.3) and Signac package (version 1.9) (https://github.com/timoast/signac), in combination with custom scripts. Cells were filtered based on quality control criteria: unique peak counts greater than 100,000 or fewer than 1,000, less than 25% of reads in peaks, blacklist ratio greater than 0.025, nucleosome signal score above 10, or transcription start site (TSS) enrichment score below 2. Gene activity scores were computed using a ±2 kb window around transcription start sites. Cell types were assigned based on marker gene activity: Spock2 for alveolar type 1 (AT1), Lamp3 for alveolar type 2 (AT2), and Sox2 for airway epithelial cells.
Assembly: mm10
Supplementary files format and content: A group of TSV, MTX, H5 and BED files containing barcodes, peaks and matrices per sample.

extract_protocol:
After being dissected in PBS and cut into pieces using forceps, the entire lung was digested in 1 ml Liebovitz media (Gibco, 21083-027) for 30 minutes at 37°C with 0.5 mg/mL of DNase I (Worthington, D, LS002007), 2 mg/mL of collagenase type I (Worthington, CLS-1, LS004197), and 2 mg/mL of elastase (Worthington, ESL, LS002294). By pipetting up and down, a mechanical trituration was performed on the tissue at 15 minutes during the digestion until the piece were small enough to go through pipet tip. Following the addition of 20% fetal bovine serum, 300 µl (FBS, Invitrogen, 10082–139) to stop the enzymatic reaction, the tissue was homogenized by trituration. The samples were put on ice in the cold room, filtered through a 70 μm cell strainer (Falcon, 352350), and spun down for one minute at 5000 rpm. This was followed by the removal of the supernatant, the addition of 1 ml of red blood cell lysis buffer (15 mM NH₄Cl, 12 mM NaHCO₃, 0.1 mM EDTA, pH 8.0), and the samples' incubation on ice for 3 minutes. Cells were pelleted again by centrifugation at 5000 g for 1 min, washed with once Liebovitz + 10% FBS, resuspended with 1 ml Liebovitz + 10% FBS and filtered through 70 μm cell strainer into a 5 ml glass tube. Samples were stained with CD45-PE/Cy7 (BioLegend, 103114), ECAD-PE (BioLegend, 147304), and ICAM2-A647 (Invitrogen, A15452) antibodies (1:250 dilutions for all antibodies) for 30 min on ice. SYTOX Blue (1:1000, Invitrogen, S34857) was added for viability. A BD FACS Aria Fusion Cell Sorter was used to sort the samples. Dead cells and doublets were excluded. For scRNA-seq and scATAC-seq, CD45-positive cells were collected as the immune cell lineage; from the CD45-negative population, ICAM2-positive cells were collected as the endothelial cell lineage; from the ICAM2-negative population, ECAD-positive cells were collected as the epithelial cell lineage; and the remaining triple-negative population was collected as the mesenchymal lineage. Epithelial cell lineage was submitted for the 10x Genomics library.
Lung epithelial cells and immune cells (CD45+) were sorted from 8-week-old mice and processed using the 10x Genomics Chromium Single Cell ATAC platform with the 3′ Library and Gel Bead Kit, following the manufacturer’s protocol.


title: PBS4/Basal4

description: Library name: sample4


title: PBS_PBS2

description:
Library name: Sample 8
Column name in 4_genes_fpkm_expression.txt: FPKM.PBS_PBS2

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases. Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/). We used HISAT2 to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/. The mapped reads of each sample were assembled using StringTie. Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. After the ﬁnal transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) was used to estimate the expression levels of all transcripts.
Assembly: GRCm38
Supplementary files format and content: A XSLX file containing gene level counts, normalized using the FPKM (Fragments Per Kilobase of transcript per Million mapped reads) method.

source_name: Whole lungs

extract_protocol:
After mice anesthesia, the thoracic cavity was dissected, lungs were removed after PBS perfusion via the heart and subsequently placed in a 15 mL test tube containing 5 mL RNAlater (Millipore Sigma). Lungs were weighted and homogenized in RNAlater until smooth using bead beater. RNA was isolated from lungs using Qiagen RNeasy mini kits (Qiagen, CA, USA) according to the manufacturers' instructions, then submitted for RNA-sequencing at LC sciences (Houston, Texas)
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: A solution of ODN (1 μM) and Pam2CSK4 (4 μM) in 8 ml of endotoxin-free sterile PBS or PBS control  was placed in an Aerotech II nebulizer (Biodex Medical Systems, Shirley, NY) driven by 10 L/min of 5% CO2 in air to promote deep breathing. Polyethylene tubing (30 cm × 22 mm) was used to connect the nebulizer to a 10-L polyethylene container that was vented to a biosafety hood. Mice were exposed to the aerosol for ∼ 40 minutes.

value: Whole lungs


title: PBS_PBS3

description:
Library name: Sample 9
Column name in 4_genes_fpkm_expression.txt: FPKM.PBS_PBS3


title: PBS_PBS1

description:
Library name: Sample 7
Column name in 4_genes_fpkm_expression.txt: FPKM.PBS_PBS1


title: scATAC_HDM-only

description:
Library name: Sample 1
10x Genomics


title: PBS_HDM2

description:
Library name: Sample 5
Column name in 4_genes_fpkm_expression.txt: FPKM.PBS_HDM2


title: Wt2/PBS

description: Library name: sample16


title: PBS_HDM1

description:
Library name: Sample 4
Column name in 4_genes_fpkm_expression.txt: FPKM.PBS_HDM1


title: Pam2ODN_HDM3

description:
Library name: Sample 3
Column name in 4_genes_fpkm_expression.txt: FPKM.Pam2ODN_HDM3


title: PBS_HDM3

description:
Library name: Sample 6
Column name in 4_genes_fpkm_expression.txt: FPKM.PBS_HDM3


title: Pam2ODN_HDM1

description:
Library name: Sample 1
Column name in 4_genes_fpkm_expression.txt: FPKM.Pam2ODN_HDM1


title: LPS_2

description: Library name: sample10


title: LPS3

description: Library name: sample7


title: musP7_cd1cranial_3

city: La Jolla

first: Ceri

middle: J

last: Weber

state: CA

address: 9500 Gilman Dr

institute: University of California San Diego

description: Library name: Mus2

data_processing:
Samples were demultiplexed using bcl2fastq Conversion Software
Quality control analysis and trimming of raw fastq files were performed using Trim Galore, a wrapper around Cutadapt and FastQC.
Trimmed reads were mapped to TOGA-annotated one-to-one and one-to-zero transcripts using STAR and read counts per gene were acquired by “--quantMode GeneCounts” option.
STAR aligned gene counts were used to perform differential expression analysis between mouse and jerboa TV1 and TV6 with DESeq2.
Assembly: Mus musculus (mm10) and Jaculus jaculus (mJacJac1.mat.Y.cur)
Supplementary files format and content: SR50 files are the raw count matrices

source_name: Tail vertebra 1 cranial growth cartilage

growth_protocol: Mouse pups were raised to postnatal day 7 and jerboa pups were raised to postnatal day 16

extract_protocol:
Three cranial growth plates per vertebral identity per species was pooled into RNAlater (Invitrogen) and equilibrated overnight at 4˚C. Samples were removed from RNAlater and snap frozen in liquid nitrogen the next day and stored at -80˚C or immediately processed for RNA extraction. Tissue was disrupted over liquid nitrogen using a mortar and pestel, then homogonized using Qiagen QIAshredder system. RNA was extracted using the Qiagen RNAeasy Micro kit with on-column DNA-digest
UCSD IGM used Illumina mRNA Stranded Library kits to prepare libraries from samples with Agilent Tapestation 4200 RIN scores >8

treatment_protocol: Tails were incubated in Proteinase K to remove connective tissues. Cranial growth cartilages were dissected from mouse and jerboa tail vertebra 1 and tail vertebra 6 in ice cold PBS.

value: CD-1 WT

tag: time

value: postnatal day 7


title: musP7_cd1cranial_2

description: Library name: Mus1

value: Tail vertebra 1 cranial growth cartilage


title: musP7_cd6cranial_5

description: Library name: Mus6

source_name: Tail vertebra 6 cranial growth cartilage


title: musP7_cd6cranial_6

description: Library name: Mus7

value: Tail vertebra 6 cranial growth cartilage


title: musP7_cd1cranial_13

description: Library name: Mus3


title: musP7_cd6cranial_4

description: Library name: Mus5


title: E3CT6SAN

city: New York

first: Li

last: Gan

state: NY

address: 413 East 69th Street, 9th Floor BB904

department: Helen and Robert Appel Alzheimer’s Disease Research Institute

institute: Weill Cornell Medicine

description:
Library name: Sample 28
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv

data_processing:
RNA-seq reads were mapped using the BlueBee genomics platform and the GENCODE GRCm38 mouse genome (Lexogen QuantSeq 2.2.3) as reference genome.
Counts were normalized using the median of ratios method.
Differential gene expression was analyzed with the DESeq2 1.38.3 package
To control for multiple testing, we used the Benjamini–Hochberg approach to constrain the FDR
Assembly: mm10 genome
Supplementary files format and content: csv: read counts

source_name: primary microglia

extract_protocol:
RNA was isolated from microglia using the Quick-RNA MicroPrep Kit (Zymo Research, R1051)
cDNA library generation was done using the QuantSeq 3′ mRNA-Seq Library Prep Kit (FWD) for Illumina (K01596, Lexogen) following manufacturer’s instructions.

value: primary microglia

value: Christchurch

value: Tau


title: E3CT5SAN

description:
Library name: Sample 27
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: musP7_cd1cranial_15

description: Library name: Mus4


title: musP7_cd6cranial_17

description: Library name: Mus8


title: E3CC_6

description:
Library name: Sample 25
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: E3CT4SAN

description:
Library name: Sample 26
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: E3T4SAN

description:
Library name: Sample 18
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv

value: WT


title: E3CC_4

description:
Library name: Sample 23
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: E3CC_3

description:
Library name: Sample 22
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv

value: Control


title: E3CC_2

description:
Library name: Sample 21
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: E3T6SAN

description:
Library name: Sample 20
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: E3T5SAN

description:
Library name: Sample 19
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: E3_3

description:
Library name: Sample 14
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: E3_6

description:
Library name: Sample 17
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: E3_4

description:
Library name: Sample 15
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: Pam2ODN_HDM2

description:
Library name: Sample 2
Column name in 4_genes_fpkm_expression.txt: FPKM.Pam2ODN_HDM2

value: Wild type


title: E3_2

description:
Library name: Sample 13
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: GLY2

city: TREVOUX

first: joel

last: lachuer

state: Veuillez sélectionner une région, une état ou une province.

address: 11 allée des acacias

country: France

institute: University Lyon1

data_processing:
Then sequencing was performed on the MGI DNBSEQ-G400, run Single Read 100 bp on a Flow Cell FCL SE100 (MGI)
Data were demultiplexed with BasecallLite v1.5.0.323 producing fastQ file.
Data analysis were performed using Partek suite software (version 8.0). Reads trimming was performed using cutadapt v4.2 software
Reads trimming was performed using cutadapt v4.2 software
Then the reads were mapped using STAR aligner (ver2.7.8a) with default parameters on the human genome GRCh38
Data normalization was realized using median ratio calculation and differential expression was performed by DEseq algorithm. Genes were considered as differentially expressed for a fold change of 1.8 and P-value < 0.05
Assembly: GRCh38
Supplementary files format and content: 1 file .TXT ( raw_counts processed.txt) including raw counts for all samples

source_name: human embryonic kidney cell lines

extract_protocol:
RNA isolation was performed, as previously described (Thollet et al. 2010; Vendrell et al. 2012), from three independent cell culture replicates of each tested cell line (HEK293 cells stably expressing Halo-tagged ZNF217-WT, ZNF217-ΔE4 or ZNF217-G1013 isoforms; control cells were HEK293 cells stably transfected with pHTN-Halo-CMV empty vector)
mRNA was enriched from 200 ng of total RNA, then library preparation was realized with the MGIEasy RNA Directional Library Prep Set (MGI). Quality of libraries were checked by Fragment Analyzer (Agilent) and quantified by Qubit 1X dsDNA HS Assay Kit. Samples were pooled and after circularization in ssDNA, DNB (DNA NanoBalls) were prepared, following the manufacturer protocol.

treatment_protocol:
ZNF217-WT and ZNF217-∆E4 sequences we previously cloned into the pcDNA6 plasmid (Invitrogen, Cergy Pontoise, Paris) (Bellanger et al. 2021; Thollet et al. 2010), we constructed and cloned into the pHTN HaloTag® CMV-neo vector (pHTN-Halo-CMV) (Promega, Madison, WI, USA) three ZNF217-derived constructs, all in frames at their respective N-terminus with the HaloTag sequence: (i) the ZNF217-WT isoform; (ii) the ZNF217-∆E4 isoform; (iii) the truncated ZNF217-G1013 variant, encoding the first 1013 aa sequence present on both ZNF217-WT and ZNF217-∆E4 protein
HEK293 and HEK293T human embryonic kidney cell lines were purchased from the American Type Culture Collection (ATCC) and cultured according to recommendations in DMEM medium supplemented with 10% fetal bovine serum (FBS) and 1% penicillin (10,000 units/ml) –streptomycin (10,000 μg/ml) antibiotics (Thermo Fisher Scientific)
Cell lines were stably transfected with pHTN-Halo-CMV empty vector, pHTN-Halo-CMV-ZNF217-WT, pHTN-Halo-CMV-ZNF217-∆E4 or pHTN-Halo-CMV-ZNF217-G1013 plasmids, then selected in the presence of 1 mg/ml geneticin/G418 (Thermo Fisher Scientific).

value: human embryonic kidney cell lines

value: HEK293 cells

value: ZNF217 G1013 isoform transfected


title: GLY3


title: DE3

value: ZNF217 deletedE4 isoform transfected


title: E3_1

description:
Library name: Sample 12
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: E3CC_5

description:
Library name: Sample 24
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: DE2


title: E3CA9SAN

description:
Library name: Sample 11
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_amyloid_file.csv

value: Amyloid


title: E3CB2SAN

description:
Library name: Sample 7
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: CMV1

value: empty vector transfected


title: E3CA7SAN

description:
Library name: Sample 9
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_amyloid_file.csv


title: E3CB3SAN

description:
Library name: Sample 8
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: CMV3


title: CMV2


title: DE1


title: E3A9SAN

description:
Library name: Sample 6
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_amyloid_file.csv


title: E3A7SAN

description:
Library name: Sample 4
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_amyloid_file.csv


title: E3CA8SAN

description:
Library name: Sample 10
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_amyloid_file.csv


title: WT2

value: ZNF217 Wild type transfected


title: WT3


title: E3B3SAN

description:
Library name: Sample 3
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: E3A8SAN

description:
Library name: Sample 5
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_amyloid_file.csv


title: E3_5

description:
Library name: Sample 16
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: GLY1


title: NSUN2 RIP-seq from ddH2O-treated PANC-1 cells

description: Library name: PANC1_nc_IP

data_processing:
Raw reads were processed using fastp v0.20.1 to trim adapters and filter low-quality reads.
Reads aligned to rRNA were removed using SortMeRNA v2.1.
Clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2 v2.1.0.
Peaks were called using MACS2 v2.2.7.1 with input as control. Peaks were annotated with BEDTools v2.29.2. Motif analysis was performed with HOMER v4.11.1.
Assembly: GRCh38 / Ensembl release 107
Supplementary files format and content: Processed files include BED files of peaks, bigWig tracks for visualization, and count matrices of RIP signal intensity and gene-level expression.
Supplementary files format and content: Additional files include differential peak analysis results (MAnorm or DiffBind), annotated peaks, and GO/KEGG enrichment result tables.

growth_protocol: PANC-1 cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin at 37°C in a 5% CO₂ humidified incubator.

extract_protocol:
RIP was performed using anti-NSUN2 antibody bound to Protein A/G magnetic beads. Cell lysates were prepared in polysome lysis buffer (PLB), immunoprecipitated for 4 hours at 4°C, washed, and RNA was extracted using TRIzol reagent. Input samples were collected before immunoprecipitation.
Libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Takara, Cat# 634888), following the manufacturer’s protocol.

treatment_protocol: Cells were treated with 30 mM sodium lactate or ddH₂O (vehicle control) for 24 hours before RNA immunoprecipitation.

value: pancreatic ductal adenocarcinoma cell

value: wild-type

tag: antibody


title: Input control RNA from lactate-treated PANC-1 cells

description: Library name: PANC1_lac_Input

value: lactate


title: E3B1SAN

description:
Library name: Sample 1
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: E3B2SAN

description:
Library name: Sample 2
primary microglia from APOE3 or APOE3S/S mice treated with nothing, amyloid or tau
gene_count_final_tau_file.csv


title: LG852-NY-258

description:
Library name: Sample 30
mRNA expression in mouse hippocampus

data_processing:
Gene counts were obtained by aligning reads to the mouse genome (mm10) with Cell Ranger software (v.6.1.2) (10x Genomics).
To account for unspliced nuclear transcripts, reads mapping to pre-mRNA were counted. Cell Ranger 6.1.2 default parameters were used to call cell barcodes. We further removed genes expressed in no more than 3 cells, cells with a unique gene count over 5000 or less than 300, cells with UMI counts over 15000, and cells with a high fraction of mitochondrial reads (>1%).
Potential doublet cells were predicted and removed using DoubletFinder for each sample.
SoupX was used to identify and remove ambient RNA from the dataset (Young et al., 2020)
Seurat v4.0.0 R package used for analysis
Assembly: mm10 genome
Supplementary files format and content: barcodes.tsv.gz: cellular barcodes present in datase
Supplementary files format and content: features.tsv.gz: IDs of quantified genes
Supplementary files format and content: matrix.mtx.gz: a matrix of count values, where rows are associated with the gene IDs above and columns correspond to the cellular barcodes.

molecule: nuclear RNA

source_name: brain hippocampus

extract_protocol:
Nuclei isolation adapted from Grubman et al. 2019
Chromium Single Cell 3' Reagent Kits v3.1 (10x Genomics)

value: brain hippocampus

tag: Sex

value: Male

tag: age


title: LG852-NY-257

description:
Library name: Sample 29
mRNA expression in mouse hippocampus

value: ApoE3WT;P301S Tau+


title: [PRO-Seq] K562 cells, single-allele eNMU landing pad knock-in, clonal line E5, rep1

city: Ithaca

first: Zhou

last: Zhou

state: New York

address: 526 Campus Rd, 417 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

description:
Library name: Sample 9
"merge" bw files are merged from rep1 and rep2 bw

data_processing:
For all NGS sequencing data, the quality of FASTQ files was first accessed using FastQC, and the Illumina sequencing adaptors were trimmed using fastp.
To enable accurate alignment of sequencing reads to the eNMU locus in the recombinant cell lines, we built a custom genome for each recombinant TF motif mutant using the reform command line tool. Each custom genome incorporated the exact mutant sequence flanked by Bxb1 recombination sites. For PRO-seq data analysis, rRNA read removal, alignment, and deduplication (with UMI-tools) were performed using the published bash script at https://github.com/JAJ256/PROseq_alignment.sh.
Unnormalized 3'-end bigwigs files for PRO-seq were first generated from bam alignment files by PINTS using the option “pints_visualizer -e R1_5 --reverse-complement”. To calculate scaling factors for PRO-seq data, a collapsed list of all GENCODE v46 transcripts was first generated using the reduceByGene() function in the BRGenomics R package. The unnormalized bigwig files were loaded into Rstudio, and a DESeq2 object was generated for the combined list of all PRO-seq samples using the getDESeqDataSet() function in BRGenomics, using the collapsed transcript list to specify genomic regions of interest. Scaling factors calculated by DESeq2 were applied to each bigwig file using the applyNFsGRanges() function in BRGenomics before data export. Unnormalized 5'-end bigwigs files for PRO-seq were generated from bam alignment files by PINTS using the option “pints_visualizer -e R2_5” and normalized using the same scaling factors calculated from the 3'-end bigwigs files. Normalized bigwig files of two biological replicates were merged using kentUtils of the UCSC Genome Browser for visualization.
PROseq bigwig files are all at single basepair resolution, with 3'-end read position files labled as "PRO_3p_XXX" and 5'-end read position files labled as "PRO_5p_XXX".
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: PRO-Seq

growth_protocol: All the K562 lines were cultured in RPMI 1640 media supplemented with GlutaMAX (Gibco) and 10% heat-inactivated FBS (Avantor) at 37°C with 5% CO2 in a humidified sterile incubator. Cell density was maintained between 0.1 ~ 1 × 10⁶ cells/mL, and mycoplasma testing was performed routinely.

extract_protocol:
All buffer compositions and reaction conditions followed the published protocol of Mahat and Kwak et al. (2016) unless otherwise specified. Briefly, 5 million K562 cells were mixed with 250,000 Drosophila S2 cells (5% spike-in), pelleted at 1000 r.c.f. for 5 min at 4°C, washed once with ice-cold PBS, resuspended with ice-cold permeabilization buffer at a density of 1 million cells/mL, and incubated on ice for 5 min. Cells were washed twice with the same volume of ice-cold permeabilization buffer, and resuspended in 100 μL storage buffer before immediate nuclear run-on or flash-freezing in liquid nitrogen for long-term storage at –80°C. Prior to the run-on reaction, 40 μL Dynabeads MyOne Streptavidin C1 beads (Thermo Fisher) per sample were pre-washed sequentially with Hydrolysis Buffer (0.1N NaOH + 50 mM NaCl), High Salt Wash Buffer, and Binding Buffer. Pre-washed beads were resuspended in 60 μL Binding Buffer per sample. The nuclear run-on reaction was performed at 37°C for 5 min with a final concentration of 20 µM each of Biotin-11-CTP, Biotin-11-UTP, ATP, and GTP. Following RNA extraction by Trizol LS (Invitrogen) and RNA fragmentation by base hydrolysis, 30 μL pre-washed C1 beads and 30 μL Binding Buffer were added to the ~60 μL RNA sample, and bead binding was performed at room temperature for 20 min on a rotational device. Beads were then washed twice using 500 μL High Salt Wash Buffer and once using 500 μL Low Salt Wash Buffer, with tube swap after each wash. Biotinylated RNA was eluted from beads by Trizol extraction, and 3' RNA adaptor ligation was performed in a total volume of 20 μL with 5 µM final adaptor concentration and 2 μL T4 RNA Ligase I, High Concentration (NEB). The reaction was incubated at 20°C for 4 h and held at 4°C overnight. On the next day, 50 μL Binding buffer and 30 μL pre-washed C1 beads were added to the reaction, and another round of bead binding and bead washing was performed as described above. Subsequent 5' enzymatic modifications of RNA were performed on beads with a reaction volume of 20 μL assuming 1 μL bead volume: 5' decapping reaction involved 1 μL RppH (NEB) and 1-h incubation at 37°C; 5' hydroxyl repair involved 1 μL T4 PNK (NEB) and 1-h incubation at 37°C. Beads were then washed once with 300 μL Binding Buffer, and 5' RNA adaptor ligation was performed on beads in a total volume of 20 μL with 5 µM final adaptor concentration and 2 μL T4 RNA Ligase I, High Concentration (NEB), incubated at room temperature for 1 h on a rotational device. Beads were washed twice using 500 μL High Salt Wash Buffer and once using 500 μL Low Salt Wash Buffer, with tube swap after each wash. RNA was eluted from beads by Trizol extraction and resuspended in 13 μL RT resuspension mix (8 μL DEPC H2O, 4 μL of 10 μM Illumina RP1 primer, 1 μL of 10 mM dNTPs). RNA was denatured at 65°C for 5 min and snap cooled on ice, and 7 μL RT master mix was added to the sample (4 μL of 5× RT Buffer, 1 μL of 100 mM DTT, 1 μL Invitrogen SUPERase·In RNase Inhibitor, 1 μL Thermo Scientific Maxima H Minus Reverse Transcriptase). RT reaction program was: 50°C for 30 min, 65°C for 15 min, 85°C for 5 min, hold at 4°C. The resulting cDNA was diluted with an equal volume of DEPC H2O.
A test amplification was performed on 1:4 serial dilutions of 2 μL cDNA sample and run on 6% native PAGE TBE gel to determine the optimal PCR cycle number (N). Final amplification was performed in 100 μL volume (32.5 μL DEPC H2O, 20 μL of 5× Phusion HF Buffer, 20 μL of 5 M betaine, 2.5 μL of 10 µM Illumina RP1 primer, 2.5 μL of 10 µM Illumina indexing RPI-n primer, 2.5 μL of 10 mM dNTPs, 1 μL homemade Phusion polymerase, 19 μL cDNA sample). PCR program was: initial denaturation 95°C for 2 min; 5 cycles of 95°C for 30 s, 56°C for 30 s, 72°C for 30 s; N cycles of 95°C for 30 s, 65°C for 30 s, 72°C for 30 s; final extension 72°C for 5 min. PCR products were sequentially purified using the MinElute PCR purification kit (Qiagen) and homebrew SPRI beads (1.5× bead ratio) to remove all unused primers. DNA concentration was measured by the Qubit dsDNA High Sensitivity assay (Thermo Fisher). The libraries were pooled for sequencing on the Element Biosciences AVITI (2 × 80 bp paired-end sequencing) or Illumina NovaSeq 6000/X Plus platform (2 × 150 bp paired-end sequencing). Note that the 3' and 5' RNA adaptors contain a 6-nt unique molecular identifier (UMI) to enable accurate identification of PCR duplicates in downstream bioinformatic analysis. The complete sequences of the adaptors can be found in Judd et al., 2020.

value: erythroleukemia


title: LG852-NY-256

description:
Library name: Sample 28
mRNA expression in mouse hippocampus


title: LG852-NY-252

description:
Library name: Sample 27
mRNA expression in mouse hippocampus

value: TDI


title: [PRO-Seq] K562 cells, e1 deletion, rep2

description: Library name: Sample 6

value: delta e1


title: Input control RNA from ddH2O-treated PANC-1 cells

description: Library name: PANC1_nc_Input


title: [PRO-Seq] K562 cells, e2 deletion, rep1

description:
Library name: Sample 7
"merge" bw files are merged from rep1 and rep2 bw

value: delta e2


title: WT1

value: human embryonic kidney cell lines


title: LG852-NY-244

description:
Library name: Sample 24
mRNA expression in mouse hippocampus


title: [PRO-Seq] K562 cells, wildtype, rep2

description: Library name: Sample 2

value: wildtype


title: [PRO-Seq] K562 cells, eNMU deletion, rep2

description: Library name: Sample 4

value: delta eNMU


title: [PRO-Seq] K562 cells, e1 deletion, rep1

description:
Library name: Sample 5
"merge" bw files are merged from rep1 and rep2 bw


title: patient10

city: New Haven

first: Fu

last: Gao

state: CT

address: 55 Prospect Street

institute: Yale University

description:
Library name: patient10
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the cellranger-7.1.0.
Assembly: mm10
Supplementary files format and content: matrix files

source_name: mitral valve

extract_protocol:
Single cells were processed using Chromium Controller (10X Genomics) according to the manufacturer’s protocol.
Library was performed according to the manufacturer’s instructions (scRNA seq 3’ v3 protocol, 10x Genomics).

value: mitral valve


title: LG852-NY-233

description:
Library name: Sample 22
mRNA expression in mouse hippocampus


title: [PRO-Seq] K562 cells, eNMU deletion, rep1

description:
Library name: Sample 3
"merge" bw files are merged from rep1 and rep2 bw


title: LG852-NY-227

description:
Library name: Sample 20
mRNA expression in mouse hippocampus

value: Control


title: [PRO-Seq] K562 cells, single-allele eNMU landing pad knock-in, clonal line E5, rep2

description: Library name: Sample 10


title: LG852-NY-251

description:
Library name: Sample 26
mRNA expression in mouse hippocampus


title: LG852-NY-232

description:
Library name: Sample 21
mRNA expression in mouse hippocampus


title: NSUN2 RIP-seq from lactate-treated PANC-1 cells

description: Library name: PANC1_lac_IP


title: LG852-NY-250

description:
Library name: Sample 25
mRNA expression in mouse hippocampus


title: [PRO-Seq] K562 cells, wildtype, rep1

description:
Library name: Sample 1
"merge" bw files are merged from rep1 and rep2 bw


title: LG852-NY-234

description:
Library name: Sample 23
mRNA expression in mouse hippocampus


title: patient9

description:
Library name: patient9
10x Genomics


title: [PRO-Seq] K562 cells, e2 deletion, rep2

description: Library name: Sample 8


title: LG852-NY-225

description:
Library name: Sample 19
mRNA expression in mouse hippocampus


title: Experimental group 4 vs Control group 1 – Replicate 3 (p)

type: RNA

city: Pulawy

first: Aneta

last: Pluta

state: Lublin

address: Av Partyzantow 57

department: Department of Virology and Viral Animal Diseases

institute: National Veterinary Research Institute

description: Biological replicate 6 of 6.

hyb_protocol: according to the Agilent manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C US10353831 scanner. Images were quantified using Agilent Feature Extraction Software (version 12.0.3.1).

data_processing: Agilent Feature Extraction Software (v 12.0.3.1) was used for background subtraction and LOWESS normalization.

source_name: Human embryonic kidney 293T cell line

growth_protocol: HEK293T cells were cultured in DMEM (Lonza) with 4.5 g/L glucose, 2 mM L-glutamine, 10% heat-inactivated FBS (Gibco), and 1% penicillin–streptomycin (Lonza), at 37 °C and 5% CO₂.

extract_protocol: NucleoSpin RNA Plus Kit (Macherey-Nagel, Düren, Germany) according to the manufacturer’s instructions

treatment_protocol: HEK293T cells were plated at 2×10^5 cells/well, then co‐transfected 24 h later with pDrive_miRNA and pBLVΔ‐miRNA (or controls) using Lipofectamine 3000. After 48 h, cells were washed, scraped, and pelleted.

value: V29 mutant strain + pBLVΔ-miRNA

value: 2 days post transfection

value: pDriveΔmiRNA


title: Experimental group 5 vs Control group 1 – Replicate 3

description: Biological replicate 5 of 6.

label_protocol: according to the Agilent manufacturer's protocol

value: V90 mutant strain + pBLVΔ-miRNA


title: LG851-NY-252

description:
Library name: Sample 18
mRNA expression in mouse hippocampus

value: ApoE3CC;P301S Tau+


title: Experimental group 5 vs Control group 1 – Replicate 3 (p)

description: Biological replicate 6 of 6.


title: patient8

description:
Library name: patient8
10x Genomics


title: Reference group vs Control group 1 – Replicate 3 (p)

description: Biological replicate 6 of 6.

value: 344 reference strain + pBLVΔ-miRNA


title: patient7

description:
Library name: patient7
10x Genomics


title: Reference group vs Control group 1 – Replicate 3

description: Biological replicate 5 of 6.


title: Experimental group 4 vs Control group 1 – Replicate 3

description: Biological replicate 5 of 6.


title: LG851-NY-251

description:
Library name: Sample 17
mRNA expression in mouse hippocampus

value: brain hippocampus

value: Male


title: patient3

description:
Library name: patient3
10x Genomics


title: patient4

description:
Library name: patient4
10x Genomics


title: LG851-NY-250

description:
Library name: Sample 15
mRNA expression in mouse hippocampus


title: LG851-NY-214

description:
Library name: Sample 16
mRNA expression in mouse hippocampus


title: patient5

description:
Library name: patient5
10x Genomics


title: LG852-NY-178

description:
Library name: Sample 12
mRNA expression in mouse hippocampus


title: patient2

description:
Library name: patient2
10x Genomics


title: Reference group vs Control group 1 – Replicate 2 (p)

description: Biological replicate 4 of 6.


title: Experimental group 4 vs Control group 1 – Replicate 2 (p)

description: Biological replicate 4 of 6.


title: Control group 2 vs Control group 1 – Replicate 3

description: Biological replicate 5 of 6.

value: pDriveΔmiRNA + pBLVΔ-miRNA


title: Control group 2 vs Control group 1 – Replicate 2 (p)

description: Biological replicate 4 of 6.


title: patient1

description:
Library name: patient1
10x Genomics


title: Experimental group 5 vs Control group 1 – Replicate 1 (p)

description: Biological replicate 2 of 6.


title: Control group 2 vs Control group 1 – Replicate 3 (p)

description: Biological replicate 6 of 6.


title: Experimental group 5 vs Control group 1 – Replicate 2 (p)

description: Biological replicate 4 of 6.


title: Experimental group 4 vs Control group 1 – Replicate 1 (p)

description: Biological replicate 2 of 6.


title: Control group 2 vs Control group 1 – Replicate 2

description: Biological replicate 3 of 6.


title: Experimental group 5 vs Control group 1 – Replicate 1

description: Biological replicate 1 of 6.


title: LG852-NY-133

description:
Library name: Sample 9
mRNA expression in mouse hippocampus

value: ApoE3WT;P301S Tau+


title: Sham_7d, scRNA-seq

city: Hangzhou

first: Jingyu

last: Wang

state: Zhejiang

address: No.688 Yuhangtang road

institute: Zhejiang University

data_processing:
Gene-barcode count matrices were generated after the process of sequencing output on the CeleScope recommended pipeline.
Assembly: rn7
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell

organism: Rattus norvegicus

source_name: brain

extract_protocol:
A total of 18 rats (3 rats per group) were anaesthetized and transcardially perfused with ice-cold saline. Injured or normal brain were immediately extracted and maintained in an ice-cold Hibernate-A medium (Gibco). Single-cell suspensions were obtained by using a Neural Tissue Dissociation Kit (P) (Miltenyi Biotec) according to the manufacturer’s protocol. The suspensions were then strained using a cell strainer (70 μm) and centrifuged. Cell pellets were resuspended in 33% Percoll (GE Healthcare) layered on 70% Percoll and centrifuged for 15 min at 1800 r.p.m. Cells were obtained from the 30–70% interface and washed with Hank’s Balanced Salt Solution twice. All steps were conducted at 4 °C except digestion.
libraries were prepared with Chromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol.

value: brain

value: all cells

value: sham


title: LG852-NY-171

description:
Library name: Sample 10
mRNA expression in mouse hippocampus


title: HIE_7d, scRNA-seq

value: Hypoxic ischemic encephalopathy (HIE)


title: U3180MG, HOPXKO, PDX, scRNAseq

city: Uppsala

first: Ida

last: Larsson

address: Dag Hammarskjölds Väg 20

country: Sweden

institute: Uppsala University

description:
Library name: Sample24
10X Genomics

data_processing:
Demultiplexing, counting, and alignment to the human (GRCh38) reference genome were performed using Cell Ranger 3.0.2 using default parameters.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files.

source_name: Patient derived cells isolated from mouse PDX (Brain)

growth_protocol: Patient-derived cells cultured in Neural Stem Cell Media (cells were seeded on 1% laminin-coated flasks and maintained in serum-free neural stem cell medium with B-27 and N2 supplements, as well as EGF and FGF growth factors). As well as, patient-derived cells isolated from NMRI nude (NMRI-Foxn1 nu/nu) mice or Hsd:Athymic nude-Foxn1.

extract_protocol:
Upon the experimental endpoint, mouse brains were harvested into cold HBSS buffer containing 1% Pen/Strep, 0.6% glucose, and 25nM HEPES. Then, the brain was sliced using a 1mm coronal section matrix, cut into about 1-2 mm pieces using a surgical blade, and dissociated into single cells using the Tumor Dissociation kit, human (Miltenyi, #130-095-929), used in combination with the Mouse Cell Depletion Kit (Miltenyi, #130-104-694) according to the manufacturer’s protocols. Red blood cells were removed using the Red Blood Cell Lysis Solution (Miltenyi, #130-094-183
The generation of single-cell RNA sequencing libraries followed the manufacturer’s guidelines, utilizing the Chromium Single Cell 3’ Library and Gel Bead Kit v2, v3, and v3.1 (analysis of KO-cells) (10x Genomics, Pleasanton, CA). Cryo-preserved cells underwent washing and re-suspension in 0.1% BSA in PBS just before loading onto a Chromium Single Cell B Chip (10X Genomics) with the aim of capturing 10,000 cells.

value: U3180MG HOPX-KO PDX

value: Patient-derived GBM xenografted cells

value: Male, HOPX-KO


title: Reference group vs Control group 1 – Replicate 1 (p)

description: Biological replicate 2 of 6.


title: U3054MG, PDX, replicate 2, scRNAseq, 2

description:
Library name: Sample23
10X Genomics

value: Patient derived cells isolated from mouse PDX (Brain)

value: U3054MG PDX

value: Female


title: Experimental group 4 vs Control group 1 – Replicate 2

description: Biological replicate 3 of 6.

value: V29 mutant strain + pBLVΔ-miRNA

value: 2 days post transfection

value: pDriveΔmiRNA


title: Experimental group 4 vs Control group 1 – Replicate 1

description: Biological replicate 1 of 6.


title: LG852-NY-177

description:
Library name: Sample 11
mRNA expression in mouse hippocampus

value: brain hippocampus


title: LG852-NY-132

description:
Library name: Sample 8
mRNA expression in mouse hippocampus

value: Male


title: U3054MG, PDX, replicate 1, scRNAseq, 2

description:
Library name: Sample22
10X Genomics


title: Sham_2d, scRNA-seq


title: HIE_2d, scRNA-seq


title: LG851-NY-212

description:
Library name: Sample 13
mRNA expression in mouse hippocampus

value: Control


title: LG851-NY-233

description:
Library name: Sample 14
mRNA expression in mouse hippocampus


title: Control group 2 vs Control group 1 – Replicate 1 (p)

description: Biological replicate 2 of 6.

value: pDriveΔmiRNA + pBLVΔ-miRNA


title: LG852-NY-131

description:
Library name: Sample 7
mRNA expression in mouse hippocampus


title: LIB5455517_SAM24414655_S2_L002

city: South San Francisco

first: Marc

last: Hafner

address: Building 45-1, 1 DNA Way

department: Oncology Bioinformatics

institute: Genentech

description:
SAM24414655_LIB5455517
Rapid-HiSeq9

data_processing:
CMO data was processed using CellRanger and scRNA-Seq was processed using STARsolo with standard parameters.
Cumulus workflow with default settings was used for demultiplexing
Assembly: GRCh38 (GENCODE v32/Ensembl 98)

source_name: Colon

growth_protocol: The cells were seeded to 6-well plates. All samples were treated with compound combinations starting at different days and harvested together. Upon sample collection, cells were trypsinized from the plate and hashed by using the cholesterol modified oligo (CMO) following the MULTI-seq protocol

extract_protocol:
Cells from each sample were washed and re-suspended in 180µl of PBS+1%BSA and transferred to a round-bottom 96-well plate. Then 20µl of each anchor-barcode mix was added to the suspension for a final concentration of 2µM. After the incubation for 15 minutes at room temperature, 20µl of co-anchor was added to each sample (final concentration of 2µM) and incubate for another 15 minutes at RT. Cells were then washed by 500µl of cold PBS+1% BSA twice before pooling together.
The library construction was done following the manufacturer’s manual with a few modifications to accommodate the MULTI-seq protocol: (1) during the cDNA amplification 1µl of the following primer (10µM) was added to the master mix, 5’-CTTGGCACCCGAGAATTCC-3’; (2) the supernatant from the 0.6X SPRI beads cleanup for cDNA was kept and further cleaned up by using 2.0X SPRI beads; (3) the CMO libraries were made by performing 8 cycles of the indexing PCR using the supernatant. The transcriptome and CMO libraries were then sequenced by using either the Illumina NovaSeq or NextSeq machines

tag: library name

value: Colon

value: CRC line

tag: sample name


title: Experimental group 5 vs Control group 1 – Replicate 2

description: Biological replicate 3 of 6.

value: V90 mutant strain + pBLVΔ-miRNA


title: Reference group vs Control group 1 – Replicate 1

description: Biological replicate 1 of 6.

value: 344 reference strain + pBLVΔ-miRNA


title: U3054MG, scRNAseq, 2

description:
Library name: Sample21
10X Genomics

value: Patient-derived GBM cells


title: Sham_3h, scRNA-seq

value: brain

value: all cells

value: sham


title: LG851-NY-152

description:
Library name: Sample 6
mRNA expression in mouse hippocampus


title: Reference group vs Control group 1 – Replicate 2

description: Biological replicate 3 of 6.


title: Control group 2 vs Control group 1 – Replicate 1

description: Biological replicate 1 of 6.


title: HEK293 cells stably expressing ARDrop-ALK_3 treated with BICA for 2 hours_ 3

city: Shanghai

first: Qi

last: Zhang

state: Shanghai

address: Dongfang Load 1678

institute: Shanghai Jiaotong University

description: AR BICA_3

data_processing:
The library was sequenced using an Illumina Novaseq 6000 sequencing platform and 150 bp double-ended reads were generated.
Approximately 1.5G raw reads were obtained for each sample. raw reads in fastq format were processed by fastp software, and low quality reads were removed to obtain clean reads for subsequent data analysis.
Reference genome alignment was performed using HISAT2 software and gene expression level (FPKM) calculations were performed, and the reads count for each gene was obtained by HTSeq-count (v 3.2.0).
Assembly: The clean reads were mapped to the reference genome hg38 using HISAT2. GRCh38/hg38 is the assembly of the human genome released December of 2013, that uses alternate or ALT contigs to represent common complex variation, including HLA loci. Alternate contigs were also present in past assemblies but not to the extent we see with GRCh38. Much of the improvements in GRCh38 are the result of other genome sequencing and analysis projects, including the 1000 Genomes Project.
Supplementary files format and content: tab-delimited text file include FPKM value for each sample

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer's instructions. RNA purity and quantification were identified using a NanoDrop 2000 spectrophotometer (Thermo Scientific, USA), RNA integrity was assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Transcriptome libraries were constructed using the VAHTS Universal V6 RNA-seq Library Prep kit according to the manufacturer's instructions. Transcriptome Sequencing and analysis were performed by Shanghai Ouyi Biotechnology (Shanghai, China)

value: human embryonic kidney cells


title: HEK293 cells stably expressing ARDrop-ALK_3 treated with BICA for 2 hours_ 2

description: AR BICA_2


title: LG851-NY-150

description:
Library name: Sample 4
mRNA expression in mouse hippocampus

value: ApoE3CC;P301S Tau+


title: HEK293 cells stably expressing ARDrop-ALK_3 treated with BICA for 2 hours_ 1

description: AR BICA_1


title: O1-L3

city: Murdoch

first: Viet

last: Dang

address: 90 South Street

country: Australia

institute: Murdoch University

description: Library name: O1-L3

library_source: genomic

data_processing:
Amplicon sequence variant (ASV) tables were constructed based on the DADA2 pipeline with default parameters. Read adapters were removed from raw read sequences using cutadapt, and read quality was inspected using FastQC. Chimeric sequences were removed from merged reads, and taxonomy was then assigned using the DADA2 "assignTaxonomy " function.
Assembly: metagenome
Supplementary files format and content: table files include ASV count and taxa
Supplementary files format and content: fasta files contain ASV sequences

organism: soil metagenome

source_name: 0-10cm soil

extract_protocol:
DNeasy PowerSoil Kit (Qiagen Laboratories, Inc.)
Sequencing was carried out using Amplicon sequencing on Illumina MiSeq 2 × 250-bp PE platform

value: 0-10cm soil


title: O1-L2

description: Library name: O1-L2


title: O1-L5G5

description: Library name: O1-L5G5


title: O1-L6

description: Library name: O1-L6


title: LG851-NY-143

description:
Library name: Sample 3
mRNA expression in mouse hippocampus


title: O1-L7

description: Library name: O1-L7


title: HEK293 cells stably expressing ARDrop-ALK_3 treated with DMSO for 2 hours_ 3

description: AR DMSO_3


title: HIE_3h, scRNA-seq

value: Hypoxic ischemic encephalopathy (HIE)


title: LG851-NY-142

description:
Library name: Sample 2
mRNA expression in mouse hippocampus


title: O1-L8Z8

description: Library name: O1-L8Z8


title: HEK293 cells stably expressing ARDrop-ALK_3 treated with DMSO for 2 hours_ 2

description: AR DMSO_2


title: O1-L9

description: Library name: O1-L9


title: O1-G2

description: Library name: O1-G2


title: HEK293 cells stably expressing ARDrop-ALK_3 treated with DMSO for 2 hours_ 1

description: AR DMSO_1


title: O1-Z11

description: Library name: O1-Z11


title: HEK293 cells stably expressing ARDrop-ALK_ 3


title: O1-Z1G1

description: Library name: O1-Z1G1


title: LG851-NY-151

description:
Library name: Sample 5
mRNA expression in mouse hippocampus


title: O1-L4

description: Library name: O1-L4


title: LG851-NY-135

description:
Library name: Sample 1
mRNA expression in mouse hippocampus


title: O1-Z2

description: Library name: O1-Z2


title: HEK293 cells stably expressing ARDrop-ALK_ 2


title: O1-Z10

description: Library name: O1-Z10


title: Multiome, Six2CreTGC/+;Nfkb1Null/c, GEX, rep3

city: Los Angeles

first: Shun-Yang

last: Cheng

address: 1425 San Pablo St

department: USC Stem cell - Eli and Edythe Broad Center for Regenerative Medicine

institute: University of Southern California

description: Library name: C_293S

data_processing:
Using Cell Ranger ARC software (version 2.0.1)
The samples were aggregated using cellranger-arc aggr
Assembly: mm10
Supplementary files format and content: Cell Ranger aggr output files: filtered_feature_bc_matrix.h5, atac_fragments.tsv.gz, aggr.csv

source_name: Kidney

extract_protocol:
Nuclei were isolated from flash-frozen kidney tissue and processed for single-cell multi-omics Assay for Transposase-Accessible Chromatin (ATAC)+gene expression (GEX) sequencing according to the 10× Genomics protocol (CG000338) as previously described. All reagents were prepared according to the online protocol. In brief, the tissue of a half kidney was thawed and minced on ice, transferred into 2ml of Nuclei EZ (NEZ) lysis buffer (Sigma N3408) with supplemented protease inhibitor (Roche 05892791001) , homogenized using manual bouncing  (Sigma P0485, 15 loose, 5 tight) and incubated for 3-5 minutes on ice. Loose and tight dounce homogenization were followed by lysate filtering through were 200uM filter (pluriSelect 43-50200) and 40uM filter (pluriSelect 43-50040) filters, respectively. Two mls of NEZ buffer was added to the final filtrate prior to centrifugation at 500G for 5 mins at 4°C in a swinging bucket centrifuge. Supernatants were removed and 4 ml of NEZ buffer without protease inhibitor was added before an additional spin to remove remaining cellular debris. The final pellet of nuclei was gently resuspended in nuclear resuspension buffer provided in the 10X Genomics multi-omics kit for optimal transposition and filtered through a 5uM filter (pluriSelect 43-50005) to remove clumps and reduce doublets.   All buffers for nuclear isolation were supplemented with 1U/ul Protector Rnase inhibitor (Sigma 3335402001) in 1mM DTT and all plastics used were polypropylene RNase-DNase free. Nuclei yields were targeted to be at the limit of the 10X Genomics Next GEM capability (10,000 nuclei per condition).
Library protocol:  the 10× Genomics protocol (CG000338) ATAC and GEX libraries were generated with 7 preAmp cycles, 7 ATAC cycles, 8 cDNA cycles, and 12-14 SI cycles.

value: Kidney


title: Multiome, Six2CreTGC/+;Nfkb1Null/c, GEX, rep2

description: Library name: C_291S


title: O1-Z3

description: Library name: O1-Z3


title: Multiome, Six2CreTGC/+;Nfkb1Null/c, GEX, rep1

description: Library name: C_286S


title: O1-Z4

description: Library name: O1-Z4


title: HEK293 cells stably expressing ARDrop-ALK_ 1


title: Multiome, Nfkb1c/c, GEX, rep2

description: Library name: C_278W


title: patient6

description:
Library name: patient6
10x Genomics

value: mitral valve


title: O1-Z6

description: Library name: O1-Z6


title: LIB5455516_SAM24414655_S1_L001

description:
SAM24414655_LIB5455516
Rapid-HiSeq9


title: blank HEK293 cells_3


title: O1-Z7

description: Library name: O1-Z7


title: O1-G3

description: Library name: O1-G3


title: Multiome, Nfkb1c/c, GEX, rep1

description: Library name: C_194W


title: O2-G1

description: Library name: O2-G1


title: Multiome, Nfkb1c/c, GEX

description: Library name: C_193W


title: O1-Z9

description: Library name: O1-Z9


title: blank HEK293 cells_2


title: O2-G10

description: Library name: O2-G10


title: blank HEK293 cells_1


title: O2-G11

description: Library name: O2-G11


title: Multiome, Six2CreTGC/+;Nfkb1Null/c, GEX

description: Library name: C_192S


title: O2-G2

description: Library name: O2-G2


title: Multiome, Six2CreTGC/+;Nfkb1Null/c, ATAC, rep3

description: Library name: A_293S


title: U3180MG, RFX4KO, PDX, scRNAseq

description: 10X Genomics

value: Patient derived cells isolated from mouse PDX (Brain)

value: U3180MG RFX4-KO PDX

value: Patient-derived GBM xenografted cells

value: Male


title: O1-Z5

description: Library name: O1-Z5


title: U3180MG, RFX4KO, scRNAseq

description: 10X Genomics

source_name: U3180MG RFX4-KO

value: U3180MG RFX4-KO


title: Multiome, Six2CreTGC/+;Nfkb1Null/c, ATAC, rep2

description: Library name: A_291S


title: U3013MG, ANXA1KO, PDX, scRNAseq

description: 10X Genomics

value: U3013MG ANXA1-KO PDX

value: Female


title: O2-G5

description: Library name: O2-G5


title: Multiome, Six2CreTGC/+;Nfkb1Null/c, ATAC, rep1

description: Library name: A_286S


title: O2-G3

description: Library name: O2-G3


title: O1-G11

description: Library name: O1-G11


title: O2-G6

description: Library name: O2-G6


title: U3013MG, ANXA1KO, scRNAseq

description: 10X Genomics

source_name: U3013MG ANXA1-KO

value: U3013MG ANXA1-KO

value: Patient-derived GBM cells


title: O1-G10

description: Library name: O1-G10


title: Multiome, Nfkb1c/c, ATAC, rep1

description: Library name: A_194W


title: O1-L10

description: Library name: O1-L10


title: Multiome, Nfkb1c/c, ATAC, rep2

description: Library name: A_278W


title: Petunia inflata, larger bud, 18 weeks r2

city: Davis

first: Blake

last: Meyers

address: 451 Health Sciences Drive

department: Department of Plant Sciences

institute: UC  Davis Genome Center

description:
Library name: PinfW-05_i2-29
sRNA library from Petunia inflata. These libraries were generated from 4-5 large (3-4 mm) buds at plant age 18 weeks (Plant IDs 6-10)

data_processing:
Raw small RNA sequence data was trimmed on quality at a cut-off value of > 0.05, a maximum of 2 ambiguities, adapters, and length between 15-34 nt, using the CLC Genomic Workbench (version 7.0; http://www.clcbio.com). Small RNA contaminants were filtered-out on the basis of a BLAST search 21 against a database including tRNAs from Arabidopsis thaliana (Ath) (http://lowelab.ucsc.edu/GtRNAdb/ Athal) and Rfam 11.0 (http://www.sanger.ac.uk; subset RF00005), small subunit rRNAs from Rfam (subsets RF00001;5S rRNA and RF00002;5_8S_rRNA), mtDNAs from the tomato mitochondrial genome (http://www.mitochondrialgenome.org) and GenBank: Ath, Solanum lycopersicum (Sly), Nicotiana tabacum (Nta), and Vitis vinifera (Vvi), and cpDNAs from GenBank: Ath, Sly, Solanum tuberosum (Stu), Nta, Glycine max (Gma), Medicago truncatula (Mtr) and Vvi, using an identity of ≥ 80 %.
Assembly: P. axillaris N and P. inflata S6.
Supplementary files format and content: tab-delimited file in which each line contains a unique RNA sequence and the number of times that sequence appears in the library

organism: Petunia integrifolia subsp. inflata

source_name: buds

extract_protocol:
Total RNA was isolated by a standard method using TRIzol® Reagent (Life Technologies), including a second precipitation step to increase RNA purity, and using 20 minutes centrifugation, 14.000 rpm, to optimize small RNA recovery. Samples were stored in the second precipitation, in 0.3 M Sodium Acetate (NaAc)/70 % Ethanol (EtOH), at -80 °C, upon library preparation. RNA was suspended in 10-30 μl DEPC-MQ to a final concentration of ~ 1 μg/μl, and checked on agarose for a 25S to 18S ribosomal peak ratio of > 4:5 to be used for library preparation. Small RNA libraries were prepared from 1.2 μg total RNA, using the Illumina compatible NextFlex™ Small RNA Sequencing Kit (version 1; Bioo Scientific; Sanbio BV, Uden, The Netherlands; Cat. no. 5132) and accompanying Small RNA Barcodes Primers (Cat. no. 5133). This protocol included an 18 h long 3’-adapter ligation of pre-adenylated oligonucleotides, with a modified ligase, to optimize binding to plant miRNAs and other small RNAs that contain 2’-O-methylated 3’-ends (Munafó and Robb, 2010; McCormick et al., 2011). After the 5'-adapter ligation, the recommended purification step was included, using the RNA Clean and Concentrator Kit (Zymo Research; BaseClear, Leiden, The Netherlands; Cat. no. R1015). We amplified the cDNAs by 14-16 PCR cycli. The ~ 150 nt long small RNA libraries were isolated from 3 % NuSieveTM (Lonza, Basel, Switzerland)/1 % agarose gels, and extracted by the QIAquick Gel Extraction Kit (Qiagen Benelux BV, Venlo, The Netherlands; Cat. no. 28706). Libraries were eluted in 40μl pre-warmed buffer of the Kit, and precipitated in NaAc/EtOH, at -20°C, after addition of 1 μl co-precipitant of the NextFlex Kit.
After re-suspension of the small RNA libraries in 10 μl MQ, they were sent to BaseClear (Leiden, The Netherlands) for Illumina HiSeq 2500 sequencing. Quality Control included a BioAnalyzer measurement (Agilent Technologies) and qPCR, on which basis the samples were pooled in equal amounts to 18 samples/lane in order to provide a minimum of ~ 5 Million Reads/library. Sequence data was de-multiplexed and reads delivered as '.fastq' files together with the run-statistics.

value: buds

tag: time point

value: 18 weeks


title: U3180MG, PDX,replicate 2, scRNAseq

description: 10X Genomics

value: U3180MG PDX


title: Petunia inflata, larger bud, 12 weeks

description:
Library name: PinfW-05_i3-27
sRNA library from Petunia inflata. These libraries were generated from 4-5 large (3-4 mm) buds at plant age 12 weeks (Plant IDs 6-10)

value: 12 weeks


title: U3180MG, PDX, replicate 1, scRNAseq

description: 10X Genomics


title: Multiome, Nfkb1c/c, ATAC

description: Library name: A_193W


title: O1-L11

description: Library name: O1-L11

value: 0-10cm soil


title: Petunia inflata, larger bud, 18 weeks

description:
Library name: PinfW-05_i1-33
sRNA library from Petunia inflata. These libraries were generated from 4-5 large (3-4 mm) buds at plant age 18 weeks (Plant IDs 6-10)


title: U3180MG, scRNAseq

description: 10X Genomics


title: Multiome, Six2CreTGC/+;Nfkb1Null/c, ATAC

description: Library name: A_192S


title: O2-G7

description: Library name: O2-G7


title: Petunia inflata, young bud, 18 weeks

description:
Library name: PinfW-05_i1-28
sRNA library from Petunia inflata. These libraries were generated from 4-5 large (3-4 mm) buds at plant age 18 weeks (Plant IDs 6-10)


title: U3179MG, PDX, scRNAseq

description: 10X Genomics

value: U3179MG PDX