title: Patient 3_Serum

value: Serum

value: Invasive carcinoma, cribriform


title: FX435

status: Public on Aug 05 2026

type: SRA

city: La Jolla

first: Mark

last: Antkowiak

state: CA

address: 3855 Health Sciences Dr

department: Surgery

country: USA

institute: University of California, San Diego

description: Library name: Sample 3

library_source: transcriptomic

data_processing:
Genome alignment was performed by STAR aligner with the human genome (hg38). The gene expression level were obtained by processing the RNA-sequencing reads through the BCBIO-nextGen pipeline, including alignment with STAR aligner and isoforms expression using Salmon and gene level expression using the featureCount script. The expression counts were then processed using DESeq including variance stabilization with rlog transformation.
Assembly: hg38
Supplementary files format and content: abundance.h5

molecule: total RNA

organism: Homo sapiens

source_name: GIST tumor

extract_protocol:
Total RNA was isolated from homogenized, snap-frozen human GISTs and from the corresponding cell cultures using the Qiagen RNeasy Kit. Libraries were generated from 1 µg of total RNA.
RNA libraries were prepared using Illumina's TruSeq Stranded mRNA Sample Prep Kit.

tag: tissue

value: GIST tumor

tag: genotype

value: SDHC mutant

tag: batch


title: C

city: Kunming

first: Ruixia

last: Tang

address: Jiaoling Road 935

country: China

institute: Chinese  Academy  of Medical Sciences & Peking Union Medical College

description: Library name: Sample2

data_processing:
Raw sequencing data (fastq format) were processed using Seqtk to remove adapter sequences, trim low-quality bases (Q < 20) from the 3' end, filter reads shorter than 25 nt, and remove rRNA-derived reads. Clean reads were aligned to the human reference genome (hg38) using BWA-MEM with default parameters. Circular RNAs were predicted and annotated using CIRI (v2.0). circRNA expression levels were quantified using SRPBM (Spliced Reads Per Billion Mapping) based on back-splicing junction reads. Differential expression analysis between groups was performed using edgeR (v3.32) with the following criteria: |Fold-change| ≥ 2 and p-value ≤ 0.05. Functional enrichment analyses (GO and KEGG) of parental genes of differentially expressed circRNAs were carried out using hypergeometric test with q-value ≤ 0.05 as significance threshold.
Assembly: GRCh38.p12 (hg38)
Supplementary files format and content: Format: xls; Content: circRNA_expression.xls

source_name: infected early mild

extract_protocol:
Total RNA was extracted from whole-blood samples using TRIzol reagent (Invitrogen, Catalog No. 10296028CN) per the manufacturer’s protocol. RNA concentration/purity was assessed via NanoDrop 1000 (A260/A280 ≥ 1.8, A260/A230 ≥ 2.0), and integrity via Agilent 2100 Bioanalyzer (RNA Integrity Number (RIN) ≥ 8.0). Only qualified RNA was used for subsequent sequencing.
Total RNA was subjected to ribosomal RNA (rRNA) removal using Ribo-Zero rRNA Removal Kit (Epicentre), followed by fragmentation at 94°C for 8 minutes. First-strand cDNA was synthesized using SuperScript II Reverse Transcriptase (Invitrogen) with random primers and Actinomycin D. Second-strand cDNA was synthesized using Second Strand Marking Master Mix. The double-stranded cDNA products were purified using AMPure XP beads (Beckman). After end repair and adenylation at the 3' ends, Illumina RNA adapters were ligated. Libraries were amplified by PCR (98°C for 30 sec; 10 cycles of 98°C for 10 sec, 60°C for 30 sec, 72°C for 30 sec; final extension 72°C for 5 min). The final libraries were validated on an Agilent 2100 Bioanalyzer and quantified by Qubit 2.0 Fluorometer.

value: PBMC

tag: infected with


title: C57BL6_24h_rep3

type: RNA

city: Milano

first: Stefano

last: Raffaele

state: -- Please Select (only U.S. / Can / Aus)

address: Via Balzaretti 9

department: Department of Pharmaceutical Sciences

country: Italy

institute: Università degli Studi di Milano

description:
Gene expression data from brain of C57BL/6 adult mouse 24 h post-stroke
Sample name: KL42_4

hyb_protocol: Arrays were hybridized and washed according to the manufacturer's specifications (Affymetrix Inc., Santa Clara, CA, USA).

scan_protocol: Arrays were scanned in a GeneChip® Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA).

data_processing:
Image analysis was performed using GeneChip® Operating Software (GCOS, Affymetrix). Expression data was normalized, background corrected and summarized using the GC-RMA algorithm implemented in the Partek Genomic Suite software.
Expression values are reported as log2 RMA-normalized signal intensities.

label: biotin

organism: Mus musculus

source_name: 24 h post-pMCAO C57BL/6

label_protocol: GeneChip® WT Terminal Labeling Kit (Affymetrix Inc, Santa Clara, CA, USA).

extract_protocol: Total RNA was extracted from frozen braines using Trizol reagent  (Invitrogen, Carlsbad, CA, USA) according to the manufacturers' instructions.

tag: Sex

value: Male

tag: age

value: 8 weeks

value: Brain

tag: surgery

value: pMCAO


title: Patient 2_Serum

city: Bar Harbor

first: James

middle: Leonard

last: Miller

state: ME

address: 600 Main Street

institute: The Jackson Laboratory

description: Total RNA was derived from biofluid supernatant and analyzed by the Nanostring nCounter platform. 798 c-miRNAs were assessed in each sample.

hyb_protocol: Manufacturer's instructions via Human v3b miRNA CodeSet Kit (Nanostring)

data_processing: Normalization of code-set data was performed using linear standard curves from Positive Controls (Pos A-F) and Ligation Positive Control (A and B) via nSolver Analysis Software v4.0 (Nanostring). miRNAs with maximum normalized counts below 50 were excluded to minimize background noise Ahmed et al 2022 (Cancer (Baseline)), following manufacturer’s recommendations.

label: miRTag

source_name: Serum

extract_protocol:
Participants who consented to provide unstimulated whole saliva samples for the SUNY Upstate Medical University Biorepository Core were instructed to spit into a sterile container prior to performing a routine mouthwash. Collected saliva samples were immediately chilled on ice, transferred to cryogenic vials, and subsequently stored at -80ºC. For serum collection, whole blood was drawn into sterile Vacutainer Serum Tubes (BD, Franklin Lakes, NJ), allowed to clot for 30 min at room temperature (RT), and then centrifuged at 1250 x g for 10 min at 4ºC. The serum fraction was separated, aliquoted into individual freezer tubes, flash-frozen in liquid nitrogen, and stored at -80ºC. For plasma collection, whole blood was collected in sterile Vacutainer EDTA tubes (BD), centrifuged under the same conditions (1250 x g for 10 min at 4ºC), and the plasma layer was similarly aliquoted, frozen in liquid nitrogen, and stored at -80ºC.
Total RNA for Nanostring nCounter (Nanostring, Seattle WA) analysis was extracted using the Midi Plasma/Serum RNA Purification Kit (Norgen Biotek, Thorold, Ontario, Canada). Serum, plasma, and saliva samples were thawed on ice. To remove cell debris, saliva was centrifuged at 10,000 x g for 10 min, while serum and plasma samples were spun at 400 x g for 3 min. One mL of supernatant was collected from each sample and processed according to the manufacturer’s instructions, with RNA eluted at 100 µL volumes across all treatment groups. Following extraction, RNA samples were concentrated and purified using linear acrylamide. Each 100 mL RNA sample received 300 mL of ice cold 100% EtOH, 10 mL 3M sodium acetate (pH 5.5) (Invitrogen), 3 mL linear acrylamide (5mg/mL) (Invitrogen), and were incubated at -80ºC for 16 h. Samples were centrifuged at 13,000 x g for 30 min at 4ºC to pellet the RNA, followed by two washes with 75% ethanol. After air drying, RNA pellets were responded in 10 mL of nuclease-free water.

tag: patient id

tag: patient pathology

value: Uterine-related pathology, No history of cancer

tag: receptor expression

tag: tumor grade


title: G2 - Lymph node, P toxin-induced, M#1

city: Suwon

first: Truc

middle: Do Thanh

last: Nguyen

state: All

address: 2066 Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University School of Medicine

description:
Library name: G2-Lymph Noder-Mouse 1
10x Genomics

library_source: transcriptomic single cell

data_processing:
Libraries were processed according to the manufacturer’s instructions (10x Genomics) and sequenced on a Next-Seq 2000 platforms with 100-bp paired-end sequencing. Raw sequencing data were processed using CellRanger (version 7.0.0) (10x Genomics) with default setting.
Assembly: Mouse ref. package mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Lymph node

extract_protocol:
Mouse tissues were mechanically dissociated and enzymatically digested using Tumor Dissociation Kit, mouse (Miltenyi Biotech, Germany) according to the manufacturer’s instructions. Dead cells were removed using Ficoll-Paque PLUS (GE Healthcare).
We performed 10x Genomics scRNA-seq experiments according to the manufacturer’s instruction. The library preparation was performed using a Chromium Next GEM Single Cell 5’Kit v2 (10x Genomics, CA, USA), following the manufacturer’s protocols.

value: Lymph node

tag: cell type

value: lymphocytes

tag: treatment

value: Pertussis Toxin


title: FX424

description: Library name: Sample 2

value: SDHB mutant


title: G5 - Tumor single cell, M#3

description:
Library name: G5-Tumor-Mouse 3
10x Genomics

source_name: Tumor

value: Tumor

value: cancer cells

value: non


title: Patient 1_Serum

value: Serum

value: Invasive carcinoma of no special type (NST)


title: G2 - Tumor single cell, P toxin-induced, M#3

description:
Library name: G2-Tumor-Mouse 3
10x Genomics


title: C57BL6_24h_rep2

description:
Gene expression data from brain of C57BL/6 adult mouse 24 h post-stroke
Sample name: KL42_3


title: WT, P0.5 Heart, H3K9me2 CUT&RUN, Rep1

city: Baltimore

first: Yixian

last: Zheng

state: MD

address: 3520 San Martin Dr

institute: Carnegie Institution of Washington

description:
Library name: WT_P0_5_H3K9me2_Rep1
Corresponding IgG is WT Rep3
WT_H3K9me2_log2fc.bw
P0_5_6_state_Hilands.bed

library_source: genomic

data_processing:
Samples were processed using the nf-core/cutandrun pipeline v3.2.2 with Nextflow v23.10.0. Reads were aligned to the mm10 mouse reference genome, and mitochondrial reads were removed by including the --remove_mitochondrial_reads flag during pipeline execution. The pipeline performed adapter trimming, quality control, alignment, duplicate marking, and filtering. For Hidden Markov Modeling (HMM), outputted replicate bam files were merged using samtools merge and converted to bigwig files in CPM normalized with 5kb bins. Histone and lamin CUT&RUN samples were then normalized to their corresponding IgG control by running bigwigCompare with the --operation log2 and --pseudocount 1 flags applied. Genome-wide signal tracks at 5 kb resolution for H3K9me2, H3K9me3, H3K27me3, H3K27ac, H3K4me1, H3K4me3, ATAC-seq, and lamin-associated domains (LADs) were compiled and processed, as discussed previously. ATAC-seq signals were log2-transformed with a small pseudocount, while all other datasets were used as provided. Signal values across all tracks were capped to the range of -3 to 3 to limit the influence of outliers. Analyses were restricted to autosomal chromosomes, and the first and last 3 Mb of each chromosome were excluded to reduce edge effects. Regions overlapping a combined blacklist (mm10 ENCODE blacklist v2 and low-signal regions) were removed. All datasets were then merged by genomic coordinates, and missing values were set to zero. Principal component analysis (PCA) was performed on z-score-scaled signals from all tracks. The first three principal components were retained, and their scores were appended to the genomic coordinates for downstream analyses. We then applied HMM to infer chromatin states and define HiLands domains as previously described, with emission probabilities modeled using a multivariate normal inverse Gaussian distribution. A six-state model was used throughout the analysis to capture chromatin variation across the seven markers. Model parameters were estimated using the expectation-maximization (Baum-Welch) algorithm, with 20 random initializations to reduce convergence to local optima and selection of the highest-likelihood solution. Chromatin states were assigned using the Viterbi algorithm, and adjacent genomic windows sharing the same state were merged to generate continuous HiLands regions. For lamin CUT&RUNs, additional z-score normalization was performed on the generated bigwig files to enable comparison between samples. We then identified LAD regions with the depmixS4 v1.4-0 R package was used to call a two-state HMM.
Assembly: GRCm38
Supplementary files format and content: CUT&RUN tracks for histone markers and lamins are included as bigwigs. Lamin HMM calling and HiLands calling are included as .bed files.
Library strategy: CUT&Run

molecule: genomic DNA

source_name: Heart

extract_protocol:
Hearts from P0.5 hearts were dissociated using the Pierce Primary Cardiomyocyte Isolation Kit from ThermoFisher Scientific. Cardiomyocytes were then purified with neonate cardiomyocyte isolation beads from Miltenyi Biotec.
CUT&RUN was performed with the CUTANA ChIC/CUT&RUN Kit as per manufacturer instructions using 100,000 P0.5 cardiomyocytes. Sequencing libraries were prepared with the Takara ThruPLEX DNA-seq kit according to the manufacturer’s protocol utilizing 10 cycles of PCR amplification. Libraries were quantified with the Qubit dsDNA Quantification Assay Kit and library quality was verified on the 2100 Bioanalyzer System with High Sensitivity DNA Kit. Sequencing was conducted on the Illumina NextSeq1000 using 50x50 bp length paired-end reads.

value: Heart

value: Isolated Cardiomyocyte

value: Wildtype

tag: timepoint

tag: cut&run antibody


title: FX437

description: Library name: Sample 1

value: GIST tumor

value: SDHA mutant


title: G2 - Tumor single cell, P toxin-induced, M#2

description:
Library name: G2-Tumor-Mouse 2
10x Genomics


title: Patient 6_Plasma

value: Invasive carcinoma, cribriform


title: C57BL6_24h_rep1

description:
Gene expression data from brain of C57BL/6 adult mouse 24 h post-stroke
Sample name: KL42_1

value: Male

value: 8 weeks

value: Brain

value: pMCAO


title: Nkx2-5Cre;Lmnb1Flox/+, P0.5 Heart, ATAC, Rep2

description:
Library name: P0_5_ATAC_LB1Fplus_rep2
Nkx2_5Cre_LB1Fplus_merged_ATAC_5kb.bedgraph
Nkx2_5Cre_LB1Fplus_consensus_peaks.bed

data_processing:
Samples were processed using the nf-core/atacseq pipeline version 2.1.2 with Nextflow version 23.10.0. The pipeline performed adapter trimming, quality control, alignment, duplicate marking, filtering, broad peak calling, and generation of counts per million (CPM) normalized signal tracks. Reads were aligned to the Mus musculus reference genome (mm10) with the iGenomes GTF gene annotation file (iGenomes, UCSC) also provided during execution for peak annotation. A read length of 100 bp was specified, which was used to estimate fragment size and inform background modeling during broad peak calling with MACS2. Lastly, regions in the mm10 ENCODE blacklist (v2) were also excluded during execution with the --blacklist flag.
Assembly: GRCm38
Supplementary files format and content: Bedgraph file containing merged ATAC-seq profile and bed containing conensus peaks from broad peak calling.

extract_protocol:
Hearts from P0.5 hearts were dissociated using the Pierce Primary Cardiomyocyte Isolation Kit from ThermoFisher Scientific. Cardiomyocytes were then purified with neonate cardiomyocyte isolation beads from Miltenyi Biotec.
P0.5 cardiomyocytes were isolated and purified as previously described in the cardiomyocyte isolation and culture section of these methods and an aliquot of 50,000 cells per sample was taken for further processing. ATAC-seq was performed using the Zymo-Seq ATAC Library Prep Kit (Zymo, D5458-B) as per the manufacturer’s protocol. Briefly, live cells were lysed and nuclei isolated with the supplied reagents. Nuclei were then incubated with the provided transposition mix at 37°C for 30 minutes and DNA purified with the supplied Zymo-Spin IC Columns. Libraries were made with the provided library reagents and amplified with over 10 PCR cycles. Libraries were quantified with the Qubit dsDNA Quantification Assay Kit and library quality was verified on the 2100 Bioanalyzer System with High Sensitivity DNA Kit. Sequencing was conducted on the Illumina NextSeq1000 using 50x50 bp length paired-end reads.

value: Nkx2-5Cre; Lmnb1 Flox/+


title: miRNA_PEDV_exo_3

city: nanjing

first: qiu

last: zhong

address: No. 1 Weigang, Xuanwu District

department: College of Veterinary Medicine

institute: Nanjing Agricultural University

description:
Library name: sample 18
PEDV group, miRNA-SEQ, replicate biosample 3

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to Sscrofa11.1 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Sscrofa11.1
Supplementary files format and content: tab-delimited text file includes gene counts for each sample
Supplementary files format and content: tab-delimited text file includes fpkm value for each sample

organism: Sus scrofa

source_name: IPEC-DQ

extract_protocol:
RNA was extracted from cell lines using TRIzol reagent. Briefly, cells were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: IPEC-DQ


title: VCaP  2104R

city: Ann Arbor

first: Arul

middle: M

last: Chinnaiyan

state: Michigan

address: 1500 E. Medical Center Dr

institute: University of Michigan

description:
Library name: SI_21186
RiboErase

data_processing:
Xenograft FASTQs were processed using xengsort. Then, the human FASTQs were trimmed using BBDuk. Transcripts were quantified by kallisto with human reference genome (GRCh38/hg38) and then summarized to obtain gene level counts and TPM.
Assembly: hg38
Supplementary files format and content: counts.tsv: Gene-level TPM counts obtained from kallisto.
Supplementary files format and content: tpm.tsv: Gene-level TPM values obtained from kallisto.

source_name: VCaP

growth_protocol: 1. LTL331R-CL cells were maintained in modified RPMI-1640, supplemented with 1X ITS-G, 10 nM hydrocortisone, 10 nM beta-estradiol, extra 2mM Glutamax, and 5% FBS or 0.1% FBS overnight before treatment. 2. AR+ and NEPC tumors were maintained in SCID male mice. 3. NEPC tumors were maintained in SCID male mice.

extract_protocol:
Total RNA was extracted from cultured cells or tumor tissues using the RNeasy mini kit, following the manufacturer’s instructions. 1 μg of total RNA was used to construct the sequencing libraries.
For tumor samples, ribosomal RNA was depleted using the RiboErase selection kit (Kapa Biosystems, KK8561). For cell lines and other samples, polyadenylated transcripts were enriched using Sera-Mag Oligo(dT)-Coated Magnetic Particles (GE Healthcare Life Sciences, 38152103010150). RNA libraries were constructed using the KAPA RNA HyperPrep Kit (Roche Sequencing, KK8541) from 800 ng of total RNA. Following rRNA depletion and RNA fragmentation (200-300 bp), double-stranded cDNA was synthesized, ligated with NEB adapters, and PCR-amplified using KAPA HiFi HotStart ReadyMix and NEB dual-index barcodes.

treatment_protocol: 1. NEPC cells were treated with DMSO, ESK981, Apilimod, or PIK5-33d for 6 hours. 2. No treatment for basaline comparison. 3. NEPC tumor-bearing mice were treated with Vehicle, ESK981, or Apilimod for 5 days, once per day.

value: VCaP

value: AR+ tumors

value: Vehicle


title: TNFko_Naive_rep4

description:
Gene expression data from brain of naive TNF knockout adult mouse
Sample name: KL82_1

source_name: Naive TNF_KO

value: TNFko

value: Naive


title: Patient 5_Plasma

value: Benign urothelial issue. No history of cancer


title: miRNA_PEDV_exo_1

description:
Library name: sample 16
PEDV group, miRNA-SEQ, replicate biosample 1


title: G2 - Tumor single cell, P toxin-induced, M#1

description:
Library name: G2-Tumor-Mouse 1
10x Genomics

value: Tumor

value: cancer cells

value: Pertussis Toxin


title: VCaP  2104L

description:
Library name: SI_21185
RiboErase


title: G1 - Lymph node, M#3

description:
Library name: G1-Lymph Noder-Mouse 3
10x Genomics

value: Lymph node

value: lymphocytes

value: non


title: TNFko_Naive_rep3

description:
Gene expression data from brain of naive TNF knockout adult mouse
Sample name: KL76_34

value: Male

value: 8 weeks


title: VCaP  2101R

description:
Library name: SI_21184
RiboErase


title: Patient 4_Plasma

value: Uterine-related pathology, No history of cancer


title: midgut, virgin 2

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

country: United Kingdom

institute: MRC London Institute of Medical Sciences

data_processing:
A minimum of 20 million Paired End 100bp reads per sample were generated on a HiSeq2500 with single 6bp indexing
Data was processed using RTA version 1.18.64, with default filter and quality settings
The reads were demultiplexed with CASAVA 1.8.4 (allowing no mismatch)
Sequencing reads were mapped to dm6 genome using STAR aligner. Gene based counting was performed using the STAR aligner
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.42.0)
Assembly: Ensembl Drosophila genome reference sequence assembly (dm6)
Supplementary files format and content: comma-delimited text file include raw counts for each Sample generated by STAR aligner.

organism: Drosophila melanogaster

source_name: midgut

growth_protocol: Flies were reared under standard conditions

extract_protocol:
Total RNA was extracted using TRIzol (Invitrogen) and quality was assessed using the Agilent 2100 Bioanalyser RNA 6000 Nano assay.
NGS libraries made using the Illumina TruSeq Stranded mRNA kit according to manufacturer’s instructions.

treatment_protocol: Flies were anestesised on ice and dissected in cold PBS.

value: midgut

value: wild-type (w1118)

value: virgin


title: Neurospora crassa, KTC, replicate1

city: Beijing

first: Shuting

last: Ye

address: No.1 Beichen West Road, Chaoyang District,

institute: Institute of Microbiology, Chinese Academy of Sciences

description: Library name: Sample10

data_processing:
Basecalling was performed using a software developed for DNBSEQ-T7.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence using SOAPnuke v1.5.2, then mapped to Neurospora crassa whole genome (GCA_000182925.2) using HISAT v2.0.4 with parameters -p 8 --phred64 --sensitive -I 1 -X 10000
After analyzing the efficiency of aligned clean reads to reference genome by Bowtie2 v2.2.5 with parameters -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200, gene expression were calculated as Fragments Per Kilobase of exon per Megabase of library size (FPKM) using RSME v1.2.12 with default parameters.
Differential expressed genes were caracterized using a protocol from Audic S. et al.,  Genome Research, 1997.
Assembly: GCA_000182925.2
Supplementary files format and content: excel file include FPKM values for all Samples and data for differential expressed genes between each two Samples, as well as the annotation of each genes.

organism: Neurospora crassa

source_name: mycelia

growth_protocol: Briefly, 14 small pieces of mycelial mats (1-2 mm2) were grown in liquid Vogel’s medium for 12 h and then treated with or without sterol biosynthesis inhibitors for 12 h.

extract_protocol:
Harvested samples were immediately frozen, and then ground into fine powder in liquid nitrogen. Total RNA extraction was performed according to the standard TRIzol protocol (Invitrogen, Carlsbad, CA, USA).
RNA libraries were prepared for sequencing using standard BGI protocols.

treatment_protocol: Transcriptomic profiling of the WT, emp47(NCU00162)ko strains, with or without Ketoconazole treatment, were analyzed by high-throughput RNA sequencing (RNA-seq). Ketoconazole (Sigma) was added, with final concentration of 2 μg/mL.

value: mycelia

value: WT

value: Ketoconazole


title: Patient 3_Plasma

value: Invasive carcinoma, cribriform


title: miRNA_Ctrl_exo_3

description:
Library name: sample 12
ctrl group, miRNA-SEQ, replicate biosample 3

value: IPEC-DQ


title: VCaP  2101L

description:
Library name: SI_21183
RiboErase

value: VCaP

value: AR+ tumors

value: Vehicle


title: G1 - Lymph node, M#2

description:
Library name: G1-Lymph Noder-Mouse 2
10x Genomics

value: Lymph node


title: TNFko_Naive_rep2

description:
Gene expression data from brain of naive TNF knockout adult mouse
Sample name: KL76_32

value: TNFko

value: Brain

value: Naive


title: G1 - Lymph node, M#1

description:
Library name: G1-Lymph Node-Mouse 1
10x Genomics

value: lymphocytes

value: non


title: Neurospora crassa, Control, replicate2

description: Library name: Sample8

value: No treatment


title: TNFko_Naive_rep1

description:
Gene expression data from brain of naive TNF knockout adult mouse
Sample name: KL76_31

value: Male

value: 8 weeks


title: Neurospora crassa, Control, replicate1

description: Library name: Sample7

value: mycelia


title: Patient 2_Plasma

description: Total RNA was derived from biofluid supernatant and analyzed by the Nanostring nCounter platform. 798 c-miRNAs were assessed in each sample.

value: Uterine-related pathology, No history of cancer


title: VCaP 20R

description:
Library name: SI_14324
RiboErase


title: G1 - Tumor single cell, M#3

description:
Library name: G1-Tumor-Mouse 3
10x Genomics

value: Tumor

value: cancer cells


title: Neurospora crassa emp47(NCU00162) mutant, KTC, replicate3

description: Library name: Sample6

value: emp47(NCU00162) knockout

value: Ketoconazole


title: Patient 1_Plasma

value: Invasive carcinoma of no special type (NST)


title: MDA-PCa-146-12 8L

description:
Library name: SI_14317
Poly(A)+Transcriptome

value: AR+ tumors

value: Vehicle


title: tnnt2a heterozygous and wild-type kdrl:EGFP+ cells, 48 hpf

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description: Library name: sample2

data_processing:
Reads were aligned against the zebrafish genome (DanRer11) and counted by StarSolo (Dobin et al., doi: 10.1093/bioinformatics/bts635) followed by secondary analysis in Annotated Data Format.
Preprocessed counts were further analyzed using Scanpy (Wolf et al., doi: 10.1186/s13059-017-1382-0). Basic cell quality control was conducted by taking the number of detected genes and mitochondrial content into consideration.
We removed 441 cells in total that did not express more than 1000 genes or had a mitochondrial content greater than 20%. Furthermore, we filtered 8347 genes if they were detected in less than 30 cells (<0.00%).
Raw counts per cell were normalized to the median count over all cells and transformed into log space to stabilize variance.
We initially reduced dimensionality of the dataset using PCA, retaining 50 principal components. Subsequent steps, like low-dimensional UMAP embedding (McInnes & Healy, https://arxiv.org/abs/1802.03426) and cell clustering via community detection (Traag et al., https://arxiv.org/abs/1810.08473), were based on the initial PCA. Final data visualization was done by CellxGene package (DOI 10.5281/zenodo.3235020).
Assembly: danRer11
Supplementary files format and content: starsolo outputs

organism: Danio rerio

source_name: whole embryo

growth_protocol: Zebrafish (Danio rerio) were maintained and bred at 28.5°C under standard laboratory conditions. Embryos were collected from tnnt2a mutant incrosses and raised in E3 medium at 28.5°C until 48 hpf.

extract_protocol:
At 48 hpf, embryos were dechorionated and dissociated into single-cell suspensions using enzymatic digestion and gentle trituration. Cell suspensions were filtered to remove clumps and viability was assessed. kdrl:EGFP-positive endothelial cells were FACS-sorted, washed and resuspended in 0.04% BSA/PBS for single-cell RNA-seq library preparation.
The cell suspensions were counted with Moxi cell counter and diluted according to manufacturer’s protocol to obtain 10.000 single cell data points per sample. Each sample was run separately on a lane in Chromium controller with Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10xGenomics). Single cell RNAseq library preparation was done using standard protocol.

treatment_protocol: No experimental treatment was applied prior to cell dissociation; embryos were untreated controls or tnnt2a mutants maintained under standard conditions.

value: whole embryo

value: kdrl:EGFP+ cells

value: tnnt2a+/+ and +/-


title: G1 - Tumor single cell, M#2

description:
Library name: G1-Tumor-Mouse 2
10x Genomics


title: Neurospora crassa emp47(NCU00162) mutant, KTC, replicate2

description: Library name: Sample5


title: MDA-PCa-146-12 8R

description:
Library name: SI_14316
Poly(A)+Transcriptome


title: tnnt2a mutant kdrl:EGFP+ cells, 48 hpf

description: Library name: sample1


title: G1 - Tumor single cell, M#1

description:
Library name: G1-Tumor-Mouse 1
10x Genomics


title: nac085_rab_3

status: Public on Aug 04 2026

city: Jinan

first: Pengcheng

last: Li

address: 23788 Gongye North Road

institute: Shandong Academy of Agricultural Sciences

description:
Library name: Sample18
nac085-1 rab8d-2, biological replication_3

data_processing:
To get clean sequencing reads, the sequencing data was filtered with SOAPnuke by removing reads containing sequencing adapters, with a low-quality base ratio higher than 20%, and with an unknown base ('N' base) ratio higher than 5%. The expression level of genes was calculated by RSEM (v1.3.1).
Supplementary files format and content: A xlsx file includes fpkm, tpm, and read count values of all samples

organism: Arabidopsis thaliana

source_name: Roots

growth_protocol: Seeds of WT, rab8d-2, atm-2 rab8d-2, sog1-1 rab8d-2, nac044-1 rab8d-2, and nac085-1 rab8d-2 were sterilized with a mixture containing 75% (v/v) ethanol and 0.05% (v/v) Triton X-100 for 10 minutes and then plated onto solid 1/2 Murashige and Skoog (MS) medium containing 1% (w/v) sucrose. The plates were kept in the dark in a refrigerator (4~5°C) for about 3 days and then transferred to a growth chamber (16-h light/8-h dark, 22~23°C).

extract_protocol:
Total RNA was extracted from roots of 4-day-old seedlings using the TRIzol reagent and a PureLink RNA Micro Kit (Invitrogen) according to the user manual.
mRNA purification by oligo(dT) magnetic beads, fragmentation, synthesis of the first-strand cDNA, synthesis of the second-strand cDNA, end preparation, dA-tailing, adapter ligation, library amplification, and library quality control were performed with a BGI Optimal Dual-mode mRNA Library Prep Kit (LR00R96, BGI, China) according to the user manual.The library DNA was further circulated to produce single-stranded cyclized products using an MGIEasy circularization kit.

value: Roots

value: no treatment


title: nac085_rab_1

description:
Library name: Sample16
nac085-1 rab8d-2, biological replication_1


title: nac085_rab_2

description:
Library name: Sample17
nac085-1 rab8d-2, biological replication_2


title: nac044_rab_3

description:
Library name: Sample15
nac044-1 rab8d-2, biological replication_3


title: nac044_rab_1

description:
Library name: Sample13
nac044-1 rab8d-2, biological replication_1


title: nac044_rab_2

description:
Library name: Sample14
nac044-1 rab8d-2, biological replication_2


title: sog1_rab_3

description:
Library name: Sample12
sog1-1 rab8d-2, biological replication_3

value: sog1-1 rab8d-2


title: C57BL6_Naive_rep2

description:
Gene expression data from brain of naive C57BL/6 adult mouse
Sample name: KL42_20

source_name: Naive C57BL/6

value: Male

value: Brain

value: Naive


title: sog1_rab_2

description:
Library name: Sample11
sog1-1 rab8d-2, biological replication_2


title: C57BL6_Naive_rep1

description:
Gene expression data from brain of naive C57BL/6 adult mouse
Sample name: KL42_19

value: 8 weeks


title: sog1_rab_1

description:
Library name: Sample10
sog1-1 rab8d-2, biological replication_1


title: atm_rab_3

description:
Library name: Sample9
atm-2 rab8d-2, biological replication_3

value: atm-2 rab8d-2


title: atm_rab_1

description:
Library name: Sample7
atm-2 rab8d-2, biological replication_1


title: atm_rab_2

description:
Library name: Sample8
atm-2 rab8d-2, biological replication_2


title: rab_3

description:
Library name: Sample6
rab8d-2, biological replication_3

value: Col (WT)


title: C57BL6_Naive_rep3

description:
Gene expression data from brain of naive C57BL/6 adult mouse
Sample name: KL42_24


title: rab_2

description:
Library name: Sample5
rab8d-2, biological replication_2


title: rab_1

description:
Library name: Sample4
rab8d-2, biological replication_1


title: WT_3

description:
Library name: Sample3
WT, biological replication_3


title: WT_2

description:
Library name: Sample2
WT, biological replication_2


title: X2-1-3

description: Library name: Sample12

value: PBMC


title: OX103_Spec_3

description:
Library name: Sample24
NAC103-OX, spectinomycin, biological replication_3

source_name: roots

growth_protocol: Seeds of WT, gun1-101, nac103-11, and 35S:NAC103-GFP (NAC103-OX) were sterilized with a mixture containing 75% (v/v) ethanol and 0.05% (v/v) Triton X-100 for 10 minutes and then plated onto solid 1/2 Murashige and Skoog (MS) medium containing 1% (w/v) sucrose. The plates were kept in the dark in a refrigerator (4~5°C) for about 3 days and then transferred to a growth chamber (16-h light/8-h dark, 22~23°C).

extract_protocol:
Total RNA was extracted using the TRIzol reagent and a PureLink RNA Micro Kit (Invitrogen) according to the user manual.
mRNA purification by oligo(dT) magnetic beads, fragmentation, synthesis of the first-strand cDNA, synthesis of the second-strand cDNA, end preparation, dA-tailing, adapter ligation, library amplification, and library quality control were performed with a BGI Optimal Dual-mode mRNA Library Prep Kit (LR00R96, BGI, China) according to the user manual.The library DNA was further circulated to produce single-stranded cyclized products using an MGIEasy circularization kit.

treatment_protocol: After germination and growing for about 5 days, seedlings were transferred onto solid 1/2 MS medium containing 10 mg/L spectinomycin and incubated for about 16 h.

value: roots

value: spectinomycin

value: NAC103-OX, spectinomycin


title: WT_1

description:
Library name: Sample1
WT, biological replication_1


title: OX103_Spec_2

description:
Library name: Sample23
NAC103-OX, spectinomycin, biological replication_2


title: OX103_Spec_1

description:
Library name: Sample22
NAC103-OX, spectinomycin, biological replication_1


title: nac103_Spec_1

description:
Library name: Sample19
nac103-11, spectinomycin, biological replication_1

value: nac103-11, spectinomycin


title: nac103_Spec_2

description:
Library name: Sample20
nac103-11, spectinomycin, biological replication_2


title: gun1_Spec_3

description:
Library name: Sample18
gun1-101, spectinomycin, biological replication_3

value: gun1-101, spectinomycin


title: gun1_Spec_1

description:
Library name: Sample16
gun1-101, spectinomycin, biological replication_1


title: WT_Spec_3

description:
Library name: Sample15
WT, spectinomycin, biological replication_3

value: Col

value: WT, spectinomycin


title: WT_Spec_2

description:
Library name: Sample14
WT, spectinomycin, biological replication_2


title: OX103_C_3

description:
Library name: Sample12
NAC103-OX, control, biological replication_3

value: control

value: NAC103-OX, control


title: gun1_Spec_2

description:
Library name: Sample17
gun1-101, spectinomycin, biological replication_2


title: OX103_C_1

description:
Library name: Sample10
NAC103-OX, control, biological replication_1


title: OX103_C_2

description:
Library name: Sample11
NAC103-OX, control, biological replication_2


title: WT_Spec_1

description:
Library name: Sample13
WT, spectinomycin, biological replication_1


title: nac103_C_3

description:
Library name: Sample9
nac103-11, control, biological replication_3

value: nac103-11, control


title: nac103_C_2

description:
Library name: Sample8
nac103-11, control, biological replication_2


title: gun1_C_3

description:
Library name: Sample6
gun1-101, control, biological replication_3

value: gun1-101, control


title: nac103_C_1

description:
Library name: Sample7
nac103-11, control, biological replication_1


title: WT_C_3

description:
Library name: Sample3
WT, control, biological replication_3

value: WT, control


title: WT_C_2

description:
Library name: Sample2
WT, control, biological replication_2


title: gun1_C_2

description:
Library name: Sample5
gun1-101, control, biological replication_2


title: WT_C_1

description:
Library name: Sample1
WT, control, biological replication_1


title: RCS ARSL KO_4

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

description:
Library name: MAMD-25-0009
Transcriptome profile of RCS ARSL knockout cells (ARSL KO),  biological rep 4

data_processing:
Illumina NovaSeq 6000 base call (BCL) files were converted in fastq file through bcl2fastq Trimming and cleaning with bbduk "Alignment was performed with STAR 2.7.11a The expression levels of genes were determined with HTseq-counts 0.9.1"
Assembly: rn6
Supplementary files format and content: Vst_NormalizedCounts.txt

organism: Rattus norvegicus

source_name: RCS cells

growth_protocol: RCS cells were grown in Dulbecco Minimal Essential Medium (DMEM), supplemented with 10% Fetal Bovine Serum (FBS), penicillin/streptomycin anf 2mM L-Glutammine

extract_protocol:
Total RNA was isolated using the RNEasy Mini Kit (Qiagen, Germantown, MD, USA)
NEGEDIA Digital mRNA-seq research grade sequencing service (Next Generation Diagnostic srl)

treatment_protocol: No treatment was performed on RCS cells

tag: cell line

value: RCS cells

value: ARSL KO


title: RCS ARSL KO_3

description:
Library name: MAMD-25-0008
Transcriptome profile of RCS ARSL knockout cells (ARSL KO),  biological rep 3


title: RCS ARSL KO_2

description:
Library name: MAMD-25-0007
Transcriptome profile of RCS ARSL knockout cells (ARSL KO),  biological rep 2


title: RCS ARSL KO_1

description:
Library name: MAMD-25-0006
Transcriptome profile of RCS ARSL knockout cells (ARSL KO),  biological rep 1


title: RCS WT-5

description:
Library name: MAMD-25-0005
Transcriptome profile of RCS WT cells (Control),  biological rep 5

value: Wild type


title: RCS WT-1

description:
Library name: MAMD-25-0001
Transcriptome profile of RCS WT cells (Control),  biological rep 1


title: RCS WT-3

description:
Library name: MAMD-25-0003
Transcriptome profile of RCS WT cells (Control),  biological rep 3


title: RCS WT-2

description:
Library name: MAMD-25-0002
Transcriptome profile of RCS WT cells (Control),  biological rep 2


title: Bone marrow, NDEA, rep2

city: Jefferson

first: Li

last: Xia

state: AR

address: 3900 NCTR Rd

institute: National Center for Toxicological Research

description: Library name: Sample 14

data_processing:
Sequencing was performed on an Illumina NextSeq 2000 platform, using 100 nt single end reads, with 5 million reads on average per sample. Data analysis was processed via aligning sequencing reads to a reference genome using the STAR (Spliced Transcripts Alignment to a Reference) aligner, which enables fast and accurate mapping through a pre-built genome index. Following alignment, the number of RNA molecules per gene was quantified to assess gene expression levels, and differentially expressed genes (DEGs) were identified for downstream analysis. DESeq2 was used to perform differential expression analysis with the adjusted p-value < 0.05. Downstream analyses include pathway enrichment and data visualization to interpret biological relevance were performed via Ingenuity Pathway analysis (IPA, Qiagen).
Assembly: The STAR aligner (Spliced Transcripts Alignment to a Reference) is Lexogen’s preferred tool for aligning reads from its products. It aligns sequencing reads directly to a reference genome using a pre-built genome index.
Supplementary files format and content: txt. file includes raw counts for each Sample

source_name: Bone marrow

growth_protocol: Six-week-old female Big Blue rats obtained from Gentronix (Alderley Edge, UK) were housed at 24 °C with a 12-hour light/dark cycle. The rats had ad libitum access to water and an NIH-41 irradiated pelleted diet. After one week of acclimation, they were randomly assigned to different treatment groups, with 3 rats per cage.

extract_protocol:
Total RNA was isolated from liver and bone marrow using the Mini RNeasy Kit (Qiagen, Hilden, Germany). The quality and concentration of the RNA samples were assessed using the Qubit RNA Broad Range Assay Kits (Invitrogen, Waltham, MA).
Library preparation, sequencing, and initial data processing were subsequently performed by Lexogen GmbH, Austria. Briefly, RNA samples were characterized using UV-Vis spectrophotometry (NanoDrop 2000c, Thermo Fisher), and RNA integrity was assessed on a Fragment Analyzer System with the DNF-471 RNA Kit (15 nt) (Agilent). Libraries were constructed using Lexogen’s QuantSeq 3' mRNA-Seq Library Prep Kit FWD, incorporating the BC1-block add-on, following UG version 191UG444V0111. The quality of the prepared libraries was verified on a Fragment Analyzer System with the DNF-474 HS-DNA Kit (1-6000 bp) (Agilent).

treatment_protocol: All rats were gavaged with NDEA at doses of 0, 5 and 10 mg/kg/day with a volume of 2 ml/kg for 28 consecutive days. Dose volumes were calculated individually based on the animal’s most recent body weight. Six rats per dose group were treated, except for the positive control group that consisted of three rats. Positive control animals received B(a)P at a dose of 75 mg/kg/day for the same duration.

value: Bone marrow

tag: strain

value: Blig Blue

value: female

value: Transgenic for vector carrying cII and lacI reporter genes

value: Treated with NDEA


title: Bone marrow, NDEA, rep3

description: Library name: Sample 15

tag: tissue


title: Bone marrow, NDEA, rep4

description: Library name: Sample 16

tag: genotype


title: Bone marrow, NDEA, rep1

description: Library name: Sample 13


title: Bone marrow, control, rep4

description: Library name: Sample 12

value: Treated with Control


title: Bone marrow, control, rep2

description: Library name: Sample 10


title: Bone marrow, control, rep1

description: Library name: Sample 9


title: Liver, NDEA, rep3

description: Library name: Sample 7

source_name: Liver

value: Liver


title: Liver, NDEA, rep4

description: Library name: Sample 8


title: Col-0, 3-week-old, young true leaf

city: Hefei

first: Wenjie

last: Wang

state: Anhui

address: No. 130, Changjiang West Road

institute: Anhui Agricultrual University

data_processing:
The duplicated reads with both the same forward and reverse reads were removed according to scripts (https://github.com/PEHGP/DEtail-seq/blob/master/RemoveSamReads.py)
The rest reads were aligned to the reference genome with Bowtie2 using --local settings.
For visualization and splitting strands, the aligned reads files (BAM) including the second read in pairs were converted to the first single base bigWig file with 1bp bins using bamCoverage from deepTools with --binSize 1 --Offset 1 --samFlagInclude 128 --filterRNAstrand forward/reverse. The option --filterRNAstrand forward means Crick strand and -- filterRNAstrand reverse means Watson strand.
Normalization was performed by deepTools based on RPGC with correction by the count of reads mapped to I-CeuI sites from each sample, and the signals around I-CeuI sites (± 2 bp) were deleted in the final normalized bigWig files.
Assembly: Tair10
Supplementary files format and content: bw

source_name: young true leaf

extract_protocol:
The chloroplasts were embedded in 0.5% low-melting-point agarose (Promega) and lysed in 1% sarkosyl, 0.45 M EDTA (pH 8.0), 10 mM Tris-HCl (pH 8.0), and 2 mg/mL proteinase K at 48°C for 16 h with shaking. The agarose plugs were washed in TE buffer six times at 37°C, with the first two washes containing 1 mM PMSF. Cut agarose plug into 12 pieces and incubated in 1 ml TE with 10 μg/ml RNase A at 37°C overnight. The agarose pieces were washed five times with 1 ml TE buffer at 37°C for 6 min, then stored in plug storage solution (0.05 M EDTA pH 8.0, 60% glycerol) at -20°C until all samples were ready for the next step.
The DNA library was constructed with Scale ssDNA-seq Lib Prep Kit for Illumina V2 (ABclonal, RK20228). Five agarose pieces (~30 mg) were washed three times with 200 μl 1× CutSmart buffer (NEB) at 37°C for 6 min. The spike-in was performed by incubating the agarose pieces with 15 U I-CeuI (NEB) in 150 μl 1× CutSmart buffer at 37°C for 12 h. After digestion, the agarose pieces were washed three times with 500 μl TE buffer at 37°C for 6 min, followed by twice washes with 200 μl Low EDTA TE (ABclonal) at 37°C for 6 min. The agarose pieces were incubated in 80 μl T7 Tailing & Ligation buffer (ABclonal) at 37°C for 12 h. Then, heated the agarose pieces at 98°C for 2 min. The DNA in the agarose was recovered using a DNA purification kit (Magen, Catalog No D2111-02) and eluted with Low EDTA TE. The DNA was then sonicated to ~250 bp using Focused-ultrasonicator (Covaris S220). To finish the library preparation, the subsequent steps were performed according to the manufacturer's protocol exactly.

treatment_protocol: For tissue at different ages, the seeds were sown at the same time, while the tissues were collected every week as indicated for chloroplast isolation. For temperature treatment, the seedlings were grown on plates for 19 days, then transferred into growth chambers and grown under different temperatures with long-day conditions as indicated for 2 days. The aerial parts were harvested for chloroplast isolation. For photoperiod treatment, the seedlings were grown on plates for 16 days, then transferred into growth chambers and grown under different photoperiods as indicated for 5 days. The aerial parts were harvested for chloroplast isolation.

value: young true leaf

tag: developmental stage

value: 16 h light/8 h dark, 22C/20C


title: Liver, NDEA, rep2

description: Library name: Sample 6


title: Liver, NDEA, rep1

description: Library name: Sample 5


title: Liver, control, rep4

description: Library name: Sample 4


title: Liver, control, rep2

description: Library name: Sample 2

value: Big Blue


title: Liver, control, rep3

description: Library name: Sample 3


title: NAC103-Halo, DAP, rep2

description: Library name: NAC103-Halo, DAP, rep2

data_processing:
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 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.
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences. The clean reads were then aligned to reference genome sequences using the BWA program.
The bam file generated by the unique mapped reads as an input file, using macs2 software for callpeak with cutoff qvalue < 0.05.
Assembly: TAIR10
Supplementary files format and content: bw, narrowPeak

source_name: Whole seedlings

growth_protocol: Seedlings were grown on 1/2 MS medium in a growth chamber (16-h light/8-h dark, 22~23°C).

extract_protocol:
About 5 g of materials were collected from the liquid 1/2 MS medium and fixed with 1% formaldehyde. After nuclei extraction, the chromatin was sonicated using a Bioruptor (on, 30s; off, 30s; 15 cycles).
For ChIP-seq, the DNA library was prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to the manufacturer’s instructions. For DAP-seq, the DNA library was prepared using a VAHTS Universal DNA Library Prep Kit for Illumina V3 (ND607, Vazyme, China).

treatment_protocol: For ChIP-seq, 35S:NAC103-GFP seedlings were treated with 20 µM MG132 for 24 h before collection.

value: Whole seedlings

value: Col


title: NAC103-Halo, input

description: Library name: NAC103-Halo, input


title: NAC103-GFP, ChIP, rep3

description: Library name: NAC103-GFP, ChIP, rep3


title: NAC103-GFP, ChIP, rep2

description: Library name: NAC103-GFP, ChIP, rep2


title: NAC103-GFP, input, rep1

description: Library name: NAC103-GFP, input, rep1


title: NAC103-GFP, ChIP, rep1

description: Library name: NAC103-GFP, ChIP, rep1


title: Whole rosette tissue, hta9 hta11, 17 day, RNA, rep2

city: West Lafayette

first: Joe

last: Ogas

state: Indiana

address: 175 S. University Street

department: Department of Biochemistry

institute: Purdue University

description: Library name: HTA_2

data_processing:
Short reads were trimmed for adapter, polyG and low quality sequences using fastp (v 0.23.2) (parameters: -g -x -q 5 -u 50 -n 15)
Trimmed reads were mapped to the TAIR10 reference gemome assembly using hisat2 (v 2.2.1)
The mapped SAM files were converted, sorted and indexed to BAM files using SAMtools (v 1.17)
The gene feature was counted in DESeq2 and limma packages in Bioconductor
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Whole rosette tissue

growth_protocol: Plants used for RNA-sequencing were sown directly on soil pots. Seeds were cold-treated in dark at 4°C for three days before moving to a Percival AR75 growth chamber. Plants were grown under 16-hour light/8-hour dark photoperiod cycle at 150μE light (Phillip F32T8/TL941) with far-red supplements (soft white 25W incandescent light) at 22°C prior to sample collection. Samples for the following analyses were harvested 6 hours after the light was turned on.

extract_protocol:
Total RNA was extracted from 17-day-old shoot tissue of 5 plants that had not bolted and that were randomly selected from 5 individual pots using a RNeasy Plant Mini Kit (Qiagen; catalog no. 74904) following with the DNase I digestion and RNA clean up included in an RNA Clean & Concentrator kit (Zymo Research; catalog no. 1014). Three biological replicates were collected for each indicated genotype.
1 μg of total RNA of each sample was used for cDNA library construction. cDNA library construction was performed using an NEBNext Ultra II Directional RNA Library Prep C (NEB; catalog no. E7760S) combined with an NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB; catalog no. E7490S) according to the manufacturer’s manual.

value: Whole rosette tissue

tag: ecotype

value: hta9 hta11

tag: development stage


title: Whole rosette tissue, hta9 hta11, 17 day, RNA, rep3

description: Library name: HTA_3


title: Whole rosette tissue, hta9 hta11, 17 day, RNA, rep1

description: Library name: HTA_1


title: Whole rosette tissue, wild type, 17 day, RNA, rep3

description: Library name: WT_3


title: Whole rosette tissue, hta9 hta11, 17 day, H3K27me3, ChIP, rep3

description: Library name: HTA_H3K27me3_3

data_processing:
Short reads were trimmed for adapter, polyG and low quality sequences using fastp (v 0.23.2) (parameters: -g -x -q 5 -u 50 -n 15)
Trimmed reads were mapped to the TAIR10 reference gemome assembly using Bowtie2 (v 2.2.1) in very-sensitive-end-to-end mode
The mapped SAM files were converted, sorted and indexed to BAM files using SAMtools (v 1.17)
The reads of individual biological replicate were merged into one BAM file using SAMtools (v 1.17)
The BAM files of individual replicate and the merged sample were converted to paired-end BED files using BEDTools
ChIP-seq quantification was conducted using the annotated code was deposited on GitHub (https://github.com/BradleyDickson/Arabidopsis_H2AZ_H3K27me3_siQ-ChIP).
Assembly: TAIR10
Supplementary files format and content: TXT files include the quantification of the normalized distribution at indicated genomic regions in all included samples with a p-value < 0.05 threshold (-pv)
Supplementary files format and content: TXT files include the quantification of the normalized distribution at indicated genomic regions in all included samples (-DB)
Supplementary files format and content: BED files include the normalized distribution (NC) at the indicated genomic regions
Supplementary files format and content: BED files include the number of ChIP DNA fragemtents (NA) at the indicated genomic regions

source_name: Whole Rosette tissue

growth_protocol: Plants used for ChIP-sequencing were sown directly on soil pots. Seeds were cold-treated in dark at 4°C for three days before moving to a Percival AR75 growth chamber. Plants were grown under 16-hour light/8-hour dark photoperiod cycle at 150μE light (Phillip F32T8/TL941) with far-red supplements (soft white 25W incandescent light) at 22°C prior to sample collection. Samples for the following analyses were harvested 6 hours after the light was turned on.

extract_protocol:
4 g of 17-day-old whole rosette tissue were collected for each biological replicate. Nuclear lysis buffer was replaced with 1.7 mL of ChIP Lysis Buffer (50 mM HEPES-NaOH (pH =7.4), 16.7 mM Tris-HCl (pH = 8), 1 mM EDTA (pH = 8), 150 mM NaCl, 0.1% SDS, 1% Triton X-100, 0.1% Sodium deoxycholate, 1 cOmpleteTM mini tablet / 10 mL solution). The total chromatin samples were sonicated using Bioruptor Pico. Sheared chromatin samples were stored at -80 °C overnight prior to the immunoprecipitation. The following antibodies were used in the analysis: Anti-H3 (ab1791, Abcam) (1:200 dilution), Anti-H3K27me3 (07-449, Millipore) (1:100 dilution), and Anti-H2A.Z (1.5 µg for a 500 µL IP sample) (Deal et al., 2007). The QIAquick MinElute PCR purification kit was replaced with ChIP DNA Clean & Concentrator purification kit (D5205, Zymo research) for elution of the ChIP DNA. The eluted ChIP DNA was quantified us a Qubit 2.0 Fluorometer and used immediately in library construction.
0.5 ng eluted ChIP DNA was used for each library construction. ChIP DNA libraries were constructed using a NEBNext Ultra II DNA Library Prep Kit (NEB; catalog no. E7645L) according to the manufacturer’s manual. Illumina Multiplexing adapter was used for indexing. Pair-ended,150-bp sequencing was performed using an Illumina Novaseq S4 lane.

value: Whole Rosette tissue


title: Whole rosette tissue, hta9 hta11, 17 day, H2A.Z, ChIP, rep2

description: Library name: HTA_H2A.Z_2


title: Whole rosette tissue, hta9 hta11, 17 day, H2A.Z, ChIP, rep1

description: Library name: HTA_H2A.Z_1


title: Whole rosette tissue, hta9 hta11, 17 day, input, ChIP, rep2

description: Library name: HTA_input_2


title: Whole rosette tissue, hta9 hta11, 17 day, input, ChIP, rep1

description: Library name: HTA_input_1


title: Whole rosette tissue, wild type, 17 day, H3K27me3 ChIP, rep3

description: Library name: WT_H3K27me3_3


title: Whole rosette tissue, wild type, 17 day, H3K27me3 ChIP, rep2

description: Library name: WT_H3K27me3_2


title: Whole rosette tissue, wild type, 17 day, H3K27me3 ChIP, rep1

description: Library name: WT_H3K27me3_1


title: Whole rosette tissue, wild type, 17 day, H2A.Z, ChIP, rep3

description: Library name: WT_H2A.Z_3


title: Whole rosette tissue, wild type, 17 day, H2A.Z, ChIP, rep2

description: Library name: WT_H2A.Z_2


title: Whole rosette tissue, wild type, 17 day, input, ChIP, rep3

description: Library name: WT_input_3


title: Bone marrow, control, rep3

description: Library name: Sample 11

tag: Sex


title: Whole rosette tissue, wild type, 17 day, input, ChIP, rep2

description: Library name: WT_input_2


title: Whole rosette tissue, wild type, 17 day, input, ChIP, rep1

description: Library name: WT_input_1


title: eIF4A3-GEX1A-1.total-RNA-seq

city: Hangzhou

first: Fengli

last: Zhao

state: Zhejiang

address: No. 28 of Shuidaosuo Road

department: State Key Laboratory of Rice Biology and Breeding

institute: China National Rice Research Institute

description: RNA-seq

data_processing:
The adapters, Ns, and low-quality bases were removed from raw data using the Trimmomatic package (version 0.39)
The clean reads were mapped to the TAIR10 genome using HISAT2 (version 2.2.0) with default parameters.
RNA-seq: The uniquely mapped reads were retained for further processing using SAMtools [3] (version 1.3.1)
Assembly: TAIR10 genome
Supplementary files format and content: BigWig, or tab-separated text

source_name: seedling

extract_protocol:
Total RNA was extracted using E.Z.N.A. Plant RNA Kit (Omega)
The resulting total RNA and mRNA were used to construct the strand-specific sequencing library with NEBNext Ultra II Directional RNA Library Prep Kit (NEB)

value: seedling

value: Herboxidiene; FLAG antibody (Sigma F1804)

tag: time


title: eIF4A3-GEX1A-2.total-RNA-seq

description: RNA-seq


title: Whole rosette tissue, hta9 hta11, 17 day, RNA, rep4

description: Library name: HTA_4


title: eIF4A3-DMSO-2.total-RNA-seq

description: RNA-seq

value: DMSO; FLAG antibody (Sigma F1804)


title: eif4a3-beta-est-3.mRNA-seq

description: RNA-seq

molecule: polyA RNA

value: eif4a3 RNAi

value: Beta-estradiol


title: Whole rosette tissue, wild type, 17 day, RNA, rep4

description: Library name: WT_4

value: Wild type


title: eif4a3-beta-est-2.mRNA-seq

description: RNA-seq


title: eif4a3-beta-est-1.mRNA-seq

description: RNA-seq


title: C57BL6_Naive_rep4

description:
Gene expression data from brain of naive C57BL/6 adult mouse
Sample name: KL42_28

data_processing:
Image analysis was performed using GeneChip® Operating Software (GCOS, Affymetrix). Expression data was normalized, background corrected and summarized using the GC-RMA algorithm implemented in the Partek Genomic Suite software.
Expression values are reported as log2 RMA-normalized signal intensities.

extract_protocol: Total RNA was extracted from frozen braines using Trizol reagent  (Invitrogen, Carlsbad, CA, USA) according to the manufacturers' instructions.

value: Male

tag: age

value: 8 weeks

value: Brain

tag: surgery

value: Naive


title: eif4a3-Mock-3.mRNA-seq

description: RNA-seq

value: Ethanol


title: Whole rosette tissue, hta9 hta11, 17 day, H2A.Z, ChIP, rep3

description: Library name: HTA_H2A.Z_3


title: Whole rosette tissue, hta9 hta11, 17 day, input, ChIP, rep3

description: Library name: HTA_input_3


title: eif4a3-Mock-2.mRNA-seq

description: RNA-seq


title: eif4a3-Mock-1.mRNA-seq

description: RNA-seq


title: eIF4A3-3.mRNA-seq

description: RNA-seq


title: eIF4A3-GEX1A-2.CLIP

description: eCLIP-seq


title: eIF4A3-1.mRNA-seq

description: RNA-seq


title: eIF4A3-DMSO-2.CLIP

description: eCLIP-seq


title: eIF4A3-DMSO-1.CLIP

description: eCLIP-seq


title: eIF4A3-2.CLIP

description: eCLIP-seq

value: FLAG antibody (Sigma F1804)


title: eIF4A3-1.CLIP

description: eCLIP-seq


title: Col-0-1.CLIP

description: eCLIP-seq

value: wildtype


title: Col-0-2.CLIP

description: eCLIP-seq


title: IL2KO, rep3

city: Bethesda

first: Tom

last: Hill

state: Maryland

address: NIHBC 10 - CLINICAL CENTER BG RM 11N244A, 10 CENTER DR

institute: NIAID

description: Library name: IL2KO_msLN_TCR

data_processing:
Samples demultiplexed using Seurat
gene expression and antibodies integrated with scRepetoire
Samples integrated using Harmony
Assembly: mm10
Supplementary files format and content: RDS

source_name: PBMC

growth_protocol: All mice were bred and maintained under specific pathogen free (SPF) conditions at the University of Alabama at Birmingham (UAB) and at the National Institutes of Health (NIH) facilities.

extract_protocol:
Cells enriched via centrifugation then washed and stained for flow cytometry.
Cells were labeled with BioLegend TotalSeq-Hashtag antibodies for 30 min at 4°C, washed, stained with fluorochrome-labeled antibodies, and TCRβ+CD8-CD4+CD44hi activated cells were sorted using a FACSAriaTM (BD Biosciences). Dead cells excluded with 7-AAD. Libraries were generated with the 10x Genomics Chromium Next GEM Single Cell 5' Kit v2 and sequenced on an illumina novaseq

treatment_protocol: Mice were treated intraperitoneally with 30,000 units of human recombinant IL-2

value: PBMC

tag: library type

value: TCR


title: WT, rep3

description: Library name: WT_msLN_TCR

value: WT


title: WT, rep1

description: Library name: WT_msLN_FB

library_source: other

molecule: protein

value: FB


title: IL2KO, rep2

description: Library name: IL2KO_msLN_GEX

value: GEX


title: Female Tau transgenic

city: Nagoya

first: Ryohei

last: Uenishi

state: Aichi

address: 1 Kawasumi, Mizuho-cho, Mizuho-ku,

department: Neurocognitive Science

country: Japan

institute: Nagoya City University

hyb_protocol: A total of 5,006 genes were included in the analysis using the Xenium Mouse 5K Pan Tissue & Pathways Panel. Gene panel probe hybridization was performed overnight for 18 hours at 50 °C. The slides were washed the following day to remove unbound probes. Ligase was then added to circularize the paired ends of the bound probes (30 minutes at 42 °C), followed by amplification enhancement (2 hours at 4 °C) and enzymatic rolling circle amplification (1.5 hours at 30 °C). The slides were subsequently washed with TE buffer before background fluorescence was chemically quenched.

scan_protocol: Image processing, transcript decoding, quality score generation, and multimodal cell segmentation were automatically performed onboard the Xenium platform. Cell boundaries were determined using a deep-learning-based algorithm that integrates DAPI nuclear staining with cell boundary markers (ATP1A1, E-Cadherin, and CD45) and interior staining (18S rRNA) provided in the Xenium Cell Segmentation Stain Mix. Data were acquired using instrument software version 3.2.1.2 and processed with Xenium Onboard Analysis (XOA) software version 3.2.0.7.

data_processing: Xenium onborded analysis: 3.2.0.7.

label: Xenium probe set

source_name: Brain

label_protocol: Xenium probe set

extract_protocol: tissue preparation protocol: FFPE tissue sections were cut at a thickness of 5 µm and placed onto a Xenium slide, followed by deparaffinization and decrosslinking according to the manufacturer's protocol.

tag: tissue preservation method

value: FFPE

value: Female

value: Tau transgenic


title: Female wild-type

value: Wild-type


title: Male wild-type


title: Male Tau transgenic


title: Stereo-seq spatial transcriptome of ileum from SPF KM mouse

city: Guangzhou

first: Xiaodong

last: Fang

address: No. 111 Dade Road, Yuexiu District

institute: Guangdong Provincial Hospital of Chinese Medicine

description:
Library name: ST_SPF_ileum
Seurat object of Stereo-seq spatial transcriptomic data from ileum of SPF KM mouse.

data_processing:
Spatial transcriptomic sequencing data were processed as follows. ST_BarcodeMap was employed to extract read pairs containing valid cell identifiers (CIDs), converting CID sequences into spatial coordinate information. Quality control of raw reads was performed using Fastp (v0.23.1). Cleaned reads were aligned to the mouse reference genome GRCm39 using STAR aligner. Bam2Gem was utilized to establish correspondence between uniquely mapped reads and genes, with MID correction applied to determine final gene expression levels. The output was stored in Gene Expression Matrix (GEM) format. Cellular segmentation was performed based on ssDNA staining images, enabling reconstruction of spatial expression data at single-cell resolution. Cell type composition in spatial spots was deconvoluted using RCTD (Robust Cell Type Decomposition) with the Level2 single-cell dataset as the reference.
Assembly: GRCm39
Supplementary files format and content: RDS files containing Seurat objects with spatial gene expression matrices, spatial coordinates, and cell type deconvolution results.
Library strategy: Spatial Transcriptomics

source_name: ileum

growth_protocol: Adult male SPF and GF Kunming (KM) mice were obtained from the experimental animal center of Huazhong Agricultural University in Wuhan, China. After three weeks of weaning, they were fed the same diet for seven weeks. All mice were raised to 10 weeks of age for sampling.

extract_protocol:
OCT-embedded tissue blocks were sectioned in a cryostat at a thickness of 10 μm. Sections with RNA Integrity Number (RIN) > 7 were selected for subsequent experiments.
Spatial transcriptomic profiling was performed using the BGI Stereo-seq platform. Sections were mounted onto Stereo-seq FC chips and fixed in pre-chilled methanol (-20°C). Permeabilization was optimized across a time-gradient series (6, 12, 18, and 24 minutes), and 6 minutes was determined as the optimal duration. For final library preparation, sections were mounted onto Stereo-seq SC chips, fixed in pre-chilled methanol, and stained with ssDNA. Permeabilization was performed for 6 minutes at 37°C, followed by reverse transcription at 42°C for 1 hour. After tissue removal, cDNA was released at 55°C for 3 hours, amplified by PCR, and purified using magnetic beads. The cDNA was then circularized, fragmented, and size-selected to generate the final sequencing library. Qualified libraries were sequenced on the DNBSEQ-T7 platform (BGI, Qingdao, China).

treatment_protocol: Mice were divided into SPF and GF groups. For spatial transcriptomic analysis, intestinal tissues adjacent or corresponding to those used for single-cell analysis were collected from ileum, cecum, and colon. The luminal contents were cleared by rinsing with ice-cold PBS. Tissues were blotted dry, embedded in OCT, snap-frozen on dry ice, and stored at -80°C.

value: ileum

tag: cell type

value: tissue sections

value: KM

value: SPF


title: eIF4A3-DMSO-1.total-RNA-seq

description: RNA-seq

value: seedling

tag: treatment

value: DMSO; FLAG antibody (Sigma F1804)


title: Stereo-seq spatial transcriptome of colon from SPF KM mouse

description:
Library name: ST_SPF_colon
Seurat object of Stereo-seq spatial transcriptomic data from colon of SPF KM mouse.

source_name: colon

value: colon


title: Stereo-seq spatial transcriptome of ileum from germ-free KM mouse

description:
Library name: ST_GF_ileum
Seurat object of Stereo-seq spatial transcriptomic data from ileum of germ-free KM mouse.

value: germ-free


title: Stereo-seq spatial transcriptome of cecum from SPF KM mouse

description:
Library name: ST_SPF_cecum
Seurat object of Stereo-seq spatial transcriptomic data from cecum of SPF KM mouse.

source_name: cecum

value: cecum


title: Stereo-seq spatial transcriptome of colon from germ-free KM mouse

description:
Library name: ST_GF_colon
Seurat object of Stereo-seq spatial transcriptomic data from colon of germ-free KM mouse.


title: nac103_Spec_3

description:
Library name: Sample21
nac103-11, spectinomycin, biological replication_3

value: roots

value: spectinomycin

tag: batch

value: nac103-11, spectinomycin


title: Single-cell transcriptome of intestinal segments from KM mice

description:
Library name: KM_scRNAseq_intestinal_segments
Integrated Seurat object containing single-cell transcriptomic data from jejunum, ileum, cecum, and colon of KM mice under SPF and GF conditions.

data_processing:
Raw sequencing data were processed with Cell Ranger (v6.0.2) for demultiplexing, alignment to the mm10/GRCm38 reference genome, and UMI counting. The resulting gene expression matrices were imported into Seurat (v4.0.3) for downstream analysis. Quality control was performed by filtering out cells expressing 200 or fewer genes, genes detected in fewer than 3 cells, and cells with mitochondrial UMIs accounting for 50% or more of the total. Dimensionality reduction was performed on the top 2,000 highly variable genes using PCA, followed by UMAP projection and graph-based clustering. Cell types were manually annotated by cross-referencing cluster-specific gene expression with canonical marker genes from the literature and the Mouse Cell Atlas.
Assembly: mm10/GRCm38
Supplementary files format and content: RDS file containing a Seurat object with gene expression matrix, cell metadata, and dimensionality reduction coordinates.

source_name: intestine (jejunum, ileum, cecum, colon)

extract_protocol:
Mice were euthanized by cervical dislocation and intestinal tissues were dissected with sterile instruments. Tissues were dissected into small fragments and stored in fresh tissue storage solution. Cells were obtained from fresh tissues by enzymatic digestion within 36 hours at BGI-QingDao's Single Cell Laboratory in Qingdao, China.
Single-cell libraries were constructed using the Dnbelab C series single-cell library preparation kit (MGI, 100001082) following the manufacturer's instructions. The protocol involved droplet encapsulation, bead collection, reverse transcription, cDNA amplification, and purification. The generated library was sequenced on the DNBSEQ-T7 sequencing platform (BGI, Qingdao, China).

treatment_protocol: Mice were divided into specific pathogen-free (SPF) and germ-free (GF) groups. Intestinal tissues (jejunum, ileum, cecum, and colon) were collected from 10-week-old male mice for scRNA-seq.

value: mixed intestinal cells

value: SPF and germ-free


title: eIF4A3-2.mRNA-seq

description: RNA-seq


title: eIF4A3-GEX1A-1.CLIP

description: eCLIP-seq

value: Herboxidiene; FLAG antibody (Sigma F1804)


title: Stereo-seq spatial transcriptome of cecum from germ-free KM mouse

description:
Library name: ST_GF_cecum
Seurat object of Stereo-seq spatial transcriptomic data from cecum of germ-free KM mouse.


title: Single-cell transcriptome of myeloid cells from colon of C57BL/6 mice under SPF and germ-free conditions

description:
Library name: C57_colon_myeloid_cells
Seurat object containing myeloid cell single-cell transcriptomic data from colon of C57BL/6 mice at 4 weeks of age under SPF and GF conditions, used as validation cohort.

data_processing:
Raw sequencing data were processed with Cell Ranger (v6.0.2) for demultiplexing, alignment to the mm10/GRCm38 reference genome, and UMI counting. The resulting gene expression matrices were imported into Seurat (v4.0.3) for downstream analysis. Quality control, dimensionality reduction, clustering, and cell type annotation were performed as described for the KM cohort. B cell, T cell, and myeloid cell subsets were extracted from the full colon dataset and re-clustered for validation analysis.
Assembly: mm10/GRCm38
Supplementary files format and content: RDS files containing Seurat objects with gene expression matrices, cell metadata, and dimensionality reduction coordinates for B cell, T cell, and myeloid cell subsets, respectively.

growth_protocol: SPF and GF C57BL/6 mice were maintained under controlled diet and housing. Mice were sampled at 4 weeks of age for colon tissue collection.

extract_protocol:
Mice were euthanized and colon tissues were dissected with sterile instruments. Cells were obtained from fresh tissues by enzymatic digestion for single-cell analysis.
Single-cell libraries were constructed using the Dnbelab C series single-cell library preparation kit (MGI, 100001082) following the manufacturer's instructions. The protocol involved droplet encapsulation, bead collection, reverse transcription, cDNA amplification, and purification. Libraries were sequenced on the DNBSEQ-T7 sequencing platform (BGI, Qingdao, China).

treatment_protocol: Mice were divided into SPF and GF groups. Colon tissues were collected from 4-week-old male C57BL/6 mice for scRNA-seq validation.

value: myeloid cells

value: SPF; germ-free


title: Single-cell transcriptome of T cells from colon of C57BL/6 mice under SPF and germ-free conditions

description:
Library name: C57_colon_T_cells
Seurat object containing T cell single-cell transcriptomic data from colon of C57BL/6 mice at 4 weeks of age under SPF and GF conditions, used as validation cohort.

value: T cells


title: Single-cell transcriptome of B cells from colon of C57BL/6 mice under SPF and germ-free conditions

description:
Library name: C57_colon_B_cells
Seurat object containing B cell single-cell transcriptomic data from colon of C57BL/6 mice at 4 weeks of age under SPF and GF conditions, used as validation cohort.

value: B cells


title: gun1_C_1

description:
Library name: Sample4
gun1-101, control, biological replication_1

value: control

value: gun1-101, control


title: RCS ARSL KO_5

description:
Library name: MAMD-25-0010
Transcriptome profile of RCS ARSL knockout cells (ARSL KO),  biological rep 5

value: RCS cells

value: ARSL KO


title: 32D cells transfected with biotinylated ED-miR-675-3p mimic, input, replicate 1

city: Tianjin

first: Shuangshuang

last: Pu

state: China

address: 288 Nanjing Road

institute: State Key Laboratory of Experimental Hematology National Clinical Research Center for Blood Diseases Institute of Hematology

description:
Library name: Sample 45
Column name in miRNA_pulldown_raw_counts.tsv.gz: edit-input

data_processing:
Raw paired-end reads were processed using fastp v0.23.1. Read pairs were removed when either read contained adapter contamination, more than 10% undetermined bases, or more than 50% bases with Phred quality scores below 5. Clean reads were aligned to the Mus musculus GRCm38/mm10 reference genome using HISAT2. Alignment files were converted to BAM format, name-sorted, and filtered to remove unmapped reads using SAMtools. Gene-level unnormalized read counts were generated using HTSeq-count with the Ensembl Mus musculus GRCm38.101 annotation.
Raw single-end reads were processed to remove reads containing adapter contamination, poly-N sequences, homopolymeric sequences, low-quality bases, or reads lacking the expected 3′ adapter or insert sequence. Clean reads within the selected small-RNA length range were retained for downstream analysis. Clean reads were mapped to the Mus musculus GRCm38/mm10 reference genome using Bowtie. Seed-based alignment was performed using a 20-nt seed, allowing no more than one mismatch within the seed region. Mapped reads were annotated against known mouse miRNA sequences in miRGeneDB 2.1 and used to quantify known miRNAs.
Assembly: GRCm38/mm10
Supplementary files format and content: 32D_H19_Adar_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for nine bulk RNA-seq libraries generated from 32D-LV-H19 cells expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A.
Supplementary files format and content: ckit_h19_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for 12 bulk RNA-seq libraries generated from primary mouse c-Kit-positive cells expressing empty vector, wild-type editable H19-A, the H19-G edited mimic, or the editing-resistant H19-T mutant.
Supplementary files format and content: AN_GN_TN_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for nine bulk RNA-seq libraries generated from poly(I)-treated Ki67-eGFP-negative LT-HSCs carrying H19-A, H19-G, or H19-T alleles.
Supplementary files format and content: miRNA_pulldown_raw_counts.tsv.gz contains gene-level unnormalized read counts for 12 RNA-seq libraries generated from input and biotinylated miRNA pulldown fractions of 32D cells transfected with scrambled-control, unedited wild-type miR-675-3p, or edited miR-675-3p mimics.
Supplementary files format and content: ki67_eGFP_gene_count_matrix.tsv.gz contains gene-level unnormalized read counts for six bulk RNA-seq libraries generated from steady-state Ki67-eGFP-negative and Ki67-eGFP-positive LT-HSCs.
Supplementary files format and content: miRNA_RCadj_libraryRPM.tsv.gz contains reverse-complement-adjusted miRNA abundance values for 21 small RNA-seq libraries. The matrix includes 32D-LV-H19 cells expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A, and primary mouse c-Kit-positive cells expressing empty vector, H19-A, H19-G, or H19-T.

growth_protocol: 32D and 32D-LV-H19 mouse myeloid progenitor cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 10 ng/mL recombinant mouse interleukin-3, penicillin, and streptomycin at 37°C in a humidified incubator containing 5% CO₂. Primary mouse c-Kit-positive hematopoietic progenitor cells were isolated from bone marrow by magnetic enrichment using CD117 MicroBeads (Miltenyi Biotec). Cells were cultured in serum-free expansion medium supplemented with 100 ng/mL stem cell factor, 100 ng/mL thrombopoietin, penicillin, and streptomycin at 37°C in a humidified incubator containing 5% CO₂. Mice were maintained under specific-pathogen-free conditions. Bone marrow cells were collected from 8- to 10-week-old female mice. LT-HSCs were identified and purified by fluorescence-activated cell sorting using the Lin⁻Sca-1⁺c-Kit⁺CD34⁻Flt3⁻ phenotype. In Ki67-eGFP reporter mice, Ki67-eGFP-negative LT-HSCs were defined as quiescent cells, whereas Ki67-eGFP-positive LT-HSCs were defined as cycling cells.

extract_protocol:
Total RNA was extracted using TRIzol reagent according to the manufacturer’s instructions. Samples were treated with DNase I to remove residual genomic DNA. For miRNA pulldown experiments, RNA was extracted separately from the input lysate and the streptavidin-enriched pulldown fraction using TRIzol reagent. RNA concentration was determined using a Qubit fluorometer or NanoDrop spectrophotometer. RNA integrity was evaluated using an Agilent RNA analysis system when sample yield permitted.
For conventional bulk RNA-seq, libraries were prepared from 200 ng total RNA using the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L). Poly(A)-positive RNA was enriched using poly-T oligo-attached magnetic beads, fragmented, reverse-transcribed, adapter-ligated, and PCR-amplified according to the manufacturer’s instructions. For miRNA pulldown RNA-seq, libraries were prepared from RNA recovered from the corresponding input and pulldown fractions using the NEBNext Ultra RNA Library Prep Kit for Illumina. Libraries were generated using the same poly(A) enrichment, fragmentation, reverse-transcription, adapter-ligation, and PCR-amplification workflow. Conventional bulk RNA-seq and miRNA pulldown RNA-seq libraries were sequenced using a paired-end 150-bp strategy on an Illumina NovaSeq 6000 or DNBSEQ-T7 platform, as specified for each sample. For small RNA-seq, libraries were prepared from total RNA using the NEBNext Multiplex Small RNA Library Prep Set for Illumina (NEB, E7300L). Following sequential 3′- and 5′-adapter ligation, reverse transcription, and PCR amplification, library fragments containing 18–40-nt inserts were size-selected. Qualified libraries were sequenced using a single-end 50-bp strategy on an Illumina NovaSeq 6000.

treatment_protocol: For ADAR1-dependent experiments, 32D-LV-H19 cells were transduced with lentiviral vectors expressing empty vector, wild-type ADAR1 p110, or catalytically inactive ADAR1 p110 E861A. Cells were collected 48 h after transduction. For H19 allele-dependent experiments, primary mouse c-Kit-positive cells were transduced with lentiviral vectors expressing empty vector, wild-type editable H19-A, the H19-G edited mimic, or the editing-resistant H19-T mutant. GFP-positive transduced cells were purified by fluorescence-activated cell sorting before RNA extraction. For inflammatory-stress experiments, H19-A, H19-G, and H19-T mice carrying the Ki67-eGFP reporter were administered polyinosinic acid [poly(I)] at 10 mg/kg. Bone marrow was collected 24 h after treatment, and Ki67-eGFP-negative LT-HSCs were purified by fluorescence-activated cell sorting. For miRNA pulldown experiments, 32D cells were transfected with a biotinylated scrambled-control miRNA mimic, biotinylated unedited wild-type miR-675-3p mimic, or biotinylated edited miR-675-3p mimic. Cells were harvested 48 h after transfection. An aliquot of each cell lysate was retained as the input fraction, and biotinylated miRNA-associated RNA complexes were isolated using streptavidin-coated beads. Steady-state Ki67-eGFP-negative and Ki67-eGFP-positive LT-HSCs were isolated without additional experimental treatment.

value: myeloid progenitor cell line

value: wild type

value: transfection with ED-miR-675-3p for 48 h


title: 32D cells transfected with biotinylated ED-miR-675-3p mimic, pulldown, replicate 1

description:
Library name: Sample 47
Column name in miRNA_pulldown_raw_counts.tsv.gz: edit


title: 32D cells transfected with biotinylated ED-miR-675-3p mimic, pulldown, replicate 2

description:
Library name: Sample 48
Column name in miRNA_pulldown_raw_counts.tsv.gz: edit-1


title: 32D cells transfected with biotinylated WT-miR-675-3p mimic, pulldown, replicate 2

description:
Library name: Sample 44
Column name in miRNA_pulldown_raw_counts.tsv.gz: WT-1

value: transfection with WT-miR-675-3p for 48 h


title: 32D cells transfected with biotinylated ED-miR-675-3p mimic, input, replicate 2

description:
Library name: Sample 46
Column name in miRNA_pulldown_raw_counts.tsv.gz: edit-input-1


title: RCS WT-4

description:
Library name: MAMD-25-0004
Transcriptome profile of RCS WT cells (Control),  biological rep 4

value: Wild type


title: 32D cells transfected with biotinylated WT-miR-675-3p mimic, pulldown, replicate 1

description:
Library name: Sample 43
Column name in miRNA_pulldown_raw_counts.tsv.gz: WT


title: 32D cells transfected with biotinylated WT-miR-675-3p mimic, input, replicate 2

description:
Library name: Sample 42
Column name in miRNA_pulldown_raw_counts.tsv.gz: WT-input-1


title: 32D cells transfected with biotinylated WT-miR-675-3p mimic, input, replicate 1

description:
Library name: Sample 41
Column name in miRNA_pulldown_raw_counts.tsv.gz: WT-input


title: 32D cells transfected with biotinylated scrambled-control miRNA mimic, pulldown, replicate 2

description:
Library name: Sample 40
Column name in miRNA_pulldown_raw_counts.tsv.gz: random-1

value: transfection with scrambled mimic for 48 h


title: 32D cells transfected with biotinylated scrambled-control miRNA mimic, pulldown, replicate 1

description:
Library name: Sample 39
Column name in miRNA_pulldown_raw_counts.tsv.gz: random


title: 32D cells transfected with biotinylated scrambled-control miRNA mimic, input, replicate 1

description:
Library name: Sample 37
Column name in miRNA_pulldown_raw_counts.tsv.gz: random-input


title: 32D cells transfected with biotinylated scrambled-control miRNA mimic, input, replicate 2

description:
Library name: Sample 38
Column name in miRNA_pulldown_raw_counts.tsv.gz: random-input-1


title: WT, rep2

description: Library name: WT_msLN_GEX

value: PBMC

value: WT

value: GEX


title: IL2KO, rep1

description: Library name: IL2KO_msLN_FB

value: FB


title: Ki67-eGFP-negative LT-HSCs, replicate 3

description:
Library name: Sample 33
Column name in ki67_eGFP_gene_count_matrix.tsv.gz: KN3

source_name: bone marrow

value: bone marrow

value: long-term hematopoietic stem cell

value: Ki67-eGFP reporter


title: Ki67-eGFP-positive LT-HSCs, replicate 3

description:
Library name: Sample 36
Column name in ki67_eGFP_gene_count_matrix.tsv.gz: KP3


title: Ki67-eGFP-positive LT-HSCs, replicate 1

description:
Library name: Sample 34
Column name in ki67_eGFP_gene_count_matrix.tsv.gz: KP1


title: Ki67-eGFP-positive LT-HSCs, replicate 2

description:
Library name: Sample 35
Column name in ki67_eGFP_gene_count_matrix.tsv.gz: KP2


title: Ki67-eGFP-negative LT-HSCs, replicate 1

description:
Library name: Sample 31
Column name in ki67_eGFP_gene_count_matrix.tsv.gz: KN1


title: Ki67-eGFP-negative LT-HSCs, replicate 2

description:
Library name: Sample 32
Column name in ki67_eGFP_gene_count_matrix.tsv.gz: KN2


title: Poly(I:C)-treated H19-T Ki67-eGFP-negative LT-HSCs, replicate 2

description:
Library name: Sample 29
Column name in AN_GN_TN_gene_count_matrix.tsv.gz: TN_2

value: H19-T editing-resistant allele; Ki67-eGFP reporter

value: poly(I:C), 10 mg/kg, 24 h


title: Poly(I:C)-treated H19-T Ki67-eGFP-negative LT-HSCs, replicate 1

description:
Library name: Sample 28
Column name in AN_GN_TN_gene_count_matrix.tsv.gz: TN_1


title: Poly(I:C)-treated H19-G Ki67-eGFP-negative LT-HSCs, replicate 3

description:
Library name: Sample 27
Column name in AN_GN_TN_gene_count_matrix.tsv.gz: GN_3

value: H19-G edited-mimic allele; Ki67-eGFP reporter


title: Poly(I:C)-treated H19-G Ki67-eGFP-negative LT-HSCs, replicate 2

description:
Library name: Sample 26
Column name in AN_GN_TN_gene_count_matrix.tsv.gz: GN_2


title: Poly(I:C)-treated H19-G Ki67-eGFP-negative LT-HSCs, replicate 1

description:
Library name: Sample 25
Column name in AN_GN_TN_gene_count_matrix.tsv.gz: GN_1


title: single cell RNA-seq of Tbet and Runx3 KO

city: Suzhou

first: Qiang

last: Shan

address: No. 100, Chongwen Road

institute: Suzhou Institute of Systems Medicine

description: Library name: Sample 4

data_processing:
The sequencing data were processed using an open-source pipeline (https://github.com/MGI-tech-bioinformatics/DNBelab_C_Series_scRNA-analysis-software ). Briefly, all samples were performed sample de-multiplexing, barcode processing, and single-cell 3' unique molecular identifier (UMI) counting with default parameters. Processed reads were then aligned to GRCh38 genome reference using STAR (2.5.1b). Valid cells were automatically identified based on the UMI number distribution of each cell by using the “barcodeRanks()” function of the DropletUtils tool to remove background beads and the beads that had UMI counts less than the threshold value. Finally, we used PISA to calculate the gene expression of cells and create a gene x cell matrix for each library.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: CD8+ T cells

extract_protocol:
The collected tissues were washed by 1× PBS, then quickly frozen and stored in liquid nitrogen. Nuclei extraction was separated by mechanical extraction method. Firstly, put the tissues into 2ml Dounce homogenizer set and thawed in homogenization buffer (containing 20mM Tris pH8.0, 500mM sucrose, 0.1% NP-40, 0.2U/μL RNase inhibitor, 1× protease inhibitor cocktail, 1% bovine serum albumin (BSA), and 0.1mM DTT. Use Dounce pestle A to grind the tissue 10 times, filter with 70μm cell filter, and then grind with Dounce pestle B 10 times, filter with 30um cell filter. Centrifuge at 500 × g for 5 minutes at 4°C to pellet the nuclei, and resuspend in the blocking buffer containing 1% BSA and 0.2U/μL RNase inhibitor in 1× PBS. Centrifuge again at 500 × g for 5 minutes and resuspend with Cell Resuspension Buffer (MGI).
DNBelab C Series High-throughput Single-Cell RNA Library Preparation Set was utilized for scRNA-seq library preparation. In brief, the single-cell suspensions were converted to barcoded scRNA-seq libraries through steps including droplet encapsulation, emulsion breakage, mRNA captured beads collection, reverse transcription, cDNA amplification and purification. cDNA production was sheared to short fragments with 300-500 bp, and indexed sequencing libraries were constructed according to the manufacturer’s protocol. Qualification was performed using Qubit ssDNA Assay Kit (Thermo Fisher Scientific) and Agilent Bioanalyzer 2100. All libraries were further sequenced by the DNBSEQ-T7 sequencing platform with pair-end sequencing. The sequencing reads contained 30-bp read 1 (including the 10-bp cell barcode 1, 10-bp cell barcode 2 and 10-bp unique molecular identifiers (UMI)), 100-bp read 2 for gene sequences and 10-bp barcodes read for sample index.

value: CD8+ T cells

value: Tbet/Runx3 double knockout


title: single cell RNA-seq of Tbet KO

description: Library name: Sample 3

value: Tbet knockout


title: Poly(I:C)-treated H19-A Ki67-eGFP-negative LT-HSCs, replicate 1

description:
Library name: Sample 22
Column name in AN_GN_TN_gene_count_matrix.tsv.gz: AN_1

value: H19-A control allele; Ki67-eGFP reporter


title: single cell RNA-seq of Control

description: Library name: Sample 1

value: wild type


title: Poly(I:C)-treated H19-A Ki67-eGFP-negative LT-HSCs, replicate 2

description:
Library name: Sample 23
Column name in AN_GN_TN_gene_count_matrix.tsv.gz: AN_2


title: gCeO_N4_ATAC-seq

city: Dresden

first: Mareike

last: Albert

address: Fetscherstr. 105

department: Center for Regenerative Therapies TU Dresden

institute: TUD Dresden University of Technology

description:
Library name: 127116
gCeO_N_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz

data_processing:
sequence data files were created with bcl2fastq2 v2.20.0
ATAC-seq libraries were mapped and processed using the ENCODE pipeline (Lee et al. 2016) with default settings. This includes that creating narrowPeak files with MACS2, conversion of bed files to bw files and count tables
consensusPeak.narrowPeak files represent IDR-filtered high-confidence ATAC-seq peaks representing reproducible chromatin accessibility regions across biological replicates.
Assembly: gorGor6
Supplementary files format and content: bigWig: Normalized ATAC-seq signal tracks for genome browser visualization.
Supplementary files format and content: narrowPeak: Called accessible chromatin peaks with genomic coordinates and peak statistics.
Supplementary files format and content: GEO_gorilla_ATAC_counts.tsv.gz: Raw counts per peak across samples with genomic/gene annotations with liftover coordination for human (hg38) and chimpanzee (panTro6)

organism: Gorilla gorilla gorilla

source_name: cerebral organoid

growth_protocol: iPSC line grown under standard conditions (5 % CO2, 37 °C) on Matrigel-coated plates in StemFlex.

extract_protocol:
ATAC-seq was performed as previously described with minor alterations to the protocol (Corces et al. 2017). Briefly, sorted cells are pelleted at 500x g and 4 °C for 5 min. All supernatant was aspirated, cells were re-suspended in 50 µL ice-cold lysis buffer by pipetting up-and-down three times and incubated on ice for 3 min. Lysis was washed out with 1 mL ice-cold wash buffer, and the tubes were inverted to mix. Cells were again pelleted at 500x g and 4 °C for 10 min. Supernatant was fully aspirated and cells re-suspended in 50 µL transposition mix containing 100 mM transposase. Reactions were incubated at 37 °C and 1,000 rpm in a thermoshaker for 2 hours and then quenched by the addition of 40 mM EDTA. Reactions were pelleted at 500x g for 5 min, re-suspended in 200 µL reverse-crosslink solution and incubated O/N at 65 °C and 1,000 rpm in a thermoshaker as previously reported for ATAC-seq on fixed cells (Chen et al. 2020). The next day, the original protocol was continued, and reactions were cleaned up using a Zymo DNA Clean and Concentrator-5 Kit.
libraries were amplified with determination of amplification cycles by qPCR as described (Corces et al. 2017) and unique adapter combinations (i5 and i7), and final PCR reactions were cleaned up using a Zymo DNA Clean and Concentrator-5 Kit. Final libraries were size selected using SPRIselect Beads at 0.5x and 1.3x ratios, to retain fragments of 150–1,000 bp.

value: cerebral organoid

value: BCL11B+ neuron


title: gCeO_bIP5_ATAC-seq

description:
Library name: 127115
gCeO_bIP_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz

value: basal intermediate progenitor cell


title: gCeO_bRG2_ATAC-seq

description:
Library name: 127114
gCeO_bRG_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz

value: basal radial glia


title: gCeO_bRG1_ATAC-seq

description:
Library name: 127113
gCeO_bRG_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz


title: gCeO_aRG3_ATAC-seq

description:
Library name: 127112
gCeO_aRG_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz

value: apical radial glia


title: gCeO_N3_ATAC-seq

description:
Library name: 127111
gCeO_N_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz


title: gCeO_bIP4_ATAC-seq

description:
Library name: 127110
gCeO_bIP_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz


title: gCeO_bIP3_ATAC-seq

description:
Library name: 105218
gCeO_bIP_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz


title: RTN_24hr_CO2_5

city: Wauwatosa

first: Ibrahim

last: Vazirabad

state: Wisconsin

address: 8915 W Connell Ave

department: Physiology

institute: Medical College of Wisconsin

description: Library name: R2023.1493

data_processing:
Filtered reads were obtained by running fastp v0.24.0 with default parameters.
Filtered reads were aligned to the goat reference (ARS1) using STAR v2.7.10b with gene-level counts generated by FeatureCounts v2.0.6.
Differential expression analysis was performed by EdgeR v4.6
Assembly: ARS1
Supplementary files format and content: gene name, log2 fold change, log2CPM, and FDR per comparison are included for all differentially expressed genes.

organism: Capra hircus

source_name: RTN

growth_protocol: Five groups (n = 6) of adult (≥ 2 years) outbred (Alpine, Saanen, Toggenburg, etc.) female goats were assigned to the protocol.

extract_protocol:
RNA was isolated using the Qiagen RNeasy Lipid Tissue Kit per the manufacturer’s recommendations, including on-column DNase digestion
RNA-seq libraries were constructed using the SMART-SEQ v4 Ultra Low Input RNA Kit for Sequencing and the Nextera XT DNA Library Preparation Kit. Sequencing produced 100-bp paired end reads across up to two lanes.

treatment_protocol: The five groups were randomly assigned to different environmental CO2 exposures, either 24 hr of control (room air), 3 hours of 6% CO2, 24 hours of 6% CO2, 7 days of 6% CO2, or 7 days of control (room air).

value: RTN


title: gCeO_N2_ATAC-seq

description:
Library name: 105217
gCeO_N_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz


title: gCeO_N1_ATAC-seq

description:
Library name: 105216
gCeO_N_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz


title: RTN_24hr_CO2_6

description: Library name: R2023.1494


title: gCeO_bIP2_ATAC-seq

description:
Library name: 105215
gCeO_bIP_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz


title: gCeO_bIP1_ATAC-seq

description:
Library name: 105214
gCeO_bIP_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz


title: gCeO_aRG2_ATAC-seq

description:
Library name: 105213
gCeO_aRG_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz


title: gCeO_aRG1_ATAC-seq

description:
Library name: 105212
gCeO_aRG_consensusPeak.narrowPeak.gz
GEO_gorilla_ATAC_counts.tsv.gz