title: Rabbit_10dpi_replicate_1_scRNA-seq_10x

description:
Library name: Rabbit_10dpi_replicate_1_scRNA-seq
Note: because the file1 is larger than 100G, the file 1 was split into two files(part1, part2)

value: injury, 10dpi


title: Crypt_organoids_ATAC_seq_WT_day3_rep1

status: Public on Jul 06 2025

type: SRA

city: Incheon

first: Ik Soo

last: Kim

address: Gaetbeol-ro, Yeonsu-gu

country: South Korea

institute: Gachon University college of Medicine

library_source: genomic

data_processing:
ATAC-Seq: After trimming adapter sequences by Trim Galore (V0.5.0), paired-end reads were aligned onto mm10 using Bowtie2 (v2.3.5.1)51 and peak calling was conducted by Model-based Analysis for ChIP-Seq (MACS) (v2.1.2) General analysis of chromatin accessibility including annotation of genomic coordinates, peak counts, and normalization was performed using ChrAccR (v.0.9.17).
RNA-Seq : The reads were pre-processed to remove adaptors and bases with low quality by Trimmomatic (v0.36). Next, STAR (v2.5.3) was used to align the reads, and Transcripts Per Million (TPM) was calculated with RSEM (v1.3.0).
Assembly: mm10
Supplementary files format and content: *.bw : The bigWig format is for display of dense, continuous data that will be displayed as a graph in IGV or UCSC browser.
Supplementary files format and content: *.gtf : Output of StringTie mediated assembly of RNA-Seq alignments into potential transcripts.
Supplementary files format and content: *.txt : Combined output of StringTie mediated assembly of transcripts into genes (counts, FPKM, TPM)

molecule: genomic DNA

organism: Mus musculus

growth_protocol: Mouse crypts were isolated and resuspended in DMEM/F-12 (Hyclone Laboratories).  Single intestinal organoid cells which were incubated by 1× TrypLE™ Express (Gibco) were subcultured with Matrigel matrix (Corning) in 24well plates. Each well was supplemented with 600µl of IntestiCult Organoid Growth Medium (OGM). Organoids were grown at 37 °C in a humidified incubator with 5% CO2.

extract_protocol:
DNA: ATAC-seq libraries were prepared for sequencing using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (#20034197, Illumina) and paired-end sequencing was performed by Illumina platform
ATAC-seq libraries were prepared for sequencing using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits (#20034197, Illumina)
RNA: Total RNAs were extracted from WT and Phf16-/Y intestinal organoid cells on days1-3. Then, the stranded mRNA-seq library was prepared following Illumina's TruSeq protocol.
RNA-seq library was prepared following Illumina's TruSeq protocol

tag: tissue

tag: cell line

tag: cell type

value: Intestinal epithelium

tag: genotype

value: WT

tag: treatment

tag: time


title: Rabbit_0dpi_replicate_1_scRNA-seq_10x

city: Beijing

first: Weifeng

last: Lin

state: Beijing

address: 7 Science Park Road ZGC Life Science Park

country: China

institute: National Institute of Biological Sciences

description:
Library name: Rabbit_0dpi_replicate_1_scRNA-seq
Note: because the file1 is larger than 100G, the file 1 was split into two files(part1, part2)

library_source: transcriptomic single cell

data_processing:
Raw reads were aligned to the mouse and rabbit reference genomes to produce the single-cell gene expression matrixes using Cell Ranger (Version 7.0), respectively.
The file 1 was split into two files(part1, part2) with linux command 'split' because it's more than 100G.
Assembly: GRCm39 and oryCun2
Supplementary files format and content: Cell Ranger software output files (barcodes.tsv, features.tsv, matrix.mtx)

molecule: polyA RNA

organism: Oryctolagus cuniculus

source_name: ear-pinna

extract_protocol:
The ear hole tissues were collected using biopsy punches and washed with ice-cold PBS. Subsequently, the tissues were dissected into small pieces quickly and transferred into tubes with Collagenase dissociation buffer containing 2mg/ml Collagenase type I (Sigma, C2674) and 100ug/ml DNase I (Roche, 10104159001). After incubating at 37 ℃, the dissociated cell suspension was filtered through a 70 μm filter. The remaining incompletely digested tissue pellets were further dissociated with TrypLE (Gibco, 12605010) and then filtered and mixed with dissociated cells digested with collagenase. For separate living cells, the dissociated cell mixtures were resuspended with ice-cold PBS containing 5% fetal bovine serum (FBS) and incubated with Propidium Iodide (PI) to stain dead cells. The PI-negative cells were sorted using BD FACSAria II Flow cytometry. To ensure single-cell sample quality, the proportion of living cells was evaluated by Trypan blue staining before library preparation with the 10X Genomics platform.
The scRNA library construction were performed according to the manufacturer’s protocol

treatment_protocol: For RA treatment, RA solutions were intraperitoneally injected into mice every two days upon injury at the dose of 20 μg/g until 15 dpi, equal volume DMSO solution were used as control

value: ear-pinna

value: injury, 0dpi


title: Crypt_organoids_ATAC_seq_WT_day3_rep2


title: SK-N-SH cells, DA+,rep1

city: Shanghai

first: Yang

last: Yaqi

address: No.1678 Dongfang Road, Pudong, Shanghai, China

institute: Shanghai Children Medical Centre

library_source: transcriptomic

data_processing:
For quality control of the raw sequencing data, FastQ Screen (version 0.13.0) and FastQC (version 0.11.9) were utilized.
The STAR software (version 2.7.1a) was employed for mapping the reads to the human genome (hg19) or hybrid human(hg19)-ERCC genome. Read counts within each gene were computed using HTSeq count (version 0.11.2).
Gene transcription was quantified by calculating Fragments Per Kilobase of exon per Million mapped reads (FPKM). Statistical significance was assessed using DESeq2 (version 1.40.2)
Assembly: hg19
Supplementary files format and content: 6h_DA+_DA-.fpkm_all_fpkm.txt

molecule: total RNA

organism: Homo sapiens

source_name: SK-N-SH

growth_protocol: EMEM/F12 medium supplemented with 10% FBS. cells were cultured in an incubator at 37°C with 5% CO2.

extract_protocol:
Lyse cells directly in a culture dish by adding 1 mL TRIzol reagent and mix thoroughly. add 200μL chloroform, vortex mix for 15 seconds. incubate the mix for 5 minutes at room temperature and two layer should form. centrifuge at 12000 g at 4 °C for 10 minutes. Carefully transfer the top layer into the new tubes.add 1:1V of isopropanol to each tube and mix by inversion. Centrifuge at 12000 g at 4 °C for 15 minutes. Discard the supernatant and wash the pellet with 1 mL 75%  ethanol. Centrifuge at 12000g at 4 °C for 10 minutes. Remove all of residential ethanol with a pipet and air dry for 5 min. redissolve RNA in 30-50 μL  DEPC treated water.
The rRNA-depleted sequencing libraries from total RNA were prepared using Illumina TruSeq® Stranded Total RNA Gold preparation Kit. About 1 μg total RNA was used as input material, and Ribo-Zero Gold kit was used to remove both cytoplasmic and mitochondrial rRNA. Purified RNA was then fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments were copied into first strand cDNA using reverse transcriptase and random primers, followed by second strand cDNA synthesis. These cDNA fragments were then subjected to end-repair, phosphorylation and 'A' base addition according to Illumina's library construction protocol.

treatment_protocol: SK-N-SH cells were cultured for 24 hours in standard medium, and then cells were treated with medium (control) or DA at 40 M for 6 h.

value: SK-N-SH

value: neuroblastoma cells

value: Wild Type

value: dopamine


title: Primed Astrocytes with Aβ treatement_ATAC-seq_1

city: Seoul

first: Jinsoo

last: Seo

address: 50 Yonsei-ro

department: Department of Systems Biology

institute: Yonsei University

data_processing:
40-bp end sequences were trimmed for bowtie2 (version 2.3.4) alignment against the hg38 human genome with specific parameters (--end-to-end --very-sensitive --no-mixed --no-discordant -q --phred33 -I 10 -X 700)
Aligned bam files were sorted and indexed using samtools (version 1.6).
After the alignment step, fragment size histograms were visualized using a customized R script as quality control.
Genrich peak caller was used for ATAC-seq peak calling.
Assembly: Human hg38
Supplementary files format and content: ATAC-seq signal bigwig tracks

source_name: hiPSC-derived astrocytes

growth_protocol: hiPSC-astrocytes were cultured in astrocyte media (ScienCell)

extract_protocol:
Transposition reaction was performed with Illumina Tagment DNA TDE1 Enzyme and Buffer Kit and DNA was isolated using the Qiagen MinElute Reaction Cleanup Kit.
DNA was amplified using NEBNext 2X PCR Master Mix and Illumina/Nextera i5 common adapters and i7 index adapters

treatment_protocol: 10 μM Aβ42 oligomer for 6 hours

value: hiPSC-derived astrocytes

value: Astrocytes

value: Control (APOE3)

value: Aβ


title: Primed Astrocytes with Aβ treatement_ATAC-seq_3


title: SK-N-SH cells, DA-,rep3


title: SK-N-SH cells, DA+,rep2


title: Crypt_organoids_ATAC_seq_WT_day2_rep1


title: Rabbit_10dpi_replicate_2_scRNA-seq_10x

description:
Library name: Rabbit_10dpi_replicate_2_scRNA-seq
Note: because the file1 is larger than 100G, the file 1 was split into two files(part1, part2)


title: SK-N-SH cells, DA-,rep2


title: Crypt_organoids_ATAC_seq_WT_day1_rep2


title: Rabbit_5dpi_scRNA-seq_10x

description:
Library name: Rabbit_5dpi_scRNA-seq
Note: because the file1 is larger than 100G, the file 1 was split into two files(part1, part2)

value: injury, 5dpi


title: Primed Astrocytes without Aβ treatement_ATAC-seq_1


title: SK-N-SH cells, DA-,rep1


title: small intestine, 4w, scRNA-seq

city: Fukuoka

first: Shinichiro

last: Sawa

address: 3-1-1 Maidashi, Higashiku

country: Japan

institute: Kyushu University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were performed using the Cell Ranger software v7.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: small intestine

extract_protocol:
Intestines were collected, cut into 1cm pieces, and then washed with EDTA-free cold PBS. Gut tissue was incubated in 30mM EDTA-containing PBS for 13 minutes at room temperature then immediately washed with EDTA-free cold PBS to remove epithelium.  Washed gut specimens were incubated in DMEM containing 1 mg/mL Collagenase P , 0.2 mg/mL Liberase TH and 0.33 mg/mL DNase I  at 37ºC. Dissociated cells were collected every 30 min and strained with a 100 μm nylon mesh, and then were subjected to density gradient centrifugation using 40%/80% Percoll system (Cyvita). The cells at the intermediate layer were collected by centrifuge and resuspended in 2% FBS/2 mM EDTA/PBS. The isolated cells were stained with antibodies against PDPN, CD45 and CD31. Fixable viability dye (eBioscience) was used to stain dead cells. Alive PDPN+CD45-CD31- cells were sorted for single cell 3' gene expression library construction.
Library construction was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, 10x Genomics) with slight modification.  Cells up to 10,000 were directly sorted into the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). .

value: small intestine

tag: strain

value: wild type

tag: age


title: Primed Astrocytes without Aβ treatement_ATAC-seq_2


title: Sample 1 (IL15 KO)

status: Public on Jul 05 2025

city: Toulouse

first: Joost

last: van Meerwijk

address: CHU Purpan BP 3028

department: CPTP U1043

country: France

institute: INSERM

data_processing:
Illumina Casava 2.20 was used for basecalling
LongRanger mkfastq v.2.1.4 was used to de-multiplex samples and converted files .bcl2 to FASTQ format.
Alignment, de-duplication, barcode filtering and gene quantification for all four samples were handled by the 10X Genomics proprietary software, Cell Ranger v.2.0.2 (expect-cells = 3000)
Quality control, filtering of low quality genes and cells with R (version 3.4.1) and scater (version 1.4.0): outliers filtered with 'nmads = 3'
Cell cycle prediction with R (version 3.4.1) and scran (version 1.4.5): cyclone method
Quick clustering and normalization performed with R (version 3.4.1) and scran (version 1.4.5)
Filtering of cells not in G1 phase
Genome_build: mm10 (refdata-cellranger-mm10-1.2.0)
Supplementary_files_format_and_content: Raw count matrix and Filtered and normalized counting matrix

source_name: Thymic regulatory T cells

growth_protocol: NA, Sorting

extract_protocol:
RNA was extracted by Nucleospin RNA XS
Chromium Controller Single-Cell Instrument and Chromium Single Cell 3' Library & Gel Bead Kit v2, A Chip Kit and i7 Multiplex Kit

tag: sorting

value: Rag2-Gfp Foxp3-Thy1a IL15 o/o B6

value: 3 weeks


title: Crypt_organoids_ATAC_seq_WT_day1_rep1

value: Intestinal epithelium


title: Sample 1 (IL2 KO)

value: Rag2-Gfp Foxp3-Thy1a IL2 o/o B6


title: Sample 1 (WT IL2)

value: Rag2-Gfp Foxp3-Thy1a IL2 wt/wt B6


title: C57BL/6 cells, shVdac 3-1, Week4

city: Hangzhou

first: Yani

last: Chen

state: Zhejiang

address: No. 268, Kaixuan Rd.

institute: Zhejiang University

description: Library name: Sample 6

data_processing:
Raw FASTQ files were processed using Cutadapt (v1.9.1) with parameters
Genome indexing using HISAT2 (v2.0.1). Clean reads were aligned to the reference genome using HISAT2 with default parameters.
Transcript abundance was estimated using HTSeq (v0.6.1) . Raw counts were generated for each gene/transcript.
Normalization and differential expression were analyzed using DESeq2 (v1.30.1).
Assembly: GRCm39
Supplementary files format and content: CSV files containing normalized expression values (FPKM).

source_name: bone mesenchymal stem cells

extract_protocol:
1 ug of total RNA was used for the construction of sequencing libraries.
Libraries were pooled and sequenced on an Illumina HiSeq/NovaSeq/MGI2000 platform with 2×150 bp paired-end configuration.

value: bone mesenchymal stem cells

value: Vdac knockdown


title: C57BL/6 cells, shVdac 2-1, Week4

description: Library name: Sample 5


title: C57BL/6 cells, shVdac 1-1, Week4

description: Library name: Sample 4


title: Primed Astrocytes with Aβ treatement_ATAC-seq_2


title: C57BL/6 cells, shControl 3-1, Week4

description: Library name: Sample 3

value: WT


title: C57BL/6 cells, shControl 1-1, Week4

description: Library name: Sample 1


title: C57BL/6 cells, shControl 2-1, Week4

description: Library name: Sample 2


title: NIH-3T3 MCMV 72 hpi no AB

city: Würzburg

first: Florian

last: Erhard

address: Versbacher Str. 7

department: Institut für Virologie und Immunbiologie

country: Germany

institute: Julius-Maximilians-Universität Würzburg

data_processing:
The 3’ adapter sequence (AGATCGGAAGAGCGGTT) was trimmed using reaper, and library barcode sequences (first 9 nt of read=3 random bases followed by 4 bases of sample-specific barcode followed by 2 random bases) were removed from all reads and stored for later use.
All reads were mapped using bowtie 1.2 (REF) against the murine genome and transcriptome (Ensembl version 90) and the MCMV genome and transcriptome (Genbank KY348373.1).
). To collapse random barcodes for each mapped read location, the most frequently observed sequence (composed of random barcode and mapped read sequence) was determined. This sequence and all sequences with exactly one mismatch (to account for sequencing errors) were removed. This procedure was repeated until no sequences remained. The number of iterations was used as the read count. This procedure was repeated separately for each sample-specific barcode. Barcodes not matching any sample-specific sequence were discarded.
Mismatch frequencies and miRNA read counts were determined using GRAND-SLAM 2.0.7.
Assembly: Ensembl version 90 and Genbank KY348373.1
Supplementary files format and content: counts

source_name: NIH-3T3 murine embryonic fibroblasts

growth_protocol: NIH-3T3 fibroblasts (ATCC: CRL-1658) were cultured in DMEM medium containing 5% fetal calf serum and penicillin/streptomycin. TCMK-1 murine kidney epithelial cells (ATCC: CCL-139) were cultured in DMEM containing 10% fetal calf serum and penicillin/streptomycin. Cells at passage 6-15 were infected at MOI=10 with WT MCMV.

extract_protocol:
mAgo2-bound RNA was purified using the iCLIP protocol as described
Library construction was performed using the iCLIP protocol, which comprises 3'-adaptor ligation and circularisation. Random nucleotide barcodes enable the removal of PCR duplicates

treatment_protocol: For MCMV infection, cells from seven 15 cm dishes (80% confluent) per condition (for MCMV infection) were trypsinized 3-4 days after the last split. Cells were resuspended in 1 ml cell culture medium per plate. MCMV virus stock was added at an MOI of 10 (t=0). Similar to centrifugal enhancement, infecting cells in suspension rather than on plates results improves infection by about 10-fold.). 1h later, cells were transfered to a bottle with 195 ml cell culture media containing a final concentration of 25 µM 4sU. Cells were plated to ten 15 cm dishes (20 ml per plate). At 24 and 48 h post infection, an additional 25µM (24hpi) and 50 µM (48hpi) 4sU was added to the cell culture medium. Uninfected cells were split 24h prior to beginn of 4sU labeling (100µM 24h).

value: Immortalized embryonic fibroblasts

tag: time post infection

value: MCMV 72hpi

tag: infection with

value: MCMV

tag: rip antibody

tag: replicate

value: Replicate 1

tag: protocol

value: iCLIP protocol

value: 100 uM 4sU labeling for 24h prior to harvest


title: TCMK-1 MCMV 72 hpi Exp 1

description: Experiment 1 = PC17

source_name: TCMK-1 murine epithelial cells

value: SV40 transformed murine kidney epithelial cells

value: anti-mAgo2, Wako Chemicals (cat. no.:018-22021)


title: NIH-3T3 Mock no AB

value: Mock


title: TCMK-1 MCMV 72 hpi Exp 2

description: Experiment 2 = PC25

value: Replicate 2

value: 25 + 25 +50 uM 4sU at 0, 24 and 48 hpi; harvest at 72 hpi


title: NIH-3T3 Mock Exp 2

description: Experiment 2 = PC25


title: TCMK-1 Mock Exp 1

description: Experiment 1 = PC17


title: NIH-3T3 Mock Exp 1

description: Experiment 1 = PC17


title: NIH-3T3 MCMV 72 hpi Exp 2

description: Experiment 2 = PC25


title: NIH-3T3 MCMV 72 hpi Exp 1

description: Experiment 1 = PC17


title: ChIP_MCF10AT1_H3K4me3_rep2

city: Burlington

first: Seth

last: Frietze

state: VT

address: 149 Beaumont Avenue

department: Biomedical and Health Sciences

country: USA

institute: University of Vermont

data_processing:
Basecalls were performed using bcl2fastq v2.20 for HiSeq output.
ChIP-seq reads were aligned to the hg38 genome using STAR version v2.7.9a using  the options “--alignIntronMax 1 --alignEndsType EndToEnd”. Only uniquely mapping reads with at most two mismatches were retained.
ChIP-seq coverage plots were generated based on the locations of the mapped ChIP-seq reads which were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
narrowPeak files were generated using MACS v2 with default settings using correpsonding input control.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Supplementary files format and content: ChromHMM (version 1.2.4) was used to binarize BAM files and used to generate a 23-state model of chromatin states based on seven histone modifications across all four cell lines.

growth_protocol: Cells were grown in DMEM: F12 with 5%  horse serum supplmented with 10mg/ml human insulin + 20ng/ml recombinant hEGF + 100 ng/ml cholera toxin + 0.5 mg/ml hydrocortisone + penicillin/streptomycin and 2 mM glutamine. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching with 0.125M glycine and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the NEB UltraII Library Preparation Kit according to manufacturer's instructions.

tag: chip antibody


title: ChIP_MCF10DCIS_H3K4me3_rep2


title: Sample 1 (WT IL15)

value: Rag2-Gfp Foxp3-Thy1a IL15 wt/wt B6

value: 3 weeks


title: ChIP_MCF10A_H3K4me3_rep2


title: ChIP_MCF10A_H3K4me3_rep1


title: ChIP_MCF10DCIS_H3K9me3_rep2


title: ChIP_MCF10CA1a_H3K4me3_rep2


title: ChIP_MCF10DCIS_H3K9me3_rep1


title: ChIP_MCF10CA1a_H3K9me3_rep1


title: ChIP_MCF10CA1a_H3K9me3_rep2


title: ChIP_MCF10A_H3K9me3_rep2


title: ChIP_MCF10A_H3K9me3_rep1


title: ChIP_MCF10AT1_H3K9me3_rep1


title: ChIP_MCF10DCIS_H3K27ac_rep2


title: ChIP_MCF10DCIS_H3K27ac_rep1


title: ChIP_MCF10CA1a_H3K27ac_rep2


title: ChIP_MCF10AT1_H3K27ac_rep2


title: ChIP_MCF10A_H3K27ac_rep2


title: ChIP_MCF10AT1_H3K27ac_rep1


title: Patient_P1858_ATAC_MM_Pre_Treatment

city: Calgary

first: nizar jacques

last: Bahlis

state: AB

address: 3330 Hospital Dr NW HMRB328

department: Medicine

country: Canada

institute: University of Calgary

description: Library name: P1858_ATAC_MM

library_source: genomic single cell

data_processing:
All raw FASTQs reads were aligned against the human reference genome GRCh38 with default parameters.
Assembly: Human referene genome GRCh38
Supplementary files format and content: Filtered feature - barcode HDF5 file output from CellRanger pipeline

source_name: Bone marrow

extract_protocol:
Primary CD138+ MM cells  were obtained from the BM aspirates of MM patients pre- and post- treatment with anti-GPRC5D T cell engagers treatment, using positive selection with CD138 microbeads (Miltenyi Biotech, Auburn, CA) and accordingly to manufacturer’s instructions.
For single-cell library preparation for ATAC-seq the desired number of nuclei were targeted and processed according to 10X Genomics Reagent Kits User Guide (CG000168). The Nuclei Isolation was performed ad indicated in the nuclei Isolation protocol for Single Cell ATAC Sequencing (10x Genomics). Based on the starting number of cells and desired final nuclei concentration primary MM cells were washed, lysed and re-suspended in appropriate volume of chilled Diluted Nuclei Buffer. The resulting nuclei were then immediately used to generate scATAC-seq libraries. ScATAC-seq libraries were prepared according to 10X Genomics Reagent Kits User Guide. Briefly, the desired number of nuclei were combined with ATAC Buffer and master mix to form transposed Nuclei. Single-cell GEMs were then generated, amplified and subjected to bead clean-ups. Indexed sequencing libraries were constructed using Chromium i7 Sample Index and the barcode sequencing libraries subjected to a final bead clean-up prior to quantification.

value: Bone marrow

tag: disease state

value: multiple myeloma

tag: batch


title: Patient_P4520_ATAC_MM_Post_Treatment

description: Library name: P4520_ATAC_MM

tag: tissue


title: ChIP_MCF10AT1_H3K4me3_rep1

tag: cell line


title: Patient_P4585_ATAC_MM_Pre_Treatment

description: Library name: P4585_ATAC_MM

tag: cell type


title: ChIP_MCF10CA1a_H3K4me3_rep1


title: ChIP_MCF10A_H3K27ac_rep1


title: Patient_P1695_MM_Pre_Treatment

description: Library name: P1695_MM

extract_protocol:
Primary CD138+ MM cells  were obtained from the BM aspirates of MM patients pre- and post- treatment with anti-GPRC5D T cell engagers treatment, using positive selection with CD138 microbeads (Miltenyi Biotech, Auburn, CA) and accordingly to manufacturer’s instructions.
Single-cell library preparation for RNA-sequencing primary MM CD138+ cells were processed according to 10X Genomics reagent Kits User Guide (CG00052 v2 Chemistry). Cells were partitioned into nanoliter-scale Gel Bead-In-Emulsions (GEMs) using 10X GemCode Technology. Primers containing (i) an Illumina R1 sequence, (ii) a 16 bp 10x barcode, (iii) a 10 bp Unique Molecular Identifier (UMI) and (iv) a poly-dT primer sequence were incubated with partitioned cells resulting in barcoded, full-length cDNA from poly-adenylated mRNA. Silane magnetic beads were used to remove leftover biochemical reagents/primers, then cDNA was amplified by PCR. Enzymatic Fragmentation and Size Selection was used to optimize cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) were added during GEM incubation, whereas P5, P7, a sample index (i7), and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation and PCR.


title: Patient_P4585_MM_Pre_Treatment

description: Library name: P4585_MM


title: input_unstim_siIGF2BP3_5

city: London

first: Paniz

last: Khooshemehri

address: Great Maze Pond

department: Infectious diseases

country: United Kingdom

institute: King's college London

description: Library name: SAMPLE 39

data_processing:
CGC cloud platform for QC (multiQC), trimming (trimmomatic) and alignment (Salmon index & quant)
R studio for differential gene expression (DESeq2)
Assembly: gencode.v34
Supplementary files format and content: quant file - output from salmon

growth_protocol: shControl and shIGF2BP3 constitutive cell lines were grown in RPMI 10%FBS.Cells were starved in 2% media overnight and stimulated with 100 ng/ml IL-13 cytokine and harvested 24h later for Frac-seq.

extract_protocol:
TRIzol LS followed by DNAse digestion and lilbrary prep using polyA selection and Ultra II Stranded Library prep (NEB)
Stranded, paired-end sequencing libraries were prepared according to Illumina protocols using Truseq kit

value: Immortalized human lung epithelial cells

tag: genotype

value: knockdown

value: unstim

tag: fraction

value: input


title: Patient_P1858_MM_Pre_Treatment

description: Library name: P1858_MM


title: ChIP_MCF10CA1a_H3K27ac_rep1


title: ChIP_MCF10CA1a_H3K27me3_rep1


title: ChIP_MCF10AT1_H3K9me3_rep2


title: ChIP_MCF10CA1a_H3K27me3_rep2


title: input_IL13_siC_5

description: Library name: SAMPLE 38

value: control

tag: treatment


title: input_IL13_siIGF2BP3_5

description: Library name: SAMPLE 40


title: Patient_P1695_ATAC_MM_Pre_Treatment

description: Library name: P1695_ATAC_MM


title: Patient_P4520_MM_Post_Treatment

description: Library name: P4520_MM


title: ChIP_MCF10DCIS_H3K4me3_rep1


title: ChIP_MCF10DCIS_H3K27me3_rep2


title: input_unstim_siC_5

description: Library name: SAMPLE 37


title: polysome_unstim_siIGF2BP3_5

description: Library name: SAMPLE 35

value: polysome


title: polysome_IL13_siIGF2BP3_5

description: Library name: SAMPLE 36


title: ChIP_MCF10DCIS_H3K27me3_rep1


title: Bulk human ILC2 transcriptome, University of North Carolina - Set 3

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

address: 125 Mason Farm Road, CB #7599 5105-5106 Marsico Hall

institute: University of North Carolina at Chapel Hill

description: Library name: Serody_23_Bulk

data_processing:
Sequencing QA with FastQC v0.11.9 and Picard v2.22.4
Alignment with STAR v2.4.2
Quantified with Salmon v1.4.0
Differential gene expression with DESeq2 v1.34.0
Assembly: Hg38
Supplementary files format and content: Salmon count data

growth_protocol: ILC2 cells were enriched from a non-mobilized peripheral blood leukapheresis product by RosetteSep human ILC2 enrichment kit according to the manufacturer’s instructions. ILC2s were cultured in aMEM with 20% fetal bovine serum, with 1% penicillin/streptomycin with cytokine described as follows. Recombinant human IL-2, IL-7, IL-4, IL-17E (IL-25), IL-33 and TSLP were used for expansion in culture.

extract_protocol:
ILC2 cells were prepared in suspension and nuclei were isolated by pelleting 25,000–200,000 in a fixed-angle centrifuge before total RNA extraction.
Illumina TruSeq Stranded mRNA Prep

treatment_protocol: ILC2 cells were cultured as described above and RNA was extracted after expansion followed by cDNA synthesis and genomic DNA elimination prior to PCR amplification.


title: polysome_IL13_siC_5

description: Library name: SAMPLE 34


title: Bulk human ILC2 transcriptome, University of North Carolina - Set 2

description: Library name: Serody_22_Bulk


title: ChIP_MCF10AT1_H3K27me3_rep2


title: P6_cWT_M_Jejunum_L41830-8

city: Durham

first: Staci

last: Bilbo

state: North Carolina

address: 207 Research Dr, GSRB2

department: Psychology and Neuroscience

institute: Duke University

description: Library name: Sample12

data_processing:
Trimmomatic(v0.38) was used to trim sequencing adapters
Reads were aligned to the mouse genome (mm10)  using STAR 2.5.3.a
Reads were counted using featureCounts in the Subread package (v1.6.3)
Assembly: mm10
Supplementary files format and content: tab-delimited text files includes counts for each sample

source_name: Intestine

extract_protocol:
The small intestine was dissected and a 2 cm segment of the region of interested was collected and opended. The flat tissue sheet was in HBSS with EDTA for ~15 mins and the epithelial cells were released by using mechanical force. Epithelial cells were washed 2 times in HBSS then snap frozen in liquid nitrogen. Total RNA was extracted using trizol.
RNA-sequencing libraries were made from ≥500ng of purified mouse intestinal cells using the Kapa Stranded mRNA-seq kit

value: Intestine

tag: tissue region

value: Jejunum

tag: Sex

value: Male

value: Dab2 cWT


title: polysome_unstim_siC_5

description: Library name: SAMPLE 33


title: ChIP_MCF10AT1_H3K27me3_rep1


title: P6_cWT_M_Jejunum_L41820-1

description: Library name: Sample11

tag: age


title: input_IL13_siIGF2BP3_4

description: Library name: SAMPLE 32


title: Bulk human ILC2 transcriptome, University of Minnesota - Set 2

description: Library name: Blazar_46_Bulk


title: Fallopian tube_normal tissue_N7

type: RNA

city: Harbin

first: Mengke

last: Yuan

state: Heilongjiang

address: 24 heping, xiangfang

institute: Heilongjiang University of Chinese Medicine

hyb_protocol: cRNAs were fragmented and hybridized in reference to Agilent Human ceRNA The Microarray 2019 (4*180k, Design ID: 086188, Agilent) chip process instruction. Gene Expression Wash Pack (Agilent) was adapted to wash the chip

scan_protocol: Slides were scanned immediately by DNA microarray scanner (Agilent)

data_processing: Microarray array images were examined with Feature Extraction software (version10.7.1.1, Agilent Technologies), and raw data extracted from images were processed into quantile normalization form through Gene Spring GX

source_name: Fallopian tube, collected from the patients who suffered from hysteromyoma during their total hysterectomy and bilateral adnexectomy

label_protocol: RNAs were amplified and labeled by Cy3 using Low Input Quick Amp Labeling Kit, One-color (Agilent, Santa Clara, CA). QIAGEN RNeasy Mini kit (Qiagen) was applied to purify the labeled cRNAs

growth_protocol: After the residues of blood and other impurities were removed from them by PBS, the samples were stored in -80 ℃ refrigerator

extract_protocol: Total RNAs were extracted and purified using the QIAGEN miRNeasy Micro Kit (QIAGEN, Hilden, Germany), and qualified by NanoDrop ND-2000 (Thermo Scientific), and their integrality was tested by Agilent Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA)

tag: tissure

value: Fallopian tube

tag: gender

value: female

tag: subject status

value: normal tissure was comfirmed through confirmed through postoperative pathology


title: Fallopian tube_normal tissue_N6


title: input_unstim_siIGF2BP3_4

description: Library name: SAMPLE 31


title: ChIP_MCF10A_H3K27me3_rep2


title: Bulk human ILC2 transcriptome, University of Minnesota - Set 1

description: Library name: Blazar_45_Bulk


title: P6_cWT_M_Jejunum_L41662-1

description: Library name: Sample10


title: Human ILC2 ATAC Library - Donor B

description: Library name: Serody_2B_ATAC

data_processing:
QC with FastQC v0.11.9
Adapter trimming with Trim Galore! V0.6.7
Alignment with BWA v0.7.17
Duplicate marking  and alignments merged with picard v3.0.0
Peak calling with MACS2 v2.2.7.1
Concensus peak set created with BEDTools v2.30.0
Data processing coordinated with nf-core ATACseq v2.1.2
Assembly: Hg38
Supplementary files format and content: library-normalized bigWig files of processed ATAC-seq reads

growth_protocol: ILC2 cells were enriched from a non-mobilized peripheral blood leukapheresis product by RosetteSep human ILC2 enrichment kit according to the manufacturer’s instructions. ILC2s were cultured in alpha Minimum Essential Media with 20% fetal bovine serum, with 1% penicillin/streptomycin with cytokine combinations as described in a 5% CO2 incubator at 37°C. Recombinant human IL-2, IL-7, IL-4, IL-17E (IL-25), IL-33 and TSLP were used for expansion in culture.

extract_protocol:
Cells of interest were prepared in suspension and nuclei were isolated by pelleting 25,000–200,000 in a fixed-angle centrifuge. Cells were lysed with 10 mM Tris-HCl (pH 7.4), 10 mM NaCl, and 3 mM MgCl2 prior to 30 min of transposition with an in house Tn5 transposase (generated at UNC CICBDD with Addgene construct #60240 as adapted from Picelli et al., Genome Res, 2014) at 37 °C. Immediately following transposition, samples were purified with Zymo Conc & Clean (Genesee) and stored at −20 °C prior to library amplification.
Fragments were amplified using 1× NEBnext PCR master mix (New England BioSciences) and custom Nextera PCR primers 1 and 2 (Illumina). Full libraries were amplified for five cycles (Thermo Fisher), after which a test aliquot of each sample was taken to test 20 cycles to determine the additional number of cycles needed for the remaining 45 μL reaction (QuantStudio 6 K, Applied Biosystems). After the additional cycles were complete (average of 5–15 additional cycles), libraries were purified using a Zymo Conc & Clean (Genesee) prior to a two-sided Ampure bead (Beckman Coulter) size selection to enrich nucleosome-free fragments. Fragment size and concentration were determined by TapeStation 2000 and Qubit 4 (Agilent). Following QAQC, samples were sequenced on the Illumina HiSeq4000 (75x paired-end HO).


title: ChIP_MCF10DCIS_H3K4me1_rep2


title: Fallopian tube_chonic salpingitis_N9

source_name: Fallopian tube, collected during  unilateral or bilateral adnexectomy operation of patients who had hydrosalpinx or empyema

value: chonic salpingitis was comfirmed through confirmed through postoperative pathology


title: Fallopian tube_normal tissue_N4


title: Bulk human ILC2 transcriptome, University of North Carolina - Set 1

description: Library name: Serody_21_Bulk


title: input_unstim_siC_4

description: Library name: SAMPLE 29


title: Fallopian tube_chonic salpingitis_N3


title: Human ILC2 ATAC Library - Donor A

description: Library name: Serody_2A_ATAC


title: ChIP_MCF10DCIS_H3K4me1_rep1


title: P6_cWT_M_Ileum_L41830-8

description: Library name: Sample9

value: Ileum


title: ChIP_MCF10A_H3K27me3_rep1


title: Fallopian tube_chonic salpingitis_N1


title: polysome_IL13_siIGF2BP3_4

description: Library name: SAMPLE 28


title: Fallopian tube_normal tissue_N2


title: Small RNA-Seq sample of CIPD in Rat_LPD_3

city: Hyderabad

first: Pankaj

middle: Singh

last: Dholaniya

state: Telangana

address: S46 School of Life Sciences

department: Biotechnology and Bioinformatics

country: India

institute: University of Hyderabad

description: Library name: LPD_3

data_processing:
Raw reads were checked for different quality parameters, including: phred score, length, contamination, GC%, etc. Depending on the Raw data QC, we used the Fastp filtration tool to filter out high-quality reads from the raw data. quality control, adapter trimming, quality filtering, per-read quality pruning and many other operations with a single scan of the FASTQ data.
Assembly: mRatBN7.2
Supplementary files format and content: .tsv

organism: Rattus norvegicus

source_name: Serum

extract_protocol:
Total small RNA was isolated using miRNeasy serum Advanced serum kit and followed the manufacturer instructions
For RNA Sequencing library was prepared using QIAseq® miRNA Library Kit

treatment_protocol: All rats from different groups of rats were treated using Rotenone, a herbicide which modulated the function of oxidative pathyays and hampered the ATP production.

value: Serum

value: Wildtype

value: RIPD


title: input_IL13_siC_4

description: Library name: SAMPLE 30

value: Immortalized human lung epithelial cells


title: Fallopian tube_chonic salpingitis_N5


title: P6_cWT_M_Ileum_L41820-1

description: Library name: Sample8


title: P6_cKO_M_Jejunum_L41830-2

description: Library name: Sample6

value: Dab2 cKO


title: P6_cKO_M_Jejunum_L41820-3

description: Library name: Sample5


title: ChIP_MCF10CA1a_H3K4me1_rep1


title: polysome_unstim_siIGF2BP3_4

description: Library name: SAMPLE 27

value: knockdown

value: unstim


title: P6_cWT_M_Ileum_L41662-1

description: Library name: Sample7


title: ChIP_MCF10CA1a_H3K4me1_rep2


title: polysome_IL13_siC_4

description: Library name: SAMPLE 26

value: control

value: polysome


title: Small RNA-Seq sample of CIPD in Rat_LPD_2

description: Library name: LPD_2


title: ChIP_MCF10AT1_H3K4me1_rep2


title: polysome_unstim_siC_4

description: Library name: SAMPLE 25


title: P6_cKO_M_Jejunum_L41662-7

description: Library name: Sample4

value: Intestine

value: Jejunum


title: Small RNA-Seq sample of CIPD in Rat_LPD_1

description: Library name: LPD_1


title: input_IL13_siIGF2BP3_3

description: Library name: SAMPLE 24

value: input


title: Small RNA-Seq sample of CIPD in Rat_EPD_2

description: Library name: EPD_2


title: ChIP_MCF10A_H3K4me1_rep2


title: P6_cKO_M_Ileum_L41830-2

description: Library name: Sample3

value: Male


title: Small RNA-Seq sample of CIPD in Rat_EPD_3

description: Library name: EPD_3


title: input_unstim_siIGF2BP3_3

description: Library name: SAMPLE 23


title: ChIP_MCF10A_H3K4me1_rep1


title: P6_cKO_M_Ileum_L41820-3

description: Library name: Sample2


title: Small RNA-Seq sample of CIPD in Rat_EPD_1

description: Library name: EPD_1


title: input_IL13_siC_3

description: Library name: SAMPLE 22


title: ChIP_MCF10DCIS_H4K8ac_rep2

value: epicypher 19091001


title: Small RNA-Seq sample of CIPD in Rat_Control_3

description: Library name: CNT_3


title: P6_cKO_M_Ileum_L41662-7

description: Library name: Sample1


title: input_unstim_siC_3

description: Library name: SAMPLE 21


title: Small RNA-Seq sample of CIPD in Rat_Control_2

description: Library name: CNT_2


title: XEN_DeltXp2_Xist_VP1-rep2

city: Bangalore

first: SRIMONTA

last: GAYEN

state: Karnataka

address: GE14, new biological science building, Indian institute of Science

department: Department of Developmental biology and Genetics

institute: Indian Institute of Science, Bangalore, India

description: Library name: Sample 6

data_processing:
4C-seq data was processed using the R tool pipe-4C (v1.16) (https://github.com/deLaatLab/pipe4C)
Assembly: mm10
Supplementary files format and content: bigWig
Library strategy: 4C-Seq

source_name: XEN

growth_protocol: XEN cells were cultures in DMEM supplemented with FBS, L-glutamine, Pen-strep, NEAA etc.

extract_protocol:
XEN cells were fixed with formaldehyde and scrapped to isolate the nuclei. 4C DNA was prepared for library after two round of restriction digestion and ligation.
4C-seq library was prepared following  a in house Illumina compatible protocol.

value: XEN

tag: breed

value: Hybrid (Mus musculus molossinus X Mus musculus)

value: Extra-embryonic endoderm stem cell

value: WT


title: ChIP_MCF10DCIS_H4K8ac_rep1


title: polysome_IL13_siIGF2BP3_3

description: Library name: SAMPLE 20


title: XEN_DeltXp1_Xist_VP1-rep2

description: Library name: Sample 4


title: Small RNA-Seq sample of CIPD in Rat_Control_1

description: Library name: CNT_1

value: Serum

value: Wildtype


title: ChIP_MCF10AT1_H3K4me1_rep1


title: XEN_DeltXp1_Xist_VP1-rep1

description: Library name: Sample 3


title: polysome_IL13_siC_3

description: Library name: SAMPLE 18

value: Immortalized human lung epithelial cells


title: hid2, dehydrated (4 h), rep 3

city: Changchun

first: Liangliang

last: Li

address: 4888 Shengbei Street, Kuancheng District

department: Northeast Institute of Geography and Agroecology

institute: Chinese Academy of Sciences

description: Library name: hid2-4 h-3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0). The parameters were as follows: 1) removing reads containing adapters; 2) removing reads containing more than 10% of unknown nucleotides(N); 3) removing low quality reads containing more than 50% of low quality (Q-value≤20) bases.
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
An index of the reference genome was built, and paired-end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default.
The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference-based approach. For each transcription region, a TPM (Transcripts Per Kilobase of exon model per Million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Correlation analysis was performed by R. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1, the better the repeatability between two parallel experiments. Principal component analysis (PCA) was performed with R package gmodels (http://www.r-project.org/) in this experience. PCA is a statistical procedure that converts hundreds of thousands of correlated variables (gene expression) into a set of values of linearly uncorrelated variables called principal components. PCA is largely used to reveal the structure/relationship of the samples/datas.
RNAs differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes/transcripts with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts.
Assembly: tair_TAIR10
Supplementary files format and content: The txt files include the AGI code, count and FPKM for each sample.

organism: Arabidopsis thaliana

source_name: Rosette leaves

growth_protocol: 12-day-old WT and hid2 mutant seedlings were transferred from 1/2 Murashige and Skoog (MS) plates to soil and grown for 12 additional day.

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo (dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#7530,New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired. A base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X).And polymerase chain reaction (PCR) amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000.

treatment_protocol: The rosette leaves of 24-day-old WT and hid2 mutant seedlings were harvested after dehydration for 0, 2, and 4 h, and then frozen in liquid nitrogen immediately.

value: Rosette leaves

value: hid2 mutant

value: dehydrated (4 h)

tag: replicate

value: replicate 3


title: WT_XEN_Xist_VP1-rep2

description: Library name: Sample 2


title: ChIP_MCF10CA1a_H4K8ac_rep1

tag: chip antibody


title: WT_XEN_Xist_VP1-rep1

description: Library name: Sample 1


title: hid2, dehydrated (4 h), rep 2

description: Library name: hid2-4 h-2

value: replicate 2


title: input_IL13_siIGF2BP3_2

description: Library name: SAMPLE 16

value: knockdown


title: hid2, dehydrated (4 h), rep 1

description: Library name: hid2-4 h-1

value: replicate 1


title: ChIP_MCF10CA1a_H4K5ac_rep2

value: invitrogen WE3292211


title: input_unstim_siIGF2BP3_2

description: Library name: SAMPLE 15

value: unstim

value: input


title: ChIP_MCF10DCIS_H4K5ac_rep2


title: polysome_unstim_siIGF2BP3_3

description: Library name: SAMPLE 19

value: polysome


title: ChIP_MCF10CA1a_H4K5ac_rep1


title: input_IL13_siC_2

description: Library name: SAMPLE 14

value: control


title: ChIP_MCF10AT1_H4K8ac_rep2

value: epicypher 19091001


title: ChIP_MCF10AT1_H4K8ac_rep1


title: ChIP_MCF10DCIS_H4K5ac_rep1


title: 7160

first: Zilong

last: Geng

address: 800 Dongchuan Rd, Minhang District, Shanghai, China

institute: Shanghai Jiao Tong University

description:
RH_RQ.csv
RH_RQ_DEG.csv

data_processing:
The resulting FASTQ files were aligned to the mouse reference genome (mm10) using HISAT2
mRNA abundance was quantified in counts per million (CPM) by HTseq
Differential expression analysis was conducted using DESeq2
Assembly: mm10
Supplementary files format and content: All processed files are in CSV format, containing the results of transcriptomic differential analysis statistics.

source_name: heart

extract_protocol:
Total RNA was then extracted and purified using the RNAprep Pure Micro Kit (TIANGEN).
mRNA was purified from 1μg of total RNA using poly-T oligo magnetic beads, and the libraries were constructed using the TIANSeq Fast RNA Library Kit (TIANGEN ).

value: heart


title: hid2, dehydrated (2 h), rep 4

description: Library name: hid2-2 h-4

value: dehydrated (2 h)

value: replicate 4


title: hid2, dehydrated (2 h), rep 2

description: Library name: hid2-2 h-2


title: Input

city: Chongqing

first: Ting

last: Zeng

address: No. 1 Medical College Road

institute: Chongqing medical university

description: Library name: Sample 1

data_processing:
Library Preparation and Quantification, Quality control for raw data, Reads mapping to the reference genome, Peak detection, Peak annotation, Peak annotation
Library quality was assessed on the Agilent Bioanalyzer 2100 system. The libraries were sequenced on an Illumina Novaseq platform with a paired-end read length of 150 bp according to the standard protocols
Raw data of fastq format were firstly processed using fastp software
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. After mapping reads to the reference genome, we used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. Different peak analysis was based on the fold enrichment of peaks of different experiments.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes peak foldenrichment

source_name: iWAT SVF differentiated adipocytes

extract_protocol:
RIP experiment was conducted according to millipore RIP kit construction.Total RNA was harvested using Trizol (Invitrogen). Total RNA was used for the construction of sequencing libraries.
The RNA fragment size distribution and concentration of the immunoprecipitated (IP) products were analyzed using an Agilent 2100 Bioanalyzer (Agilent Technologies) and a simpleNano spectrophotometer (GE Healthcare). Subsequently, the IP and Input libraries were constructed with the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs, E7770). Library quality was verified on the Agilent 2100 Bioanalyzer. Paired-end sequencing (PE150) was performed on the Illumina NovaSeq platform.

value: iWAT SVF differentiated adipocytes

value: WT

value: isoproterenol

tag: antibody

value: Input


title: 6160

description:
RH_RQ.csv
RH_RQ_DEG.csv


title: hid2, dehydrated (2 h), rep 3

description: Library name: hid2-2 h-3

value: Rosette leaves

value: hid2 mutant

value: replicate 3


title: hid2, dehydrated (4 h), rep 4

description: Library name: hid2-4 h-4

value: dehydrated (4 h)


title: polysome_unstim_siC_3

description: Library name: SAMPLE 17

value: Immortalized human lung epithelial cells


title: polysome_IL13_siIGF2BP3_2

description: Library name: SAMPLE 12

value: knockdown


title: hid2, dehydrated (2 h), rep 1

description: Library name: hid2-2 h-1

value: replicate 1


title: ChIP_MCF10AT1_H4K5ac_rep2

value: invitrogen WE3292211


title: polysome_unstim_siIGF2BP3_2

description: Library name: SAMPLE 11

value: unstim

value: polysome


title: hid2, dehydrated (0 h), rep 4

description: Library name: hid2-0 h-4

value: dehydrated (0 h)


title: IP

description: Library name: Sample 2

value: CELF1 antibody


title: ChIP_MCF10AT1_H4K5ac_rep1


title: polysome_IL13_siC_2

description: Library name: SAMPLE 10

value: control


title: hid2, dehydrated (0 h), rep 3

description: Library name: hid2-0 h-3


title: input_unstim_siC_2

description: Library name: SAMPLE 13

value: input


title: 7159

description:
RH.csv
RH_DEG.csv

value: heart

value: vehicle


title: ChIP_MCF10A_H4K8ac_rep2

value: epicypher 19091001


title: XEN_DeltXp2_Xist_VP1-rep1

description: Library name: Sample 5

value: XEN

value: Hybrid (Mus musculus molossinus X Mus musculus)

value: Extra-embryonic endoderm stem cell

value: WT


title: polysome_unstim_siC_2

description: Library name: SAMPLE 9

value: Immortalized human lung epithelial cells


title: ChIP_MCF10A_H4K8ac_rep1


title: hid2, dehydrated (0 h), rep 1

description: Library name: hid2-0 h-1

value: Rosette leaves

value: hid2 mutant


title: hid2, dehydrated (0 h), rep 2

description: Library name: hid2-0 h-2

value: replicate 2


title: knockout MSc, d7, Has-tKO-M264

city: Leipzig

first: Ulf

last: Anderegg

address: Johannisallee 30

department: Dept. of Dermatology

institute: Leipzig University, Faculty of Medicine

data_processing:
demultiplexing with bcl2fastq software (Illumina, v2.20)
polishing using fastp (Chen et al., 2018)
Reads were mapped against the mouse reference genome (hg38) using HISAT2.
Stringtie and the R package Ballgown [49] were employed to calculate differential expression.
Expression data were normalized using the DESeq2 R bioconductor package.
Assembly: GRCm39
Supplementary files format and content: Excel file includes DESeq2 R bioconductor package processed counts for each sample
Supplementary files format and content: tab-delimited txt files include FPKM for each sample

source_name: bone

growth_protocol: Mesenchymal stem cells were purified from femora and tibiae of the hind legs of wildtype and Has-tKO mice (n=4). The cells were cultured for 4 passages in a-MEM (Lonza, 12-169) supplemented with stabilized glutamine (ThermoFisherScientific, 25030081) and 10% FCS (anprotec, AC-SM-0190). Addition of 4-hydroxytamoxifen (2mM, Hycultec, HY-16950) for 48h during passages 2 and 3 introduced the inducible knockout of Has2 in the cells which was verified by HA-ELISA of the supernatants and Has2-qRT PCR.

extract_protocol:
RNA was isolated using the column extraction kit ReliaPrep™ RNA Miniprep System (Promega, Z6112).
Briefly,100 ng of total RNA was depleted of ribosomal RNA using the NEBNext® rRNA Depletion Kit v2 (NEB) according to the instructions of the manufacturer. Depleted RNA was transcribed using SuperScript IV reverse transcriptase (ThermoFisher, 18090200) for 2 h at 55°C. After second strand synthesis (TargetAmp kit, Epicentre). DNA was treated with the Illumina Tagment DNA TDE1 Enzyme and Buffer Kits, which fragments the DNA and inserts partial sequencing adapter (Nextera) sequences. Final PCR amplification of the libraries was done using KAPA HiFi HotStart Library Amplification Kit with unique dual indexing by IDT® for Illumina Nextera DNA Unique Dual Indexes Sets. The purified barcoded libraries were quantified using Qubit Fluorometric Quantification (ThermoFischer Scientific). The size distribution of the library DNA was analyzed using the FragmentAnalyzer (Agilent).

treatment_protocol: Osteogenic differentiation of 3d confluent cultures was induced with the StemXVivo Osteogenic medium and supplement (Biotechne, CCM007/9) for 7 days with medium exchange every 3 days.

value: bone

value: differentiating MSc

value: Has-tKO

tag: time


title: input_IL13_siIGF2BP3_1

description: Library name: SAMPLE 8

value: knockdown


title: input_unstim_siIGF2BP3_1

description: Library name: SAMPLE 7

value: unstim


title: 7162

city: Shanghai

description:
RH_RQ.csv
RH_RQ_DEG.csv
RH.csv
RH_DEG.csv

tag: tissue


title: ChIP_MCF10DCIS_input

description: MCF10DCIS input

tag: cell line


title: knockout MSc, d7, Has-tKO-M263

tag: cell type


title: ChIP_MCF10A_H4K5ac_rep1

value: invitrogen WE3292211


title: 6159

description:
RH.csv
RH_DEG.csv

value: heart

tag: genotype


title: ChIP_MCF10A_H4K5ac_rep2


title: WT, dehydrated (4 h), rep 4

description: Library name: WT-4 h-4

value: dehydrated (4 h)

value: replicate 4


title: WT, dehydrated (4 h), rep 3

description: Library name: WT-4 h-3

value: replicate 3


title: input_IL13_siC_1

description: Library name: SAMPLE 6

value: control

tag: fraction

value: input


title: input_unstim_siC_1

description: Library name: SAMPLE 5

tag: treatment


title: 6162

value: vehicle


title: knockout MSc, d7, Has-tKO-M262


title: ChIP_MCF10CA1a_input

description: MCF10CA1a input


title: WT, dehydrated (4 h), rep 2

description: Library name: WT-4 h-2

value: WT


title: polysome_IL13_siIGF2BP3_1

description: Library name: SAMPLE 4

value: Immortalized human lung epithelial cells

value: polysome


title: knockout MSc, d7, Has-tKO-M261


title: ChIP_MCF10CA1a_H4K8ac_rep2

value: epicypher 19091001


title: WT, dehydrated (4 h), rep 1

description: Library name: WT-4 h-1

value: Rosette leaves

value: replicate 1


title: wildtype MSc, d7, WT4

value: bone

value: differentiating MSc

value: wildtype


title: polysome_unstim_siIGF2BP3_1

description: Library name: SAMPLE 3

value: knockdown

value: unstim


title: ChIP_MCF10A_input

description: MCF10A input


title: WT, dehydrated (2 h), rep 4

description: Library name: WT-2 h-4

value: dehydrated (2 h)


title: wildtype MSc, d7, WT3


title: WT, dehydrated (2 h), rep 3

description: Library name: WT-2 h-3


title: SKOV3 cells, LDL treatment group, T3

first: Song

last: Tang

address: School of Medicine C233, Zijingang Campus of Zhejiang University, 866 Yuhangtang Road, Hangzhou, P.R. China.

description: Library name: Sample 7

data_processing:
Raw sequence reads were mapped to the reference genome (Homo sapiens, ensemble, GRCh38) using Hisat2 tools soft.
Numbers of reads assigned to genes were counted by featureCounts.
Differential expression analysis of two conditions/groups was performed using the DESeq2 R package (1.26.0).
Assembly: GRCh38
Supplementary files format and content: txt file includes raw counts for each sample
Supplementary files format and content: txt file includes fpkm values for each sample

growth_protocol: SKOV3 cells were maintained in McCoy’s 5A medium (Gibco, USA) supplemented with 10% fetal bovine serum (FBS) and antibiotics, incubated in 37°C, 5% CO2 condition

extract_protocol:
Total RNA of SKOV3 cells was extracted Trizol reagent (B511311, Sangon Biotech, China) following the manufacturer’s instructions. 2μg of total RNA was used for the construction of sequencing libraries.
RNA libraries were constructed according to the illumina's instructions using TruSeq Stranded mRNA Kit.

treatment_protocol: The control groups (C1-4) were cultured with ordinary medium, while the treatment groups (T1-4) were treated with 50 μg/mL LDL for 48 hours.

value: Ovarian cancer cells

value: LDL treatment


title: polysome_unstim_siC_1

description: Library name: SAMPLE 1

value: control


title: wildtype MSc, d7, WT2


title: SKOV3 cells, LDL treatment group, T4

description: Library name: Sample 8


title: polysome_IL13_siC_1

description: Library name: SAMPLE 2


title: WT, dehydrated (2 h), rep 2

description: Library name: WT-2 h-2

value: replicate 2


title: SKOV3 cells, LDL treatment group, T2

description: Library name: Sample 6


title: SARS_96H

city: Melbourne

first: Dylan

last: Sheerin

state: VIC

address: 1G Royal Parade

country: Australia

institute: WEHI

data_processing:
Fastq files were QC'd using fastQC
Fastq files were aligned to the reference genome and transcripts were quantified using the Honeycomb beenet pipeline.
Assembly: GRCh38
Supplementary files format and content: tab-separated variable files include transcript count information for each sample

source_name: Whole blood cells

extract_protocol:
A total of eight Honeycomb HIVE devices, one device per condition, were loaded with 30,000 cells each and processed as per manufacturer's instructions to generate cDNA libraries
cDNA libraries were sequenced using an Illumina NextSeq500 instrument and with custom primers provided by Honeycomb Biotechnologies.

treatment_protocol: Human blood samples were infected with the indicated pathogen for 24 or 96 hours, or left uninfected for the same time intervals.

value: Whole blood cells

value: 96h post-infection


title: wildtype MSc, d7, WT1


title: UN_96H

value: Uninfected


title: WT, dehydrated (2 h), rep 1

description: Library name: WT-2 h-1

value: WT


title: WT, dehydrated (0 h), rep 3

description: Library name: WT-0 h-3

value: dehydrated (0 h)

value: replicate 3


title: SKOV3 cells, control group, C4

description: Library name: Sample 4

value: Without special treatment


title: CO_96H

value: Mycobacterium tuberculosis + SARS-CoV-2


title: WT, dehydrated (0 h), rep 4

description: Library name: WT-0 h-4

value: Rosette leaves

value: replicate 4


title: home_cage_r2

city: Blacksburg

first: Timothy

last: Jarome

address: Mail Stop: 0306,ANIMAL SCIENCES  MC0306,LITTON REEVES   STE 3490

institute: Virginia Tech

description: FFPE spatial transcriptome sequencing

data_processing:
The FFPE Visium sequencing reads were mapped to the mouse reference genome (mm10) using the short-read probe alignment algorithm for FFPE ‘count’ method in Space Ranger (v2.1.0) from the 10x Genomics.
The FFPE Visium data was filtered by (1) removal of spots with fewer than 100 unique genes, (2) removal of spots with fewer than 500 unique molecular identifiers (UMIs).
Normalization, dimensionality reduction, clustering, UMAP embedding and Marker genes identification were conducted using the Seurat R package (v5.0.3).
The differential gene expression analysis was performed using FindMarkers function, which applies a pairwise Wilcoxon Rank Sum test the spots within the same cluster between CFC and CC groups.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz:list of spatial barcodes
Supplementary files format and content: features.tsv: list of gene lDs
Supplementary files format and content: matrix.mtx.gz: gene expresion count data in Matrix Market Exchange Format
Supplementary files format and content: aligned fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected tissue image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors json.json.gz: scalefactors in json format
Supplementary files format and content: tissue hires image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue lowres image.png.gz: low-res image of tissue
Supplementary files format and content: tissue positions list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics

source_name: brain

growth_protocol: Adult male C57BL/6J mice (12 weeks) were purchased from Jaxson laboratory and maintained in a 12-hour light/dark cycle under standard pathogen-free conditions.

extract_protocol:
Mice were harvested and fresh mouse brain tissues were fixed in 10% neutral buffered formalin (NBF) at room temperature (RT) overnight for preparing formalin-fixed paraffin-embedded (FFPE) tissue blocks.
Visium Spatial Gene Expression (VGSE) libraries were prepared using the Visium Spatial Gene Expression Slide Kit (10x genomics, cat# PN-1000185) following the manufacturer’s User Guide (CG000407).

treatment_protocol: Adult C57BL/6 male mice (12~15 weeks) were subjected to contextual fear conditioning (CFC), mice without foot shock were used as context control (CC), and mice stayed in the home cage until sample harvest were used as home cage control (HC). Mice were harvested 1h or 4h after foot shock on the training day (day 0) and 4h after memory retrieval on day 1 to assess fear memory consolidation and reconsolidation.

value: brain

value: wild-type

tag: day

tag: time after_foot_shock


title: home_cage_r1

description: FFPE spatial transcriptome sequencing


title: SKOV3 cells, control group, C3

description: Library name: Sample 3


title: ChIP_MCF10AT1_input

description: MCF10AT1 input

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching with 0.125M glycine and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the NEB UltraII Library Preparation Kit according to manufacturer's instructions.


title: WT, dehydrated (0 h), rep 2

description: Library name: WT-0 h-2


title: d1_cfc_4h_r2

description: FFPE spatial transcriptome sequencing

value: cfc


title: SARS_24H

value: 24h post-infection


title: d1_cfc_4h_r1

description: FFPE spatial transcriptome sequencing


title: SKOV3 cells, control group, C2

description: Library name: Sample 2

value: Ovarian cancer cells


title: WT, dehydrated (0 h), rep 1

description: Library name: WT-0 h-1

value: replicate 1


title: d1_cc_4h_r2

description: FFPE spatial transcriptome sequencing

value: cc


title: CO_24H

value: Whole blood cells


title: SKOV3 cells, LDL treatment group, T1

description: Library name: Sample 5

value: LDL treatment


title: ncr1, dehydrated (4 h), replicate 3

description: Library name: ncr1-4 h-3

growth_protocol: 12-day-old WT and ncr1 mutant seedlings were transferred from 1/2 Murashige and Skoog (MS) plates to soil and grown for 12 additional day.

treatment_protocol: The rosette leaves of 24-day-old WT and ncr1 mutant seedlings were harvested after dehydration for 0, 2, and 4 h, and then frozen in liquid nitrogen immediately.

value: ncr1 mutant

value: dehydrated (4 h)


title: SKOV3 cells, control group, C1

description: Library name: Sample 1


title: ncr1, dehydrated (4 h), replicate 4

description: Library name: ncr1-4 h-4


title: UN_24H

value: Uninfected


title: ncr1, dehydrated (4 h), replicate 2

description: Library name: ncr1-4 h-2


title: d0_cfc_4h_r2

description: FFPE spatial transcriptome sequencing


title: WT_XEN_H3K9me3

description: Library name: Sample 11

data_processing:
Quality of ChIP-seq reads was checked
For allele-specific enrichment analysis a GRCm38 (mm10) SNP N-masked in-silico genome was created using SNPsplit genome preparation
ChIP-seq reads were mapped to the N-masked genome using Bowtie2
Enrichment was calculated using bamCompare from deeptools (v.3.5.0) with BPM normalization
Assembly: mm10
Supplementary files format and content: bigWig

extract_protocol:
ChIP was performed using the Simple ChIP Chromatin IP kit with magnetic beads (Cell Signaling Technology, #9003) following the manufacturer’s protocols.
ChIP-seq library was prepared following the manufacturer’s guidelines using the NEXTflex Rapid DNA sequencing Bundle kit (BIOO Scientific, Inc. U.S.A.) compatible with Illumina sequencing. Approximately, 1 ng of ChIP DNA was used for the library preparation.

value: XEN

tag: strain

value: Hybrid (Mus Molassinus X Mus Musculus)

value: Extra-embryonic endoderm stem cell

value: WT


title: TB_96H

value: Mycobacterium tuberculosis

value: 96h post-infection


title: ncr1, dehydrated (4 h), replicate 1

description: Library name: ncr1-4 h-1

value: Rosette leaves


title: WT_clone2_rep2

description:
Library name: Sample 9
Raw_count_WT clones.txt

data_processing:
Quality of RNA-seq reads was checked using FastQC
Reads were mapped to the mouse genome GRCm38 (mm10) using STAR (2.7.9a)
Read counting was done using featureCounts (2.0.1)
Assembly: mm10
Supplementary files format and content: text file includes raw counts for each samples

extract_protocol:
Total RNA was extracted from XEN cells following the Trizol RNA extraction method
RNA-seq library was prepared following the manufacturer’s guidelines using the NEBNext Ultra/Tru-seq stranded RNA library preparation kit for Illumina.


title: RPS4Y1 knockout cell line 48 hours after TGFb stimulation, KO 2

city: Ultimo

first: Karosham

middle: Diren

last: Reddy

state: NSW

address: 15 Broadway

department: Life Sciences

institute: University of Technology Sydney

description:
Library name: FRCB3_TGFb_48hr
FRCB3_TGFb_48hr
RPS4Y1_48hr_raw_counts.txt
RPS4Y1_48hr_normalised.txt

data_processing:
Sequenced reads were trimmed for the adaptor sequence using Trimmomatic version 0.39
Reads were aligned using STAR aligner version 2.7.4a to GRCh38
Assembly: hg38
Supplementary files format and content: tab-deliminted text files include raw CPM or log2CPM normalised values for each sample

growth_protocol: All cell lines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and 1% antibiotics/antimycotic and incubated at 37 deg celcius and 5% CO2

extract_protocol:
RNA was harvested using the Bioline Isolate II Mini RNA kit
Library construction was completed by Ramaciotti Centre for Genomics, NSW, Australia

treatment_protocol: All cell lines were serum starved (quiesced) in DMEM supplemented with 0.1% bovine serum albumin (BSA) and antibiotics/antimycotics and incubated at 37 deg celsius and 5% CO2. Cells were either left in quiescent media (not treated [NT]) or stimulated with TNF-alpha (10ng/ml) for 6 hours or with TGF-beta (10ng/ml) for 48 hours.

value: Adenocarcinomic human alveolar basal epithelial cell

value: RPS4Y1 knockout

value: TGF-beta (10ng/ml)

value: 48 hours


title: RPS4Y1 knockout cell line 48 hours after TGFb stimulation, KO 3

description:
Library name: RYF12_TGFb_48hr
RYF12_TGFb_48hr
RPS4Y1_48hr_raw_counts.txt
RPS4Y1_48hr_normalised.txt


title: d0_cfc_1h_r2

description: FFPE spatial transcriptome sequencing

value: brain

value: wild-type

value: cfc


title: Wild type cell line at baseline 48 hours after TGFb stimulation,  WT 3

description:
Library name: RC5A5_TGFb_48hr
RC5A5_TGFb_48hr
RPS4Y1_48hr_raw_counts.txt
RPS4Y1_48hr_normalised.txt

value: wild type


title: ncr1, dehydrated (2 h), replicate 3

description: Library name: ncr1-2 h-3

value: ncr1 mutant

value: dehydrated (2 h)


title: d0_cfc_1h_r1

description: FFPE spatial transcriptome sequencing


title: ncr1, dehydrated (2 h), replicate 4

description: Library name: ncr1-2 h-4


title: RPS4Y1 knockout cell line 48 hours after TGFb stimulation, KO 1

description:
Library name: RYA2_TGFb_48hr
RYA2_TGFb_48hr
RPS4Y1_48hr_raw_counts.txt
RPS4Y1_48hr_normalised.txt


title: WT_clone1_rep1

description:
Library name: Sample 8
Raw_count_WT clones.txt

value: XEN


title: WT_XEN_H3K27me3

description: Library name: Sample 10

value: Hybrid (Mus Molassinus X Mus Musculus)


title: Wild type cell line at baseline 48 hours after TGFb stimulation, WT 1

description:
Library name: RCH12_TGFb_48hr
RCH12_TGFb_48hr
RPS4Y1_48hr_raw_counts.txt
RPS4Y1_48hr_normalised.txt


title: TB_24H

value: Whole blood cells

value: 24h post-infection


title: d0_cc_4h_r2

description: FFPE spatial transcriptome sequencing

value: cc


title: XEN_Input

tag: Sex

value: Female

value: Hybrid (Mus musculus molossinus X Mus musculus)

value: Extra-embryonic endoderm stem cell

value: WT


title: d1_cc_4h_r1

description: FFPE spatial transcriptome sequencing


title: d0_cc_4h_r1

description: FFPE spatial transcriptome sequencing


title: RPS4Y1 knockout cell line 48 hours after serum starvation, KO 3

description:
Library name: RYF12_NT_48hr
RYF12_NT_48hr
RPS4Y1_48hr_raw_counts.txt
RPS4Y1_48hr_normalised.txt

value: Adenocarcinomic human alveolar basal epithelial cell

value: RPS4Y1 knockout

value: no treatment


title: ncr1, dehydrated (2 h), replicate 1

description: Library name: ncr1-2 h-1

value: Rosette leaves


title: XEN_CTCF_DeltXp_1

value: CTCF ( Diagenode, #C15410210)

value: Paternal Xist deletion


title: d0_cc_1h_r2

description: FFPE spatial transcriptome sequencing

value: brain

value: wild-type


title: RPS4Y1 knockout cell line 48 hours after serum starvation, KO 2

description:
Library name: FRCB3_NT_48hr
FRCB3_NT_48hr
RPS4Y1_48hr_raw_counts.txt
RPS4Y1_48hr_normalised.txt

value: 48 hours


title: ncr1, dehydrated (0 h), replicate 4

description: Library name: ncr1-0 h-4

value: ncr1 mutant

value: dehydrated (0 h)


title: RPS4Y1 knockout cell line 48 hours after serum starvation, KO 1

description:
Library name: RYA2_NT_48hr
RYA2_NT_48hr
RPS4Y1_48hr_raw_counts.txt
RPS4Y1_48hr_normalised.txt


title: d0_cfc_4h_r1

description: FFPE spatial transcriptome sequencing

value: cfc


title: ncr1, dehydrated (0 h), replicate 3

description: Library name: ncr1-0 h-3


title: WT_EV_3 rep3

value: XEN

value: Mus musculus molossinus X Mus musculus


title: Wild type cell line at baseline 48 hours after TGFb stimulation, WT 2

description:
Library name: RC4D3_TGFb_48hr
RC4D3_TGFb_48hr
RPS4Y1_48hr_raw_counts.txt
RPS4Y1_48hr_normalised.txt

value: wild type

value: TGF-beta (10ng/ml)


title: WT_XEN_CTCF rep1

value: Female

value: Hybrid (Mus musculus molossinus X Mus musculus)

value: Extra-embryonic endoderm stem cell

value: WT


title: WT_XEN_CTCF rep2


title: WT_EV_2 rep2


title: d0_cc_1h_r1

description: FFPE spatial transcriptome sequencing

value: cc


title: Wild type cell line at baseline 48 hours after serum starvation,  WT 3

description:
Library name: RC5A5_NT_48hr
RC5A5_NT_48hr
RPS4Y1_48hr_raw_counts.txt
RPS4Y1_48hr_normalised.txt

value: Adenocarcinomic human alveolar basal epithelial cell

value: no treatment


title: Wild type cell line at baseline 48 hours after serum starvation, WT 2

description:
Library name: RC4D3_NT_48hr
RC4D3_NT_48hr
RPS4Y1_48hr_raw_counts.txt
RPS4Y1_48hr_normalised.txt


title: XEN_Rad21_DeltXp_1 rep1

value: Rad21 (Abcam, #ab992 )

value: Paternal Xist deletion


title: ncr1, dehydrated (2 h), replicate 2

description: Library name: ncr1-2 h-2

value: Rosette leaves

value: dehydrated (2 h)


title: Wild type cell line at baseline 48 hours after serum starvation, WT 1

description:
Library name: RCH12_NT_48hr
RCH12_NT_48hr
RPS4Y1_48hr_raw_counts.txt
RPS4Y1_48hr_normalised.txt

value: 48 hours


title: WT, dehydrated (4 h), replicate 4

description: Library name: WT-4 h-4

value: dehydrated (4 h)


title: ncr1, dehydrated (0 h), replicate 2

description: Library name: ncr1-0 h-2

value: ncr1 mutant

value: dehydrated (0 h)


title: WT_XEN_Rad21

value: XEN


title: RPS4Y1 knockout cell line 6 hours after TNFa stimulation, KO 3

description:
Library name: RYF12_TNFa_6hr
RYF12_TNFa_6hr
RPS4Y1_6hr_raw_counts.txt
RPS4Y1_6hr_normalised.txt

value: RPS4Y1 knockout

value: TNF-alpha (10ng/ml)

value: 6 hours


title: WT, dehydrated (4 h), replicate 3

description: Library name: WT-4 h-3


title: WT_XEN_H3K27ac

value: Female

value: Hybrid (Mus musculus molossinus X Mus musculus)

value: Extra-embryonic endoderm stem cell


title: a, spleen

city: Beijing

first: Yujia

last: Wang

address: 38 Xueyuan Road, Haidian District

department: Department of Immunology

institute: Peking university school of basic medical sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting were made using the Cell Ranger software (https://support.10xgenomics.com/single-cell-gene-expression/software/downloads/latest)
We use Seurat(v4.0.2) to determine clusters,dimensionality reduction was performed using PCA and the first twenty principle compoments were used to generate clusters by K-means algorithm and graph-based algorithm, respectively.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: spleen

extract_protocol:
A certain number of liver/spleen lymphocytes were taken from mouse tagged with Foxp3GFP (C57BL/6), and CD4+ T cells were obtained by positive screening of CD4 (L3T4) Microbeads (Miltenyi Biotec), then CD4+ Foxp3GFP+ Treg cells were obtained by flow sorting after cell surface staining.
According to the manufacturer’s introduction, single-cell RNA-seq libraries were constructed using Single Cell 5’ Library and Gel Bead Kit, Single Cell V(D)J Enrichment Kit.The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100,000 reads per cell with pair-end 150 bp (PE150) reading strategy.

value: spleen

value: Treg

tag: age

value: 7 week

tag: developmental stage

value: aged


title: RPS4Y1 knockout cell line 6 hours after TNFa stimulation, KO 2

description:
Library name: FRCB3_TNFa_6hr
FRCB3_TNFa_6hr
RPS4Y1_6hr_raw_counts.txt
RPS4Y1_6hr_normalised.txt

value: Adenocarcinomic human alveolar basal epithelial cell


title: WT, dehydrated (4 h), replicate 2

description: Library name: WT-4 h-2

value: Rosette leaves

value: WT


title: n, spleen

description: 10x Genomics

value: 12 day

value: neonatal


title: WT_XEN_H3K4me1

tag: breed


title: WT, dehydrated (4 h), replicate 1

description: Library name: WT-4 h-1

value: dehydrated (4 h)


title: RPS4Y1 knockout cell line 6 hours after TNFa stimulation, KO 1

description:
Library name: RYA2_TNFa_6hr
RYA2_TNFa_6hr
RPS4Y1_6hr_raw_counts.txt
RPS4Y1_6hr_normalised.txt


title: n, liver

description: 10x Genomics

source_name: liver

value: liver


title: D1_DeltXp_2 rep1

value: XEN

value: Mus musculus molossinus X Mus musculus

value: Paternal Xist deletion


title: WT_EV_1 rep1

value: Female


title: Wild type cell line at baseline 6 hours after TNFa stimulation,  WT 3

description:
Library name: RC5A5_TNFa_6hr
RC5A5_TNFa_6hr
RPS4Y1_6hr_raw_counts.txt
RPS4Y1_6hr_normalised.txt

value: wild type

value: TNF-alpha (10ng/ml)

value: 6 hours


title: XEN_Rad21_DeltXp_2 rep2

value: Hybrid (Mus musculus molossinus X Mus musculus)

value: Extra-embryonic endoderm stem cell

value: Rad21 (Abcam, #ab992 )


title: WT, dehydrated (2 h), replicate 4

description: Library name: WT-2 h-4

value: dehydrated (2 h)


title: Wild type cell line at baseline 6 hours after TNFa stimulation, WT 2

description:
Library name: RC4D3_TNFa_6hr
RC4D3_TNFa_6hr
RPS4Y1_6hr_raw_counts.txt
RPS4Y1_6hr_normalised.txt

value: Adenocarcinomic human alveolar basal epithelial cell


title: D1_DeltXp_1 rep2


title: WT3

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 N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Index of the reference genome was built using Hisat2 (v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2 (v2.0.5).
featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
After the liver was taken out and frozen with liquid nitrogen, total RNA was extracted by Trizol.Total amounts and integrity of RNA were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit following manufacturer's protocols.

tag: strain background


title: D3_DeltXp_DeltXm_2 rep2

value: Homozygous Xist deletion


title: WT2


title: WT, dehydrated (2 h), replicate 2

description: Library name: WT-2 h-2

value: Rosette leaves

value: WT


title: WT, dehydrated (2 h), replicate 3

description: Library name: WT-2 h-3


title: RPS4Y1 knockout cell line at baseline 6 hours after serum starvation, KO 3

description:
Library name: RYF12_NT_6hr
RYF12_NT_6hr
RPS4Y1_6hr_raw_counts.txt
RPS4Y1_6hr_normalised.txt

value: RPS4Y1 knockout

value: no treatment


title: Wild type cell line at baseline 6 hours after TNFa stimulation, WT 1

description:
Library name: RCH12_TNFa_6hr
RCH12_TNFa_6hr
RPS4Y1_6hr_raw_counts.txt
RPS4Y1_6hr_normalised.txt


title: WT1

value: liver


title: D3_DeltXp_DeltXm_1 rep1

value: XEN

value: Mus musculus molossinus X Mus musculus


title: a, liver

description: 10x Genomics

value: Treg

value: 7 week

value: aged


title: cKO3


title: RPS4Y1 knockout cell line at baseline 6 hours after serum starvation, KO 2

description:
Library name: FRCB3_NT_6hr
FRCB3_NT_6hr
RPS4Y1_6hr_raw_counts.txt
RPS4Y1_6hr_normalised.txt

value: 6 hours


title: cKO2


title: WT, dehydrated (2 h), replicate 1

description: Library name: WT-2 h-1


title: WT, dehydrated (0 h), replicate 4

description: Library name: WT-0 h-4

value: dehydrated (0 h)


title: Midgut cells, Xrp1 O/E EE, all gut cells

city: Tsukuba

first: Ryusuke

last: Niwa

state: Ibaraki

address: 1 Chome-1-1 Tennodai

institute: University of Tsukuba

description:
Library name: pros-Xrp1OE
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger version 6.0.2. Quality control and analyses were conducted using Seurat version 5.1.0. Cells with 500-5000 genes detected and mitochondrial content less than 10% were selected for PCA and UMAP analysis.
Assembly: BDGP6.46
Supplementary files format and content: Tab-separated values files and matrix files

organism: Drosophila melanogaster

source_name: Adult midguts

extract_protocol:
Midguts were dissociated with elastase on a rotator with periodic pipetting for 1 hour at 27°C. The cell suspension was filtered through a 100 μm cell strainer, and pelleted at 200g for 5 min at 4°C. Cells were pooled together, resuspended in 1× PBS with 0.1% ultra-pure BSA, and filtered through a 70 μm cell strainer. For collecting EE lineages, GFP-positive cells were sorted out by FACS.
scRNA-seq libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1, following the manufacter's instructions.

value: Adult midguts

value: Midgut epithelial cells

value: Female


title: RPS4Y1 knockout cell line at baseline 6 hours after serum starvation, KO 1

description:
Library name: RYA2_NT_6hr
RYA2_NT_6hr
RPS4Y1_6hr_raw_counts.txt
RPS4Y1_6hr_normalised.txt

value: Adenocarcinomic human alveolar basal epithelial cell


title: WT, dehydrated (0 h), replicate 3

description: Library name: WT-0 h-3


title: Wild type cell line at baseline 6 hours after serum starvation,  WT 3

description:
Library name: RC5A5_NT_6hr
RC5A5_NT_6hr
RPS4Y1_6hr_raw_counts.txt
RPS4Y1_6hr_normalised.txt

value: wild type


title: Wild type cell line at baseline 6 hours after serum starvation, WT 2

description:
Library name: RC4D3_NT_6hr
RC4D3_NT_6hr
RPS4Y1_6hr_raw_counts.txt
RPS4Y1_6hr_normalised.txt


title: Midgut cells, Control, all gut cells

description:
Library name: pros-control
10X Genomics


title: Midgut cells, EE lineages, rep 2

description:
Library name: EE-lineages_rep 2
10X Genomics


title: Wild type cell line at baseline 6 hours after serum starvation, WT 1

description:
Library name: RCH12_NT_6hr
RCH12_NT_6hr
RPS4Y1_6hr_raw_counts.txt
RPS4Y1_6hr_normalised.txt


title: WT, dehydrated (0 h), replicate 2

description: Library name: WT-0 h-2

value: Rosette leaves


title: Flox_3

data_processing:
Data Trimming，mRNA Annotation，Gene Quantification
Sequence reads were trimmed for adaptor sequence/low-quanlity sequence using SQAPnuke
The trimmed sequence were mapped to GrCM38/mm10 using HISAT2
mRNA expression level of genes was calculated by RSEM (v1.3.1)
Assembly: mmu10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM for each sample

source_name: iWAT

extract_protocol:
Total RNA was harvested using Trizol (Invitrogen). 200ng of total RNA was used for the construction of sequencing libraries.
Sample QC, mRNA Isolation, mRNA Fragmentation,  cDNA Synthesis,  End Repair, Add A and Adaptor Ligation, PCR, Library QC, Circularization, Sequencing

value: iWAT

value: littermate control

value: cold stimulation at 4℃ for 6 hours


title: Midgut cells, EE lineages, rep 1

description:
Library name: EE-lineages_rep 1
10X Genomics


title: WT, dehydrated (0 h), replicate 1

description: Library name: WT-0 h-1

value: WT


title: cKO1

value: liver


title: Flox_2


title: HCT116 treated with PLOD3 siRNA 3

city: Bishan

first: Hong

last: Peng

state: ChongQing

address: Shuangxing avenue 9

institute: AffiliatedBishan hospital of Chongqing Medical  University

data_processing:
Cutadapt software (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9) was used to remove the reads that contained adaptor contamination,(command line: ~cutadapt -a ADAPT1 -A ADAPT2 -o out1.fastq -p out2.fastq in1.fastq in2.fastq -O 5 -m 100).
And After removed the low quality bases and undetermined bases ,we used HISAT2 software (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) to map reads to the genome (for example:Homo sapiens Ensembl v96),(command line: ~hisat2 -1 R1.fastq.gz -2 R1.fastq.gz -S sample_mapped.sam).
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d.Linux_x86_64) with default parameters (command line: ~stringtie -p 4 -G genome.gtf -o output.gtf -l sample input.bam). Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8.Linux_x86_64).
After the final transcriptome was generated, StringTie and ballgown(http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]),(command line: ~stringtie -e -B -p 4 -G merged.gtf -o samples.gtf samples.bam).
Assembly: StringTie
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: colon and rectum

growth_protocol: HCT116 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃

extract_protocol:
Total RNA was isolated using RNAiso Plus (Takara, Shiga, Japan), and 1 µg RNA was used to synthesize cDNA with the PrimeScript™RT reagent Kit with gDNA Eraser (Takara).
Libraries were constructed by depleting ribosomal RNA using the Human/Mouse/Rat Ribo-Zero rRNA Removal Kit for Illumina (Epicentre, Madison, WI, USA).

treatment_protocol: HCT116 cells were treated with PLOD3 siRNA or siNC for 2 days.

value: colon and rectum

value: colorectal cancer cell

value: si RNA

value: PLOD3 si RNA


title: BL6_joint

city: Livermore

first: Stephen

middle: Patrick

last: Wilson

state: CA

address: 7000 East Ave

department: BBTD

institute: LLNL

data_processing:
Cellranger mkfastq to generate FASTQ
Cellranger count to generate count matrix
Assembly: mm10
Supplementary files format and content: gene list (features.tsv) and cell barcodes (barcodes.tsv) as well as gene/barcode matrices (matrix.mtx) are provided for each experimental group.

source_name: Immune cells from the knee joints

extract_protocol:
Mice were euthanized and femur and tibia of uninjured hindlimbs were dissected, and superficial tissue were thoroughly removed, taking care to maintain the integrity of the knee joint. Joint residing cells were liberated by first dissociating the two bones into 7.5 mL of 3% Collagenase 1 solution (Worthington Biochemical, Lakewood, NJ; CLS-1) and 100 µg/mL DNase I (Roche, Basel, Switzerland; 11284932001) in DMEM/F12 shaking at 37 °C for two 1-hour digests followed by PBS wash steps between digests. Cells released from the joint were filtered through a 70 μm nylon cell strainer prior to red blood cell (RBC) lysis using ammonium-chloride-potassium (ACK) lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA; A1049201). Separation of immune cells was performed using CD45 conjugated magnetic microbeads followed by Miltenyi Biotech MACS separation with LC columns for CD45+ cell enrichment.
Immune (CD45+) cell populations were independently sequenced using a Chromium Single Cell 3' Reagent Kit and Chomium instrument (10X Genomice, Pleasanton, CA). Library preparation was performed according to manufacturer’s protocol.

value: Uninjured Synovial joints

value: CD45+ cells


title: HCT116 treated with PLOD3 siRNA 2


title: BL6_95wk_D7

extract_protocol:
Mice were euthanized and femur and tibia of injured and uninjured hindlimbs were dissected, and superficial tissue were thoroughly removed, taking care to maintain the integrity of the knee joint. Joint residing cells were liberated by first dissociating the two bones into 7.5 mL of 3% Collagenase 1 solution (Worthington Biochemical, Lakewood, NJ; CLS-1) and 100 µg/mL DNase I (Roche, Basel, Switzerland; 11284932001) in DMEM/F12 shaking at 37 °C for two 1-hour digests followed by PBS wash steps between digests. Cells released from the joint were filtered through a 70 μm nylon cell strainer prior to red blood cell (RBC) lysis using ammonium-chloride-potassium (ACK) lysis buffer (Thermo Fisher Scientific, Waltham, MA, USA; A1049201). Separation of immune cells was performed using CD45 conjugated magnetic microbeads followed by Miltenyi Biotech MACS separation with LC columns for CD45+ cell enrichment.
Immune (CD45+) cell populations were independently sequenced using a Chromium Single Cell 3' Reagent Kit and Chomium instrument (10X Genomice, Pleasanton, CA). Library preparation was performed according to manufacturer’s protocol.

treatment_protocol: 10-week-old and 95-week-old C57BL/6  mice were subjected to anterior cruciate ligament injury using a non-invasive single dynamic tibial compressive overload model

value: Injured joints

value: CD45- cells


title: BL6_marrow

value: Uninjured Femur Bone Marrow


title: HCT116 treated with PLOD3 siRNA 1


title: AKO_3

value: adipocyte-specific Celf1 knockout


title: HCT116 treated with si NC 3

value: NC

value: si NC


title: BL6_95wk_D0

value: Uninjured joints


title: AKO_2

value: iWAT


title: ncr1, dehydrated (0 h), replicate 1

description: Library name: ncr1-0 h-1

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, Carlsbad, CA,USA) according to the manufacturer’s protocol.
RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis. After total RNA was extracted, eukaryotic mRNA was enriched by Oligo (dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB#7530,New England Biolabs, Ipswich, MA, USA). The purified double-stranded cDNA fragments were end repaired. A base added, and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads (1.0X).And polymerase chain reaction (PCR) amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000.

value: Rosette leaves

value: ncr1 mutant

value: dehydrated (0 h)


title: Midgut cells, unsorted baseline, all gut cells

description:
Library name: EE-lineage-traced_allcelltypes
10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger version 6.1.2. Quality control and analyses were conducted using Seurat version 5.1.0. Cells with 500-5000 genes detected and mitochondrial content less than 10% were selected for PCA and UMAP analysis.
Assembly: BDGP6.46
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Midguts were dissociated with elastase on a rotator with periodic pipetting for 1 hour at 27°C. The cell suspension was filtered through a 100 μm cell strainer, and pelleted at 200g for 5 min at 4°C. Cells were pooled together, resuspended in 1× PBS with 0.1% ultra-pure BSA, and filtered through a 70 μm cell strainer.
scRNA-seq libraries were prepared using Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1, following the manufacter's instructions.

value: Adult midguts

value: Midgut epithelial cells

value: Female


title: BL6_10wk_D7


title: HCT116 treated with si NC 2

value: colon and rectum

value: colorectal cancer cell


title: Control spleen, scRNAseq

city: Seoul

first: JAE

middle: YONG

last: HAN

address: 1 Gwanak-ro, Gwanak-gu

department: Department of Agricultural Biotechnology

institute: Seoul National University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, and aggregation were made using the Cell Ranger v7.0.1 (10x Genomics; https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: GRCg7b
Supplementary files format and content: features.tsv.gz
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: matrix.mtx

organism: Gallus gallus

source_name: Spleen

extract_protocol:
Spleen of 3 weeks-old wild-tpye and RAG1 knockout chicken were freshly collected and washed with Phosphate Buffered Saline (PBS without Ca2+/Mg2+, pH 7.0-7.2). The tissue was mechanically digested with blade and chemically digested with 0.05% trypsin-EDTA diluted in Hank's Balanced Salt Solution (HBSS, without Mg2+/Ca2+, pH 7.2) for 10 minutes at 37°C. The 0.05% trypsin-EDTA was inactivated by filtered Fetal Bovine Serum (FBS) with 10% volume of trpysin-EDTA. The red blod cells were removed using Red Blood Cell Lysis Solution (Miltenyil Biotech) and filtered out by 40μm cell strianer.
Libraries were prepared using the Chromium controller according to the 10x chromium Next GEM Single Cell 3’ v3.1 protocol(CG000315). Briefly, the cell suspensions were diluted in nuclease  free water to achieve a targeted cell count of 10,000. Cell suspension was mixed with master mix and loaded with Single Cell 3’V3.1 Gel Beads and Partitioning Oil into a chromium Next GEM chip G. RNA transcripts from single cells were uniquely barcoded and reverse transcribed within droplets. cDNA molecules were pooled and the cDNA pool then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library. The purified libraries were quantified using   qPCR according to the qPCR Quantification Protocol Guide(KAPA) and qualified using the Agilent Technologies 4200 TapeStation (Agilent technologies).  And then the libraries were sequenced using HiSeq platform(Illumina) according to the read length in the user guide.

value: Spleen

value: Not applicable

value: Spleen cells

value: wild-type


title: HCT116 treated with si NC 1


title: BL6_10wk_D0

value: CD45+ cells


title: Hlfnegative_TRM_C-3

status: Public on Jul 04 2025

city: chiba city

first: Masahiro

last: Kiuchi

state: chiba

address: cyuoku inohana1-8-1

institute: Chiba univercity

description: Library name: Hlfnegative_TRM_C-3

data_processing:
Sequencing reads were aligned to the mouse reference genome (GRCm38) using Bowtie 2 and TopHat (v1.3.2) for RNA-seq, and Hisat2 (v2.2.1) for ChIP-seq and ATAC-seq.
For RNA-seq, transcript abundance was quantified as FPKM using Cufflinks (v2.0.2). For ChIP-seq and ATAC-seq, peaks were called using MACS2 with optimized parameters (ChIP-seq: window_size = 300; ATAC-seq: window_size = 100; FDR = 0.01).
Differentially expressed genes (DEGs) in RNA-seq were identified using DESeq2 (v1.10.1) on pseudobulk data, with thresholds of log2(fold change) > 1 or < –1 and p-value < 0.01. For ATAC-seq, differentially accessible regions (DARs) were detected using HOMER's getDifferentialPeaks.
ChIP-seq and ATAC-seq peaks were annotated using HOMER (annotatePeaks.pl). Overlapping peaks between assays were identified using mergePeaks, and motifs were enriched using findMotifsGenome.pl with a 200-bp window.
Co-expression networks for RNA-seq were constructed using Simpson's coefficient and visualized with Cytoscape (v3.7.1). Signal intensity tracks (BigWig) were generated using SAMtools, BEDtools, and deepTools, and visualized in the Integrative Genomics Viewer (IGV).
Assembly: Mouse genome GRCm38 (mm10).
Supplementary files format and content: Processed RNA-seq data are provided as gene-level FPKM tables. ChIP-seq and ATAC-seq data include peak BigWig signal tracks.

source_name: Lung

extract_protocol:
For RNA-seq, total RNA was extracted using TRIzol reagent (Invitrogen) according to the manufacturer’s instructions. For ChIP-seq, chromatin was extracted from paraformaldehyde-fixed cells lysed with SDS lysis buffer, followed by sonication. For ATAC-seq, nuclei were isolated by cell lysis and immediately subjected to transposition.
RNA-seq libraries were prepared using the TruSeq RNA Sample Prep Kit v2 (Illumina) following the manufacturer’s protocol. ChIP-seq libraries were constructed using the NEBNext Ultra II DNA Library Prep Kit for Illumina, including adapter ligation and PCR amplification. ATAC-seq libraries were prepared from transposed DNA fragments using PCR amplification (11–12 cycles) prior to sequencing. All libraries were sequenced on an Illumina NextSeq500 system.

value: Lung

value: Asp-Ag

tag: term

tag: hlf

value: negative

tag: iv staining


title: Hlfpositive_TRM_D-2

description: Library name: Hlfpositive_TRM_D-2

tag: tissue

value: positive


title: Hlfnegative_TRM_B-3

description: Library name: Hlfnegative_TRM_B-3


title: Hlfnegative_TRM_A-3

description: Library name: Hlfnegative_TRM_A-3


title: HLF_FLAG_Th17

description: Library name: HLF_FLAG_Th17


title: Empty_FLAG_Th2

description: Library name: Empty_FLAG_Th2


title: HLF_FLAG input

description: Library name: HLF_FLAG input


title: Hlfpositive_TRM_A-2

description: Library name: Hlfpositive_TRM_A-2


title: Flox_1

value: iWAT

value: littermate control

value: cold stimulation at 4℃ for 6 hours


title: Hlfpositive_TRM_B-2

description: Library name: Hlfpositive_TRM_B-2


title: HLF_FLAG_Th2

description: Library name: HLF_FLAG_Th2


title: Circulating_B-1

description: Library name: Circulating_B-1


title: Sample Spleen, scRNAseq

description: 10x Genomics

tag: cell line

value: RAG1 knockout (RAG1-/-)

value: chicken RAG1 was disrupted