title: KCL_1Dpci_62


title: Ileum, Control, Non-inflamed, rep 1, scTCR-seq

status: Public on Jul 31 2025

type: SRA

city: New York

first: Emma

middle: Claire

last: Erlich

state: NY

address: 417 E 68th St

country: USA

institute: Memorial Sloan Kettering

description: 10x Genomics

library_source: transcriptomic

data_processing:
Illumina base call (BCL) files were converted to FASTQ using Cell Ranger "mkfastq"
Expression data was processed using Cell Ranger "multi", pipeline version cellranger-7.1.0
Assembly: GRCh38-2020-A for 5' RNA expression, vdj_GRCh38_alts_ensembl-7.1.0 for BCR and TCR alignment
Supplementary files format and content: Tab-seperated values files and matrix files for the 5' RNA data
Supplementary files format and content: filtered_contig_annotations.csv analyzed by Cell Ranger 7.1.0 for the BCR and TCR data
Library strategy: scTCR-seq

molecule: total RNA

organism: Homo sapiens

source_name: Ileum

extract_protocol:
Two pieces of matched ileum and the associated mesentery was collected from consenting patients who were undergoing surgical resection of their ileum to treat Crohn's disease. Under a pathologist’s supervision, one piece of tissue was collected from an area of the ileum with active inflammation and the other piece was from adjoining normal region. Control ileum and mesentery was collected from gastrointestinal cancer patients from regions of the intestine upstream of their tumors. After collection, tissue was stored for under an hour in RPMI-1640 before undergoing single cell digestion. In the lab, the tissue was first rinsed in fresh HBSS before the mesentery, intestinal lamina propria, and muscularis were separated using a scalpel. To remove mucus and epithelial cells, the lamina propria was cut into thin 0.5 cm thick strips and then placed in 10 ml of HBSS with 5 mM EDTA and digested at 37° C for 20 minutes, before vortexing the tubes for 20 seconds, removing the tissue from the HBSS/ETDA, placing it in fresh HBSS and vortexing the tissue again. The lamina propria was then minced into small pieces and weighed. Mesentery was also minced into small pieces with a scalpel, before being weighed. Then tissue was digested in 1 g of tissue per 5 ml of RPMI-1640 media containing 10% FBS, 1 mg/ml Collagenase IV, 0.2 mg/ml DNase I at 37° C for 45 minutes (for mesentery) or 1 hour (for ileum) on an orbital at 100 rpm. Tissue was then vortexed, filtered through a 100m filter into a fresh tube, and washed with an equal volume of FACS buffer (2% FBS, 5mM EDTA, 0.2% sodium azide in PBS). Cells were then spun down for 10 minutes at 500 x g at 4° C, RBC lysis was performed for 5 minutes on the cells, which were washed with additional 10 ml of FACS buffer. After spinning cells down at 10 minutes at 500 x g at 4C, they were resuspended in 1 ml of FACS buffer, counted using an automatic cell counter and frozen at -80° C in 10% DMSO in 90% FBS before being moved to long-term storage in liquid nitrogen. On a later day, aliquots of cells were rapidly thawed in a 37° C water bath, stained for flow cytometry sorting and live, CD45+ immune cells were sorted for sequencing.
The 10x Genomics Chromium Single Cell 5' Library and Gel Bead Kit was used. We sequenced 5' RNA expression, TCR sequencing, and BCR sequencing as per the manufacturer's protocol.

tag: tissue

value: Ileum

tag: cell type

value: TCR+ cells

tag: disease

value: Control (Gastrointestinal cancer)

tag: disease state

value: Non-inflamed

tag: Sex

value: M


title: subject4 day3 timepoint4

city: Yushima, Bunkyo-ku, Tokyo

first: Atsushi

last: Satomura

address: 5F ITP Hongo Office , 2-25-7

country: Japan

institute: Craif

description: Library name: library93

library_source: other

data_processing:
Raw sequencing reads were initially processed using UMI-tools. The 5′-end bases, corresponding to miRNA sequences located upstream of the 3’ adapter, were extracted. Simultaneously, 12 bp unique molecular identifiers (UMIs), positioned immediately downstream of the 3′-adapter, were appended to the read identifiers to enable deduplication and subsequent analyses. Reads longer than 19 bases were retained and aligned to the human miRNA reference database provided by miRge 3.0 using Bowtie v1.2.3. Alignment settings allowed no mismatches within a 25-base seed and disallowing reverse complement matches.
Assembly: miRge 3.0
Supplementary files format and content: comma separated file with raw miRNA counts

molecule: other

source_name: Urine

extract_protocol:
Approximately 3.5 mL of urine was centrifuged at 2,000 × g for 30 minutes at 4°C to remove cells and debris. From the resulting supernatant, 3 mL was mixed with an equal volume of Total Exosome Isolation Reagent for urine (Thermo Fisher Scientific, Waltham, MA) and incubated at room temperature on a shaker at 100 rpm for 1 hour. The mixture was then centrifuged at 3,000 × g for 1 hour at 4°C to precipitate the EVs. The resulting EV pellet was resuspended in 250 μL of phosphate-buffered saline and subjected to RNA extraction using the MagMAX mirVana Total RNA Isolation Kit with the KingFisher Apex automated system (Thermo Fisher Scientific), following the manufacturer’s instructions. RNA was initially eluted in 30 μL of elution buffer. The eluate was then concentrated at 60°C for 30 to 45 minutes using a centrifugal concentrator (Eppendorf, Hamburg, Germany) and finally resuspended in 5 μL of nuclease-free water. Purified RNA samples were stored at −80°C until further analysis.
Small RNA libraries were prepared using 5 μL of total RNA and the QIAseq miRNA Library Kit (QIAGEN, Hilden, Germany), following the manufacturer’s instructions. Library concentrations were quantified using the Qubit Flex Fluorometer (Thermo Fisher Scientific) with the Qubit™ dsDNA High Sensitivity Assay Kit. Prepared libraries were stored at −20°C until sequencing. Sequencing was performed on a NextSeq 550 system (Illumina, San Diego, CA) using 2 pmol of denatured libraries and single-end 75 bp reads, following the manufacturer’s protocol.

value: Urine

tag: batch


title: striatum, 6 months old, Q140, female, replicate 3

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

data_processing:
Basecalls/demultiplexing performed using Illumina Bcl2fastq2 v 2.17
Alignment to mouse genome using STAR spliced read aligner
Counting reads using HTSeq with GRCm38(mm10) as reference
Normalization using trimmed mean of M values method, and differential expression analysis using Biocoductor packages.
Assembly: mm10
Supplementary files format and content: Counts

organism: Mus musculus

source_name: Striatum

extract_protocol:
Brain striatal tissues were dissected from all mice at 6 months of age. RNA was extracted using a Qiagen RNeasy kit.
Library was prepared using TruSeq Stranded mRNA (Poly-A)
RNA samples were barded into cDNA libraries and sequencing was carried out as paired end, 2X100bp, Novaseq S4

value: Striatum

tag: genotype

value: Q

value: female


title: WIK_7Dpci_61

city: Oxford

first: Mathilda

last: Mommersteeg

address: | Institute of Developmental and Regenerative Medicine (IDRM) | IMS-Tetsuya Nakamura Building, Old Road Campus, Roosevelt Drive

department: Department off Physiology, Anatomy and Genetics

country: United Kingdom

institute: University of Oxford

data_processing:
Reads were demultiplexed using bcl2fastq (v2.20.0, Illumina)
Adapter trimming and quality control was performed with Trim Galore! (v.0.6.4_dev)
Reads from 2 lanes of sequencing were combined
Alignment and gene counting was performed using STAR (v.2.7.6a)
Assembly: GRCz11 (soft-masked, primary assembly, ftp://ftp.ensembl.org:21/pub/release-104/fasta/danio_rerio/dna/Danio_rerio.GRCz11.dna_sm.primary_assembly.fa.gz)
gene annotations: Ensembl v.104 (ftp.ensembl.org/pub/release-104/gtf/danio_rerio/Danio_rerio.GRCz11.104.gtf.gz)

organism: Danio rerio

source_name: cardiac ventricle

extract_protocol:
RNA was extracted from individual ventricles using the Quick-RNA MicroPrep kit (Zymo Research). 1.5 ug of total RNA was used for the construction of sequencing libraries.
Libraries were generated using the QuantSeq 3' mRNA-Seq Library Prep Kit (FWD) from Lexogen.

treatment_protocol: Cryo-injury was induced on the tip of the ventricle using a copper probe pre-chilled in liquid nitrogen.

value: cardiac ventricle

tag: strain

value: WIK

tag: treatment

value: cryo-injury

tag: time (days)


title: WIK_7Dpci_60


title: Ileum, Control, Non-inflamed, rep 1, scBCR-seq

description: 10x Genomics

data_processing:
Illumina base call (BCL) files were converted to FASTQ using Cell Ranger "mkfastq"
Expression data was processed using Cell Ranger "multi", pipeline version cellranger-7.1.0
Assembly: GRCh38-2020-A for 5' RNA expression, vdj_GRCh38_alts_ensembl-7.1.0 for BCR and TCR alignment
Supplementary files format and content: Tab-seperated values files and matrix files for the 5' RNA data
Supplementary files format and content: filtered_contig_annotations.csv analyzed by Cell Ranger 7.1.0 for the BCR and TCR data
Library strategy: scBCR-seq

value: BCR+ cells


title: subject4 day3 timepoint3

description: Library name: library92


title: Ileum, Control, Non-inflamed, rep 1, scRNA-seq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Illumina base call (BCL) files were converted to FASTQ using Cell Ranger "mkfastq"
Expression data was processed using Cell Ranger "multi", pipeline version cellranger-7.1.0
Assembly: GRCh38-2020-A for 5' RNA expression, vdj_GRCh38_alts_ensembl-7.1.0 for BCR and TCR alignment
Supplementary files format and content: Tab-seperated values files and matrix files for the 5' RNA data
Supplementary files format and content: filtered_contig_annotations.csv analyzed by Cell Ranger 7.1.0 for the BCR and TCR data

value: CD45+ immune cells


title: subject4 day3 timepoint6

description: Library name: library95


title: subject4 day3 timepoint2

description: Library name: library91


title: WIK_7Dpci_58


title: Mesentery, Control, Non-inflamed, rep 1, scRNA-seq

description: 10x Genomics

source_name: Mesentery

value: Mesentery


title: RPE-choroid complex, shSerpinb2-4

city: 广州

first: Min

last: Xie

state: 广东省

address: 广东省广州市天河区金穗路7号

department: State Key Laboratory of Ophthalmology

country: China

institute: Zhongshan Ophthalmic Center, Sun Yat-sen University

data_processing:
The RNA sequencing reads were first trimmed to remove poly-A and unguallied reads were elminated using Cutadapt.
The remainina reads were then aligned to theHomo sapiens relerence aenome GRch38 usina HISAT2 (V2.1.0).
Gene expression values were calculaled from fraqments per kilobases per miion fragmenls (fPKlw) values.
Assembly: http://www.ensembl.org/Mus_musculus/Info/Annotation; http://asia.ensembl.org/Homo_sapiens/Info/Index

source_name: RPE-choroid complex

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were maintained in an ECM supplemented with 5% fetal bovine serum (FBS), 1% Endothelial Cell Growth Supplement（ECGS）and 1% antibiotics in a humidified atmosphere of 5% CO2 at 37°C.

extract_protocol:
The collected cells were lvsed withTrizoseacent dnvirooen l ifeTechnolodies) accordina to the manufacturer's protocol.
The cDNA libraries were constructed and sequenced using an lumina NovaSeg 6000 platomm (umina) Shanghai Personal Biotechnology Cp. Ltd.

treatment_protocol: (1)Laser-induced CNV model, and shSerpinb2 (1 µg/µl) injection in vitreous cavity immediately after CNV.(2)The siRNA was transfected into HUVEC using Escot(Sigma) Transfection Reagent, and samples were collected 48 hours later and sent for sequencing.

value: RPE-choroid complex

value: choroidneovascularization


title: striatum, 6 months old, Q140, female, replicate 1


title: subject4 day3 timepoint1

description: Library name: library90


title: WIK_1Dpci_57


title: HCT116 cell FSTL3 rep3

city: Nanjing

first: Leqian

last: Ying

state: Jiangsu

address: Ding Jiaqiao street

department: Oncology

institute: Southeast University

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer's instructions. After cluster generation, the library preparations weresequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Quality control-Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, 030 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads mapping to the reference genome-Reference genome and gene model annotation files were downloaded from genome website directly. 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. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Quantification of gene expression level- 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 geneand reads count mapped to this gene. FPKM, expected number of Fragments PerKilobase of transcript sequence per Millions base pairs sequenced, considers theeffect of sequencing depth and gene length for the reads count at the same time, and iscurrently the most commonly used method for estimating gene expression levels.
Assembly: Reads mapping to the reference genome-Reference genome and gene model annotation files were downloaded from genome website directly. 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. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
Supplementary files format and content: Raw counts for each sample
Supplementary files format and content: FPKM values for each sample

source_name: Colon cancer

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

extract_protocol:
The study involved the exogenous addition of humanized FSTL3 protein (MCE) to the culture medium of HCT116 cells. We then performed gene expression profiling analysis using data obtained from RNA-seq after 24 hours.
A total amount of 1 ug RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTMRNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.

value: Colon cancer

tag: cell line

value: Colon cancer cell

value: WT

value: FSTL3 (300ng/mL) 24 hours


title: RPE-choroid complex, shSerpinb2-3

address: 广东省广州市天河区金穗路7号


title: HCT116 cell FSTL3 rep2


title: subject4 day3 timepoint9

description: Library name: library89


title: HCT116 cell FSTL3 rep1


title: WIK_1Dpci_56


title: RPE-choroid complex, shSerpinb2-2

address: 广东省广州市天河区金穗路7号


title: WIK_1Dpci_55


title: subject4 day2 timepoint8

description: Library name: library88


title: RPE-choroid complex, shSerpinb2-1

address: 广东省广州市天河区金穗路7号


title: striatum, 6 months old, Q140, female, replicate 2


title: subject4 day2 timepoint7

description: Library name: library87


title: HCT116 cell control rep3

value: Control


title: HCT116 cell control rep2


title: TU_7Dpci_52

value: TU


title: subject4 day2 timepoint6

description: Library name: library86

value: Urine


title: RPE-choroid complex, shControl-3

address: 广东省广州市天河区金穗路7号

value: shControl


title: HCT116 cell control rep1


title: TU_7Dpci_51


title: subject4 day2 timepoint5

description: Library name: library85


title: subject4 day2 timepoint4

description: Library name: library84


title: RPE-choroid complex, shControl-2

address: 广东省广州市天河区金穗路7号


title: RO d192 CTRL2, AAV9.hCLN2-treated CLN2-2

city: Tuebingen

first: Kevin

last: Achberger

address: Oesterbergstrasse 3

department: Institute of Neuroanatomy and Developmental Biology

country: Germany

institute: University of Tuebingen

description: 1=Doublets, 2=CTRL2, 3=AAV9.hCLN2-treated CLN2-2, 4=Not assigned

data_processing:
Samples were demultiplexed using Illumina's bcl2fastq conversion. A 10x Genomics custom reference package was created via Cell Ranger mkgtf v7.0.1 with the GENCODE GRCh38.p13 (release version 41) primary assemble reference sequence and main gene annotation file in GTF format along with the AAV vector genome sequence from the full-length 5’ flop ITR to the full-length 3’ flop ITR and the annotation of the transgene TPP1 sequence in the vector genome. Read alignments were performed in Cell Ranger count v7.0.1 against the pre-built reference package to generate gene-by-cell UMI count matrices with intronic reads included.
BAM files from cell ranger were used as input for sample demultiplexing and doublet removal by SNP genotyping using Souporcell v2.0 (Heaton et al., 2020).
Gene-barcode matrices were then loaded into Seurat (R, Version 4.3, (Butler et al., 2018)) and demultiplexed cells were annotated.
Assembly: GRCh38
Supplementary files format and content: Tab-separated value files and matrix files

source_name: Retinal Organoids

growth_protocol: ROs were differentiated from hiPSCs based on a previously described protocol by Zhong et al., 2014 with additional modifications  (Achberger et al., 2019)

extract_protocol:
The ROs were dissociated with the Neurosphere Dissociation Kit (P) (Miltenyi Biotec, Germany) according to manufacturer’s instruction. Then, the cells were filtered with a 30 µm MACS strainer (Miltenyi Biotec, Germany) and centrifuged for 2 min at 400 g. Subsequently, the cells were resuspended in proper volumes of 10% FBS in PBS for sequencing. All steps were performed at RT. Single cell suspension concentration and cell viability were determined by automatic cell counting (DeNovix CellDrop, DE, USA) using an AO/PI viability assay (DeNovix, DE, USA).
Gene expression libraries were generated using the 10X Chromium Next gel beads-in-emulsion (GEM) Single Cell 3’ Reagent Kit v3.1 (10X Genomics, CA, USA) according to manufacturer’s instructions. In brief, 18,000 cells originating from two different cell lines, were loaded on the Chromium Next GEM Chip G, which was subsequently run on the Chromium Controller (10X Genomics, CA, USA) to partition cells into GEMs. Cell lysis and reverse transcription of poly-adenylated mRNA occurred within the GEMs and resulted in cDNA with GEM-specific barcodes and transcript-specific unique molecular identifiers (UMIs). After breaking the emulsion, cDNA was amplified by PCR, enzymatically fragmented, end-repaired, extended with 3′ A-overhangs, and ligated to adapters. P5 and P7 sequences, as well as sample indices (Chromium i7 Multiplex kit, 10X Genomics, CA, USA), were added during the final PCR amplification step. The fragment size of the final libraries was determined using the Bioanalyzer High-Sensitivity DNA Kit (Agilent, CA, USA). Library concentration was determined using the Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific, MA, USA). scRNA libraries were pooled and paired-end-sequenced on the Illumina NovaSeq 6000 platform using for the read 1 28 cycles, i7 index 10 cycles, i5 index 10 cycles and read 2 90 cycles.

treatment_protocol: On day 0 of treatment, one RO was placed in each well of non-adherent 96-well plates in 80 µl BRDM with 10% FBS and 100 µM taurine (depending on the age of the ROs, the medium was additionally supplemented with RA, as mentioned above). AAVs were thawed in ice and added via a 50% medium change to obtain a genome copy number of 1.67x10^11 gc/well. On day 1, 20 µl of medium were added per well in order to have a final volume of 100 µl/well. The medium was changed twice per week by a 70% replacement. On day 7 the medium volume was increased to 150 µl/well and on day 35 the ROs were transferred to a 48-well plate with 300 µl culture medium. From day 49, the ROs were cultured in 500 µl/well. A. For the scRNA-seq analysis, the organoids were cultured for 70 days after treatment.

value: Retinal Organoids

value: CTRL2, AAV9.hCLN2-treated CLN2-2

tag: timepoint

value: no and AAV9.hCLN2


title: RO d192 CTRL2, CLN2-2

description: 1=Doublets, 2=CTRL2, 3=CLN2-2, 4=Not assigned

value: CTRL2, CLN2-2

value: no


title: TU_7Dpci_49

value: cardiac ventricle

value: cryo-injury


title: RPE-choroid complex, shControl-1

address: 广东省广州市天河区金穗路7号

value: RPE-choroid complex


title: RPE-choroid complex, shControl-4

address: 广东省广州市天河区金穗路7号

value: choroidneovascularization


title: RPE-choroid complex, No CNV-3

address: 广东省广州市天河区金穗路7号

description: No CNV_3

value: No treatment


title: subject4 day2 timepoint2

description: Library name: library82


title: RO d192 CTRL1, CLN2-1

description: 1=Doublets, 2=CTRL1, 3=CLN2-1, 4=Not assigned

value: CTRL1, CLN2-1


title: TL_7Dpci_46

value: TL


title: TU_1Dpci_54


title: subject4 day2 timepoint1

description: Library name: library81


title: RO d192 CTRL1, AAV9.hCLN2-treated CLN2-1

description: 1=Doublets, 2=CTRL1, 3=AAV9.hCLN2-treated CLN2-1, 4=Not assigned

value: CTRL1, AAV9.hCLN2-treated CLN2-1


title: TU_1Dpci_48


title: TL_7Dpci_44


title: TL_7Dpci_45


title: RPE-choroid complex, No CNV-2

address: 广东省广州市天河区金穗路7号

description: No CNV_2

value: WT


title: Skin_Donor C (36Y)_Single-hair region_Sample C5

city: Chuo-ku, Kobe

first: Hironobu

last: Fujiwara

state: Hyogo

address: 2-2-3 Minatojima-minamimachi

department: Center for Biosystems Dynamics Research

institute: RIKEN

description: 10x Genomics

data_processing:
Demultiplexing, barcoded processing, and gene counting were conducted using Cell Ranger software v3.1.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Skin

extract_protocol:
To generate single-cell suspensions from human skin samples, the following four experimental steps were performed: Firstly, skin tissues were dissected into small pieces containing only a single hair (single-hair samples) or no hairs (non-hair samples); Secondly, to maximize the number of dermal cells for analysis, the interfollicular epidermis was removed from each sample using tweezers after treating skin tissues with 2.4 U/mL dispase (Corning) in PBS at 4ºC for 20 minutes and then at 37ºC for 20 minutes. In this process, care was taken not to remove hair follicle keratinocytes; Thirdly, remaining skin tissues were placed in a mixture of the following enzymes: 0.20% collagenase I (Thermo Fisher Scientific), 0.05% collagenase II (Thermo Fisher Scientific), 0.05% collagenase IV (Thermo Fisher Scientific), 0.01% Hyaluronidase (Nakalai Tesque), and 5 U/mL DNase I (Sigma) in HBSS. The skin tissue was minced using surgical scissors and incubated at 37ºC with gentle rotation (20 rpm) until the tissue was completely digested (for about one hour). Finally, a skin cell suspension was obtained from each sample. The obtained cell suspension was passed through 70- and 30-µL cell strainers (Miltenyi Biotec) and centrifuged at 3000 rpm for seven minutes. After removal of the supernatant, cells were resuspended with FBS-containing DMEM.
For each skin tissue sample, a single-cell cDNA library was individually prepared using Single Cell 3’ Reagent Kit of version 3 chemistry (10x Genomics) following the manufacturer’s protocol. The prepared cDNA libraries were then sequenced using NovaSeq 6000 Sequencing System (Illumina).

value: Skin

value: Various cell types residing in the dermis

value: Female

tag: age

value: 36 years old


title: subject4 day2 timepoint3

description: Library name: library83

value: Urine


title: RPE-choroid complex, No CNV-1

address: 广东省广州市天河区金穗路7号

description: No CNV_1


title: subject4 day2 timepoint9

description: Library name: library80


title: Skin_Donor C (36Y)_Single-hair region_Sample C4

description: 10x Genomics


title: Skin_Donor C (36Y)_Single-hair region_Sample C3

description: 10x Genomics


title: subject4 day1 timepoint6

description: Library name: library77


title: subject4 day1 timepoint8

description: Library name: library79


title: subject4 day1 timepoint7

description: Library name: library78


title: WT, PNX

city: Chengdu

first: Liyin

last: Zhang

state: Sichuan

address: Remin nan Road

institute: Sichuan University

data_processing:
Sample data were aggregated using Cell Ranger software and raw data were processed further in R (version 3.4.4). The following quality control steps were performed: (i) genes expressed by less than 10 cells or with a row average of < 0.002 were not considered; (ii) cells that expressed fewer than 300 genes (low quality), and cells that expressed over 4,000 genes (potential doublets) were excluded from further analysis; (iii) cells in which over 10% of unique molecular identifiers (UMIs) were derived from the mitochondrial genome were removed. The whole workflow included quality control, data normalization, sample integration, clustering and visualization.
Assembly: mm10
Supplementary files format and content: Table-separated values and matrix market files

source_name: Right lobe of mouse lung after PNX

extract_protocol:
Briefly, the Sheep anti Rat magnetic beads were pre-coated with CD31 and CD45 respectively. Harvested mouse lungs were washed with pre-cooled DPBS, cut into pieces, digested with digestion buffer containing type 1 collagenase (2mg/mL) in 37°C for 40min. After erythrocytes were lysed, lung cells were incubated with CD45 coated magnetic beads in 4°C for 30 min. The CD45 positive cells were absorbed by magnetic rack, the remaining cell suspension was incubated with CD31 coated magnetic beads in 4°C for 30 min, and CD31-positive and CD45-negative lung endothelial cells were obtained by elution of magnetic beads.
Library was performed according to manufactors' instruction: GEM generation,  Barcoding, GEM-RT clean-up, cDNA amplification and library construction.  Sequencing was performed on Illumina Nova-seq 6000 (Illumina, America),  followed by de-multiplexing and mapping to the mouse genome (build mm10)  using Cell Ranger (10x Genomics, version 2.1.1).

value: Right lobe of mouse lung after PNX

value: Primary cell

value: Endothelilal cell

value: Wild type


title: TL_1Dpci_43

value: cardiac ventricle

value: cryo-injury


title: TL_1Dpci_42


title: Skin_Donor C (36Y)_Single-hair region_Sample C1

description: 10x Genomics


title: M3KO, PNX


title: TL_1Dpci_41


title: Skin_Donor C (36Y)_Single-hair region_Sample C2

description: 10x Genomics


title: subject4 day1 timepoint5

description: Library name: library76


title: SAT_7Dpci_40

value: SAT


title: subject4 day1 timepoint3

description: Library name: library74


title: WT, Sham

source_name: Right lobe of mouse lung before PNX

value: Right lobe of mouse lung before PNX


title: Skin_Donor C (36Y)_Non-hair region_Sample C0

description: 10x Genomics


title: SAT_7Dpci_39


title: SAT_7Dpci_38


title: BMDMs, IFNrA

city: hangzhou

first: huan

last: chen

state: Zhejiang

address: Hangzhou, Zhejiang Province, China

institute: Zhejiang Chinese Medical University

description: IFNrA

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost 3length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited txt file includes count values for each Sample

source_name: BMDM

growth_protocol: BMDMs were maintained in DMEM supplementred with 10%fetal bovine serum (FBS) under conditions of 37℃ in an atmosphere with 5% CO2.

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3ug of total RNA was used for the construstion of sequencing livraries
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufactruer's protocols

treatment_protocol: IFNγ 40ng/ml  (GSKJ1 200μM，MCE)

value: BMDM

value: IFNγ


title: BMDMs, IFNrB

description: IFNrB


title: subject4 day1 timepoint4

description: Library name: library75


title: BMDMs, IFNrGSKB

description: IFNrGSKB

value: IFNγ GSKJ1


title: SAT_1Dpci_37


title: Skin_Donor B (37Y)_Single-hair region_Sample B6

description: 10x Genomics

value: 37 years old


title: Skin_Donor B (37Y)_Single-hair region_Sample B5

description: 10x Genomics

value: Skin


title: SAT_1Dpci_36


title: BMDMs, CONB

description: CONB

value: WT

value: control


title: subject4 day1 timepoint1

description: Library name: library72


title: BMDMs, IFNrGSKA

description: IFNrGSKA


title: subject3 day3 timepoint8

description: Library name: library71


title: subject4 day1 timepoint2

description: Library name: library73


title: Skin_Donor B (37Y)_Single-hair region_Sample B7

description: 10x Genomics

value: Various cell types residing in the dermis

value: Female


title: Skin_Donor B (37Y)_Single-hair region_Sample B4

description: 10x Genomics


title: BMDMs, CONA

description: CONA


title: NA_7Dpci_33


title: Skin_Donor B (37Y)_Single-hair region_Sample B3

description: 10x Genomics


title: Skin_Donor B (37Y)_Single-hair region_Sample B2

description: 10x Genomics


title: AR113Q-ASO, 52W, 6, replicate_2

city: New Haven

first: Changwoo

last: Lee

state: CT

address: 295 Congress

department: Neuroscience

institute: Yale University

description:
10x Genomics
230926_ctype.h5ad

data_processing:
CellRanger v7.1.0
Preprocessing quality control including doublet detection using Scrublet
Normalization and square root transformation
BBKNN batch correction
Cell type annotation
Assembly: mm10
Supplementary files format and content: h5ad files

molecule: nuclear RNA

source_name: lumbar cord

extract_protocol:
Nuclei isolation from frozen tissue followed a previously established protocol (24). Lumbar cords from three animals per genotype (WT and AR113Q) at each timepoint (26 and 52 weeks) were utilized, with six animals for the ASO-injected 52-week AR113Q group. Briefly, frozen tissue underwent gentle dounce homogenization in 2 mL of ice-cold Nuclei EZ Prep buffer (Sigma; NUC101-1KT) using a large clearance pestle "A" followed by a small clearance pestle "B," each for 25 strokes. Subsequently, the homogenized tissue was incubated on ice for five minutes with an additional 2 mL of cold EZ Prep buffer. The homogenates were then centrifuged at 500xg for five minutes at 4°C. The nucleus pellets were resuspended in 4 mL of cold EZ Prep buffer, followed by incubation on ice for five minutes and a repeated centrifugation at 500xg for five minutes at 4°C. The nuclei were washed in 4 mL of Nuclei Suspension Buffer (NSB), which contained 1x phosphate-buffered saline (PBS), 0.01% BSA, and 0.1% RNase inhibitor (Clontech/Takara; 2313B). The final washing step was followed by centrifugation at 500xg for five minutes at 4°C. The purified nuclei were resuspended in 1 mL of NSB, filtered through a 40 μm cell strainer (Fisher Scientific; 22-363-547), and quantified using a Countess III FL Cell Counter (Thermo Fisher Scientific; AMQAF2000). Single-nucleus suspensions were then appropriately diluted to achieve a concentration of approximately 1000 nuclei per μL in NSB for library preparation.
Libraries were prepared from diluted single-nucleus suspensions using the 10x Genomics Chromium Single Cell 3’ Reagent Kits v.3.1 at the Yale Center for Genome Analysis (YCGA). Briefly, 10,000 cells per sample were mixed with RT Master Mix, loaded onto the Single Cell A Chip, and combined with approximately 750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). Each gel bead has primers containing the following: an Illumina R1 sequence (read 1 sequencing primer), a 16-nucleotide barcode, a 12-nucleotide unique molecular identifier (UMI), and a 30-nucleotide poly-dT primer sequence. After dissolution of the Gel Beads in a GEM, the released primers were mixed with the cell lysate and Master Mix, resulting in barcoded, full-length cDNA from poly-adenylated mRNA after incubation. Silane magnetic beads were then used to remove leftover biochemical reagents from the post-GEM reaction mixture.  Subsequently, full-length, barcoded cDNA underwent PCR amplification to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size before library construction. During library construction, P5, P7, a sample index, and R2 (read 2 primer sequence) were added via end repair, A-tailing, adaptor ligation, and PCR. The final libraries contained the P5 and P7 primers used in Illumina bridge amplification. Sequencing was performed using the NovaSeq6000 at the YCGA.  Sample concentrations were normalized to 1. 2nM and loaded onto an Illumina NovaSeq S4 flow cell at a concentration that yielded 20k-50k passing filter clusters per cell per sample. Paired-end sequencing was conducted on an Illumina NovaSeq6000 instrument following Illumina protocols and 10x sequencing specifications. The 8bp index was read during an additional sequencing read that automatically followed the completion of read 1. Data generated during sequencing runs were simultaneously transferred to the YCGA high-performance computing cluster. To monitor quality in real time, a positive control (prepared bacteriophage Phi X library) provided by Illumina was spiked into every lane at a concentration of 0.3%. Signal intensities were converted to individual base calls during a run using the system’s Real Time Analysis (RTA) software. Base calls were transferred from the machine’s dedicated personal computer to the Yale high-performance computing cluster via a 1 Gigabit network mount for downstream analysis.

treatment_protocol: ASOs were made of a 16-mer, 3-10-3 constrained ethyl gapmer containing the following sequence: AAGTTGTAGTAGTCGC, which is complementary to human and mouse AR transcripts as detailed previously (13); this ASO is designated ASO1 in Supplemental Fig. 2. Alternatively, ASO1 conjugated to palmitic acid via an amide linkage at the 5’ end is designated ASO2 in Supplemental Fig. 2. ASOs were diluted in PBS, pH 7 and administered subcutaneously to C57BL/6J males (5 – 50 mg/kg) or AR113Q males (25 mg/kg) weekly for the indicated durations. AR113Q mice were administered ASO2 or vehicle (PBS, pH 7) for the treatment study. For this longitudinal trial, AR113Q males were randomly assigned to vehicle or ASO treatment group. The CAG repeat range for the vehicle group ranged from 97-111 repeats with a mean of 105; the CAG repeat range for the treatment group ranged from 95-110 repeats with a mean of 104 (p>0.05 by Student’s t-test).

value: lumbar cord

value: ASO-AR113Q knock-in

value: 52 weeks


title: subject3 day3 timepoint6

description: Library name: library69

value: Urine


title: subject3 day3 timepoint7

description: Library name: library70


title: NA_1Dpci_30

value: cardiac ventricle


title: subject3 day3 timepoint5

description: Library name: library68


title: NA_7Dpci_31

value: cryo-injury


title: Skin_Donor B (37Y)_Single-hair region_Sample B1

description: 10x Genomics


title: subject3 day3 timepoint4

description: Library name: library67


title: Skin_Donor A (40Y)_Single-hair region_Sample A7

description: 10x Genomics

value: 40 years old


title: Skin_Donor B (37Y)_Non-hair region_Sample A0

description: 10x Genomics


title: AR113Q-ASO, 52W, 5, replicate_2

description:
10x Genomics
230926_ctype.h5ad


title: AR113Q-ASO, 52W, 4, replicate_2

description:
10x Genomics
230926_ctype.h5ad


title: AR113Q-ASO, 52W, 6, replicate_1

description:
10x Genomics
230926_ctype.h5ad


title: subject3 day3 timepoint3

description: Library name: library66


title: NA_1Dpci_28


title: AR113Q-ASO, 52W, 4, replicate_1

description:
10x Genomics
230926_ctype.h5ad


title: subject3 day3 timepoint2

description: Library name: library65


title: NA_7Dpci_34


title: AB_7Dpci_27

value: AB


title: subject3 day2 timepoint9

description: Library name: library63


title: subject3 day3 timepoint1

description: Library name: library64


title: AB_7Dpci_24


title: AR113Q-ASO, 52W, 3

description:
10x Genomics
230926_ctype.h5ad


title: Skin_Donor A (40Y)_Single-hair region_Sample A5

description: 10x Genomics


title: NA_1Dpci_29


title: AR113Q-ASO, 52W, 2

description:
10x Genomics
230926_ctype.h5ad


title: Skin_Donor A (40Y)_Single-hair region_Sample A4

description: 10x Genomics


title: subject3 day2 timepoint8

description: Library name: library62


title: Skin_Donor A (40Y)_Single-hair region_Sample A3

description: 10x Genomics


title: AB_1Dpci_23


title: AR113Q-ASO, 52W, 1

description:
10x Genomics
230926_ctype.h5ad


title: AB_1Dpci_22


title: WT, 52W, 3

description:
10x Genomics
230926_ctype.h5ad

value: Wild-type


title: Skin_Donor A (40Y)_Single-hair region_Sample A2

description: 10x Genomics


title: subject3 day2 timepoint7

description: Library name: library61


title: AR113Q-ASO, 52W, 5, replicate_1

description:
10x Genomics
230926_ctype.h5ad


title: WT, 52W, 2

description:
10x Genomics
230926_ctype.h5ad


title: subject3 day2 timepoint6

description: Library name: library60


title: TU_unop_3

value: TU

value: uninjured


title: AB_1Dpci_21


title: Skin_Donor A (40Y)_Non-hair region_Sample A0

description: 10x Genomics


title: Skin_Donor A (40Y)_Single-hair region_Sample A6

description: 10x Genomics


title: Skin_Donor A (40Y)_Single-hair region_Sample A1

description: 10x Genomics


title: TU_unop_2


title: WT, 52W, 1

description:
10x Genomics
230926_ctype.h5ad


title: subject3 day2 timepoint4

description: Library name: library58


title: subject3 day2 timepoint5

description: Library name: library59


title: H3

city: Suzhou

first: Juan

last: Yin

address: 80 Tian'e Dang Road

department: Suzhou Key Laboratory of Gut Microecology

institute: The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University

data_processing:
Illumina Bcl2FastQ  software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using Hisat2 v2.1.0 with default parameters.
HTSeq v0.11.2 was subsequently employed to convert aligned short reads into read counts for each gene model.
Transcripts Per Kilobase of exon model per Million mapped reads(TPM) were calculated.
Assembly: hg38
Supplementary files format and content: text files include TPM/counts for each Sample
Supplementary files format and content: text files include all/different mRNAs/genes for each Sample

source_name: Peripheral Blood

extract_protocol:
Total RNA was isolated from cells/tissues using the Magzol Reagent (Magen, China)according to the manufacturer’s protocol. The quantity and integrity of RNA yield was assessed by using the K5500(BeijingKaiao, China) and the Agilent 2200 TapeStation (Agilent Technologies, USA) separately.
The mRNA was enriched by oligodT according to instructions of NEBNext® Poly(A) mRNA Magnetic Isolation Module (NEB,USA).And then fragmented to approximately 200bp. Subsequently, the RNA fragmentswere subjected to first strand and second strand cDNA synthesis following by adaptor ligation and enrichment with a low-cycleaccording to instructions ofNEBNext® Ultra™ RNA Library Prep Kit for Illumina. The purified library products were evaluated using the Agilent 2200 TapeStation and Qubit(Thermo Fisher Scientific, USA).
The libraries were sequenced by Illumina (Illumina, USA) with paired-end 150bp at Ribobio Co. Ltd (Ribobio, China).

value: Peripheral Blood

value: Human Acute Monocytic Leukemia Cells

value: hsa_circRNA_103124 overexpressed


title: AR113Q, 52W, 3

description:
10x Genomics
230926_ctype.h5ad

value: AR113Q knock-in


title: TU_unop_1


title: AR113Q, 52W, 2

description:
10x Genomics
230926_ctype.h5ad


title: H2


title: SAT_unop_5

value: SAT


title: subject3 day2 timepoint3

description: Library name: library57


title: AR113Q, 52W, 1

description:
10x Genomics
230926_ctype.h5ad


title: H1


title: C3

value: WT


title: SAT_unop_4


title: subject3 day2 timepoint1

description: Library name: library55


title: subject3 day1 timepoint10

description: Library name: library54


title: WT, 26W, 3

description:
10x Genomics
230926_ctype.h5ad

value: lumbar cord

value: 26 weeks


title: SAT_unop_3


title: WT, 26W, 2

description:
10x Genomics
230926_ctype.h5ad


title: subject3 day1 timepoint9

description: Library name: library53


title: C2


title: NA_unop_1


title: WT, 26W, 1

description:
10x Genomics
230926_ctype.h5ad


title: NA_unop_2


title: C1


title: NA_unop_4


title: R194_rW44SC400.R1

city: Urbana

first: Lila

middle: O.

last: Vodkin

state: IL

address: 1201 W. Gregory Dr.

department: Crop Sciences

institute: University of Illinois

data_processing:
Illumina pipeline for demultiplexing and adaptor removal
Sequenced reads were aligned to 88,647 Glyma1 cDNA soybean gene models determined by the Soybean Genome Project (Schmutz et al. 2010) using Bowtie (Langmead et al. 2009). Bowtie parameters allowed up to three mismatches and up to 25 alignments per read.
Reads per kilobase of gene model per million mapped reads (RPKM) were calculated according to Mortazavi et al. (2008).
Assembly: Glycine max cv. Williams 82 Wm82.a2 at https://phytozome-next.jgi.doe.gov/
Supplementary files format and content: Excel file of the RPKM (reads per million per kilobase) of RNA-seq hits to each soybean Glyma transcript model for each library.

organism: Glycine max

source_name: immature seed coat

growth_protocol: Plants were grown under optimal greenhouse conditions. The developing seed were harvested at the stated mg fresh weight ranges. Whole seeds were dissected by hand into cotyledons and seed coats. Other tissues as seedling cotyledons, vegetative buds, or shoots tips, were extracted from germinating seedlings or 1 month-old plants.

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform, lithium chloride precipitation, and ethanol precipitation.
Libraries were constructed with Illumina Tru Seq or Stranded Tru Seq kits by the University of Illinois DNA Services Laboratory and sequenced using Illumina machines.

treatment_protocol: Standard greenhouse conditions unless otherwise noted in each sample.

value: immature seed coat

tag: stage or_seed_fresh_wt

tag: cultivar

value: Williams 44, i mutation

tag: lab names

tag: phenotype descriptors

value: black seed coat

value: i RT w1

tag: other

value: i inversion

tag: grin l_number_(or_other_designation)

tag: grin pi_number


title: subject3 day1 timepoint8

description: Library name: library52

tag: tissue

value: Urine


title: R193_rW44SC300.R1


title: AR113Q, 26W, 3

description:
10x Genomics
230926_ctype.h5ad


title: subject3 day1 timepoint7

description: Library name: library51


title: R219_44SC50

value: iRT w1


title: WIK_unop_3

tag: cell type

value: cardiac ventricle

value: WIK


title: subject3 day2 timepoint2

description: Library name: library56

tag: batch


title: subject3 day1 timepoint6

description: Library name: library50


title: AR113Q, 26W, 1

description:
10x Genomics
230926_ctype.h5ad

tag: genotype


title: WIK_unop_2

tag: strain

value: uninjured


title: R192_rW44SC75.R1


title: subject3 day1 timepoint5

description: Library name: library49


title: WIK_unop_1

tag: treatment


title: R191_rW44SC25.R1


title: subject3 day1 timepoint4

description: Library name: library48


title: Saline rep_03

city: 北京

first: aking

last: Eco

state: 北京

address: 11# Xizhimen South Street, Xicheng District

department: Rheumotology and Immunology

institute: Peking University People's Hospital

description: single-cell 5' transcriptome library by 10x Genomics

data_processing:
Cell Ranger 6.1.2
The 10× Genomics barcode and UMI sequences were extracted from R1 reads, as well as the insertion fragment sequences from R2 Reads.
The insert fragment extracted reads from R2 in the step above were mapped to the mm10 reference genome using the STAR software.
Barcode correction.
UMI filtering and calibration.
Assembly: mm10 (refdata-gex-mm10-2020-A.tar.gz)
Supplementary files format and content: Tab-delimited text files include filtered counts, genes, barcodes for each sample.

molecule: polyA RNA

source_name: Spleen

growth_protocol: Male DBA1/J mouse aged 8–10 weeks was kept under SPF condition.

extract_protocol:
Spleen was harvested from CIA model treatment with AgTCV, TCV or Saline. The spleen tissue was initially homogenized using a grinding rod. Subsequently, an optimal quantity of digestive enzymes was introduced to facilitate tissue digestion, resulting in the generation of a single-cell suspension.
Single-cells were submitted to 10X Genomics Chromium Controller to generate single-cell 5’ and V(D)J libraries production, using the 10X Genomics Chromium Single Cell Immune Profiling Solution following the manufacturer’s protocol.

treatment_protocol: Collagen-induced arthritis (CIA) mouse was administrated with different conditions, including AgTCV, TCV or Saline.

value: Spleen

tag: Sex

value: Male

tag: condition

value: Collagen-induced arthritis (CIA)

value: Saline


title: Saline rep_02

value: WT


title: R217_44SC10


title: AB_unop_7

value: AB

tag: time (days)


title: Saline rep_01


title: subject3 day1 timepoint2

description: Library name: library46


title: TL_unop_3

value: TL


title: TCV rep_03

value: TCV


title: subject3 day1 timepoint1

description: Library name: library45


title: TL_unop_1


title: subject3 day1 timepoint3

description: Library name: library47


title: D172_CG, Small RNA-Seq

description:
Raw _smRNA_total_and_unique_counts_by_strand.xlsx
CHS_RPMs.xlsx

data_processing:
Adapter trimming was performed using Illumina’s Flicker pipeline which finds the presence of the adapter in each read by finding the best alignment of the adapter to the read, and then removing it from the read.
Alignments of raw sequences were performed using the Bowtie v.1 program (Langmead et al., 2009) allowing 2 mismatches.
Assembly: Williams 82 Wm82a.4 soybean reference genome
Supplementary files format and content: Excel file of the total number or unique number of hits of small RNA sequences to each soybean Glyma transcript model by strand
Supplementary files format and content: Excel file of total and normalized CHS7 and CHS8 reads per million (RPM) for each library.

source_name: shoot tips from Clark glabrous

extract_protocol:
Total RNA was extracted from tissues using phenol:chloroform and ethanol precipitation.
Libraries were constructed with Illumina True-Seq Small RNA kit or Perkin Elmer NextFlex Small RNA sample kit v. 2 by the University of Illinois DNA Services Laboratory using an Illumina HiSeq 2000, or HiSeq 2500 sequencing.

value: shoot tips from Clark glabrous

tag: stage or_seed_fresh_weight

value: shoot tips, 1 cm from adult glaborous plants

tag: lab name

value: CG

tag: phenotype

value: yellow seed coat, black hilum

tag: i locu_genotype

value: i-i R T, P1

tag: other genotype

tag: grin l_number


title: TL_unop_2


title: R215_43SC50

value: immature seed coat

tag: stage or_seed_fresh_wt

tag: cultivar

value: Williams, W43

tag: lab names

tag: phenotype descriptors

value: i-i RT w1

tag: other

tag: grin l_number_(or_other_designation)


title: D170_CS2, Small RNA-Seq

source_name: shoot tips,1 cm, Clark standard

tag: tissue

value: shoot tips,1 cm, Clark standard

value: shoot tips, 1 cm from adult standard plants

value: Clark, UC2

value: CS or UC2

value: i-i R T

tag: grin pi_number


title: TCV rep_01

value: Spleen

tag: genotype

value: WT

tag: strain

tag: Sex

value: Male

value: Collagen-induced arthritis (CIA)

tag: treatment


title: AB_unop_6

tag: cell type

value: cardiac ventricle

value: AB

value: uninjured

tag: time (days)


title: TCV rep_02

tag: condition

value: TCV


title: AgTCV rep_03

value: AgTCV


title: AB_7Dpci_5

value: cryo-injury


title: subject2 day3 timepoint8

description: Library name: library44

source_name: Urine

value: Urine

tag: batch


title: subject2 day3 timepoint6

description: Library name: library42


title: subject2 day3 timepoint7

description: Library name: library43


title: AgTCV rep_02


title: AB_unop_4


title: subject2 day3 timepoint5

description: Library name: library41


title: R213_43SC10

value: immature seed coat

value: Williams, W43

value: yellow seed coat, black hilum

value: i-i RT w1


title: D169_CS, Small RNA-Seq

value: shoot tips,1 cm, Clark standard

tag: stage or_seed_fresh_weight

value: shoot tips, 1 cm from adult standard plants

value: Clark, UC2

tag: lab name

value: CS or UC2

tag: phenotype

tag: i locu_genotype

tag: other genotype

tag: grin l_number


title: KCL_unop_3

value: KCL


title: D175_CGVb, Small RNA-Seq

source_name: vegetative buds from Clark glabrous

value: vegetative buds from Clark glabrous

value: vegetative buds, 5-7 wk plants

tag: cultivar

value: CG

value: i-i R T, P1


title: D171_CF, Small RNA-Seq

source_name: shoot tips from Clark five foliate

tag: tissue

value: shoot tips from Clark five foliate

value: shoot tips, 1 cm from adult five leaflet plants

value: CF

value: i-i R T, Lf1


title: subject2 day3 timepoint4

description: Library name: library40

value: Urine


title: AgTCV rep_01

value: Spleen

value: WT

value: Male

value: Collagen-induced arthritis (CIA)

value: AgTCV


title: KCL_unop_2

source_name: cardiac ventricle

value: cardiac ventricle

value: uninjured


title: P_7d_3

city: Shanghai

first: Yongliang

last: Chen

state: Shanghai

address: No 399. Middle Yanchang Road, JingAn District.

department: Stomatological Hospital and Dental School

institute: Tongji University

data_processing:
Hisat2 for sequence alignment
Stringtie tools for transcript assembly, transcript abundance estimation, gene structure optimization
Samtools tools for related file processing
Assembly: mm9
Supplementary files format and content: Xls file include expression  values for each sample

source_name: the mandibular first molar

extract_protocol:
TRIzol (Thermo Fisher, 15596018) was used to separate and purify total RNA from the samples, following the manufacturer's instructions. The quantity and purity of the total RNA were assessed using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the integrity of RNA was evaluated using Bioanalyzer 2100 (Agilent, CA, USA).
Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: the mandibular first molar

value: periodontitis


title: P_7d_2


title: subject2 day3 timepoint3

description: Library name: library39

data_processing:
Raw sequencing reads were initially processed using UMI-tools. The 5′-end bases, corresponding to miRNA sequences located upstream of the 3’ adapter, were extracted. Simultaneously, 12 bp unique molecular identifiers (UMIs), positioned immediately downstream of the 3′-adapter, were appended to the read identifiers to enable deduplication and subsequent analyses. Reads longer than 19 bases were retained and aligned to the human miRNA reference database provided by miRge 3.0 using Bowtie v1.2.3. Alignment settings allowed no mismatches within a 25-base seed and disallowing reverse complement matches.
Assembly: miRge 3.0
Supplementary files format and content: comma separated file with raw miRNA counts


title: D173_CSVb, Small RNA-Seq

source_name: vegetative buds from Clark standard

value: vegetative buds from Clark standard

value: vegetative buds, 5-7 wk plants

value: Clark, UC2

value: CS or UC2

value: yellow seed coat, black hilum

value: i-i R T

tag: grin pi_number


title: D174_CFVb, Small RNA-Seq

source_name: vegetative buds from Clark five foliate

value: vegetative buds from Clark five foliate

value: CF

value: i-i R T, Lf1


title: KCL_unop_1

value: KCL


title: subject2 day3 timepoint2

description: Library name: library38

value: Urine


title: P_7d_1

tag: genotype


title: sample13-2201

city: Durham

first: Leah

last: Wehmas

state: NC

address: 109 T.W. Alexander Drive

institute: US EPA

description: Library name: sample13-2201

data_processing:
Reads were trimmed at both ends using a minimum Phred score of 20 and a minimum read length of 25 base pairs.
After trimming, reads were aligned to rn7 reference index using Star v2.7.8a with default setting and quantified to Ensembl transcript release 108 using Partek Expectation Maximization.
Genes with a median count <10 across all samples were filtered. The count matrix was used for DESeq2 analysis (Love et al., 2014) implemented in R.4.4.0 (R Core Team 2024). For DESeq2, the noise filtered counts were rounded to the nearest integer.
For benchmark dose response analysis, the the noise filtered targeted RNA-Seq count matrix was adjusted for BioSpyder attenuation, normalized to counts per million mapped reads (CPM), log2 transformed with a 1 positive count adjustment.
Assembly: rn7/ensembl108
Supplementary files format and content: tab delimited file format containing raw count matrix for all samples. Genes in rows, samples as columns
Supplementary files format and content: tab delimited file format containing raw count matrix for all samples adjusted for BioSpyder attenuation. Genes in rows, samples as columns
Supplementary files format and content: tab delimited file format containing attenuation adjusted, noise filtered, counts per million mapped reads normalized, log2 transformed with positive 1 offset matrix for all samples. Genes in rows, samples as columns

organism: Rattus norvegicus

source_name: testis pooled by litter

growth_protocol: Dams were housed individually in clear polycarbonate cages (20 cm × 25 cm × 47 cm) with laboratory grade heat-treated pine shavings (Northeastern Products, Warrensburg, NY) as bedding. Pregnant dams were fed NIH07 Rat Chow and filtered (5 μm filter) municipal drinking water (Durham, NC) ad libitum. Pregnant rats were maintained on a 12:12 h photo period (light/dark cycle, lights off at 7:00 p.m.) and 20–22º C temperature with a 45–55% relative humidity. Water was tested monthly for Pseudomonas and every 4 months for a suite of chemicals, including pesticides and heavy metals. The study was conducted under protocols approved by the National Health and Environmental Effects Research Laboratory Institutional Animal Care and Use Committee and the Association for Assessment and Accreditation of Laboratory Animal Care.

extract_protocol:
RNA was extracted from the pooled fetal testes homogenates (all remaining testes per litter minus three for testosterone measurements) and analyzed for changes in gene expression across all dose groups.  RNA was isolated and purified using Qiagen RNeasy Mini Kit with DNAse digestion according to manufacturer instructions (Valencia, California). RNA concentration and purity were assessed by NanoDrop 2000 Spectrophotometer (Thermo Scientific, Wilmington, Delaware).
Aliquots of testes RNA from Gray et al. 2021 were then submitted to BioSpyder for Templated Oligo-Sequencing (TempO-Seq, BioSpyder Technologies, Carlsbad, CA, USA) using the rat whole transcriptome assay, which targets 21,119 protein coding genes using detector oligo probes. A full description of the assay can be found in Yeakley et al. (2017). Libraries were sequenced on an Illumina Hi-Seq 2500 (San Diego, CA, USA).

treatment_protocol: Pregnant Harlan Sprague Dawley rat dams were randomly assigned to the DCHP treatment group by weight to ensure similar means and variances on gestation day (GD) 14. From GD 14 through 18, the dams were dosed via oral gavage with either the vehicle control (laboratory-grade corn oil; CASRN 8001-30-7) or one of four doses of DCHP (100 mg/kg-day, 300 mg/kg-day, 600 mg/kg-day, n=3 and 900 mg/kg-day, n=2) at 2.5 ml/kg bodyweight. On GD 18, dams were euthanized, and the fetuses removed, and testes dissected before being pooled by litter, homogenized, and stored at -80°C for future analysis.

value: testis pooled by litter

tag: strain

value: Harlan Sprague Dawley

value: male

tag: age at_termination

value: gestational day 18

tag: exposure

value: in utero

tag: exposure duration

value: gestational day 14 to 18

value: dicyclohexyl phthalate (CASRN 84-61-7)

tag: biospyder platform

value: BioSpyder whole transcriptome targeted RNA-seq (21,119 protein coding genes using detector oligo probes) for rat


title: Xenografted microglia library 5, mRNA-derived cDNA

city: Leuven

first: Bart

last: de Strooper

address: Campus Gasthuisberg, Herestraat 49, bus 602

department: VIB-KU Leuven Center for Brain & Disease Research

country: Belgium

institute: KULeuven

description:
Library name: GAL005_cDNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

data_processing:
Cell Ranger v6.1.2 (10x Genomics) was used to align reads to the joint GRCh38/mm10 human/mouse reference genome and to generate feature-barcode matrices.
Further processing was done with Seurat v4.2.3 (cell and gene filtering, hashtag identification, clustering, differential gene expression analysis, gene set enrichment analysis)
Gene co-expression analysis was performed using hdWGCNA (0.3.0)
Assembly: GRCh38/mm10
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Brain

growth_protocol: Mice were housed in groups of 2-5, under a 14/10 h light/dark cycle at 21°C, with food and water ad libitum.

extract_protocol:
Human microglia were freshly isolated from the mouse brain of AppNL-G-F mice. In brief, mice were anesthetized with an overdose of sodium pentobarbital and perfused with ice-cold 1x DPBS (+5U heparin). Freshly collected mouse brains were placed in ice-cold FACS buffer (1x DPBS + 2% FCS + 2 mM EDTA) + 5 μM Actinomycin D (ActD, Sigma, Cat#A1410-5MG). After removal of olfactory bulbs and cerebellum, tissue was dissociated using the Miltenyi neural tissue dissociation kit P (Miltenyi, Cat#130-092-628) by means of mechanical and enzymatic dissociation. Cell suspension was filtered and washed with FACS buffer + 5 μM Actinomycin D and spun at 300g for 5 minutes at 4o degrees. After washing, cell pellet was resuspended in 30% isotonic Percoll and centrifuged for 5 minutes at 300g to remove cell debris and myelin layers. Pelleted cells were incubated for 10 minutes with FcR blockers (mouse, 0.1 mg ml-1, 500 Miltenyi, #130-092-575; human, 0.1 mg ml-1, Miltenyi, # 130-059-901) on ice. After washing, cell pellet was stained with: PE-PanCD11b (1:50, Miltenyi, Cat#130-113-806), BV421-mCD45 (1:500, BD Biosciences, Cat#563890), APC-hCD45 (1:50, BD Biosciences, Cat#555485), TotalSeqTM-A cell hashing antibodies (1:500, Biolegend) and viability dye (eFluor 780, Thermo Fisher Scientific, Cat#65-0865-14) in cold FACS buffer during 30 minutes at 4°C. Cells were washed in ice-cold FACS buffer and resuspended and filtered on a 35 μm strainer with 500 ml of FACS buffer for sorting. Alive human microglia sorting was done on a MACSQuant Tyto Cartridge and human cells were sorted based on CD11b and hCD45 expression at 4 °C.
For single-cell RNA sequencing, 15,000–20,000 human microglia (CD11b+, hCD45+) from each mouse were sorted on the MACSQuant Tyto and diluted to a final concentration of 1,000 cells μl-1. Since all the samples were individually hashed using Total-Seq A cell hashing antibodies, 2,000-4,000 human microglia per animal were pooled and loaded onto the Chromium Next GEM Chip G (PN no. 2000177). The DNA library preparations were generated following the manufacturer’s instructions (CG000204 Chromium Next GEM Single Cell 3′ Reagent Kits v3.1). In parallel, the hashtag oligo libraries were prepared according to the manufacturer’s instructions (BioLegend, Total-Seq A Antibodies and Cell Hashing with 10x Single Cell 3′ Reagent Kit v3 3.1 Protocol) using 16 cycles for the index PCR. A total of 5 libraries containing 12 biological replicates were sequenced (GAL002, GAL004, GAL005, H1 and H2), targeting a 90% messenger RNA and 10% hashtag oligo library (50,000 reads per cell), on a HiSeq4000 (Illumina) platform with the recommended read lengths by the 10X Genomics workflow.

treatment_protocol: The ability of Lecanemab (or mAb158) to reduce Aβ burden was assessed following chronic treatment of 4-month-old male and female AppNL-G-F Csf1rΔFIRE/ΔFIRE mice (or AppNL-G-F mice) dosed weekly intraperitoneally for 8 weeks with 10 mg kg−1 Lecanemab (mAb158), Lecanemab 101 LALA-PG (mAb158 LALA-PG) or IgG1 (IgG2a).

value: Brain

tag: cell line

tag: cell type

value: Microglia

value: APP-NLGF:AB39/AB41/AB53/AB49/AB45; APP-NLGF x FIRE KO:AB79/AB90/AB92/AB93/AB88

tag: treatment

tag: library type

value: mRNA

tag: antibodies/tags


title: P_3d_2

value: the mandibular first molar

value: periodontitis


title: Xenografted microglia library 5, HTO-derived cDNA

description:
Library name: GAL005_HTO
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

value: HTO

value: Anti CD298 and β2 microglobulin: AB01/TotalSeq-A0251; AB02/TotalSeq-A0252; AB03/TotalSeq-A0253; AB04/TotalSeq-A0254; AB05/TotalSeq-A0255; AB08/TotalSeq-A0256; AB09/TotalSeq-A0257; AB12/TotalSeq-A0258; AB13/TotalSeq-A0259; AB14/TotalSeq-A0260; AB16/TotalSeq-A0262


title: sample14-2202

description: Library name: sample14-2202

tag: Sex


title: subject2 day2 timepoint8

description: Library name: library35

extract_protocol:
Approximately 3.5 mL of urine was centrifuged at 2,000 × g for 30 minutes at 4°C to remove cells and debris. From the resulting supernatant, 3 mL was mixed with an equal volume of Total Exosome Isolation Reagent for urine (Thermo Fisher Scientific, Waltham, MA) and incubated at room temperature on a shaker at 100 rpm for 1 hour. The mixture was then centrifuged at 3,000 × g for 1 hour at 4°C to precipitate the EVs. The resulting EV pellet was resuspended in 250 μL of phosphate-buffered saline and subjected to RNA extraction using the MagMAX mirVana Total RNA Isolation Kit with the KingFisher Apex automated system (Thermo Fisher Scientific), following the manufacturer’s instructions. RNA was initially eluted in 30 μL of elution buffer. The eluate was then concentrated at 60°C for 30 to 45 minutes using a centrifugal concentrator (Eppendorf, Hamburg, Germany) and finally resuspended in 5 μL of nuclease-free water. Purified RNA samples were stored at −80°C until further analysis.
Small RNA libraries were prepared using 5 μL of total RNA and the QIAseq miRNA Library Kit (QIAGEN, Hilden, Germany), following the manufacturer’s instructions. Library concentrations were quantified using the Qubit Flex Fluorometer (Thermo Fisher Scientific) with the Qubit™ dsDNA High Sensitivity Assay Kit. Prepared libraries were stored at −20°C until sequencing. Sequencing was performed on a NextSeq 550 system (Illumina, San Diego, CA) using 2 pmol of denatured libraries and single-end 75 bp reads, following the manufacturer’s protocol.

value: Urine

tag: batch


title: subject2 day2 timepoint9

description: Library name: library36


title: P_3d_3


title: sample12-2199

description: Library name: sample12-2199

value: testis pooled by litter


title: AR113Q, 26W, 2

description:
10x Genomics
230926_ctype.h5ad

value: lumbar cord

value: AR113Q knock-in

tag: age

value: 26 weeks


title: subject2 day3 timepoint1

description: Library name: library37


title: P_3d_1


title: sample11-2198

description: Library name: sample11-2198

value: Harlan Sprague Dawley

value: male

value: gestational day 18

value: in utero


title: P_0d_3


title: subject2 day2 timepoint7

description: Library name: library34


title: Xenografted microglia library 4, mRNA-derived cDNA

description:
Library name: GAL004_cDNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: Brain

value: APP-NLGF:AB38/AB40/AB52; APP-NLGF x FIRE KO:AB56/AB57/AB86


title: Xenografted microglia library 3, HTO-derived cDNA

description:
Library name: GAL002_HTO
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

value: Microglia

value: Anti CD298 and β2 microglobulin: AB38/TotalSeq-A0251; AB40/TotalSeq-A0252; AB52/TotalSeq-A0253; AB56/TotalSeq-A0257; AB57/TotalSeq-A0258; AB86/TotalSeq-A0259


title: sample10-2197

description: Library name: sample10-2197

value: gestational day 14 to 18

value: dicyclohexyl phthalate (CASRN 84-61-7)

value: BioSpyder whole transcriptome targeted RNA-seq (21,119 protein coding genes using detector oligo probes) for rat


title: subject2 day2 timepoint6

description: Library name: library33


title: Xenografted microglia library 3, mRNA-derived cDNA

description:
Library name: GAL002_cDNA
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: mRNA


title: Xenografted microglia library 4, HTO-derived cDNA

description:
Library name: GAL004_HTO
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

value: HTO

value: Anti CD298 and β2 microglobulin: AB01/TotalSeq-A0251; AB02/TotalSeq-A0252; AB03/TotalSeq-A0253; AB04/TotalSeq-A0254; AB08/TotalSeq-A0256; AB09/TotalSeq-A0257; AB12/TotalSeq-A0258; AB13/TotalSeq-A0259; AB14/TotalSeq-A0260; AB16/TotalSeq-A0262


title: subject2 day2 timepoint5

description: Library name: library32

value: Urine


title: sample09-2196

description: Library name: sample09-2196

value: testis pooled by litter


title: sample08-2195

description: Library name: sample08-2195


title: subject2 day2 timepoint4

description: Library name: library31


title: Xenografted microglia library 2, HTO-derived cDNA

description:
Library name: H2_H
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

value: APP-NLGF:AB01/AB02/AB03/AB04/AB05/AB08/AB09/AB12/; APP-NLGF x FIRE KO:AB13/AB14/AB16

value: Anti CD298 and β2 microglobulin: AB01/TotalSeq-A0251; AB02/TotalSeq-A0252; AB03/TotalSeq-A0253; AB04/TotalSeq-A0254; AB05/TotalSeq-A0255; AB08/TotalSeq-A0256; AB09/TotalSeq-A0257; AB12/TotalSeq-A0258; AB13/TotalSeq-A0259; AB14/TotalSeq-A0260; AB16/TotalSeq-A0262


title: C_7d_3

value: the mandibular first molar

value: Control


title: C_7d_2


title: C_7d_1


title: subject2 day2 timepoint2

description: Library name: library29


title: Xenografted microglia library 2, mRNA-derived cDNA

description:
Library name: H2_R
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA


title: sample07-2194

description: Library name: sample07-2194

value: Harlan Sprague Dawley

value: male

value: gestational day 18

value: in utero


title: sample06-2193

description: Library name: sample06-2193


title: Xenografted microglia library 1, mRNA-derived cDNA

description:
Library name: H1_R
3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript
poly A RNA

value: Brain

value: Microglia


title: RF023_K562_sh93v4_6D

city: Lausanne

first: Julien

last: Duc

state: VAUD

address: Station 19 CH-1015 Lausanne

department: School of Life Science

country: Switzerland

institute: EPFL

description:
Library name: 2021_09_29_L13
RNAseq on K562 transducedWith pLKO_ZNF93

data_processing:
Raw reads were mapped with hisat2 with -k5 optino to the human hg19 genome
Gene summaziation performed with featureCounts using -Q 10 as option
Assembly: hg19
Supplementary files format and content: countTable raw unique read counts

growth_protocol: K562 were grown in RPMI supplemented with FCS and PSG

extract_protocol:
NucleoSpin RNA Plus, Mini kit for RNA purification with DNA removal column MACHEREY-NAGEL Item number: 740984.50
Illumina mRNA LT Truseq

value: Myeloid

value: WT


title: sample05-2192

description: Library name: sample05-2192

value: gestational day 14 to 18

value: dicyclohexyl phthalate (CASRN 84-61-7)

value: BioSpyder whole transcriptome targeted RNA-seq (21,119 protein coding genes using detector oligo probes) for rat


title: subject2 day2 timepoint1

city: Yushima, Bunkyo-ku, Tokyo

first: Atsushi

last: Satomura

institute: Craif

description: Library name: library28

value: Urine


title: sample04-2191

description: Library name: sample04-2191

value: testis pooled by litter


title: subject2 day1 timepoint9

description: Library name: library27


title: C_3d_3


title: C_3d_2


title: P_0d_1

value: periodontitis


title: C_3d_1


title: RF026_K562_sh93v4_6D

description:
Library name: 2021_09_29_L08
RNAseq on K562 transducedWith pLKO_ZNF93


title: subject2 day1 timepoint8

description: Library name: library26


title: subject2 day2 timepoint3

description: Library name: library30


title: sample01-2188

description: Library name: sample01-2188

value: corn oil vehicle control (CASRN 8001-30-7)


title: Xenografted microglia library 1, HTO-derived cDNA

description:
Library name: H1_H
Cell Hashing library: read1 file contains cell barcode and UMI; read2 file contains Hashtag Antibody Derived Tag reads
Hashtag-derived oligonucleotide (HTO)

value: APP-NLGF:AB01/AB02/AB03/AB04/AB05/AB08/AB09/AB12/; APP-NLGF x FIRE KO:AB13/AB14/AB16

value: HTO

value: Anti CD298 and β2 microglobulin: AB01/TotalSeq-A0251; AB02/TotalSeq-A0252; AB03/TotalSeq-A0253; AB04/TotalSeq-A0254; AB05/TotalSeq-A0255; AB08/TotalSeq-A0256; AB09/TotalSeq-A0257; AB12/TotalSeq-A0258; AB13/TotalSeq-A0259; AB14/TotalSeq-A0260; AB16/TotalSeq-A0262


title: subject2 day1 timepoint6

description: Library name: library24


title: C_0d_2

value: the mandibular first molar

value: Control


title: primary cells, EGK.X stage embryo, sample 3

city: Pasadena

first: Xi

state: California

address: 1200 E. California Blvd

institute: California Institute of Technology

data_processing:
Raw fastq files were ran through FASTQC program for quality control
Raw fastq files were then aligned to chicken genome Gg6 using STAR software
Reads were counted by RSEM software
Raw counts were processed in R for downstream analysis -- Differentially expressed genes analyzed by DESeq2; Plots generated by ggplot2; etc.
Assembly: Gg6
Supplementary files format and content: text file containg gene ID and raw counts

organism: Gallus gallus

source_name: freshly laid EGK.X embryo

growth_protocol: Freshly laid avian fertile eggs at EGK.X-XII stages were kept at 16 °C before extraction. To harvest cells from yolk, a filter paper-based method was applied (Chapman et al., 2001). Filter paper with a hole at center was placed on top of the embryo. The outer edge of the filter paper was cut together with the vitelline membranes. Embryo were then released from yolk together with the filter paper and washed in PBS solution. Next, embryo was transferred into a 15ml tube free of the paper ring and dissociated by pipetting inside N2B27 medium. Dissociated cells were cultured in tissue plates coated with irradiated mouse embryonic fibroblast (MEF) cells as feeder layer. Basal medium used for routine ESC maintenance was N2B27 medium composed of DMEM/F12:Neuralbasal (1:1) plus 0.5x N2, 0.5x B27 supplement and 10ng/ml ovotransferrin with the addition of 1x penicillin-streptomycin. Avian ESC self-renewal was kept with 2.5µM IWR-1, 2µM Gö6983, 2µM SB431542 plus chicken LIF (10ng/ml for cESCs and 20ng/ml for other avian ESCs). ESCs were cultured at 38 °C in 5% CO2 with daily medium change. To passage, TrypLE was used to incubate the cells for 5 min and neutralized with basal medium in triple amount. Cells were handled with 5ml pipette all the time to avoid dissociation into singles.

extract_protocol:
Total RNA of chicken embryos and in-vitro expanded cells was extracted using the RNeasy Mini Kit (QIAGEN) according to manufacturer’s instructions.
BGISEQ-500 library construction protocol

value: freshly laid EGK.X embryo

value: primary cells


title: RF022_K562_sh93v4_6D

description:
Library name: 2021_09_29_L03
RNAseq on K562 transducedWith pLKO_ZNF93


title: C_0d_1


title: subject2 day1 timepoint4

address: 5F ITP Hongo Office , 2-25-7

description: Library name: library22


title: RF022_K562_shscr_6D

description:
Library name: 2021_09_29_L01
RNAseq on K562 transducedWith pLKO_scr


title: primary cells, EGK.X stage embryo, sample 2


title: RF023_K562_shscr_6D

description:
Library name: 2021_09_29_L11
RNAseq on K562 transducedWith pLKO_scr


title: KO_3

source_name: alveolar bone

value: alveolar bone

value: MSCs


title: sample02-2189

description: Library name: sample02-2189

value: Harlan Sprague Dawley

value: male

value: gestational day 18

value: in utero


title: sample03-2190

description: Library name: sample03-2190

value: gestational day 14 to 18

value: BioSpyder whole transcriptome targeted RNA-seq (21,119 protein coding genes using detector oligo probes) for rat


title: subject2 day1 timepoint3

description: Library name: library21

value: Urine


title: primary cells, EGK.X stage embryo, sample 1

value: WT


title: P_0d_2

value: periodontitis


title: C_0d_3


title: subject2 day1 timepoint7

description: Library name: library25


title: RF026_K562_shscr_6D

description:
Library name: 2021_09_29_L06
RNAseq on K562 transducedWith pLKO_scr

value: Myeloid


title: UM-Chor1, T-DARPin_D4, rep2

city: Heidelberg

first: Cihan

last: Erkut

address: Im Neuenheimer Feld 581

department: Applied Functional Genomics

institute: German Cancer Research Center

data_processing:
DKFZ ODCF RNA-seq workflow 1.3.0 (https://github.com/DKFZ-ODCF/RNAseqWorkflow)
Basecalling was performed using bcl2fastq 2.20.0.422.
FASTQ reads for individual samples were aligned by a 2-pass alignment using the STAR aligner 2.5.3a.
Duplicate marking of the resultant main alignment file was done with sambamba 0.6.5.
The chimeric file was sorted using samtools 1.6.
BAM indexes were generated using sambamba 0.6.5.
Quality control analysis was performed using samtools flagstat and the rnaseqc tool version 1.1.8. Depth of coverage analysis for rnaseqc was turned off.
Gene-specific read counting was performed using featureCounts version 1.5.1 over exon features based on the GENCODE 19 gene models. Only unique alignments were counted. Strand specific counting was also used.
A custom script was used to calculate RPKM and TPM expression values. For total library abundance calculations, all genes on chromosomes X, Y, MT as well as rRNA and tRNA genes were omitted, as they are likely to introduce library size estimation biases.
Assembly: 1000 Genomes Project Phase II Reference Genome (hs37d5) based on NCBI GRCh37, and GENCODE 19 gene models.
Supplementary files format and content: Tab-delimited text files with gene IDs, gene names, raw counts, RPKM and TPM values.

growth_protocol: Cells were cultured in IMDM:RPMI-1640 (4:1, Gibco) with 10% FBS (Sigma-Aldrich), 1% penicillin/streptomycin (P/S, Gibco), and 1x non-essential amino acids (NEAA, Sigma-Aldrich) on collagen I-coated flasks under standard conditions (37 ˚C, 5% CO2).

extract_protocol:
Cell pellets were resuspended with 350 μL RLT buffer on ice, lysed with a 26-gauge needle, and processed with the RNAeasy Mini Kit (Qiagen), including a DNAse I digestion step. Eluted RNA was immediately frozen at −80°C with 1 µL RNaseOUT (Invitrogen) after quantification with a NanoDrop One system (Thermo Scientific). RNA purity was confirmed (RIN > 8) on a TapeStation (Agilent).
Libraries were prepared using Illumina TruSeq Stranded Kit according to manufacturer's recommendations.

value: Chordoma

value: T-DARPin D4


title: UM-Chor1, T-DARPin_D4, rep3


title: subject2 day1 timepoint2

description: Library name: library20


title: KO_1


title: chicken embryonic stem cells, p10, sample 3

value: cES p10

value: embryonic stem cells


title: subject2 day1 timepoint5

description: Library name: library23


title: chicken embryonic stem cells, p10, sample 2

value: freshly laid EGK.X embryo


title: KO_2

value: alveolar bone


title: WT_3

value: MSCs


title: chicken embryonic stem cells, p10, sample 1


title: UM-Chor1, T-DARPin_D4, rep1


title: subject2 day1 timepoint1

description: Library name: library19


title: UM-Chor1, T-DARPin_B1, rep3

value: T-DARPin B1


title: subject1 day3 timepoint6

description: Library name: library18


title: WT_2


title: subject1 day3 timepoint5

description: Library name: library17


title: UM-Chor1, T-DARPin_B1, rep1


title: subject1 day3 timepoint4

description: Library name: library16


title: UM-Chor1, T-DARPin_B1, rep2


title: UM-Chor1, T-DARPin_A2, rep3

value: T-DARPin A2


title: subject1 day3 timepoint3

description: Library name: library15


title: HFD, skin,  IL-23 4

city: Inchon

first: YunJae

last: Jung

address: 155 Gaetbeol-ro, Yeonsu-gu

department: Microbiology

country: South Korea

institute: College of Medicine, Gachon University

description:
HFD9_IL-23_2
Normalized.txt

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Read count were calculated by using StringTie version 2.1.3b, with parameter --rf -l -o -G -A -e
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count, FPKM, TPM values for each Sample

source_name: HFD Skin IMQ + IL-23

growth_protocol: Six week-old C57BL/6 male mice were purchased from Orientbio (Gyeonggi-do, Korea). The mice were kept under standard temperature and humidity conditions in a specific pathogen-free environment. All procedures involving mice were reviewed and approved by the Center of Animal Care and Use of the Lee Gil Ya Cancer and Diabetes Institute, Gachon University.

extract_protocol:
RNA from the skin and small intestines of the mice was extracted using QIAzol and purified using an RNeasy mini kit. The purified RNA was processed with DNase I  to remove genomic DNA.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Prior to the start of the experimentation, the mice underwent a shaving procedure. Following a 12-week dietary period, the mice received a daily topical application of 62.5 mg of IMQ cream (5%) (Aldara™) on their shaved back continuously for a period of 5 consecutive days. Additionally, to induce intradermal IL-23-induced psoriatic skin inflammation, the mice were administered daily injections of 1 μg of rmIL-23 in PBS at a designated location on their shaved backs for five days.

value: male

value: Adipose tissue

tag: diet

value: HFD

value: Imiqiumod + Recombinant IL-23

tag: condition

value: Psorisis


title: HFD, skin,  IL-23 5

description:
HFD9_IL-23_3
Normalized.txt

tag: tissue


title: subject1 day3 timepoint2

description: Library name: library14

value: Urine


title: HFD, skin,  IL-23 3

description:
HFD9_IL-23_1
Normalized.txt


title: UM-Chor1, T-DARPin_A2, rep2


title: UM-Chor1, T-DARPin_A2, rep1


title: subject1 day3 timepoint1

description: Library name: library13


title: UM-Chor1, DARPin_E3_5, rep2

value: DARPin E3_5


title: HFD, skin,  IL-23 1

description:
HFD7_IL-23_1
Normalized.txt


title: subject1 day2 timepoint6

description: Library name: library11


title: HFD, skin,  IMQ 5

description:
HFD12_IMQ_14
Normalized.txt

source_name: HFD Skin IMQ

value: Imiqiumod


title: subject1 day2 timepoint7

description: Library name: library12


title: UM-Chor1, DARPin_E3_5, rep3

value: Chordoma


title: UM-Chor1, DARPin_E3_5, rep1


title: WT_1

tag: genotype

value: WT


title: HFD, skin,  IMQ 4

description:
HFD12_IMQ_12
Normalized.txt

tag: strain


title: shV-3

city: harbin

first: Lei

last: Gao

address: nagang street

institute: harbin medical university

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 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. GTF file:https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz.
Using macs3 (v3.0) to identify peaks in m6A sequencing data, and annotating the gene information and location of the peaks with ChIPseeker (v1.26.2).
Assembly: CRCh38
Supplementary files format and content: Count/FPKM, peaks, bw files

growth_protocol: The human pancreatic cancer cell lines were purchased from the Shanghai Cell Bank of Chinese Academy of Sciences (Shanghai, China). The cancer cell lines were cultured in DMEM medium containing 10% fetal bovine serum (FBS), 100 U/mL penicillin, 100 U/mL streptomycin and 0.03% glutamine at 37 oC in 5% CO2.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer’s procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA), and the RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA).
For mRNA-seq: A total amount of 1.5 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA) following manufacturer's recommendations and index codes were added to attribute sequences to each sample.
For m6A-seq: Poly (A) RNA was purified from 50μg total RNA using Dynabeads Oligo (dT) 25-61005 (Thermo Fisher, CA, USA) by two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 86℃ 7min. The cleaved RNA fragments were in cubated for 2h at 4℃ with m6A-specific antibody (No. 202003, Synaptic Systems, Germany) in IP buffer (50 mM Tris-HCl, 750 mM NaCl and 0.5% Igepal CA-630). The IP RNA was reverse-transcribed to cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which was next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA. An A-base was added to the blunt ends of each strand, preparing for ligation to the indexed adapters. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min.

treatment_protocol: The human cell lines transfected with Lentivirus, and digested for next studies.

value: pancreatic cancer cell

value: VIRMA knockdown

value: lv-sh-virma


title: subject1 day2 timepoint4

description: Library name: library9


title: HFD, skin,  IMQ 3

description:
HFD8_IMQ_5
Normalized.txt


title: shV-2


title: HFD, skin,  IL-23 2

description:
HFD7_IL-23_4
Normalized.txt


title: HFD, skin,  IMQ 2

description:
HFD8_IMQ_4
Normalized.txt


title: subject1 day2 timepoint3

description: Library name: library8


title: HFD, skin,  IMQ 1

description:
HFD8_IMQ_1
Normalized.txt


title: shV-1


title: subject1 day2 timepoint1

description: Library name: library6


title: subject1 day2 timepoint5

description: Library name: library10


title: subject1 day2 timepoint2

description: Library name: library7


title: 24W-Head3

type: RNA

city: Fuzhou

first: Jinyan

address: No.7 Wusi Road

institute: Fufian Academy of Medical Sciences

description: lncRNA and mRNA expression profiles

hyb_protocol: The fluorescent cRNAs were hybridized onto the lncRNA expression microarray slide. The hybridized slides were then washed, fixed, and scanned by the Agilent DNA Microarray Scanner (part number G2505C).

data_processing: The array images were acquired and analyzed with using Agilent Feature Extraction software (version 11.0.1.1). Quantile normalization of the raw data was performed with using the GeneSpring GX v12.1 software package (Agilent Technologies).

source_name: Islets from head region of pancreatic

label_protocol: rRNA and tRNA were removed to purify total RNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre, Madison, WI, USA). Then, each sample was amplified and transcribed into fluorescent cRNAs along the entire length of the transcript without 3’ bias utilizing a random priming method.

extract_protocol: Total RNA from the isolated islets was extracted using TRIzol Reagent (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. RNA integrity was assessed by standard denaturing agarose gel electrophoresis, and quantity and quality were measured by NanoDrop ND-1000 spectrophotometer (OD 260 nm, NanoDrop Technologies, Wilmington, DE, USA).

treatment_protocol: The common bile duct of the anesthetized rats were isolated, clamped off and cannulated near the junction of the small intestine. Then 10 mL of 0.5mg/mL ductal collagenase (Type XI, Sigma, Cat. # C7657) solution (1% BSA in Hank’s Balanced Salt Solution, HBSS, Gibco) was dispensed to perfuse the pancreas. After removed from the rat, the perfused pancreas was cut into two parts, the head (duodenal part) and the tail (spleen part) that placed in 50 ml conical tube respectively. The digestion was performed at 37° C for 16 min with hand-shaking for 15 seconds to dissociate the suspension into a homogeneous slurry and stopped by the HBSS on ice. After three washes, the pellet was re-suspended with 30% BSA in HBSS and filtered through a 850 μm cell strainer to remove impurities. In order to acquirean adequate quality, quantity, and purity of islets, the filtrate was collected and purified with density gradient centrifugation using a Biocoll Separating Solution (Biochrom AG) at 4° C. Islet yield were then picked up manually and the purity and specificity were evaluated by dithizone staining.

value: head region of pancreatic

value: Pancreatic islet


title: shNC-2

value: NC


title: shNC-3


title: 24W-Tail2

description: lncRNA and mRNA expression profiles

scan_protocol: The hybridized slides were then washed, fixed, and scanned by the Agilent DNA Microarray Scanner (part number G2505C).

source_name: Islets from tail region of pancreatic

value: tail region of pancreatic


title: 24W-Tail3

description: lncRNA and mRNA expression profiles

value: male


title: shNC-1


title: 24W-Tail1

description: lncRNA and mRNA expression profiles


title: Chow, skin,  IMQ 4

description:
Set8-2ChowIMQ4
Normalized.txt

source_name: Chow Skin IMQ

value: Adipose tissue

value: Chow


title: subject1 day1 timepoint4

description: Library name: library4


title: shV-input

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reads were mapped to human genome assembly GRCh38 (ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz) using HISAT2.
HTSeq v0.13.5 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. GTF file:https://ftp.ensembl.org/pub/release-104/gtf/homo_sapiens/Homo_sapiens.GRCh38.104.gtf.gz.
Using macs3 (v3.0) to identify peaks in m6A sequencing data, and annotating the gene information and location of the peaks with ChIPseeker (v1.26.2).
Assembly: CRCh38
Supplementary files format and content: Count/FPKM, peaks, bw files
Library strategy: m6A-Seq


title: Chow, skin,  IMQ 3

description:
Set8-1ChowIMQ3
Normalized.txt


title: subject1 day1 timepoint2

description: Library name: library2


title: Chow, skin,  IMQ 5

description:
Set8-2ChowIMQ6
Normalized.txt


title: shV-m6A


title: 24W-Head2

description: lncRNA and mRNA expression profiles


title: subject1 day1 timepoint3

description: Library name: library3


title: Chow, skin,  IMQ 1

description:
Set8-1ChowIMQ1
Normalized.txt


title: subject1 day1 timepoint5

description: Library name: library5


title: Chow, skin,  IMQ 2

description:
Set8-1ChowIMQ2
Normalized.txt


title: shNC-m6A


title: 24W-Head1

description: lncRNA and mRNA expression profiles


title: tumor tissues,CM-ZIF8 at Ce6/Lon+L, rep3

city: Beijing

first: yanghong

last: liu

address: No.2 Nanwei Road, Xicheng District

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

data_processing:
Bioinformatics analysis of RNA-seq data was performed with R software(V 4.1.0). Differentially expressed genes (DEGs) were got using the DESeq2 package (v1.26.0) (10.1186/s13059-014-0550-8), with the following creteria: p < 0.01 and absolute log2 fold change > 1. Pathway enrichment were performed using kobas (doi.org/10.1093/nar/gkab447). Gene pathway network were plotted using the cluster Profiler package (v 4.2.2). The heatmap was plotted using the pheatmap package (v1.0.12). Protein-protein interaction network analysis were performed by String DB.
Assembly: GRCm38

source_name: tumor tissues

extract_protocol:
the total RNA of tumor tissues in 5% glucose and CM-ZIF8 at Ce6/Lon+L group were  extracted using Trizol reagent.
RNA-seq libraries were prepared according to the manufacturer's library construction protocol.RNA quality was evaluated by Agilent 2100 BioAnalyzer (Agilent RNA 6000 Nano Kit). mRNA was purified via an oligo (dT) and subjected to sequencing library constructions. The  library quality  was performed using an Agilent 2100 Bioanalyzer and ABI StepOnePlus Real-Time PCR System. RNA-seq was carried out using an Novaseq600 with 150 base pair reads.

value: tumor tissues

value: BALB/c mice


title: H3K4_93v2

description:
Library name: nxid21414
H3K4 ZNF93 KD

library_source: genomic

data_processing:
Raw data were mapped using bowtie2 with --sensitive-local mode
Peaks were called using seacr with parameters stringent
Assembly: hg19
Supplementary files format and content: Bedfile as outputed by SEACR of the Cut&Tag peaks
Library strategy: Cut & Tag

molecule: genomic DNA

growth_protocol: HEK293T were grown in DMEM supplemented with FCS and PSG

extract_protocol:
According to protocol from Zhao et al ., 2020
BrdU-Seq (NEBNext UltraII DNA Library Prep for Illumina)
NEBNext Ultra DNA Library Prep Kit for Illumina (NEB, cat. no. E7370)

treatment_protocol: No

value: Myeloid

tag: chip antibody

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9756


title: H3K4_93v3

description:
Library name: nxid21415
H3K4 ZNF93 KD

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9757


title: Healthy3_ADT

city: Stanford

first: Asiri

last: Ediriwickrema

address: 265 Campus Dr

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

data_processing:
raw data was processed using sevenbridges per BD Rhapsody protocol recommendations
Assembly: hg38
Supplementary files format and content:  output files are count tables for both genes and adts in a csv file.

molecule: protein

source_name: bone marrow

extract_protocol:
cryopreserved bone marrow cells were thawed and submitted for single cell capture and processing using the BD Rhapsody workflow
libraries were generated according to manufacter's instructions.

value: bone marrow

tag: ethnicity

value: Other

value: ADT


title: shNC-input

value: pancreatic cancer cell


title: Healthy2_ADT

value: female

value: White


title: H3K4_93v1

description:
Library name: nxid21413
H3K4 ZNF93 KD

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9755


title: tumor tissues, CM-ZIF8 at Ce6/Lon+L, rep1


title: tumor tissues, CM-ZIF8 at Ce6/Lon+L, rep2


title: Healthy1_ADT


title: H3K4_scr4

description:
Library name: nxid21412
H3K4 scranble

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9754


title: H3K4_93v4

description:
Library name: nxid21416
H3K4 ZNF93 KD

value: Tri-Methyl-Histone H3 (Lys4) (C42D8) Rabbit mAb #9758


title: Healthy3_WTA

value: male

value: GEX


title: tumor tissues, 5% glucose, rep2


title: ST-LPD2 (LPD treated  Raw264.7 cells with Salmonella infection)

city: Changchun

first: Jiazhang

last: Qiu

address: Xi'an Road 5333

institute: Jilin University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: Mus musculus  Ensembl_v101
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Murine monocyte-macrophage leukemia cells


title: ST-LPD3 (LPD treated  Raw264.7 cells with Salmonella infection)


title: tumor tissues, 5% glucose, rep1

value: tumor tissues


title: subject1 day1 timepoint1

description: Library name: library1

source_name: Urine

value: Urine


title: Healthy2_WTA