title: Mouse_cerebellum_E18_female_replicate2

description: 10x Genomics

value: female


title: MKN45 cells, Negative control -1

status: Public on Mar 25 2026

type: SRA

city: Ji'nan

first: Shi

last: Duanbo

state: Shandong

address: wenhua xi road 44#

country: China

institute: Shandong University

library_source: transcriptomic

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded fromgenome website directly. Index of the reference genome was built using Hisat2 v2.0.5and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
feature Counts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Assembly: GRCh38
Supplementary files format and content: ab-delimited text flies include RPKM values for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: stomach

growth_protocol: MKN45 cells were supplemented with 10% fetal bovine serum (FBS) in humidifed atmosphere with 5% CO2 at 37℃

extract_protocol:
RNA was harvested using Trizol reagent. NEBNext® Ultra™ RNA Library Prep Kit for Illumina®(NEB #E7530S/L) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: INHBA was overexpressed in MKN45 cells by transfecting LV-GV493-IHNBA, while the other cells was transfected with LV-GV493-Negative control as control group. All the cells were cultrued for 48 hours.

tag: tissue

value: stomach

tag: cell line

tag: cell type

value: gastric cancer cell line

tag: genotype

value: Negative control

tag: treatment

value: MKN45 cells transfected with LV-GV493-Negative contol


title: Mouse_cerebellum_E18_male_replicate1

city: Toronto

first: Michael

middle: D.

last: Taylor

state: Ontario

address: 555 University Ave

department: DSCB

country: Canada

institute: The Hospital for Sick Children

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger software v.3.0.2 default pipeline
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: cerebellum

extract_protocol:
Hindbrain structures were dissected from mice, dissociated into single cell suspensions using papain and were run on the 10X Genomics Chromium Controller using the Chromium Single Cell 3' Solution V3 protocols
10x Genomics Chromium Single Cell 3' Solution V3 protocols

value: cerebellum

tag: developmental stage

value: Embryonic day 18.5

tag: Sex

value: male

tag: strain

value: wild type


title: MKN45 cells, INHBA overexpressing -2

value: INHBA overexpressing

value: MKN45 cells transfected with LV-GV493-INHBA


title: CD4 positive sorted CAR T-cell (pooled from 5 mice), unirradiated (NRT, 0 Gy) from mouse Lung tumor

city: New York

first: Laszlo

last: Halasz

state: NY

address: 1470 Madison Avenue

department: Department of Oncological Sciences

country: USA

institute: Mount Sinai Icahn School of Medicine

data_processing:
RNA-seq data was performed by nf-core/rnaseq pipeline (version 3.9).
In brief, adapters and low quality reads were filtered by trimgalore (0.6.6). Cleaned reads were aligned to the mouse reference genome with STAR and genes were quantified using Salmon.
Assembly: mm39
Supplementary files format and content: Comma separated tables containing Salmon quantified raw gene counts for each sample. CPM values were created using EdgeR's cpm function.

molecule: polyA RNA

source_name: Lung

extract_protocol:
Total RNA was extracted from cells following the Trizol Reagent User Guide (Thermo Fischer Scientific). Extracted RNA were quantified using Qubit 2.0 Fluorometer and RNA integrity was checked using Qubit 2.0 Fluorometer.
SMARTSeq HT Ultra Low Input Kit was used for full-length cDNA synthesis and amplification, and Illumina Nextera XT library was used for library preparation.
Low count RNA-seq

value: Lung

value: CAR T cells

tag: cell subset

value: CD4 positive

value: 0 Gy


title: Mouse_cerebellum_E18_female_replicate1

description: 10x Genomics


title: CV051T

city: Singapore

first: Oleg

last: Grinchuk

address: 61 Biopolis Dr, Proteos

country: Singapore

institute: IMCB

description: Library name: Sample 39

data_processing:
RNA-seq data quality was monitored via FASTQC package (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Reads preprocessing was performed by Trim_galore with default parameters.
Mapping of RNA-seq reads was done using bowtie2 with default parameters for paired  RNA-seq data.
RSEM software (Li and Dewey, 2011)  were used to quantify the gene-level expression.
Assembly: hg19
Supplementary files format and content: txt format; processed counts, TPM (Transcripts Per Kilobase Million).

source_name: colorectal tumor

extract_protocol:
RNA was isolated using EZNA total RNA Kit (Omega #R6834-02) according to manufacturer’s instructions.
The mRNA is fragmented randomly by adding fragmentation buffer, then the cDNA is synthesized by using mRNA template and random hexamers primer, after which a custom second-strand synthesis buffer (Illumina) , dNTPs, RNase H and DNA polymerase I are added to initiate the second-strand synthesis. Second, after a series of terminal repair, a ligation and sequencing adaptor ligation, the double-stranded cDNA library is completed through size selection and PCR enrichment.

value: colorectal tumor

tag: batch


title: MKN45 cells, INHBA overexpressing -1


title: CV050T

description: Library name: Sample 38


title: 2642, Homo sapiens, Blood,Blood

city: Groton

first: Darien

last: Capunitan

state: CT

address: 255 Shennecossett Rd

institute: Pfizer

description: Library name: itox002642

data_processing:
The BCL files were demultiplexed using BaseSpace software with bcl2fastq function. Reads were processed to count values through a modified nf-core RNAseq pipeline (v3.14.0) executed with Nextflow (v23.10.0). The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1). Resulting counts were stored in MySQL database and linked to human orthologs through ensembl annotation and sequence similarity.
Assembly: The selected workflow included pseudo-alignmentto respective ensembl transcriptome (v110) and quantitation with salmon (v1.10.1).
Supplementary files format and content: csv file includes read counts for each Sample
Supplementary files format and content: rds of read count mapped to human

source_name: Blood,Blood

extract_protocol:
RNA was isolated from tissues using the RNeasy mini kit (Qiagen #74534) according to manufacturer’s protocol. RNAseq cDNA libraries were prepared from 1 μg total RNA using the Illumina TruSeq stranded mRNA kit (Cat. No. RS-122-2101) according to the manufacturer's instructions.
After elution, libraries were quantified using the Qubit 4 Fluorometer (ThermoFisher Scientific, #Q33238) using the Qubit 1X dsDNA Assay Kit (ThermoFisher Scientific, #Q32853).

value: Blood,Blood


title: Mouse_cerebellum_E16_male_replicate2

description: 10x Genomics

value: Embryonic day 16.5


title: 2640, Homo sapiens, Blood,Blood

description: Library name: itox002640


title: CV045T

description: Library name: Sample 37


title: 2644, Homo sapiens, Blood,Blood

description: Library name: itox002644


title: CV044T

description: Library name: Sample 36


title: 2643, Homo sapiens, Blood,Blood

description: Library name: itox002643


title: TSC2

city: New Haven

first: Tyler

middle: Barry

last: Jensen

address: 10 Amistad Street 214A

department: Genetics

institute: Yale University

data_processing:
Star aligner, samtools, subread featurecounts
Assembly: hg38
Supplementary files format and content: counts table

source_name: H1 hESC mTeSR

extract_protocol:
Rneasy total rna extraction
NEB Poly-A selection kit, NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina

value: H1 hESC mTeSR

value: Trophoblast stem cell

value: WT


title: 2641, Homo sapiens, Blood,Blood

description: Library name: itox002641


title: Mouse_cerebellum_E16_male_replicate1

description: 10x Genomics


title: TSC1


title: 2468, Homo sapiens, Eye-Cornea,Eye-Cornea

description: Library name: itox002468

source_name: Eye-Cornea,Eye-Cornea

value: Eye-Cornea,Eye-Cornea


title: CV041T

description: Library name: Sample 34


title: Mouse_cerebellum_E16_female_replicate1

description: 10x Genomics

value: cerebellum

value: female


title: STB2

value: Syncytiotrophoblast


title: Mouse_cerebellum_E16_female_replicate2

description: 10x Genomics

value: wild type


title: CV042T

description: Library name: Sample 35


title: ESC2

value: hESC primed


title: 2469, Homo sapiens, Eye-Retina,Eye-Retina

description: Library name: itox002469

source_name: Eye-Retina,Eye-Retina

value: Eye-Retina,Eye-Retina


title: 2470, Homo sapiens, Eye-Cornea,Eye-Cornea

description: Library name: itox002470


title: STB1


title: CV038T

description: Library name: Sample 32


title: CV039T

description: Library name: Sample 33


title: Mouse_cerebellum_E14_male_replicate1

description: 10x Genomics

value: Embryonic day 14.5

value: male


title: CV036T

description: Library name: Sample 31


title: 2471, Homo sapiens, Eye-Cornea,Eye-Cornea

description: Library name: itox002471


title: Mouse_cerebellum_E14_female_replicate2

description: 10x Genomics


title: ESC1


title: KD_hBlastoid

data_processing:
Cell ranger
Assembly: hg38
Supplementary files format and content: Cells, counts, indexes

source_name: H1 hESC PXGL

extract_protocol:
Poly A
!0x Library Prep

value: H1 hESC PXGL

value: hBlastoid


title: 2472, Homo sapiens, Eye-Retina,Eye-Retina

description: Library name: itox002472


title: Mouse_cerebellum_E14_female_replicate1

description: 10x Genomics


title: Mouse_cerebellum_E14_male_replicate2

description: 10x Genomics


title: WT_hBlastoid

value: shControl


title: LEC, R&D rhAng2, 6h, rep4

city: Helsinki

first: Pipsa

last: Saharinen

address: Haartmaninkatu 8

country: Finland

institute: University of Helsinki

description:
Library name: A2_6h_4
10x Genomics

data_processing:
Raw sequencing reads were quality assessed using FastQC and adapter sequences were removed using Trim Galore. Trimmed reads were aligned to the human reference genome using STAR. Duplicate reads were marked using Picard. Gene-level read counts were generated using featureCounts, and transcript-level expression was quantified using StringTie. Quality control metrics were assessed using RNA-SeQC, RSeQC, Preseq, dupRadar, and gene body coverage analysis.
Assembly: GRCh38
Supplementary files format and content: Tab-separeted value files and matrix files

source_name: skin

growth_protocol: Human dermal Lymphatic endothelial cells (LECs, Promocell)  were maintained in EBMV2 (PromoCell). Media was supplemented with fetal bovine serum (5% final concentration, FBS) and growth supplements, provided by the manufacturers.

extract_protocol:
RNA was isolated from LECs using RNeasy Micro Kit by Qiagen (Cat. No. 74004).
Bulk RNA-seq libraries were prepared using the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs, Ipswich, MA) following the manufacturer’s protocol.

treatment_protocol: LECs were starved for 2.5 h in starvation media consisting of a final FBS concentration 0.5% after which the cells were stimulated with 500ng mL-1 R&D rhAngpt2 for 3 hrs and 6 hrs.

value: skin

value: Human Dermal Lymphatic Endothelial Cells (HDLEC)

value: R&D rhAng2


title: Mouse_cerebellum_E13_male_replicate1

description: 10x Genomics

value: Embryonic day 13.5


title: MMPLACENTA2

data_processing:
star aligner, samtools, subread featurecounts
Assembly: hg38, mm10
Supplementary files format and content: counts table

source_name: Term Placenta

extract_protocol:
Rneasy total RNA
Epicentre Ribo-zero™ rRNA Removal Kit followed by the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina

value: Term Placenta

value: WT


title: Mouse_cerebellum_E13_male_replicate2

description: 10x Genomics

value: cerebellum


title: LEC, R&D rhAng2, 6h, rep3

description:
Library name: A2_6h_3
10x Genomics


title: MMPLACENTA1


title: Mouse_cerebellum_E13_female_replicate2

description: 10x Genomics

value: female


title: CV034T

description: Library name: Sample 30

value: colorectal tumor


title: CV031_T

description: Library name: Sample 28


title: LEC, R&D rhAng2, 6h, rep1

description:
Library name: A2_6h_1
10x Genomics


title: CV030_T

description: Library name: Sample 27


title: Mouse_cerebellum_E13_female_replicate1

description: 10x Genomics

value: wild type


title: LEC, R&D rhAng2, 6h, rep2

description:
Library name: A2_6h_2
10x Genomics


title: LEC, R&D rhAng2, 3h, rep4

description:
Library name: A2_3h_4
10x Genomics


title: CV033_T

description: Library name: Sample 29


title: HSPLACENTA1


title: CV026_T

description: Library name: Sample 25


title: Mouse_hindbrain_E12_male_replicate2

description: 10x Genomics

source_name: hindbrain

value: hindbrain

value: Embryonic day 12.5


title: LEC, R&D rhAng2, 3h, rep3

description:
Library name: A2_3h_3
10x Genomics


title: CV025_T

description: Library name: Sample 24


title: shH2AJ_TSC-Primed_Rep1

data_processing:
star aligner, samtools, subread featurecounts
Assembly: hg38
Supplementary files format and content: counts table

value: H1 hESC mTeSR

value: Trophoblast stem cell

value: shH2AJ stable line

value: H2AJ knockdown


title: shH2AJ_TSC-Primed_Rep2


title: Mouse_hindbrain_E12_female_replicate2

description: 10x Genomics


title: HSPLACENTA2


title: CV028_T

description: Library name: Sample 26


title: CV023_T

description: Library name: Sample 23


title: shH2AJ_TSC-Naive_Rep1

value: H1 hESC PXGL


title: Mouse_hindbrain_E12_female_replicate1

description: 10x Genomics


title: LEC, R&D rhAng2, 3h, rep2

description:
Library name: A2_3h_2
10x Genomics

value: skin


title: CV021_T

description: Library name: Sample 22


title: Mouse_hindbrain_E12_male_replicate1

description: 10x Genomics

value: male


title: LEC, BSA, rep 4

description:
Library name: CTRL_4
10x Genomics

value: Human Dermal Lymphatic Endothelial Cells (HDLEC)

value: BSA


title: LEC, R&D rhAng2, 3h, rep1

description:
Library name: A2_3h_1
10x Genomics

value: R&D rhAng2


title: Mouse_hindbrain_E11_male_replicate2

description: 10x Genomics

value: Embryonic day 11.5


title: shH2AJ_STB-Primed_Rep1

value: Syncytiatrophoblast


title: LEC, BSA, rep 1

description:
Library name: CTRL_1
10x Genomics


title: shH2AJ_Okae_Rep2

source_name: Okae Trophoblast

value: Okae Trophoblast


title: CV020_T

description: Library name: Sample 21

value: colorectal tumor


title: CV40_N

description: Library name: Sample 20

source_name: matched normal

value: matched normal


title: shH2AJ_STB-Primed_Rep2


title: LEC, BSA, rep 2

description:
Library name: CTRL_2
10x Genomics


title: LEC, BSA, rep 3

description:
Library name: CTRL_3
10x Genomics


title: Mouse_hindbrain_E11_male_replicate1

description: 10x Genomics

value: hindbrain

value: wild type


title: Mouse_hindbrain_E11_female_replicate1

description: 10x Genomics

value: female


title: shH2AJ_TSC-Naive_Rep2

value: Trophoblast stem cell


title: CV050N

description: Library name: Sample 18


title: LEC, multimeric Ang2, 6h, rep4

description:
Library name: MA_6h_4
10x Genomics

treatment_protocol: LECs were starved for 2.5 h in starvation media consisting of a final FBS concentration 0.5% after which the cells were stimulated with 500ng mL-1 multimeric Angpt2 for 3 hrs and 6 hrs.

value: multimeric Ang2


title: CV051N

description: Library name: Sample 19


title: shH2AJ_Okae_Rep1

value: shH2AJ stable line

value: H2AJ knockdown


title: Mouse_hindbrain_E10_male_replicate2

description: 10x Genomics

value: Embryonic day 10.5


title: shH2AJ_ESC-Primed_Rep2

value: H1 hESC mTeSR

value: hESC primed


title: shH2AJ_ESC-Primed_Rep1


title: Mouse_hindbrain_E10_male_replicate1

description: 10x Genomics

value: male


title: CV044N

description: Library name: Sample 16


title: Mouse_hindbrain_E10_female_replicate2

description: 10x Genomics


title: LEC, multimeric Ang2, 6h, rep3

description:
Library name: MA_6h_3
10x Genomics

value: skin

value: Human Dermal Lymphatic Endothelial Cells (HDLEC)


title: CV042N

description: Library name: Sample 15


title: CV041N

description: Library name: Sample 14


title: shH2AJ_ESC-Naive_Rep2

value: H1 hESC PXGL

value: hESC naive


title: CV045N

description: Library name: Sample 17


title: LEC, multimeric Ang2, 6h, rep2

description:
Library name: MA_6h_2
10x Genomics


title: Mouse_hindbrain_E11_female_replicate2

description: 10x Genomics

value: Embryonic day 11.5


title: LEC, multimeric Ang2, 6h, rep1

description:
Library name: MA_6h_1
10x Genomics


title: Mouse_hindbrain_E10_female_replicate1

description: 10x Genomics


title: shH2AJ_ESC-Naive_Rep1


title: CV039N

description: Library name: Sample 13

value: matched normal


title: Mouse_hindbrain_E9_male_replicate1

description: 10x Genomics

value: hindbrain

value: Embryonic day 9.5


title: LEC, multimeric Ang2, 3h, rep4

description:
Library name: MA_3h_4
10x Genomics


title: shCon_TSC-Primed_Rep2

value: shControl stable line

value: control shRNA


title: CV034N

description: Library name: Sample 10


title: Mouse_hindbrain_E9_female_replicate2

description: 10x Genomics

value: female

value: wild type


title: Mouse_hindbrain_E9_male_replicate2

description: 10x Genomics


title: CV036N

description: Library name: Sample 11


title: Mouse_hindbrain_E9_female_replicate1

description: 10x Genomics


title: CV038N

description: Library name: Sample 12


title: LEC, multimeric Ang2, 3h, rep1

description:
Library name: MA_3h_1
10x Genomics

value: multimeric Ang2


title: shCon_TSC-Naive_Rep2

value: Trophoblast stem cell


title: LEC, BSA, rep2

description:
Library name: MA_ctrl_2
10x Genomics

value: BSA


title: shCon_TSC-Primed_Rep1

value: H1 hESC mTeSR


title: Mouse_cerebellum_E18_XY_Testes_replicate1

description: 10x Genomics

data_processing:
Cell Ranger software v.5.0.1 default pipeline
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Cerebellar structures were dissected from mice, dissociated into single cell suspensions using papain and were run on the 10X Genomics Chromium Controller using the Chromium Single Cell 3' Solution V3 and V3.1 protocols
10x Genomics Chromium Single Cell 3' Solution V3 and V3.1 protocols

value: cerebellum

value: Embryonic day 18.5

tag: chromosomes

value: XY

tag: gonads

value: Testes

tag: mouse line

value: Four Core Genotype

value: XY-Sry


title: CV031_N

description: Library name: Sample 8

value: matched normal


title: shCon_STB-Primed_Rep1

value: Syncytiatrophoblast


title: LEC, multimeric Ang2, 3h, rep3

description:
Library name: MA_3h_3
10x Genomics

value: skin

value: Human Dermal Lymphatic Endothelial Cells (HDLEC)


title: LEC, BSA, rep4

description:
Library name: MA_ctrl_4
10x Genomics


title: Mouse_cerebellum_E18_XY_Ovaries_replicate1

description: 10x Genomics

value: Ovaries

value: XY-


title: LEC, multimeric Ang2, 3h, rep2

description:
Library name: MA_3h_2
10x Genomics


title: CV030_N

description: Library name: Sample 7


title: LEC, BSA, rep3

description:
Library name: MA_ctrl_3
10x Genomics


title: CV033_N

description: Library name: Sample 9


title: shCon_STB-Primed_Rep2

value: shControl stable line

value: control shRNA


title: CV028_N

description: Library name: Sample 6


title: LEC, BSA, rep1

description:
Library name: MA_ctrl_1
10x Genomics


title: shCon_TSC-Naive_Rep1

value: H1 hESC PXGL

value: Trophoblast stem cell


title: RR40_IP_NVP2_and_5-ethynyluridine

city: Houston

first: Eric

last: Van Nostrand

state: TX

address: 1 Baylor Plaza Rm T334

department: Therapeutic Innovation Center

institute: Baylor College of Medicine

description: Library name: RR40

data_processing:
Standard processing of eCLIP data was performed as previously described (Blue SB, et al. Nature Protocols 2022), with mapping performed to a hg19 as described below.
UMI removal and cut adapt:  umi_tools extract   --random-seed 1   --bc-pattern NNNNNNNNNN   --stdin 23145FL-08-01-37_S37_L001_R1_001.fastq.gz   --log /dev/null | cutadapt   -j 8   --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 1   -   --report minimal   2> AST378.cut.adapt.log | cutadapt   -j 8  --match-read-wildcards   --times 1   -e 0.1   --quality-cutoff 6   -m 18   -a a_adapters.fasta   -O 5   -   -o AST378.trim.gz   --report minimal   >>AST378.cut.adapt.log
Repeat mapping (takes adapter-trimmed fastq files, and maps to a repeat database to filter repeat elements prior to genome mapping:     STAR     --runMode alignReads     --runThreadN 8     --alignEndsType EndToEnd     --genomeDir  homo_sapiens_repbase_v2   --genomeLoad NoSharedMemory     --outBAMcompression 10     --outFileNamePrefix AST378.repeat.map     --outFilterMultimapNmax 100     --outFilterMultimapScoreRange 1     --outFilterScoreMin 10     --outFilterType BySJout     --outReadsUnmapped Fastx    --outSAMattrRGline ID:foo     --outSAMattributes All     --outSAMmode Full     --outSAMtype BAM Unsorted     --outSAMunmapped None     --outStd Log     --readFilesCommand zcat     --readFilesIn AST378.trim.gz
Unique genomic mapping (takes repeat-removed reads and maps to the reference genome: STAR   --runMode alignReads   --runThreadN 8   --alignEndsType EndToEnd   --genomeDir hg19 --genomeLoad NoSharedMemory   --outBAMcompression 10   --outFileNamePrefix AST378.genome.map   --outFilterMultimapNmax 1   --outFilterMultimapScoreRange 1   --outFilterScoreMin 10   --outFilterType BySJout   --outReadsUnmapped Fastx   --outSAMattrRGline ID:foo   --outSAMattributes All   --outSAMmode Full   --outSAMtype BAM Unsorted   --outSAMunmapped None   --outStd Log   --readFilesIn AST378.repeat.mapUnmapped.out.mate1
Sort mapped reads: samtools sort -@ 8 -m 2G -o AST378.genome.map.bam *Aligned.out.bam
Remove PCR duplicate reads: samtools index AST378.genome.map.bam umi_tools dedup   --random-seed 1   --stdin AST378.genome.map.bam   --method unique   --stdout AST378.bam
Make bigwigs: samtools index AST378.bam b2bw AST378.bam  --cpus 1
Finds peak region clusters:clipper --species hg19 --processors 16 --bam AST378.bam --outfile AST378.peak.bed
(IDR) Irreproducible Discovery Rate between replicates Geometric mean passing log2fc cutoff of >=3 and log10pval >=3 :  process_peak --ip_bams AST378.bam RR34.bam \ --input_bams AST379.bam  RR33.bam \ --peak_beds AST378.bed  RR34.bed  \ --outdir output/directory/ \ --ids AST378 RR34  \ --read_type SE --species hg19  --l2fc 3 --l10p 3 --report AST378_RR34_IDR.html --cpus 1
Assembly: hg19
Supplementary files format and content: .bw files contain read density (per million mapped, non-PCR duplicate reads); .bed files contain

source_name: Hela

growth_protocol: A monoclonal HeLa-61 cell line (derived from polyclonal ATCC stock) was maintained OptiMEM (Gibco) with 4% FBS and were grown to ~80% confluence in 15 cm dishes. All cells were grown at 37°C in humidified air containing 5% CO2. Cell lines were validated by STR profiling (ATCC), verified to be mycoplasma negative (Genlantis), and routinely refreshed from frozen stocks.

extract_protocol:
eCLIP was performed as previously described (Blue SB, et al. Nature Protocols 2022). Briefly, 10 million HeLa cells were UV crosslinked (254 nM, 400 mJ/cm2), snap frozen, and lysed as previously described.
RNA fragmentation was performed, 2% of the sample was removed for size-matched input, and the remainder was subjected to immunoprecipitation of TDP43-bound RNA with antibody against TDP43 (Proteintech 10782-2-AP). Dephosphorylation, RNA adapter ligation, SDS-PAGE electrophoresis and nitrocellulose membrane transfer, RNA isolation, reverse transcription, and PCR amplification were performed as previously described (Blue, SM. et al, Nat Protocols 2022). Libraries are as previously described for eCLIP (Blue, SM. et al, Nat Protocols 2022), based on the Illumina RNA TruSeq HT adapter strategy.

treatment_protocol: HeLa cells were treated for 24 h with or without 100 µM 5EU, followed by a 5EU washout and a 2 h pulse of 250 nM NVP2.

value: Hela

value: WT

value: 100 µM 5EU 24h, then 250 nM NVP2 2h

tag: antibody

value: TDP-43 Protein Tech 10782-2-AP


title: Mouse_cerebellum_E18_XX_Ovaries_replicate1

description: 10x Genomics

value: cerebellum

value: Embryonic day 18.5

value: XX


title: shCon_ESC-Primed_Rep2

value: H1 hESC mTeSR

value: hESC primed


title: shCon_ESC-Naive_Rep2

value: hESC naive


title: Mouse_cerebellum_E18_XX_Testes_replicate1

description: 10x Genomics

value: Testes

value: Four Core Genotype

value: XXSry


title: Mouse_cerebellum_E16_XY_Ovaries_replicate1

description: 10x Genomics

value: Embryonic day 16.5

value: XY

value: Ovaries

value: XY-


title: Mouse_cerebellum_E16_XY_Testes_replicate1

description: 10x Genomics

value: XY-Sry


title: RR37_input_5-ethynyluridine

description: Library name: RR37

value: Hela

value: WT


title: shCon_Okae_Rep2

value: Okae Trophoblast

value: Trophoblast stem cell

value: shControl stable line

value: control shRNA


title: shCon_Okae_Rep1


title: mCherry-6h-rep3

city: Guangzhou

first: Shu

last: Meng

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou National Laboratory

description: Library name: mChe-6h-rep3

data_processing:
Raw sequencing reads were first subjected to basic quality control including removal of potential sequencing adapters, and poor quality bases or reads using TrimGalore (v0.6.10). Then, clean reads were aligned to the human reference genome (GRCh38) using STAR (v2.7.10b) with default arguments, and only uniquely mapped reads were retained. Reads quantification on the gene level was performed using featureCounts (v2.0.6). Genes with a minimal raw count of 10 and detected in at least three samples were retained. Differentially gene expression analysis was conducted using DESeq2 package (v1.40.2, p < 0.05 and fold change > 1.5).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file with raw counts for each sample

source_name: HUVEC

extract_protocol:
HUVECs were collected at 6h and 24h after IVT mRNA transfection. Then, total RNA was extracted using RNeasy Plus Mini Kit (Cat# 74134, QIAGEN).
RNA-seq libraries were prepared according to the standard protocol of VAHTSTM Total RNA-seq (H/M/R) Library Prep Kit for Illumina® (Cat# NR603).

treatment_protocol: We co-transfected 6μg mCherry mRNA with 1.2μg Luc, M, and SOCS1 mRNA into HUVECs, respectively.

value: HUVEC


title: Mouse_cerebellum_E16_XX_Ovaries_replicate1

description: 10x Genomics

value: cerebellum

value: XX


title: Mouse_cerebellum_E16_XX_Testes_replicate1

description: 10x Genomics

value: Testes


title: CV026_N

description: Library name: Sample 5

value: matched normal


title: RR38_IP_5-ethynyluridine

description: Library name: RR38

value: TDP-43 Protein Tech 10782-2-AP


title: CV023_N

description: Library name: Sample 3


title: shCon_ESC-Primed_Rep1

value: H1 hESC mTeSR

value: hESC primed


title: shCon_ESC-Naive_Rep1

value: H1 hESC PXGL

value: hESC naive


title: liver, mut3,7 dpf

city: Qingdao

first: xinkai

last: cheng

address: No. 5 Yushan Road

institute: zebrafish liver

description: Library name: Sample 6

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.Differential expression analysis was performed using the DESeq2. Based on the hypergeometric distribution, GO, KEGG pathway, Reactome and WikiPathways enrichment analysis of DEGs were performed to screen the significant enriched term using R (v 3.2.0), respectively.
Assembly: GRCz11
Supplementary files format and content: csv file includes FPKM values for each Sample

organism: Danio rerio

source_name: liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: liver

value: 7 dpf

value: mrpl13 mutant


title: CV020_N

description: Library name: Sample 1


title: mice cardiomyocytes, Ang II+JV001_2

city: shanghai

first: yinlong

last: zhao

address: Shanghai 200125, China A419, Bldg #2, 115 Jinzun Road,

institute: Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

description: AngII.txt

data_processing:
The raw reads were firstly processed with fastp and low quality reads were removed.
Mapping to the reference genome (mm39) was done with HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: mm39
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Heart

extract_protocol:
Total RNA was extracted with the TRIzol reagent (Invitrogen, CA, USA) according to the protocol. RNA was purified, then quantified with NanoDrop 2000 (Thermo Scientific, USA). RNA integrity was assessed with Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
Libraries were constructed with VAHTS Universal V6 RNA-seq Library Prep Kit according to the instructions provided by the manufacturer. The transcriptome sequencing and analysis were conducted by OE Biotech Co., Ltd. (Shanghai, China).

value: Heart

value: cardiomyocytes

value: WT

value: Ang II+JV001


title: RR39_input_NVP2_and_5-ethynyluridine

description: Library name: RR39

value: Hela

value: 100 µM 5EU 24h, then 250 nM NVP2 2h


title: CV021_N

description: Library name: Sample 2


title: liver, mut2,7 dpf

description: Library name: Sample 5


title: mice cardiomyocytes, Ang II+JV001_3

description: AngII.txt


title: OE-H2AJ_TSC_H2AJ_Rep2_R1.fastq

description: OEH2AJ_TSC_H2AJ_mean.scaled.hg38.smooth200.bw

library_source: genomic

data_processing:
Trimmomatic, Bowtie2, Samtools, MACS2, Bedtools, IDR
Assembly: hg38
Supplementary files format and content: Bigwig and peak calls
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: H1 hESC mTeSR derived

extract_protocol:
Column Cleanup
Cutana Cut and Run Library Kit

value: H1 hESC mTeSR derived

value: Trophoblast Stem Cell

value: OE H2AJ Flag


title: OE-H2AJ_TSC_FLAG_Rep1_R1.fastq

description:
OE-H2AJ_TSC_FLAG_PEAKS.bed
OEH2AJ_TSC_FLAG_mean.scaled.hg38.smooth200.bw


title: RR36_IP_NVP2

description: Library name: RR36

value: 250 nM NVP2 2h

value: TDP-43 Protein Tech 10782-2-AP


title: RR35_input_NVP2

description: Library name: RR35


title: RR33_input_UNT

description: Library name: RR33


title: OE-H2AJ_TSC_H2AJ_Rep1_R1.fastq


title: OE-H2AJ_TSC_FLAG_Rep2_R1.fastq


title: CV025_N

description: Library name: Sample 4

value: matched normal


title: RR34_IP_UNT

description: Library name: RR34


title: AST384_IP_NVP2_and_5-ethynyluridine

description: Library name: AST384


title: EV_TSC_FLAG_Rep2_R1.fastq

value: OE Empty Vector


title: liver, mut1,7 dpf

description: Library name: Sample 4


title: shH2AJ_STB_S5_Rep1

description: shH2AJ_STB_S5_Rep1.hg38.binSize50.smoothLength200

value: Syncytiotrophoblast


title: EV_TSC_FLAG_Rep1_R1.fastq


title: mice cardiomyocytes, Saline_2

description: AngII.txt

value: Saline


title: mice cardiomyocytes, Ang II+JV001_1

description: AngII.txt


title: mice cardiomyocytes, Ang II+Vector_2

description: AngII.txt

value: Ang II+Vector


title: mice cardiomyocytes, Ang II+Vector_1

description: AngII.txt


title: cas9_control4

city: Hangzhou

first: Xiang

last: Qiu

state: Zhejiang

address: No.1 Xueshi Road, Shangcheng District

institute: Zhejiang University

description: Library name: cas9_4

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by thesoftware of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated. Then we use fastp (v0.20.0) software to filter the sequencing data to get high quality sequence (Clean Data) for further analysis.
Differential expression analysis was performed using DESeq2 R package (v1.46.0)
The clusterProfiler R package (v4.14.4) was used to perform the functional pathway enrichment analysis.
The WGCNA R package (v1.73) was employed to analyze the co-expression gene networks and cluster-specific modules.
Machine learning were performed using glmnet (v4.1-8), randomForest (v4.7-1.2), e1071 (v1.7-16) R package.
Assembly: Not applicable.
Supplementary files format and content: CSV file including Reads count for each sample.

source_name: whole body

extract_protocol:
Norgen, Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit
IDT, xGenTM Broad-Range RNA Library Prep Kit

value: whole body

value: whole body cell


title: liver, sib2,7 dpf

description: Library name: Sample 2

value: liver

value: 7 dpf

value: sib


title: mice cardiomyocytes, Ang II+Vector_3

description: AngII.txt

value: Heart

value: cardiomyocytes

value: WT


title: liver, sib3,7 dpf

description: Library name: Sample 3


title: AST383_input_NVP2_and_5-ethynyluridine

description: Library name: AST383

value: Hela

value: 100 µM 5EU 24h, then 250 nM NVP2 2h


title: shH2AJ_STB_S2_Rep2

description:
shH2AJ_STB_S2_mean.scaled.orig.hg38.smooth200.bw
shH2AJ_STB_S2.macs.idr.filtered.bed

value: H1 hESC mTeSR derived


title: liver, sib1,7 dpf

description: Library name: Sample 1


title: AST382_IP_5-ethynyluridine

description: Library name: AST382

value: TDP-43 Protein Tech 10782-2-AP


title: mice cardiomyocytes, Saline_3

description: AngII.txt


title: cas9_control3

description: Library name: cas9_3


title: AST379_input_NVP2

description: Library name: AST379

value: 250 nM NVP2 2h


title: shH2AJ_STB_S2_Rep1


title: cas9_control2

description: Library name: cas9_2


title: mice cardiomyocytes, Saline_1

description: AngII.txt


title: AST381_input_5-ethynyluridine

description: Library name: AST381


title: AST380_IP_NVP2

description: Library name: AST380


title: shH2AJ_STB_IgG_Rep2


title: shH2AJ_STB_IgG_Rep1


title: AST378_IP_UNT

description: Library name: AST378


title: mice cardiomyocytes, TAC+JV001_3

description: TAC.txt


title: cas9_control1

description: Library name: cas9_1


title: shCon_STB_S2_Rep2

description:
shCon_STB_S2_mean.scaled.orig.hg38.smooth200.bw
shCon_STB_S2.macs.idr.filtered.bed

value: shControl


title: shCon_STB_S5_Rep1

description: shCon_STB_S5_Rep1.hg38.binSize50.smoothLength200

value: Syncytiotrophoblast


title: mice cardiomyocytes, TAC+Vector_3

description: TAC.txt

value: TAC+Vector


title: mice cardiomyocytes, TAC+JV001_2

description: TAC.txt


title: mice cardiomyocytes, TAC+JV001_1

description: TAC.txt


title: agmat_KO3

description: Library name: agmat_3


title: agmat_KO4

description: Library name: agmat_4


title: VAT-EVs miRNA-seq sample C2

city: Harbin

first: LI

last: YANCHAO

state: Heilongjiang

address: 2nd Affiliated Hospital of Harbin Medical University, No. 157 Baojian Road, Nangang District, Harbin, Heilongjiang, China.

department: Cardiology Organization

institute: The Second Affiliated Hospital of Harbin Medical University

description:
Library name: E-micA957-06h
VAT-derived extracellular vesicles isolated from epididymal white adipose tissue of ApoE-/- mice fed a high-fat diet with nicotine treatment

data_processing:
Raw sequencing reads were processed to remove adaptor sequences, low-quality reads, and reads shorter than 15 nt or longer than 35 nt.
Clean reads were aligned to reference databases to filter rRNA, tRNA, snRNA, snoRNA, and repetitive sequences, and subsequently mapped to the mouse genome and miRBase to identify known and novel miRNAs.
miRNA expression levels were quantified based on mapped reads and normalized as transcripts per million (TPM).
Differential expression analysis between experimental groups was performed using edgeR with multiple testing correction.
Assembly: Mus musculus reference genome (GRCm38/mm10)
Supplementary files format and content: Processed data files include a matrix of miRNA expression levels normalized as TPM for all samples and a table of differentially expressed miRNAs between experimental groups.

source_name: eWAT

growth_protocol: Male ApoE−/− mice (8 weeks old) were maintained under specific-pathogen-free (SPF) conditions with controlled temperature and humidity and a 12-hour light/dark cycle, with free access to food and water.

extract_protocol:
Extracellular vesicles were isolated from epididymal white adipose tissue (eWAT) of ApoE−/− mice. Total RNA, including small RNAs, was extracted from adipose tissue-derived EVs using a commercial RNA isolation protocol.
Small RNA libraries were constructed from EV-derived total RNA following the manufacturer’s protocol for miRNA sequencing.

treatment_protocol: Mice were fed a high-fat diet (HFD) or a high-fat diet combined with nicotine administration (HFD+Ni, 2 mg/kg/day) for 12 weeks prior to tissue collection.

value: eWAT

value: ApoE-/-

value: high-fat diet + nicotine (HFD+Ni)


title: mice cardiomyocytes, TAC+Vector_2

description: TAC.txt


title: VAT-EVs miRNA-seq sample C3

description:
Library name: E-micA957-07h
VAT-derived extracellular vesicles isolated from epididymal white adipose tissue of ApoE-/- mice fed a high-fat diet with nicotine treatment


title: shCon_STB_IgG_Rep2


title: VAT-EVs miRNA-seq sample C1

description:
Library name: E-micA957-05h
VAT-derived extracellular vesicles isolated from epididymal white adipose tissue of ApoE-/- mice fed a high-fat diet with nicotine treatment


title: shCon_STB_S2_Rep1


title: AST377_input_UNT

description: Library name: AST377


title: agmat_KO2

description: Library name: agmat_2

value: whole body

value: whole body cell


title: mice cardiomyocytes, TAC+Vector_1

description: TAC.txt


title: mice cardiomyocytes, Sham_3

description: TAC.txt

value: Sham


title: VAT-EVs miRNA-seq sample B3

description:
Library name: E-micA957-03h
VAT-derived extracellular vesicles isolated from epididymal white adipose tissue of ApoE-/- mice fed a high-fat diet

value: high-fat diet (HFD)


title: shCon_STB_IgG_Rep1


title: agmat_KO1

description: Library name: agmat_1


title: VAT-EVs miRNA-seq sample B4

description:
Library name: E-micA957-04h
VAT-derived extracellular vesicles isolated from epididymal white adipose tissue of ApoE-/- mice fed a high-fat diet


title: RNA-seq of Arabidopsis thaliana: 40 day-old Col-0 under short-day replicate 3

city: Taipei city

first: Chin-Mei

last: Lee

address: No. 1, Sec. 4, Roosevelt Rd.

department: Institute of Plant Biology

country: Taiwan

institute: National Taiwan University

data_processing:
The paired end reads sequencing data were trimmed with Trimmomatic to remove undesired Illumina adaptor sequences and repetitive poly-G sequences.
For the alternative splicing event analysis, the following procedures were performed. Firstly, the reads were mapped onto the coordinate of transcripts indexed from Araport11 201606 released with Bowtie2 with a filtering identity threshold of 0.95, and the coordinates of reads passing the filter were translated into coordinates on the genome TAIR10.
To enhance the identification efficiency toward alternative splicing events, the unmapped reads were mapped onto the coordinate of the genome with BLAT with a filtering identity threshold as 0.9 and at least 8 bases matched on both sides of reads.
The resulting mapped sequences by both methods were collected together as input of the RackJ pipeline.
Assembly: TAIR10
Supplementary files format and content: DEseq2.GEO.csv: ouput spreadsheet from DEseq2
Supplementary files format and content: RackJ_SSESs_WT-mutant.csv: ouput spreadsheet from RackJ, Exon skipping
Supplementary files format and content: RackJ_SSDAs_WT-mutant.csv: ouput spreadsheet from RackJ, donor/accepter
Supplementary files format and content: RackJ_SSIRs_WT-mutant.csv: ouput spreadsheet from RackJ, Intron retention

organism: Arabidopsis thaliana

source_name: rosette leaves

growth_protocol: 40 day-old leaves of mac3amac3b mutants and Col-0, which were still in the vegetative phase under short days. Seed vernalization was performed by soaking in sterilized water at 4°C for three days in darkness, followed by sowing on soil. For seedlings grown on plates, seeds underwent sterilization with 70% ethanol and 0.1% TRITON® X-100, then were plated on 1/2 strength Murashige and Skoog (MS) medium (Caisson, Cat# MSP02) supplemented with 0.8% agar (Duchefa Biochemie, Cat# P1003). Plates were kept at 4°C in the dark for three days before being moved to growth chambers. Growth conditions for plants, whether in soil ,  under short-day (SD) conditions (8 hours of light/16 hours of dark), maintained at 22°C with light intensities ranging from 85 to 120 µmol m-2 s-1.

extract_protocol:
Total RNA was extracted using the RNeasy Plant Mini Kit (QIAGEN, Cat# 74904), with subsequent removal of genomic DNA contamination employing the RNase-Free DNase Set (Qiagen, Cat# 79254).
The RNA sequencing libraries of triple replicates of both Col-0 and mac3amac3b were prepared by Genomic Technology Core at the Institute of Plant and Microbial Biology in Academia Sinica with the Illumina TrueSeq toolkit.

value: rosette leaves

value: 40-day-old non-flowering mature plant grown under short-day


title: mice cardiomyocytes, Sham_2

description: TAC.txt

value: Heart

value: cardiomyocytes

value: WT


city: Los Angeles

first: Zhiyuan

last: Mao

state: California

address: 675 Charles E. Young Dr. South

department: Microbiology Immunology & Molecular Genetics

institute: University of California, Los Angeles

description: Library name: 32Ma selection pHLA-A2 R3 9mer yeast library

library_source: other

data_processing:
Extract round 3 or 4 selection data with barcodes, extract the antigen sequences, filter the sequence with pre-mature stop codon, and count frequencies of amino acids at each position as described previously (Gee, M.H. et al. Cell 2018)
Supplementary files format and content: count frequencies of amino acids

molecule: other

organism: Saccharomyces cerevisiae

source_name: EBY 100

extract_protocol:
DNA of 5X10^7 yeast from selections were isolated by miniprep (Zymoprep II kit, Zymo Research).
Library construction is described in previous publication (Gee, M.H. et al. Cell 2018)

value: EBY 100

value: Yeast


title: mice cardiomyocytes, Sham_1

description: TAC.txt


title: RNA-seq of Arabidopsis thaliana: 40 day-old Col-0 under short-day replicate 2


title: OE-H2AJ_STB_H2A_Rep2

value: H1 hESC mTeSR derived

value: OE H2AJ Flag


title: VAT-EVs miRNA-seq sample B2

description:
Library name: E-micA957-02h
VAT-derived extracellular vesicles isolated from epididymal white adipose tissue of ApoE-/- mice fed a high-fat diet


title: OE-H2AJ_STB_H2A_Rep1

value: Syncytiotrophoblast


title: Hind limb rbp4-cre:Ai14+ CSNs, layer 5 M1

first: William

middle: Ben

last: Cafferty

address: 300 George Street

department: Neurology

description:
Library name: HL_rbp4_CSN
10X Genomics

data_processing:
Demultiplexing, barcode processing, aligment, gene counting and aggregation were perfomed using Cell Ranger software. Subsequent processing was perfomed were performed with Python 3.8.5 and the scipy (1.5.2) and numpy (1.19.2) modules. After extracting the single-cell gene expression matrix, we used the scprep (1.0.3) package in python to eliminate non-neurons and normalize the data (Gigante, 2021). Briefly, we filtered out cells that had a library size of less than 2500 unique molecular identifiers (UMIs) as well as cells that had mitochondrial gene expression in the top tenth percentile. To exclude doublets, we used two methods: 1) We used the python package scrublet and removed all cells that were detected as doublets (Wolock et al., 2019). 2) We removed cells that expressed both the male specific genes (Eif2s3y or Ddx3y) and female specific genes (Xist or Tsix).  After a library size normalization, we used the python package MAGIC (3.0.0) to impute missing data (van Dijk et al., 2018). Using the MAGIC output gene expression matrix, we filtered out contaminating cell types (endothelial cells, microglia, astrocytes, and oligodendrocytes) as well as inhibitory interneurons (via negative expression of vglut2), resulting in an approximate 1% reduction from the starting neuronal population. We then square root transformed the data for further downstream analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values and matrix files

source_name: cortical

extract_protocol:
Adult intact cell isolation was done following our previously published protocol (Golan and Cafferty, 2021). Briefly, mice that received retrograde injections into either the lumbar or cervical cord were anesthetized with isoflurane and transcardially perfused with artificial cerebrospinal fluid (aCSF) ten days after retro-AAV injection.  The brain was dissected and submerged in ice-cold carbogenated aCSF for three minutes before being transferred to a brain matrix (Braintree Scientific, Inc.) where four 500 µm sections through M1 were sliced and sections were transferred to a petri dish containing ice cold carbogenated aCSF. Regions of M1 (+1.0 to -0.5 mm relative to Bregma) containing labeled CSNs were dissected under a fluorescent microscope and transferred to a 5 ml Eppendorf tube with dissociation buffer with papain. The sample in dissociation buffer with papain was incubated at 34℃ for 70 minutes on a shaker at medium speed. After 70 minutes, the dissociation solution with papain was replaced with a Stop buffer. The Stop solution was then replaced with 800 µl of dissociation buffer and triturated with Pasteur pipettes with decreasing diameters (600 µm, 300 µm and 150 µm) and placed on ice. To differentiate between intact neurons and nuclei, a cell-permeable dye was added at a concentration of 1:1000 for 5 minutes (Invitrogen, L34974). The sample was then centrifuged at 300 g for 10 minutes at 4℃ and resuspended in 500 µl of dissociation buffer. Fluorescent single cells were isolated from rbp4 cre: Ai14 mice and C57Bl/6J mice injected with retro-AAV-CAG-GFP.  Sorting was performed on the Sony SH800 sorter with a 130 µm nozzle, ensuring a sheath pressure and sample pressure of less than 9 PSI. To ensure pyramidal neurons were sorted, size reference beads were used to set a minimum diameter of 10 µm (Spherotech, PPS-5 and PPS-6) for all collected cells. To exclude non-intact cells, the cells were sorted for the presence of the cell-permeable dye. A sample of non-fluorescent tissue from adjacent regions of the cortex was used as negative control to set the gate for the presence of fluorescence (GFP or tdTomato). The sample was then sorted into Eppendorf tubes containing 4℃ dissociation buffer and immediately sequenced at the Yale Center for Genome Analysis (YCGA).
Library construction was perfomed according to manufacturers instructions. Single cell suspension in RT Master Mix was loaded on the Single Cell A Chip and partitioned with a pool of about 750,000 barcoded gel beads to form nanoliter-scale Gel Beads-In-Emulsions (GEMs). Each gel bead has primers containing (i) an Illumina® R1 sequence (read 1 sequencing primer), (ii) a 16 nt 10x Barcode, (iii) a 12 nt Unique Molecular Identifier (UMI), and (iv) a poly-dT primer sequence (30nt). Upon dissolution of the Gel Beads in a GEM, the primers were released and mixed with cell lysate and Master Mix. Incubation of the GEMs then produced barcoded, full-length cDNA from poly-adenylated mRNA.Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic Fragmentation and Size Selection were used to optimize the cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) was added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers were used in Illumina bridge amplification. The Single Cell 3’ Protocol produces Illumina-ready sequencing libraries. A Single Cell 3’ Library comprises standard Illumina paired-end constructs which begin and end with P5 and P7. The Single Cell 3’ 16 bp 10x Barcode and 12 bp UMI are encoded in Read 1, while Read 2 is used to sequence the cDNA fragment (91bp). Minimum sequencing depth is 20,000 read pairs per cell.

treatment_protocol: To label the forelimb (FL) and hindlimb (HL) corticospinal tract for projection analysis, two groups of adult C57/blk6 mice received dual injections of pAAV-CAG-FLEX-tdTomato (Addgene, 28306-AAV1) into either the caudal FL motor cortex (n=4, AP: between 0.0 mm and 0.5 mm rostral to bregma, ML: between 1.0 mm and 1.3 mm lateral to bregma, 4 injections 100 nl/site) or the HL motor cortex (n=4, AP: between  -0.5 mm and -1 mm caudal to bregma, ML: between 1.5 mm to 2.0 mm lateral to bregma, 4 injections 100 nl/site), and pENN.AAV.hSyn.Cre.WPRE.hGH (Addgene 105553-AAVrg) into either the cervical (C6/7) or lumbar spinal cord (L4/5).

value: cortical

value: layer 5 neurons

tag: age

value: 8-10 weeks

value: pooled male and female

value: naïve


title: VAT-EVs miRNA-seq sample B1

description:
Library name: E-micA957-01h
VAT-derived extracellular vesicles isolated from epididymal white adipose tissue of ApoE-/- mice fed a high-fat diet

source_name: epididymal white adipose tissue (eWAT)

value: epididymal white adipose tissue (eWAT)

value: ApoE-/-


title: OE-H2AJ_STB_FLAG_Rep1

description:
OE-H2AJ_STB_FLAG_mean.hg38.smooth200.bw
H2AJ-Flag_Peaks_Overlap.bed


title: RNA-seq of Arabidopsis thaliana: 40 day-old Col-0 under short-day replicate 1

value: rosette leaves


title: Forelimb and hindlimb rbp4-cre:Ai14- non-CSNs, layer 5 M1

description:
Library name: FL_HL_rbp4_control
10X Genomics


description: Library name: TCR156wt selection pHLA-A2 R3 9mer yeast library


title: snRNAseq, O_Post-LVAD

city: Boston

first: Krishan

last: Gupta

state: MASSACHUSETTS

address: 300 Longwood Avenu, Boston children's Hospital

institute: Boston Children's Hospital/Harvard Medical School

description: 10x Genomics

data_processing:
Cell Ranger (version 7.1.0) to map the raw reads of RNA sequencing data to the mouse genome (version mm10) and to count UMI for each gene.
Assembly: GRCh38
Supplementary files format and content: csv files, in metaData file some columns starts with ABC, that’s means after batch correction

extract_protocol:
We isolated nuclei from frozen human heart tissue samples and constructed 3’ single cell gene expression libraries (Next GEM v3.1) using the 10x Genomics Chromium system. The libraries were sequenced with ~200 million PE150 reads per sample on Illumina NovaSeq. After sequencing, clean reads were analyzed with human reference genome GRCh38 using Cell Ranger v6.1.2. Introns were included in the analysis.
single-nuclei RNA-seq library construction following the protocol provided by 10X Genomics.


title: replicate2,scONT

city: Chengdu

first: chen

last: li

address: Renmin South Road

institute: Sichuan Univercity

description:
Library name: Rep2scONT
OXFORD_NANOPORE

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger software v4.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest) [CITE-seq].  The demultiplexing, barcoded processing, gene counting and aggregation were made using the cellranger software v4.0.0 (https://www.10xgenomics.com/support/software/cell-ranger/latest) [3' scRNA-seq].  The Pychopper (v2.5.0) software was used to identify, orient and trim long-read sequencing reads with default parameters. The number of reads, read length and quality were analyzed using NanoComp software (v1.33.1) with the parameter of “–raw–store–tsv_stats” and visualized using R package ggplot2 (v3.5.1). Pychopper processed reads were aligned to the reference genome GRCm38 with annotation from ENSEMBL release 101 for mouse and the reference genome GRCh38 using minimap2 (v2.17) with the following parameters: minimap2 -ax splice -uf --secondary=no -C5 --MD. Then, mismatches, insertions, deletions, and non-canonical splice sites in alinged reads were corrected using TranscriptClean (v2.0.3) software. Finally, TranscriptClean-corrected reads were aligned again to the reference mentioned before. Finally, reads were assigned to known genes to generate comprehensive count matrices, enabling the quantification of expression at both the gene and isoform levels for each individual cell [scONT].
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: bone marrow

extract_protocol:
C57BL/6J mice were purchased from Jiangsu JCYK Bioscience Co. Ltd (Jiangsu, China), housed and bred under SPF condition (Specific Pathogen Free) at the Laboratory Animal Center of West China Second University Hospital, and were allowed access to diet and water ad libitum. All animal experiments were carried out following the protocols approved by the Institutional Animal Care and Use Committee of West China Second University Hospital [(2018) Animal Ethics Approval No. 004]. The bone marrow cells were obtained from the femur and tibia of C57BL/6 mice aged about 8 weeks and filtered via a 70-μm cell strainer (BD Biosciences). After centrifuging (300 g, 5 min, 4℃), the cells were resuspended in 200 mL EasySep Buffer and CD117 MicroBeads (20 μL/one mouse). The whole solution was transferred to a 1.5 mL centrifuge tube and incubated on ice for 20~30 min. A 1 mL sample was added to the MS separation column. The MS separation column was cleared with EasySep Buffer 3 times on the Magnetic Separation Rack, and then the MS separation column was eluted with 5 mL of EasySep Buffer off the Magnetic Separation Rack to obtain Lin- cells. 20 μL cells were taken and counted, and the remaining samples were centrifuged (300 g, 5 min, 4℃). SCM (+) medium was used to resuspend (4 mL/one mouse) and then placed in an incubator (37℃, 5% CO₂) at constant temperature for 12~24 hr.
RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA) and the concentration was measured using Qubit® 2.0 Fluorometer (Life Technologies, CA, USA). The integrity of RNA was assessed using the Qubit® 1.0 Fluorometer. Single cells were prepared in the Chromium Single Cell Gene Expression Solution using the Chromium Single Cell 5′ Gel Bead, Chip and Library Kits v2 (10x Genomics) as per the manufacturer’s protocol. Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq) is a single-cell multi-omics technology that measures RNA and protein expression simultaneously in single cells. We generated a 5’ CITE-seq dataset of mouse bone marrow lineage negative (LIN−) cells, which consists of 388 cells and 8 proteins. The cells were then partitioned into Gel Beads in Emulsion in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, which was under the action of poly(dT) and enzyme. In GEMs, each pair-end contains read 1 (R1) and read 2 (R2), the former consists of (i) a 16nt 10x Barcode, (ii) a 10nt unique molecular identifier (UMI), and (iii) a 13nt TSO. Libraries were sequenced on the Illumina NovaSeq 6000 platform at Novogene, Beijing, China [CITE-seq].  The collected cells were resuspended in PBS containing 1% BSA at the concentration at 1 × 106 cells/mL and prepared for single cell library preparation. Single cells were prepared in the Chromium Single Cell Gene Expression Solution using the Chromium Single Cell 3 Gel Bead, Chip and Library Kits v2 (10× Genomics) as per the manufacturer’s protocol. The cells were then partitioned into Gel Beads in Emulsion in the Chromium instrument, where cell lysis and barcoded reverse transcription of RNA occurred, followed by amplification, shearing 5 adaptor, and sample index attachment. Libraries were sequenced on the Illumina NovaSeq 6000 platform at Novogene, Beijing, China [3' scRNA-seq].  The Pychopper (v2.5.0) software was used to identify, orient and trim long-read sequencing reads with default parameters. The number of reads, read length and quality were analyzed using NanoComp software (v1.33.1) with the parameter of “–raw–store–tsv_stats” and visualized using R package ggplot2 (v3.5.1). Pychopper processed reads were aligned to the reference genome GRCm38 with annotation from ENSEMBL release 101 for mouse and the reference genome GRCh38 using minimap2 (v2.17) with the following parameters: minimap2 -ax splice -uf --secondary=no -C5 --MD. Then, mismatches, insertions, deletions, and non-canonical splice sites in alinged reads were corrected using TranscriptClean (v2.0.3) software. Finally, TranscriptClean-corrected reads were aligned again to the reference mentioned before. Finally, reads were assigned to known genes to generate comprehensive count matrices, enabling the quantification of expression at both the gene and isoform levels for each individual cell [scONT].

value: bone marrow

value: hematopoietic stem and progenitor cells


title: RNA-seq of Arabidopsis thaliana: 40 day-old mac3a/mac3b mutants under short-day replicate 3

value: 40-day-old non-flowering mature plant grown under short-day


title: Forelimb rbp4-cre:Ai14+ CSNs, layer 5 M1

description:
Library name: FL_rbp4_CSN
10X Genomics


title: RNA-seq of Arabidopsis thaliana: 40 day-old mac3a/mac3b mutants under short-day replicate 2


title: EV_STB_FLAG_Rep2

description:
EV_STB_FLAG_mean.hg38.smooth200.bw
H2AJ-Flag_Peaks_Overlap.bed

value: OE Empty Vector


title: 3q gain cell, mRNA, biological replicate 3

city: West Haven

first: Wenxue

last: Li

state: CT     Connecticut

address: 300 Heffernernan Dr Bldg A42,, Bldg 840, Room ABC 367

description:
Library name: Sample 9
Chr3_isogenic_system_mRNA.xlsx

data_processing:
Total mRNA:RNA sequencing from chromosoe 3/chromosome 8 aneuploidy system data was processed using the nf-core/rnaseq pipeline (v3.14.0). The RNAseq were also aligned to the human genome GRCh38. Ribosome Profiling: The analysis of ribosome footprint data was performed using RiboDoc (v0.9.1.1) on Podman (v3.4.4). RPFs ranging from 25 to 45 nucleotides were aligned to the human genome (GRCh38) within the analysis pipeline. For identification and removal of human rRNA contaminants, the SILVA database was utilized.
Assembly: GRCh38
Supplementary files format and content: TPM values:Chr8_isogenic_system_mRNA.xlsx
Supplementary files format and content: TPM values:Chr3_isogenic_system_mRNA.xlsx
Supplementary files format and content: raw counts for each sample:Chr3_isogenic_Riboseq.xlsx

source_name: lung epithelial cell

extract_protocol:
Total mRNA:Cells from the chromosome 3 isogenic aneuploidy system (3p loss/3q gain/WT) were washed three times with PBS, snap-frozen, and then lysed with the QIAShredder columns (#79654, QIAGEN) according to the manufacturer’s instructions. For each cell line, three biological replicates were processed. Total RNA was isolated with the Qiagen RNeasy Mini Kit (#74104, QIAGEN), including the DNA digestion step using the RNAase-Free DNAase set kit (#79254, QIAGEN). Ribosome Profiling:3p loss cells and 3p WT cells were subjected to ribosome profiling. For each cell line, three biological replicates were processed. Cells were cultured under standard conditions until they reached 80% confluency. They were then treated with 10 µg/µL cycloheximide for 5 minutes at 37°C. Following treatment, cells were harvested and lysed. Ribosome-protected fragments (RPFs) were generated and purified using RiboLace Pro (Immagina Biotech; catalog # RL00P-12). The RPFs underwent end repair using the Small RNA Library Prep Kit (NEB; catalog # E7300S) and size selection using the RNA Clean & Concentrator-5 Kit (Zymo; catalog # R1015) to enrich RNA fragments sized smaller than 200 nt.
Total mRNA:PolyA isolation and sequencing library preparation was performed using the NEB Next Ultra Directional RNA Library Prep Kit (#E7760, NEB). Each set of samples were pooled and sequenced in one lane of HiSeq2500 RR, 100 basepair paired end. For the transcriptome analysis of chromosome 8 isogenic aneuploidy system (8p loss/8p WT), total mRNA samples were prepared as described above with three biological replicates, and the following library preparation was conducted in Yale Center for Genomic Analysis (YCGA). Sequencing was conducted on NovaSeq X Plus platform (Illumina). Ribosome Profiling:RPFs were reverse transcribed and tagged by Small RNA Library Prep Kit (NEB; catalog # E7300S) following the recommended conditions. RPF libraries were then amplified by Phusion High-Fidelity PCR Kit (NEB; E0553L). Further size selection and purification of RPF libraries was conducted using Mag-Bind TotalPure NGS beads (Omega Bio-tek; catalog # M1378-01) at a beads-to-product ratio of 1.3:1. The NGS libraries were quantified using the sparQ Universal Library Quant Kit (Quantabio; catalog # 95210-100) and analyzed using a TapeStation (Agilent) before being sequenced with NovaSeq X Plus (Illumina) in YCGA or NextSeq 1000 system in Quintara Biosciences. The target sequencing depth for the RPF libraries was 200 million reads per library.

value: lung epithelial cell

value: 3q gain


title: snRNAseq, X_Pre-LVAD

description: 10x Genomics

value: Heart


title: EV_STB_FLAG_Rep1

value: H1 hESC mTeSR derived


title: Hind limb non-CSNs, layer 5 M1, replicate 2

description:
Library name: HL2_control
10X Genomics

value: WT


title: RNA-seq of Arabidopsis thaliana: 40 day-old mac3a/mac3b mutants under short-day replicate 1


title: RA 4

type: RNA

city: Chandigarh

first: Jyotdeep

last: Kaur

state: Chandigarh

address: PGIMER, Sector 12

department: Department of Biochemistry

country: India

institute: Postgraduate Institute of Medical Education and Research (PGIMER)

description: miRNA expression

hyb_protocol: Labelled miRNAs were then hybridized using a Microarray Hybridization Chamber Kit. Blocking agents and hybridization samples were prepared following kit protocol.The hybridization chamber was assembled and loaded into the oven rotator rack set at 20 rpm.Samples were hybridized at 55°C for 20-24 h.

scan_protocol: Following hybridization, arr×ays were washed using wash buffers containing 0.005% Triton X-102 (10%) at 37°C for 5 min and scanned on a SureScan microarray scanner using 1 color scan setting for 8×60k platform

data_processing: Data was extracted using Agilent Feature Extraction software using default parameters and was analyzed using Genespring GX software.

source_name: Rheumatoid arthritis patient 4

label_protocol: 100ng of total RNA was used. Fluorescently-labeled miRNAs were generated with a miRNA complete labeling and hybridization kit( Agilent p/n 5190-04-56) following the manufacturer's instructions.Thus Cyanine 3-pCp molecules were ligated to the 3'end of RNA molecule

extract_protocol: For cellular miRNA isolation, the synovial fluid cell pellet was immediately processed for RNA isolation using RNeasy cells/tissue kit, Qiagen Inc.,USA following the manufacturer’s protocol.

treatment_protocol: Synovial fluid was aseptically aspirated from the affected knee of subjects. Samples were collected in sterile vial on ice. To reduce viscosity of the synovial fluids, samples were diluted with nuclease free water (1:1 dilution) and were centrifuged at 10,000 g for 15 minutes.

tag: disease state

value: Rheumatoid arthritis

tag: gender

value: F


title: RA 3

description: miRNA expression

source_name: Rheumatoid arthritis patient 3


title: OE-H2AJ_STB_FLAG_Rep2

value: Syncytiotrophoblast

value: OE H2AJ Flag


title: replicate1,scONT

description:
Library name: Rep1scONT
OXFORD_NANOPORE

tag: tissue


title: Hind limb non-CSNs, layer 5 M1, replicate 3

description:
Library name: HL3_control
10X Genomics

value: cortical

value: layer 5 neurons

value: 8-10 weeks

value: pooled male and female

value: naïve


title: Hind limb CSNs, layer 5 M1, replicate 3

description:
Library name: HL3_CSN
10X Genomics


title: RA 2

description: miRNA expression

source_name: Rheumatoid arthritis patient 2


title: Hind limb CSNs, layer 5 M1, replicate 2

description:
Library name: HL2_CSN
10X Genomics


title: Late OA 6

description: miRNA expression

source_name: KL-grade III Late OA patient 6

value: KL-grade III Late OA


title: Hind limb non-CSNs, layer 5 M1, replicate 1

description:
Library name: HL1_control
10X Genomics


title: Embryonic stem cell (ES cell)

city: Bunkyo

first: Zhennan

last: Yang

state: Tokyo

department: Graduate School of Medicine, Department of Cellular and Tissue Communications

country: Japan

institute: The University of Tokyo

data_processing:
Adapter trimming of sequencing data was performed by using cutadapt 2.10.   Filtered reads were chunked to 16 parts for parallel processing by using Seqkit 0.9.0.
Filtered cell barcode reads were annotated by Python script provided by BD with minor modification for compatible to Python3.7, associated cDNA reads were mapped to Ensembl cDNA and ncRNA (build GRCh38, release-101) with reporter gene EGFP-IRES2-Puromycin-3'UTR by using Bowtie2-2.3.4.1 by the following parameters: -N 1 - -very-sensitive-local --seed 656565 --reorder, and associated Hashtag reads were mapped to Known barcode sequence+BAAAAA by using Bowtie2-2.4.2 by the following parameters:-D 50 -R 20 -N 0 -L 8 -i S,1,0.75 --norc --seed 656565 --reorder --trim-to 3:21 --score-min L,-9,0 --mp 3,3 --np 3 --rdg 3,3.
Cell barcode information of each read was added to the bowtie2-mapped BAM files, and read counts of same gene symbols of each cell barcode were counted.   Inflection point of the knee-plot of cell barcode/read number was detected by using DropletUtils package in R 3.5.3, and cell barcodes below the inflection threshold were filtered out.
Each hashtag read was normalized by total read counts into the smallest total read counts linearly and each cell were annotated to each hashtag based on fold-change between first- and second-most highly counted hashtags.   Cells were ordered ascending by the fold-change, and top 3.82 % cells were filtered out as doublet cells (probability of the % of doublet was estimated by Poisson's distribution calculated by load cell number and total number of Rhapsody wells).
Distribution-based error correction for background subtraction of gene-expression matrix was performed as described previously (Shichino et al., 2021) with the following parameters (maximum expression of log2(x+1) was over 8, maximum average expression of first component was over 5.5, and minimum difference of average expression between first- and second-components was over 5). We then analyzed cells assigned to hashtag 7-10 for this work.
A total of 3,314 out of 12,033 cells after quality check were normalized and analyzed by Seurat package version 4.0.2. (Hao et al., 2021) in R version 4.0.5. Twelve clusters (cluster 0-11) were obtained with 2000 most highly variable genes under the parameters of PCA dimension=37, k.param=50, and resolution=2.0, and two-dimensional t-SNE is drawn by the package.
RNA velocity analysis was performed as follows. After adapter trimming, quality filtering raw scRNA-seq fastq data, cell barcode reads were annotated by Python script provided by BD with minor modification for compatible to Python3.7. Associated cDNA reads were mapped to reference genome (build GRCh38 release-101 with reporter gene) by using HISAT2-2.2.1. (Kim et al., 2019) by the following parameters: -q -p 6 –rna-strandness F –very-sensitive –seed 656565 –reorder –omit-sec-seq –mm. For HISAT2 index build, Corresponded ensembl gtf file was filtered to retain protein-coded RNA, long non-coding RNA and T cell chain/immunoglobulin chain annotations according to 10X Genomics’s method(https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/advanced/references#mkgtf).   Addition of reporter gene (EGFP-IRES2-Puromycin-3'UTR) into reference genome and GTF files was performed according to 10X Genomics's method (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_mr, "Add a Marker Gene to the FASTA and GTF" section).
Cell barcode information of each read were added to the HISAT2-mapped BAM files, and associated gene annotations were assigned by using featureCounts v2.0.2 by following parameters: -T 2 -Q 0 -s 1 -t gene -g gene_name –primary -M -O –largestOverlap –fraction -R BAM.
In featureCounts analysis,“gene”annotation was used for capturing un-spliced RNA information for RNA velocity analysis, and primary annotations were kept. Then, resulted BAM file was splitted by valid cell barcodes by using nim 1.0.6 and hts-nim v0.2.23.
For each BAM file, we ran velocyto-0.17.17 by python-3.6.10 under anaconda3 environment. The resulted 3,314 loom files are combined into single loom file by loompy-3.0.6 package and imported into Seurat object. In Seurat, we used velocyto.R-0.6 library to calculate the velocity direction with kCells=100 on PCA space and draw the arrow embedding figure with n=50 on the original tSNE space.
For volcano plot comparing gene expression, we first extracted cells of cluster 7,8,9, and 10 with tSNE_2 < -15 condition.   Then we reassign clusters with higher resolution of 5 and obtained 26 clusters (A-Z).   We analyzed differentially expressed genes by volcano plots between the cluster A and the cluster B for all of 37,273 genes and the results are drawn in Figure 5G by using ggplot2-3.3.3 package in R.
Assembly: hg38
Supplementary files format and content: tsv

source_name: human blastocysts

growth_protocol: Primed hESCs were maintained on Matrigel coated dishes in StemFit AK02N, and Naive hESCs were maintained on Matrigel coated dishes in PXGL medium after being cultured in feeder-free conditions for more than 10 passages. We also treated primed hESCs  with AICAR in PXGL medium on MEF feeder cells. After 14 or 28 days, single cells were colltected.

extract_protocol:
Primed hESCs maintained without feeder cells were collected without any selection. Naive hESCs were sorted EOS-GFP+ (the purity was more than 95%) by using flow cytometry. AICAR-treated hESCs on MEF feeder cells were collected after MEF feeder cells (mouse-MHC+) depletion using flow cytometry. Each cell was determined by FlowCount beads (Beckman Coulter).
For scRNA-seq, cDNA libraries and hashtag libraries were prepared combined by an BD Rhapsody system and an optimized process similar to the magnetic bead-based bulk RNA-seq method (Shichino et al. JCI insight 2019). Sequencing libraries were generated by using NEBNext UltraII FS library prep kit (New England Biolabs), and QC of cDNA/Hashtag libraries was performed by MultiNA (Shimazu) and qPCR library quantification assay (KAPA).
BD Rhapsody WTA

value: Embryonic stem cell (ES cell)

value: human blastocysts

value: blastocyst stage

value: mixed sample (non-demultiplexed)


title: 3q gain cell, mRNA, biological replicate 2

description:
Library name: Sample 8
Chr3_isogenic_system_mRNA.xlsx

tag: cell line

value: lung epithelial cell

value: 3q gain


title: Rheumatoid Arthritis (RA) Human Synovium_FGRA-RA2

city: los angeles

first: yizhou

last: wang

address: 8700 beverly blvd

institute: cedars-sinai medical center

description:
Section_B1
10x Genomics

data_processing:
library strategy: Spatial Transcriptomic
Raw sequencing data was demultiplexed and converted to fastq format by using bcl2fastq v2.20 (Illumina). Space Ranger software v2.0.0 (10X Genomics) was used for reads alignment, tissue detection, fiducial detection, and barcode/UMI counting with default parameter. Briefly, raw reads were aligned to the human erence transcriptome (GRCh38, version=2020-A), then reads with the same barcode, UMI and gene annotation were grouped for UMI counting. For image processing, the slides’ barcoded spot pattern was aligned to the input image, and tissue and background were discriminated. A UMI count matrix was generated, with gene identities as rows and spatial barcodes as columns. Seurat v4.2.1 in R v4.1.3 was used for advanced downstream analysis. The matrix was loaded into Seurat to create a Seurat object and low-quality spots were filtered out based on the total number of UMI (< 600 and > 30,000) and total number of genes expressed (< 300). Further, spots with > 15% reads mapped to mitochondrial genes were removed. Count data of the remained spots was normalized using sctransform. To obtain two-dimensional projections of the population’s dynamics, principal component analysis (PCA) was run on the top 5,000 most variable genes to reduce the number of features. The top 5,000 most variable genes were identified based on their mean and dispersion. After running PCA, t-distributed stochastic neighbor embedding (t-SNE) analysis was performed to further reduce these components to visualize spots in a two-dimensional space. SPATA2 was used to calculate the average expression of exTh17 and fibroblast marker genes. MistyR (v1.6.0) was used to investigate the associations between the exTh17 and fibroblast maker genes. In MistyR, the neighborhood parameter was set to 5 spots and the cutoff threshold for the importance scores of markers was set to 0.5 standard deviation.
Assembly: GRCh38
Supplementary files format and content: JPEG images for slides
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Human Synovium

extract_protocol:
Frozen synovial tissues specimens were provided by Pini Orthopedic Hospital, University of Milan Italy. Tissues sections were generated by cryosectioning and fixed prior to permeabilization and reverse trascription to obtain cDNA for library generation
Visium Spatial Gene Expression libraries comprise standard Illumina paired-end constructs that are flanked with P5/P7, necessary for binding to the Illumina flow cell. TruSeq Read 1 is used for priming and sequencing the 16 bp Spatial Barcode and 12 bp UMI, and TruSeq Read 2 is used for priming and sequencing the cDNA insert. The two 10 bp sample indexes are sequenced in the i5 and i7 read respectively. Sequencing these libraries produce a standard Illumina BCL data output folder.
SP_28x10x10x90_Dual Index library piered-end, dual indexed sequencing. P5 (index i5:10) - TueSeq Read1 (Spatial BC+UMI+poly(dT)VN) - TueSeq Read2 (2:90 insert) - P7 (Index i7:10)

value: Human Synovium

tag: subject status

value: ACPA and RF positive RA patients with active disease

value: Female


title: 3q gain cell, mRNA, biological replicate 1

description:
Library name: Sample 7
Chr3_isogenic_system_mRNA.xlsx

tag: genotype


title: RA 1

description: miRNA expression

source_name: Rheumatoid arthritis patient 1

value: Rheumatoid arthritis

value: M


title: H1-EOS AICAR_naive_2

description:
Bulk RNA-Seq data
64

data_processing:
Total sequence was sequenced by Novaseq 6000 (PCR1: 5cycles and PCR2: 14 cycles).
Reads were aligned to human genome build GRCh38.p13 and Reads Per Kilobase of transcript, per Million mapped reads (RPKM) calculation were performed by using RSEM (RNA-Seq by Expectation-Maximization).
Comparative data were downloaded from the European Nucleotide Archive (ENA) under accessions ERP006823 (Takashima et al., 2014), SRP059279 (Ji et al., 2016), SRP045911 (Sperber et al., 2015), SRP055810 (Blakeley et al., 2015), and SRP074076 (Yang et al., 2017).  All 29 fastq files are adapter trimmed by cutadapt-1.15 using trim_galore-0.4.4_dev with –stringency 3 option, and then mapped to Ensembl GRCh38 release 100 reference cDNA and ncRNA sequences using Bow-tie2 v2.2.5 with the very-sensitive-local option. Among a total of 1,800,071,774 (single or paired) reads, 1,254,839,844 (69.7%) were successfully mapped and quantified as genes with a threshold of MAPQ score ≥ 1. A total of 61,222 genes (43,813 on average) were detected for 29 samples.
The following analyses were performed using R ver. 4.0.3 after non-categorized limma voom normalization (Law et al., 2014). A total of 25 samples from naive hESCs, primed hESCs, AICAR- and CA-p38 induced naive hPSCs were analyzed.
Genome_build: hg38
Supplementary_files_format_and_content: A matrix table of calculation of gene expression value and normalization were performed by RPKM for every sample and every gene
ENSG_summary_ID name_20220308.xlsx contains the public accession ID for the reanalyzed samples included in the processed data file.

source_name: Embryonic stem cell (ES cell)

growth_protocol: Primed hESCs were maintained on Matrigel coated dishes in StemFit AK02N. Naive human PSCs were cultured in the PXGL medium (Ndiff227 medium supplemented with PD0325901, XAV939, Go6983, human Lif, and penicillin/streptomycin) on Matrigel-coated 6 well plates with mitomycin C inactivated mouse embryonic fibroblast (MEF) feeder.  AICAR and DOX (CA-p38) was added to the PXGL medium with penicillin/streptomycin, and VPA was added to Ndiff227 basal medium with PD0325901, human Lif, and penicillin/streptomycin for naive state induction.  After naive conversion, bulk cells were reculutred in PXGL condition. After several passages, we sorted CD75- and SUSD2-positive cells, and collected them.

extract_protocol:
For sample preparation, primed state cells were dissociated by TrypLE™ Select CTS™, and CD75+/SUSD2+ naive state cells were sorted in by using FACS. Total RNA was isolated by using the RNeasy Mini kit (Qiagen) and purified with the RNA Clean & Concentrator-5 kit (Zymo Research) according to the manufacturer’s instructions. Polyadenylated RNA (polyA) was enriched by using NEBNext® Poly(A) mRNA Magnetic Isolation Module (New England BioLabs).
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell type

value: naive ES cell

tag: treatment

value: treated with AICAR


title: Forelimb CSNs, layer 5 M1, replicate 3

description:
Library name: FL3_CSN
10X Genomics

value: cortical

value: layer 5 neurons

value: WT

value: 8-10 weeks

tag: Sex


title: Late OA 2

description: miRNA expression

source_name: KL-grade IV Late OA patient 2

value: KL-grade IV Late OA

value: F


title: Forelimb non-CSNs, layer 5 M1, replicate 2

description:
Library name: FL2_control
10X Genomics

value: pooled male and female

value: naïve


title: H1-EOS AICAR_naive_1

description:
Bulk RNA-Seq data
63


title: Late OA 5

description: miRNA expression

source_name: KL-grade III Late OA patient 5

value: KL-grade III Late OA


title: Chr3 WT cell, mRNA, biological replicate 2

description:
Library name: Sample 5
Chr3_isogenic_system_mRNA.xlsx

value: lung epithelial cell

value: Chr3 WT


title: Rheumatoid Arthritis (RA) Human Synovium_CPRA-RA1

description:
Section_A1
10x Genomics

value: Human Synovium

value: ACPA and RF positive RA patients with active disease


title: Chr3 WT cell, mRNA, biological replicate 3

description:
Library name: Sample 6
Chr3_isogenic_system_mRNA.xlsx


title: Chr3 WT cell, mRNA, biological replicate 1

description:
Library name: Sample 4
Chr3_isogenic_system_mRNA.xlsx


title: Hind limb CSNs, layer 5 M1, replicate 1

description:
Library name: HL1_CSN
10X Genomics


title: CA-p38 H1-EOS_naive

description:
Bulk RNA-Seq data
67

value: treated with DOX (CA-p38)


title: CA-p38 H1-EOS_primed

description:
Bulk RNA-Seq data
YH1-EOS

value: primed ES cell

value: untreated


title: Forelimb non-CSNs, layer 5 M1, replicate 3

description:
Library name: FL3_control
10X Genomics


title: H1-EOS_primed

description:
Bulk RNA-Seq data
H1-EOS


title: Late OA 3

description: miRNA expression

source_name: KL-grade IV Late OA patient 3


title: 3p loss cell, mRNA, biological replicate 2

description:
Library name: Sample 2
Chr3_isogenic_system_mRNA.xlsx

value: 3p loss


title: 3p loss cell, mRNA, biological replicate 3

description:
Library name: Sample 3
Chr3_isogenic_system_mRNA.xlsx


title: Late OA 1

description: miRNA expression

source_name: KL-grade IV Late OA patient 1

value: M


title: Late OA 4

description: miRNA expression

source_name: KL-grade III Late OA patient 4


title: Forelimb non-CSNs, layer 5 M1, replicate 1

description:
Library name: FL1_control
10X Genomics

source_name: cortical

value: cortical

value: layer 5 neurons


title: SI_38887_SW480_Thapsigargin_BRD4

city: Ann Arbor

first: Abhijit

last: Parolia

state: MI

address: 1500 E Medical Center Dr

institute: Michigan Medicine

data_processing:
Alignment performed to hg38 using bwa (“bwa mem” command with options -5SP -T0, version 0.7.17-r1198-dirty). Filter with samtools and picard MarkDuplicates (removed duplicates).  MACS2 peak calling  using narrowpeak setting and bedtools to remove blacklisted regions of the genome from the peaks list (Encode’s list ENCFF356LFX.bed). UCSC’s tool wigtoBigwig for converting to bigwig formats.
Assembly: Hg38
Supplementary files format and content: Bigwig and BED files

source_name: Large intestine

growth_protocol: Cells were grown in full media.

extract_protocol:
Diagenode iDeal ChIP-seq kit for Transcription Factors
Chromatin immunoprecipitation experiments were carried out using the Ideal ChIP-seq Kit for Transcription Factors (Diagenode) as per the manufacturer’s protocol. Chromatin from 2 × 106 cells (for transcription factors) was used for each ChIP reaction with 4 μg of the target protein antibody respectively. In brief, cells were trypsinized and washed twice with 1× PBS, followed by cross-linking for 8 min in 1% formaldehyde solution. Crosslinking was terminated by the addition of 1/10 volume 1.25 M glycine for 5 min at room temperature followed by cell lysis and sonication (Bioruptor, Diagenode), resulting in an average chromatin fragment size of 200 bp. Fragmented chromatin was then used for immunoprecipitation using various antibodies, with overnight incubation at 4 °C. ChIP DNA was de-crosslinked and purified using the iPure Kit V2 (Diagenode) using the standard protocol. Purified DNA was then prepared for sequencing as per the manufacturer’s instructions (Illumina). ChIP samples (1–10 ng) were converted to blunt-ended fragments using T4 DNA polymerase, Escherichia coli DNA polymerase I large fragment (Klenow polymerase), and T4 polynucleotide kinase (New England BioLabs (NEB)). A single adenine base was added to fragment ends by Klenow fragment (3′ to 5′ exo minus; NEB), followed by ligation of Illumina adaptors (Quick ligase, NEB). The adaptor-ligated DNA fragments were enriched by PCR using the Illumina Barcode primers and Phusion DNA polymerase (NEB). PCR products were size-selected using 3% NuSieve agarose gels (Lonza) followed by gel extraction using QIAEX II reagents (Qiagen). Libraries were quantified and quality checked using the Bioanalyzer 2100 (Agilent) and sequenced on the Illumina HiSeq 2500 Sequencer (125-nucleotide read length).

treatment_protocol: SW480 cell were culture in regular media and treated with DMSO (control), Fedratinib, (1 uM for 4 hr), or Thapsigargin (50 nM for 4 hr)

value: Large intestine

value: Primary colon Adenocarcinoma

value: Male

tag: chip antibody

value: BRD4 Diagenode, Cat# C15410338

value: Thapsigargin (50 nM for 4 hr)


title: 3p loss cell, mRNA, biological replicate 1

description:
Library name: Sample 1
Chr3_isogenic_system_mRNA.xlsx


title: SI_38886_SW480_Fedratinib_BRD4

value: Fedratinib, (1 uM for 4 hr)


title: Early OA 4

description: miRNA expression

source_name: KL-grade II Early OA patient 4

value: KL-grade II Early OA

value: F


title: Kidney, DKD class III, rep4

status: Public on Mar 24 2026

city: Calgary

first: Justin

last: Chun

state: Alberta

address: 3330 Hospital Drive NW

institute: University of Calgary

description:
Run5830_Slide4A-polygons.csv
Run5830_Slide4A_exprMat_file.csv
Run5830_Slide4A_fov_positions_file.csv
Run5830_Slide4A_metadata_file.csv
Run5830_Slide4A_tx_file.csv
CellComposite_slide4A.tar
CellLabels_slide4A.tar
CellOverlay_slide4A.tar
CompartmentLabels_slide4A.tar
RawMorphologyImages_slide4A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide4A file package. Slide4A FOVs 22-34 and 47-55 correspond to this sample

hyb_protocol: NanoString CosMx spatial transcriptomics slides were prepared with NanoString 1000-plex human RNA probe assay according to manufacturer protocols.

scan_protocol: Spatial probe hybridization was measured on the NanoString CosMx Spatial Molecular Imager.

data_processing:
Raw data files were assembled including cell segmentation assembled by NanoString AtoMx software.
Cells having fewer than 20 total transcripts counts were excluded from downstream analyses.

source_name: kidney biopsy, DKD class III

extract_protocol: Paraffin embedded kidney biopsies from control and patients with diabetic kidney diseases were obtained from the Biobank for the Molecular Classification of Kidney Disease, Calgary, AB, Canada. Tissue was sectioned at 5 µm thickness with a microtome.

value: Kidney cortex

value: Class III


title: Kidney, DKD class IV, rep3

description:
Run5830_Slide4A-polygons.csv
Run5830_Slide4A_exprMat_file.csv
Run5830_Slide4A_fov_positions_file.csv
Run5830_Slide4A_metadata_file.csv
Run5830_Slide4A_tx_file.csv
CellComposite_slide4A.tar
CellLabels_slide4A.tar
CellOverlay_slide4A.tar
CompartmentLabels_slide4A.tar
RawMorphologyImages_slide4A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide4A file package. Slide4A FOVs 7-15 and 57 correspond to this sample

source_name: kidney biopsy, DKD class IV

value: Class IV


title: Kidney, DKD class IV, rep1

description:
Run5830_Slide4A-polygons.csv
Run5830_Slide4A_exprMat_file.csv
Run5830_Slide4A_fov_positions_file.csv
Run5830_Slide4A_metadata_file.csv
Run5830_Slide4A_tx_file.csv
CellComposite_slide4A.tar
CellLabels_slide4A.tar
CellOverlay_slide4A.tar
CompartmentLabels_slide4A.tar
RawMorphologyImages_slide4A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide4A file package. Slide4A FOVs 71-79 correspond to this sample


title: Forelimb CSNs, layer 5 M1, replicate 2

city: New Haven

institute: Yale University

description:
Library name: FL2_CSN
10X Genomics

value: WT

value: 8-10 weeks

value: pooled male and female

value: naïve


title: Kidney, DKD class II, rep3

description:
Run5830_Slide3A-polygons.csv
Run5830_Slide3A_exprMat_file.csv
Run5830_Slide3A_fov_positions_file.csv
Run5830_Slide3A_metadata_file.csv
Run5830_Slide3A_tx_file.csv
CellComposite_slide3A.tar
CellLabels_slide3A.tar
CellOverlay_slide3A.tar
CompartmentLabels_slide3A.tar
RawMorphologyImages_slide3A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide3A file package. Slide3A FOVs 28-35 correspond to this sample

source_name: kidney biopsy, DKD class II

value: Class II


title: Early OA 3

description: miRNA expression

source_name: KL-grade II Early OA patient 3

value: M


title: Kidney, DKD class IV, rep2

description:
Run5830_Slide4A-polygons.csv
Run5830_Slide4A_exprMat_file.csv
Run5830_Slide4A_fov_positions_file.csv
Run5830_Slide4A_metadata_file.csv
Run5830_Slide4A_tx_file.csv
CellComposite_slide4A.tar
CellLabels_slide4A.tar
CellOverlay_slide4A.tar
CompartmentLabels_slide4A.tar
RawMorphologyImages_slide4A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide4A file package. Slide4A FOVs 58-70 correspond to this sample


title: Forelimb CSNs, layer 5 M1, replicate 1

description:
Library name: FL1_CSN
10X Genomics

value: cortical

value: layer 5 neurons


title: H1-EOS VPA_naive

description:
Bulk RNA-Seq data
70

value: naive ES cell

value: treated with VPA


title: kidney, DKD class I, rep1

description:
Run5830_Slide1A-polygons.csv
Run5830_Slide1A_exprMat_file.csv
Run5830_Slide1A_fov_positions_file.csv
Run5830_Slide1A_metadata_file.csv
Run5830_Slide1A_tx_file.csv
CellComposite_slide1A.tar
CellLabels_slide1A.tar
CellOverlay_slide1A.tar
CompartmentLabels_slide1A.tar
RawMorphologyImages_slide1A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide1A file package. Slide1A FOV 34-39 and 59-67 correspond to this sample

source_name: kidney biopsy, DKD class I

value: Class I


title: Kidney, DKD class III, rep3

description:
Run5830_Slide3A-polygons.csv
Run5830_Slide3A_exprMat_file.csv
Run5830_Slide3A_fov_positions_file.csv
Run5830_Slide3A_metadata_file.csv
Run5830_Slide3A_tx_file.csv
CellComposite_slide3A.tar
CellLabels_slide3A.tar
CellOverlay_slide3A.tar
CompartmentLabels_slide3A.tar
RawMorphologyImages_slide3A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide3A file package. Slide3A FOVs 1-8, 19-27, and 92 correspond to this sample


title: Kidney, DKD class I, rep3

description:
Run5830_Slide3A-polygons.csv
Run5830_Slide3A_exprMat_file.csv
Run5830_Slide3A_fov_positions_file.csv
Run5830_Slide3A_metadata_file.csv
Run5830_Slide3A_tx_file.csv
CellComposite_slide3A.tar
CellLabels_slide3A.tar
CellOverlay_slide3A.tar
CompartmentLabels_slide3A.tar
RawMorphologyImages_slide3A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide3A file package. Slide3A FOVs 36-48 and 53-68 correspond to this sample


title: Kidney, non-disease control, rep3

description:
Run5830_Slide3A-polygons.csv
Run5830_Slide3A_exprMat_file.csv
Run5830_Slide3A_fov_positions_file.csv
Run5830_Slide3A_metadata_file.csv
Run5830_Slide3A_tx_file.csv
CellComposite_slide3A.tar
CellLabels_slide3A.tar
CellOverlay_slide3A.tar
CompartmentLabels_slide3A.tar
RawMorphologyImages_slide3A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide3A file package. Slide3A FOVs 82-91 correspond to this sample

source_name: Kidney biopsy, non-diseased control

value: Non-disease control


title: kidney, non-disease control, rep1

description:
Run5830_Slide1A-polygons.csv
Run5830_Slide1A_exprMat_file.csv
Run5830_Slide1A_fov_positions_file.csv
Run5830_Slide1A_metadata_file.csv
Run5830_Slide1A_tx_file.csv
CellComposite_slide1A.tar
CellLabels_slide1A.tar
CellOverlay_slide1A.tar
CompartmentLabels_slide1A.tar
RawMorphologyImages_slide1A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide1A file package. Slide1A FOV 41-58 correspond to this sample


title: Kidney, DKD class II, rep1

description:
Run5830_Slide1A-polygons.csv
Run5830_Slide1A_exprMat_file.csv
Run5830_Slide1A_fov_positions_file.csv
Run5830_Slide1A_metadata_file.csv
Run5830_Slide1A_tx_file.csv
CellComposite_slide1A.tar
CellLabels_slide1A.tar
CellOverlay_slide1A.tar
CompartmentLabels_slide1A.tar
RawMorphologyImages_slide1A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide1A file package. Slide1A FOV 11-33 correspond to this sample


title: Kidney, DKD class III, rep5

description:
Run5830_Slide4A-polygons.csv
Run5830_Slide4A_exprMat_file.csv
Run5830_Slide4A_fov_positions_file.csv
Run5830_Slide4A_metadata_file.csv
Run5830_Slide4A_tx_file.csv
CellComposite_slide4A.tar
CellLabels_slide4A.tar
CellOverlay_slide4A.tar
CompartmentLabels_slide4A.tar
RawMorphologyImages_slide4A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide4A file package. Slide4A FOVs 1-6 and 21 correspond to this sample


title: Kidney, DKD class III, rep1

description:
Run5830_Slide1A-polygons.csv
Run5830_Slide1A_exprMat_file.csv
Run5830_Slide1A_fov_positions_file.csv
Run5830_Slide1A_metadata_file.csv
Run5830_Slide1A_tx_file.csv
CellComposite_slide1A.tar
CellLabels_slide1A.tar
CellOverlay_slide1A.tar
CompartmentLabels_slide1A.tar
RawMorphologyImages_slide1A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide1A file package. Slide1A FOV 1-11 correspond to this sample


title: v_3

city: Wuhan

first: Kailun

last: Zhang

address: No. 1 Shizishan Road

institute: Huazhong Agricultural University

description: control group

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 NC_012207.1 using CLC genomic benchwork (parameter-mismath cost:2 insertion cost:3 deletion cost: 3 length fraction:0.8 similarity fraction:0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NC_012207.1
Supplementary files format and content: tab-delimited text files includes RPKM values for each sample

organism: Mycobacterium tuberculosis variant bovis BCG

growth_protocol: BCG was cultured to mid-log phase in 20 mL Middlebrook 7H9 medium supplemented with 10% oleic acid, albumin, dextrose, and catalase medium and 0.05% Tween-80 and incubated at 37℃ for 2-4 weeks. The recombinant BCG strains were grown in the above media and condition with supplementation of kanamycin (50 μg/mL).

extract_protocol:
Extracellular bacterial total RNA was extracted using Trizol reagent (Invitrogen, USA) according to the manufacturer’s instructions.
NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, USA, Catalog #: E7530L)

treatment_protocol: BCG_ncBCG427 and BCG_Vector were cultured to the mid-log phase in Middlebrook 7H9 medium for 2-4 weeks. Subsequently, the RNA of two bacterial strains was extracted for transcriptomic analysis

value: vector


title: Kidney, DKD class II, rep2

description:
Run5830_Slide2A-polygons.csv
Run5830_Slide2A_exprMat_file.csv
Run5830_Slide2A_fov_positions_file.csv
Run5830_Slide2A_metadata_file.csv
Run5830_Slide2A_tx_file.csv
CellComposite_slide2A.tar
CellLabels_slide2A.tar
CellOverlay_slide2A.tar
CompartmentLabels_slide2A.tar
RawMorphologyImages_slide2A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide2A file package. Slide2A FOVs 15-34 and 60 correspond to this sample


title: Early OA 2

description: miRNA expression

source_name: KL-grade II Early OA patient 2

value: KL-grade II Early OA

value: F


title: ncBCG427_1

description: experimental group

source_name: Mycobacterium tuberculosis variant bovis BCG

value: ncBCG427 overexpression


title: ncBCG427_2

description: experimental group


title: ZD055_KIRpos

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

institute: University of Ottawa

description: Library name: ZD055_KIRpos

data_processing:
Raw reads processed using fastp v0.20.1 to remove low quality sections and trim adapter sequences
Trimmed reads aligned to the hg38 genome using STAR v.2.7.8a, retaining reads aligning uniquely on the genome
Aligned reads counted for overlap with exons and summarized to genes using Subread featureCounts v2.0.1 with -s2 option for reverse-stranded library and using ENSEMBL Homo_sapiens.GRCh38.104 GTF file
Assembly: hg38
Supplementary files format and content: Individual tab-delimited text files produced by Subread featureCounts giving the number of reads aligning to exons, and summarized over genes

source_name: Gamma-delta T cells

growth_protocol: Peripheral blood mononuclear cells (PBMCs) were isolated from whole blood using Hypaque density gradient centrifugation and cryopreserved in FBS with 10% DMSO. After thawing, cells were rested overnight in RPMI supplemented with 10% FBS. Total γδ T cells were purified by negative magnetic selection, and KIR⁻ and KIR⁺ subsets were subsequently sorted by flow cytometry.

extract_protocol:
Total RNA was extracted using the RNeasy Micro Kit (Qiagen)
NEBNext Ultra II Directional RNA-Poly(A) Library Prep

treatment_protocol: Cells were not treated.

value: Gamma-delta T cells

tag: donor id

tag: kir status

value: KIRpos


title: Kidney, non-disease control, rep2

description:
Run5830_Slide2A-polygons.csv
Run5830_Slide2A_exprMat_file.csv
Run5830_Slide2A_fov_positions_file.csv
Run5830_Slide2A_metadata_file.csv
Run5830_Slide2A_tx_file.csv
CellComposite_slide2A.tar
CellLabels_slide2A.tar
CellOverlay_slide2A.tar
CompartmentLabels_slide2A.tar
RawMorphologyImages_slide2A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide2A file package. Slide2A FOV 48-63 correspond to this sample

value: Kidney cortex


title: v_2

description: control group


title: ncBCG427_3

description: experimental group


title: ZD055_KIRneg

description: Library name: ZD055_KIRneg

value: KIRneg


title: v_1

description: control group


title: ZD038_KIRpos

description: Library name: ZD038_KIRpos


title: ZD034_KIRpos

description: Library name: ZD034_KIRpos


title: ZD050_KIRpos

description: Library name: ZD050_KIRpos


title: ZD050_KIRneg

description: Library name: ZD050_KIRneg


title: Kidney, DKD class I, rep2

description:
Run5830_Slide2A-polygons.csv
Run5830_Slide2A_exprMat_file.csv
Run5830_Slide2A_fov_positions_file.csv
Run5830_Slide2A_metadata_file.csv
Run5830_Slide2A_tx_file.csv
CellComposite_slide2A.tar
CellLabels_slide2A.tar
CellOverlay_slide2A.tar
CompartmentLabels_slide2A.tar
RawMorphologyImages_slide2A.tar
ALL_SLIDES_processed_metadata.h5ad
processed_metadata.csv
All raw data is in slide2A file package. Slide2A FOVs 11-14 and 35-42 correspond to this sample


title: ZD038_KIRneg

description: Library name: ZD038_KIRneg


title: ZD034_KIRneg

description: Library name: ZD034_KIRneg


title: ZD030_KIRpos

description: Library name: ZD030_KIRpos


title: ZD026_KIRpos

description: Library name: ZD026_KIRpos