title: Sample6 Term GFP (-) non NPCs At PC19.5

description: Library name: S6_term19


title: Healthy Control 2, Fluorophore positive, Tetramer positive, IGG targeted

status: Public on Apr 17 2026

type: SRA

city: Chapel Hill

first: Office of Genomics Research

last: UNC Lineberger Comprehensive Cancer Center

state: NC

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

country: USA

institute: University of North Carolina at Chapel Hill

description: Library name: HC TPOS IGG

library_source: transcriptomic

data_processing:
Airrflow NF-core pipeline v4.1.1
Assembly: Hg38
Supplementary files format and content: IgH/K/L consensus clonotypes, TSV format
Library strategy: BCR-Seq

molecule: total RNA

organism: Homo sapiens

source_name: Peripheral blood mononuclear cells

growth_protocol: Cells were cultured inImmunoCult Human B cell expansion kit media (StemCell Catalog #100-0645) media containing CD40L (Bio-Techne, 6245-CL, 0.5 μg/mL), CpG oligodeoxynucleotide (InvivoGen, tlrl-2006, 1 μg/mL) in humidified conditions with 5% CO2 at 37degrees

extract_protocol:
RNeasy Plus Micro Kit
Takara SMARTer Human BCR IgG IgM H/K/L Profiling Kit

treatment_protocol: MPO antigen (Elastin, No. MY862, 1 ng/mL) was added to all cells

tag: tissue

value: Peripheral blood mononuclear cells

tag: cell type

value: B cells


title: Healthy Control 2, Fluorophore negative, IGG targeted

description: Library name: HC2 ANEG IGG


title: BM_CMP_rep3

city: Münster

first: Carlos

last: Silvestre Roig

address: Von Esmarch Str. 56

country: Germany

institute: University of Münster

description: Library name: lane2_AGGCAG

data_processing:
STAR alignment, Gene quantification using Salmon, differential expression was made using Deseq2
Assembly: mm10
Supplementary files format and content: csv file with FPKM values for each sample

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
TotalRNA was isolated using PicoPure Kit (Thermofisher) following manufacturer's protocol.
SMARTer smRNA-Seq Kit was used to generate Illumina libraries.

value: Bone marrow

value: CMP

tag: genotype

value: WT

tag: treatment

tag: batch


title: Healthy Control 1, Fluorophore positive, Tetramer positive, IGK/L targeted

description: Library name: HC1 TPOS IGKL


title: Sample2 Term GFP (-) non NPCs At PC19.5

city: Melbourne

first: Mehran

last: Piran

state: VIC

address: 19 Innovation Walk

department: Anatomy and Developmental Biology

country: Australia

institute: Monash University

description: Library name: S2_term19

data_processing:
FASTQ files were first assessed for quality using base-level metrics including per-base sequence content, GC content, adaptor contamination, and sequence duplication levels. Overrepresented sequences and adaptor content were flagged and used to guide preprocessing decisions. Trimming of nucleotides at both the 3′ and 5′ ends, as well as removal of overrepresented sequences using TrimGlore and BBDuK, was carried out using a combination of trimming strategies and overrepresented sequence removal. Pre-processed reads were aligned to the mouse reference genome, GRCm39, using STAR. Read count quantification was implemented using featureCounts tool. MultiQC was used to summarise alignment metrics across samples.
Assembly: GRCm39
Supplementary files format and content: Each file is a gene-level annotation and quantification table, in tab-delimited text format, where each row represents an Ensembl gene ID, with accompanying genomic and expression information. The "Chr", "Start", and "End" columns list the chromosome and genomic coordinates, sometimes with multiple semicolon-separated entries reflecting exons or transcript variants, while the **Strand** column indicates the DNA strand orientation (`+` or `-`, or multiple values if features span both). The "Length" column gives the size of the annotated region in base pairs, and the "Counts"  column reports the number of sequencing reads mapped to each gene, serving as a measure of expression.

source_name: kidney

growth_protocol: All animal experiments were approved by the Institutional Animal Care and Use Committee of the Hadassah Hebrew University. All mice were housed in the Hebrew University Specific Pathogen–Free Animal Facility Unit. The study utilized CD1 outbred mice, including transgenic mice. Specifically, we used the transgenic mice line Tg(Six2-EGFP/cre) Amc (herein Six2 Cre+/tg). Heterozygous Six2 Cre+/tg embryos were generated by mating male Six2 Cre+/tg  mice (8 to 10 weeks old) with wild-type (WT) CD1 females (8 to 10 weeks old). The day of vaginal plug detection was considered embryonic day 0.5 of pregnancy. Pregnant females were randomly assigned to the different experimental groups. At PC19.5 and PC 20.5, kidneys from each letter and each group were dissected from all pups, and no gender-specific analysis was performed.

extract_protocol:
The pups kidney were carefully dissected and excised in ice-cold HBSS buffer. Using a surgical scalpel, the kidneys were sliced and chopped into approximately 0.5- to 1-mm pieces on ice. The chopped kidney fragments were then transferred into an HBSS solution supplemented with 1 mg/ml collagenase (11213865001; Sigma-Aldrich) and dispase (D4693-1G; Sigma-Aldrich) and incubated at 37°C for 30 minutes. The cell suspension was filtered through a 40-mm nylon cell strainer (Corning) and washed twice with cold HBSS. Six2 Cre+/tg GFP(+) and GFP(-) NPCs were isolated by cell flow cytometry-based cell sorting at the Hebrew University Faculty of Medicine Core Facility. For RNA extraction, 50,000-100,000 cells were washed in cold HBSS, and total RNA was extracted using the Qiagen RNeasy Micro Kit (74004; Qiagen).
Libraries were prepared from RNA samples using a SMARTer® Stranded Total RNA-Seq Kit v4 (Takara Bio). The libraries were barcoded and pooled for multiplex sequencing. The pooled DNA library was loaded on a NovaSeq 6000 SP Reagent Kit v1.5 (100 cycles) cartridge (Illumina) and sequenced on an Illumina Novaseq 6000 System using a single-read sequencing condition of 100 cycles.

treatment_protocol: The pregnant mice were randomly assigned to one of two groups : Preterm group,pregnant females were injected with a single subcatanouse dose of mifepristone at the post conception (PC) day 17.5 leading to delivery at PC18.5 and Term group. pregnant mice were injected with the same dose at PC18.5 to deliver at PC19.5. On PC19.5 and PC20.5, the pups were dissected, kidneys were extracted and the nephron progenitor cells and non nephron progenitor cells were sorted.

value: kidney

value: non NPC

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos

value: Mifepristone at PC18.5


title: PACE234

city: New York City

first: Matthew

last: Muller

state: NY

address: 550 First Avenue

department: Department of Medicine

institute: New York University

description: Library name: Sample 18

data_processing:
Data processing and quality control were performed using the SeqNSlide Pipeline
Quality control of sequencing reads was assessed using FastQC (v.0.11.9) and MultiQC (v.1.10.1)
Reads were trimmed using fastqc (v.0.20.1) and trimmomatic, and mapped to human reference genome hg38 using STAR (v.2.7.7a).
Genomic features were then assigned using Subread featureCounts (v.1.6.3)
Assembly: hg38
Supplementary files format and content: space-delimited text file includes raw counts per sample per gene

source_name: whole blood

extract_protocol:
Peripheral whole blood RNA was collected into PAXgene Blood RNA tubes (Becton Dickinson and Company, Franklin Lakes, New Jersey) and stored at −80 C. Automated RNA extraction was performed using the QIAsymphony PAXgene Blood RNA Kit (PreAnalytiX, Qiagen/BD). RNA yield and integrity were evaluated prior to sequencing.
Library preparation was performed with the Illumina TruSeq kit (Illumina, San Diego, CA) using 200 ng of total RNA per sample as input. Libraries were amplified for 12 PCR cycles, then quantified, normalized, and pooled for sequencing. Sequencing was carried out on an Illumina HiSeq 4000 platform (v4 chemistry, single-read configuration).

value: whole blood

tag: phenotype

value: PAD

tag: age

tag: Sex

value: Male

tag: race

value: White

tag: ethnicity

value: Non-Hispanic


title: BM_CMP_rep1

description: Library name: lane1_AGGCAG


title: PACE152

description: Library name: Sample 16

value: Female

value: Black


title: Sample31 Preterm GFP (+) NPCs At PC20.5

description: Library name: S31_preterm20_np

value: nephron progenitor cells

value: Mifepristone at PC17.5


title: Healthy Control 1, Fluorophore negative, IGK/L targeted

description: Library name: HC1 ANEG IGKL

value: Peripheral blood mononuclear cells

value: B cells


title: Healthy Control 1, Fluorophore positive, Tetramer positive, IGG targeted

description: Library name: HC1 TPOS IGG


title: LAD2_Coculture_R3

city: Bloomington

first: Heather

last: O'Hagan

state: IN

address: 1001 E 3RD ST

department: School of Medicine

institute: Indiana University

description:
Library name: Sample 12
Column name in Raw_counts_all_samples: LAD2_Coculture_R3

data_processing:
Sequencing read quality control for all samples was assessed with FastQC (v0.11.9)
An index of the hg38 genome was created, and reads were aligned with STAR (v2.7.10a) with the additional parameter --quantMode GeneCounts to generate count matrix
Deseq2 (v3.24.0) was used for differential expression analysis. Gene Set Enrichment Analysis using the Reactome database was performed.
Assembly: hg38
Supplementary files format and content: Excel file includes gene count values for each sample

growth_protocol: HT-29 cells were maintained in McCoy 5A media supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C. LAD2 cells were maintained in SP34 media supplemented with SP34 nutrients in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen) for HT-29 samples and Rneasy micro kit (Qiagen) for LAD2 cells.
RNA libraries for RNA-seq were prepared using NEB NextUltra DNA Library following the manufacturer's protocol.

treatment_protocol: HT-29 cells and LAD2 cells were incubated in direct coculture for 12 hours.

tag: cell line

value: Mast cell line

value: In Coculture

value: 12 hours


title: Sample4 Term GFP (-) non NPCs At PC19.5

description: Library name: S4_term19

value: kidney

value: non NPC


title: PACE149

description: Library name: Sample 15


title: Sample29 Preterm GFP (+) NPCs At PC20.5

description: Library name: S29_preterm20_np

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos


title: BM_CMP_rep2

description: Library name: lane1_CTCTCT

value: Bone marrow

value: CMP

value: WT


title: PACE169

description: Library name: Sample 17

value: whole blood

value: PAD

value: Male

value: White

value: Hispanic/Latino


title: Healthy Control 1, Fluorophore negative, IGG targeted

description: Library name: HC1 ANEG IGG


title: LAD2_Coculture_R2

description:
Library name: Sample 11
Column name in Raw_counts_all_samples: LAD2_Coculture_R2


title: Sample27 Preterm GFP (+) NPCs At PC20.5

description: Library name: S27_preterm20_np

value: nephron progenitor cells

value: Mifepristone at PC17.5


title: LAD2_Coculture_R1

description:
Library name: Sample 10
Column name in Raw_counts_all_samples: LAD2_Coculture_R1


title: PACE122

description: Library name: Sample 13

value: Black

value: Non-Hispanic


title: Sample25 Preterm GFP (+) NPCs At PC20.5

description: Library name: S25_preterm20_np


title: Patient 4 (MPO-ANCA), Fluorophore positive, Tetramer positive, IGK/L targeted

description: Library name: P4 MPO-ANCA TPOS IGKL

value: Peripheral blood mononuclear cells

value: B cells


title: LAD2_Alone_R3

description:
Library name: Sample 9
Column name in Raw_counts_all_samples: LAD2_Alone_R3

value: Mast cell line

value: Alone

value: 12 hours


title: Patient 4 (MPO-ANCA), Fluorophore negative, IGK/L targeted

description: Library name: P4 MPO-ANCA ANEG IGKL


title: PACE121

description: Library name: Sample 12


title: LAD2_Alone_R2

description:
Library name: Sample 8
Column name in Raw_counts_all_samples: LAD2_Alone_R2


title: PACE120

description: Library name: Sample 11

value: Female


title: Patient 4 (MPO-ANCA), Fluorophore positive, Tetramer positive, IGG targeted

description: Library name: P4 MPO-ANCA TPOS IGG


title: LAD2_Alone_R1

description:
Library name: Sample 7
Column name in Raw_counts_all_samples: LAD2_Alone_R1


title: Sample21 Term GFP (+) NPCs At PC20.5

description: Library name: S21_term20_np

value: kidney

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos

value: Mifepristone at PC18.5


title: Patient 4 (MPO-ANCA), Fluorophore negative, IGG targeted

description: Library name: P4 MPO-ANCA ANEG IGG


title: PACE136

description: Library name: Sample 14

value: whole blood

value: PAD


title: Sample19 Term GFP (+) NPCs At PC20.5

description: Library name: S19_term20_np


title: Patient 3 (MPO-ANCA), Fluorophore positive, Tetramer positive, IGK/L targeted

description: Library name: P3 MPO-ANCA TPOS IGKL


title: PACE087

description: Library name: Sample 9

value: Male

value: Other


title: Sample17 Term GFP (+) NPCs At PC20.5

description: Library name: S17_term20_np

value: nephron progenitor cells


title: HT29_Coculture_R2

description:
Library name: Sample 5
Column name in Raw_counts_all_samples: HT29_Coculture_R2

value: Colorectal cancer cell line

value: In Coculture


title: Patient 3 (MPO-ANCA), Fluorophore negative, IGK/L targeted

description: Library name: P3 MPO-ANCA ANEG IGKL


title: Sample15 Preterm GFP (+) NPCs At PC19.5

description: Library name: S15_preterm19_np

value: Mifepristone at PC17.5


title: HT29_Coculture_R1

description:
Library name: Sample 4
Column name in Raw_counts_all_samples: HT29_Coculture_R1


title: PACE117

description: Library name: Sample 10

value: Hispanic/Latino


title: PACE077

description: Library name: Sample 8


title: HT29_Coculture_R3

description:
Library name: Sample 6
Column name in Raw_counts_all_samples: HT29_Coculture_R3


title: Sample13 Preterm GFP (+) NPCs At PC19.5

description: Library name: S13_preterm19_np


title: PACE037

description: Library name: Sample 6


title: Patient 3 (MPO-ANCA), Fluorophore negative, IGG targeted

description: Library name: P3 MPO-ANCA ANEG IGG

value: Peripheral blood mononuclear cells

value: B cells


title: HT29_Alone_R3

description:
Library name: Sample 3
Column name in Raw_counts_all_samples: HT29_Alone_R3

value: Alone


title: PACE076

description: Library name: Sample 7

value: Asian

value: Non-Hispanic


title: Sample11 Preterm GFP (+) NPCs At PC19.5

description: Library name: S11_preterm19_np

value: kidney


title: PACE036

description: Library name: Sample 5

value: Black


title: Sample9 Preterm GFP (+) NPCs At PC19.5

description: Library name: S9_preterm19_np

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos


title: HT29_Alone_R1

description:
Library name: Sample 1
Column name in Raw_counts_all_samples: HT29_Alone_R1

value: 12 hours


title: Sample23 Term GFP (+) NPCs At PC20.5

description: Library name: S23_term20_np

value: Mifepristone at PC18.5


title: Patient 3 (MPO-ANCA), Fluorophore positive, Tetramer positive, IGG targeted

description: Library name: P3 MPO-ANCA TPOS IGG


title: Patient 2 (MPO-ANCA), Fluorophore negative, IGK/L targeted

description: Library name: P2 MPO-ANCA ANEG IGKL


title: Sample7 Term GFP (+) NPCs At PC19.5

description: Library name: S7_term19_np


title: PACE035

description: Library name: Sample 4

value: whole blood

value: PAD

value: Male


title: R3, responder 3

city: Bethesda

first: Kristi

last: Briggs

address: 10 Center Drive

institute: NIDDK

description:
Library name: Sample 6_R3
10X Genomics

library_source: transcriptomic single cell

data_processing:
Gene counting was done using CellRanger software
Assembly: Homo Sapien GRCh38
Supplementary files format and content: tab seperated matrix and values files

source_name: sigmoid colon

extract_protocol:
Cryopreserved tissue was thawed at 37 °C and immediately washed and placed in solution of RPMI and 5% fetal bovine serum (FBS) with the addition of and disassociated using DNAse 1 and Collagenase P at 37 °C for 40 minutes. Digestion was stopped with 100 mM EDTA. Cells were filtered through a 70-µm pore size filter to obtain a single-cell suspension and washed with solution of RPMI + 5% FBS + 2 mM EDTA. Cells were spun down and resuspended in phosphate-buffered saline (PBS) to count. Cells were then stained with Live/Dead Fixable Aqua (Thermo Fisher Scientific) for 20 minutes. Cells were then washed and stained with CD45 (BV510; BD), CD3 (APC; BD), and EpCAM (BV605; BioLegend) with the addition of human Fc block and Brilliant buffer plus (BD). CD45+ and CD3+ cells (T cells) and CD45− and EpCAM+ (epithelial cells) were sorted on the BD FACSAria II and collected into tubes with PBS + 1% bovine serum albumin. Cells were then stained with trypan blue and manually counted with a hemocytometer and resuspended with the desired concentration of 1000 cells/µL. Any cell population with <10 000 cells were combined with another population. Cells were then sent to the Johns Hopkins Sidney Kimmell Comprehensive Cancer Center Experimental and Computational Genetics Core for library preparation and sequencing.  output.
The single-cell 5′ V(D)J and 5′ digital gene expression kits (10x Genomics) were used with an emulsion-based protocol provided by the manufacturer. Cells and barcoded gel beads were partitioned into nanoliter-scale droplets using the 10x Genomics Chromium platform to partition up to 10 000 cells per sample (when possible) followed by RNA capture and cell-barcoded complementary DNA synthesis using the manufacturer’s standard protocols. Libraries were generated and sequenced on an Illumina NovaSeq instrument using 2 × 150-bp paired end sequencing. The 5′ VDJ libraries were sequenced to a depth of ∼5000 reads per cell and the 5′ differential gene expression libraries were sequenced to a target depth of ∼50 000 reads per cell. Cell Ranger (v9.0; 10x Genomics) was used to align reads to reference (GRCh38-3.0.0) and generate feature-barcodematrices from the Chromium scRNAseq

value: sigmoid colon

value: responder


title: Patient 2 (MPO-ANCA), Fluorophore positive, Tetramer positive, IGG targeted

description: Library name: P2 MPO-ANCA TPOS IGG


title: HT29_Alone_R2

description:
Library name: Sample 2
Column name in Raw_counts_all_samples: HT29_Alone_R2

value: Colorectal cancer cell line


title: PACE029

description: Library name: Sample 3

value: Female

value: Other

value: Hispanic/Latino


title: Patient 2 (MPO-ANCA), Fluorophore positive, Tetramer positive, IGK/L targeted

description: Library name: P2 MPO-ANCA TPOS IGKL

value: Peripheral blood mononuclear cells

value: B cells


title: R2, responder 2

description:
Library name: Sample 5_R2
10X Genomics


title: Sample5 Term GFP (+) NPCs At PC19.5

description: Library name: S5_term19_np

value: nephron progenitor cells


title: PACE011

description: Library name: Sample 2

value: Non-Hispanic


title: Sample3 Term GFP (+) NPCs At PC19.5

description: Library name: S3_term19_np

value: kidney


title: Patient 1 (MPO-ANCA), Fluorophore positive, Tetramer positive, IGK/L targeted

description: Library name: P1 MPO-ANCA TPOS IGKL


title: Sample1 Term GFP (+) NPCs At PC19.5

description: Library name: S1_term19_np

value: Heterozygous CD-1 WT/ Six2 Cre+/tg embryos


title: NR3, non-responder 3

description:
Library name: Sample 4_NR3
10X Genomics

value: non-responder


title: Patient 1 (MPO-ANCA), Fluorophore positive, Tetramer positive, IGG targeted

description: Library name: P1 MPO-ANCA TPOS IGG


title: PACE005

description: Library name: Sample 1

value: Asian


title: NR2, non-responder 2

description:
Library name: Sample 2_NR2
10X Genomics


title: A5345_73746 CD4+ T cells

city: San Francisco

first: Tongcui

last: Ma

state: CA

address: 1650 Owens street

institute: UCSF

description: Library name: Sample74

data_processing:
The sequencing reads were trimmed for known adapters and low-quality regions of reads were performed using Fastq-mcf for the CLEAR, TEACH, and REDUC sample, and using Trim-galore for the A5345 samples. For both sets of samples, sequence quality control was assessed using FastQC and RSeQC.
Alignment of the reads to the human hg38 genome was performed using STAR.
Reads for the CLEAR, TEACH, and REDUC samples were assigned to genes using "featureCounts", part of the Subread suite (http://subread.sourceforge.net/). The transcript levels for A5345 samples were quantified using Salmon and summarized as gene-level counts using tximport. The filterByExpr function in the edgeR bioconductor package with the min.count argument set to 5 was used to filter out lowly expressed genes
Assembly: human hg38 genome
Supplementary files format and content: csv, different expressed genes

source_name: Blood

growth_protocol: Cryopreserved PBMCs were rapidly thawed in a 37°C water bath, and then washed once with complete RPMI (Corning) containing 20% FBS (Avantor), 2 mM L-glutamine (Gibco), 100 ug/mL Penicillin-streptomycin (Gibco) and 10 mM HEPES (Gibco). The PBMCs were then resuspended in 10 mL of RPMI-1640 with 20% FBS and transferred to 15 mL conical tubes. The cells were treated with 10 mL of RNase free DNase I (Sigma) (10 units/uL) processed for RNAseq.

extract_protocol:
Total RNA was extracted from PBMCs (CLEAR, TEACH and REDUC) or CD4+ T cells (ACTG A5345) using the Qiagen RNeasy Micro Kit per manufacturer’s protocol. RNA yields ranged from 300 ng to 3,500 ng. RNA quality was tested using a Qubit 2 fluorometer (Thermo Scientific).
Sequencing libraries were prepared by Azenta Life Sciences employing the NEB Next Ultra II RNA Library Prep Kit for Illumina.  Briefly, mRNA was enriched using oligo (dT) beads, then fragmented for 15 minutes at 94°C followed by cDNA synthesis. Fragments were then end-repaired and adenylated. Universal adapters were ligated to cDNA fragments, then indexes were added with library enrichment by PCR. RNA integrity and library size was assessed by Agilant Tapestation, and concentrations were determined by Qubit 2 fluorometer with final quantification by qPCR. Flow cells were prepared with multiplexed and clustered sequencing libraries, then loaded onto an Illumina HiSeq instrument.

tag: cohort

tag: pid

value: Blood

value: CD4+ T cells

value: WT


title: PC03

city: Lishui

first: Yahong

last: Lu

state: Zhejiang

address: No.289, Kuocang Road, Liandu District, Lishui City, Zhejiang Province, China

country: China

institute: The Fifth Affiliated Hospital of Wenzhou Medical University

description:
Library name: Sample 9
PC03_FPKM

data_processing:
Software trim_galore (version 0.6.4): de-joining, low quality, short reads.  Software bowtie2 (version 2.4.2): compare rRNA databases of corresponding species, remove rRNA.  Software hisat2 (version 2.2.0): compare reference genome Human:GRCh38.104 ; Mouse: GRCm39.104 ; Rattus: Rnor_6.0.  Software htseq-count (version 0.13.5): for RNA quantification.  Software edgeR : for differential analysis.
Assembly: GRCm39.104
Supplementary files format and content: Supplementary file format content processed date.xlsx

growth_protocol: C2C12 cells (a mouse myoblast cell line) were cultured in DMEM + 10% FBS at 37°C in a 5% CO2 incubator. When the cells reached a confluence of 90%, the medium was changed to DMEM containing 2% horse serum, and the cells were cultured for 5–7 days to form multinucleated myotubes.

extract_protocol:
Total RNA extraction of samples was performed using the RNeasy (Qiagen) RNA extraction kit and according to the standard procedure provided by the manufacturer.  The resulting RNA was subjected to electrophoretic QC by Agilent 4200 TapeStation (Cat#G2991A, Agilent) and quantitative QC by Qubit 3.0 Fluorometer (Cat#Q33216, Thermo Fisher Scientific)/NanoDrop One (ND-ONE, Thermo Fisher Scientific). (Cat#Q33216, Thermo Fisher Scientific)/NanoDrop One (ND-ONE, Thermo Fisher Scientific) for quantitative QC. Qualified RNA can be used for subsequent library construction.  Translated with DeepL.com (free version)
Experiments were performed using the VAHTS Stranded mRNA-seq Library Prep Kit (NR602, Vazyme) and according to the manufacturer's product instruction manual. The constructed mRNA libraries were quality checked by Qubit fluorometer (#Q33216, Thermo Fisher Scientific) and Agilent 4200 TapeStation (Cat#G2991A, Agilent). The libraries were uploaded using the illumina sequencing platform.

treatment_protocol: The palmitic acid group was treated with 200 μM palmitic acid for 48 disappearance. Palmitic acid + carnitine group treated with 200 μM palmitic acid and 1000 μM carnitine 48 disappeared.

value: Mouse myoblasts

value: palmitic acid + carnitine


title: A5345_73718 CD4+ T cells

description: Library name: Sample73


title: NR3, non-responder 1

description:
Library name: Sample 1_NR3
10X Genomics

value: sigmoid colon


title: A5345_73709 CD4+ T cells

description: Library name: Sample72


title: PC02

description:
Library name: Sample 8
PC02_FPKM


title: Patient 2 (MPO-ANCA), Fluorophore negative, IGG targeted

description: Library name: P2 MPO-ANCA ANEG IGG


title: R1, non-responder 1

description:
Library name: Sample 3_R1
10X Genomics


title: Patient 1 (MPO-ANCA), Fluorophore negative, IGG targeted

description: Library name: P1 MPO-ANCA ANEG IGG


title: ARID_Domain_Deletion_IP_2

city: La Jolla

first: Brian

last: Yee

address: 9500 Gilman Dr

department: Health

institute: UCSD

description: Library name: Domain_Deletion_IP_2

data_processing:
Reads were aligned using STAR v. 2.6.7a
IP enrichment was calculated by normalizing with corresponding inputs
Domain and domain deletion bound libraries were compared folllowing input normalixation
Assembly: GRCh38
Supplementary files format and content: comma separated value file of annotated domain vs domain deletion (no domain) transcripts enriched in IP samples compared to inputs
Supplementary files format and content: csv files of rpkm for all samples used in ribosome profiling

extract_protocol:
THP-1 macrophages were nucleofected with ARID5A domain and domain deletion constructs with V5 tags. Cells were pelleted and IP samples were generated by immunoprecipitation wtih an anti-V5 antibody. Inputs and IP samples were then lysed with Trizol and RNA was extracted using phenol/chloroform.
For RNA samples, libraries were constructed using the Illumina Stranded mRNA Ligation preparation kit. In brief, equal amounts of RNA are subjected to polyA selection and subsequent fragmentation. Samples are reverse transcribed and adapters are ligated. The products are then purified and amplified for sequencing.

value: THP-1 Macrophages


title: A5345_73705 CD4+ T cells

description: Library name: Sample71


title: ARID_Domain_Deletion_Input_2

description: Library name: Domain_Deletion_Input_2


title: Patient 1 (MPO-ANCA), Fluorophore negative, IGK/L targeted

description: Library name: P1 MPO-ANCA ANEG IGKL


title: PA03

description:
Library name: Sample 6
PA03_FPKM

value: palmitic acid


title: PSE-9

city: Linz

first: Anna

middle: Regina

last: Tröscher

address: Krankenhausstraße 5

department: Center for Medical Research

country: Austria

institute: Johannes Kepler University Linz

description: Library name: 9

data_processing:
basecall: DRAGEN CSL Convert v4.2.7.
CLC Genomics Workbench v24.0.2.
Trimming: Phred score <13, ambigious nucleotides >2, lenght <8, adapter trimming
Aligning: miRBase v22 (homo sapiens)
TMM normalization and FDR correction
Assembly: miRBase v22 (homo sapiens)
Supplementary files format and content: Excel file includes raw read counts of every sample

source_name: Serum

extract_protocol:
Qiagen miRNeasy Serum/Plasma Advanced Kit
TruSeq Small RNA Library Prep Kit - Illumina

value: Serum

tag: group

value: Stroke


title: A5345_73701 CD4+ T cells

description: Library name: Sample70


title: ARID_Domain_Deletion_IP_1

description: Library name: Domain_Deletion_IP_1


title: PSE-42

description: Library name: 42


title: A5345_73672 CD4+ T cells

description: Library name: Sample69


title: PA01

description:
Library name: Sample 4
PA01_FPKM


title: PC01

description:
Library name: Sample 7
PC01_FPKM


title: PSE-35

description: Library name: 35


title: PA02

description:
Library name: Sample 5
PA02_FPKM


title: PSE-23

description: Library name: 23


title: ARID_Domain_Deletion_Input_1

description: Library name: Domain_Deletion_Input_1


title: NC03

description:
Library name: Sample 3
NC03_FPKM

value: control


title: PSE-25

description: Library name: 25


title: PSE-24

description: Library name: 24


title: ARID_Domain_IP_2

description: Library name: Domain_IP_2


title: A5345_73482 CD4+ T cells

description: Library name: Sample67


title: NC02

description:
Library name: Sample 2
NC02_FPKM


title: NC01

description:
Library name: Sample 1
NC01_FPKM


title: ARID_Domain_IP_1

description: Library name: Domain_IP_1


title: ARID_Domain_Input_2

description: Library name: Domain_Input_2


title: A5345_73373 CD4+ T cells

description: Library name: Sample66


title: A5345_73619 CD4+ T cells

description: Library name: Sample68


title: A5345_73315 CD4+ T cells

description: Library name: Sample65


title: MEC, Home cage, rep3

city: Palo Alto

first: Xiao

last: Han

state: California

address: 265 Campus Drive

institute: Stanford University

data_processing:
Raw reads were stripped of adaptor sequences and removed low quality bases using Trimmomatic (version 0.33). The processed reads with lengths greater than 35 nt were defined as clean reads. Then the filtered reads were aligned to the mm10 genome with STAR (version 2.7.10b). The number of reads mapped to each Ensemble gene was counted using the HTSeq (version 2.0.1).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

molecule: polyA RNA

source_name: MEC

growth_protocol: Wild type BL-6 mice were individually housed in a single cage before starting the behavioural scheme. Mice were habituated to the hander for 3 minutes each day over a period of 5 days.

extract_protocol:
RNA was extracted using standard TRIzol (15596018, ThermoFisher) method.
RNA libraries were generated using the Illumina TruSeq Stranded mRNA kit, following the manufacturer's protocol

treatment_protocol: The mice were divided into three groups: home cage, context exposure, and foot shock.

value: MEC

value: Home cage


title: A5345_72119 CD4+ T cells

description: Library name: Sample64


title: PSE-7

description: Library name: 7

value: PSE


title: PSE-10

description: Library name: 10


title: PSE-8

description: Library name: 8


title: A5345_610671 CD4+ T cells

description: Library name: Sample63


title: MEC, Home cage, rep2


title: PSE-45

description: Library name: 45


title: ARID_Domain_Input_1

description: Library name: Domain_Input_1


title: GEM4

city: 종로구

first: Hyunsung

last: Nam

state: 서울특별시

address: 대학로 1

country: South Korea

institute: Seoul National University

description:
Library name: SVF_Re_GEM2
10x Genomics

data_processing:
FASTQ reads of 10x scRNA-seq data were processed by Cell Ranger (version 7.2.0, 10x Genomics; Pleasanton, CA, USA) using GRCH38-2020-A as a reference genome. All analyses were performed in Python (v3.11.9) using the following packages: anndata (v0.11.4), matplotlib (v3.10.0), numpy (v1.24.4), pandas (v2.2.3), scanpy (v1.9.8),22 scipy (v1.15.2), scvi-tools (v1.3.0)23, seaborn (v0.13.2). R studio (v4.4.0) and Seurat (v5.3.0) were also used.
Assembly: hg38
Supplementary files format and content: Cellranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Demultiplexing output files: demuxalot_result.csv.gz

source_name: Adipose tissue

extract_protocol:
RNA was harvested with 10X genomics Single-cell protocols.
Single-cell dissociated liquid nitrogen-stored samples were resuspended and counted using Luna automated cell counter. A total of 20,000 cells were loaded per channel on a Chromium X using Chromium Next GEM Single Cell 5’ v2 reagents (10X Genomics, Pleasanton, CA, USA), and scRNA-seq libraries were prepared according to the manufacturer’s instructions. The libraries were analyzed and quantified using TapeStation D1000 screening tapes (Agilent, Santa Clara, CA, USA) and sequenced using the NovaSeq 6000 system (Illumina, San Diego, CA, USA).

value: Adipose tissue


title: PSE-40

description: Library name: 40


title: GEM3

description:
Library name: SVF_Re_GEM1
10x Genomics


title: MEC, Fear, rep3

value: Fear


title: A5345_363331 CD4+ T cells

description: Library name: Sample61


title: A5345_363340 CD4+ T cells

description: Library name: Sample62


title: GEM2

description:
Library name: SVF_GEM_2
10x Genomics


title: PSE-36

description: Library name: 36


title: A5345_363323 CD4+ T cells

description: Library name: Sample60


title: PSE-3

description: Library name: 3


title: A5345_363300 CD4+ T cells

description: Library name: Sample59


title: MEC, Context, rep3

value: Context


title: GEM1

description:
Library name: SVF_GEM_1
10x Genomics


title: MEC, Fear, rep1


title: MEC, Fear, rep2


title: PSE-2

description: Library name: 2


title: siASCL2-3

city: Guang Zhou

first: Tingting

last: Guo

state: Guang Dong

address: University Town Campus (South Campus): 382 Zhonghuan Road East, Panyu District, Guangzhou Higher Education Mega Centre,

institute: South China University of Technology

description: Library name: Sample6

data_processing:
we used Fastp (version 0.19.7) to perform basic statistics on the quality of the raw reads.
Discard a paired reads if either one read contains adapter contamination;
Discard a paired reads if more than 10% of bases are uncertain in either one read;
Discard a paired reads if the proportion of low quality (Phred quality <5) bases is over 50% in either one read
reads from each sample in FASTQ format were aligned to the genome using Hisat2 to generate SAM files, which were then converted to BAM format using Samtools. Gene quantification was performed using FeatureCounts to obtain a raw count matrix.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: liver cancer

extract_protocol:
Total RNAs from cells were extracted using Universal RNA Extraction Kit (TaKaRa)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: liver cancer

value: liver cancer stem cell

value: ASCL4  knockdown

value: ASCL5  knockdown


title: siASCL2-2

description: Library name: Sample5

value: ASCL3  knockdown


title: A5345_362477 CD4+ T cells

description: Library name: Sample57

value: Blood

value: CD4+ T cells

value: WT


title: PSE-1

description: Library name: 1

value: Serum


title: MEC, Context, rep1


title: PSE-5

description: Library name: 5

value: Epilepsy


title: siASCL2-1

description: Library name: Sample4

value: ASCL2  knockdown


title: MEC, Context, rep2

value: MEC


title: A5345_363294 CD4+ T cells

description: Library name: Sample58


title: NC3

description: Library name: Sample3

value: control


title: A5345_322670 CD4+ T cells

description: Library name: Sample56


title: PSE-4

description: Library name: 4


title: A5345_3093693 CD4+ T cells

description: Library name: Sample55


title: LEC, Home cage, rep2

source_name: LEC

value: LEC

value: Home cage


title: LEC, Home cage, rep3


title: NC2

description: Library name: Sample2


title: PSE-46

description: Library name: 46


title: NC1

description: Library name: Sample1


title: A5345_3093690 CD4+ T cells

description: Library name: Sample53


title: LEC, Home cage, rep1


title: PSE-30

description: Library name: 30


title: PSE-26

description: Library name: 26


title: LEC, Fear, rep3

value: Fear


title: HCC1143 cells, METTL3 siRNA, Rep 2

city: Izmir

first: Bünyamin

last: Akgül

state: Urla

address: Gulbahce Campus

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

description:
Library name: si-METTL3-KD-2
column name in final_counts_genes.txt: si-METTL3-2

data_processing:
Raw FASTQ files were preprocessed using Trim Galore! Tool. Then adapter-trimmed sequences were mapped to human genome GRCh38.p14 with GENCODE.v44 annotation.
The mapped data were counted using featureCounts tool from Subread package.
Differential expression analysis was performed using DESeq2 package from Bioconductor.
Assembly: GRCh38.p14
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample.

growth_protocol: The transfected cells were then incubated for 72 hours in a humidified atmosphere of 5% CO₂ at 37°C prior to harvesting for subsequent experiments. The cells are passaged approximately twice a week before reaching saturation.

extract_protocol:
RNA samples to be used for RNA-sequencing were isolated using the RNeasy Mini Kit (QIAGEN) according to the manufacturer's protocol.
Illumina Stranded Total RNA Prep with Ribo-Zero Plus kit was used.

treatment_protocol: 4 × 10⁵ HCC1143 cells were seeded into 10 cm dishes and incubated overnight. The cells were transfected with 25 nM of METTL3 siRNA pool (si-METTL3) or a non-target negative control siRNA (si-NC) using Dharmafect. The transfected cells were then incubated for 72 hours in a humidified atmosphere of 5% CO₂ at 37°C prior to harvesting for subsequent experiments.

value: breast carcinoma


title: HCC1143 cells, METTL3 siRNA, Rep 1

description:
Library name: si-METTL3-KD-1
column name in final_counts_genes.txt: si-METTL3-1


title: A5345_3093689 CD4+ T cells

description: Library name: Sample52


title: PSE-18

description: Library name: 18


title: LEC, Fear, rep2


title: A5345_3093691 CD4+ T cells

description: Library name: Sample54


title: PSE-17

description: Library name: 17


title: HCC1143 cells, Negative Control siRNA, Rep 2

description:
Library name: si-NC-2
column name in final_counts_genes.txt: si-NC-2

value: Negative Control siRNA


title: A5345_3093688 CD4+ T cells

description:
Library name: Sample51
Only the R1 fastq file is available for this sample.


title: PSE-16

description: Library name: 16


title: HCC1143 cells, Negative Control siRNA, Rep 1

description:
Library name: si-NC-1
column name in final_counts_genes.txt: si-NC-1


title: A5345_3038151 CD4+ T cells

description: Library name: Sample50


title: LEC, Context, rep3

value: Context


title: LEC, Fear, rep1


title: CD34+ MKs, IFNγ 100 ng/mL, D4

description:
Library name: 32
IFNgamma_d4

data_processing:
Data processing and quality control were performed using the RNAseq PE snakemake pipeline [https://github.com/mgildea87/RNAseq_PE].
Quality control of sequencing reads was assessed using FastQC (v.0.11.9) and MultiQC (v.1.10.1)
Reads were trimmed using fastp (v.0.20.1), and mapped to human reference genome hg38 using STAR (v.2.7.7a).
Genomic features were then assigned using Subread featureCounts (v.1.6.3)
Assembly: hg38
Supplementary files format and content: space-delimited text file includes raw counts per sample per gene

source_name: CD34+ cells

growth_protocol: Cells were cultured in StemSpan SFEM II (STEMCELL Technologies) supplemented with stem cell factor (25 ng/ml; STEMCELL Technologies) and thrombopoietin (TPO; 25 ng/ml; R&D Systems) for 5 days. Then, cells were cultured only with TPO (25 ng/ml) until day 12.

extract_protocol:
Total RNA was isolated using Direct-zol RNA MicroPrep columns (Zymo Research).
Sequencing libraries were barcoded and prepared using the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA), and libraries were sequenced single end (51bp) on an Illumina NovaSeq 6000 at the Genome Technology Center at NYU Langone.

treatment_protocol: On day 11, cells were stimulated for 24 hours with IFNα 1000 U/mL, IFNγ 100 ng/mL or PBS (vehicle control)

value: CD34+ cells

value: Hematopoietic Stem and Progenitor Cells

tag: donor

value: Treated

tag: treatment type

value: IFNγ 100 ng/mL

tag: time of_treatment

value: 24 hours


title: A5345_3038013 CD4+ T cells

description: Library name: Sample48

tag: tissue

value: Blood

value: CD4+ T cells

value: WT


title: LEC, Context, rep1


title: PSE-12

description: Library name: 12

value: Serum

value: Epilepsy


title: CD34+ MKs, IFNγ 100 ng/mL, D3

description:
Library name: 31
IFNgamma_d3

tag: cell type


title: A5345_3038056 CD4+ T cells

description: Library name: Sample49

tag: genotype


title: LEC, Context, rep2

tag: treatment


title: MEC, Home cage, rep1

value: MEC


title: A5345_3010657 CD4+ T cells

description: Library name: Sample47

tag: batch


title: CD34+ MKs, IFNγ 100 ng/mL, D2

description:
Library name: 30
IFNgamma_d2


title: Y1mock_term_NOB2020_S28

city: Belfast

first: Guillermo

last: López-Campos

state: Northern Ireland

address: 97 Lisburn road

department: Welcome-Wolfson Institute for Experimental Medicine

country: United Kingdom

institute: Queen's University of Belfast

data_processing:
Sequence quality wwas analysed using FASTQC program
Sequence reads were mapped to human genome GRCh38/hg38 (Gencode release 38 for the annotation) using Rsubread package in R (v2.6.4 Jul 2021) including a low quality sequence trimming parameter (nTrim5 = 12, nTrim3 = 1) and all other parameters were ekpt as default.
Read counts were generated using FeatureCounts function of R subread package (using Genecode 38 annotation)
Assembly: GRCh38/hg38
Supplementary files format and content: A single multicolumn csv file containing some gene annotation details in the first 8 columns (uniqueId, EnsemblGeneId, chr, start, end, strand, lenth and gene_name) followed by raw counts columns for each of the samples analysed

source_name: Well-differentiated primary nasal epithelial cell

growth_protocol: Nasal brushings were performed on healthy newborn term infants, (37–42 weeks gestation) and preterm infants (28–34 weeks gestation) at birth and repeated in the same infants at one-year-old.   Harvested pediatric nasal cells were cultured to differentiation using established methods.  In brief, cells were expanded in airway epithelial cell basal medium with addition of an airway epithelial cell growth medium supplement pack (Promocell, Heidelberg, Germany).  Cells were seeded at passage 3 onto collagen-coated 6 mm diameter Transwells (Corning, Tewksbury, Massachusetts) and on reaching 100% confluence, an air-liquid interface was established and maintained until complete differentiation as defined by extensive cilia coverage and mucus production observed under light microscopy.  Transepithelial electrical resistances (TEER) were also measured.

extract_protocol:
WD-PNEC cultures at 24, 48, 72, 96 hpi were trypsinized in 200 μL 0.05% Trypsin-ethylenediaminetetraacetic acid (EDTA) (v/v).  Once cells were singular and detached as determined by light microscopy observation, the cell suspensions was transferred to RNAse free microcentrifuge tubes and the trypsin was inactivated by 400 μL of low glucose DMEM supplemented with 5% FBS (v/v).  The cells were centrifuged at 489 x g and the resulting supernatant carefully removed.  Cells were resuspended in 200 μL ice-cold sterile RNAse-free PBS.  RNA extraction then proceeded according to manufacturer’s instructions (High pure RNA isolation kit, Roche diagnostics, Indianapolis, USA).  Purified RNA was stored at -80oC until used. Agilent 2100 Bioanalyzer was used to assess RNA purity and integrity using the RNA 6000 Nano kit (Agilent Technologies, Santa Clara, CA, USA) according to manufacturer’s instructions.  Software analysis (Agilent Technologies, version 2.6) calculated RNA concentration and RNA integrity number (RIN) (a measure of RNA integrity) for each sample.  The vast majority of RNA samples demonstrated RIN values between 8.0 and 10. Samples with RIN values <7 were considered of insufficient quality and discarded.
KAPA RNA HyperPrep Kit with RiboErase (HRM), using ribosomal depletion to enrich for mRNA

treatment_protocol: Duplicate WD-PNEC cultures were infected with RSV BT2a or mock-infected.  A multiplicity of infection (MOI) of 3 was chosen with the aim of achieving infection in all susceptible cells in the culture.  In brief, 100 μL RSV BT2a inoculum or media-only were added to the apical surface of WD-PNEC cultures and incubated for 2 h at 37oC, 5% CO2.   Subsequently, the inoculum was removed, and the apical surface washed four times with 250 μL low glucose DMEM.  After the final wash, and every 24 h thereafter, the apical surface was rinsed with 250 μL low glucose DMEM, which was harvested, snap frozen in liquid nitrogen and stored at -80oC.  Simultaneously, the basal medium (300 μL) of each culture Transwell was harvested, snap frozen and stored at -80oC. Harvested medium was replaced with 300 μL of fresh airway epithelial cell growth medium (Promocell, Heidelberg, Germany).  Apical rinses and basal medium were used to determine virus growth kinetics and cytokine/chemokine responses. All cultures were monitored daily by light microscopy using NIKON ECLIPSE T5100 or NIKON ECLIPSE TE-2000 U (Nikon, UK).

value: Female

tag: gestational age

tag: infection status

value: mock

tag: chronological age

tag: sample origin


title: CA3, Home cage, rep3

value: Home cage


title: Y1RSV_term_NOB2020_S14

value: Well-differentiated primary nasal epithelial cell

tag: Sex

value: RSV


title: A5345_3010648 CD4+ T cells

description: Library name: Sample45


title: Y1mock_term_NOB2020_S27


title: A5345_3010649 CD4+ T cells

description: Library name: Sample46


title: CD34+ MKs, IFNα 1000 U/mL, D4

description:
Library name: 28
IFNalpha_d4

tag: cell line

value: IFNα 1000 U/mL


title: CD34+ MKs, IFNγ 100 ng/mL, D1

description:
Library name: 29
IFNgamma_d1

value: CD34+ cells


title: CA3, Home cage, rep2


title: CA3, Home cage, rep1


title: A5345_3010598 CD4+ T cells

description: Library name: Sample44

tag: cohort


title: CD34+ MKs, IFNα 1000 U/mL, D3

description:
Library name: 27
IFNalpha_d3

value: Hematopoietic Stem and Progenitor Cells


title: Y1mock_term_NOB2020_S25

value: Male


title: Y1mock_term_NOB2020_S26


title: A5345_271986 CD4+ T cells

description: Library name: Sample42

tag: pid


title: CD34+ MKs, PBS, D4

description:
Library name: 24
PBS_d4

value: Control

value: PBS


title: CD34+ MKs, IFNα 1000 U/mL, D1

description:
Library name: 25
IFNalpha_d1

value: Treated

value: 24 hours


title: A5345_272835 CD4+ T cells

description: Library name: Sample43

value: Blood

value: CD4+ T cells

value: WT


title: CD34+ MKs, IFNα 1000 U/mL, D2

description:
Library name: 26
IFNalpha_d2


title: Y1RSV_term_NOB2020_S11


title: CA3, Fear, rep3

value: Fear


title: Y1mock_term_NOB2020_S13

value: Female


title: A5345_271973 CD4+ T cells

description: Library name: Sample41


title: Y1RSV_term_NOB2020_S12


title: CA3, Fear, rep1


title: A5345_271217 CD4+ T cells

description: Library name: Sample40


title: CA3, Fear, rep2


title: CD34+ MKs, PBS, D1

description:
Library name: 21
PBS_d1


title: Y1mock_term_NOB2020_S24

value: mock


title: CD34+ MKs, PBS, D2

description:
Library name: 22
PBS_d2


title: A5345_15249 CD4+ T cells

description: Library name: Sample39


title: CA3, Context, rep2

value: Context


title: CA3, Context, rep3


title: CA3, Context, rep1


title: CA1, Home cage, rep3

value: Home cage


title: CD34+ MKs, PBS, D3

description:
Library name: 23
PBS_d3


title: A5345_15239 CD4+ T cells

description: Library name: Sample38


title: Y1mock_term_NOB2020_S23

value: Well-differentiated primary nasal epithelial cell


title: Y1RSV_term_NOB2020_S10

value: RSV


title: CA1, Home cage, rep1


title: nGD MLO # Biol rep 3 from GD2-1260 iPSC cells, 8 weeks

city: Cincinnati

first: Stuart

last: Adler

state: OH

address: 3333 Burnet Ave

department: Human Genetics

institute: Cincinnati Children's Hospital Medical Center

description: Library name: Sample 6

data_processing:
Reads were trimmed to remove adapters and low-quality reads using default parameters in Trimmomatic (Version 0.33). A quality control check on the fastq files was performed using FastQC.
The trimmed reads were then mapped to a reference genome using default parameters with strandness option in Hisat2 (Version 2.0.5)
Transcript or gene abundance was determined using kallisto (Version 0.43.1)
A transcriptome index in kallisto was created using Ensembl cDNA sequences for the reference genome. This index was then used to quantify transcript abundance in raw counts and transcript per million (TPM)
Assembly: GRCh38
Supplementary files format and content: Excel file includes raw counts for all samples with each transcript and corresponding gene ID

source_name: midbrain-like organoid tissue

extract_protocol:
Total RNAs were extracted from brain tissues using RNeasy Mini Kit (Qiagen, Tokyo, Japan).
Total RNA (150 to 300 ng) determined by Invitrogen Qubit high-sensitivity spectrofluorometric measurement was poly-A selected and reverse transcribed using Illumina’s TruSeq® stranded mRNA library preparation kit (Illumina, San Diego, CA, USA).

value: midbrain-like organoid tissue

value: Midbrain-like organoid

value: Midbrain-like organoid differentiation


title: A5345_14859 CD4+ T cells

description: Library name: Sample37


title: Y1RSV_term_NOB2020_S09

value: Male


title: CA1, Home cage, rep2


title: A5345_111714 CD4+ T cells

description: Library name: Sample35


title: A5345_14651 CD4+ T cells

description: Library name: Sample36


title: Y1RSV_term_NOB2020_S08


title: Y1mock_term_NOB2020_S22


title: CA1, Fear, rep3


title: TEACH_120 PBMC

description: Library name: Sample34

value: TEACH

value: PBMC


title: nGD MLO # Biol rep 2 from GD2-1260 iPSC cells, 8 weeks

description: Library name: Sample 5


title: nGD MLO # Biol rep 1 from GD2-1260 iPSC cells, 8 weeks

description: Library name: Sample 4


title: WT MLO # Biol rep 2 from WT-75.1 iPSC cells, 8 weeks

description: Library name: Sample 2


title: CA1, Fear, rep1


title: TEACH_116 PBMC

description: Library name: Sample32


title: Y0RSV_term_NOB2020_S07


title: Y0mock_term_NOB2020_S21


title: WT MLO # Biol rep 1 from WT-75.1 iPSC cells, 8 weeks

description: Library name: Sample 1


title: CA1, Context, rep3


title: WT MLO # Biol rep 3 from WT-75.1 iPSC cells, 8 weeks

description: Library name: Sample 3


title: THP1_Macrophage_NegativeControl_IgG_Rep2

description: Library name: IgG_CUTRUN_2

library_source: genomic

data_processing:
Data was processed using a modified version of CUT&RUN tools
Adapters were trimmed using Trimmomatic (v0.36), and subjected to a second round
Reads were aligned using bowtie2 (v2.3.5.1)  --very-sensitive-local, minimum fragment length 10, and maximum fragment length 700
PCR duplicates were removed using Picard (v0.1.8)
Peaks were called using MACS2 (v2.2.7.1) on the default narrowPeak setting with IgG as a normalization controls
Assembly: GRCh38
Supplementary files format and content: narrowPeak files output by MACS2

molecule: genomic DNA

extract_protocol:
Nuclei were isolated per Epicypher CUTANA CUT&RUN protocol and subjected to immobilization and permeabilization using Concanavalin-coated beads and complexes were immunoprecipitated using ARID5A specific antibody from Atlas Antibodies, and positive (H3K4Me) and negative (IgG) control antibodies from EpiCypher. pAG-MNAse is used to cleave target complex.
Isolated DNA fragments are repaired to generate blunt ended DNA, and 5'end is phosphorylated and 3' end is labeled with dAMP (non-templated). Adapter is ligated and uracil is added to digest hairpin loops. DNA is purified, amplified by PCR and sequenced using EpiCypher CUT&RUN library prep kit.

value: Macrophages


title: Y0mock_term_NOB2020_S20


title: TEACH_115 PBMC

description: Library name: Sample31

value: Blood


title: CA1, Fear, rep2


title: THP1_Macrophage_NegativeControl_IgG_Rep1

description: Library name: IgG_CUTRUN_1


title: Y0RSV_term_NOB2020_S06


title: CA1, Context, rep1


title: CA1, Context, rep2


title: TEACH_114 PBMC

description: Library name: Sample30


title: THP1_Macrophage_PositiveControl_H3K4me3_Rep2

description: Library name: H3K4me3_CUTRUN_2


title: TEACH_113 PBMC

description: Library name: Sample29


title: TEACH_117 PBMC

description: Library name: Sample33


title: Y0mock_term_NOB2020_S19


title: Y0RSV_term_NOB2020_S05


title: Y0mock_term_NOB2020_S18


title: THP1_Macrophage_ARID5A_Rep2

description: Library name: ARID5A_CUTRUN_2


title: 1A9CP80rev_replicate_2

city: East Lansing

first: Sachi

last: Horibata

state: MI

address: 766 Service Rd, Room 2014

institute: Michigan State University

description:
Library name: Sample 8
column name in counts All Sample.txt: rev2

data_processing:
CCBR pipeliner https://ccbr.github.io/
Statistical analyses were conducted using R (v3.5). After applying quantile normalization for log2 transformed expression values, principal component analysis (PCA) showed consistency between replicates as well as distinct separation among the three groups. Differential expression analysis was performed by fitting the generalized linear models (GLM, Gaussian) using glm function. The FDR (false discovery rate) was calculated by the Benjamini-Hochberg method for each gene. Genes with FDR < 0.01 and |log2 fold-change| > 2 were considered as significantly differentially expressed.
Assembly: hg38
Supplementary files format and content: text files include normalized counts for each sample

growth_protocol: 1A9CP80 cells are grown in the presence of 80 uM cisplatin. Before the experiments, cells were passaged without cisplatin before conducting the RNA-seq. All cells were cultured in the absence of cisplatin.

extract_protocol:
RNA was isolated from the cells using Rneasy Kit (Qiagen). The quality of the RNA was determined using an Agilent D1000 ScreenTape System Bioanalyzer. Only the samples with RNA Integrity Number (RIN) 10 were used for the RNA-seq.
Illumina TruSeq mRNA Prep Kit

treatment_protocol: No treatment

value: ovarian cancer cell

value: cisplatin revertant_resensitized


title: TEACH_112 PBMC

description: Library name: Sample28

value: WT


title: 1A9CP80rev_replicate_3

description:
Library name: Sample 9
column name in counts All Sample.txt: rev3


title: THP1_Macrophage_ARID5A_Rep1

description: Library name: ARID5A_CUTRUN_1


title: 1A9CP80rev_replicate_1

description:
Library name: Sample 7
column name in counts All Sample.txt: rev1


title: TEACH_101 PBMC

description: Library name: Sample26


title: Y0mock_term_NOB2020_S17

value: Female


title: 1A9CP80, replicate 3

description:
Library name: Sample 6
column name in counts All Sample.txt: res3

value: cisplatin resistant


title: iTF_Microglia_RPF_Arid5aKD_Rep2

description: Library name: RPF_KD_2

data_processing:
For splicing reads were aligned using STAR v. 2.6.7a
Differential splicing analysis was performed on STAR-aligned reads using rMATS v 4.3
Reads were aligned using Bowtie v.1.1.229 for ribosome profiling.
For ribosome profiling: ribosome P site was calculated using the 5′ end of the reads using the canonical ORFs with +12 for reads that were 28–29 bp and +13 for reads that were 30–33 bp
RPKM were calculated for mRNA and ribosome profiling footprints
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include differential skipped exon splicing analysis for each knockdown (SE.MATS.JC.txt from rMATS)
Supplementary files format and content: csv files of rpkm for all samples used in ribosome profiling

source_name: iPSC-derived microglia

extract_protocol:
For RNA samples, cells were lysed with Trizol and RNA was extracted using phenol/chloroform. For RPF samples, cells were harvested in cyclohexamide and lysed and treated with RNase I. Lysates were subjected to a sucrose gradient and the polysome pellet was resuspended in Trizol. RNA extracted using phenol/chloroforml.
For RNA samples, libraries were constructed using the Illumina Stranded mRNA Ligation preparation kit. In brief, equal amounts of RNA are subjected to polyA selection and subsequent fragmentation. Samples are reverse transcribed and adapters are ligated. The products are then purified and amplified for sequencing. For RPF samples, linkers are ligated to ribosome protected RNA fragments and subsequently reverse transcribed and gel purified. After purification, products are circularized and subjected to rRNA depletion prior to amplification with sequencing barcodes.

value: iPSC-derived microglia

value: KD


title: Y0RSV_term_NOB2020_S03

value: Well-differentiated primary nasal epithelial cell


title: 1A9CP80, replicate 2

description:
Library name: Sample 5
column name in counts All Sample.txt: res2


title: REDUC_44 PBMC

description: Library name: Sample25

value: REDUC


title: REDUC_43 PBMC

description: Library name: Sample24


title: TEACH_107 PBMC

description: Library name: Sample27


title: Y0mock_term_NOB2020_S16

value: mock


title: iTF_Microglia_RPF_Arid5aKD_Rep1

description: Library name: RPF_KD_1


title: 1A9CP80, replicate 1

description:
Library name: Sample 4
column name in counts All Sample.txt: res1


title: THP1_Macrophage_PositiveContro_H3K4me3_Rep1

description: Library name: H3K4me3_CUTRUN_1


title: 1A9, replicate 2

description:
Library name: Sample 2
column name in counts All Sample.txt: sen2

value: cisplatin sensitive


title: iTF_Microglia_RPF_Nontargeting_Rep2

description: Library name: RPF_NT_2

value: NT


title: Y0mock_term_NOB2020_S15

value: Male


title: REDUC_41 PBMC

description: Library name: Sample22


title: Y0RSV_term_NOB2020_S01

value: RSV


title: Y0RSV_term_NOB2020_S02


title: iTF_Microglia_RPF_Nontargeting_Rep1

description: Library name: RPF_NT_1


title: Y1mock_termB2019_S14

value: term


title: iTF_Microglia_RNA_Arid5aKD_Rep3

description: Library name: RNA_KD_3


title: 1A9, replicate 3

description:
Library name: Sample 3
column name in counts All Sample.txt: sen3


title: 1A9, replicate 1

description:
Library name: Sample 1
column name in counts All Sample.txt: sen1


title: REDUC_42 PBMC

description: Library name: Sample23

value: PBMC


title: iTF_Microglia_RNA_Arid5aKD_Rep2

description: Library name: RNA_KD_2


title: REDUC_34 PBMC

description: Library name: Sample20

value: Blood


title: iTF_Microglia_RNA_Arid5aKD_Rep1

description: Library name: RNA_KD_1


title: Y1RSV_termB2019_S9


title: Y1mock_termB2019_S6


title: Cd4CreTet2KO CD4+ TILs, biol rep 3

city: Tsukuba

first: AI NHAN THI

last: LE

state: Ibaraki Prefecture

address: 2-1-1 Amakubo, University of Tsukuba Global Village, 305-8575

department: Department of Hematology

country: Japan

institute: Graduate School of Comprehensive Human Sciences, University of Tsukuba

description:
Library name: CD4Cre_188_CD4
CD4+ TILs sorted from liver metastases at day 30 post-injection

data_processing:
Sequencing reads were trimmed for adapter sequence and low-quality bases using CLC Genomics Workbench v11.0.1 (Qiagen).
Trimmed reads were mapped to the mouse GRCm38/mm10 reference genome using CLC Genomics Workbench v11.0.1 with parameters: mismatch cost 2, insertion cost 3, deletion cost 3, length fraction 0.8, similarity fraction 0.8.
Gene expression quantification and normalization were performed using CLC Genomics Workbench v11.0.1. Differentially expressed genes were identified using the Wald test with Tet2fl/fl as the control group (FDR < 0.05).
Assembly: mm10
Supplementary files format and content: CSV files contain gene-level expression values (Total counts, RPKM, TPM, CPM) per sample, together with differential expression statistics (fold change, log fold change, p-value, FDR p-value, Bonferroni) for Vav1CreTet2KO vs. Tet2fl/fl and Cd4CreTet2KO vs. Tet2fl/fl comparisons.

source_name: liver metastatic tumor

extract_protocol:
Tumor-infiltrating leukocytes were isolated from liver metastatic tumors by enzymatic digestion with collagenase A (0.75 mg/ml) and DNase I (50 µg/ml) followed by density gradient centrifugation using Histopaque-1083. CD45+ cells were enriched by MACS separation. CD4+ and CD8+ TILs were sorted by flow cytometry using anti-CD45, anti-CD3ε, anti-CD4, and anti-CD8α antibodies on a BD FACSAria III cell sorter. Total RNA was extracted from sorted cells using the RNeasy Micro Kit (Qiagen).
RNA integrity was assessed using the Agilent 2100 Bioanalyzer. Samples with RIN > 7 were used for library preparation with the SMARTer Stranded Total RNA-seq Kit v2 - Pico Input Mammalian (Takara Bio, Cat#634413) according to the manufacturer's protocol.

value: liver metastatic tumor

value: CD4+ tumor-infiltrating lymphocytes


title: REDUC_36 PBMC

description: Library name: Sample21

value: WT


title: REDUC_32 PBMC

description: Library name: Sample18


title: REDUC_33 PBMC

description: Library name: Sample19


title: Cd4CreTet2KO CD4+ TILs, biol rep 2

description:
Library name: CD4Cre_184_CD4
CD4+ TILs sorted from liver metastases at day 30 post-injection


title: Y1RSV_termB2019_S11

value: Female


title: iTF_Microglia_RNA_Nontargeting_Rep2

description: Library name: RNA_NT_2


title: iTF_Microglia_RNA_Nontargeting_Rep1

description: Library name: RNA_NT_1


title: Cd4CreTet2KO CD8+ TILs, biol rep 4

description:
Library name: CD4Cre_188_CD8
CD8+ TILs sorted from liver metastases at day 30 post-injection

value: CD8+ tumor-infiltrating lymphocytes


title: THP1_Macrophage_ARID5A_eCLIP_Input2

description: Library name: ARID5A_IN2

data_processing:
Data was processed using Skipper, available at: http://github.com/yeolab/skipper
Reads were trimmed for adapter sequences and barcode sequences (eCLIP samples) using skewer.
Unique Molecular Identifiers (UMIs) were extracted from raw sequencing reads with fastp
Extracted reads were aligned using STAR: --alignEndsType EndToEnd --genomeDir {params.star_sjdb} --genomeLoad NoSharedMemory --outBAMcompression 10 --outFileNamePrefix {params.outprefix} --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100 --outFilterMultimapScoreRange 1 --outSAMmultNmax 1 --outMultimapperOrder Random --outFilterScoreMin 10 --outFilterType BySJout --limitOutSJcollapsed 5000000 --outReadsUnmapped None --outSAMattrRGline ID:{wildcards.replicate_label} --outSAMattributes All --outSAMmode Full --outSAMtype BAM Unsorted --outSAMunmapped Within --readFilesCommand zcat --outStd Log --readFilesIn {input.fq} --runMode alignReads --runThreadN {threads}
Custom scripts called reproducible enriched windows and repetitive elements as part of Skipper
Assembly: GRCh38
Supplementary files format and content: reproducible enriched window files contain p values, q values, enrichment, and annotations for significantly bound transcriptome tiled windows
Supplementary files format and content: reproducible enriched re files contain p values, q values, enrichment, and annotations for significantly bound repetitive elements

extract_protocol:
Cells were lysed and and sonicated in eCLIP lysis buffer, and RNA was fragmented using RNase I (Ambion) and complexes were immunoprecipitated with ARID5A-specific antibody from Atlas Antibodies
RNA was reverse transcripted with Superscript III, and adaptor was ligated with T4 RNA Ligase 1, then libraries were constructed with Q5 High-Fidelity 2x Master Mix (NEB)

value: Macrophages


title: Cd4CreTet2KO CD4+ TILs, biol rep 1

description:
Library name: CD4Cre_182_CD4
CD4+ TILs sorted from liver metastases at day 30 post-injection


title: REDUC_29 PBMC

description: Library name: Sample17


title: THP1_Macrophage_ARID5A_eCLIP_Input1

description: Library name: ARID5A_IN1


title: Cd4CreTet2KO CD8+ TILs, biol rep 3

description:
Library name: CD4Cre_182_CD8
CD8+ TILs sorted from liver metastases at day 30 post-injection


title: REDUC_28 PBMC

description: Library name: Sample16


title: Cd4CreTet2KO CD8+ TILs, biol rep 2

description:
Library name: CD4Cre_122_CD8
CD8+ TILs sorted from liver metastases at day 30 post-injection


title: REDUC_27 PBMC

description: Library name: Sample15


title: Y1mock_termB2019_S3


title: Y1mock_termB2019_S18


title: Y1RSV_termB2019_S12


title: Cd4CreTet2KO CD8+ TILs, biol rep 1

description:
Library name: CD4Cre_98_CD8
CD8+ TILs sorted from liver metastases at day 30 post-injection


title: THP1_Macrophage_ARID5A_eCLIP_IP2

description: Library name: ARID5A_IP2


title: REDUC_26 PBMC

description: Library name: Sample14


title: THP1_Macrophage_ARID5A_eCLIP_IP1

description: Library name: ARID5A_IP1


title: Y1RSV_termB2019_S_S10


title: REDUC_25 PBMC

description: Library name: Sample13


title: Vav1CreTet2KO CD4+ TILs, biol rep 3

description:
Library name: VAV1_316_CD4
CD4+ TILs sorted from liver metastases at day 30 post-injection


title: Y1mock_termB2019_S13


title: REDUC_23 PBMC

description: Library name: Sample11


title: Y1RSV_termB2019_S8


title: granulosa cells, hCG+RU486, 12h, rep 2

city: Lexington

first: Hayce

last: Jeon

state: KENTUCKY

address: 800 Rose Street

department: Dept. of OB/GYN

institute: University of Kentucky

description: Library name: Sample_RH_2

data_processing:
FASTQ files were generated and demultiplexed with the bcl2fastq v2.20 Conversion Software (Illumina). Adaptors were trimmed from the 3' end of the reads, resulting in 2,332,045,900 filtered reads.
Trimmed reads were aligned to the human genome version of GRCh38 from NCBI using STAR (2.7.10a) and SAMtools, and transcript levels were then quantified using Salmon (1.10.1).
Differential gene expression analysis was performed using the Limma-trend method on edgeR package.
Assembly: GRCh38
Supplementary files format and content: Jo_12h_AllResults.xlsx

source_name: Ovary

growth_protocol: Cells were obatined from IVF patients at the time of oocyte retrieval and subjected to a Percoll gradient to isolate granulosa cells. Isolated granulosa cells were then cultured in Opti-MEM supplemented with 1x antibiotics/antimycotics and 10% fetal bovine serum for 6 days to regain the responsiveness to hCG.

extract_protocol:
Total RNA was isolated from the cultured cells using a RNeasy mini kit (Qiagen) and eluted in 40 ul of nuclease-free water.
Libraries for RNA-Seq were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina). The libraries were quantitated by qPCR and sequenced on a single lane for 101 cycles from one end of the fragments on a NovaSeq 6000 with a NovaSeq S2 reagent kit (Illumina).

treatment_protocol: After the acclimation period, the cells were undergone serum startvation for 1 h and then treated with or without hCG in the presence or absence of RU486 for 12 h.

value: Ovary

value: primary human granulosa/lutein cells

tag: time


title: Y0RSV_termB2019_S20

value: Well-differentiated primary nasal epithelial cell


title: granulosa cells, hCG+RU486, 12h, rep 3

description: Library name: Sample_RH_3


title: granulosa cells, hCG+RU486, 12h, rep 4

description: Library name: Sample_RH_4


title: REDUC_22 PBMC

description: Library name: Sample10

data_processing:
The sequencing reads were trimmed for known adapters and low-quality regions of reads were performed using Fastq-mcf for the CLEAR, TEACH, and REDUC sample, and using Trim-galore for the A5345 samples. For both sets of samples, sequence quality control was assessed using FastQC and RSeQC.
Alignment of the reads to the human hg38 genome was performed using STAR.
Reads for the CLEAR, TEACH, and REDUC samples were assigned to genes using "featureCounts", part of the Subread suite (http://subread.sourceforge.net/). The transcript levels for A5345 samples were quantified using Salmon and summarized as gene-level counts using tximport. The filterByExpr function in the edgeR bioconductor package with the min.count argument set to 5 was used to filter out lowly expressed genes
Assembly: human hg38 genome
Supplementary files format and content: csv, different expressed genes

extract_protocol:
Total RNA was extracted from PBMCs (CLEAR, TEACH and REDUC) or CD4+ T cells (ACTG A5345) using the Qiagen RNeasy Micro Kit per manufacturer’s protocol. RNA yields ranged from 300 ng to 3,500 ng. RNA quality was tested using a Qubit 2 fluorometer (Thermo Scientific).
Sequencing libraries were prepared by Azenta Life Sciences employing the NEB Next Ultra II RNA Library Prep Kit for Illumina.  Briefly, mRNA was enriched using oligo (dT) beads, then fragmented for 15 minutes at 94°C followed by cDNA synthesis. Fragments were then end-repaired and adenylated. Universal adapters were ligated to cDNA fragments, then indexes were added with library enrichment by PCR. RNA integrity and library size was assessed by Agilant Tapestation, and concentrations were determined by Qubit 2 fluorometer with final quantification by qPCR. Flow cells were prepared with multiplexed and clustered sequencing libraries, then loaded onto an Illumina HiSeq instrument.

value: REDUC


title: Vav1CreTet2KO CD4+ TILs, biol rep 2

description:
Library name: VAV1_310_CD4
CD4+ TILs sorted from liver metastases at day 30 post-injection


title: granulosa cells, hCG+RU486, 12h, rep 1

description: Library name: Sample_RH_1


title: Vav1CreTet2KO CD8+ TILs, biol rep 2

description:
Library name: VAV1_310_CD8
CD8+ TILs sorted from liver metastases at day 30 post-injection


title: Y0mock_termB2019_S16

value: mock


title: Y0mock_termB2019_S7


title: CLEAR_8 PBMC

description: Library name: Sample8

value: CLEAR


title: granulosa cells, hCG, 12h, rep 4

description: Library name: Sample_H_4

value: hCG


title: REDUC_24 PBMC

description: Library name: Sample12


title: Vav1CreTet2KO CD8+ TILs, biol rep 1

description:
Library name: VAV1_305_CD8
CD8+ TILs sorted from liver metastases at day 30 post-injection


title: granulosa cells, hCG, 12h, rep 3

description: Library name: Sample_H_3


title: Vav1CreTet2KO CD8+ TILs, biol rep 3

description:
Library name: VAV1_316_CD8
CD8+ TILs sorted from liver metastases at day 30 post-injection


title: Tet2fl/fl CD4+ TILs, biol rep 3

description:
Library name: WT_187_CD4
CD4+ TILs sorted from liver metastases at day 30 post-injection


title: CLEAR_4 PBMC

description: Library name: Sample7


title: Y0RSV_termB2019_S2

value: Male

value: RSV


title: granulosa cells, hCG, 12h, rep 2

description: Library name: Sample_H_2


title: CLEAR_2 PBMC

description: Library name: Sample6

value: PBMC


title: Vav1CreTet2KO CD4+ TILs, biol rep 1

description:
Library name: VAV1_305_CD4
CD4+ TILs sorted from liver metastases at day 30 post-injection


title: CLEAR_9 PBMC

description: Library name: Sample9

value: Blood


title: Tet2fl/fl CD8+ TILs, biol rep 3

description:
Library name: WT_187_CD8
CD8+ TILs sorted from liver metastases at day 30 post-injection

value: liver metastatic tumor


title: granulosa cells, hCG, 12h, rep 1

description: Library name: Sample_H_1


title: Y0mock_termB2019_S4

value: term


title: CLEAR_1 PBMC

description: Library name: Sample5

value: WT


title: Tet2fl/fl CD4+ TILs, biol rep 2

description:
Library name: WT_185_CD4
CD4+ TILs sorted from liver metastases at day 30 post-injection

value: CD4+ tumor-infiltrating lymphocytes


title: Y0RSV_termB2019_S17

value: Female


title: Y0RSV_termB2019_S19


title: CLEAR_19 PBMC

description: Library name: Sample4


title: Y0mock_termB2019_S5


title: granulosa cells, Control, 12h, rep 3

description: Library name: Sample_C_3

value: Control


title: CLEAR_17 PBMC

description: Library name: Sample3


title: Y0mock_termB2019_S15


title: Tet2fl/fl CD8+ TILs, biol rep 1

description:
Library name: WT_178_CD8
CD8+ TILs sorted from liver metastases at day 30 post-injection

value: CD8+ tumor-infiltrating lymphocytes


title: Tet2fl/fl CD4+ TILs, biol rep 1

description:
Library name: WT_178_CD4
CD4+ TILs sorted from liver metastases at day 30 post-injection


title: CLEAR_12 PBMC

description: Library name: Sample2


title: granulosa cells, Control, 12h, rep 1

description: Library name: Sample_C_1

value: Ovary

value: primary human granulosa/lutein cells


title: Y0RSV_termB2019_S1

value: Well-differentiated primary nasal epithelial cell


title: CLEAR_10 PBMC

description: Library name: Sample1


title: granulosa cells, Control, 12h, rep 2

description: Library name: Sample_C_2


title: granulosa cells, Control, 12h, rep 4

description: Library name: Sample_C_4


title: Ureter, 2w, COL17KO2

status: Public on Apr 16 2026

city: Sapporo

first: Takashi

last: Namba

state: Hokkaido

address: Kita 18-Nishi 9, Kita-ku

department: Department of Basic Veterinary Sciences, Faculty of Veterinary Medicine

institute: Hokkaido University

description: Library name: KO_2w_Ur_3

data_processing:
Raw read quality was assessed using FastQC (v0.12.1).
Adapter sequences and low-quality bases were removed using Trimmomatic (v0.38).
Processed reads were mapped to the reference genome (GRCm39/mm39) using RNA aligner HISAT2 (v2.1.0).
Gene expression levels were quantified as transcripts per million (TPM).
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text file includes raw counts for all samples
Supplementary files format and content: tab-delimited text file containing TPM values for all samples

source_name: ureter

extract_protocol:
Total RNA was isolated using the NucleoSpin RNA (MACHEREY-NAGEL) accoriding to the manufacture's instructions. 1.0 µg of total RNA was used for the construction of sequencing libraries.
Strand-specific RNA-seq libraries were constructed using the NEBNext Poly(A) RNA Magnetic Isolation Module and the NEBNext Ultra II Directional RNA Library Prep Kit (New England Biolabs).

value: ureter


title: Ureter, 2w, COL17KO3

description: Library name: KO_2w_Ur_4


title: Ureter, 2w, WT3

description: Library name: WT_2w_Ur_4


title: Ureter, 2w, COL17KO1

description: Library name: KO_2w_Ur_2


title: Ureter, 2w, WT1

description: Library name: WT_2w_Ur_2


title: Tet2fl/fl CD8+ TILs, biol rep 2

description:
Library name: WT_185_CD8
CD8+ TILs sorted from liver metastases at day 30 post-injection


title: iasl14_6

city: Seoul

first: Sangwoo

last: Kim

state: State...

address: 50-1 Yonsei-ro, Seodaemun-gu

department: Dept. of Biomedical Systems Informatics

institute: Yonsei University College of Medicine

description:
Library name: Sample 36
Column name in raw_counts_All_Samples.txt: iasl14_6

data_processing:
Raw FASTQ files were filtered and trimmed using FASTP (version 0.21.0), removing reads shorter than 50 bp and low-complexity sequences. Trimmed reads were aligned to the genome reference using STAR (version 2.7.10). Transcript quantification was performed using HTSeq (version 2.7.17) in intersection-strict mode.
Assembly: GRCm39 (Ensembl release 112)
Supplementary files format and content: Tab-delimited text files. The processed data includes a raw read count matrix (from HTSeq) for each sample.

source_name: Hippocampus

extract_protocol:
Ipsilateral hippocampal tissues were harvested at 3, 7, and 14 days post-injection. Samples were preserved in RNAlater prior to total RNA extraction. Total RNA was extracted, with resulting RNA Integrity Number (RIN) values ranging between 8.0 and 9.5.
Libraries were constructed using the TruSeq Stranded mRNA Sample Preparation Kit (Illumina). The preparation followed a poly(A) selection and strand-specific protocol. High-throughput sequencing was performed on the Illumina NovaSeq X Plus platform. The process generated 100 bp paired-end reads.

treatment_protocol: Adult male C57BL/6 mice (8–10 weeks old) received a unilateral microinjection of kainic acid (0.3 μg in 0.15 μL PBS) into the basolateral amygdala. Stereotaxic coordinates used were AP -1.31 mm, ML -3.0 mm, and DV -4.5 mm relative to Bregma. To standardize status epilepticus duration and reduce mortality, diazepam (10 mg/kg) was administered intraperitoneally 40 minutes after injection. Control animals received an equivalent volume of vehicle (saline).

value: Hippocampus

value: Intra-amygdala saline injection


title: iasl14_4

description:
Library name: Sample 34
Column name in raw_counts_All_Samples.txt: iasl14_4


title: iasl14_3

description:
Library name: Sample 33
Column name in raw_counts_All_Samples.txt: iasl14_3


title: iasl14_2

description:
Library name: Sample 32
Column name in raw_counts_All_Samples.txt: iasl14_2


title: iasl14_1

description:
Library name: Sample 31
Column name in raw_counts_All_Samples.txt: iasl14_1


title: iaka14_9

description:
Library name: Sample 30
Column name in raw_counts_All_Samples.txt: iaka14_9

value: Intra-amygdala kainate injection


title: iaka14_7

description:
Library name: Sample 29
Column name in raw_counts_All_Samples.txt: iaka14_7


title: iaka14_3

description:
Library name: Sample 27
Column name in raw_counts_All_Samples.txt: iaka14_3


title: Ureter, 2w, WT2

description: Library name: WT_2w_Ur_3


title: iasl14_5

description:
Library name: Sample 35
Column name in raw_counts_All_Samples.txt: iasl14_5


title: iaka14_1

description:
Library name: Sample 25
Column name in raw_counts_All_Samples.txt: iaka14_1


title: iasl7_6

description:
Library name: Sample 24
Column name in raw_counts_All_Samples.txt: iasl7_6


title: iaka14_2

description:
Library name: Sample 26
Column name in raw_counts_All_Samples.txt: iaka14_2


title: iaka7_6

description:
Library name: Sample 17
Column name in raw_counts_All_Samples.txt: iaka7_6


title: iasl7_3

description:
Library name: Sample 21
Column name in raw_counts_All_Samples.txt: iasl7_3


title: iasl7_5

description:
Library name: Sample 23
Column name in raw_counts_All_Samples.txt: iasl7_5


title: iaka14_5

description:
Library name: Sample 28
Column name in raw_counts_All_Samples.txt: iaka14_5


title: iaka7_7

description:
Library name: Sample 18
Column name in raw_counts_All_Samples.txt: iaka7_7


title: iaka7_5

description:
Library name: Sample 16
Column name in raw_counts_All_Samples.txt: iaka7_5


title: iasl7_2

description:
Library name: Sample 20
Column name in raw_counts_All_Samples.txt: iasl7_2


title: iasl3_5

description:
Library name: Sample 10
Column name in raw_counts_All_Samples.txt: iasl3_5


title: iasl3_7

description:
Library name: Sample 12
Column name in raw_counts_All_Samples.txt: iasl3_7


title: iasl7_4

description:
Library name: Sample 22
Column name in raw_counts_All_Samples.txt: iasl7_4


title: iasl3_6

description:
Library name: Sample 11
Column name in raw_counts_All_Samples.txt: iasl3_6


title: iaka7_4

description:
Library name: Sample 15
Column name in raw_counts_All_Samples.txt: iaka7_4


title: iaka7_3

description:
Library name: Sample 14
Column name in raw_counts_All_Samples.txt: iaka7_3


title: iasl3_4

description:
Library name: Sample 9
Column name in raw_counts_All_Samples.txt: iasl3_4


title: iaka3_7

description:
Library name: Sample 6
Column name in raw_counts_All_Samples.txt: iaka3_7


title: iasl7_1

description:
Library name: Sample 19
Column name in raw_counts_All_Samples.txt: iasl7_1


title: iasl3_3

description:
Library name: Sample 8
Column name in raw_counts_All_Samples.txt: iasl3_3


title: iaka3_3

description:
Library name: Sample 3
Column name in raw_counts_All_Samples.txt: iaka3_3


title: iaka3_2

description:
Library name: Sample 2
Column name in raw_counts_All_Samples.txt: iaka3_2


title: iaka7_2

description:
Library name: Sample 13
Column name in raw_counts_All_Samples.txt: iaka7_2


title: iaka3_5

description:
Library name: Sample 5
Column name in raw_counts_All_Samples.txt: iaka3_5


title: iaka3_4

description:
Library name: Sample 4
Column name in raw_counts_All_Samples.txt: iaka3_4


title: iaka3_1

description:
Library name: Sample 1
Column name in raw_counts_All_Samples.txt: iaka3_1


title: Fourth instar larvae, Treated , 72hour, rep 2

city: CALICUT UNIVERSITY

first: ANUSRUTHI

last: RAMAKRISHNAN

address: THENHIPALAM

department: ZOOLOGY

country: India

institute: UNIVERSITY OF CALICUT

description: Library name: Sample 4

data_processing:
The library was quantified using the Qubit dsDNA HS assay kit (Invitrogen) and sequenced on the Illumina Novaseq 6000 platform
The adapter sequences and low-quality bases from the raw sequence reads were removed using fastp v0.12.4
The rRNA reads were removed from quality-trimmed data using bbmap’s v38.18 bbduk algorithm
The system-generated base call files were converted to fastq files using the “Illumina DRAGEN Bio-IT Platform or bcl2fastq
Assembly: The pre-processed reads were mapped to an Ae index. albopictus (Asian tiger mosquito) Genome assembly: (GCF_035046485.1) reference genome using STAR v2.7.10a aligner
Supplementary files format and content: Excel sheet with rows contain genes and coloumns contain samples with expression counts

organism: Aedes albopictus

source_name: whole fourth instar larvae

extract_protocol:
Aedes albopictus RNA was extracted using Zymo Direct-Zol RNA miniprep extraction method
The library preparation was prepared using the “NEBNext® Ultra™ II RNA Library Prep Kit for Illumina”

value: whole fourth instar larvae

value: herbicide Diquat treatment


title: Fourth instar larvae, Control , 72hour, rep 2

description: Library name: Sample 2


title: iasl3_2

description:
Library name: Sample 7
Column name in raw_counts_All_Samples.txt: iasl3_2


title: Fourth instar larvae, Control , 72hour, rep 1

description: Library name: Sample 1


title: Lung Alternaria

city: Pittsburgh

first: Amanda

middle: Catherine

last: Poholek

state: Pennsylvania

address: 4401 Penn Ave., Rangos Research Center 8129

department: Pediatrics

institute: University of Pittsburgh

description: Library name: Alternaria

data_processing:
Raw sequencing data were processed using the Cell Ranger multi pipeline (v9.0.1; 10x Genomics) for alignment, filtering, and quantification. Reads were aligned to the mouse reference genome (GRCm39). Demultiplexing of pooled samples was performed based on assignment to specific oligonucleotide tags. This resulted in filtered unique molecular identifier (UMI) feature-barcode matrices for each individual sample, which were used for downstream analysis.
Downstream analysis was performed using the Scanpy toolkit (v1.10.3)68. After importing raw gene expression matrices, cells expressing fewer than 200 genes or exhibiting high mitochondrial content (>20%) were excluded. To remove potential multiplets, cells with abnormally high gene counts (>6,000) were filtered out. Doublet detection was performed using Scrublet69 . Detected doublets were removed with a high-confidence doublet score threshold of 0.3. Following quality control, raw counts were normalized to the median total counts per cell and log-transformed. The top 2,000 highly variable genes were identified and used for Principal Component Analysis (PCA). Dimensionality reduction was performed using Uniform Manifold Approximation and Projection (UMAP) based on the nearest neighbor graph, and cells were clustered using the Leiden algorithm70 . Non-ILC2 contamination was identified via canonical marker expression (e.g., Epcam for epithelial cells, Col1a1 for fibroblasts, Cd79a for B cells) and excluded from downstream analysis.
After excluding low-quality cells and contamination, 18,414 ILC2 cells were identified from the scRNA-seq dataset. These cells underwent standard normalization, log-transformation, PCA, and UMAP processing as described above. ILC2 subsets (corresponding to those in Fig. 7a) were identified using Leiden clustering with a resolution of 0.7. Differentiation trajectories were modeled using Palantir (v1.4.1)71 . A starting cell with a representative transcriptomic profile was selected from Cluster 1, which contained the majority of untreated naive ILC2s. Pseudotime values were calculated to reconstruct the developmental timeline. To verify the robustness of the inferred trajectory, Diffusion Pseudotime (DPT)72 analysis was independently performed using Scanpy (v1.10.3). Both analyses were conducted on the same combined dataset (including both WT and KO conditions) and rooted in the same starting cluster (Cluster 1) to ensure a unified and directly comparable pseudotime axis across conditions.
Assembly: GRCm39

source_name: Lung

extract_protocol:
ILC2s from each sample were loaded to GEM-X OCM Chip
RNA barcoding, on-chip multiplexing and library generation was performed with GEM-X Universal 3' Gene Expression v4 4-plex kit. 3 pooled libraries were generated for sequencing on an Illumina NovaseqXPlus paired end 150bp with approximately 250 million reads per sample.

value: Lung

value: Blimp-1 KO, NMur1Cre Control

value: Alternaria


title: Lung Papain

description: Library name: Papain

value: papain


title: Lung Untreated

description: Library name: Untreated

value: PBS


title: Coris batuensis, non-cleaner, forebrain section, sample 9

city: Austin

first: Rebecca

middle: L

last: Young

state: TX

address: 2415 Speedway

department: Integrative Biology

institute: University of Texas at Austin

description: Library name: CHO-9

data_processing:
Custom perl scripts using the FASTX-toolkit and CUTADAPT v. 2.8 were used to remove reads with a homo-polymer run of “A”≥8 bases, retain reads with minimum 20 bases, removal PCR duplicates – defined as sequences sharing the same degenerate header and 20 bases of sequence – and filtered for quality (Phred quality score > 20 for 90% of the nucleotides).
We aligned preprocessed reads using the Burrows-Wheeler Aligner (bwa-mem) and process reads using samtools.
Assembly: Oreochromis niloticus reference (Orenil1.0 Ensembl cdna) and Labroides dimidiatus genome (Accession: PRJNA937036)
Supplementary files format and content: Processed data .counts are raw counts aligned to the Oreochromis niloticus reference
Supplementary files format and content: Processed data .LdimAlign.counts are raw counts aligned to the Labroides dimidiatus genome

organism: Coris batuensis

source_name: Female, forebrain section

extract_protocol:
Total RNA was extracted using Maxwell 16LEV simplyRNA tissue kit (Promega Corporation, Madison, WI, USA) following manufacturer instructions, including DNase treatment. RNA samples were then eluted into 40uL of nuclease-free water.
Libraries are constructed using the University of Texas Genome Sequencing Analysis Facility protocol for 3'tag-seq. Total RNA was fragmented via Mg+ buffer and cDNA was synthesized with poly-dT oligo. cDNA was amplified using PCR and purified with DNA-binding magnetic beads. Sequencing was perfored on an Illumina HiSeq 2000 instrument.

treatment_protocol: Whole heads were transferred into 30 mL conical tubes with RNAlater (ThermoFischer, Waltham, MA, USA) to preserve the integrity of the RNA. The elapsed time between capture and death ranged from 6 to 28 minutes. After 3 hours (on average) in RNAlater, the samples were transferred into O.C.T. Compound (Sakura, Torrance, CA, USA) and flash frozen in liquid nitrogen and shipped to The University of Texas at Austin for RNA isolation.frozen heads were sectioned on a cryostat microtome into 300µm thick slices. The second most rostral slice of the brain, containing pallial areas Dl and Dm (i.e., the putative teleost homologs of the mammalian hippocampus and basolateral amygdala (areas Dl and Dm, respectively), along with partial portions of septal and striatal territories, was collected and stored in 200ul of ice-cold homogenization buffer with 1-thioglycerol (Promega Corporation, Madison, WI, USA) and stored at -80C until further processing.

value: Female, forebrain section


title: Coris batuensis, non-cleaner, forebrain section, sample 4

description: Library name: CHO-4


title: Coris batuensis, non-cleaner, forebrain section, sample 3

description: Library name: CHO-3


title: Coris batuensis, non-cleaner, forebrain section, sample 2

description: Library name: CHO-2


title: Coris batuensis, non-cleaner, forebrain section, sample 1

description: Library name: CHO-1


title: Coris batuensis, non-cleaner, forebrain section, sample 10

description: Library name: CHO-10


title: Coris batuensis, non-cleaner, forebrain section, sample 8

description: Library name: CHO-8


title: Coris batuensis, non-cleaner, forebrain section, sample 6

description: Library name: CHO-6


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 9

description: Library name: BLA-9

organism: Hemigymnus melapterus


title: Fourth instar larvae, Treated , 72hour, rep 1

description: Library name: Sample 3


title: Coris batuensis, non-cleaner, forebrain section, sample 5

description: Library name: CHO-5


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 8

description: Library name: BLA-8


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 7

description: Library name: BLA-7


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 6

description: Library name: BLA-6


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 5

description: Library name: BLA-5


title: H3

city: Bareilly

first: Pushpendra

last: Kumar

state: Uttar pradesh

address: Izatnagar

department: Animal Genetics

institute: ICAR-IVRI

data_processing:
Illumina HiSeq X10 used for basecalling.
The sequenced raw Illumina reads were subjected to Trim galore to automate the quality and adapter trimming as well as quality control of fastq files.
Kallisto pipeline used to create “transcriptome index”. Tximport was used to import and summarize the transcript-level abundance estimates from kallisto for gene-level analysis with DESeq2.
Genome_build: Mus_musculus.GRCm38.cdna.all.fa
Supplementary_files_format_and_content: gene_counts.txt: Matrix table with raw gene counts for every gene and every sample.

source_name: ovary

extract_protocol:
Total RNA from samples was extracted by AgriGenome Labs Pvt. Ltd., Kochi, as per their standard protocol. Poly “A” selection was undertaken to enhance the concentration of mRNA.
TruSeq RNA sample preparation kit_ Poly A capture method was used for library preparation.

tag: strain

value: F4 inbred Swiss albino

value: estrous-phased ovarian tissue

value: female

tag: age

value: Adult (135-140 days)

tag: litter size

value: high


title: L2

tag: tissue

value: low


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 10

description: Library name: BLA-10


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 3

description: Library name: BLA-3


title: L5


title: L1


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 4

description: Library name: BLA-4


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 2

description: Library name: BLA-2


title: RNA-seq_PTBP3_KO-1

city: Beijing

first: Zongchang

last: Du

address: 15 Datun Road, Chaoyang District, Beijing, China

institute: IBP

data_processing:
Illumina bcl2fastq-1.8.4 conversion software was used for base calling.
After sequencing of single-cell RNA-seq libraries, adapters and low-qaulity bases were removed by Trimmomatic (Bolger et al., 2014) program. The retained paired-end reads were aligned to the mouse reference genome (mm9) using HISAT2 (Kim et al., 2015) tool with default parameters. The uniquely mapped reads count matrix were subject to DESeq2 (Michael, et al., 2014)  package to identify differentially expressed genes. Alternative splicing events were detected using rMATS (Shihao Shen, et al., 2014) software with defualt parameters.
2P-seq reads were filtered by trimming adaptors and A’s from the end of reads using the Cutadapt (Martin et al., 2014) program. The remaining reads were mapped to the mouse genome, and only uniquely mapped reads were retained. All samples were combined together and reads adjacent to each other were merged to cluster to identify robust polyadenylation sites. The alternative polyadenylation events were detected using DEXSeq (Anders Simon et al,. 2012) package with defualt parameters.
Genome_build: mm9
Supplementary_files_format_and_content: Bigwig files were generated using bamCoverage.

source_name: spleen

growth_protocol: Wild type and PTBP3 knockout mice were bred at six- to eight-weeks-old.

extract_protocol:
Total RNAs were extracted with Trizol regent and chloroform.
RNA-seq libraries were generated with some modifications (Mortazavi et al, 2008), 2P-seq libraries were generated with modification (Spies et al., 2013) .

treatment_protocol: Naive B cells were isolated from spleen using MojoSort™ Mouse Pan-B Cell Isolation Kit (Biolegend, 480052) following the manufacture’s protocol.

tag: method

value: RNA-Seq

value: PTBP3 knockout

tag: cell type

value: Naive B cells

value: spleen


title: SP_FD_D3_S74

city: Ås

first: Byron

last: Morales Lange

address: Arboretveien 6

country: Norway

institute: Norwegian University of Life Sciences

description: Library name: Sample114

data_processing:
RNA-seq raw files were processed in Orion High-Performance Computing Cluster (Norwegian University of Life Sciences) to remove adapter sequences and low-quality reads through BBDuk v.34.56. After, cleaned reads were aligned to Atlantic salmon genome SSAL_v3.1 (GenBank: GCA_905237065.2) by HISAT v2.2.1. Then, mapped fragments were counted with FeatureCounts v1.4.6-p1
Assembly: Atlantic salmon genome SSAL_v3.1 (GenBank: GCA_905237065.2)
Supplementary files format and content: Count files with mapped fragments

organism: Salmo salar

source_name: Spleen

extract_protocol:
Total RNA was isolated from head kidney and spleen from 10 fish per dietary group at each location. Briefly, a 5 mm stainless steel bead and 900 μL QIAzol lysis reagent (Qiagen) were added to 50 mg of each sample. Then, a TissueLyser bead mill (Qiagen) at 20 Hz for 2 min was used (twice) to lyse the samples. The homogenate was recovered and 180 μL chloroform were added before vortexing and centrifugation at 14,000 x g (4 °C for 15 min). Each upper phase was recovered in a new tube and 450 μL isopropanol were added. After gentle manual shaking and incubation at room temperature, the samples were centrifuged again (14,000 x g at 4 °C for 15 min). The supernatants were removed and 200 μL 70% ethanol were added before centrifugation (14,000 x g at 4 °C for 10 min). The pellets were left to dry for 5-10 min at room temperature. Finally, each pellet was resuspended in 40 μL RNAse-free water and incubated for 10 min incubation at 55 °C.
The RNA concentration of the samples was estimated with a NanoDrop™ 8000 spectrophotometer (Thermo Fisher Scientific) according to instructions from the manufacturer. Then, RNA integrity (RIN values) was measured with an Agilent 4150 TapeStation (Agilent) following the supplier's protocols. All samples had RIN values ≥ 7. Novogene (United Kingdom) performed the libraries and RNA-seq through an Illumina NovaSeq 6000 System (150 bp paired-end RNA-seq and 30 million reads depth).

value: Spleen

tag: diet

value: Diet 3

tag: treatment

value: 10% Fermented sunflower meal

tag: farm location

value: Fjord (FD)


title: SP_FD_D3_S80

description: Library name: Sample120


title: RNA-seq_PTBP3_WT-2

tag: genotype

value: wild type


title: Hemigymnus melapterus, facultative cleaner. forebrain section, sample 1

description: Library name: BLA-1


title: SP_FD_D3_S73

description: Library name: Sample113


title: SP_FD_D3_S75

description: Library name: Sample115