title: ATRi 1

description: Library name: A1

source_name: GP33+ CD8+ T cells


title: UPN827 cells, TN1689 TrailNet 3or6 month T1D plasma

status: Public on Jun 01 2026

type: RNA

city: Milwaukee

first: Martin

last: Hessner

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

country: USA

institute: Medical College of Wisconsin

description: Gene expression data from UPN827 cells stimulated with T1D plasma

hyb_protocol: The Affymetrix GeneChip Human Genome U133 plus 2.0 array was selected for these studies for its overall comprehensive coverage.

scan_protocol: After hybridization, arrays were washed and stained with Affymetrix fluidics protocol FS450_0001 and scanned with a 7G Affymetrix GeneChip Scanner

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

label: biotin

molecule: total RNA

organism: Homo sapiens

source_name: UPN827 cells stimulated with TN1689 TrailNet 3or6 month T1D plasma

label_protocol: cRNA was synthesized, labeled, fragmented, and hybridized to an array in accordance to the Affymetrix GeneChip expression analysis technical manual.

growth_protocol: Commercial cryopreserved PBMCs of healthy Caucasian male donor UPN827 were thawed and washed per the manufacturer’s protocol (Cellular Technology Ltd., Shaker Heights, OH).

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Gene expression was accomplished by culturing PBMCs at 37°C in 5% CO2 with 40% of participant plasma  that was sampled at baseline or the 3-6 months post-baseline from six TrailNet new-onset T1D intervention trails, or from our local Recent onset T1DM cohort. Cultures were prepared in a Costar 24-well plate (Corning) using 500,000 cells/well and in RPMI 1640 medium supplemented with 100U/ml penicillin and 100ug/ml streptomycin in a total of 500 µl.  After culture (9 hours optimal for cryopreserved PBMCs) total RNA was extracted using TRIzol reagent (Invitrogen Life Technologies).

tag: responder cells

value: UPN827 cells

tag: sample timepoint

value: TrailNet 3 or 6 month


title: Patient-rep16

type: SRA

city: New York

first: Bettina

last: Nadorp

state: NY

address: 500 1st Ave

department: Medicine/Pathology

institute: NYU Langone Health

library_source: transcriptomic

data_processing:
Read alignment: STAR aligner version 2.5.0c was used to map reads against the reference genome hg19. Only uniquely mapping reads were kept (specific parameters: --trim5p=13, --outFilterMultimapNmax 1, --outFilterMismatchNoverLmax 0.05)
Deduplication: Duplicated reads were excluded using picard-tools version 2.6.0.
Read counting: Reads were counted on a stranded gene-basis within annotated exons downloaded from Ensembl Genes V75 using the ngsutils tool bamutils count (special paramters: -uniq, -multiple complete, -library RF).
Normalization: edgeR version 3.14.0 was used to normalize read counts per sample and genes were filtered for counts-per-million > 1. CDS length from Ensembl Genes V75 was used to calculate FPKM values for filtered genes.
Assembly: hg19
Supplementary files format and content: xlsx file with containing FPKM values for each sample

source_name: bone marrow

extract_protocol:
RNA was extracted using the RNEasy micro kit following manufacturer's guidelines
RNA libraries for RNA-seq were prepared using Truseq library prep protocol

tag: tissue

value: bone marrow

tag: cell type

value: whole BM


title: Transduction of Clone # 7 mESCs at day 6 of SMC differentiation with cgRNA library, Replicate 3, GFP+ cells

city: Vancouver

first: Arman

middle: Foyez

last: Adel

state: British Columbia

address: 6088 University Boulevard

department: The School of Biomedical Engineering

country: Canada

institute: the University of British Columbia

description:
Library name: Day6-GFPpos-Rep3_S18_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt

library_source: genomic

data_processing:
miRNA targets were extracted and counted from raw reads using a whitelist of cgRNA targets (mmuSequences.csv) and a modified version of the barcode counting script (cgLibV2_BC_counter.ipynb) from Joung et al., Cell, 2023 (PMID 36608654).
miRNA target counts were then paired to their corresponding miRNA target names and samples were ordered in a matrix using the mmuSequences.csv file and either multiClonal_cgRNA_matrix.ipynb script for the multi-clonal mESC screen or the SMC_cgRNA_matrix.ipynb for the clonal mESC, SMC differentiation Day 3, SMC differentiation Day 6 and cumulative recording screens.
All analysis scripts and associated files to generate process counts data can be found at https://github.com/yachielab
Assembly: miRbase v22
Supplementary files format and content: raw counts for each sample labelled in the columns and the miRNA target named in the rows
Supplementary files format and content: miRNA target seqeunce and subsequent raw read count for each target for each sample
Library strategy: CRISPR Screen

molecule: genomic DNA

organism: Mus musculus

source_name: Mouse ES cells differentiated to smooth muscle cells

growth_protocol: mESCs were grown in DMEM low-glucose (Thermo Fisher #11885084) supplemented with 15% FBS (Thermo Fisher #A5256501), 1% Glutamax (Gibco #35050061), 1% Non-essential amino acids (Gibco #11140050), 1% Sodium Pyruvate (Gibco #11360070), 20µM 2-Mercaptoethanol (Sigma-Aldrich #M6250-100ML), 3µM of GSK-3 inhibitor CHIR99021 (Sigma-Aldrich # SML1046-5MG), 1µM MEK1 and MEK2 inhibitor PD0325901 (Sigma-Aldrich # PZ0162-5MG), 10^3 U LIF (Biotechnie R&D Systems # 8878-LF-500/CF) and 200µg/ml of Geneticin (G418 Sulfate) (Gibco #10131035). Prior to transduction, media was supplemented with 10µg/ml of polybrene (Sigma-Aldrich# H9268-5G). 24 hours after the transduction of the cgRNA library, the media was further supplemented with 3µg/ml of Puromycin (Thermo Fisher #A1113803).

extract_protocol:
The genomic DNA of cells that were either taken from the population or EGFP+ FACS sorted cells were extracted using Monarch® Spin gDNA Extraction Kit (T3010S) as per the manufacturers protocols.
miRNA targets were then amplified from the extracted gDNA using a two step PCR process where in the first process, targets were amplified with primers containing partial Truseq adapter seqeunces. In the second PCR, the rest of the Truseq adapters and subsequent index and flow-cell adapter sequences were added on to the first round PCR product.

treatment_protocol: Differentiation of mESCs to SMCs was carried out in DMEM-F12 (Gibco # 11320033) supplemented with 10% FBS (Gibco #A5256701), 1mM Glutamax (Gibco #35050061), 0.1mM Non-essential amino acids (Gibco #11140050), 0.1 mM Sodium Pyruvate (Gibco #11360070), 0.2µM 2-Mercaptoethanol (Sigma-Aldrich #M6250-100ML), 10µM RA (Stem Cell Technologies #100-1045) and 200µg/ml of Geneticin (G418 Sulfate) (Gibco #10131035). Prior to transduction, media was supplemented with 10µg/ml of polybrene (Sigma-Aldrich# H9268-5G). 24 hours after the transduction of the cgRNA library, the media was further supplemented with 3µg/ml of Puromycin (Thermo Fisher #A1113803).

tag: cell line

tag: treatment

value: Transduction of Clone # 7 mESCs at day 6 of SMC differentiation with cgRNA library,GFP+ cells


title: Patient-rep15


title: Cochlear outer sulcus , Euthyroid rep1

city: Shanghai

first: zhifang

last: xie

address: 1665 Kongjiang Road

department: Ministry of Education-Shanghai Key Laboratory of Children's Environmental Health

country: China

institute: Xinhua Hospital, Shanghai Jiaotong University School of Medicine

data_processing:
The sequencing data was filtered with SOAPnuke(V1.5.2) by removing reads containing adaptors, removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%, removing reads whose unknown base ratio is more than 5%.
The clean reads were mapped to the reference genome (Mus musculus, GCF_000001635.26_GRCm38.p6) with HISAT2 (v2.0.4) program and aligned to reference coding gene set with Bowtie2 (v2.2.5).
Expression levels of gene was calculated by RSEM (v1.2.12)
Assembly: GCF_000001635.26_GRCm38.p6
Supplementary files format and content: Excel files include read counts and FPKM, tpm, read count values for each Sample

molecule: polyA RNA

source_name: Cochlear outer sulcus

extract_protocol:
Articular cartilage total RNA was extracted from bilateral femoral heads of each mouse at P22 using Trizol combined with Qiagen RNeasy Micro kit.
Oligo(dT)-attached magnetic beads were used to purified mRNA. Purified mRNA was fragmented into small pieces with fragment buffer at appropriate temperature. Then First-strand cDNA was generated using random hexamer-primed reverse transcription, followed by a second-strand cDNA synthesis. Afterwards, A-Tailing Mix and RNA Index Adapters were added by incubating to end repair. The cDNA fragments obtained from previous step were amplified by PCR, and products were purified by Ampure XP Beads, then dissolved in EB solution. The product was validated on the Agilent Technologies 2100 bioanalyzer for quality control. The double stranded PCR products from previous step were heated denatured and circularized by the splint oligo sequence to get the final library. The single strand circle DNA (ssCir DNA) was formatted as the final library. The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol: Timed-pregnant C57BL/6J mice were treated with either antithyroid agents (0.05% methimazole, 1.0% sodium perchlorate monohydrate, and 5.0% sucrose in drinking water) or vehicle from embryonic day 17. The treatment was continued during lactation and stopped at P10.

value: Cochlear outer sulcus

tag: age

tag: strain

value: Euthyroid


title: Transduction of Clone # 7 mESCs at day 6 of SMC differentiation with cgRNA library, Replicate 2, GFP+ cells

description:
Library name: Day6-GFPpos-Rep2_S17_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt

value: Mouse ES cells differentiated to smooth muscle cells


title: Patient-rep14


title: UPN827 cells, TN1761 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1761 TrailNet 3or6 month T1D plasma


title: RNA-seq, flagleaf, Nijinokirameki, chemical fertilizer, Year 2024, rep1

city: Tsukuba

first: Hirofunmi

last: Fukuda

state: Ibaraki

address: 1-31-1 Kannondai

country: Japan

institute: National Agriculture and Food Research Organization (NARO)

description:
Library name: rna_Niji_flagleaf_CF_2024_rep1
column name in Niji_flagleaf_5DAF_CF_GM_RNA_rawdata_UniqueExonReads_2024.csv: 2024_CF_rep1

data_processing:
The libraries were sequenced using the Illumina NovaSeq X Plus. Sequencing was performed on the 25B flow cell with paired-end 150-bp and unique dual-index reads. The reads were preprocessed by CLC Genomics Workbench version 25.0 (Qiagen). Reads were first trimmed using the following parameters: quality limit of 0.05, maximum number of ambiguities 2. Next, raw reads were mapped to the genome assembly and gene sets of Os-Nipponbare-IRGSP-1.0 with the following parameters: mismatch cost of 2, insertion–deletion cost of 3, length fraction of 0.8, similarity fraction of 0.8, and maximum number of hits of a read of 10. Then, uniquely mapped read counts were quantified. Genes with at least one raw read count in all of the library samples for each comparison were analyzed.
Assembly: Os-Nipponbare-IRGSP-1.0
Supplementary files format and content: csv file includes RNA-seq raw count on whole transcripts for each sample.

organism: Oryza sativa

source_name: flag leaf

growth_protocol: Hairy vetch (Vicia villosa), a legume species, was grown as a cover crop in paddy fields in Kannondai, Tsukuba City, Ibaraki Prefecture, Japan (36°01′29″N, 140°06′25″E, 21 m a.s.l.). Nutrient element contents in the field soils were analyzed by Tokachi Federation of Agricultural Cooperatives (https://www.nokyoren.or.jp/; Obihiro, Japan). The seeds (Fujiemon [Massa], Snow Brand Seed Co., Ltd.) were sown in field by hand on October 31 and again on November 15, 2023 (i.e., 60 kg/ha in total) since the germination rate of the first-sown seeds was low. The plants were grown for 5 months until April in 2024 and then directly plowed into the soil in the Kannondai paddy fields.  Seeds of rice plants were soaked in water at 30 °C for 2 d, sown in trays filled with synthetic granular soil (Sumitomo Chemical Company Co., Ltd., Tokyo, Japan), and incubated at 30 °C in the dark for 2 d. The seeds were sown on April 22, 2024. Those trays placed in a field for nearly 3 weeks to 1 month and then transplanted by hand or with a rice planter (18 cm apart × 30 cm apart, planting density 18.5 hills/m2) into the desired field conditions and grown for approximately 5 more months from mid-May to September. A normal paddy field condition (fertilization with 56:176:56 kg/ha of N:PO4:K) was set as the control condition. No chemical fertilizers were added to the green manure–treated soil.

extract_protocol:
For both flag leaves and caryopses sampling, spikelets in our field were marked on the day of flowering and collected at five days after flowering (DAF) (i.e., six days after heading) in rice plants cultivated for approximately 15 weeks after sowing. More than ten spikelets were taken from the upper third of three panicles collected from the same plant from 9:00 to 10:00 am, immediately frozen in liquid nitrogen, combined as one biological replicate of endosperms, and stored in a deep freezer. Husk was removed from frozen caryopses. Endosperms were sampled separately from embryonic bud on the cold base and then stored  in a deep freezer until sample crushing. Frozen samples were crushed by a multi-specimen cell disruption device (BMS-A20TP; BMS) just before RNA extraction. Total RNA from each sample was extracted using an RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany) according to the manufacturer’s protocol.
RNA-sequencing (RNA-seq) libraries were prepared using the NEBNext Ultra II Directional mRNA-seq kit for Illumina (New England Biolabs), following the manufacturer’s protocols.

treatment_protocol: Chemical fertilizer was applied as a basal dressing at 56:176:56 kg/ha (N:PO4:K). Green-manure treatment consisted of hairy vetch–derived nutrients with no additional chemical fertilizer.

value: flag leaf

tag: genotype

value: WT

value: CF


title: UPN827 cells, TN1687 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1687 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1686 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1686 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1728 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1728 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1685 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1685 TrailNet 3or6 month T1D plasma


title: LCN2 KO DE_Recovery_rIL10_16

city: San Jose

first: Eleana

middle: Stephanie

last: Guardado

address: 3166 Kimlee Dr

institute: Stanford

description: Mouse 36

scan_protocol: Chip was imaged and quantified by a nCounter Sprint profiler.

data_processing: All samples passed the NanoString system quality control (QC) test. Data were analyzed using nSolver 4.0 and by performing a NanoString Advanced analysis. The following housekeeping genes showing the strongest correlation with each other were used for normalization of gene expression: Acad9, Cnot10, Mtmr14, Nol7, Nubp1, Pgk1, Ppia, and Rplp0. The agglomerative analysis on nSolver was used to generate heatmaps. Per NanoString’s recommendation, 50 transcript counts was taken as the “count threshold”. The 20 most upregulated genes among all treatments were identified by the differential expression analysis. The STRING database (https://string-db.org) was used to explore protein-protein interactions among differentially regulated genes from NanoString that were statistically significant based on the unadjusted p-values [20].

source_name: RNA from lung tissue

growth_protocol: Male C57BL/6J and B6.129P2-Lcn2tm1Aade/AkiJ mice 8-13 weeks of age were received from The Jackson Laboratory (Bar Harbor, ME, USA) and housed in micro-isolator cages (five per cage) at the University of California, Riverside animal barrier facilities. Mice were allowed unrestricted access to food and water, monitored for any behavioral or physiological changes, and weighed weekly. All experiments and procedures were approved by the University of California River-side Institutional Animal Care and Use Committee.

extract_protocol: Animals were euthanized with isoflurane and collection of bronchoalveolar lavage fluid (BALF) and lung tissue was performed as described below. For BALF collection, a cannula was first inserted into the trachea and secured by tying a knot with a suture around the trachea. A syringe was used to rinse/wash the whole lung with 1 ml of sterile 1X PBS, which was collected in a separate tube to prevent over-dilution in subsequent enzyme-linked immunoassays (ELISAs). The lungs were washed two additional times with 1 ml PBS, and combined in a second tube for downstream cellular analyses. After BALF collection, the left lung lobe was tied off, excised and frozen in RNAlater to be used for NanoString analyses.

treatment_protocol: WT and LCN-2 KO mice were repetitively exposed to DE prepared from dusts collected from swine confinement facilities or their saline vehicle control. An aqueous solution of dust extract was prepared as described above and published previously and administered to mice as a 50 l intranasal instillation (IN) of 12.5% DE or saline under light isoflurane anesthesia. Male mice of 8-13 weeks old were given IN instillations in the mornings for 15 weekdays.  For this work, we evaluated two time points after repetitive DE exposure: 1) five hours after last IN (no recovery period), and 2) 72 hours after last IN (recovery period). For studies that included IL-10 administration, 1 ug of recombinant mouse IL-10 per 25 g mouse body weight was administered to LCN-2 KO animals on the day of the final DE IN and at 48 hr post final DE IN.

tag: gender

value: Male

value: Lung

value: LCN2 KO


title: Patient-rep13


title: UPN827 cells, TN1697 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1697 TrailNet 3or6 month T1D plasma


title: Cochlear outer sulcus , Euthyroid rep2


title: LCN2 KO DE_Recovery_rIL10_12

description: Mouse 35


title: Transduction of Clone # 7 mESCs at day 6 of SMC differentiation with cgRNA library, Replicate 2, unsorted cells

description:
Library name: Day6-Unsort-Rep2_S14_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt

value: Transduction of Clone # 7 mESCs at day 6 of SMC differentiation with cgRNA library,unsorted cells


title: LCN2 KO DE_Recovery_IL10_8

description: Mouse 34


title: Transduction of Clone # 7 mESCs at day 6 of SMC differentiation with cgRNA library, Replicate 1, unsorted cells

description:
Library name: Day6-Unsort-Rep1_S13_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt


title: Patient-rep01


title: UPN827 cells, TN1682 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1682 TrailNet 3or6 month T1D plasma


title: LCN2 KO Sal_Recovery_rIL10_14

description: Mouse 33


title: LCN2 KO Sal_Recovery_rIL10_10

description: Mouse 32


title: Transduction of Clone # 7 mESCs at day 3 of SMC differentiation with cgRNA library, Replicate 3, GFP+ cells

description:
Library name: Day3-GFPpos-Rep3_S12_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt

value: Transduction of Clone # 7 mESCs at day 3 of SMC differentiation with cgRNA library,GFP+ cells


title: UPN827 cells, TN1679 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1679 TrailNet 3or6 month T1D plasma


title: CD34-rep2

value: CD34+ cells


title: UPN827 cells, TN1680 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1680 TrailNet 3or6 month T1D plasma

value: UPN827 cells


title: LCN2 KO Sal_Recovery_rIL10_6

description: Mouse 31


title: Transduction of Clone # 7 mESCs at day 3 of SMC differentiation with cgRNA library, Replicate 2, GFP+ cells

description:
Library name: Day3-GFPpos-Rep2_S11_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt


title: UPN827 cells, TN1677 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1677 TrailNet 3or6 month T1D plasma

value: TrailNet 3 or 6 month


title: SK_GSKJ4_72h reps 1 and 2

city: Cardiff

first: Marcos

last: Quintela

state: --- Select One ---

address: 52 Maindy Rd, Hadyn Ellis Building

department: European Cancer Stem Cell Research Institute

country: United Kingdom

institute: Cardiff University

data_processing:
FastQ files that contained high quality RNA sequencing reads were aligned to the 'GRCh38/hg38' genome build using STAR
Gene count tables were generated using the --quantMode GeneCounts argument in STAR
DESeq2 was used to identify significant differential expression between control and experimental samples
Assembly: hg38
Supplementary files format and content: Tab-delimited text file including per sample: Ensembl gene ID, total counts

source_name: SKOV3 cell line

growth_protocol: OVCAR-3, CAOV3 and SKOV3 cells were grown in 12-well TC plates using RMPI 1640, DMEM/F12 and McCoys media respectively (Life Scientific)

extract_protocol:
Following 48h and 72h of JMJD3/UTX inhibition, total RNA samples were extracted using the Qiagen Rneasy mini kit (74106)
cDNA libraries were prepared at Novogene (Eukaryotic RNA-Seq, cDNA library)

treatment_protocol: OVCAR-3, CAOV3 and SKOV3 cells were treated with GSK-J5 (control) and GSK-J4 (Stripped media, 2.5uM) for 48h and 72h prior to RNA extraction

tag: treatment length


title: Transduction of Clone # 7 mESCs at day 3 of SMC differentiation with cgRNA library, Replicate 1, GFP+ cells

description:
Library name: Day3-GFPpos-Rep1_S10_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt


title: CD34-rep1

value: bone marrow


title: LCN2 KO DE_Recovery_NO rIL10_15

description: Mouse 30


title: UPN827 cells, TN1671 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1671 TrailNet 3or6 month T1D plasma


title: Transduction of Clone # 7 mESCs at day 3 of SMC differentiation with cgRNA library, Replicate 3, unsorted cells

description:
Library name: Day3-Unsort-Rep3_S9_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt

value: Transduction of Clone # 7 mESCs at day 3 of SMC differentiation with cgRNA library,unsorted cells


title: SK_GSKJ5_72h reps 1 and 2

value: GSK-J5 (Control)


title: LCN2 KO DE_Recovery_NO rIL10_11

description: Mouse 29


title: UPN827 cells, TN1670 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1670 TrailNet 3or6 month T1D plasma


title: ATAC_J4_rep1

data_processing:
Nextflow (v 23.10.1) was used to run the nf-core/atacseq pipeline.
The command used was: nextflow run nf-core/atacseq -profile singularity -params-file parameters.json --input samples.csv --genome GRCh38 --outdir output
Briefly, fastQ files were aligned to the 'GRCh38/hg38' genome build assembly using Bowtie2 and peak calling was performed using MACS2.
DiffBind was used to identify significant differential peak enrichment between control and experimental samples.
Assembly: hg38
Supplementary files format and content: Indexed Bigwig files (bw).

source_name: Ovarian cancer cell line

growth_protocol: OVCAR-3 cells were grown in 12-well TC plates using RPMI 1640 (20% FBS) media (Thermo Fisher Scientific).

extract_protocol:
After 48h of treatment, cells were lysed, nuclei extracted and DNA tagmented and purified using the ATAC-Seq kit (C01080002, Diagenode) following manufacturer's instructions.
DNA libraries were prepared using the unique dual indexes (UDI) for Tagmeneted libraries kit (C01011034, Diagenode). AMPure XP beads (A63880, Beckman Coulter) were used for library clean up.
DNA libraries were sequenced at Novogene (PE150).

treatment_protocol: OVCAR-3 cells were treated with GSK-J5 (control) and GSK-J4 (2.5µM) for 48h prior to chromatin extraction.

value: Ovarian cancer cell line


title: LCN2 KO DE_Recovery_NO rIL10_7

description: Mouse 28


title: UPN827 cells, TN1668 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1668 TrailNet 3or6 month T1D plasma


title: Transduction of Clone # 7 mESCs at day 3 of SMC differentiation with cgRNA library, Replicate 2, unsorted cells

description:
Library name: Day3-Unsort-Rep2_S8_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt

source_name: Mouse ES cells differentiated to smooth muscle cells


title: CA_GSKJ4_72h reps 1 and 2

source_name: CAOV3 cell line


title: Transduction of Clone # 7 mESCs at day 3 of SMC differentiation with cgRNA library, Replicate 1, unsorted cells

description:
Library name: Day3-Unsort-Rep1_S7_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt


title: UPN827 cells, TN1706 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1706 TrailNet 3or6 month T1D plasma


title: CA_GSKJ5_72h reps 1 and 2


title: LCN2 KO Sal_Recovery_NO rIL10_13

description: Mouse 27


title: LCN2 KO Sal_Recovery_NO rIL10_9

description: Mouse 26


title: SK_GSKJ4_72h rep3

data_processing:
FastQ files that contained high quality RNA sequencing reads were aligned to the 'GRCh38/hg38' genome build assembly using STAR.
Gene count tables were generated using the --quantMode GeneCounts argument in STAR.
DESeq2 was used to identify significant differential expression between control and experimental samples.
Assembly: hg38
Supplementary files format and content: Processed_OVCAR3.txt: Tab-delimited text file including Ensembl gene ID and total counts per sample
Supplementary files format and content: Processed_CAOV3.txt: Tab-delimited text file including Ensembl gene ID and total counts per sample
Supplementary files format and content: Processed_SKOV3.txt: Tab-delimited text file including Ensembl gene ID and total counts per sample

source_name: Cell line

growth_protocol: OVCAR-3, CAOV3 and SKOV3 cells were grown in 12-well TC plates using RPMI 1640 (20% FBS), DMEM/F12 (10% FBS) and McCoys 5A (10%) media respectively (Thermo Fisher Scientific).

extract_protocol:
Following 48-72h of treatment, total RNA samples were extracted using the Qiagen RNeasy Plus kit (74134).
cDNA libraries were prepared using the polyA enrichment mRNA library preparation following manufacturer's instructions (Novogene).

treatment_protocol: OVCAR-3, CAOV3 and SKOV3 cells were treated with GSK-J5 (control) and GSK-J4 (2.5µM) for 48-72h prior to RNA extraction.

value: Cell line

value: GSKJ4 72h 2.5uM


title: UPN827 cells, TN1660 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1660 TrailNet 3or6 month T1D plasma


title: Transduction of Clone # 7 mESCs with cgRNA library, Replicate 3, EGFP+ cells

description:
Library name: mESC-GFPpos-Rep3_S6_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt

value: Mouse ES cells differentiated to smooth muscle cells

value: Transduction of Clone # 7 mESCs with cgRNA library,EGFP+ cells


title: UPN827 cells, TN1655 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1655 TrailNet 3or6 month T1D plasma


title: Transduction of Clone # 7 mESCs with cgRNA library, Replicate 2, EGFP+ cells

description:
Library name: mESC-GFPpos-Rep2_S5_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt


title: LCN2 KO Sal_Recovery_NO rIL10_5

description: Mouse 25

source_name: RNA from lung tissue


title: OV_GSKJ5_72h reps 1 and 2

source_name: OVCAR-3 cell line


title: Transduction of Clone # 7 mESCs with cgRNA library, Replicate 1, EGFP+ cells

description:
Library name: mESC-GFPpos-Rep1_S4_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt


title: OV_GSKJ4_48h reps 1 and 2


title: LCN2 KO DE_Recovery_NO rIL10_1_F

description: Mouse 24


title: Transduction of Clone # 7 mESCs with cgRNA library, Replicate 3, unsorted cells

description:
Library name: mESC-Unsort-Rep3_S3_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt

value: Transduction of Clone # 7 mESCs with cgRNA library,unsorted cells


title: OV_GSKJ5_48h reps 1 and 2


title: UPN827 cells, TN1647 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1647 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1702 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1702 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1643 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1643 TrailNet 3or6 month T1D plasma


title: LCN2 KO DE_Recovery_NO rIL10_1_C

description: Mouse 23

value: Male


title: Transduction of Clone # 7 mESCs at day 6 of SMC differentiation with cgRNA library, Replicate 1, GFP+ cells

description:
Library name: Day6-GFPpos-Rep1_S16_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt

value: Transduction of Clone # 7 mESCs at day 6 of SMC differentiation with cgRNA library,GFP+ cells


title: PAD Gastroc 1

city: Omaha

first: Hanjun

last: Wang

state: Nebraska

address: 984455 University of Nebraska Medical Center 985850 University of Nebraska Medic

department: Anesthesiology

institute: University of Nebraska Medical Center

description: Library name: Sample Gastroc 10

data_processing:
Sequencing and bioinformatical analysis were completed by LC Sciences, LLC, TX, USA.
Assembly: Sequencing and bioinformatical analysis were completed by LC Sciences, LLC, TX, USA.
Supplementary files format and content: CSV file including PFKM values for each sample

organism: Rattus norvegicus

source_name: skeletal muscle

extract_protocol:
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using a divalent cation buffer at elevated temperatures.
The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: sham and hindlimb ischemia

value: skeletal muscle

value: Sprague Dawley

value: hindlimb ischemia


title: UPN827 cells, TN1639 TrailNet 3or6 month T1D plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with TN1639 TrailNet 3or6 month T1D plasma


title: LCN2 KO DE_Recovery_NO rIL10_1_B

description: Mouse 22

value: Lung

value: LCN2 KO


title: UPN827 cells, TN1638 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1638 TrailNet 3or6 month T1D plasma

value: UPN827 cells

value: TrailNet 3 or 6 month


title: Transduction of Clone # 7 mESCs with cgRNA library, Replicate 1, unsorted cells

description:
Library name: mESC-Unsort-Rep1_S1_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt


title: LCN2 KO Sal_Recovery_NO rIL10_1_E

description: Mouse 21


title: UPN827 cells, TN1684 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1684 TrailNet 3or6 month T1D plasma


title: Patient-rep12

source_name: bone marrow

value: bone marrow

value: whole BM


title: PAD Gastroc 2

description: Library name: Sample Gastroc 9


title: Transduction of Clone # 7 mESCs at day 6 of SMC differentiation with cgRNA library, Replicate 3, unsorted cells

description:
Library name: Day6-Unsort-Rep3_S15_L001_R1_001
C7_SMC_cgRNA_count_matrix.txt

value: Transduction of Clone # 7 mESCs at day 6 of SMC differentiation with cgRNA library,unsorted cells


title: Patient-rep11


title: Transduction of multi-clonal mESCs with cgRNA library, Replicate 3 (Clone # 10), EGFP+ cells

description:
Library name: C10-GFPpos-mmu_S3_L001_R1_001
multiClonal_cgRNA_count_matrix.txt

source_name: Mouse ES cells

value: Mouse ES cells

value: Transduction of multi-clonal mESCs with cgRNA library,EGFP+ cells


title: LCN2 KO Sal_Recovery_NO rIL10_1_B

description: Mouse 20


title: PAD Gastroc 4

description: Library name: Sample Gastroc 7


title: PAD Gastroc 3

description: Library name: Sample Gastroc 8


title: Transduction of multi-clonal mESCs with cgRNA library, Replicate 3 (Clone # 10), unsorted cells

description:
Library name: C10-Unsort-mmu_S6_L001_R1_001
multiClonal_cgRNA_count_matrix.txt

value: Transduction of multi-clonal mESCs with cgRNA library,unsorted cells


title: LCN2 KO Sal_Recovery_NO rIL10_1_A

description: Mouse 19


title: WT DE_Recovery_NO rIL10_E

description: Mouse 18

value: WT


title: UPN827 cells, TN1631 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1631 TrailNet 3or6 month T1D plasma


title: PAD Gastroc 5

description: Library name: Sample Gastroc 6


title: Transduction of multi-clonal mESCs with cgRNA library, Replicate 2 (Clone # 7), EGFP+ cells

description:
Library name: C7-GFPpos-mmu_S2_L001_R1_001
multiClonal_cgRNA_count_matrix.txt


title: UPN827 cells, TN1633 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1633 TrailNet 3or6 month T1D plasma


title: WT DE_Recovery_NO rIL10_B

description: Mouse 17


title: UPN827 cells, TN1629 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1629 TrailNet 3or6 month T1D plasma


title: Transduction of multi-clonal mESCs with cgRNA library, Replicate 2 (Clone # 7), unsorted cells

description:
Library name: C7-Unsort-mmu_S5_L001_R1_001
multiClonal_cgRNA_count_matrix.txt


title: Transduction of multi-clonal mESCs with cgRNA library, Replicate 1 (Clone # 3), EGFP+ cells

description:
Library name: C3-GFPpos-mmu_S1_L001_R1_001
multiClonal_cgRNA_count_matrix.txt


title: WT DE_Recovery_NO rIL10_A

description: Mouse 16


title: UPN827 cells, TN1630 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1630 TrailNet 3or6 month T1D plasma


title: Sham Gastroc 2

description: Library name: Sample Gastroc 4

value: Sham


title: UPN827 cells, TN1628 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1628 TrailNet 3or6 month T1D plasma


title: Sham Gastroc 4

description: Library name: Sample Gastroc 2


title: WT Sal_Recovery_NO rIL10_F

description: Mouse 15

value: Male


title: UPN827 cells, TN1624 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1624 TrailNet 3or6 month T1D plasma


title: GvHD_4plex_scRNAseq

city: Suwon

first: Truc

middle: Do Thanh

last: Nguyen

state: All

address: 2066 Seobu-ro, Jangan-gu

country: South Korea

institute: Sungkyunkwan University School of Medicine

description:
Library name: GvHD_4plex_scRNAseq
Multiplexed 10x run

library_source: transcriptomic single cell

data_processing:
Sparse matrix files in Matrix Market format (matrix.mtx.gz) with accompanying barcodes (barcodes.tsv.gz) and gene annotation files (features.tsv.gz) produced by Cell Ranger.
Each processed dataset contains cell-by-gene UMI count matrices for a single demultiplexed sample.
Assembly: mm10 (GRCm38)
Supplementary files format and content: Matrix Market sparse matrices and accompanying barcode and feature tables.

source_name: CD4+ and CD8+ T cells

extract_protocol:
Donor-derived T cells were isolated from acute GvHD recipient mice, stained, and sorted by flow cytometry. Single-cell suspensions were prepared according to 10x Genomics recommendations.
Single-cell 5′ gene expression libraries were generated using the 10x Genomics GEM-X Universal 5′ Gene Expression v3 chemistry with 4-plex on-chip multiplexing. GEM generation, reverse transcription, cDNA amplification, and library construction were performed following the manufacturer’s protocol. Indexed libraries were sequenced on an Illumina NextSeq 2000 using a 100-bp paired-end configuration.

treatment_protocol: Recipient mice received total body irradiation followed by donor bone marrow and T-cell infusion to induce acute GvHD. Rapamycin or PBS control was administered according to experimental group

value: CD4+ and CD8+ T cells

value: BALB/c (H-2d)


title: UPN827 cells, TN1623 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1623 TrailNet 3or6 month T1D plasma


title: Cochlear outer sulcus , Hypothyroid rep2

source_name: Cochlear outer sulcus

value: Cochlear outer sulcus

value: Hypothyroid


title: Transduction of multi-clonal mESCs with cgRNA library, Replicate 1 (Clone # 3), unsorted cells

description:
Library name: C3-Unsort-mmu_S4_L001_R1_001
multiClonal_cgRNA_count_matrix.txt


title: WT Sal_Recovery_NO rIL10_A

description: Mouse 13

source_name: RNA from lung tissue

value: Lung


title: ATRi 5

city: Annandale

first: Thomas

last: Conrads

state: VA

address: 3289 Woodburn Rd, Suite 375

institute: Women’s Health Integrated Research Center

description: Library name: A5

data_processing:
Quality controlled sequencing reads was aligned to the mouse reference genome (GRCm39/mm39, Ensembl release 104) using the STAR algorithm (v2.7.1) within the RSEM workflow (v1.3.3) generating of both raw read counts and Transcripts Per Million (TPM) expression values for each transcript. TPM values were normalized using the formula log₂(TPM + 1) to stabilize variance and approximate a normal distribution for downstream statistical analyses
Assembly: GRCm39/mm39, Ensembl release 104
Supplementary files format and content: tab-delimited text file includes raw count for all samples

source_name: GP33+ CD8+ T cells

extract_protocol:
RNA was “harvested” by sorting cells directly into lysis buffer: live GP33-specific (GP33⁺) CD8⁺ T cells were FACS-sorted (500–1,000 cells/well) into a 96‑well plate containing cell lysis buffer. Lysates were stored: the plate was stored at −80 °C.
RNA libraries for RNA-seq were prepared using the SMART-seq HT Ultra Low input protocol

treatment_protocol: Female C57BL/6 mice were purchased from The Jackson Laboratory and were 6-8 weeks old at the time of infection with 1.5 x 106 PFU LCMV Armstrong (in 150 µL), administered intraperitoneally on day 0. Mice received 75 mg/kg ATRi (ceralasertib) or Vehicle (10% DMSO, 40% Propylene Glycol, 50% dH2O) via oral gavage on days 5, 6, and 7 post LCMV Armstrong infection. Spleens were harvested at 6 weeks after infection for sorting of GP33+ memory CD8+ T cells.

value: GP33+ CD8+ T cells

value: ATRi (75 mg/kg ceralasertib) on days 5, 6, and 7


title: Sham Gastroc 5

description: Library name: Sample Gastroc 1

source_name: skeletal muscle

value: skeletal muscle

value: Sprague Dawley


title: UPN827 cells, TN1618 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1618 TrailNet 3or6 month T1D plasma

value: UPN827 cells

value: TrailNet 3 or 6 month


title: RNA-seq, endosperm, Nijinokirameki, green manure, Year 2024, rep2

description:
Library name: rna_Niji_endosperm_GM_2024_rep2
column name in Niji_endosperm_5DAF_CF_GM_RNA_rawdata_UniqueExonReads_2024.csv: 2024_GM_rep2

source_name: endosperm

value: endosperm

value: GM


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_6h_D4_Pol2-NTD

city: Bethesda

first: Kai

last: Ge

state: MD

address: 50 South Dr Rm 4154

department: NIDDK

institute: NIH

description: Library name: Sample 45

data_processing:
Basecalls performed using Bcl2fastq.
ChIP-seq reads were aligned to the mm9 genome assembly using bowtie2.
Peaks were called using SICER (v2) with following configuration: For ChIP-seq of HIRA and SPT6, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-10 were used. For S5P-Pol II, S2P-Pol II, and CDK9, a window size of 50 bp, gap size of 50 bp, and a false discovery rate of 1E-3 were used. For H3K27ac, a window size of 200 bp, gap size of 200 bp, and a false discovery rate of 1E-3 were used. The effective genome fraction of 0.8 was applied to all ChIP-Seq data.
Paired-end reads of RNA-seq were aligned to the mm9 genome assembly using STAR.
SICER v1.1 was used to calculate the reads per kilo base per million (RPKM) on exonic regions as expression measurements for each gene.
Assembly: mm9
Supplementary files format and content: wig files were generated using in-house script and the scores represent RPKM; tab-delimited text files include FPKM values for each gene.

growth_protocol: Mouse 3T3-L1 white preadipocytes were maintained in growth (DMEM +10%BS) medium

extract_protocol:
Total RNA was subjected to rRNA depletion using theNEBNext® rRNA Depletion Kit v2 (Human/Mouse/Rat) with RNA Sample Purification Beads (NEB, E7405L) before using Click-iT™ Nascent RNA Capture Kit (C10365) to capture nascent RNA.
Isolated nascent RNAs were reverse-transcribed into cDNA using  SuperScript™ VILO™ cDNA Synthesis Kit (Thermo, 11754050) and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.

treatment_protocol: For the adipogenesis assay, cells were plated in growth medium (DMEM plus 10% BS) 4 days before the induction and were induced with 10 μg/mL insulin, 0.5 mM IBMX and 1 μM DEX in FBS medium (DMEM plus 10% FBS) for 2 days. After 2 days of induction, the culture medium was changed to DMEM supplemented with FBS and insulin only.

value: Differentiating preadipocytes

value: wild type

value: adipogenic differentiation

tag: time

value: day 4

tag: chip antibody

value: Anti-Rbp1 NTD(D8L4Y) (14958, Cell Signaling Technology)


title: LCN2 KO DE_NO Recovery_NO rIL10_116

description: Mouse 12

value: Male

value: LCN2 KO


title: LCN2 KO DE_NO Recovery_NO rIL10_24

description: Mouse 11


title: UPN827 cells, TN1616 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1616 TrailNet 3or6 month T1D plasma


title: PAD Soleus 2

description: Library name: Sample Soleus 9

value: hindlimb ischemia


title: snRNA seq of striatum of 2 mouse models of PD: MitoPark18_1

city: Stockholm

first: Konstantinos

last: Meletis

address: Solnavagen 9

department: Neuroscience

country: Sweden

institute: Karolinska Institutet

description:
Library name: snRNAseq_mouse_models_Mitopark18_1
18a

data_processing:
We generated the count matrix from the sequencing data for each sample (fastq) using the software commercialized by 10x Genomics Cellranger (10x Genomics Cell Ranger v7.1.0)
Assembly: mm10-2020-A
Supplementary files format and content: filtered_feature_bc_matrix_<filename>.h5, sparse matrix of gene expression counts. Rows = Genes (Features), Columns = Cell Barcodes (IDs) and Expression Counts

source_name: Brain

extract_protocol:
Striatum from one hemisphere of 19 brains was collected for nuclei isolation. Brain tissue was placed into a tube together with lysis buffer (10?mM Tris-HCl, 10?nM NaCl, 3?nM MgCl2, 0.1% Nonidet P40 Substitute 0.1%, 1?mM DTT, 1U/µl RNAse inhibitor and Nuclease free water), homogenized by pestle homogenization in a tissue grinder tube and incubated on ice for 5?min. The nuclei were extracted by following 10x Genomics protocol for Nuclei Isolation from Complex Tissues for Single Cell Multiome ATAC?+?Gene Expression Sequencing (User Guide, CG000375 Rev A). Each sample was filtered through a 70?µm cell strainer, sorted and permeabilized nuclei were pelleted at 500?×?g for 5?min at 4?°C, and resuspended in 1 ml PBS 1x, 1% BSA + 1 U/?l RNase inhibitor, for two times. After the second centrifuge nuclei were stained with 7-AAD Ready Made Solution (SML 633-1ML) 0.01% for FACS sorting.
The nuclei were processed according to the 10X Genomics Chromium Next GEM Single Cell 3' Reagent Kits v3.1 (Dual Index) protocol (User Guide CG000315 Rev C). For each sample, we aimed to recover between 2,000 and 7,000 nuclei. Libraries were constructed for sequencing in accordance with the protocol and manufacturer's recommendations. Sequencing was performed using an Illumina NextSeq 2000, targeting a depth of 300 to 400 million reads per sample. The sequencing read lengths were as follows: Read 1, 28 cycles; i7 and i5 index, 10 cycles each; Read 2, 90 cycles.

treatment_protocol: Mild Neurotoxin Model (6-OHDA): Adult wild-type mice received unilateral injections of 6-hydroxydopamine (6-OHDA) at a low dose (0.6 µg/µL) into the medial forebrain bundle (MFB), selectively damaging nigrostriatal dopaminergic neurons and inducing mild Parkinsonian pathology. Untreated wild-type mice served as controls.  Progressive Genetic Model (MitoPark): The MitoPark model (Slc6a3-cre; Tfam^flx/flx) induces mitochondrial dysfunction specifically in dopaminergic neurons, leading to progressive neurodegeneration. Samples were collected at two timepoints:

value: Brain

value: no cell line

value: all cells

value: +/DAT-cre, TfamloxP/TfamloxP

value: transgenic animals


title: snRNA seq of striatum of 2 mouse models of PD: MitoPark18_2

description:
Library name: snRNAseq_mouse_models_Mitopark18_2
18b


title: UPN827 cells, TN1615 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1615 TrailNet 3or6 month T1D plasma

value: UPN827 cells


title: LCN2 KO DE_NO Recovery_NO rIL10_5

description: Mouse 10

value: Lung


title: PAD Soleus 4

description: Library name: Sample Soleus 7

value: skeletal muscle

value: Sprague Dawley


title: UPN827 cells, TN1611 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1611 TrailNet 3or6 month T1D plasma

value: TrailNet 3 or 6 month


title: LCN2 KO Sal_NO Recovery_NO rIL10_113

description: Mouse 9


title: snRNA seq of striatum of 2 mouse models of PD: MitoPark15_3

description:
Library name: snRNAseq_mouse_models_Mitopark15_3
15c


title: UPN827 cells, TN1605 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1605 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1610 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1610 TrailNet 3or6 month T1D plasma


title: LCN2 KO Sal_NO Recovery_NO rIL10_19

description: Mouse 8


title: LCN2 KO Sal_NO Recovery_NO rIL10_1

description: Mouse 7


title: Sham Soleus 1

description: Library name: Sample Soleus 5

value: Sham


title: PAD Soleus 5

description: Library name: Sample Soleus 6


title: snRNA seq of striatum of 2 mouse models of PD: MitoPark15_2

description:
Library name: snRNAseq_mouse_models_Mitopark15_2
15b


title: snRNA seq of striatum of 2 mouse models of PD: MitoPark15_1

description:
Library name: snRNAseq_mouse_models_Mitopark15_1
15a


title: UPN827 cells, TN1602 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1602 TrailNet 3or6 month T1D plasma


title: Sham Soleus 2

description: Library name: Sample Soleus 4


title: WT DE_NO Recovery_NO rIL10_111

description: Mouse 6

value: WT


title: snRNA seq of striatum of 2 mouse models of PD: MitoPark11_3

description:
Library name: snRNAseq_mouse_models_Mitopark11_3
MP3


title: Sham Soleus 3

description: Library name: Sample Soleus 3


title: UPN827 cells, TN1596 TrailNet 3or6 month T1D plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with TN1596 TrailNet 3or6 month T1D plasma


title: WT DE_NO Recovery_NO rIL10_17

description: Mouse 5


title: UPN827 cells, TN1595 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1595 TrailNet 3or6 month T1D plasma


title: snRNA seq of striatum of 2 mouse models of PD: MitoPark11_2

description:
Library name: snRNAseq_mouse_models_Mitopark11_2
MP2


title: Sham Soleus 4

description: Library name: Sample Soleus 2


title: WT DE_NO Recovery_NoO rIL10_5

description: Mouse 4


title: Sham Soleus 5

description: Library name: Sample Soleus 1


title: WT Sal_NO Recovery_NO rIL10_107

description: Mouse 3


title: WT Sal_NO Recovery_NO rIL10_15

description: Mouse 2


title: UPN827 cells, TN1583 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1583 TrailNet 3or6 month T1D plasma


title: genomic DNA from AML patient AD034

type: genomic

city: singapore

first: yi

last: chai

department: CSI

country: Singapore

institute: National University of SIngapore

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to human Infinium MethylationEPIC BeadChip (Illumina) according to the manufacturer's standard protocol.

scan_protocol: Arrays were imaged using BeadArray Reader (HiScan) and standard recommended Illumina scanner settings

data_processing: ChAMP pipeline with quality control

label: Cy3 and Cy5

source_name: bone marrow

label_protocol: Standard Illumina Protocol for Infinium MethylationEPIC BeadChip arrays.

extract_protocol: Genomic DNA was extracted from bone marrow samples with standard DNA extraction protocols

value: primary cells


title: snRNA seq of striatum of 2 mouse models of PD: mild 6OHDA_2

description:
Library name: snRNAseq_mouse_models_mild_6OHDA_2
6OHDA_2

value: mild 6OHA injeciton (0.6 ug)


title: genomic DNA from AML patient AD358


title: UPN827 cells, TN1580 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1580 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1571 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1571 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1567 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1567 TrailNet 3or6 month T1D plasma


title: VOC3

city: Suzhou

first: Xiaoyu

last: Lin

address: No. 100, Chongwen Road, Suzhou Industrial Park

institute: Suzhou Institute of Systems Medicine

description: Library name: Sample6

data_processing:
Gene quantification employed RSEM v1.3.1. Differential expression analysis (log₂(fold change) >1, adjusted P<0.05) used DESeq2 v1.40.2, with visualizations generated via ggplot2 v3.5.1 and ComplexHeatmap v2.20.0. Gene Set Enrichment Analysis (GSEA) was performed using clusterProfiler v4.12.6 with GO Biological Pathways (MSigDB) and gene ranking by signal-to-noise ratio. Enrichment patterns were visualized using enrichplot v1.24.4.
Assembly: Aspergillus_niger_ASM285v2

organism: Aspergillus niger

source_name: fungal culture

extract_protocol:
(1) cytology: the concentration of cells is adjusted to the desired concentration, usually 700-1200 cells/ΜL. (2)10X labeled cDNA fragments: gel beads containing barcode information bind to a mixture of cells and enzymes and are then coated with Surfactant droplets located in a microfluidic system to form GEMs. Gems flow into the reservoir and are collected, the gel beads dissolve to release Barcode sequences, cDNA fragments are reverse transcribed, and samples are labeled. The gel beads were broken and the oil droplets were broken, and the cDNA was used as a template for PCR amplification. The products of all GEMs were mixed to construct a standard sequencing library.
Construction of mRNA library: DNA library was constructed by cutting cDNA into 200 ~ 300 BP fragments, sequencing adapters and primers, and PCR amplification.

value: fungal culture

value: VOC is exposed to the bacteria 7 days


title: genomic DNA from AML patient AD546


title: snRNA seq of striatum of 2 mouse models of PD: mild 6OHDA_1

description:
Library name: snRNAseq_mouse_models_mild_6OHDA_1
6OHDA_1


title: VOC2

description: Library name: Sample5


title: VOC1

description: Library name: Sample4


title: snRNA seq of striatum of 2 mouse models of PD: control_7

description:
Library name: snRNAseq_mouse_models_control_6
C1_S7

value: -/DAT-cre, TfamloxP/TfamloxP

value: Control  animals


title: UPN827 cells, TN1558 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1558 TrailNet 3or6 month T1D plasma


title: CK3

description: Library name: Sample3

value: not exposed to the bacteria of volatile organic compounds


title: UPN827 cells, TN1556 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1556 TrailNet 3or6 month T1D plasma


title: genomic DNA from AML patient AD532


title: snRNA seq of striatum of 2 mouse models of PD: control_6

description:
Library name: snRNAseq_mouse_models_control_5
C2_S5

value: Brain

value: no cell line

value: all cells


title: CK2

description: Library name: Sample2


title: snRNA seq of striatum of 2 mouse models of PD: control_4

description:
Library name: snRNAseq_mouse_models_control_4
C1_S4


title: UPN827 cells, TN1555 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1555 TrailNet 3or6 month T1D plasma

value: UPN827 cells


title: genomic DNA from AML patient AD594


title: CK1

description: Library name: Sample1


title: snRNA seq of striatum of 2 mouse models of PD: control_3

description:
Library name: snRNAseq_mouse_models_control_3
Control_1

source_name: Brain


title: UPN827 cells, TN1553 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1553 TrailNet 3or6 month T1D plasma


title: genomic DNA from AML patient AD550


title: SI Infected Red Clover 7

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

description: Library name: F7

data_processing:
Adaptor sequences and low quality reads removed
Mapped to Sheep genome
DEG determined using DESeq2
Assembly: GCA_016772045.1
Supplementary files format and content: excel file with count data and gene symbol for each sample

organism: Ovis aries

source_name: Small Intestine

extract_protocol:
RNA was extracted using RNeasy kit (Qiagen) following instructions provided by the manufacturer
standard Illumina

value: Small Intestine

value: Infected Red Clover


title: snRNA seq of striatum of 2 mouse models of PD: control_2

description:
Library name: snRNAseq_mouse_models_control_2
new_control_2


title: SI Infected Red Clover 6

description: Library name: F6


title: snRNA seq of striatum of 2 mouse models of PD: control_1

description:
Library name: snRNAseq_mouse_models_control_1
new_control_1


title: genomic DNA from AML patient AD556


title: SI Infected Red Clover 5

description: Library name: F5


title: UPN827 cells, TN1538 TrailNet 3or6 month T1D plasma

data_processing: Image data were normalized and analyzed Partek Genomic Suite (Partek GS) to determine signal log intensity/ratios.  The statistical significance of differential gene expression and false discovery rates (FDR) were derived through ANOVA function in Partek GS.

source_name: UPN827 cells stimulated with TN1538 TrailNet 3or6 month T1D plasma

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.


title: ST_mild 6OHDA_12

description: Library name: Spatial_Transcriptomics_mouse_model_PD_mild_6OHDA_12

data_processing:
Spatial gene expression profiling was conducted using the Visium platform, strictly following the manufacturer's instructions [CG000239 Rev D], generating a total of 24 libraries. Sequencing of the 24 libraries was performed on a NextSeq2000 platform, with cDNA libraries diluted to a final concentration of 2 nM and pooled for sequencing. Each sample was sequenced to a depth of 150-200 million reads, with read lengths configured as 28 bp for Read 1, 10 bp for both i7 and i5 indices, and 90 bp for Read 2, in line with the Visium protocol [CG000239 Rev D].
The sequenced libraries from the Visium experiments were processed using the 10x Genomics Spaceranger pipeline (10x Genomics Space Ranger v1.3.1) to generate the gene count matrices for the downstream data analysis. For the mapping, the Mus musculus reference genome (mm10-2020-A, prebuilt reference from 10X genomics; GENCODE Release M23; Ensembl version Ensembl98) was used.
Assembly: mm10-2020-A
Supplementary files format and content: filtered_feature_bc_matrix_<filename>.h5, sparse matrix of gene expression counts. Rows = Genes (Features), Columns = Cell Barcodes (IDs) and Expression Counts
Library strategy: Spatial Transcriptomics

extract_protocol:
fresh frozen tissue
The tissue sections mounted on Visium slides were fixed in pre-chilled methanol at -20°C for 30 minutes, in accordance with the 10X Genomics protocol [CG000160 Rev B]. Following fixation, hematoxylin was applied for 5 minutes, followed by a 45-second application of eosin to enhance contrast. Brightfield images were captured using a Zeiss Axiolmager.Z2 microscope equipped with Metafer 5 software. We optimized the tissue permeabilization process specifically for the striatal region, following the 10X Genomics tissue optimization guidelines [CG000238 Rev D]. Preliminary testing identified 14 minutes as the optimal permeabilization time for this brain region.

treatment_protocol: Adult wild-type mice received unilateral injections of 6-hydroxydopamine (6-OHDA) at a low dose (0.6 µg/µL) into the medial forebrain bundle (MFB), selectively damaging nigrostriatal dopaminergic neurons and inducing mild Parkinsonian pathology. Untreated wild-type mice served as controls. Spatial gene expression profiling was conducted on the striata of mice from the mild 6-OHDA model to preserve anatomical context.

tag: section name

value: All cells

tag: batch


title: genomic DNA from AML patient AD535


title: SI Infected Red Clover 4

description: Library name: F4


title: UPN827 cells, TN1537 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1537 TrailNet 3or6 month T1D plasma

value: TrailNet 3 or 6 month


title: ST_mild 6OHDA_11

description: Library name: Spatial_Transcriptomics_mouse_model_PD_mild_6OHDA_11


title: genomic DNA from AML patient AD320


title: ST_mild 6OHDA_10

description: Library name: Spatial_Transcriptomics_mouse_model_PD_mild_6OHDA_10


title: genomic DNA from AML patient AD307


title: UPN827 cells, TN1535 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1535 TrailNet 3or6 month T1D plasma


title: SI Infected Red Clover 2

description: Library name: F2


title: ST_mild 6OHDA_9

description: Library name: Spatial_Transcriptomics_mouse_model_PD_mild_6OHDA_9


title: genomic DNA from AML patient AD634


title: UPN827 cells, TN1534 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1534 TrailNet 3or6 month T1D plasma


title: SI Infected Red Clover 1

description: Library name: F1


title: ST_mild 6OHDA_8

description: Library name: Spatial_Transcriptomics_mouse_model_PD_mild_6OHDA_8


title: UPN827 cells, TN1549 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1549 TrailNet 3or6 month T1D plasma


title: genomic DNA from AML patient AD549


title: UPN827 cells, TN1547 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1547 TrailNet 3or6 month T1D plasma


title: genomic DNA from AML patient AD584

source_name: bone marrow


title: SI Infected 7

description: Library name: E7

value: Infected


title: ST_mild 6OHDA_7

description: Library name: Spatial_Transcriptomics_mouse_model_PD_mild_6OHDA_7


title: genomic DNA from AML patient AD564a


title: UPN827 cells, TN1532 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1532 TrailNet 3or6 month T1D plasma


title: SI Infected 6

description: Library name: E6


title: ST_mild 6OHDA_6

description: Library name: Spatial_Transcriptomics_mouse_model_PD_mild_6OHDA_6


title: genomic DNA from AML patient AD217


title: UPN827 cells, TN1529 TrailNet 3or6 month T1D plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with TN1529 TrailNet 3or6 month T1D plasma


title: SI Infected 5

description: Library name: E5


title: ST_mild 6OHDA_5

description: Library name: Spatial_Transcriptomics_mouse_model_PD_mild_6OHDA_5


title: UPN827 cells, TN1527 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1527 TrailNet 3or6 month T1D plasma


title: genomic DNA from AML patient AD155


title: UPN827 cells, TN1536 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1536 TrailNet 3or6 month T1D plasma


title: SI Infected 4

description: Library name: E4


title: genomic DNA from AML patient AD046


title: UPN827 cells, TN1526 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1526 TrailNet 3or6 month T1D plasma


title: SI Infected Red Clover 3

description: Library name: F3


title: ST_mild 6OHDA_4

description: Library name: Spatial_Transcriptomics_mouse_model_PD_mild_6OHDA_4


title: UPN827 cells, TN1525 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1525 TrailNet 3or6 month T1D plasma


title: SI Infected 3

description: Library name: E3


title: ST_mild 6OHDA_3

description: Library name: Spatial_Transcriptomics_mouse_model_PD_mild_6OHDA_3


title: genomic DNA from AML patient AD572


title: UPN827 cells, TN1520 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1520 TrailNet 3or6 month T1D plasma


title: SI Infected 2

description: Library name: E2


title: genomic DNA from AML patient AD569b


title: ST_mild 6OHDA_2

description: Library name: Spatial_Transcriptomics_mouse_model_PD_mild_6OHDA_2

source_name: Brain


title: SI Infected 1

description: Library name: E1


title: genomic DNA from AML patient AD587


title: ST_mild 6OHDA_1

description: Library name: Spatial_Transcriptomics_mouse_model_PD_mild_6OHDA_1


title: UPN827 cells, TN1518 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1518 TrailNet 3or6 month T1D plasma


title: SI Control 6

description: Library name: D6

source_name: Small Intestine

value: Control


title: UPN827 cells, TN1516 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1516 TrailNet 3or6 month T1D plasma


title: ST_control_12

description: Library name: Spatial_Transcriptomics_mouse_model_PD_Control_12


title: genomic DNA from AML patient AD408

value: primary cells


title: SI Control 5

description: Library name: D5


title: UPN827 cells, TN1514 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1514 TrailNet 3or6 month T1D plasma


title: ST_control_11

description: Library name: Spatial_Transcriptomics_mouse_model_PD_Control_11


title: genomic DNA from AML patient AD559


title: SI Control 4

description: Library name: D4


title: ST_control_10

description: Library name: Spatial_Transcriptomics_mouse_model_PD_Control_10


title: genomic DNA from AML patient AD568


title: UPN827 cells, TN1512 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1512 TrailNet 3or6 month T1D plasma


title: SI Control 3

description: Library name: D3


title: ST_control_9

description: Library name: Spatial_Transcriptomics_mouse_model_PD_Control_9


title: UPN827 cells, TN1509 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1509 TrailNet 3or6 month T1D plasma


title: genomic DNA from AML patient AD399


title: SI Control 2

description: Library name: D2


title: UPN827 cells, TN1503 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1503 TrailNet 3or6 month T1D plasma


title: ST_control_8

description: Library name: Spatial_Transcriptomics_mouse_model_PD_Control_8


title: genomic DNA from AML patient AD194


title: SI Control 1

description: Library name: D1


title: ST_control_7

description: Library name: Spatial_Transcriptomics_mouse_model_PD_Control_7


title: genomic DNA from AML patient AD018


title: Ab Infected Red Clover 7

description: Library name: C7

source_name: Abomasum

value: Abomasum


title: UPN827 cells, TN1494 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1494 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1496 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1496 TrailNet 3or6 month T1D plasma


title: ST_control_6

description: Library name: Spatial_Transcriptomics_mouse_model_PD_Control_6


title: genomic DNA from AML patient AD385

source_name: bone marrow


title: UPN827 cells, TN1492 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1492 TrailNet 3or6 month T1D plasma


title: Ab Infected Red Clover 6

description: Library name: C6


title: ST_control_5

description: Library name: Spatial_Transcriptomics_mouse_model_PD_Control_5


title: genomic DNA from AML patient AD466


title: Ab Infected Red Clover 5

description: Library name: C5


title: snRNA seq of striatum of 2 mouse models of PD: MitoPark11_1

description:
Library name: snRNAseq_mouse_models_Mitopark11_1
MP1

value: +/DAT-cre, TfamloxP/TfamloxP

value: transgenic animals


title: genomic DNA from AML patient AD063


title: ST_control_4

description: Library name: Spatial_Transcriptomics_mouse_model_PD_Control_4


title: Ab Infected Red Clover 4

description: Library name: C4


title: UPN827 cells, TN1489 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1489 TrailNet 3or6 month T1D plasma


title: UPN827 cells, TN1488 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1488 TrailNet 3or6 month T1D plasma


title: ST_control_3

description: Library name: Spatial_Transcriptomics_mouse_model_PD_Control_3


title: genomic DNA from AML patient AD355


title: Ab Infected Red Clover 3

description: Library name: C3


title: ST_control_2

description: Library name: Spatial_Transcriptomics_mouse_model_PD_Control_2


title: UPN827 cells, TN1485 TrailNet 3or6 month T1D plasma

description: Gene expression data from UPN827 cells stimulated with T1D plasma

source_name: UPN827 cells stimulated with TN1485 TrailNet 3or6 month T1D plasma


title: Ab Infected Red Clover 2

description: Library name: C2


title: ST_control_1

description: Library name: Spatial_Transcriptomics_mouse_model_PD_Control_1


title: UPN827 cells, TN1482 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1482 TrailNet 3or6 month T1D plasma


title: liver, 7d old mice, TRAF2/Casp-8LPC-KO null, replicate 4

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

country: Netherlands

institute: Wageningen University

hyb_protocol: Hybridization and washing of the Affymetrix GeneChip Mouse Gene 1.1 ST peg arrays were performed on a GeneTitan Instrument according to the manufacturer's recommendations.

scan_protocol: Arrays were scanned on an Affymetrix GeneTitan instrument (Affymetrix, Santa Clara, CA).

data_processing: Expression estimates were calculated applying the RMA algorithm in the Bioconductor library 'Oligo' (v1.34.2).

source_name: whole liver, 7 days old, TRAF2/Casp-8LPC-KO

label_protocol: One hundred nanogram of RNA was used for whole transcript cDNA synthesis with the Ambion WT Expression Kit [catalog number 4411974] (Applied Biosystems/Life Technologies, Nieuwekerk a/d IJssel, The Netherlands).

growth_protocol: Mice carrying LoxP-site-flanked alleles of Traf2 (Grech et al., 2004) were crossed to alfp-Cre transgenic mice (Kellendonk et al., 2000) to generate LPC-specific knockout mice (TRAF2LPC-KO). Mice with combined conditional deletions of Traf2 and Caspase-8 (Salmena et al., 2003) (TRAF2/Casp-8LPC-KO) or additional conditional deletion of Mlkl (Murphy et al., 2013), Nemo (Beraza et al., 2009) or Ikkβ (Greten et al., 2007), or rather constitutive deletion of Ripk3 (Newton et al., 2004) were generated by intercrossing the respective lines to TRAF2/Casp-8LPC-KO mice. In all experiments, littermates carrying the respective loxP-flanked alleles but lacking expression of Cre recombinase were used as wild-type (WT) controls. Mice were bred on a mixed C57/BL6 - SV129Ola genetic background. Only sex- and age-matched animals were compared.

extract_protocol: Total RNA was prepared from the liver tissue samples using TRIzol reagent, whereafter purified total RNA was isolated using Qiagen RNeasy columns. RNA integrity was checked on chip analysis (Agilent 2100 Bioanalyzer, Agilent Technologies, Amsterdam, The Netherlands) according to the manufacturer's instructions. RNA was judged as suitable for array hybridization only if samples exhibited intact bands corresponding to the 18S and 28S ribosomal RNA subunits, and displayed no chromosomal peaks or RNA degradation products (RNA Integrity Number > 8.0).

treatment_protocol: Mice had free access to standard laboratory chow and water. Mice were used at the age of 7 days, at which they were killed and livers were removed.

tag: strain/background

value: C57/BL6 - SV129Ola mix

tag: genotype/variation

tag: Sex

value: male

tag: age (days)

value: liver

tag: mouse id


title: Ab Infected Red Clover 1

description: Library name: C1

tag: tissue


title: liver, 7d old mice, TRAF2/Casp-8/IKKβLPC -/- null, replicate 4

source_name: whole liver, 7 days old, TRAF2/Casp-8/IKKbetaLPC-KO


title: UPN827 cells, TN1480 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1480 TrailNet 3or6 month T1D plasma

tag: responder cells

tag: sample timepoint


title: Ab Infected 7

description: Library name: B7

tag: treatment


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_6h_D4_input

description: Library name: Sample 44

extract_protocol:
ChIP-Seq: Cells were cross-linked with 1.5% formaldehyde for 10 min and quenched by 125 mM glycine for 10 min. 10 million fixed cells were resuspended in ice cold buffer containing 5mM PIPES, pH 7.5, 85mM KCl, 1% NP-40 and protease inhibitors, incubated on ice for 15 min, and centrifuged at 500 g for 5 min at 4°C. Nuclei were resuspended with 1mL buffer containing 50mM Tris-HCl, pH8.0, 10mM EDTA, 0.1% SDS and protease inhibitors, and subjected to sonication. Sheared chromatin was clarified by centrifugation at 13,000 g for 10 min at 4°C. The supernatant was transferred to a new tube and further supplemented with 1% Triton-X100, 0.1% sodium deoxycholate and protease inhibitors. 2% of the mixture was set aside as input and 20ng of spike-in chromatin (Active Motif, #53083) was added to the rest. For each ChIP, 4 - 10 µg of target antibodies and 2μg of spike-in antibody (anti-H2Av, Active Motif, #61686) were added and incubated on a rotator at 4°C overnight. ChIP samples were added with 50μL prewashed protein A Dynabeads (ThermoFisher) and incubated for 3h at 4°C. Beads were then collected on a magnetic rack and washed twice with 1mL cold RIPA buffer, twice with 1mL cold RIPA buffer containing 300mM NaCl, twice with 1mL cold LiCl buffer and once with PBS. Beads were then eluted with 100 μL buffer containing 0.1M NaHCO3, 1% SDS, and 20μg Proteinase K at 65°C overnight. Input sample volumes were adjusted to 100μL with the elution buffer. Samples were then purified using QIAquick PCR purification kit (Qiagen) and eluted in 30 μL 10mM Tris-HCl.
ChIP-Seq: Libraries were prepared according to NEB (Illumina kit) instructions. DNA were used to construct libraries using NEBNext® Ultra™ II DNA Library Prep kit with AMPure XP magnetic beads (Beckman Coulter).
RNA-Seq: Total RNA was subjected to mRNA purification using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490).
RNA-Seq: Isolated mRNAs were reverse-transcribed into double stranded cDNA and subjected to sequencing library construction using the NEBNext Ultra™ II RNA Library Prep Kit for Illumina (NEB, E7770) according to the manufacturer’s instructions.

tag: cell line

tag: cell type

value: Differentiating preadipocytes

value: HIRA depleted

value: adipogenic differentiation

value: day 4


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_6h_D4_input

description: Library name: Sample 43

tag: genotype

value: wild type


title: UPN827 cells, TN1477 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1477 TrailNet 3or6 month T1D plasma

value: UPN827 cells


title: liver, 7d old mice, TRAF2/Casp-8LPC-KO null, replicate 3


title: liver, 7d old mice, TRAF2/Casp-8/IKKβLPC -/- null, replicate 3


title: Ab Infected 6

description: Library name: B6


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_6h_D4_SPT6

description: Library name: Sample 42

value: Anti-SPT6(D6J9H) (15616, Cell Signaling Technology)


title: UPN827 cells, TN1474 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1474 TrailNet 3or6 month T1D plasma

value: TrailNet 3 or 6 month


title: Ab Infected 5

description: Library name: B5

value: Infected


title: liver, 7d old mice, TRAF2/Casp-8LPC-KO null, replicate 2


title: UPN827 cells, TN1467RH TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1467RH TrailNet 3or6 month T1D plasma


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_6h_D4_SPT6

description: Library name: Sample 41


title: liver, 7d old mice, TRAF2/Casp-8/IKKβLPC -/- null, replicate 2


title: UPN827 cells, TN1466 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1466 TrailNet 3or6 month T1D plasma


title: Ab Infected 4

description: Library name: B4


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_6h_D4_CDK9

description: Library name: Sample 40

value: Anti-CDK9(C12F7) (2316T, Cell Signaling Technology)


title: liver, 7d old mice, TRAF2/Casp-8LPC-KO null, replicate 1


title: UPN827 cells, TN1460RH TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1460RH TrailNet 3or6 month T1D plasma


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_6h_D4_CDK9

description: Library name: Sample 39


title: Ab Infected 3

description: Library name: B3

source_name: Abomasum


title: Ab Infected 2

description: Library name: B2


title: UPN827 cells, TN1456 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1456 TrailNet 3or6 month T1D plasma


title: liver, 7d old mice, TRAF2/Casp-8/IKKβLPC -/- null, replicate 1


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_6h_D4_Pol2ser2

description: Library name: Sample 38

value: Anti-Phospho-Rpb1 CTD (Ser2) (E1Z3G) (13499S, Cell Signaling Technology)


title: Ab Infected 1

description: Library name: B1

value: Abomasum


title: liver, 7d old mice, TRAF2/Casp-8LPC-KO/RIPK3-/- null, replicate 4

source_name: whole liver, 7 days old, TRAF2/Casp-8LPC-KO/RIPK3-/-


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_6h_D4_Pol2ser2

description: Library name: Sample 37


title: UPN827 cells, TN1455 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1455 TrailNet 3or6 month T1D plasma


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_6h_D4_Pol2ser5

description: Library name: Sample 36

value: Anti-Phospho-Rpb1 CTD (Ser5) (D9N5I) (13523, Cell Signaling Technology)


title: UPN827 cells, TN1453 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1453 TrailNet 3or6 month T1D plasma


title: liver, 7d old mice, wild-type, replicate 4

source_name: whole liver, 7 days old, WT

value: WT


title: Ab Control 6

description: Library name: A6

value: Control


title: Ab Control 5

description: Library name: A5


title: liver, 7d old mice, TRAF2/Casp-8LPC-KO/RIPK3-/- null, replicate 3

value: C57/BL6 - SV129Ola mix

value: male


title: UPN827 cells, TN1450 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1450 TrailNet 3or6 month T1D plasma


title: Ab Control 4

description: Library name: A4


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_6h_D4_Pol2ser5

description: Library name: Sample 35

value: Differentiating preadipocytes


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_6h_D4_H3K27ac

description: Library name: Sample 34

value: HIRA depleted

value: Anti-H3K27ac (ab4729, Abcam)


title: UPN827 cells, TN1447 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1447 TrailNet 3or6 month T1D plasma


title: liver, 7d old mice, wild-type, replicate 3

value: liver


title: UPN827 cells, TN1444 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1444 TrailNet 3or6 month T1D plasma


title: liver, 7d old mice, TRAF2/Casp-8LPC-KO/RIPK3-/- null, replicate 2


title: Ab Control 3

description: Library name: A3


title: Ab Control 2

description: Library name: A2


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_6h_D4_H3K27ac

description: Library name: Sample 33

value: wild type

value: adipogenic differentiation

value: day 4


title: UPN827 cells, TN1441 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1441 TrailNet 3or6 month T1D plasma

value: UPN827 cells

value: TrailNet 3 or 6 month


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_dTAG13_6h_D4_HA

description: Library name: Sample 32

value: Anti-HA (13-2010, Epicypher)


title: liver, 7d old mice, wild-type, replicate 2


title: liver, 7d old mice, TRAF2/Casp-8LPC-KO/RIPK3-/- null, replicate 1


title: Ab Control 1

description: Library name: A1


title: UPN827 cells, TN1438 TrailNet 3or6 month T1D plasma

source_name: UPN827 cells stimulated with TN1438 TrailNet 3or6 month T1D plasma


title: 3T3-L1_hHIRA-dTAG-HA_HiraKO_DMSO_6h_D4_HA

description: Library name: Sample 31


title: Cebpa-KO-Tfr-2

status: Public on May 31 2026

city: Pohang

first: Haena

last: Lee

state: Kyungbuk

address: POSTECH Biotech Center, 77 Cheongam-ro

department: Department of Life Sciences

institute: Pohang University of Science and Technology

description: Library name: Sample 5

data_processing:
The raw reads from the sequencer to remove low quality and adapter sequence before analysis and aligned the processed reads to genomic DNA references [UCSC mm39 (mus musculus)] using STAR-2.7.11b
Transcript assembly of known transcripts was processed by StringTie v2.1.3b
Expression abundance of transcript and gene were calculated as read count or FPKM value (Fragments Per Kilobase of exon per Million fragments mapped) per sample.
Genes with one more than zeroed read count values in the samples were excluded. Filtered data were log2-transformed and subjected to quantile Normalization
Independent t-test with raw p-value was used for statistical processing
Assembly: mouse UCSC mm39
Supplementary files format and content: tab-delimited text files with TPM and FPKM values for every gene and every sample

source_name: Spleen

extract_protocol:
Total RNA was extracted through an Rneasy Micro Kit (Qiagen) and subjected to RNA-seq.
RNA libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA for Sequencing Nextera XT DNA Library Preparation Kit following manufacturer's protocols. (SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing User Manual, Nextera XT DNA Library Prep Kit Reference Guide)

value: Spleen

tag: cell source

value: Ex Vivo Sorted spleen cells

value: Tfr cells

value: Treg-specific Cebpa knock-out (KO)

value: Imiquimod treatment

value: 21 days


title: UPN827 cells, TN1437 TrailNet 3or6 month T1D plasma

city: Milwaukee

first: Martin

last: Hessner

institute: Medical College of Wisconsin

source_name: UPN827 cells stimulated with TN1437 TrailNet 3or6 month T1D plasma


title: Lola KD adult midgut, microbial challenge pool-2, dslola-mch-datab-r2

city: Mexico

first: Veronica

last: Valverde-Garduño

state: Morelos

address: Av Universidad

department: Centro de Investigaciones en Enfermedades Infecciosas

country: Mexico

institute: Instituto Nacional de Salud Pública

description:
Library name: dslola-chall-datab-r2
Column name in all.dslola.counts.txt: dslola.dslolareto2

data_processing:
The fastq were subjected to quality check by FastQC
The raw reads were performed using Trimmomatic v0.39
The trimmed reads paired were subjected to mapping using STAR v.2.7.5 mapper
Read count were performed using FeatureCounts
The analysis between sample groups was performed by DEseq2 package
Assembly: Anopheles albimanus STECLA reference genome AalbS3
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

organism: Anopheles albimanus

source_name: midgut

growth_protocol: Mosquitoes treated with lola dsRNA and GFP dsRNA were collected 24 h post-injection

extract_protocol:
Total RNA was extracted using TRIzol® reagent
Libraries were pooled and sequenced on the Illumina NextSeq 500.

treatment_protocol: 25 midguts were pooled for each sample

value: midgut

tag: strain

value: Tapachula

value: Lola knockdown

value: microbial challenge


title: Cebpa-KO-Tfr-1

description: Library name: Sample 4

tag: time


title: liver, 7d old mice, wild-type, replicate 1

value: C57/BL6 - SV129Ola mix

value: WT

value: male

value: liver


title: Lola KD adult midgut, microbial challenge pool-1, dslola-mch-datab-r1

description:
Library name: dslola-chall-datab-r1
Column name in all.dslola.counts.txt: dslola.dslolareto1


title: WT-Tfr-3

description: Library name: Sample 3

value: Wild-type (WT)


title: OSS3

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

hyb_protocol: The labeled cRNAs were hybridized onto the Arraystar Human lncRNA Arrays (4x44K, Arraystar), and incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: After washing, slides were scanned with the Agilent Scanner G2505C.

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed using the R software limma package. Differentially expressed circRNAs with statistical significance between two groups were identified through Volcano Plot filtering. Differentially expressed circRNAs between two samples were identified through Fold Change filtering. Hierarchical Clustering was performed to show the distinguishable circRNAs expression pattern among samples.

source_name: hVECs-EVs

label_protocol: Total RNA from each sample was amplified and transcribed into fluorescent cRNA utilizing ramdom primer according to Arraystar Super RNA Labeling protocol (Arraystar, Inc.)

growth_protocol: Human valvular endothelial cells (hVECs) and human valvular interstitial cells (hVICs) were co-cultured using a parallel-plate flow system (Ibidi pump system 10902, Ibidi, Munich, Germany). A 0.5 µm pore-size ibiPore SiN membrane (85216-S, Falcon cell culture inserts, Becton Dickinson; 1.6 × 10⁶ pores/cm²) was used to separate the two cell types. hVECs were first seeded on the underside of the membrane and allowed to adhere for 6 hours. The membrane was then inverted and placed into a 6-well plate containing endothelial growth medium-2 (EGM-2, CC-3202, Lonza) supplemented with 2% fetal bovine serum, 100 μg/mL streptomycin, and 100 U/mL penicillin. hVICs were then seeded onto the upper surface of the insert. After firm attachment of both cell types, the inserts were transferred into the parallel-plate flow chamber equipped with a polycarbonate holder.

treatment_protocol: To investigate which components in human valvular endothelial cell-derived extracellular vesicles (hVECs-EVs) orchestrate human valvular interstitial cells （hVICs）osteogenic reprogramming, we isolated EVs from hVECs exposed to bi-directional OSS (± 5 dyne/cm² at 1Hz) and laminar shear stress (LSS, 5 dyne/cm²), respectively. We then conducted a two-stage case-control study to investigate circRNAs in hVECs-EVs. The circRNA profiles of these EVs were examined using the Arraystar Human Circular RNA Microarray. extracellular vesicles (EVs) isolated from OSS (hVECsOSS-EVs) and LSS (hVECsLSS-EVs)

value: hVECs

tag: group

value: OSS


title: WT-Tfr-2

description: Library name: Sample 2

value: Spleen


title: WT-Tfr-1

description: Library name: Sample 1

value: Ex Vivo Sorted spleen cells


title: dLN monocytes, 6 hours post dose 2, mouse ID MOD845

status: Public on May 26 2026

city: Lausanne

first: Gustavo

middle: Agustín

last: Ruiz Buendía

state: Vaud

address: Amphipôle, Quartier UNIL-Sorge

country: Switzerland

institute: Swiss Institute of Bioinformatics

description: Library name: LN_dose2_MOD845

data_processing:
nfcore rnaseq pipeline (release 3.12.0) using the mouse genome (GRCm38.p6) from ensembl.
Pseudoalignment and quantification was performed with Salmon (1.10.3). Gene-level quantification was obtained with the tximport R package (1.20.1).
Assembly: GRCm38.p6
Supplementary files format and content: Tab-delimited text file includes raw gene-level counts for each sample.

source_name: dLN

growth_protocol: Draining lymph node and blood samples were collected from mice, 6 hours after 1 dose or 2 doses of COVID-19 mRNA vaccine. Monocytes were sorted by FACS and stored in RLT buffer at -80ºC.

extract_protocol:
RNA was extracted using RNeasy midi kit (Qiagen) according to the manufacturer's instructions. RNA concentration and quality were assessed using a 2100 Bioanalyzer (Agilent).
RNA libraries for RNA-seq were prepared using the SMARTer Ultra Low + Nextera XT kit from Illumina according to the manufacturer's instructions. 100 ng of total RNA were used for the construction of RNA-seq libraries. Library molarity and quality were assessed with a Qubit and Tapestation using a DNA high sensitivity chip (Agilent Technologies). Libraries were pooled at a 1.1 nM concentration and sequenced with an Illumina NovaSeq 6000 sequencer for a minimum of 30 million single-end 100 bp reads per sample.

treatment_protocol: C57BL/6J mice were vaccinated intramuscularly with 1 dose or 2 doses (21 days apart) of 1 µg of a COVID-19 mRNA vaccine.

value: dLN

value: Monocytes

value: Dose 2


title: dLN monocytes, 6 hours post dose 2, mouse ID MOD842

description: Library name: LN_dose2_MOD842


title: dLN monocytes, 6 hours post dose 2, mouse ID MOD841

description: Library name: LN_dose2_MOD841


title: dLN monocytes, 6 hours post dose 1, mouse ID MOD843

description: Library name: LN_dose1_MOD843

value: Dose 1


title: dLN monocytes, 6 hours post dose 1, mouse ID MOD839

description: Library name: LN_dose1_MOD839


title: dLN monocytes, 6 hours post dose 1, mouse ID MOD840

description: Library name: LN_dose1_MOD840


title: dLN monocytes, 6 hours post dose 2, mouse ID MOD846

description: Library name: LN_dose2_MOD846


title: dLN monocytes, 6 hours post dose 1, mouse ID MOD844

description: Library name: LN_dose1_MOD844


title: Blood monocytes, 6 hours post dose 2, mouse ID MOD846

description: Library name: blood_dose2_MOD846

source_name: Blood

value: Blood


title: Blood monocytes, 6 hours post dose 2, mouse ID MOD845

description: Library name: blood_dose2_MOD845


title: Blood monocytes, 6 hours post dose 2, mouse ID MOD842

description: Library name: blood_dose2_MOD842


title: Blood monocytes, 6 hours post dose 2, mouse ID MOD841

description: Library name: blood_dose2_MOD841


title: Blood monocytes, 6 hours post dose 1, mouse ID MOD843

description: Library name: blood_dose1_MOD843


title: Blood monocytes, 6 hours post dose 1, mouse ID MOD844

description: Library name: blood_dose1_MOD844


title: Blood monocytes, 6 hours post dose 1, mouse ID MOD840

description: Library name: blood_dose1_MOD840


title: Blood monocytes, 6 hours post dose 1, mouse ID MOD839

description: Library name: blood_dose1_MOD839


title: Control 3

status: Public on May 22 2026

city: Harbin

first: Mingming

last: Wu

state: Heilongjiang

address: 23 Youzheng St

department: Departments of Cardiology

institute: The First Affiliated Hospital of Harbin Medical University

description: Library name: Sample 7

data_processing:
Raw data were processed using Cell Ranger software v5.0.0 (10x Genomics) for alignment to the human reference genome (GRCh38/hg38) and transcript quantification.
Assembly: Homo sapiens (GRCh38/hg38)
Supplementary files format and content: Filtered gene-barcode expression matrices in HDF5 (.h5) formats.

source_name: PBMC

extract_protocol:
Venous blood (2 mL) was collected in EDTA anticoagulant tubes and processed within 4 h. Peripheral blood mononuclear cells (PBMCs) were isolated by density gradient centrifugation using Ficoll-Paque medium. Cell viability exceeded 85%, determined by trypan blue staining. Approximately 15,000 cells per sample were prepared for downstream capture.
Libraries were constructed using the Chromium Single Cell V(D)J 5' Reagent V2 Kit (10x Genomics). For each sample, 15,000 cells were loaded for gel bead-in-emulsion (GEM) generation. Released RNA was barcoded through reverse transcription. cDNA was amplified and library quality was assessed via Agilent 2100 Bioanalyzer. Paired-end sequencing (2 × 150 bp) was performed on an Illumina NovaSeq platform (Novogene).

treatment_protocol: The cohort comprised patients with anti-PD-1 antibody therapy-associated cardiac injury (diagnosed as “possible myocarditis”; n = 4), and control patients without signs of cardiac injury after anti-PD-1 antibody therapies (n = 3).

value: PBMC

tag: subject status

tag: antibody

value: anti-PD-1 antibody


title: Control 2

description: Library name: Sample 6

value: control patients without signs of cardiac injury


title: Control 1

description: Library name: Sample 5


title: myocarditis 4

description: Library name: Sample 4

value: patients with therapy-associated cardiac injury


title: Ocy454 cells, FACS-sorted CD61 high, Rep 3

city: Boston

first: Courtney

last: Mazur

state: MA

address: 50 Blossom Street

department: Endocrine Unit

institute: Massachusetts General Hospital

description: Library name: CD61 High 3

data_processing:
For differentiation samples, STAR aligner was used to map sequencing reads to transcripts in reference genome. Read counts for individual transcripts were produced with HTSeq-count.
For FACS-sorted samples, transcript abundances were calculated using Salmon
Assembly: GRCm39
Supplementary files format and content: Tab-delimited file contains counts per million for all 8 differentiation samples.
Supplementary files format and content: Tab-delimited files contain Salmon-calculated transcript abundances for each FACS sample

growth_protocol: Ocy454 cells were grown on standard tissue culture plastic in MEM alpha supplemented with 10% FBS and 1% antibiotic/antimycotic. Cells are cultured at 33C until confluent, then cultured at 37C to induce differentiation.

extract_protocol:
Differentiated cells were lysed in RLT buffer. Lysates were passed through QIAshredder columns, then total RNA was isolated using the PureLink RNA Mini Kit with on-column DNase. FACS-sorted cells were pelleted and lysed in RLT buffer. Lysates were passed through QIAshredder columns, then total RNA was isolated using the Arcturus PicoPure RNA isolation kit with on-column DNase treatment.
mRNA molecules were purified from total RNA using oligo(dT)-magnetic beads. After fragmentation and reverse transcription, adapters were ligated and products amplified by PCR. The double stranded PCR products were heat denatured and circularized by the splint oligo sequence. The ssCir DNA was formatted as the final library.

treatment_protocol: Differentiation samples were collected after the indicated days at 37C. CD61-sorted samples were prepared for flow cytometry after 17 days of differentiation by labeling with CD61-PE antibody and DAPI. The top 10% and bottom 10% of live cells were collected based on CD61-PE fluorescence intensity. Sorted cells were collected into PBS with 2% FBS and RNase inhibitor.


title: myocarditis 3

description: Library name: Sample 3


title: myocarditis 2

description: Library name: Sample 2


title: myocarditis 1

description: Library name: Sample 1


title: aly mutant, biological replicate3

status: Public on May 20 2026

city: Cambridge

first: Yukiko

last: Yamashita

address: 455 main ST

institute: Whitehead Institute for Biomedical Research

description: Library name: aly mutant, biological replicate3

data_processing:
Paired-end reads (250 x 250 bp) were align using STAR aligner (v. 2.7.1a)
trimmed using fastp default option
gene count was generate using featureCounts
Assembly: Dmel Release 6.38
Supplementary files format and content: FeatureCount output

organism: Drosophila melanogaster

source_name: testis

extract_protocol:
Total RNA was extracted from dissected testes by Trizol extraction.
Libraries were prepared using the KAPA Biosystems RNA HyperPrep Kit with RiboErase. 500 ng of total RNA was used for library construction.

value: testis


title: aly mutant, biological replicate2

description: Library name: aly mutant, biological replicate2


title: aly mutant, biological replicate1

description: Library name: aly mutant, biological replicate1


title: sa mutant, biological replicate2

description: Library name: sa mutant, biological replicate2


title: sa mutant, biological replicate3

description: Library name: sa mutant, biological replicate3


title: sa mutant, biological replicate1

description: Library name: sa mutant, biological replicate1


title: AX

status: Public on May 18 2026

city: London

first: Probir

last: Chakravarty

address: 1Midland Road

institute: Francis Crick

description:
Library name: RIZA2
10X Genomics

data_processing:
All subsequent analyses were performed in R v.4.1.0 using the Seurat (v4) package.  Genes were considered to be ‘expressed’ if the estimated (log10) count was at least 0.1. Primary filtering was then performed by removing from consideration: cells expressing fewer than 50 genes and cells for which mitochondrial genes made up greater than 10% of all expressed genes.
Assembly: mm10
Supplementary files format and content: tab delimited text containing raw counts obtained from CellRanger version 6.0.1

source_name: Pituitary

extract_protocol:
Chromium Controller and Chromium10x 3 prime v2.0, Chromium Single Cell 30 Reagent Kits UserGuide (v3 Chemistry)
Chromium Next GEM Single Cell

treatment_protocol: Adrenalectomised/Sham operated animals

value: Pituitary

value: Stem cell

value: AX


title: ShamAX

description:
Library name: RIZA1
10X Genomics

value: Sham


title: NEC, P5, technical replicate 2

status: Public on May 05 2026

city: Berlin

first: Michael

last: Sigal

address: Augustenburger Platz 1

department: Dept. Hepatology and Gastroenterology

country: Germany

institute: Charité Universitätsmedizin

description: Library name: SP084_028

data_processing:
Single-nucleus RNA reads were aligned to the GRCh38-2020-A reference using CellRanger v6.0.1 [PMID: Zheng 28091601], incorporating both exonic and intronic (nuclear pre-mRNA) reads.  Sample P5 was processed as two technical replicates, which were subsequently merged during analysis. The background reads were removed using the R package SoupX [PMID: Young 33367645], with parameters set to tfidfMin = 0.6, soupQuantile = 0.9, and priorRho = 0.1. After background subtraction, expression values were rounded to integers. Cells were filtered based on criteria including fewer than 300 or more than 4000 RNA features, over 5% mitochondrial read content, or genes with fewer than two reads across all samples. Mitochondrial and ribosomal genes were excluded from further analysis to minimize technical noise.
Assembly: Homo sapiens, GRCh38
Supplementary files format and content: Tab separated values files and matrix files

source_name: Tumor tissue

extract_protocol:
Tumor tissue preserved by cryopreservation was disrupted in NP-40 lysis buffer (10 mM Tris-HCl at pH 7.4, 10 mM NaCl, 3 mM MgCl₂, 0.01% NP-40, 1 mM DTT, 2% BSA, 1 U/µl RNAse inhibitor, and Complete EDTA-free protease inhibitor) in a 1.5 ml Eppendorf tube using a plastic pestle. After a 5-minute incubation on ice, the suspension was filtered through a 70 µm pre-separation strainer, then centrifuged at 4°C and resuspended in nuclei wash buffer (PBS, 1% BSA, and 0.4 U/µl RNAse inhibitor). DAPI (3.5 µl) was added, and the mixture was passed through a 40 µm Flowmi cell strainer prior to sorting on a BD Aria Fusion instrument into an Eppendorf tube containing 200 µl of sort buffer (PBS, 2% BSA, 1 U/µl RNAse inhibitor) using a 100 µm nozzle.
Single-nuclei libraries were generated according to the protocol outlined in the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) user guide (CG0003154) from 10x Genomics. In brief, individual nuclei were encapsulated with gel beads containing barcoded primers in the Chromium controller. Within each droplet, mRNA was reverse-transcribed into barcoded cDNA, which was then amplified. The amplified cDNA was subjected to fragmentation, end-repair, A-tailing, adaptor ligation, and sample index PCR.

value: Tumor tissue


title: NEC, P4

description: Library name: SP084_021


title: NEC, P3

description: Library name: SP084_019


title: NEC, P2

description: Library name: SP084_018


title: NEC, P1

description: Library name: SP084_007


title: T212_B_BAL_TB

status: Public on May 01 2026

description: Library name: T212_B

data_processing:
nf-core/rnaseq pipeline v3.16.1; default parameters
Assembly: GRCh38, Homo sapiens
Supplementary files format and content: csv of DESeq2 normalised expression values

source_name: Bronchoalveolar lavage

extract_protocol:
Cell suspensions containing 0.5 x 106 live cells were pelleted by centrifuging at 400 x G for 5 minutes at 4oC and pellets suspended in TRI reagent (Sigma-Aldrich). Samples were vortexed at high speed for around 20 seconds before storage at -80oC until RNA extraction. RNA extraction was performed using the DirectZol RNA Microprep kit (Zymo Technologies), as per manufacturer’s instructions, including on-column DNase I digestion.
Extracted RNA from whole BAL cell pellets was subjected to Agilent TapeStation quality control analysis and RNA integrity (RIN) values determine to be ≥7.4 and ≤9.9, except for one sample (T219_1, from active TB patient #219), which had a RIN value of 4.1. 200 ng of total RNA was used for library preparation using the RNA library prep kit with Polaris ribosomal RNA depletion (Watchmaker Genomics). Approximately 2.5 x107 100 base pair paired end reads were obtained per sample using an Illumina NovaSeq X sequencer.

value: Bronchoalveolar lavage

tag: sample status

value: TB


title: T219_B_BAL_TB

description: Library name: T219_B


title: T218_B_BAL_TB

description: Library name: T218_B


title: T202_B_BAL_TB

description: Library name: T202_B


title: T196_B_BAL_TB

description: Library name: T196_B


title: NEC, P5, technical replicate 1

description: Library name: SP084_027


title: T185_B_BAL_TB

description: Library name: T185_B


title: T173_B_BAL_TB

description: Library name: T173_B


title: T166_B_BAL_TB

description: Library name: T166_B


title: T158_B_BAL_TB

description: Library name: T158_B


title: T156_B_BAL_TB

description: Library name: T156_B


title: T147_B_BAL_TB

description: Library name: T147_B


title: T132_B_BAL_TB

description: Library name: T132_B


title: T146_B_BAL_TB

description: Library name: T146_B


title: T137_B_BAL_TB

description: Library name: T137_B


title: T127_B_BAL_TB

description: Library name: T127_B


title: T123_B_BAL_TB

description: Library name: T123_B


title: T117_B_BAL_TB

description: Library name: T117_B


title: T111_B_BAL_TB

description: Library name: T111_B


title: T105_B_BAL_TB

description: Library name: T105_B


title: T095_B_BAL_TB

description: Library name: T095_B


title: T096_B_BAL_TB

description: Library name: T096_B


title: T094_B_BAL_TB

description: Library name: T094_B