title: human valvular interstitial cells from patient 3, PDK4-siRNA

city: Nanjing

first: Song

last: Wang

state: Jiangsu province

address: Guangzhou Road

institute: The First Affiliated Hospital of Nanjing Medical University

description: Library name: P3

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
Assembly: GRCh38
Supplementary files format and content: Excel file includes FPKM values for each Sample

source_name: aortic valves

growth_protocol: VICs were isolated from human aortic valve specimens collected during cardiac surgery. Valve leaflets were washed three times with 3 mL of ice-cold PBS containing 200 μL penicillin–streptomycin solution (100 U/mL penicillin, 100 μg/mL streptomycin) in 6-well plates. Tissues were enzymatically digested with 2 mg/mL collagenase type I at 37 °C for 12 hours in a humidified incubator. After digestion, the suspension was centrifuged at 1000 rpm for 5 minutes, and the resulting pellet was resuspended in DMEM supplemented with 10% FBS and 1% penicillin–streptomycin. Cells were maintained at 37 °C in a 5% CO₂ atmosphere.

extract_protocol:
Total RNA was isolated and purified using TRIzol reagent (Invitrogen, Carlsbad, CA, USA) following the manufacturer's procedure. The RNA amount and purity of each sample was quantified using NanoDrop ND-1000 (NanoDrop, Wilmington, DE, USA). The RNA integrity was assessed by Bioanalyzer 2100 (Agilent, CA, USA) with RIN number >7.0, and confirmed by electrophoresis with denaturing agarose gel
Poly (A) RNA is purified from 1μg total RNA using Dynabeads Oligo (dT)25-61005 (Thermo Fisher, CA, USA) using two rounds of purification. Then the poly(A) RNA was fragmented into small pieces using Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min. Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA）. An A-base is then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contains a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Single- or dual-index adapters are ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products are amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

treatment_protocol: VICs were transfected with small interfering RNAs (siRNAs) in osteogenic medium for 48 hours.

value: aortic valves

value: primary human valvular interstitial cells

value: interstitial cells

value: PDK4 knockdown


title: human valvular interstitial cells from patient 5, PDK4-siRNA

status: Public on May 01 2026

type: SRA

country: China

description: Library name: P5

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: H3K27ME3 KO ESC 2 (Chip)

city: Rome

first: Guido

last: Leoni

address: Via Pontina

department: Bioinformatics

country: Italy

institute: IRBM

description: Library name: KO ESC 2 (Chip)

library_source: genomic

data_processing:
Supplementary files format and content: bigWig,Broad
basecall were  performed by using bcl2fastq for Novaseq input
bigWig were generated by using the genomicRanges R package
Assembly: mm10

molecule: genomic DNA

organism: Mus musculus

source_name: ESC

extract_protocol:
The cells were crosslinked with 1% formaldehyde for 10' at room temperature and next quenched by addition of glycine (125 mM). The samples were sonicated with Bioruptor Plus (Diagenode).
libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) and NEBNext Multiplex Oligos for Illumina (NEB)

value: ESC

value: Embrionic Stem cells

value: LIN28A KO


title: Irx3KO_Irx4KO4_RNASeq

city: Ottawa

first: Kyoung-Han

last: Kim

state: Ontario

address: 40 Ruskin Street

country: Canada

institute: University of Ottawa Heart Institute

data_processing:
fastq reads were aligned to the mm9 transcriptome using kallisto 0.42.2 with default parameters
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited files containing transcript ID, transcript length, effective length, estimated counts, and abundance in TPM were generated using kallisto 0.42.2

molecule: polyA RNA

source_name: E14.5 heart

extract_protocol:
E14.5 ventricles were dissected and frozen at -80°C prior to RNA extraction with PureLink RNA Mini kit (Life Technologies). The integrity of the samples was checked on Agilent Bioanalyzer, and the samples with a RIN>8.5 were used. 1 to 2µg of RNA were used to prepare the PolyA RNA library.
Libraries were prepared according to manfacturer's instructions for the NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® kit.

tag: developmental stage

value: heart (ventricles)


title: human valvular interstitial cells from patient 6, PDK4-siRNA

description: Library name: P6


title: human valvular interstitial cells from patient 4, PDK4-siRNA

description: Library name: P4


title: human valvular interstitial cells from patient 2, PDK4-siRNA

description: Library name: P2


title: Col-0_WT_Cold 3hr_Rep1

city: Seoul

first: Nassem

last: AlBakri

address: Gwangjin-gu

department: Biomedical Science and Engineering

country: South Korea

institute: Konkuk University

description: High Output 75bp

data_processing:
Raw read QC using FASTQC tool followed by adapter trimming by Trim Galore
Trimmed reads were aligned using Burrows-Wheeler Aligner (BWA) and duplicated reads identied by suing Picard mark duplicate and merged alignments from multiple libraries of the same sample using Picard and re-marked duplicates.
Unmapped, chloropast, mitochondrial reads with >4 mismatches were filtered using SAMTools and BAMTools.
Normalized bigwig files were generated using BEDTools and bedGraphToBigWig and visualized using IGV. Genebody profile, heatmaps and genome-wide enrichment were generated using deeptools
Peak were called using MACS2 and annotated relative to gene feature using HOMER. Consensus peak peak sets isolated and filtered using BEDTools. Differential amentccessibility, PCA analysis and clustering were performed using DESeq2.
Assembly: TAIR10
Supplementary files format and content: BigWig, BroadPeak

organism: Arabidopsis thaliana

source_name: Seedling

growth_protocol: Arabidopsis (Col-0) Wild type plants were used in this study. All plants were grown in MS media contain 1% Sucrose under the condition (16 hr light/8hr dark, 20°C)

extract_protocol:
Open chromatin DNA was labeld with labeling solution for 2hr and labeled genomic DNA was isolated using Dneasy Plant Pro Kit (QIAGEN) and 200 ng of labeled genomic DNA were fragmentated by Covaris, 150bp
Pull-dwoned DNAs by adding Streptavidin Bead with high salt buffer were used for the NGS DNA library preparation described in MiMB Book Chapter 3: Chromatin Accessibility: Methods and Protocols, Chin et al., 2023
NicE-seq library

treatment_protocol: 2-3 week-old seedings (8 buds) were incubated at 0℃ for 0hr, 3hr, 6hr, 12hr, 24hr in the dark condition to treat cold stress and the nuclei sample were isolated by the following protocol described in method section.

value: Seedling

value: Wild Type

value: Cold


title: dHet_4_RNASeq


title: H3K27ME3 KO ESC 1 (Chip)

description: Library name: KO ESC 1(Chip)


title: Col-0_WT_Cold 0hr_Rep3

description: High Output 75bp


title: Col-0_WT_Cold 0hr_Rep2

description: High Output 75bp


title: human valvular interstitial cells from patient 1, PDK4-siRNA

description: Library name: P1


title: Col-0_WT_Cold 0hr_Rep1

description: High Output 75bp


title: human valvular interstitial cells form patient 5, scramble-siRNA

description: Library name: N5

value: Control

value: Scramble-siRNA


title: human valvular interstitial cells form patient 6, scramble-siRNA

description: Library name: N6


title: human valvular interstitial cells form patient 3, scramble-siRNA

description: Library name: N3


title: pulmonary artery smooth muscle cells si-NC repeat 3

first: Ruifeng

last: Zhang

address: 87 Dingjiaqiao

institute: Zhongda Hospital of Southeast University

description: Library name: Sample 3

data_processing:
Reads filtering under criteria removing reads with 20% of the base quality lower than 13
HISAT2.1.0 mapping to reference genome
count counting
Assembly: mm10
Supplementary files format and content: TXT file contain counts for each sample

source_name: pulmonary artery smooth muscle cells

extract_protocol:
RNA was harvested using Trizol reagent. The RNA quality was checked by Agilent 2200 and kept at -80℃.The RNA with RIN >8.0 is right for cDNA library construction.
mRNA libraries were prepared for sequencing using standard Illumina protocols

value: pulmonary artery smooth muscle cells


title: human valvular interstitial cells form patient 2, scramble-siRNA

description: Library name: N2


title: QFM_snRNA_seq

city: Shanghai

first: Peipei

last: Jiang

state: Shanghai

address: No. 115 Jinzun Road, Pudong New Area, Shanghai

institute: Shanghai Jiao Tong University

description:
Library name: QFM_snRNA_seq
snRNA-seq

library_source: transcriptomic single cell

data_processing:
Raw sequencing data from both scRNA-seq and snRNA-seq were processed using Cell Ranger (v7.2.0, 10x Genomics). The gene expression matrices were imported into Seurat (v5.2.1) for downstream analysis. For quality control, data from scRNA-seq (EOM) were filtered based on: nFeature_RNA > 200 & < 5000, nCount_RNA < 20000, and percent.mt < 1; for snRNA-seq, the same nFeature_RNA and nCount_RNA filters were applied. Highly variable genes were identified, and principal component analysis (PCA) was performed. The first 25 PCs were selected for dimensionality reduction using UMAP. Cell clustering was carried out using the Louvain algorithm with a resolution of 0.3. Canonical correlation analysis (CCA) was performed to integrate datasets from EOM and QFM, followed by dimensionality reduction, clustering, and differential expression analysis. Cell-type annotation was conducted manually based on canonical markers from literature and the CellMarker2 database. In the scRNA-seq analysis of EOM, a low-quality cluster lacking canonical marker gene expression and exhibiting poor clustering behavior was removed. Differentially expressed genes (DEGs) were identified with a Wilcoxon rank-sum test using |log₂(fold change)| > 0.5 and adjusted P < 0.05.
Assembly: macaca fascicularis 6.0
Supplementary files format and content: matrix.mtx: Sparse matrix in Matrix Market (MTX) format (plain text), storing sgRNA counts per cell containing sgRNA, Cell barcode, sgRNA UMI or read count. features.tsv (or genes.tsv): Tab-delimited (TSV) without header, listing all sgRNAs. barcodes.tsv: Tab-delimited (TSV) without header, containing cell barcodes.

organism: Macaca fascicularis

source_name: quadriceps femoris muscle (QFM)

extract_protocol:
Total RNA was extracted from EOM and QFM tissues of macaca fascicularis, with RNA quality assessed using the RNA Nano 6000 Assay Kit and Agilent 2100 Bioanalyzer. For scRNA-seq, mRNA was isolated via poly-T oligo magnetic beads, fragmented, and first-strand cDNA synthesized. For snRNA-seq, nuclei were isolated, and RNA extraction followed similar procedures. cDNA preparations underwent end repair, adaptor ligation, and size selection (~370–420 bp) using AMPure XP beads, followed by PCR amplification. Libraries were assessed for quality using the Qubit 2.0 Fluorometer and Bioanalyzer 2100. Sequencing was performed on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.
Total RNA was extracted from EOM and QFM tissues of macaca fascicularis, with RNA quality assessed using the RNA Nano 6000 Assay Kit and Agilent 2100 Bioanalyzer. For scRNA-seq, mRNA was isolated via poly-T oligo magnetic beads, fragmented, and first-strand cDNA synthesized. For snRNA-seq, nuclei were isolated, and RNA extraction followed similar procedures. cDNA preparations underwent end repair, adaptor ligation, and size selection (~370–420 bp) using AMPure XP beads, followed by PCR amplification. Libraries were assessed for quality using the Qubit 2.0 Fluorometer and Bioanalyzer 2100. Sequencing was performed on the Illumina NovaSeq 6000 platform with 150 bp paired-end reads.

value: quadriceps femoris muscle (QFM)


title: Plasma, IBC patient 9

city: Austin

first: Alan

last: Lambowitz

state: TX

address: 2500 Speedway

country: USA

institute: University of Texas at Austin

description: Library name: Plasma9

data_processing:
Illumina TruSeq adapters and PCR primer sequences were trimmed from the reads with Cutadapt v2.8.
Reads were mapped sequentially as described in the publication using Hisat2 v2.1.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Plasma

extract_protocol:
Total cellular RNA was extracted from FFPE tumor slices and PBMCs using a miRVana miRNA isolation kit (ThermoFisher); Plasma RNAs were isolated using a miRNeasy Serum/Plasma Advanced kit (Qiagen).
Standard TGIRT-seq protocol as described in the publication.

value: Plasma


title: rMSC cultured on flat titanium disc for 1 day under growth medium

city: Cheonansi

first: Ji-Young

last: Yoon

state: Chungnam

address: Dandaero 119

department: Nanbiomedical science

institute: Dankook University

data_processing:
Basecalls were performed using bcl2fastq v2.20.0 for NovaSeq ouput.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to GRCh38 whole genome by using Bowtie2 v2.3.4.1 with parameter --maxins 5000 --very-sensitive --no-discordant --no-mixed --no-unal --mm
After removing reads aligned to the mitochondrial genome from the indexed BAM file, duplicate reads were removed using MarkDuplicates in Picard version 1.118.
Peak were called using MACS2 v2.1.1 with parameter -t ATAC-seq.bam -g hs --bdg --nolambda --keep-dup all --broad -q 0.05
ChIPseeker v1.20.0 was used to annotate the overlap or closest gene of the called peak.
Assembly: GRCh38
Supplementary files format and content: bedGraph

organism: Rattus norvegicus

source_name: rat Bone marrow-derived mesenchymal stem cells

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

extract_protocol:
Transposition reaction was performed using Illumina Tagment DNA TDE1 Enzyme and Buffer Kits, followed by DNA purification was proceeded using MinElute PCR purification Kit (Qiagen).
Amplify transposed DNA fragment. To reduce GC and size bias in PCR, the appropriate number of cycles is determined using qPCR. Run a qPCR side reaction.Calculate the additional number of cycles needed, plot liner Rn versus cycle and determine the cycle number that corresponds to 1/4 of maximum fluorescent intensity. Run the remaining PCR reaction to the cycle number determined by qPCR. Purify amplified library.
ThepurifiedlibrarieswerequantifiedusingqPCRaccordingtotheqPCRQuantificationProtocol Guide (KAPA)andqualifiedusingBioanalyzer (Agilenttechnologies). And then the libraries were sequencedusingHiSeq platform (Illumina).

treatment_protocol: rMSCs were cultured for 1 day under growth medium on flat titanium or titanium with wave-forming nanotextures.

value: Growth medium

tag: culture condition

value: flat titanium disc


title: dHet_2_RNASeq


title: rMSC cultured on wave-forming nanotextured titanium disc for 1 day under growth medium

value: rat Bone marrow-derived mesenchymal stem cells

value: wave-forming nanotextured titanium disc


title: pulmonary artery smooth muscle cells si-NC repeat 1

description: Library name: Sample 1


title: Plasma, IBC patient 8

description: Library name: Plasma8


title: pulmonary artery smooth muscle cells si-Snhg18 repeat 1

description: Library name: Sample 4

value: Snhg18 knockdown


title: human valvular interstitial cells from patient 1, scramble-siRNA

description: Library name: N1

value: aortic valves

value: primary human valvular interstitial cells

value: interstitial cells


title: Plasma, IBC patient 7

description: Library name: Plasma7


title: dHet_3_RNASeq

value: heart (ventricles)


title: pulmonary artery smooth muscle cells si-Snhg18 repeat 3

description: Library name: Sample 6


title: EOM_snRNA_seq

description:
Library name: EOM_snRNA_seq
snRNA-seq

source_name: extraocular muscle (EOM)

value: extraocular muscle (EOM)


title: Plasma, IBC patient 6

description: Library name: Plasma6


title: pulmonary artery smooth muscle cells si-NC repeat 2

description: Library name: Sample 2


title: Irx3KO_Irx4KO2_RNASeq


title: pulmonary artery smooth muscle cells si-Snhg18 repeat 2

description: Library name: Sample 5


title: EOM_scRNA_seq

description:
Library name: EOM_scRNA_seq
scRNA-seq


title: Plasma, IBC patient 10

description: Library name: Plasma10


title: human valvular interstitial cells form patient 4, scramble-siRNA

description: Library name: N4


title: Plasma, IBC patient 5

description: Library name: Plasma5


title: WT, temperature, 22℃，rep1

city: Kunming

first: ya

middle: qi

last: xiao

state: Yunnan Province

address: Chenggong Campus of Yunnan University

department: Faculty of Ecology and Environment

institute: Yunnan University

description: Library name: WT_CO_1

data_processing:
RSEM
Assembly: TAIR10.1
Supplementary files format and content: gene.tpm.matrix.annot.txt files are files in excel format that quantify the expression levels of genes

source_name: seedling

growth_protocol: Plants were grown on half-strength MS (½MS) medium with 1.2% (w/v) sucrose.

extract_protocol:
1. Extract total RNA
2. Oligo dT enrichment of mRNA
3. Fragmented mRNA
Illumina TruseqTM RNA sample prep Kit

treatment_protocol: Some of the materials are treated at a high temperature of 37°C

value: seedling

value: WT


title: aortic valves from patient 5, calcified

description: Library name: F11

data_processing:
fastp software (https://github.com/OpenGene/fastp) were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases with default parameter. Then sequence quality was also verified using fastp.
The mapped reads of each sample were assembled using StringTie (https://ccb.jhu.edu/software/stringtie) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare (https://github.com/gpertea/gffcompare/).
After the final transcriptome was generated, StringTie and was used to estimate the expression levels of all transcripts. StringTie was used to perform expression level for mRNAs by calculating FPKM (FPKM = [total_exon_fragments / mapped_reads(millions) × exon_length(kB)]).
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: Calcified valves were collected from patients undergoing surgical replacement for clinically diagnosed CAVD, and non-calcified control valves were obtained from age-matched individuals undergoing Bentall procedures for acute aortic dissection.

tag: tissue type

value: Calcified valves collected from patients undergoing surgical replacement for clinically diagnosed CAVD


title: aortic valves from patient 6, calcified

description: Library name: F22


title: NMCMs, Ad-vector, rep3

first: LIUHUA

last: ZHOU

address: 101Longmian Avenue, Jiangning District

institute: Nanjing medical University

description: Library name: Sample3

data_processing:
FastQC V0.10.1, HISAT2  V2.2.1 , HTSEQ  V0.6.1 , Stringtie V1.3.3b
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Heart

extract_protocol:
Total RNA was extracted from primary cardiomyocytes of neonatal mice using TRIzol reagent.
The VAHTS Universal V5 RNA-sequencing Library Prep kit was employed to construct the transcriptome library.

value: Heart

value: Primary cardiomyocytes

value: Control

value: Ad-cTNT vector


title: NMCMs, Ad-HMGB2, rep2

description: Library name: Sample5

value: HMGB2 overexpression


title: NMCMs, Ad-HMGB2, rep1

description: Library name: Sample4


title: NMCMs, Ad-HMGB2, rep3

description: Library name: Sample6


title: aortic valves from patient 4, calcified

description: Library name: F5


title: Plasma, IBC patient 4

description: Library name: Plasma4

value: Plasma


title: Uveal melanoma in a singular eye from a 4-6 month old AB wildtype zebrafish

city: Iowa City

first: Zhijie

last: Li

state: IA

address: 285 Newton Road

institute: University of Iowa

description:
Library name: CK8
10x Genomics

data_processing:
The scRNA-seq reads were then mapped to custom GRCz11/danRer11 reference genome using Cell Ranger v.5.0.1 (cellranger count function), and Seurat was used for further analysis. Cells with unique RNA feature counts less than 200 and more than 5% (15% for CK8) mitochondrial contamination were removed from further processing. UMAP was generated using Seurat RunUMAP function with default settings by PCA reduction with dims 1:30, followed by FindNeighbors with dims 1:30 and FindClusters with a resolution of 0.4. Differential gene expression was then calculated by FindMarkers and FindAllMarkers with thresholds for percentage of cells between conditions. Adjusted p-value < 0.05 was used as the threshold for statistically significant difference.
Assembly: A custom reference genome including GNAQQ209L and GFP transgenes was constructed using Cell Ranger (cellranger mkref function).
Supplementary files format and content: Tab-separated values files and matrix files

organism: Danio rerio

source_name: eye

extract_protocol:
Zebrafish eyes or skin were harvested with and without tumors from 4-6 month old AB wildtype and casper (mitfa -/-, mpv17 -/-) zebrafish. Tissues were made into single cell suspension using collagenase/hyaluronidase and trypsin and prepared according to 10X Genomics cell preparation guidelines. Approximately, 10,000 cells were loaded per channel to generate single-cell gel beads-in-emulsion (GEMs).
Single-cell RNA-Seq libraries were prepared with Chromium Next GEM Single Cell 3' GEM, Library & Gel Bead Kit v3.1 (#1000128, 10X Genomics), Chromium Next GEM Chip G Single Cell Kit (#1000127, 10X Genomics), and Chromium i7 Multiplex Kit (#120262, 10X Genomics). Libraries were sequenced on an Illumina HiSeq 6000 with 150 bp paired-end reads in the genomics core at University of Iowa (Iowa City, IA).

value: eye

value: adult

value: melanocytes, retina, sclera, fibroblasts, immune cells

value: AB wildtype

value: injected with oncogenic plasmids

tag: batch


title: GNAQ+, tp53 -/-, ptena -/-, ptenb -/- skin tumor from a 4-6 month old AB wildtype zebrafish

description:
Library name: CK6
10x Genomics

source_name: skin

value: skin

value: fibroblasts, skin cells, melanocytes


title: aortic valves from patient 3, non-calcified

description: Library name: D6

value: aortic valves

value: non-calcified control valves obtained from age-matched individuals undergoing Bentall procedures for acute aortic dissection


title: aortic valves from patient 2, non-calcified

description: Library name: D4


title: Uninjected skin from a 4-6 month old AB wildtype zebrafish

description:
Library name: CK5
10x Genomics

value: control (uninjected)


title: Plasma, IBC patient 2

description: Library name: Plasma2


title: NMCMs, Ad-vector, rep2

description: Library name: Sample2


title: Uveal melanoma in a singular eye from three 4-6 month old casper (mitfa -/-, mpv17 -/-) zebrafish

description:
Library name: CK2
10x Genomics

value: melanocyte precursors, retina, sclera, fibroblasts, immune cells

value: casper (mitfa -/-, mpv17 -/-)


title: Plasma, IBC patient 1

description: Library name: Plasma1


title: Plasma, IBC patient 3

description: Library name: Plasma3


title: Plasma, breast cancer patient 6

description: Library name: PlasmaB6


title: NMCMs, Ad-vector, rep1

description: Library name: Sample1

value: Heart

value: Primary cardiomyocytes


title: Vehide

city: shanghai

first: Chen

last: kaiwen

address: shanghai jiaotong university

institute: shanghai jiaotong university

description: Library name: sample2

data_processing:
The CellRanger (v 5.0.1) was used to align the clean reads with mm10. The Seura 79 (v 5.1.0) pipeline was integrated into analysis and visualization, including clustering, dimension reduction, and cell type identification. Cell types were annotated based on the expression of known markers shown in Figure S3-E. The genes expressed in less than three cells were removed. The cells that expressed less than 200 genes were not included in the analysis. The harmony was used to remove the batch effects between samples. The dimension reduction of umap was calculated based on 40 harmony components. The significantly up-regulated genes in the specific sample and/or subpopulation were identified by FindMarkers and FindAllMarkers. The clusterProfiler was used to annotate the top markers of each subpopulation with the KEGG database. The macrophage gene score was evaluated with AddModuleScore. The ggplot2 was used to display the expression patterns of gene modules.
Assembly: Mouse mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
To control the final number of cells captured, approximately 30,000 cells per sample were loaded onto 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells per μl (Single Cell 3′ library and Gel Bead Kit v.3) as described in the manufacturer’s protocol
Library was performed according to the manufacter's instructions (single cell 3’v3protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loadedtogether with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEMwas retrotranscripted to cDNA, which contains an llumina R1 primer sequence, UniqueMolecular ldentifier (UMl) and the 10x Barcode. The pooled barcoded cDNA was thencleaned up with Silane DynaBeads, amplified by PCR and the apropiated sizedfragments were selected with SPRlselect reagent for subsequent library construction.During the library construction llumina R2 primer sequence, paired-end constructs withP5 and P7 sequences and a sample index were added.

value: tumor


title: 014K_4W_visium kidney xenograft

first: Jaeseok

last: Yang

address: 50, Yonsei-ro, Seodaemun-gu, Seoul, Republic of Korea

institute: Yonsei University

description:
Library name: 014K_4W_visium
Fresh frozen Spatial transcriptome sequencing

data_processing:
*data processing step (Bulk RNA-seq) Bulk RNA-seq raw reads were quality-checked using FastQC and trimmed using Trim Galore. Reads were aligned to the pig (Sus scrofa 11.1) and macaque (Macaca fascicularis 5.0) genomes using STAR aligner. Gene-level quantification was performed using featureCounts
*data processing step (snRNA-seq) snRNA-seq raw reads were processed using Cell Ranger (10x Genomics). Reads were aligned to pig and macaque reference genomes.
*data processing step (Visium) Visium spatial transcriptomics data were processed using Space Ranger (10x Genomics). Reads were aligned to pig and macaque reference genomes. H&E images were registered to spatial barcodes.
Assembly: Pig: Sus scrofa 11.1 (Sscrofa11.1); Macaque: Macaca fascicularis 6.0
Supplementary files format and content: Bulk RNA-seq: Raw count matrix: sample_counts.tsv (gene × sample matrix)
Supplementary files format and content: snRNA-seq: Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Visium:Space Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, Spatial coordinates: tissue_positions_list.csv, Spatial images: tissue_hires_image.png, tissue_lowres_image.png, Scale factors: scalefactors_json.json
Library strategy: Spatial Transcriptomics

organism:
Macaca fascicularis
Sus scrofa

source_name: kidney

extract_protocol:
Kidney xenograft tissues were collected from pig-to-primate transplantation models at designated timepoints. Tissues were immediately snap-frozen in liquid nitrogen and stored at -80°C until processing. Total RNA was extracted using TRIzol reagent (Invitrogen) or RNeasy Mini Kit (Qiagen) following manufacturer's protocols. RNA quality was assessed using Agilent 2100 Bioanalyzer with RIN > 7.0 required for sequencing.
*library construction protocol (Bulk RNA-seq) Bulk RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Library Prep Kit. Briefly, poly(A) mRNA was purified from total RNA using oligo-dT magnetic beads, followed by fragmentation, first-strand and second-strand cDNA synthesis, end repair, A-tailing, adapter ligation, and PCR amplification. Libraries were quantified by Qubit and quality-checked on Bioanalyzer before sequencing. *library construction protocol (snRNA-seq) Single-nucleus RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3' v3.1, v4 kit. Kidney tissues were dissociated to isolate nuclei using a Dounce homogenizer in nuclei isolation buffer. Nuclei were filtered, counted, and loaded onto the Chromium Controller to generate single-nucleus GEMs. Libraries were prepared following the manufacturer's protocol including cDNA synthesis, amplification, and library construction. *library construction protocol (Visium) Visium spatial gene expression libraries were prepared using the 10x Genomics Visium Spatial Gene Expression kit. Fresh-frozen kidney tissue sections (10 μm) were placed on Visium spatial gene expression slides, fixed, stained with H&E, and imaged. Tissue was permeabilized to release mRNA which bound to spatially-barcoded oligonucleotides on the slide. Reverse transcription, second strand synthesis, and library preparation were performed following the manufacturer's protocol.

value: kidney

value: not applicable

value: KO:GGTA1, CMAH, iGb3s, B4GalNT2; KI:CD39, CD55, CD46, TBM

value: aCD154 (5C8) + Abatacept + Tocilizumab


title: CEP

description: Library name: sample1


title: Plasma, breast cancer patient 4

description: Library name: PlasmaB4

value: Plasma


title: CITE-seq Cord Blood ADT

city: Paris

first: Alessandro

last: Donada

address: 11 rue Pierre et Marie Curie, Batiment Curie, RDC, R12, UMR168 - Equipe Perie

country: France

institute: Institut Curie

description: Library name: count_Cord_blood-53_ADT

library_source: other

data_processing:
FASTQ files for each single cell were generated using bcl2fastq (version 2.20.0), with default parameters. The Read 1 contain the TSO (constant tag sequence and a UMI) followed by cDNA or only cDNA.  The Read 2 contain cDNA only. Index1 and index2 reads correspond to cell-specific barcode. The scRNA-SmartSeq3 pipeline v1.2.1 (https://doi.org/10.5281/zenodo.15056215) was used to generate UMI count tables from FASTQ files. Briefly, reads were aligned to the human genome (hg38) using STAR (version 2.7.8a) and assigned to genes using FeatureCounts (deeptools version 3.5.0). UMIs were extracted, deduplicated and counted for each gene using umiTools (version 1.1.1). Low-quality cells were filtered out based on a minimum of 500 genes detected and a percentage of mitochondrial RNA lower than 20. Families composed of only one cell were also removed. Counts were normalised using SCTransform function with default parameters from R Seurat package (version 4.3.0).  CITE-seq: Raw sequencing reads were processed using Cellranger v3.1.0. To obtain a reads/cell/gene count table, reads were mapped to the human GRCh38 reference genome. Cells with less than 1000 genes per cell and with a high percentage (> 30%) of mitochondrial genes were removed from downstream analyses. Following our filtering procedures, the average UMI count per cell was 4406. The median number of genes detected per cell was 1662, 2.2% mapped to mitochondrial genes. Data normalization and integration were performed using the default Seurat v4 approach FindIntegrationAnchors() followed by IntegrateData(), and differentially expressed genes were determined using a logistic regression in Seurat on the non-integrated data using the FindConservedMarkers() function. Pathway based analyses were performed using the enrichR package. Unsupervised clustering was performed on the significant variable genes using the 10 first PCA followed by the nonlinear dimensionality reduction technique UMAP. Annotation of the data was obtained by mapping published signatures using the AddModuleScore() method of Seurat.
Assembly: Human hg38
Supplementary files format and content: html/raw data QC for SMART-seq3
Supplementary files format and content: mtx and h5/matrix count for CITE-seq

molecule: protein

source_name: Blood

extract_protocol:
SMART-seq3: Single cell distribution of individual cell families has been performed using the cellenONE platform (Cellenion). Briefly, we selected individual wells of 96-wells plates displaying at least four cells, harvested the entire well, centrifugated for 8’ at 300g and resuspended in 6 µL of PBS 1X (Sigma). Then, the whole volume was loaded into the machine, but due to the dead volume, effectively only 4 µL of this cell suspension could be redistributed. Individual cells were each sorted directly into single wells of 96-wells plates (90 cells per plate) at 4 °C, each well containing 3 µL of lysis buffer. The lysis buffer contains 0.03 µL Triton X100 (ThermoFisher Scientific), 0.0375 µL Recombinant RNAse Inhibitor (Takara Bio), 0.2 µL dNTP 10mM (ThermoFisher Scientific), 0.5 µL PEG 40% (Sigma), 0.04 µL SMARTseq3 oligo-dT 100 μM (/5BiosG/ACGAGCATCAGCAGCATACGATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTVN; IDT) and ultrapure RNAse water (Invitrogen).  CITE-seq: Magnetic sorted CD34+ cells from umbilical cord blood were plated at a cell density of 1x105 cells/mL, using the same culture condition described for the condition Diff. Cells were harvested after 96 hours, counted with a haemocytometer, and resuspended in cold PBS 1X (ThermoFisher Scientific) containing 2% Bovine Serum Albumin (BSA, Euromedex) and 0.01% Tween 20 (Sigma), to a final concentration of 106 cells/mL. 100 µL of this cell suspension was incubated with a mix of previously prepared CITE-seq antibodies. Cells were incubated for 30 minutes at 4 °C, washed three times with the same solution used for the incubation and resuspended in 16.5 µL, at a final concentration of 1000 cells/mL.
SMART-seq3: Reverse transcription (RT) and the subsequent steps were performed accordingly to the SMART-seq3 technique40. Briefly, lysates in each well underwent RT (42 °C for 90 mins, 10 cycles at 50 °C 2 mins + 42 °C 2 mins, and finally 85 °C for 5 mins) on ice, in presence of template switch oligonucleotide at 100 µM (/5BiosG/AGAGACAGATTGCGCAATGNNNNNNNNrGrGrGIDT), 0.04 µL Maxima H minus reverse transcriptase (ThermoFisher Scientific), TRIS-HCl 1M PH 8.3 (Invitrogen), 0.12µL NaCl 1M (Invitrogen), 0.04 µL GTP 100mM (ThermoFisher Scientific), 0,32 µL DTT 100mM (ThermoFisher Scientific), 0.1 µL MgCl2 50mM (ThermoFisher Scientific) and 0.05 µL Recombinant RNAse Inhibitor (Takara Bio) and water. The following PCR step was performed immediately after, using the Kapa Hifi HotStart Ready Mix (Roche), and forward (100 µM TCGTCGGCAGCGTCAGATGTGTATAAGAGACAGATTGCGCAATG) and reverse (25 µM ACGAGCATCAGCAGCATACGA) primers (IDT technologies) for 25 cycles. After DNA purification using AMPure XP microbeads (ratio 0.8:1) (Beckman Coulter, A63881), the cDNA was tagmented in a final volume of 2 µL, using the Nextera XT DNA Library preparation kit (Illumina). The following library amplification was performed adding 1.5 µL of UDI primers and 2,5 µL of PCR mix including the Phusion High Fidelity DNA polymerase (ThermoFisher Scientific). After tagmentation, the different samples were pooled, purified using AMPure XP microbeads (ratio 0.9:1) and sequenced at 100-bp paired end on a high-output flow cell, using a NovaSeq SP, 800M reads (Illumina).  CITE-seq: Approximately 1.65x104 cells were loaded, to obtain a final yield of 1x104 recovered cells. Cells were processed accordingly to the Chromium Single Cell 3’ library v3.1 (10x Genomics). Libraries were sequenced using a Novaseq s1 (Illumina), allocating at least 20,000 reads per cell for the mRNA library, and 5,000 reads for the Antibody Derived Tags (ADT) library

value: Blood

value: Haematopoietic stem and progenitors


title: Plasma, breast cancer patient 5

description: Library name: PlasmaB5


title: D1408T126

description: Library name: Dataset_B_125


title: 013K_7W_visium kidney xenograft

description:
Library name: 013K_7W_visium
Fresh frozen Spatial transcriptome sequencing

value: CD154 (PG405) + Abatacept + Tocilizumab


title: CITE-seq Cord Blood mRNA

description: Library name: count_Cord_blood-53_mRNA


title: D1408T127

description: Library name: Dataset_B_126


title: 012K_6W_visium kidney xenograft

description:
Library name: 012K_6W_visium
Fresh frozen Spatial transcriptome sequencing

value: KO:GGTA1, CMAH, B4GalNT2; KI:CD39, CD55


title: Mouse Buffy coat, PBS control, C16

city: Hualien

first: Hung-Jung

address: 701 Zhongyang Rd., Sec. 3

department: Institute of Medical Sciences

country: Taiwan

institute: Tzu Chi University

description: Library name: Sample C16

data_processing:
Bcl2fastq (v2.17.1.14) was used to processed the original image data for base calling.
Cutadapt (version 1.9.1) was used to processed data filtering.
Trimmed sequence reads were aligned to Mus_musculus_Ensembl_GRCm38.97 with Hisat2 (v2.0.1) with default parameters.
Assembly: Ensembl_GRCm38.97
Supplementary files format and content: Tab-deliminted text file includes raw counts for each sample

source_name: Buffy coat

extract_protocol:
RNA was extracted using TRIzol reagent (Invitrogen) and further purified with Rneasy mini plus kit (Qiagen). 1μg RNA with RIN value above 7 was used for  library preparation.
RNA libraries for RNA-seq were constracted by Genewiz Inc. The First strand cDNA was synthesized using ProtoScript II Reverse Transcriptase with random primers and Actinomycin D. The second-strand cDNA was synthesized using Second Strand Synthesis Enzyme Mix (include dACG-TP/dUTP). The purified double-stranded cDNA by AxyPrep Mag PCR Clean-up (Axygen) was then treated with End Prep Enzyme Mix to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using AxyPrep Mag PCR Clean-up (Axygen), and fragments of ~360 bp (with the approximate insert size of 300 bp) were recovered. The dUTP-marked second strand was digested with Uracil-Specific Excision Reagent (USER) enzyme (New England Biolabs). Each sample was then amplified by PCR for 11 cycles using P5 and P7 primers, with both primers carrying sequences which can anneal with flow cell to perform bridge PCR and P7 primer carrying a six-base index allowing for multiplexing. The PCR products were cleaned up using AxyPrep Mag PCR Clean-up (Axygen), validated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA), and quantified by Qubit 2.0 Fluorometer (Invitrogen, Carlsbad, CA,USA).

value: Buffy coat

value: PBS control


title: Plasma, breast cancer patient 3

description: Library name: PlasmaB3


title: Mouse Buffy coat, PBS control, C12

description: Library name: Sample C12


title: Mouse Buffy coat, PBS control, C10

description: Library name: Sample C10


title: D1408T125

description: Library name: Dataset_B_124


title: Uninjected eyes from three 4-6 month old casper (mitfa -/-, mpv17 -/-) zebrafish

description:
Library name: CK1
10x Genomics

value: eye

value: adult

value: control (uninjected)


title: D1408T124

description: Library name: Dataset_B_123


title: 011K_D_4W_visium kidney xenograft

description:
Library name: 011K_D_4W_visium
Fresh frozen Spatial transcriptome sequencing


title: Mouse Buffy coat, PBS control, C4

description: Library name: Sample C4


title: Plasma, breast cancer patient 2

description: Library name: PlasmaB2


title: Plasma, breast cancer patient 1

description: Library name: PlasmaB1


title: aortic valves from patient 1, non-calcified

description: Library name: D3

source_name: aortic valves

value: aortic valves

value: non-calcified control valves obtained from age-matched individuals undergoing Bentall procedures for acute aortic dissection


title: D1408T123

description: Library name: Dataset_B_122


title: 010K_D_34_visium kidney xenograft

description:
Library name: 010K_D_34_visium
Fresh frozen Spatial transcriptome sequencing


title: Mouse Buffy coat, PM2.5 treated, P21

description: Library name: Sample P21

value: PM2.5 exposure


title: Mouse Buffy coat, PM2.5 treated, P18

description: Library name: Sample P18


title: PBMC, IBC patient 10

description: Library name: PBMC10

source_name: PBMC

value: PBMC


title: 008K_D_34_visium kidney xenograft

description:
Library name: 008K_D_34_visium
Fresh frozen Spatial transcriptome sequencing

value: kidney

value: not applicable

value: KO:GGTA1, CMAH, iGb3s, B4GalNT2; KI:CD46, TBM


title: PBMC, IBC patient 9

description: Library name: PBMC9


title: 008K_D_49_visium kidney xenograft

description:
Library name: 008K_D_49_visium
Fresh frozen Spatial transcriptome sequencing


title: D1408T121

description: Library name: Dataset_B_120


title: PBMC, IBC patient 8

description: Library name: PBMC8


title: 006K-2W_visium kidney xenograft

description:
Library name: 006K-2W_visium
Fresh frozen Spatial transcriptome sequencing

value: aCD154 (C10)+ Abatacept


title: Mouse Buffy coat, PM2.5 treated, P9

description: Library name: Sample P9


title: PBMC, IBC patient 7

description: Library name: PBMC7


title: PBMC, IBC patient 6

description: Library name: PBMC6


title: D1408T120

description: Library name: Dataset_B_119

value: Blood


title: D1408T119

description: Library name: Dataset_B_118

value: Haematopoietic stem and progenitors


title: Mouse Buffy coat, PM2.5 treated, P17

description: Library name: Sample P17


title: 004K-4W_visium kidney xenograft

description:
Library name: 004K-4W_visium
Fresh frozen Spatial transcriptome sequencing


title: D1408T118

description: Library name: Dataset_B_117


title: D1408T122

description: Library name: Dataset_B_121


title: 004K-2W_visium kidney xenograft

description:
Library name: 004K-2W_visium
Fresh frozen Spatial transcriptome sequencing


title: PBMC, IBC patient 5

description: Library name: PBMC5


title: 006K-4W_visium kidney xenograft

description:
Library name: 006K-4W_visium
Fresh frozen Spatial transcriptome sequencing


title: T06

city: Dalian

first: Wang

last: Ziran

state: Liaoning

address: No.9 West Section Lvshun South Road

institute: Dalian Medical University

description: Library name: IS_3

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts.
The small RNA tags were mapped to reference sequence by Bowtie[1]without mismatch to analyze their expression and distribution on the reference.
Mapped small RNA tags were used to looking for known miRNA. miRBase20.0 was used as reference, modified software mirdeep2 and srna-tools-cli were used to obtain the potential miRNA and draw the secondary structures.
The characteristics of hairpin structure of miRNA precursor can be used to predict novel miRNA. The available software miREvo and mirdeep2  were integrated to predict novel miRNA through exploring the secondary structure, the Dicer cleavage site and the minimum free energy of the small RNA tags unannotated in the former steps.
Assembly: Mus_musculus_Ensembl_106
Supplementary files format and content: Readcount_TPM.txt

source_name: PBMC-EVs

extract_protocol:
The purification of total exosome-derived RNA was carried out by the exoRNeasy Maxi Kit (Qiagen).
Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: PBMC-EVs

value: WT

value: IS-stimulated


title: PBMC, IBC patient 4

description: Library name: PBMC4


title: T03

description: Library name: CTRL_3

value: untreated


title: T04

description: Library name: IS_1


title: D1408T116

description: Library name: Dataset_B_115


title: D1408T117

description: Library name: Dataset_B_116


title: 005K-2W_visium kidney xenograft

description:
Library name: 005K-2W_visium
Fresh frozen Spatial transcriptome sequencing

value: KO:GGTA1, CMAH, B4GalNT2; KI:CD46, TBM


title: 005K-4W_visium kidney xenograft

description:
Library name: 005K-4W_visium
Fresh frozen Spatial transcriptome sequencing


title: PBMC, IBC patient 3

description: Library name: PBMC3


title: T02

description: Library name: CTRL_2


title: 002K-2W_visium kidney xenograft

description: Library name: 002K-2W_visium

value: KO:GGTA1, CMAH, B4GalNT1; KI:CD39, CD54


title: PBMC, IBC patient 2

description: Library name: PBMC2


title: D1408T114

description: Library name: Dataset_B_113


title: D1408T115

description: Library name: Dataset_B_114


title: 002K-2W_snrnaseq kidney xenograft

description: Library name: Kid-20230809-2w_snrnaseq

data_processing:
*data processing step (Bulk RNA-seq) Bulk RNA-seq raw reads were quality-checked using FastQC and trimmed using Trim Galore. Reads were aligned to the pig (Sus scrofa 11.1) and macaque (Macaca fascicularis 5.0) genomes using STAR aligner. Gene-level quantification was performed using featureCounts
*data processing step (snRNA-seq) snRNA-seq raw reads were processed using Cell Ranger (10x Genomics). Reads were aligned to pig and macaque reference genomes.
*data processing step (Visium) Visium spatial transcriptomics data were processed using Space Ranger (10x Genomics). Reads were aligned to pig and macaque reference genomes. H&E images were registered to spatial barcodes.
Assembly: Pig: Sus scrofa 11.1 (Sscrofa11.1); Macaque: Macaca fascicularis 6.0
Supplementary files format and content: Bulk RNA-seq: Raw count matrix: sample_counts.tsv (gene × sample matrix)
Supplementary files format and content: snRNA-seq: Cell Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Visium:Space Ranger output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, Spatial coordinates: tissue_positions_list.csv, Spatial images: tissue_hires_image.png, tissue_lowres_image.png, Scale factors: scalefactors_json.json


title: 003K-2W_visium kidney xenograft

description:
Library name: 003K-2W_visium
Fresh frozen Spatial transcriptome sequencing

value: KO:GGTA1, CMAH, iGb3s, B4GalNT2; KI:-


title: T01

description: Library name: CTRL_1


title: PBMC, breast cancer patient 6

description: Library name: PBMCB6


title: PBMC, IBC patient 1

description: Library name: PBMC1


title: D1408T113

description: Library name: Dataset_B_112


title: 004K_4W_snrnaseq kidney xenograft

description: Library name: Kid_20231004_4W_snrnaseq

value: mixed kidney cells


title: PBMC, breast cancer patient 5

description: Library name: PBMCB5


title: D1408T111

description: Library name: Dataset_B_110


title: PBMC, breast cancer patient 4

description: Library name: PBMCB4


title: 014K_4W_snrnaseq kidney xenograft

description: Library name: 014K_4W_snrnaseq

value: KO:GGTA1, CMAH, iGb3s, B4GalNT2; KI:CD39, CD55, CD46, TBM

value: aCD154 (5C8) + Abatacept + Tocilizumab


title: D1408T110

description: Library name: Dataset_B_109


title: 013K-7W_snrnaseq kidney xenograft

description: Library name: 013K-7W_snrnaseq

value: CD154 (PG405) + Abatacept + Tocilizumab


title: D1408T112

description: Library name: Dataset_B_111


title: 4T1_DMSO_03

description: Library name: sample6

data_processing:
Before read mapping, clean reads were obtained from the raw reads by removing the adaptor sequences and low-quality reads. The clean reads were then aligned to mouse genome (GRCm38,Ensembl100) using the Hisat2. [Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods. 2015. April;12(4):357–360. doi: 10.1038/nmeth.3317] HTseq [Anders S, Pyl P T, Huber W. HTSeq–A Python framework to work with high-throughput sequencing data[J]. Bioinformatics, 2014: btu638.] was used to get gene counts and RPKM method was used to determine the gene expression.
Assembly: The clean reads were then aligned to mouse genome (GRCm38,Ensembl100) using the Hisat2.
Supplementary files format and content: We applied DESeq2 algorithm [Love M I , Huber W , Anders S . Moderated Estimation of Fold Change and Dispersion for RNA-Seq Data with DESeq2[J]. Genome Biology, 2014, 15(12):550.] to filter the differentially expressed genes, after the significant analysis, P-value and FDR analysis [Benjamini Y, et al. Controlling the false discovery rate in behavior genetics research. Behav Brain Res. 2001 Nov 1;125(1-2):279-84.] were subjected to the following criteria: i) Fold Change>1.5 or < 0.667; ii) ,P-value<0.05,FDR<0.05.

extract_protocol:
Total RNA was extracted from the samples by Trizol reagent (Invitrogen) separately. The RNA quality was checked by Agilent 2200 and kept at −80°C. The RNA with RIN (RNA integrity number) > 7.0 is acceptable for cDNA library construction.
The cDNA libraries were constructed for each RNA sample using the TruSeq Stranded mRNA Library Prep Kit (Illumina, Inc.) according to the manufacturer’s instructions. Generally, the protocol consists of the following steps: Poly-A containing mRNA was purified from 1ug total RNA using oligo(dT) magnetic beads and fragmented into 200-600 bp using divalent cations at 85℃ for 6 min. The cleaved RNA fragments were used for first- and second-strand complementary DNA (cDNA) synthesis . dUTP mix was used for second-strand cDNA synthesis, which allows for the removal of the second strand.


title: 003K_2W_snrnaseq kidney xenograft

description: Library name: Kid_20230823_2W_snrnaseq

value: kidney


title: 4T1_DMSO_01

description: Library name: sample4


title: PBMC, breast cancer patient 3

description: Library name: PBMCB3

value: PBMC


title: 4T1_CEP_03

description: Library name: sample3


title: 4T1_DMSO_02

description: Library name: sample5


title: 012K-6W_snrnaseq kidney xenograft

description: Library name: 012K-6W_snrnaseq

value: KO:GGTA1, CMAH, B4GalNT2; KI:CD39, CD55


title: 4T1_CEP_02

description: Library name: sample2


title: D1408T109

description: Library name: Dataset_B_108


title: PBMC, breast cancer patient 2

description: Library name: PBMCB2


title: 011K_4W_snrnaseq kidney xenograft

description: Library name: 011K_4W_snrnaseq


title: 4T1_CEP_01

description: Library name: sample1


title: D1408T108

description: Library name: Dataset_B_107


title: PBMC, breast cancer patient 1

description: Library name: PBMCB1


title: 010K_4W_snrnaseq kidney xenograft

description: Library name: 010K_4W_snrnaseq


title: D1408T106

description: Library name: Dataset_B_106


title: 008K_49D_snrnaseq kidney xenograft

description: Library name: 008K_49D_snrnaseq

value: KO:GGTA1, CMAH, iGb3s, B4GalNT2; KI:CD46, TBM


title: D1408T105

description: Library name: Dataset_B_105

value: Blood


title: Breast tissue FFPE, IBC patient 10

description: Library name: FFPE10

source_name: Breaset tissue FFPE

value: Breaset tissue FFPE


title: Breast tissue FFPE, IBC patient 7

description: Library name: FFPE7


title: 008K_5W_snrnaseq kidney xenograft

description: Library name: 008K_5W_srnaseq


title: Breast tissue FFPE, IBC patient 6

description: Library name: FFPE6


title: Breast tissue FFPE, IBC patient 9

description: Library name: FFPE9


title: P3-GTF Input in ADNP-FKBP12 mESC, ctrl, replicate 2

city: Basel

first: Fabio

last: Mohn

address: Maulbeerstrasse 66

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

description: Library name: Gtf3a_In_AdnpFKBP_ctrl

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 with repeat sensitive settings based on Teissandier et al (Mobile DNA, 2019)  ( --outFilterMultimapNmax 100000 --outSAMmultNmax 1 --outMultimapperOrder Random --winAnchorMultimapNmax 5000 --alignEndsType EndToEnd --alignIntronMax 1 --alignMatesGapMax 2000 --seedSearchStartLmax 30 --alignTranscriptsPerReadNmax 100000 --alignWindowsPerReadNmax 100000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 1000 --seedPerWindowNmax 300 --seedNoneLociPerWindow 1000  --outBAMsortingBinsN 100 --limitBAMsortRAM 10000000000  --alignSJDBoverhangMin 999).
Assembly: GRCm39 / mm39
Supplementary files format and content: bigWig files were generated by first using samtools to filter out only uniquely mapping reads, then per base coverage was calculated using bedtools, counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (UCSC tools).

growth_protocol: Mouse embryonic stem cells were grown under standard conditions in medium containing serum, LIF and 2i.

extract_protocol:
10^6 mES cells were crosslinked, chromatin was extracted and sonicated to an average size of 300bp. 5% of chromatin was set aside as Input control. The chromatin was incubated with antibody and protein A/G coupled Dynabeads, washed and de-crosslinked. Purified DNA was subsequently used for library preparation. For a detailed protocol, see Schnabl et al. 2025.
Libraries were prepared using the NEB Next Ultra II DNA library prep kit according to manufacturers instructions.

tag: strain

value: hybrid 129-C57BL/6

value: embryonic stem cells (ESC)

value: 24h DMSO ctrl


title: D1408T104

description: Library name: Dataset_B_104

value: Haematopoietic stem and progenitors


title: 006K_4W_snrnaseq kidney xenograft

description: Library name: 006K_4W_snrnaseq

value: aCD154 (C10)+ Abatacept


title: D1408T103

description: Library name: Dataset_B_103


title: Breast tissue FFPE, IBC patient 8

description: Library name: FFPE8


title: P3-GTF Input in ADNP-FKBP12 mESC, dTAG13, replicate 2

description: Library name: Gtf3a_In_AdnpFKBP_24h


title: 007K_8W_240326_snrnaseq kidney xenograft

description: Library name: 007K_8W_240326_snrnaseq


title: P3-GTF Input in ADNP-FKBP12 mESC, dTAG13, replicate 1

description: Library name: Gtf3c1_In_AdnpFKBP_24h


title: TBP ChIP in ADNP-FKBP12 mESC, ctrl, replicate 1

description: Library name: Tbp_ChIP_AdnpFKBP_ctrl_r1


title: TBP ChIP in ADNP-FKBP12 mESC, ctrl, replicate 2

description: Library name: Tbp_ChIP_AdnpFKBP_ctrl_r2


title: D1408T102

description: Library name: Dataset_B_102


title: P3-GTF Input in ADNP-FKBP12 mESC, ctrl, replicate 1

description: Library name: Gtf3c1_In_AdnpFKBP_ctrl


title: 006K_2W_snrnaseq kidney xenograft

description: Library name: 006K_2W_snrnaseq


title: D1408T101

description: Library name: Dataset_B_101


title: Breast tissue FFPE, IBC patient 5

description: Library name: FFPE5


title: TBP ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 2

description: Library name: Tbp_ChIP_AdnpFKBP_24h_r2


title: D1408T100

description: Library name: Dataset_B_100


title: Breast tissue FFPE, IBC patient 4

description: Library name: FFPE4


title: 005K_4W_snrnaseq kidney xenograft

description: Library name: 005K_4W_snrnaseq

value: KO:GGTA1, CMAH, B4GalNT2; KI:CD46, TBM


title: 005K_2W_snrnaseq kidney xenograft

description: Library name: 005K_2W_snrnaseq


title: TBP ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 1

description: Library name: Tbp_ChIP_AdnpFKBP_24h_r1


title: D1408T99

description: Library name: Dataset_B_99


title: Breast tissue FFPE, IBC patient 3

description: Library name: FFPE3


title: GTF3C1 ChIP in ADNP-FKBP12 mESC, ctrl, replicate 2

description: Library name: Gtf3c1_ChIP_AdnpFKBP_ctrl_r2


title: 014K_Sac_bulk kidney xenograft

description: Library name: 014K_Sac_bulk

value: not applicable


title: GTF3C1 ChIP in ADNP-FKBP12 mESC, ctrl, replicate 1

description: Library name: Gtf3c1_ChIP_AdnpFKBP_ctrl_r1


title: Breast tissue FFPE, IBC patient 1

description: Library name: FFPE1


title: D1408T97

description: Library name: Dataset_B_97


title: GTF3C1 ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 2

description: Library name: Gtf3c1_ChIP_AdnpFKBP_24h_r2


title: SNAPC3 ChIP in ADNP-FKBP12 mESC, ctrl, replicate 2

description: Library name: Snapc3_ChIP_AdnpFKBP_ctr_r2


title: 014K_D0_bulk kidney xenograft

description: Library name: 014K_D0_bulk


title: Breast tissue FFPE, IBC patient 2

description: Library name: FFPE2


title: 013K_Sac_bulk kidney xenograft

description: Library name: 013K_Sac_bulk


title: 013K-DO_bulk kidney xenograft

description: Library name: 013K-DO_bulk


title: Breast tissue FFPE, breast cancer patient 4

description: Library name: FFPEB3


title: 012K_DO_bulk kidney xenograft

description: Library name: 012K_DO_bulk


title: D1408T94

description: Library name: Dataset_B_94


title: D1408T95

description: Library name: Dataset_B_95


title: GTF3C1 ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 1

description: Library name: Gtf3c1_ChIP_AdnpFKBP_24h_r1


title: 011K-DO_bulk kidney xenograft

description: Library name: 011K-DO_bulk


title: D1408T98

description: Library name: Dataset_B_98


title: D1408T96

description: Library name: Dataset_B_96


title: Breast tissue FFPE, breast cancer patient 6

description: Library name: FFPEB4


title: Breast tissue FFPE, breast cancer patient 1

description: Library name: FFPEB1


title: Breast tissue FFPE, breast cancer patient 2

description: Library name: FFPEB2


title: D1408T93

description: Library name: Dataset_B_93


title: 010K_DO_bulk kidney xenograft

description: Library name: 010K_DO_bulk


title: D1408T92

description: Library name: Dataset_B_92


title: SNAPC3 ChIP in ADNP-FKBP12 mESC, ctrl, replicate 1

description: Library name: Snapc3_ChIP_AdnpFKBP_ctr_r1


title: SNAPC3 ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 2

description: Library name: Snapc3_ChIP_AdnpFKBP_24h_r2


title: SNAPC3 ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 1

description: Library name: Snapc3_ChIP_AdnpFKBP_24h_r1


title: Healthy Plasma, donor 12

description: Library name: PlasmaH12

value: Plasma


title: D1408T90

description: Library name: Dataset_B_90


title: 007K_DO_bulk kidney xenograft

description: Library name: 007K_DO_bulk


title: 007K_Sac_bulk kidney xenograft

description: Library name: 007K_Sac_bulk


title: Healthy Plasma, donor 13

description: Library name: PlasmaH13


title: 005K_DO_bulk kidney xenograft

description: Library name: 005K_DO_bulk


title: D1408T88

description: Library name: Dataset_B_88


title: GTF3A ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 1

description: Library name: Gtf3a_ChIP_AdnpFKBP_24h_r1


title: GTF3A ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 2

description: Library name: Gtf3a_ChIP_AdnpFKBP_24h_r2


title: Healthy Plasma, donor 11

description: Library name: PlasmaH11


title: 004K_0d_bulk kidney xenograft

description: Library name: 004K_0d_bulk


title: GTF3A ChIP in ADNP-FKBP12 mESC, ctrl, replicate 1

description: Library name: Gtf3a_ChIP_AdnpFKBP_ctrl_r1


title: GTF3A ChIP in ADNP-FKBP12 mESC, ctrl, replicate 2

description: Library name: Gtf3a_ChIP_AdnpFKBP_ctrl_r2


title: D1408T91

description: Library name: Dataset_B_91


title: Healthy Plasma, donor 8

description: Library name: PlasmaH8


title: Healthy Plasma, donor 10

description: Library name: PlasmaH10


title: BRF2 ChIP in ADNP-FKBP12 mESC, ctrl, replicate 2

description: Library name: Brf2_ChIP_AdnpFKBP_ctrl_r2


title: D1408T89

description: Library name: Dataset_B_89


title: D1408T86

description: Library name: Dataset_B_86


title: D1408T87

description: Library name: Dataset_B_87


title: Healthy Plasma, donor 7

description: Library name: PlasmaH7


title: Healthy Plasma, donor 9

description: Library name: PlasmaH9


title: 003K_0d_bulk kidney xenograft

description: Library name: 003K_0d_bulk

value: KO:GGTA1, CMAH, iGb3s, B4GalNT2; KI:-


title: BRF2 ChIP in ADNP-FKBP12 mESC, ctrl, replicate 1

description: Library name: Brf2_ChIP_AdnpFKBP_ctrl_r1


title: D1408T85

description: Library name: Dataset_B_85


title: Healthy Plasma, donor 6

description: Library name: PlasmaH6


title: 002K_0d_bulk kidney xenograft

description: Library name: 002K_0d_bulk

value: KO:GGTA1, CMAH, B4GalNT1; KI:CD39, CD54


title: BRF2 ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 2

description: Library name: Brf2_ChIP_AdnpFKBP_24h_r2


title: D1408T84

description: Library name: Dataset_B_84


title: BRF2 ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 1

description: Library name: Brf2_ChIP_AdnpFKBP_24h_r1


title: D1408T83

description: Library name: Dataset_B_83


title: STEC EDL933_Sprouts_T8_S70_R3

city: COLUMBUS

first: Ahmed

middle: E.

last: Yousef

state: Ohio

address: 2015 Fyffe Road

department: Food Science and Technology

institute: the Ohio State University

description:
Library name: Sample9
Column name in STEC EDL933_featurecounts: picard_out/T8_3.bam

data_processing:
Duplicate reads were marked with the MarkDuplicates function of PicardTools (Picard Tools - By Broad Institute, 2019). Non-duplicate reads were counted into genes with featureCounts v2.0.3 (Liao et al., 2014). Differential expression analyses were performed for each pairwise comparison of the three timepoints with DESeq2 V2.11.40.7 (Love et al., 2014) in R 4.4.2 (R Core Team, 2024) to determine differentially expressed genes (DEGs) between different samples
Supplementary files format and content: tab-delimited file  includes raw counts for each sample

organism: Escherichia coli O157:H7 str. EDL933

source_name: Bacterial cells

growth_protocol: STEC cells were grown in TSB followed by growth in sprouts for 5 days at 23 C followed by three days refrigeration at 4 C.

extract_protocol:
RNA was extract with Rneasy mini kit (Qiagen) and 100 ng RNA  was used for the construction of sequencing libraries
Nine RNA samples (3 × 3) representing three biological replicates from each of the three time points (D0, D5, and D8) were prepared for analysis using a commercial kit (Zymo-Seq RiboFree Total RNA Kit; Zymo Research, Irvine, CA, USA)

value: Bacterial cells

value: WT

value: Growth in Sprouts

value: Day 8


title: Healthy Plasma, donor 5

description: Library name: PlasmaH5


title: Healthy Plasma, donor 4

description: Library name: PlasmaH4


title: STEC EDL933_Sprouts_T8_S70_R2

description:
Library name: Sample8
Column name in STEC EDL933_featurecounts: picard_out/T8_2.bam


title: D1408T82

description: Library name: Dataset_B_82


title: BRF1 ChIP in ADNP-FKBP12 mESC, ctrl, replicate 2

description: Library name: Brf1_ChIP_AdnpFKBP_ctrl_r2


title: D1408T81

description: Library name: Dataset_B_81


title: BRF1 ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 2

description: Library name: Brf1_ChIP_AdnpFKBP_24h_r2


title: Healthy Plasma, donor 3

description: Library name: PlasmaH3


title: STEC EDL933_Sprouts_T5_S70_R2

description:
Library name: Sample5
Column name in STEC EDL933_featurecounts: picard_out/T5_2.bam

value: Day 5


title: BRF1 ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 1

description: Library name: Brf1_ChIP_AdnpFKBP_24h_r1


title: Healthy Plasma, donor 1

description: Library name: PlasmaH1


title: STEC EDL933_Sprouts_T8_S70_R1

description:
Library name: Sample7
Column name in STEC EDL933_featurecounts: picard_out/T8_1.bam


title: D1408T80

description: Library name: Dataset_B_80

value: Blood


title: Healthy Plasma, donor 2

description: Library name: PlasmaH2


title: STEC EDL933_Sprouts_T5_S70_R1

description:
Library name: Sample4
Column name in STEC EDL933_featurecounts: picard_out/T5_1.bam


title: STEC EDL933_Sprouts_T5_S70_R3

description:
Library name: Sample6
Column name in STEC EDL933_featurecounts: picard_out/T5_3.bam


title: BRF1 ChIP in ADNP-FKBP12 mESC, ctrl, replicate 1

description: Library name: Brf1_ChIP_AdnpFKBP_ctrl_r1


title: D1408T78

description: Library name: Dataset_B_78


title: STEC EDL933_TSB_T0_S70_R3

description:
Library name: Sample3
Column name in STEC EDL933_featurecounts: picard_out/T0_3.bam

value: Growth in TSB

value: Day 0


title: BDP1 ChIP in ADNP-FKBP12 mESC, ctrl, replicate 2

description: Library name: Bdp1_ChIP_AdnpFKBP_ctrl_r2

value: hybrid 129-C57BL/6

value: embryonic stem cells (ESC)


title: Healthy PBMC, donor 13

description: Library name: PBMCH13

value: PBMC


title: Healthy PBMC, donor 12

description: Library name: PBMCH12


title: BDP1 ChIP in ADNP-FKBP12 mESC, ctrl, replicate 1

description: Library name: Bdp1_ChIP_AdnpFKBP_ctrl_r1

value: 24h DMSO ctrl


title: STEC EDL933_TSB_T0_S70_R1

description:
Library name: Sample1
Column name in STEC EDL933_featurecounts: picard_out/T0_1.bam


title: D1408T77

description: Library name: Dataset_B_77

value: Haematopoietic stem and progenitors


title: D1408T76

description: Library name: Dataset_B_76


title: Healthy PBMC, donor 9

description: Library name: PBMCH9


title: Healthy PBMC, donor 10

description: Library name: PBMCH10


title: BDP1 ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 2

description: Library name: Bdp1_ChIP_AdnpFKBP_24h_r2


title: Healthy PBMC, donor 11

description: Library name: PBMCH11


title: BDP1 ChIP in ADNP-FKBP12 mESC, dTAG13, replicate 1

description: Library name: Bdp1_ChIP_AdnpFKBP_24h_r1


title: ADNP and POL3 Input in ADNP-FKBP12 mESC, ctrl

description: Library name: Adnp_P3_In_AdnpFKBP


title: STEC EDL933_TSB_T0_S70_R2

description:
Library name: Sample2
Column name in STEC EDL933_featurecounts: picard_out/T0_2.bam


title: Planktonic, CEA10, Hypoxia, rep4

city: Hanover

first: Charles

last: Puerner

state: NH

address: 1 Rope Ferry Rd

department: Microbiology and Immunology

institute: Geisel School of Medicine at Dartmouth College

description:
Library name: CEA10_H_PL4
column name in biofilm_vs_planktonic.txt is CEA10_H_PL4

data_processing:
trimming was performed with cutadapt v 2.4: nextseq-trim=20, minumum length = 1, quality cutoff = 20
Read mapping was performed with STAR v 2.7.2b: output type = BAM SortedByCoordinate, outFilterType = BySJout, genome = A1163 (v  FungiDB-52), gff file = AF293  (v FungiDB-52)
Read counting was performed with htseq-count v 0.11.2: format = BAM, stranded = no, order = pos
Assembly: FungiDB-52_AfumigatusAf293_Genome.fasta
Supplementary files format and content: tab-delimited text file included raw counts for each sample

organism: Aspergillus fumigatus

source_name: Mycelium (Planktonic)

growth_protocol: 37 °C, 5% CO2, SCN media

extract_protocol:
Tissue was harvested in TRI reagent with bead beating, RNA was purified from the aqueous phase with Qiagen RNAeasy Plus Mini kit. DNA contamination was removed with the TURBO DNA-free kit (Ambion). 100 or 200 ng of RNA was used for library construction.
RNA libraries for RNAseq were prepared using the mRNA HyperPrep kit (Kapa Bioscience) following manufacturer’s instructions.

treatment_protocol: Hypoxia treated planktonic cultures were switched to 0.2% O2 + 5% CO2 for 30 minutes

value: Mycelium (Planktonic)

value: 0.2% Oxygen expsure 30 min


title: D1408T75

description: Library name: Dataset_B_75


title: Planktonic, CEA10, Hypoxia, rep1

description:
Library name: CEA10_H_PL1
column name in biofilm_vs_planktonic.txt is CEA10_H_PL1


title: Planktonic, CEA10, Hypoxia, rep3

description:
Library name: CEA10_H_PL3
column name in biofilm_vs_planktonic.txt is CEA10_H_PL3


title: Healthy PBMC, donor 7

description: Library name: PBMCH7


title: Healthy PBMC, donor 8

description: Library name: PBMCH8


title: POL3 ChIP in ADNP-FKBP12 mESC, ctrl, replicate 1

description: Library name: Pol3_ChIP_AdnpFKBP_ctrl_r1


title: Planktonic, CEA10, Hypoxia, rep2

description:
Library name: CEA10_H_PL2
column name in biofilm_vs_planktonic.txt is CEA10_H_PL2


title: D1408T73

description: Library name: Dataset_B_73


title: POL3 ChIP in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 2

description: Library name: Pol3_ChIP_AdnpFKBP_4h_r2


title: Healthy PBMC, donor 6

description: Library name: PBMCH6


title: D1408T71

description: Library name: Dataset_B_71


title: D1408T72

description: Library name: Dataset_B_72


title: Planktonic, AF293, Hypoxia, rep4

description:
Library name: AF293_H_PL4
column name in biofilm_vs_planktonic.txt is AF293_H_PL4


title: POL3 ChIP in ADNP-FKBP12 mESC, ctrl, replicate 2

description: Library name: Pol3_ChIP_AdnpFKBP_ctrl_r2


title: POL3 ChIP in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 1

description: Library name: Pol3_ChIP_AdnpFKBP_4h_r1


title: T05

description: Library name: IS_2

value: PBMC-EVs

value: IS-stimulated


title: D1408T70

description: Library name: Dataset_B_70


title: Planktonic, AF293, Hypoxia, rep2

description:
Library name: AF293_H_PL2
column name in biofilm_vs_planktonic.txt is AF293_H_PL2


title: Healthy PBMC, donor 4

description: Library name: PBMCH4


title: Healthy PBMC, donor 3

description: Library name: PBMCH3


title: POL3 ChIP in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 1

description: Library name: Pol3_ChIP_AdnpFKBP_24h_r1


title: Planktonic, AF293, Hypoxia, rep3

description:
Library name: AF293_H_PL3
column name in biofilm_vs_planktonic.txt is AF293_H_PL3


title: Healthy PBMC, donor 2

description: Library name: PBMCH2


title: POL3 ChIP in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 2

description: Library name: Pol3_ChIP_AdnpFKBP_24h_r2


title: D1408T68

description: Library name: Dataset_B_68


title: Healthy PBMC, donor 1

description: Library name: PBMCH1


title: ADNP ChIP in ADNP-FKBP12 mESC, ctrl, replicate 2

description: Library name: Adnp_ChIP_AdnpFKBP_ctrl_r2


title: Planktonic, CEA10, Normoxia, rep4

description:
Library name: CEA10_N_PL4
column name in biofilm_vs_planktonic.txt is CEA10_N_PL4


title: Planktonic, AF293, Hypoxia, rep1

description:
Library name: AF293_H_PL1
column name in biofilm_vs_planktonic.txt is AF293_H_PL1


title: ADNP ChIP in ADNP-FKBP12 mESC, ctrl, replicate 1

description: Library name: Adnp_ChIP_AdnpFKBP_ctrl_r1


title: Planktonic, CEA10, Normoxia, rep3

description:
Library name: CEA10_N_PL3
column name in biofilm_vs_planktonic.txt is CEA10_N_PL3


title: ADNP ChIP in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 2

description: Library name: Adnp_ChIP_AdnpFKBP_4h_r2


title: Planktonic, CEA10, Normoxia, rep2

description:
Library name: CEA10_N_PL2
column name in biofilm_vs_planktonic.txt is CEA10_N_PL2


title: Frozen breast tissue, matched breast cancar tissue, patient 4

description: Library name: BC4

source_name: Frozen breast tissue

value: Frozen breast tissue


title: D1408T65

description: Library name: Dataset_B_65


title: Frozen breast tissue, matched breast cancar tissue, patient 3

description: Library name: BC3


title: D1408T66

description: Library name: Dataset_B_66


title: ADNP ChIP in ADNP-FKBP12 mESC, dTAG13, 4h, replicate 1

description: Library name: Adnp_ChIP_AdnpFKBP_4h_r1


title: D1408T64

description: Library name: Dataset_B_64


title: Planktonic, AF293, Normoxia, rep4

description:
Library name: AF293_N_PL4
column name in biofilm_vs_planktonic.txt is AF293_N_PL4


title: Frozen breast tissue, matched breast cancar tissue, patient 2

description: Library name: BC2


title: Frozen breast tissue, matched healthy tissue, patient 4

description: Library name: BCH4


title: ADNP ChIP in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 2

description: Library name: Adnp_ChIP_AdnpFKBP_24h_r2


title: 006K-DO_bulk kidney xenograft

description: Library name: 006K-DO_bulk

value: kidney

value: not applicable

value: KO:GGTA1, CMAH, iGb3s, B4GalNT2; KI:CD46, TBM

value: aCD154 (C10)+ Abatacept


title: D1408T62

description: Library name: Dataset_B_62

value: Blood


title: ADNP ChIP in ADNP-FKBP12 mESC, dTAG13, 24h, replicate 1

description: Library name: Adnp_ChIP_AdnpFKBP_24h_r1


title: D1408T67

description: Library name: Dataset_B_67


title: Planktonic, AF293, Normoxia, rep3

description:
Library name: AF293_N_PL3
column name in biofilm_vs_planktonic.txt is AF293_N_PL3


title: Planktonic, AF293, Normoxia, rep2

description:
Library name: AF293_N_PL2
column name in biofilm_vs_planktonic.txt is AF293_N_PL2


title: D1408T63

description: Library name: Dataset_B_63


title: D1408T60

description: Library name: Dataset_B_60


title: POL3 Input in GTF3C1-FKBP12 mESC, ctrl, replicate 2

description: Library name: Gtf3c1FKBP_In_ctrl_r2


title: Frozen breast tissue, matched healthy tissue, patient 3

description: Library name: BCH3


title: Frozen breast tissue, matched healthy tissue, patient 2

description: Library name: BCH2


title: Frozen breast tissue, matched breast cancar tissue, patient 1

description: Library name: BC1


title: Planktonic, AF293, Normoxia, rep1

description:
Library name: AF293_N_PL1
column name in biofilm_vs_planktonic.txt is AF293_N_PL1


title: POL3 Input in GTF3C1-FKBP12 mESC, ctrl, replicate 1

description: Library name: Gtf3c1FKBP_In_ctrl_r1


title: R62.WT2

city: Ann Arbor

first: Andrew

middle: P

last: Lieberman

state: MI

address: 1150 W Medical Center Dr.

institute: University of Michigan

description:
Library name: 15377-CK-9
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: R62-WT2

data_processing:
Reads trimmed using CutAdapt v4.8.
FastQC v0.11.8 used to ensure data quality.
Fastq Screen v0.15.3 used to screen for various types of contamination.
Reads mapped to GRCm38 using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3.
Assembly: GRCm38 (ENSEMBL)
Supplementary files format and content: The .csv file has compiled RSEM counts with gene name annotation.

source_name: Quadriceps

growth_protocol: Mice were aged in 12-hour light-dark cycles with food and water available ad libitum, to 12 or 24 weeks as indicated in sample information below, before humane euthanization.

extract_protocol:
Mice were euthanized at 12 or 24 weeks, and tibialis anterior and quadriceps were dissected and flash-frozen. Total RNA was then extracted using TRIzol, chloroform, and isopropanol. 500 ng RNA per sample was used for library prep and sequencing.
RNA libraries for RNA-seq were prepared by the University of Michigan Advanced Genomics Core, using the Illumina platform with manufacturer's protocols for polyA-enrichment.

value: Quadriceps

value: Skeletal muscle


title: Healthy PBMC, donor 5

description: Library name: PBMCH5

data_processing:
Illumina TruSeq adapters and PCR primer sequences were trimmed from the reads with Cutadapt v2.8.
Reads were mapped sequentially as described in the publication using Hisat2 v2.1.0
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample


title: D1408T69

description: Library name: Dataset_B_69


title: POL3 ChIP in GTF3C1-FKBP12 mESC, ctrl, replicate 2

description: Library name: Pol3_ChIP_Gtf3c1FKBP_ctrl_r2

value: hybrid 129-C57BL/6


title: Frozen breast tissue, matched healthy tissue, patient 1

description: Library name: BCH1


title: Planktonic, CEA10, Normoxia, rep1

description:
Library name: CEA10_N_PL1
column name in biofilm_vs_planktonic.txt is CEA10_N_PL1


title: POL3 ChIP in GTF3C1-FKBP12 mESC, dTAG13, replicate 2

description: Library name: Pol3_ChIP_Gtf3c1FKBP_24h_r2

value: embryonic stem cells (ESC)


title: R62.WT1

description:
Library name: 15377-CK-7
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: R62-WT1


title: POL3 ChIP in GTF3C1-FKBP12 mESC, ctrl, replicate 1

description: Library name: Pol3_ChIP_Gtf3c1FKBP_ctrl_r1


title: D1408T58

description: Library name: Dataset_B_58


title: Patient 73 intrahepathic cholangiocarcinoma

city: Montpellier

first: Simon

last: Cabello-Aguilar

address: Avenue du doyen Gaston Giraud

institute: CHU Montpellier

description: Library name: L73

data_processing:
Raw counts matrix were obtained using the DRAGEN RNA pipeline (v4.2.7, Illumina).
Assembly: hg19
Supplementary files format and content: tab-delimited text file containing the raw counts

source_name: bile duct

extract_protocol:
Total RNA were extracted using Maxwell® RSC FFPE RNA kit (Promega), following the manufacturer’s instructions. Concentrations were measured using Qubit RNA HS assays (Thermo Fisher Scientific).
RNA sequencing was performed using the RNA Prep with Enrichment, (L) Tagmentation in combination with the RNA Pan-cancer panel (1,362 genes, Illumina) according to the manufacturer’s recommendations. Libraries were sequenced on a NextSeq 500 instrument (2×150 cycles, Illumina).

value: bile duct


title: POL3 ChIP in GTF3C1-FKBP12 mESC, dTAG13, replicate 1

description: Library name: Pol3_ChIP_Gtf3c1FKBP_24h_r1


title: D1408T61

description: Library name: Dataset_B_61


title: D1408T57

description: Library name: Dataset_B_57


title: SCA1.dz2

description:
Library name: 15377-CK-4
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: SCA1-dz2

source_name: Tibialis anterior

value: Tibialis anterior


title: D1408T55

description: Library name: Dataset_B_55

value: Haematopoietic stem and progenitors


title: D1408T59

description: Library name: Dataset_B_59


title: Patient 71 intrahepathic cholangiocarcinoma

description: Library name: L71


title: Patient 70 intra hepathic cholangiocarcinoma

description: Library name: L70


title: ADNP Input in GTF3C1-FKBP12 mESC, ctrl, replicate 1

description: Library name: Gtf3c1FKBP_In_ctrl_r3

value: 24h DMSO ctrl


title: D1408T54

description: Library name: Dataset_B_54


title: Patient 69 intrahepathic cholangiocarcinoma

description: Library name: L69


title: ADNP Input in GTF3C1-FKBP12 mESC, ctrl, replicate 2

description: Library name: Gtf3c1FKBP_In_ctrl_r4


title: SCA1.dz1

description:
Library name: 15377-CK-2
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: SCA1-dz1


title: Patient 65 intrahepathic cholangiocarcinoma

description: Library name: L65


title: D1408T56

description: Library name: Dataset_B_56


title: ADNP ChIP in GTF3C1-FKBP12 mESC, ctrl, replicate 2

description: Library name: Adnp_ChIP_Gtf3c1FKBP_ctrl_r2


title: ADNP ChIP in GTF3C1-FKBP12 mESC, ctrl, replicate 1

description: Library name: Adnp_ChIP_Gtf3c1FKBP_ctrl_r1


title: SCA1.dz3R

description:
Library name: 15377-CK-16
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: SCA1-dz3R


title: D1408T51

description: Library name: Dataset_B_51


title: D1408T52

description: Library name: Dataset_B_52


title: SCA1.WT4

description:
Library name: 15377-CK-17
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: SCA1-WT4


title: Patient 64 extrahepathic cholangiocarcinoma

description: Library name: L64


title: Patient 63 intrahepathic cholangiocarcinoma

description: Library name: L63


title: R62.dz4

description:
Library name: 15377-CK-14
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: R62-dz4


title: D1408T50

description: Library name: Dataset_B_50


title: R62.WT4

description:
Library name: 15377-CK-13
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: R62-WT4


title: Patient 62 intra hepathic cholangiocarcinoma

description: Library name: L62


title: ADNP Input in ADNP-3xFLAG mESC

description: Library name: Adnp_P3_In_AdnpWT


title: ADNP ChIP in GTF3C1-FKBP12 mESC, dTAG13, replicate 2

description: Library name: Adnp_ChIP_Gtf3c1FKBP_24h_r2


title: D1408T49

description: Library name: Dataset_B_49


title: R62.dz3

description:
Library name: 15377-CK-12
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: R62-dz3


title: Patient 61 intra hepathic cholangiocarcinoma

description: Library name: L61


title: Patient 60 intrahepathic cholangiocarcinoma

description: Library name: L60


title: D1408T74

description: Library name: Dataset_B_74


title: ADNP ChIP in GTF3C1-FKBP12 mESC, dTAG13, replicate 1

description: Library name: Adnp_ChIP_Gtf3c1FKBP_24h_r1


title: ADNP ChIP in ADNP-3xFLAG mESC, replicate 6

description: Library name: Adnp_ChIP_AdnpWT_r6


title: SCA1.WT2

description:
Library name: 15377-CK-3
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: SCA1-WT2


title: D1408T48

description: Library name: Dataset_B_48


title: R62.WT3

description:
Library name: 15377-CK-11
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: R62-WT3


title: Patient 59 intrahepathic cholangiocarcinoma

description: Library name: L59


title: D1408T53

description: Library name: Dataset_B_53


title: ADNP ChIP in ADNP-3xFLAG mESC, replicate 5

description: Library name: Adnp_ChIP_AdnpWT_r5


title: R62.dz2

description:
Library name: 15377-CK-10
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: R62-dz2


title: Patient 58 intrahepathic cholangiocarcinoma

description: Library name: L58


title: D1408T47

description: Library name: Dataset_B_47


title: ADNP ChIP in ADNP-3xFLAG mESC, replicate 4

description: Library name: Adnp_ChIP_AdnpWT_r4


title: Patient 57 intrahepathic cholangiocarcinoma

description: Library name: L57


title: SCA1.WT1

description:
Library name: 15377-CK-1
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: SCA1-WT1


title: ADNP ChIP in ADNP-3xFLAG mESC, replicate 2

description: Library name: Adnp_ChIP_AdnpWT_r2


title: Patient 56 intrahepathic cholangiocarcinoma

description: Library name: L56


title: ADNP ChIP in ADNP-3xFLAG mESC, replicate 3

description: Library name: Adnp_ChIP_AdnpWT_r3


title: D1408T46

description: Library name: Dataset_B_46


title: Patient 55 extrahepathic cholangiocarcinoma

description: Library name: L55


title: D1408T44

description: Library name: Dataset_B_44


title: ADNP ChIP in ADNP-3xFLAG mESC, replicate 1

description: Library name: Adnp_ChIP_AdnpWT_r1


title: R62.dz1

description:
Library name: 15377-CK-8
Column name in 15377-CK_rsem.merged.gene_counts.annot.csv: R62-dz1


title: D1408T45

description: Library name: Dataset_B_45


title: D1408T43

description: Library name: Dataset_B_43


title: RNA-seq in GTF3C1-FKBP12 mESC, dTAG13, 4h, replicate 3

description: Library name: RNAseq_GTF3C1-FKBP12_dTAG13_4h_r3

data_processing:
Demultiplexing and fastq conversion were performed with bcl2fastq2 v1.17.
Sequenced reads were aligned using STAR 2.7.3 and repeat sensitive settings according to Teissandier et al (Mobile DNA, 2019) (--outFilterType BySJout --outFilterMultimapNmax 100000  --outFilterMismatchNmax 3 --winAnchorMultimapNmax 20000 --alignMatesGapMax 350 --seedSearchStartLmax 30 alignTranscriptsPerReadNmax 30000  --alignWindowsPerReadNmax 30000 --alignTranscriptsPerWindowNmax 300 --seedPerReadNmax 3000 --seedPerWindowNmax 300  --seedNoneLociPerWindow 1000--outSAMattributes NH HI NM MD AS nM --outMultimapperOrder Random --outSAMmultNmax --limitBAMsortRAM 10000000000).
Assembly: GRCm39 / mm39
Supplementary files format and content: bigWig files were generated by using samtools and bedtools to calculate per base coverage, then counts were normalized to 1 mio genome mapping reads and bigwigs were generated using bedGraphToBigWig (USCS tools).

extract_protocol:
For RNA-seq, RNA was collected using Absolutely RNA miniprep kit (Agilent) according to manufacturer's instructions. For TT-seq, RNA was isolated using Trizol according to manufacturer's instructions.
Libraries were prepared using TruSeq Ilumina total RNA-seq


title: Pdcd1 cKO, splenic CD8+ T cells baseline scRNA seq

city: Rochester

first: Haidong

last: Dong

state: MN

address: 200 First Street SW

institute: Mayo Clinic

description:
Library name: 2
PIPSeq

data_processing:
For single cell RNA sequencing, quality control, normalization, and downstream analysis were performed in R using Seurat (v4.3.0).
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: spleen

extract_protocol:
Mouse splenic and thymic CD8+ T cells were isolated using CD8a+ T cell isolation kit (Miltenyi Biotec, Cat#130-104-075). Mouse splenic naïve CD8+ T cells were isolated using Naive CD8a+ T Cell Isolation Kit, mouse (Miltenyi Biotec, Cat#130-096-543). For isolating CD8+ tumor infiltrating lymphocytes (TILs), tumors were first cut into small pieces of 2-4mm and digested using tumor dissociation kit at 37°C for 45 minutes with gentle agitation (Miltenyi Biotec, Cat#130-096-730). Dead cells were further removed using Dead cell Removal kit (Miltenyi Biotec, Cat# 130-090-101). CD8+ TILs were then isolated using CD8 (TIL) microbeads, mouse (Miltenyi Biotec, Cat#130-116-478).
Single cell libraries were prepared using Fluent Biosciences Pre-Templated Instant Partitions Sequencing (PIPseq) v3 Kit according to the manufacturer’s protocol. Briefly, cells were first filtered through a 40-μm cell strainer to remove debris and aggregates. The viability was assessed through Trypan Blue cell counting, and samples with more than 80% viability were proceeded for sample preparation. Each sample was loaded to the PIPseq microfluidic system, which partitioned individual cells into droplets containing molecular barcodes for unique transcript identification. During reverse transcription, unique molecular identifiers (UMIs) and well-specific barcodes were incorporated to enable precise quantification and tracking of individual transcripts. Subsequently, cDNA synthesis and amplification were performed to maximize transcript coverage and minimize bias.

value: spleen

value: CD8+ T cells

value: Pdcd1 cKO


title: Pdcd1fl/fl, splenic CD8+ T cells baseline scRNA seq

description:
Library name: 1
PIPSeq


title: Patient 51 extrahepathic cholangiocarcinoma

description: Library name: L51


title: Pdcd1 cKO, CD8+ TIL scRNA seq

description:
Library name: PD-1 cKO
PIPSeq

value: tumor

value: Day 12 post injection


title: Pdcd1fl/fl, CD8+ TIL scRNA seq

description:
Library name: WT
PIPSeq


title: RNA-seq in GTF3C1-FKBP12 mESC, dTAG13, 4h, replicate 2

description: Library name: RNAseq_GTF3C1-FKBP12_dTAG13_4h_r2


title: D1408T42

description: Library name: Dataset_B_42


title: Patient 52 intrahepathic cholangiocarcinoma

description: Library name: L52


title: Patient 50 extrahepathic cholangiocarcinoma

description: Library name: L50


title: RNA-seq in GTF3C1-FKBP12 mESC, dTAG13, 4h, replicate 1

description: Library name: RNAseq_GTF3C1-FKBP12_dTAG13_4h_r1


title: Patient 49 extrahepathic cholangiocarcinoma

description: Library name: L49


title: D1408T40

description: Library name: Dataset_B_40


title: Pdcd1 cKO, thymic CD8+ T cells baseline scRNA seq

description:
Library name: 6
PIPSeq

source_name: thymus

value: thymus


title: RNA-seq in GTF3C1-FKBP12 mESC, ctrl, 4h, replicate 3

description: Library name: RNAseq_GTF3C1-FKBP12_ctrl_4h_r3

value: 4h DMSO ctrl


title: D1408T38

description: Library name: Dataset_B_38


title: Patient 46 intra hepathic cholangiocarcinoma

description: Library name: L46


title: D1408T39

description: Library name: Dataset_B_39


title: Multiplexed_7

description:
Library name: 7
Parse Biosciences

data_processing:
TCR clonotype assembly, sequence annotation, and clonotype calling were performed using the Parse Biosciences TCR analysis pipeline. Productive clonotypes were defined as unique paired TRA–TRB CDR3 nucleotide sequences with detectable template counts.
The 8 uploaded libraries contain TCR sequencing dataset comprises 14 samples derived from splenic, thymic, and tumor-infiltrating CD8⁺ T cells from Pdcd1fl/fl (control) and CD8-specific Pdcd1 conditional knockout (Pdcd1 cKO) mice under baseline and tumor-bearing conditions. Baseline samples include splenic CD8⁺ T cells from Pdcd1fl/fl (Sample 1, 155A spleen) and Pdcd1 cKO (Sample 2, 155C spleen), as well as thymic CD8⁺ T cells from Pdcd1fl/fl (Sample 3, 155A thymus) and Pdcd1 cKO (Sample 4, 155C thymus). Tumor-infiltrating lymphocyte (TIL) samples include CD8⁺ T cells isolated from B16-OVA tumors in Pdcd1fl/fl (Sample 6, 160C tumor) and Pdcd1 cKO mice (Sample 5, 160B tumor; Sample 13, 160A tumor as an independent cKO replicate), and from B16-F10 tumors in Pdcd1fl/fl (Sample 8, 164C tumor) and Pdcd1 cKO mice (Sample 7, 164B tumor). Thymic CD8⁺ T cells from tumor-bearing mice include B16-OVA-bearing Pdcd1fl/fl (Sample 10, 160C thymus) and Pdcd1 cKO mice (Sample 9, 160B thymus; Sample 14, 160A thymus as an independent cKO replicate), as well as B16-F10-bearing Pdcd1fl/fl (Sample 12, 164C thymus) and Pdcd1 cKO mice (Sample 11, 164B thymus).
Assembly: GRCm39
Supplementary files format and content: Tab-delimited values file
Library strategy: TCR-Seq

source_name: CD8+ T cells

extract_protocol:
Mouse splenic and thymic CD8+ T cells were isolated using CD8a+ T cell isolation kit (Miltenyi Biotec, Cat#130-104-075). Mouse splenic naïve CD8+ T cells were isolated using Naive CD8a+ T Cell Isolation Kit, mouse (Miltenyi Biotec, Cat#130-096-543). For isolating CD8+ tumor infiltrating lymphocytes (TILs), tumors were first cut into small pieces of 2-4mm and digested using tumor dissociation kit at 37°C for 45 minutes with gentle agitation (Miltenyi Biotec, Cat#130-096-730). Dead cells were further removed using Dead cell Removal kit (Miltenyi Biotec, Cat# 130-090-101). CD8+ TILs were then isolated using CD8 (TIL) microbeads, mouse (Miltenyi Biotec, Cat#130-116-478).
In this TCR sequencing cohort, single cell suspensions were prepared using Evercode TCR kit. cDNA libraries were generated from whole-transcriptome amplification products containing V(D)J segments spanning the CDR3 regions of TCRα (TRA) and TCRβ (TRB) chains, followed by ligation of Illumina-compatible adapters.


title: Multiplexed_6

description:
Library name: 6
Parse Biosciences


title: RNA-seq in GTF3C1-FKBP12 mESC, ctrl, 4h, replicate 1

description: Library name: RNAseq_GTF3C1-FKBP12_ctrl_4h_r1


title: Patient 43 intrahepathic cholangiocarcinoma

description: Library name: L43


title: Patient 44 extrahepathic cholangiocarcinoma

description: Library name: L44


title: D1408T37

description: Library name: Dataset_B_37


title: D1408T35

description: Library name: Dataset_B_35


title: Multiplexed_4

description:
Library name: 4
Parse Biosciences


title: RNA-seq in GTF3C1-FKBP12 mESC, dTAG13, 24h, replicate 3

description: Library name: RNAseq_GTF3C1-FKBP12_dTAG13_24h_r3


title: Multiplexed_5

description:
Library name: 5
Parse Biosciences


title: RNA-seq in GTF3C1-FKBP12 mESC, ctrl, 4h, replicate 2

description: Library name: RNAseq_GTF3C1-FKBP12_ctrl_4h_r2


title: Patient 42 intrahepathic cholangiocarcinoma

description: Library name: L42


title: Pdcd1fl/fl, thymic CD8+ T cells baseline scRNA seq

description:
Library name: 5
PIPSeq


title: Multiplexed_8

description:
Library name: 8
Parse Biosciences


title: Multiplexed_3

description:
Library name: 3
Parse Biosciences


title: RNA-seq in GTF3C1-FKBP12 mESC, dTAG13, 24h, replicate 2

description: Library name: RNAseq_GTF3C1-FKBP12_dTAG13_24h_r2


title: D1408T41

description: Library name: Dataset_B_41


title: Patient 40 intrahepathic cholangiocarcinoma

description: Library name: L40


title: D1408T36

description: Library name: Dataset_B_36


title: D1408T33

description: Library name: Dataset_B_33


title: RNA-seq in GTF3C1-FKBP12 mESC, dTAG13, 24h, replicate 1

description: Library name: RNAseq_GTF3C1-FKBP12_dTAG13_24h_r1


title: Multiplexed_2

description:
Library name: 2
Parse Biosciences


title: RNA-seq in GTF3C1-FKBP12 mESC, ctrl, 24h, replicate 3

description: Library name: RNAseq_GTF3C1-FKBP12_ctrl_24h_r3


title: Patient 37 extrahepathic cholangiocarcinoma

description: Library name: L37


title: D1408T32

description: Library name: Dataset_B_32


title: Multiplexed_1

description:
Library name: 1
Parse Biosciences


title: Patient 36 extrahepathic cholangiocarcinoma

description: Library name: L36


title: RNA-seq in GTF3C1-FKBP12 mESC, ctrl, 24h, replicate 1

description: Library name: RNAseq_GTF3C1-FKBP12_ctrl_24h_r1


title: RNA-seq in GTF3C1-FKBP12 mESC, ctrl, 24h, replicate 2

description: Library name: RNAseq_GTF3C1-FKBP12_ctrl_24h_r2


title: D1408T31

description: Library name: Dataset_B_31


title: RNA-seq in CTCF-FKBP12 mESC, dTAG13, 24h, replicate 3

description: Library name: RNAseq_CTCF-FKBP12_dTAG13_24h_r3

value: mES159-2 Rosa26[(tg)Cre-ERT2/(tg)BirA-V5] Adnp[(Cterm)Avi-3F/(Cterm)Avi-3F] Ctcf[(Cterm)FKBP12F36/(Cterm)FKBP12F36]


title: Patient 32 intrahepathic cholangiocarcinoma

description: Library name: L32


title: D1408T30

description: Library name: Dataset_B_30

value: Blood


title: PUER cells, IL3, 200 nM OHT, 48h, H3K4me3

city: Grand Forks

first: Manu

last: Manu

state: ND

address: 10 Cornell Street, Stop 9019

department: Biology

institute: University of North Dakota

description:
Library name: Sample 6
CUT&RUN of PUER cells after 48 hrs of 200 nM OHT treatment using H3K4me3 antibody

data_processing:
The quality of the reads was assessed using FASTQC (v0.12.1) and trimming was performed with Trimmomatic (v0.39). Reads were aligned to the mm10 reference using Hisat2 (v2.2.0). Duplicates were marked and removed using Picard. Peaks were called using MACS2 (v2.2.9.1) with an FDR of 0.05.
Assembly: mm10
Supplementary files format and content: CUT&RUN signal in bigWig format
Library strategy: CUT&Run

source_name: PUER

growth_protocol: PUER cells were routinely maintained in complete Iscove’s Modified Dulbecco’s Glutamax medium (IMDM; Gibco, 12440061) supplemented with 10% FBS, 50μM β-mercaptoethanol, 5ng/ml IL3 (Peprotech, 213-13).

extract_protocol:
The CUT&RUN assay was performed using the CUTANA CUT&RUN kit (Epycypher, #14-1048), following the manufacturer’s instructions. Briefly, 100,000 undifferentiated and 48h IL3-OHT PUER cells were harvested, immobilized to activated Concanavalin A beads and permeabilized with digitonin. 0.5μg of α-PU.1 (Santa Cruz, #sc-390405) primary and a 1:200 dilution of Rabbit anti-Mouse IgG (Cytek, #70-8076-M002) secondary were added to the samples before treatment with pAG-MNase for 2 hours. The released DNA fragments were purified and libraries prepared.
Libraries were prepared using the CUTANA CUT&RUN Library Prep Kit (Epicypher, #14-1001) according to manufacturer's instructions.

treatment_protocol: PUER cells were expanded in T-75 flasks prior to the initiation of differentiation. The macrophage differentiation was initiated by the addition of 200nM OHT. We regard time zero (0h) of differentiation as occurring just before the addition of OHT.

value: PUER

value: bone marrow-derived progenitors

value: Tamoxifen (OHT) added at 0h for 48h

tag: antibody


title: PUER cells, IL3, 200 nM OHT, 48h, PU.1

description:
Library name: Sample 4
CUT&RUN of PUER cells after 48 hrs of 200 nM OHT treatment using PU.1 antibody

value: PU.1 ( Santa Cruz, #sc-390405)


title: Patient 35 intrahepathic cholangiocarcinoma

description: Library name: L35

value: bile duct


title: RNA-seq in CTCF-FKBP12 mESC, dTAG13, 24h, replicate 1

description: Library name: RNAseq_CTCF-FKBP12_dTAG13_24h_r1

value: hybrid 129-C57BL/6

value: embryonic stem cells (ESC)


title: RNA-seq in CTCF-FKBP12 mESC, dTAG13, 24h, replicate 2

description: Library name: RNAseq_CTCF-FKBP12_dTAG13_24h_r2


title: PUER cells, IL3, 200 nM OHT, 48h, IgG

description:
Library name: Sample 5
CUT&RUN of PUER cells after 48 hrs of 200 nM OHT treatment using IgG antibody


title: D1408T29

description: Library name: Dataset_B_29

value: Haematopoietic stem and progenitors


title: Patient 31 intrahepathic cholangiocarcinoma

description: Library name: L31


title: Patient 30 intrahepathic cholangiocarcinoma

description: Library name: L30


title: PUER cells, IL3, no OHT, 0h, H3K4me3

description:
Library name: Sample 3
CUT&RUN of undifferentiated PUER cells using H3K4me3 antibody


title: RNA-seq in CTCF-FKBP12 mESC, ctrl, 24h, replicate 3

description: Library name: RNAseq_CTCF-FKBP12_ctrl_24h_r3

value: 24h DMSO ctrl


title: D1408T28

description: Library name: Dataset_B_28


title: D1408T27

description: Library name: Dataset_B_27


title: PUER cells, IL3, no OHT, 0h, IgG

description:
Library name: Sample 2
CUT&RUN of undifferentiated PUER cells using IgG antibody


title: Patient 29 intrahepathic cholangiocarcinoma

description: Library name: L29


title: PUER cells, IL3, no OHT, 0h, PU.1

description:
Library name: Sample 1
CUT&RUN of undifferentiated PUER cells using PU.1 antibody


title: RNA-seq in CTCF-FKBP12 mESC, ctrl, 24h, replicate 2

description: Library name: RNAseq_CTCF-FKBP12_ctrl_24h_r2


title: Patient 28 intrahepathic cholangiocarcinoma

description: Library name: L28


title: RNA-seq in CTCF-FKBP12 mESC, ctrl, 24h, replicate 1

description: Library name: RNAseq_CTCF-FKBP12_ctrl_24h_r1


title: D1408T26

description: Library name: Dataset_B_26