title: IL-9 treated 3

city: Indianapolis

first: Cheuk Lam

last: Cheung

state: Indiana

address: 635 North Barnhill Drive

institute: Indiana University School of Medicine

description:
Library name: Sample 6
S3_S26

data_processing:
Using NovaSeq 6000 kit with read length 100bp
QC of the raw sequence data with FASTQC no trimming required
The sequence reads were mapped to the designated reference genome using STAR (Spliced Transcripts Alignment to a Reference) (Dobin et al. 2012). To evaluate the quality of the RNA-seq data, the number of reads that fall into different annotated regions (exonic, intronic, splicing junction, intergenic, promoter, UTR, etc.) of the reference genes was determined with bamUtils (Breese and Liu 2013).
Low quality mapped reads (including reads mapped to multiple positions) were excluded and featureCounts (Liao, Smyth, and Shi 2013) was used to quantify the gene level expression. Differential gene expression analysis was performed with edgeR (Robinson, Mccarthy, and Smyth 2010). In this workflow, the statistical methodology applied uses negative binomial generalized linear models with likelihood ratio tests.
Assembly: Reference genome UCSC hg38
Supplementary files format and content: raw counts (feature counts) for each sample

source_name: small airways

growth_protocol: human small airway epithelial cells (hSAEC) were supplemented with Lonza SingleQuot kit supplements and growth factors (CC-4124) to make small airway growth media human small airway epithelial cells were stimulated with 40ng/ml recombinant IL-9 for 6 hours vs no treatment control

extract_protocol:
RNA was harvested using Rnaeasy plus micro kit (Qiagen).
KAPA mRNA Hyperprep Kit

treatment_protocol: human small airway epithelial cells were stimulated with 40ng/ml recombinant IL-9 (biolegend)for 6 hours vs no treatment control

value: small airways

value: hSAEC

value: airway epithelial cells

value: 6h 40ng/ml IL-9

value: paired-end


title: L1a1 DNA rep1

status: Public on Apr 28 2026

type: SRA

city: Rehovot

first: Simon

last: Fishilevich

address: 234 Herzl St

country: Israel

institute: Weizmann Institute of Science

description: Library name: L1a1 DNA rep1

library_source: genomic

data_processing:
Each sample R1 and R3 reads (containing the barcode) were mapped with bowtie2 (--very-sensitive) to the barcode-oligo association list We applied several quality filters on the resulting alignments. We first filtered out read pairs that didn’t map as proper pairs, and then ensured the mapped sequence completely matched the known barcode sequence by requiring that both R1 and R3 reads have CIGAR stings = 15M, MD flags = 15 and a mapping quality of at least 20. We consolidated read abundance per barcode by selecting only reads with unique UMIs, the result being abundance counts for each barcode, across each replicate library of each cell type for both RNA and DNA.
Assembly: GRCh37
Supplementary files format and content: oligos_to_barcodes.txt file contains pairs of oligo-barcode associations. activity_and_differential_activity.txt file contains for each oligo the RNA read count, DNA read count, activity (classification, estimate and FDR), and differential activity for each pair of alleles (logFC and FDR).

molecule: genomic DNA

organism: Homo sapiens

source_name: Fetal chondrocytes

extract_protocol:
The cells were washed with PBS three times, and genomic DNA and total RNA was extracted using AllPrep DNA/RNA mini kit (Qiagen).
For DNA/RNA barcode sequencing, mRNA was treated with Turbo DNase to remove contaminating DNA, and reverse transcribed with SuperScript IV (Invitrogen) using a primer containing unique molecular identifiers (UMIs). Resulting cDNA and genomic DNA was split into multiple reactions to reduce PCR jack-potting effects and barcode amplification performed with NEBNext high-fidelity polymerase for three cycles using a forward primer containing P5 adaptor and a sample index and a reverse primer containing P7 adaptor and UMIs. PCR products were purified with AMPure XP beads (Beckman Coulter) to remove primers and concentrate samples. These products underwent a second round of amplification using P5 and P7 primers. All reactions were pooled and run on agarose gels for size selection and submitted for sequencing. For DNA-barcode association, CRE-barcode fragment is amplified with a forward primer upstream from CRE and a reverse primer downstream from barcode, using a plasmid library as a template, followed by AMPure XP beads purification and sequencing.

tag: cell line

value: Fetal chondrocytes

tag: cell type


title: A375 –R (1)

city: Amsterdam

first: Mrittika

last: Adhikary

address: Plesmanlaan 121

country: Netherlands

institute: Netherlands Cancer Institute

description: Library name: Sample 3

library_source: transcriptomic

data_processing:
Adaptors were removed from FASTQ files using cutadapt with parameters (-quality-base=33 -O 7 -e 0.15 -m 20 -q 5)
Ribosomal RNA (rRNA) and tRNA contaminants were removed by aligning FASTQ reads with Bowtie2 version 2.5.2 and parameters ( -seed 42 -p1 -local) against a reference library (rRNA reference was obtained from GENCODE v19; rRNA, MT_RNA, rRNA_pseudogene, and tRNA reference data was obtained from GtRNAdb)
Preprocessed FASTQ files were then aligned with TopHat2 version v.2.1.1 and Bowtie2 against GRCh37/hg19 and GENCODE v19/BASIC transcripts with Ensembl coordinates using the parameters (seed 41 -n 2-m 1 -novel-juncs -- no-novel-indels –no-coverage-search –segment-length 25)
Assembly: GRCh37/hg19
Supplementary files format and content: tab-delimited txt file includes raw counts for each sample
Library strategy: Ribo-Seq

molecule: total RNA

growth_protocol: A375 cells were cultured in Dulbecco’s modified Eagle’s medium (DMEM; Gibco), supplemented with 10% fetal bovine serum and 100 U/ml penicillin–streptomycin. were maintained in a humidified atmosphere containing 5% CO2 at 37 °C

extract_protocol:
Total RNA was isolated using Trizol reagent (Invitrogen), according to manufacturer’s instructions. Rapid gel extraction was used, followed by overnight precipitation at −20 °C for RNA extraction from the polyacrylamide gels. Ribosomal RNA depletion was not performed. Prepared RPF libraries were analyzed on a 2100 Bioanalyzer using a 7500 chip (Agilent, Santa Clara, CA) and quantified by qPCR (Cat.no. 07960140001, Roche, Switzerland) and subsequently diluted to a 10 nM concentration. Next, the libraries were pooled and loaded with 1.5 pM on a NextSeq550Dx system (RUO mode) and sequenced with 75-base single-read using a 75 Cycles High Output Kit v2.5 (Illumina Inc., San Diego).
The generation of Ribosome-Protected Fragment (RPF) libraries was done as previously described by Ingolia et al. 2012.

treatment_protocol: Arginine-free medium was prepared by adding glucose (Gibco), sodium pyruvate (Sigma) and all amino acids except for L-arginine to RPMI 1640 Medium without amino acids (US Biologicals). Cells were treated either with arginine-less medium, or control medium for 48 hours.

value: Melanoma cancer

tag: treatment

value: arginine depletion


title: liver, fasted, CT32, replicate 2, male

city: Manchester

first: Jessica

middle: Minnie

last: Treeby

address: Oxford Road

country: United Kingdom

institute: Manchester University

description: Library name: JMF50_S50_R1_001

data_processing:
Gencode Release M38 (GRCm39)
The Galaxy server was used for all pipelines except DryR and Masigpro. Raw reads were QCed and trimmed using Trimmomatic (Sliding window trimming, 4 bases average, average quality required 20) before being aligned to the mouse genome (Release M38 GRCm39) using HISAT2 using default options. Transcripts were assembled and counted using feature counts with GENCODE annotations for M38 (GRCm39), using default options and keeping all annotated genes including all predicted genes, pseudogenes and non-coding RNAs. Pairwise comparisons of transcriptome signatures were performed for each timepoint, with diet (ad libitium fed and fasting) as primary factor and sex (male or female) as the secondary factor using DEseq2 or DEXseq for gene and exon counts, respectively. Exon usage values equal to 0 were replaced by the smallest non-zero exon usage value (a, floor value), exon usage values equal to 1 were replaced by 1-a (ceiling value), and exon usage values equal to 0.5 were replaced by 0.4999999. To satisfy the Gaussian assumptions of the linear modeling frameworks in both maSigPro and dryR, exon usage proportions were logit-transformed (LN(exon usage/1-exon usage)). Lastly, a variance-based filter was applied where exons with >40 floor/ceiling values were discarded. Low expression genes/exons i.e., genes/exons with less than 10 counts per 20 samples (1/4 of the dataset) were filtered out in R before analyses with DryR and MaSigPro. Genes were further filtered in DryR and Masigpro based on BICW values (>0.8) or p values (<0.05), respectively. High confidence differentially expressed genes/exons passed DryR or Masigpro thresholds and DESeq2/DEXseq thresholds (adjusted p value < 0.05, LogFC [1] and adjusted p value < 0.05, LogFC [0.58], respectively) in at least two time points.
Assembly: Release M38 (GRCm39)
Supplementary files format and content: Normalised count file provided (.txt format)

organism: Mus musculus

source_name: Liver

growth_protocol: Animal experiments were licensed under the Animals (Scientific Procedures) Act of 1986 (UK) and were approved by the animal welfare committees at the University of Manchester. Eight- to twelve-weeks old C57BL/6J male and female mice were purchased from Charles River (UK) and acclimatized to the local animal unit for 1 week before the experiment. Mice were provided with a standard chow diet (TD.220157) ad libitum and group-housed (4-4 individuals) under a 12:12 h light/dark cycle at ~350 lux during the light phase and 0 lux during the dark phase for 10 days before being exposed to constant darkness (DD) for the 11th day. Ambient temperature was kept at 21 ± 5 °C, the humidity was ~51 ± 8%, with water available ad libitum.

extract_protocol:
RNA was extracted form liver samples using standard Trizol procedure (Invitrogen).
Total RNA was submitted to the Genomic Technologies Core Facility (GTCF). Quality and integrity of the RNA samples were assessed using a 4200 TapeStation (Agilent Technologies) and then libraries generated using the Illumina® Stranded mRNA Prep. Ligation kit (Illumina, Inc.) according to the manufacturer’s protocol. Briefly, total RNA (typically 0.025-1ug) was used as input material from which polyadenylated mRNA was purified using poly-T, oligo-attached, magnetic beads. Next, the mRNA was fragmented under elevated temperature and then reverse transcribed into first strand cDNA using random hexamer primers and in the presence of Actinomycin D (thus improving strand specificity whilst mitigating spurious DNA-dependent synthesis). Following removal of the template RNA, second strand cDNA was then synthesized to yield blunt-ended, double-stranded cDNA fragments. Strand specificity was maintained by the incorporation of deoxyuridine triphosphate (dUTP) in place of dTTP to quench the second strand during subsequent amplification. Following a single adenine (A) base addition, adapters with a corresponding, complementary thymine (T) overhang were ligated to the cDNA fragments. Pre-index anchors were then ligated to the ends of the double-stranded cDNA fragments to prepare them for dual indexing. A subsequent PCR amplification step was then used to add the index adapter sequences to create the final cDNA library. The adapter indices enabled the multiplexing of the libraries, which were pooled prior to cluster generation using a cBot instrument. The loaded flow-cell was then paired-end sequenced (76 + 76 cycles, plus indices) on an Illumina HiSeq4000 instrument. Finally, the output data was demultiplexed and BCL-to-Fastq conversion performed using Illumina’s bcl2fastq software, version 2.20.0.422

treatment_protocol: On the 11th day from CT8 and every 4 hours thereafter until CT44, under dim red light mice were killed humanely by cervical dislocation followed by cessation of circulation. Then, liver ( ~40 mg from the centre of the left lobe) samples were immediately dissected and frozen on dry ice.

tag: tissue

value: Liver

value: male

tag: genotype

value: fasted


title: e11.5_slide_seq

city: Pittsburgh

first: guang

last: li

state: PA

address: 530 45th St. 8116 Rangos Research Center

country: USA

institute: university of pittsburgh

description:
Library name: e11.5_slide_seq
e11.5_slide_seq;

data_processing:
We acquired the unfiltered feature-barcode matrix for each sample by using Space Ranger (v2. 1. 0) ‘count’ command with manually selected dots and reorient-images enabled) on the demultiplexed FASTQ files and associated image, along with the prebuilt mm10 genome reference 2020-A. After it detected tissue, aligned reads, generated feature-spot matrices, and positioned spots, we then used Seurat for all further analyses. In each slide, Seurat objects were created by Load10X_Spatial function and then normalized with natural-log transformation using log1p. Similarly, we obtained the unfiltered matrix of curioseq data by using Curio seeker (v2.0) with custom GRCm38 genome reference (add eGFP). Specifically, Curio seeker was first used to extract bead and molecular barcodes for the raw FASTQ files of each sample and filter beads obtained from sequencing data against the bead barcode whitelist. After filtering out beads with Hamming distance greater than 2 and creating new seurat object, we manually normalized counts with natural log.
We splitted out the Visium image which has more than one tissue. This process can facilitate the integration with scRNA-seq dataset in later section. We cut segments based on exact positions. After subsetting, we can visualize the certain stage cells either on the full image, or a cropped image. (Stage E11.5, P0, E14.5, E16.5 have two tissues in one image, E17_E11 and P2_E14 from second experiment have three tissues in same image.) In Curio seq samples, we first set filter range of each coordinate and then store the shrank image in a new Seurat object.
Assembly: GRCm38
Supplementary files format and content: rds
Library strategy: Spatial Transcriptomics

source_name: heart

extract_protocol:
Mouse hearts from CD1 wildtype, Wt1-CreER-mTmG, and Wt1-CreER-DTA mice were harvested and directly embeded in OCT. Then the hearts were sectioned and used for Visium or Slide-seq profiling.
The heart sections were processed by following the protocol for 10X Genomics Visium Spatial gene expression kit (1000187); For the Slide-seq experiments, we followed the updated protocol in 2023 October from Curio-Bio company.

value: heart

value: cardiac cells

value: CD1 wildtype


title: A375 –R (2)

description: Library name: Sample 4


title: e12.5_1_slide_seq

description:
Library name: e12.5_1_slide_seq
e12.5_1_slide_seq


title: IL-9 treated 1

description:
Library name: Sample 4
S1_S24

molecule: polyA RNA

tag: batch


title: liver, fasted, CT32, replicate 1, male

description: Library name: JMF49_S49_R1_001


title: IL-9 treated 2

description:
Library name: Sample 5
S2_S25


title: A375 CTRL (1)

description: Library name: Sample 1

value: ctrl


title: Untreated 3

description:
Library name: Sample 3
N3_S23

value: No treatment


title: TotalseqC_integrated_bone_iia-injection_1-6

city: Houston

first: Xiang

last: Zhang

address: One Baylor Plaza

institute: Baylor College of Medicine

description: for sample demultiplxing, please refer to HTO_details_README.txt file

library_source: transcriptomic single cell

data_processing:
We utilized the cellranger pipeline for processing the multiplexed raw data. In each dataset and for every patient, we generated multiplexing and count assays based on CellRanger outputs, with all subsequent steps performed using Seurat packages.
Assembly: mm10
Supplementary files format and content: tab-separated values files and matrix files

source_name: bone

extract_protocol:
Tissues were minced and homogenized in 24-well plates using scalpels and pestles, with 0.5 ml of DMEM. Subsequently, 1 ml of tissue dissociation buffer was added, and the mixture was incubated at 37°C for 45 minutes. The dissociation solution was prepared by dissolving collagenase A (Sigma, 11088793001) in a mixture of 75% (vol/vol) DMEM F12/HEPES medium (Gibco, 113300) and 25% (vol/vol) BSA fraction V (Gibco, 15260037) to achieve a working concentration of 1 mg ml⁻¹. The resulting tissue suspension was filtered through a 70-μm strainer to ensure complete homogenization, and the strainer was rinsed with DMEM to recover any remaining single cells. The flow-through was then centrifuged at 500g for 5 minutes, and the supernatant was carefully decanted. In cases where red blood cells (RBCs) were present, a 1×RBC lysis buffer (1:10 dilution of 10× RBC lysis buffer (MACS, 130-094-183) in Milli-Q water) was applied and incubated at room temperature for 10 minutes. To halt and remove RBC lysis, 20 ml of DMEM was added, and the mixture was centrifuged at 450g for 5 minutes. The supernatant was discarded, and the cell pellet was washed with 10 ml of cold DMEM at 4°C. After another centrifugation at 500g for 5 minutes, the supernatant was removed, and the cells were resuspended in cold PBS (Sigma, D8537) containing 0.04% BSA. Finally, the cell suspension was passed through a 40-μm flowmi cell strainer to ensure uniformity.
Library construction follows CellPlex and TotalSeqC sample multiplexing protocal, for CellPlex multiplexed sample, we used 3' end sequencing protocol, while we used 5' end sequencing for TotalSeqC multiplexed samples.
scRNA seq and sample multiplexing

value: bone

value: mixed sample (biotin_negative and biotin_positive)

value: iia-injection


title: A375 CTRL (2)

description: Library name: Sample 2


title: liver, control, CT28, replicate 1, female

description: Library name: JMF47_S47_R1_001

value: female

value: control


title: hsdMko_3

city: Leicester

first: Richard

middle: David

last: Haigh

state: Leicestershire

address: Medical Sciences Building, University Road

department: Department of Respiratory Sciences

institute: University of Leicester

description: Library name: ALT10124A6

data_processing:
Fastq reads were trimmed with Trimmomatic 0.36, TruSeq3-SE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:5 MINLEN:25
Trimmed fastq reads were aligned to MG1655 genome using Rockhopper2.0.3 using default settings
Read count normalisation, gene expression level determination and operon prediction were performed using Rockhopper2.0.3 with default settings
Assembly: Escherichia coli MG1655 accession NC_000913
Supplementary files format and content: tab-delimited text file contains raw counts and normalised counts for each sample
Supplementary files format and content: tab-delimited text file contains RPKM and expression values plus p and q values for each comparison

organism: Escherichia coli

extract_protocol:
Norgen Total RNA Purification Kit
Not available currently


title: liver, control, CT28, replicate 2, female

description: Library name: JMF48_S48_R1_001


title: Untreated 2

description:
Library name: Sample 2
N2_S22

value: small airways

value: hSAEC

value: airway epithelial cells

value: paired-end


title: hsdMko_2

description: Library name: ALT10124A5


title: lung_biotin_positive_intracardiac-injection_3

description: cellranger demultiplexed

source_name: lung

value: lung

value: intracardiac-injection


title: Untreated 1

description:
Library name: Sample 1
N1_S21


title: hsdMko_1

description: Library name: ALT10124A4


title: lung_biotin_positive_intracardiac-injection_2

description: cellranger demultiplexed


title: lung_biotin_positive_intracardiac-injection_1

description: cellranger demultiplexed


title: lung_biotin_positive_intracardiac-injection_4

description: cellranger demultiplexed


title: H5

city: Chicago

first: David

last: Gate

state: IL

address: 745 N Fairbanks Ct

department: Neurology

institute: Northwestern University

data_processing:
FASTQs were demultiplexed and processed using 10X CellRanger v8.0.0 and saved as Seurat objects for analysis
SoupX background contamination removal (contamination fraction was automatically estimated using SoupX::autoEstCont function and counts were adjusted using the SoupX::adjustCounts function)
DoubletFinder doublet removal (doublet formation rate of 4.4%, using 12 PCs and pN = 0.25)
Cells with more than 10% of reads reads attributed to mitochondrial genes were removed
Raw counts were separately lognormalized using Seurat's NormalizeData() and SCTransformed with Seurat's SCTransform()
Lognormalized data was integrated with Seurat's IntegrateLayers() with Harmony integration
Assembly: GRCh38
Supplementary files format and content: Each .rds processed data file is a single-sample seurat object
Supplementary files format and content: The three other processed data files are cellranger output matrices

source_name: PBMC

extract_protocol:
sorted live cells with sytox blue live/dead dye
5’ 10x Genomics with Jumpcode CRISPRclean

value: PBMC

tag: disease

value: ALS patients with C9orf72


title: liver, control, CT28, replicate 1, male

description: Library name: JMF45_S45_R1_001

value: Liver


title: H4


title: liver, control, CT28, replicate 2, male

description: Library name: JMF46_S46_R1_001


title: liver, fasted, CT28, replicate 2, female

description: Library name: JMF44_S44_R1_001

value: male


title: MG1655_3

description: Library name: ALT10124A3


title: MG1655_2

description: Library name: ALT10124A2


title: liver, fasted, CT28, replicate 1, female

description: Library name: JMF43_S43_R1_001


title: MG1655_1

description: Library name: ALT10124A1


title: H2

value: ALS slow


title: liver, fasted, CT28, replicate 2, male

description: Library name: JMF42_S42_R1_001


title: lung_biotin_negative_intracardiac-injection_2

description: cellranger demultiplexed


title: lung_biotin_negative_intracardiac-injection_4

description: cellranger demultiplexed


title: RAD21deg-G1-5PhIAA-T-RS-R3

city: PHILADELPHIA

first: Yu

middle: Sunny

last: Liu

address: 333 Cottman Ave, P3165

department: Cancer Epigenetics Institute

institute: Fox Chase Cancer Center

description: Library name: AS444

data_processing:
Fastq files of Hi-C were first trimed to keep 50bp and then mapped and parsed to generate cooler files using Distiller
Cooler files were then processed for all analysis including contact heatmaps, insulation, scaling plot, loop pileup, compartment and TAD boundary pileup analysis using cooltools. All Hi-C processing and analystic tools are from Open2C (https://open2c.github.io/)
Fastq files of ChIPseq were mapped using Bowtie to generate sam files
HOMER (PMID 20513432) was used to generate tag and bigwig files and call peaks from sam files
DeepTools was used for ChIP signal stacking up
Assembly: hg19
Supplementary files format and content: cooler for Hi-C and BigWig files for ChIPseq

source_name: Colon

growth_protocol: HAP1-RAD21-TEV and HAP1 cells were grown in IMDM medium with10% FBS and 1% penicillin-streptomycin; HCT116 Degron cells were grown in MyCoy's 5A medium with 10% Medium and 1% penicillin-streptomycin. All cells were cultured at 37C in 5% CO2

extract_protocol:
Nuclei were purified using hytonic buffer and after treatments, nuclei and cells were fixed by FA for Hi-C or ChIPseq protocols
Hi-C 2.0 (PMID28435001) and HOMER (PMID 20513432)

treatment_protocol: 1. For HADC inhibitors, all cells are treated with DMSO or 500nM TSA for 3 hours. 2. To degrade CTCF, HCT-116-CTCF degron cells were treated with 1uM 5'-Ph-IAA, or DMSO as a negative control for 6 hours. 3. TEV protease treatment: 15U/ml at 4C for overnight; NB contains 10mM PIPES pH 7.4, 2mM MgCl2 and 10mM KCl; NBS1 buffers are NB with 132mM NaCl. NBS1 is physical conditional buffer.

value: Colon


title: H1


title: liver, control, CT24, replicate 2, female

description: Library name: JMF40_S40_R1_001

value: fasted


title: lung_biotin_negative_intracardiac-injection_3

description: cellranger demultiplexed


title: liver_biotin_positive_intracardiac-injection_4

description: cellranger demultiplexed

source_name: liver

value: liver


title: RAD21deg-G1-5PhIAA-D-RS-R3

description: Library name: AS443


title: H3


title: liver, fasted, CT28, replicate 1, male

description: Library name: JMF41_S41_R1_001


title: G5


title: lung_biotin_negative_intracardiac-injection_1

description: cellranger demultiplexed


title: G4

value: ALS fast


title: liver, control, CT24, replicate 1, female

description: Library name: JMF39_S39_R1_001

value: female


title: RAD21deg-G1-D-T-RS-R3

description: Library name: AS442

value: DMSO+TSA


title: liver, control, CT24, replicate 2, male

description: Library name: JMF38_S38_R1_001


title: G3


title: RAD21deg-G1-D-D-RS-R3

description: Library name: AS441

value: DMSO+DMSO


title: liver_biotin_positive_intracardiac-injection_2

description: cellranger demultiplexed


title: RAD21deg-G1-5PhIAA-D-RS-R1

description: Library name: AS431


title: liver_biotin_positive_intracardiac-injection_3

description: cellranger demultiplexed


title: RAD21deg-G1-5PhIAA-T-RS-R1

description: Library name: AS432


title: G2


title: G1


title: liver, fasted, CT24, replicate 2, female

description: Library name: JMF36_S36_R1_001


title: liver_biotin_negative_intracardiac-injection_4

description: cellranger demultiplexed


title: liver, fasted, CT24, replicate 1, female

description: Library name: JMF35_S35_R1_001


title: RAD21deg-G1-D-D-RS-R1

description: Library name: AS429


title: RAD21deg-G1-D-T-RS-R1

description: Library name: AS430


title: liver_biotin_positive_intracardiac-injection_1

description: cellranger demultiplexed


title: liver_biotin_negative_intracardiac-injection_3

description: cellranger demultiplexed


title: liver, fasted, CT24, replicate 2, male

description: Library name: JMF34_S34_R1_001


title: F4


title: F3


title: liver_biotin_negative_intracardiac-injection_1

description: cellranger demultiplexed


title: R4-16-cRAD21-RS-R2

description: Library name: AS194

source_name: Blood

value: Blood

value: TSA, RAD21 antibody


title: liver_biotin_negative_intracardiac-injection_2

description: cellranger demultiplexed


title: R4-16-WAPAL-RS-R2

description: Library name: AS193

value: TSA, WAPL antibody


title: F5


title: brain_biotin_positive_intracardiac-injection_4

description: cellranger demultiplexed

source_name: brain

value: brain


title: liver, fasted, CT24, replicate 1, male

description: Library name: JMF33_S33_R1_001


title: R4-16-IgG-T-RS-R2

description: Library name: AS192

value: TSA, IgG


title: F1

value: PBMC

value: control


title: liver, control, CT20, replicate 1, female

description: Library name: JMF31_S31_R1_001

value: Liver


title: brain_biotin_positive_intracardiac-injection_3

description: cellranger demultiplexed

value: intracardiac-injection


title: R4-16-cRAD21-D-RS-R2

description: Library name: AS191

value: DMSO, RAD21 antibody


title: F2


title: liver, control, CT20, replicate 2, female

description: Library name: JMF32_S32_R1_001


title: brain_biotin_positive_intracardiac-injection_2

description: cellranger demultiplexed


title: E5

value: ALS slow


title: R4-16-IgG-D-RS-R2

description: Library name: AS189

value: DMSO, IgG


title: E4


title: liver, control, CT20, replicate 1, male

description: Library name: JMF29_S29_R1_001


title: liver, control, CT24, replicate 1, male

description: Library name: JMF37_S37_R1_001

value: fasted


title: liver, fasted, CT20, replicate 2, female

description: Library name: JMF28_S28_R1_001

value: male


title: brain_biotin_negative_intracardiac-injection_4

description: cellranger demultiplexed


title: E3


title: R4-16-cRAD21-T-RS-R1

description: Library name: AS188


title: E2


title: liver, control, CT20, replicate 2, male

description: Library name: JMF30_S30_R1_001

value: female


title: brain_biotin_positive_intracardiac-injection_1

description: cellranger demultiplexed


title: liver, fasted, CT20, replicate 1, female

description: Library name: JMF27_S27_R1_001


title: R4-16-WAPAL-T-RS-R1

description: Library name: AS187


title: R4-16-IgG-T-RS-R1

description: Library name: AS186


title: R4-16-WAPAL-D-RS-R2

description: Library name: AS190

value: DMSO, WAPL antibody


title: liver, fasted, CT20, replicate 2, male

description: Library name: JMF26_S26_R1_001


title: brain_biotin_negative_intracardiac-injection_3

description: cellranger demultiplexed


title: D5

value: ALS fast


title: brain_biotin_negative_intracardiac-injection_2

description: cellranger demultiplexed


title: brain_biotin_negative_intracardiac-injection_1

description: cellranger demultiplexed


title: bone_biotin_positive_intracardiac-injection_4

description: cellranger demultiplexed

value: bone


title: D4


title: liver, control, CT16, replicate 2, female

description: Library name: JMF24_S24_R1_001


title: E1


title: R4-16-WAPAL-D-RS-R1

description: Library name: AS184

value: Blood


title: liver, control, CT16, replicate 1, female

description: Library name: JMF23_S23_R1_001


title: bone_biotin_positive_intracardiac-injection_3

description: cellranger demultiplexed


title: R4-16-IgG-D-RS-R1

description: Library name: AS183


title: R4-16-cRAD21-D-RS-R1

description: Library name: AS185


title: liver, control, CT16, replicate 2, male

description: Library name: JMF22_S22_R1_001


title: liver, fasted, CT20, replicate 1, male

description: Library name: JMF25_S25_R1_001


title: TSA-H3K9Ac-R3

description: Library name: AS165

value: TSA, H3K9Ac antibody


title: bone_biotin_positive_intracardiac-injection_2

description: cellranger demultiplexed


title: D1


title: liver, control, CT16, replicate 1, male

description: Library name: JMF21_S21_R1_001


title: D2


title: bone_biotin_positive_intracardiac-injection_1

description: cellranger demultiplexed


title: TSA-IgG-R3

description: Library name: AS164


title: D3

value: ALS patients with C9orf72


title: liver, fasted, CT16, replicate 2, female

description: Library name: JMF20_S20_R1_001


title: bone_biotin_negative_intracardiac-injection_4

description: cellranger demultiplexed


title: DMSO-H3K9Ac-R3

description: Library name: AS162

value: DMSO, H3K9Ac antibody


title: DMSO-IgG-R3

description: Library name: AS161


title: liver, fasted, CT16, replicate 1, female

description: Library name: JMF19_S19_R1_001


title: C4

value: PBMC


title: liver, fasted, CT16, replicate 2, male

description: Library name: JMF18_S18_R1_001


title: C5


title: C3


title: bone_biotin_negative_intracardiac-injection_2

description: cellranger demultiplexed


title: C2


title: TSA-H3K9Ac-R4

description: Library name: AS171


title: liver, fasted, CT16, replicate 1, male

description: Library name: JMF17_S17_R1_001


title: bone_biotin_negative_intracardiac-injection_3

description: cellranger demultiplexed


title: TSA-IgG-R4

description: Library name: AS170

value: TSA, IgG


title: DMSO-H3K9Ac-R4

description: Library name: AS168


title: DMSO-IgG-R4

description: Library name: AS167


title: C1


title: bone_biotin_negative_intracardiac-injection_1

description: cellranger demultiplexed


title: liver, control, CT12, replicate 2, female

description: Library name: JMF16_S16_R1_001

value: Liver

value: control


title: liver, control, CT12, replicate 1, female

description: Library name: JMF15_S15_R1_001


title: Colon, Il10KO W14, replicate 2

city: Stockholm

first: Jennifer

last: Fransson

address: Karolinska Institutet

country: Sweden

institute: Karolinska Institutet

data_processing:
Read quality was inspected using FastQC and further processed for abundance estimation using Kallisto.
Read abundances and TPM values estimated with Kallisto were compiled into gene expression matrices (counts and tpm)
Assembly: mm10
Supplementary files format and content: .csv-files with count and TPM matrices

source_name: colon

extract_protocol:
Tissue biopsies (approximately 0.5 cm long) were collected from the distal colon and stored at -80°C in RNAlater (Invitrogen). To extract RNA, tissue was lysed in RLT Plus Buffer (QIAGEN) + 2% b-mercaptoethanol by bead-beating (Precellys). RNA was isolated with the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's instructions and quantified using a Nanodrop spectrophotometer (ThermoFisher).
cDNA libraries were sequenced by Novogene Co. Ltd (UK) at a sequencing depth of 20 million reads per sample using paired-end 150 bp reads on a NovaSeq 6000 sequencer with a v1.0 reagent kit. Samples were sequenced using paired-end 150bp sequencing, aiming at a coverage of 20M reads.

value: colon

value: BALB/c Il10KO

tag: time

tag: cage

value: C

tag: rin

tag: lipocalin (ng/g)


title: TSA-RAD21-R2

description: Library name: AS75

value: TSA, RAD21 antibody


title: Colon, Il10KO W12, replicate 3

value: E


title: B4


title: Colon, Il10KO W14, replicate 3


title: liver, control, CT12, replicate 2, male

description: Library name: JMF14_S14_R1_001

value: female


title: B2


title: Colon, Il10KO W14, replicate 1

value: A


title: liver, fasted, CT12, replicate 2, female

description: Library name: JMF12_S12_R1_001

value: male


title: B3

value: ALS slow


title: Colon, Il10KO W12, replicate 2

value: B


title: B1

value: ALS fast


title: TSA-CTCF-R2

description: Library name: AS74

value: Blood

value: TSA, CTCF antibody


title: liver, fasted, CT12, replicate 1, female

description: Library name: JMF11_S11_R1_001


title: TSA-IgG-R2

description: Library name: AS73


title: B5

value: PBMC


title: DMSO-RAD21-R2

description: Library name: AS71

value: DMSO, RAD21 antibody


title: liver, control, CT12, replicate 1, male

description: Library name: JMF13_S13_R1_001

value: Liver


title: liver, fasted, CT12, replicate 2, male

description: Library name: JMF10_S10_R1_001

value: control


title: DMSO-CTCF-R2

description: Library name: AS70

value: DMSO, CTCF antibody


title: A5


title: Colon, Il10KO W12, replicate 1

value: colon

value: BALB/c Il10KO


title: Colon, Il10KO W10, replicate 2

value: C


title: DMSO-IgG-R2

description: Library name: AS69

value: DMSO, IgG


title: A3


title: liver, control, CT8, replicate 1, female

description: Library name: JMF7_S7_R1_001

value: female

value: fasted


title: liver, control, CT8, replicate 2, female

description: Library name: JMF8_S8_R1_001


title: Colon, Il10KO W10, replicate 3

value: F


title: Colon, Il10KO W10, replicate 1


title: Colon, Il10KO W8, replicate 3

value: D


title: A2


title: TSA-RAD21-R1

description: Library name: AS67

value: TSA, RAD21 antibody


title: A4


title: A1

value: ALS slow


title: Colon, Il10KO W8, replicate 2


title: liver, control, CT8, replicate 2, male

description: Library name: JMF6_S6_R1_001


title: liver, fasted, CT12, replicate 1, male

description: Library name: JMF9_S9_R1_001

value: male


title: TSA-CTCF-R1

description: Library name: AS66

value: Blood

value: TSA, CTCF antibody


title: TSA-IgG-R1

description: Library name: AS65

value: TSA, IgG


title: 552_S5_Arthemeter [ATAC-Seq]

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

country: Germany

institute: Helmholtz Zentrum München German Research Center for Environmental Health

description: 10x Genomics single cell multiome (ATAC)

library_source: genomic single cell

data_processing:
Raw reads were aligned to the improved pig genome and pre-processed using the 10x Genomics CellRangerARC pipeline (v 2.0.0) for downstream analyses.
Assembly: ensembl home sampiens v107
Supplementary files format and content: gex.h5ad: Gene expression AnnData as h5ad file
Supplementary files format and content: atac.h5ad: ATAC AnnData as h5ad file

source_name: hiPSC

extract_protocol:
For flow cytometry, differentiating aggregates were incubated with Accutase for 5 minutes in a water bath and dispersed to single cells.  Cells were then stained with SYTOX-Blue for 5 min at RT. Cells were sorted using a FACS Aria III (Becton Dickinson) operated with BD FACSDiva software.
For nuclei isolation and library construction, a low input nuclei isolation protocol adapted from 10X Genomics was performed. In brief, sorted cells were washed once with 1 mL PBS + 1% BSA, counted, centrifuged, and supernatant was aspirated. Subsequently, the washed cell pellet was resuspended in chilled lysis buffer with 0.1x detergent concentration (50 μL per sample) and placed on ice for 5 min. Then wash buffer (500 μL per sample) was added and nuclei were centrifuged. To gradually change from wash to diluted nuclei buffer, cells were washed once in a 1:1 mixture of wash buffer and diluted nuclei buffer and subsequently one with pure diluted nuclei buffer. The washed isolated nuclei were then resuspended in 7-10 μl diluted nuclei buffer and were directly added to the transposition reaction after quality control and counting. In all following steps, 10X Genomics’ Single Cell Multiome ATAC and gene-expression protocols were followed according to the manufacturer’s specifications and guidelines.

value: hiPSC

value: ARXnCFP/nCFP; PAX4mCherry/mCherry

tag: age

value: Stage 5, day 4

tag: enrichment

value: SYTOX-


title: DMSO-RAD21-R1

description: Library name: AS63

value: DMSO, RAD21 antibody


title: 552_S5_Arthemeter [RNA-Seq]

description: 10x Genomics single cell multiome (RNA)

molecule: nuclear RNA


title: Colon, Il10KO W8, replicate 1

value: colon

value: BALB/c Il10KO

value: B


title: liver, fasted, CT8, replicate 2, female

description: Library name: JMF4_S4_R1_001

value: Liver

value: fasted


title: liver, control, CT8, replicate 1, male

description: Library name: JMF5_S5_R1_001

value: female


title: DMSO-CTCF-R1

description: Library name: AS62

value: DMSO, CTCF antibody


title: Colon, Il10KO W6, replicate 3

value: F


title: liver, fasted, CT8, replicate 1, female

description: Library name: JMF3_S3_R1_001

value: male


title: DMSO-IgG-R1

description: Library name: AS61

value: Blood

value: DMSO, IgG


title: 551_S5_CTRL_All [ATAC-Seq]


title: 551_S5_CTRL_All [RNA-Seq]

description: 10x Genomics single cell multiome (RNA)


title: Colon, Il10KO W6, replicate 1

value: A


title: 550_S5_PAX4 [ATAC-Seq]

value: hiPSC


title: liver, fasted, CT8, replicate 2, male

description: Library name: JMF2_S2_R1_001


title: liver, fasted, CT8, replicate 1, male

description: Library name: JMF1_S1_R1_001


title: 550_S5_PAX4 [RNA-Seq]

description: 10x Genomics single cell multiome (RNA)

value: ARXnCFP/nCFP; PAX4mCherry/mCherry


title: YL-TSA-NBS1-R3

description: Library name: YL-TSA-NBS1-R3

value: TSA


title: YL-TSA-NBS1-TEV-R3

description: Library name: YL-TSA-NBS1-TEV-R3


title: Colon, WT W6, replicate 3

value: BALB/c WT

value: G


title: NonDiabetic, rep3

city: Rochester

first: Yuanhang

state: MN

address: 200 1ST ST SW

institute: Mayo Clinic

description:
Library name: Sample3
10x Genomics

data_processing:
Raw BCL files were processed using the Cell Ranger version 3.1 suite from 10x Genomics, resulting in fastq sequencing files, aligned BAM files, and a raw feature count matrix for each sample.
Assembly: mm10
Supplementary files format and content: Tab-seperated values files and matrix files

source_name: Muscle layer of stomach

extract_protocol:
Gastric muscularis propria was placed in a dissociation buffer (collagenase type II, 1.3 mg/mL; Worthington Biochemical, Lakewood, NJ; 41B12533, BSA 2.0 mg/mL; Sigma, St Louis, MO; A7906, trypsin inhibitor 2.0 mg/mL; Sigma T9128-5g, ATP 0.27 mg/mL; Sigma A7699-1g, HEPES: 25 mM , H3375; Sigma) for 2 hours at 37°C. The dissociated cells were centrifuged at 300g for 5 minutes at 4°C, and the supernatant was discarded. The pellet was resuspended in the presence of Ca2+-Free Hanks (without phenol red) with 1% BSA (fluorescence-activated cell sorting [FACS] - buffer) and passed through a Falcon cell strainer into a 50-mL conical tube. After adding 6 mL of buffer, the cells were centrifuged at 300g for 5 minutes at 4°C. Cells were labeled with a combination of antibodies described previously. Sorting was carried out using a Becton-Dickinson 15-color LSR II Special Order flow cytometer running FACS Diva 6 software (BD, San Jose, CA) located in the Mayo Clinic Flow Cytometry Core Facility. Data were analyzed using FlowJo X software (Tree Star, Ashland, OR).
The CD45+ cells were assessed for viability using the Vi-Cell XR Cell Viability Analyzer (Beckman-Coulter), and their count was determined. Following this, barcoded Gel Beads were thawed, and a cDNA master mix was prepared according to Chromium Single Cell 3’ v3 library kit instructions. A live volume cells was mixed with the master mix and Gel Beads, then processed using the Chromium Controller to capture individual cells in uniquely labeled Gel Beads-In-Emulsion (GEMs). After collecting the GEMs, reverse transcription, dissolution, and cDNA clean-up were performed, resulting in a pool of barcoded cDNA. This cDNA was then used to construct libraries, incorporating Illumina sequencing primers and unique i7 Sample index, and assessed for quality using Qubit High Sensitivity assays (Thermo Fisher Scientific), Agilent Bioanalyzer High Sensitivity chips (Agilent), and Kapa DNA Quantification reagents (Kapa Biosystems).

value: Muscle layer of stomach

tag: Sex

value: Female

tag: strain


title: Colon, WT W6, replicate 2

value: colon


title: Colon, WT W6, replicate 1


title: YL-TSA-NB-TEV-R3

description: Library name: YL-TSA-NB-TEV-R3


title: 549_S5_ARX_PAX4 [RNA-Seq]

description: 10x Genomics single cell multiome (RNA)

value: Stage 5, day 4


title: Colon, Il10KO, Week 14 with rectal prolapse

data_processing:
*library strategy: Spatial Transcriptomics
Reads were trimmed from poly-A and TSO sequences
Trimmed reads were analyzed using SpaceRaw sequences from spatial transcriptomics samples were processed using SpaceRanger v 2.0.0 (10X genomics).
SpaceRanger output was analyzed using the STUtility pipeline in R. Genes annotated as protein coding or part of the TCR/BCR complex according to ENSEMBL were retained, excluding mitochondrial genes which were removed from the dataset.
Assembly: mm10
Supplementary files format and content: .tar.gz compressed folders containing spaceranger output

extract_protocol:
Colonic tissue was collected on W6 in WT and W10 and W14 in the Il10-/- background. Samples were cleaned from adipose tissue, opened longitudinally and the luminal content was removed by washing in cold PBS. Starting from the distal portion and with the luminal side facing upward, the colon was rolled resulting in a Swiss roll with the distal colon in the center and the proximal colon in the outer part of the roll. The Swiss roll was placed in a histology plastic cassette and snap frozen in a bath of liquid nitrogen-cooled isopentane for 1 minute. The frozen tissue was embedded in Optimal Cutting Temperature compound (OCT, Sakura Tissue-TEK) on dry ice and stored at -80°C. 10 mm thick sections were cut and transferred to oligo-barcoded capture areas on the Visium 10x Genomics slide. The Visium Spatial Tissue Optimization (10x Genomics) was performed according to manufacturer's instructions and 30 minutes was selected as the optimal permeabilization time. Colonic tissue was fixed and stained with H&E and imaged on a Leica DM5500 B microscope (Leica Microsystems) at 5x magnification. Leica Application Suite X (LAS X) was used to acquire tile scans of the entire slide and subsequently merge images.
Sequence libraries were then processed according to manufacturer's instructions (Visium Spatial Transcriptomics, 10x Genomics). After the second cDNA strand synthesis, cDNA was quantified with qRT-PCR ABI 7500 Fast Real-Time PCR System and analyzed with ABI 7500 Software 2.3.
cDNA libraries were sequenced by NGI Sweden on a NovaSeq 6000 sequencer with a sequencing depth of 100-140M reads per sample at a read length of 28-10-10-90.


title: 549_S5_ARX_PAX4 [ATAC-Seq]


title: YL-DMSO-NBS1-TEV-R3

description: Library name: YL-DMSO-NBS1-TEV-R3

value: DMSO


title: NonDiabetic, rep2

description:
Library name: Sample2
10x Genomics


title: Sample 3 EBV CD8 (CD3+TCRab+CD8+CD38+)

city: Freiburg

first: Geoffroy

last: Andrieux

address: Breisacherstr 153

institute: University clinics Freiburg

description: Library name: EBV_CD8_3

data_processing:
Basecalls performed using RTA 2.7.3
Bad quality reads were filtered out using Trimmomatic (v 0.36) with the following paramters: HEADCROP:5 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:25
Reads were aligned to the mm9 genome assembly using STAR (v2.5.2b), and read count per gene was subsequently estimated with the following parameters: --outFilterType BySJout --outFilterMultimapNmax 10 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.05 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMatchNmin 16 --quantMode GeneCounts
Assembly: hg19
Supplementary files format and content: tab-delimited txt file including read count per gene for each sample

source_name: peripheral blood

extract_protocol:
RNA was isolated using the Qiagen RNAeasy microkit
Barcoded RNA-sequencing libraries were prepared from 100 ng total RNA using the Ovation Human RNA-Seq system for small amounts of RNA (Nugen, San Carlos, CA). For selective depletion of rRNAs, the insert-dependent adapter cleavage method from Nugen was used prior to cDNA synthesis. To control sources of variability during sample and data processing, a common set of external spike-in RNA controls, developed by the external RNA controls consortium (ERCC), was used (Ambion).

value: peripheral blood

value: T cells


title: Colon, Il10KO W6, replicate 2

value: BALB/c Il10KO

value: B


title: 548_S5_ARX [ATAC-Seq]

value: SYTOX-/ARX-CFP+


title: YL-DMSO-NBS1-R3

description: Library name: YL-DMSO-NBS1-R3

value: Blood


title: Sample 2 EBV CD8 (CD3+TCRab+CD8+CD38+)

description: Library name: EBV_CD8_2


title: NonDiabetic, rep1

description:
Library name: Sample1
10x Genomics


title: YL-TSA-NB-R3

description: Library name: YL-TSA-NB-R3


title: Colon, Il10KO, Week 14


title: Colon, IL10KO, Week 10


title: Donor10

city: Copenhagen

first: Kelvin

last: Yeung

address: Blegdamsvej 3B

country: Denmark

institute: LEO SIC

description: 10x Genomics

data_processing:
Demultiplexing and data preprocessing including quality control, read alignment (hg38), and gene quantification was conducted using the 10x Cell Ranger software (v7.1.0).
Assembly: hg38
Supplementary files format and content: Tab separated values files and matrix files

source_name: Epidermis

extract_protocol:
Skin samples were incubated overnight in 2.4 mg/ml Dispase (Roche) in phosphate buffered saline (PBS) solution at 4°C. Epidermis and dermis were separated. Epidermis was digested in 0.5 mg/ml Collagenase D (Roche) with deoxyribonuclease (0.1%, Sigma-Aldrich) in PBS for a total of 1 hour at 37°C, quenched with 2% bovine serum albumin (BSA) (Sigma Aldrich) in PBS, and strained through a 70-μm mesh strainer. The strainer was washed through with 2% BSA in PBS to collect any remaining cells. The single cell suspension was always kept on ice.
We used 10X Genomics Chromium Next GEM Single Cell 5’ kit, v2 with 5’ Feature Barcode kit alongside Chromium Single Cell Human TCR Amplification kit for TCRαβ and Dual Index Kit TT and TN Set A. The kit was used to the manufacturer’s instructions. The samples were multiplexed, using TotalSeq-C hashtag antibodies (Biolegend). The sequencing was carried out on an Illumina NovaSeq 6000 using a S4 flow cell, 200 cycles, to the manufacturer’s instructions.

value: Epidermis

tag: contact allergen

value: Nickel

value: Allergic contact dermatitis

value: Anakinra


title: YL-DMSO-NB-TEV-R3

description: Library name: YL-DMSO-NB-TEV-R3


title: Sample 1 EBV CD8 (CD3+TCRab+CD8+CD38+)

description: Library name: EBV_CD8_1


title: 548_S5_ARX [RNA-Seq]

description: 10x Genomics single cell multiome (RNA)

value: hiPSC

value: ARXnCFP/nCFP; PAX4mCherry/mCherry


title: Colon, Il10KO W14, Immune fraction, antibody capture

data_processing:
Reads were analyzed using CellRanger v 6.0.2 (10X Genomics)
Gene expression matrices were analyzed using the Seurat 4.1.1 pipeline
Assembly: mm10
Supplementary files format and content: .h5-files for each sample

extract_protocol:
Tissue biopsies (approximately 0.5 cm long) were collected from the distal colon and stored at -80°C in RNAlater (Invitrogen). To extract RNA, tissue was lysed in RLT Plus Buffer (QIAGEN) + 2% b-mercaptoethanol by bead-beating (Precellys). RNA was isolated with the RNeasy Plus Mini Kit (QIAGEN) according to the manufacturer's instructions and quantified using a Nanodrop spectrophotometer (ThermoFisher).
Libraries were constructed following the manufacturer’s guidelines (Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein (10X Genomics)), with TotalSeq-derived barcodes being retained only for the immune cell fractions.
Sequencing was performed by Novogene Co. Ltd (UK) on NovaSeq 6000 sequencers with a targeted sequencing depth of 300M reads per gene expression sample and 50M reads per TotalSeq-derived sample. Read length was PE150 (Novogene) or 28-10-10-150 for gene expression samples and 28-10-10-25 (NGI) for TotalSeq-derived samples.


title: H21193_Control_MMP

city: Lübeck

first: Axel

last: Künstner

address: Ratzeburger Allee 160

department: LIED

institute: University of Lübeck

description: Library name: H21193

data_processing:
Transcript-level quantification was performed using salmon (v0.13.0), which pseudoaligned reads to the human transcriptome, including both coding and non-coding RNAs, based on Ensembl release 94 (GRCh38).
Assembly: GRCh38
Supplementary files format and content: Processed data contains TPM values.

source_name: iPSC

extract_protocol:
RNA was extracted from whole cell lysates using the RNeasy kit (Qiagen) according to the manufacturer’s recommendations.
Total RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit with poly-A enrichment and sequenced on an Illumina HiSeq 4000 platform generating single-read 50 bp reads.

value: iPSC

value: skin fibroblasts

tag: group

value: Control

value: MMP


title: Donor9

description: 10x Genomics


title: Donor6, run 2

description: 10x Genomics

value: Placebo


title: YL-DMSO-NB-R3

description: Library name: YL-DMSO-NB-R3

tag: cell line

value: DMSO


title: Colon, Il10KO W12, Immune fraction, antibody capture

value: colon


title: YL-TSA-NBS1-TEV-R1

description: Library name: YL-TSA-NBS1-TEV-R1

tag: cell type

value: TSA


title: YL-TSA-NBS1-R1

description: Library name: YL-TSA-NBS1-R1

tag: treatment


title: H21192_Patient_MMP

description: Library name: H21192

value: Patient


title: H21191_Control_Rotenone

description: Library name: H21191

value: Rotenone


title: Colon, Il10KO W10, Immune fraction, antibody capture

tag: tissue


title: Colon, Il10KO W8, Immune fraction, antibody capture

tag: genotype


title: YL-TSA-NB-R1

description: Library name: YL-TSA-NB-R1

value: Blood

tag: batch


title: Donor5, run 2

description: 10x Genomics

value: Epidermis

tag: disease


title: YL-TSA-NB-TEV-R1

description: Library name: YL-TSA-NB-TEV-R1


title: H21188_Patient_Rotenone

description: Library name: H21188


title: Colon, Il10KO W6, Immune fraction, antibody capture

tag: time


title: H21190_Control_Rotenone

description: Library name: H21190


title: Colon, WT, Week 6

value: WT


title: YL-DMSO-NBS1-TEV-R1

description: Library name: YL-DMSO-NBS1-TEV-R1


title: Donor6, run 1

description: 10x Genomics

value: Nickel

value: Allergic contact dermatitis


title: Donor5, run 1

description: 10x Genomics

value: Anakinra


title: Colon, WT W6, Immune fraction, antibody capture


title: Donor4

description: 10x Genomics


title: Donor3

description: 10x Genomics


title: H21186_Control_NT

description: Library name: H21186

value: No treatment


title: H21187_Control_NT

description: Library name: H21187

value: iPSC


title: Colon, Il10KO W14, Stromal fraction, gene expression


title: YL-DMSO-NB-TEV-R1

description: Library name: YL-DMSO-NB-TEV-R1


title: H21185_Patient_NT

description: Library name: H21185

value: skin fibroblasts


title: Donor1

description: 10x Genomics


title: YL-DMSO-NBS1-R1

description: Library name: YL-DMSO-NBS1-R1


title: H21184_Patient_NT

description: Library name: H21184


title: YL-DMSO-NB-R1

description: Library name: YL-DMSO-NB-R1


title: Colon, Il10KO W14, Immune fraction, gene expression


title: Colon, Il10KO W14, Epithelial fraction, gene expression


title: HEK293T_TM_24h_r3 [A21]

city: London

first: Eleni

last: Maniati

address: John Vane Science Centre, Charterhouse Square

department: Barts Cancer Institute

institute: Queen Mary University of London

data_processing:
RNA-Seq reads were quality trimed and mapped to the human genome (hg38, Genome Reference Consortium GRCh38)  using STAR.
Number of reads aligned to the exonic region of each gene were counted using rsem-count based on the Ensembl annotation.
Assembly: hg38
Supplementary files format and content: tab-delimited text file of rsem gene counts  for each sample

source_name: cell line

growth_protocol: Oci AML3 cells were grown at a concentration of 300,000/mL in 10% RPMI. HEK293T cells were grown at 50% confluency in 10% DMEM.

extract_protocol:
RNA extraction
mRNA library preparation (poly A enrichment)

treatment_protocol: Cells were then treated with DMSO or 1μg/mL tunicamycin for 4 or 24h

value: cell line

value: 1μg/mL tunicamycin for 24H


title: Colon, Il10KO W12, Stromal fraction, gene expression


title: HAP1-DMSO-R2

description: Library name: AS129

value: Wild-type


title: H21183_Control_MMP

description: Library name: H21183

value: Control

value: MMP


title: Colon, Il10KO W12, Immune fraction, gene expression

value: colon


title: HEK293T_TM_24h_r2 [A20]


title: HEK293T_DMSO_24h_r3 [A18]

value: DMSO


title: HAP1-DMSO-R1

description: Library name: AS87


title: Colon, Il10KO W12, Epithelial fraction, gene expression


title: HAP1-TSA-R2

description: Library name: AS130

value: TSA


title: Donor2

description: 10x Genomics


title: H21181_Control_Rotenone

description: Library name: H21181

value: Rotenone


title: H21179_Patient_Rotenone

description: Library name: H21179

value: Patient


title: HAP1-TSA-R1

description: Library name: AS88

value: Blood


title: H21182_Patient_MMP

description: Library name: H21182


title: Colon, Il10KO W10, Immune fraction, gene expression


title: HAP1-RAD21TEV-TSA-R2

description: Library name: AS33


title: Colon, Il10KO W10, Stromal fraction, gene expression


title: HEK293T_TM_24h_r1 [A19]


title: H21178_Patient_Rotenone

description: Library name: H21178


title: HAP1-RAD21TEV-DMSO-R2

description: Library name: AS32


title: Colon, Il10KO W10, Epithelial fraction, gene expression


title: HEK293T_DMSO_24h_r1 [A16]


title: Oci_AML3_24H_TM_r3 [A15]

value: OCI AML3


title: HAP1-RAD21TEV-TSA-R1

description: Library name: AS126


title: H21176_Control_NT

description: Library name: H21176


title: HEK293T_DMSO_24h_r2 [A17]


title: Colon, Il10KO W8, Stromal fraction, gene expression


title: Colon, Il10KO W8, Immune fraction, gene expression


title: HAP1-RAD21TEV-DMSO-R1

description: Library name: AS125


title: Oci_AML3_24H_TM_r2 [A14]


title: H21175_Patient_NT

description: Library name: H21175


title: H21177_Control_NT

description: Library name: H21177


title: H21174_Patient_NT

description: Library name: H21174


title: Oci_AML3_24H_TM_r1 [A13]


title: QAG370-QAG372-QAG373, AVEGFA-AVEGFA-AVEGFA, LOW_HYPOXIA-HIGH_HYPOXIA-LOW_HYPOXIA, scRNAseq

city: Madrid

first: Manuel

last: Moradiellos Corpus

address: Calle Melchor Fernández Almagro 3

department: Human Genetics

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description:
Library name: Sample 5
10x Genomics with v2.5 reagent kits; CMO-OLIGOS for each of mouse QAG370:1-2-3-4, QAG372:5-6-7-8, QAG373:9-10-11-12

data_processing:
Image analysis, per-cycle basecalling and quality score assignment was performed with Illumina RTA software  (RTA v2). Conversion of BCL files to FASTQ format was performed with "cellranger mkfastq" (10xGenomics), a wrapper for "bcl2fastq" (Illumina).
The bollito pipeline (García-Jimeno et al., 2022) was used to perform the initial steps of the single-cell analysis, checking cell-level quality control by removing outlier cells based on read counts, number of expressed genes and the percentage of mitochondrial counts distributions. All of its parameters were set as default. After this preliminary filtering, the samples were merged into a single object that would be analyzed by Seurat v4.3.0.
Seurat was employed to exclude cells with low quality (those with fewer than 2,500 UMIs) or cells identified as potential multiplets (those with more than 27500 UMIs). Only cells expressing a minimum of 50 house-keeping genes from a curated list specific to quality control (Tirosh et al., 2016) were retained for analysis. The expression levels were normalized to log transcripts per 10,000 cells (TP10K).
Assembly: mm10
Supplementary files format and content: Samples' cell barcodes, genes/features and metadata (supplementary) as tab-separated values files
Supplementary files format and content: Samples' expression values as matrix files

source_name: Breast cancer

growth_protocol: All animal experiments were performed in the CNIO (Spanish National Cancer Research Centre) in accordance with protocols approved by the Research Ethics and Animal Welfare Committee on Animal Experimentation of the Instituto de Salud Carlos III (PROEX 387/15 and PROEX 206.7/21). Experiments were performed in accordance with the guidelines stated in the International Guiding Principles for Biomedical Research Involving Animals developed by the Council for International Organizations of Medical Sciences. MMTV-PyMT mice (FVB/N-Tg (MMTV-PyVT)634Mul/J) and BALB/c were bred at the CNIO Animal Facility. Mouse strains were maintained under specific pathogen-free conditions at the CNIO Animal Facility. Animals were kept in a climate-controlled environment (22±2ºC) with cycles of 12h light/dark and with ad libitum access to food and water.

extract_protocol:
Tumors were extracted from mice and dissagregated using Tumor Dissociation Kit, mouse (Miltenyi, #130-096-730). Single cell tumor cell suspension were stained with DAPI and DAPI- cells were sorted in BD-FACS-ARIA into PBS. After that, three different tumors were multiplexed using oligo labeling was by 3’CellPlex Kit Set A (10xGenomics, cat no. 1000261). Next, a secondary sort of DAPI- cells was executed with the BD FACS ARIA to further enrich for viable cells. Multiplexed-single-cell suspensions sourced from three distinct tumors were processed together into one sample, which was drop encapsulated with Chromium device (10xGenomics). Finally, it was sequenced in Illumina Nextseq 550 (with v2.5 reagent kit)
Cell multiplexed samples were processed with the "Chromium Next GEM Single Cell 3' Kit v3.1" (10xGenomics  PN-1000268). Generation of gel beads in emulsion (GEMs), barcoding, post GEM-RT clean-up, cDNA amplification and both 3’ Gene Expression and Cell Multiplexing library construction were all performed as recommended by the manufacturer.

treatment_protocol: Treatments with the different drugs were started at 7th weeks of age of MMTV-PyMT mouse models. Anti-VEGFA clone B20-4.1.1 or Isotype mouse IgG2a clone C1.18.4 were prepared in 1x PBS and administered at 5 mg/kg intraperitoneally twice per week during 6 weeks

value: Breast cancer


title: H21173_Control_MMP

description: Library name: H21173


title: Colon, Il10KO W6, Stromal fraction, gene expression


title: QAG432-QAG452-QAG465, CONT-CONT-CONT, CONTROL-CONTROL-CONTROL, scRNAseq

description:
Library name: Sample 4
10x Genomics with v2.5 reagent kits; CMO-OLIGOS for each of mouse QAG432:1-2-3-4, QAG452:5-6-7-8, QAG465:9-10-11-12

value: IgG2a isotype


title: H21172_Patient_MMP

description: Library name: H21172


title: Colon, Il10KO W8, Epithelial fraction, gene expression


title: Oci_AML3_24H_DMSO_r3 [A12]


title: Oci_AML3_24H_DMSO_r1 [A10]


title: Colon, Il10KO W6, Epithelial fraction, gene expression


title: Colon, Il10KO W6, Immune fraction, gene expression


title: H21167_Control_NT

description: Library name: H21167

value: No treatment


title: QAG359-QAG360-QAG365, AVEGFA-AVEGFA-AVEGFA, LOW_HYPOXIA-HIGH_HYPOXIA-HIGH_HYPOXIA, scRNAseq

description:
Library name: Sample 3
10x Genomics with v2.5 reagent kits; CMO-OLIGOS for each of mouse QAG359:1-2-3-4, QAG360:5-6-7-8, QAG365:9-10-11-12


title: Oci_AML3_24H_DMSO_r2 [A11]


title: Oci_AML3_4H_TM_r3 [A9]

value: 1μg/mL tunicamycin for 4H


title: QAG364-QAG397-QAG404, CON-CONT-CONT, CONTROL-CONTROL-CONTROL, scRNAseq

description:
Library name: Sample 1
10x Genomics  with v2.5 reagent kits; CMO-OLIGOS for each of mouse QAG364:1-2-3-4, QAG397:5-6-7-8, QAG404:9-10-11-12


title: Colon, WT W6, Stromal fraction, gene expression

value: WT


title: H21166_Control_NT

description: Library name: H21166

value: iPSC

value: skin fibroblasts


title: QAG356-QAG357-QAG348, AVEGFA-AVEGFA-AVEGFA, LOW_HYPOXIA-LOW_HYPOXIA_HIGH_HYPOXIA,scRNAseq

description:
Library name: Sample 2
10x Genomics with v2.5 reagent kits; CMO-OLIGOS for each of mouse QAG348:1-2-3-4, QAG356:5-6-7-8, QAG357:9-10-11-12


title: Oci_AML3_4H_TM_r2 [A8]

value: cell line


title: e11.5_visium

description:
Library name: e11.5_visium
visium_e11.5 sections

value: heart

value: cardiac cells

value: CD1 wildtype


title: H21165_Patient_NT

description: Library name: H21165


title: Colon, WT W6, Epithelial fraction, gene expression

value: colon


title: H21164_Patient_NT

description: Library name: H21164


title: Colon, WT W6, Immune fraction, gene expression


title: e14.5_visium

description:
Library name: e14.5_visium
visium_e14.5 sections


title: Oci_AML3_4H_TM_r1 [A7]


title: Oci_AML3_4H_DMSO_r3 [A6]

value: DMSO


title: e17.5_visium

description:
Library name: e17.5_visium
visium_e17.5 sections


title: p2_visium

description:
Library name: p2_visium
visium_p2 sections


title: Colon, day 50, anti-IL-12p40-treated

data_processing:
Reads were analyzed using SpaceRaw sequences from spatial transcriptomics samples were processed using SpaceRanger v 1.2.0 (10X genomics). Ranger v 6.0.2 (10X Genomics)
SpaceRanger output was analyzed using the STUtility pipeline in R. Genes annotated as protein coding or part of the TCR/BCR complex according to ENSEMBL were retained, excluding mitochondrial genes which were removed from the dataset. NMF was performed on the three samples from mouse not treated with anti-IL-12p40, using RunNMF from the STUtility package to produce 20 factors. Gene expression was visualized in all four samples, i.e. including the sample from an anti-IL-12p40-treated mouse.
Assembly: mm10
Supplementary files format and content: .tar.gz compressed folders containing spaceranger output
Library strategy: Spatial Transcriptomics

extract_protocol:
Colonic tissue was collected on d0 (untreated), d30 (untreated) and d50 (anti-IL-12p40 treated and untreated) in the Rag2-/- background. Samples were cleaned from adipose tissue, opened longitudinally and the luminal content was removed by washing in cold PBS. Starting from the distal portion and with the luminal side facing upward, the colon was rolled resulting in a Swiss roll with the distal colon in the center and the proximal colon in the outer part of the roll. The Swiss roll was placed in a histology plastic cassette and snap frozen in a bath of liquid nitrogen-cooled isopentane for 1 minute. The frozen tissue was embedded in Optimal Cutting Temperature compound (OCT, Sakura Tissue-TEK) on dry ice and stored at -80°C. 10 mm thick sections were cut and transferred to oligo-barcoded capture areas on the Visium 10x Genomics slide. The Visium Spatial Tissue Optimization (10x Genomics) was performed according to manufacturer's instructions and 30 minutes was selected as the optimal permeabilization time. Colonic tissue was fixed and stained with H&E and imaged on a Leica DM5500 B microscope (Leica Microsystems) at 5x magnification. Leica Application Suite X (LAS X) was used to acquire tile scans of the entire slide and subsequently merge images.
Sequence libraries were then processed according to manufacturer's instructions (Visium Spatial Transcriptomics, 10x Genomics). After the second cDNA strand synthesis, cDNA was quantified with qRT-PCR ABI 7500 Fast Real-Time PCR System and analyzed with ABI 7500 Software 2.3.
cDNA libraries were sequenced by NGI Sweden on a NovaSeq 6000 sequencer with a sequencing depth of 100-170M reads per sample at a read length of 28-10-10-90.

value: Rag2 KO

value: CD45RBhi transfer + anti-IL12p40

value: yes


title: H21156_Control_NT

description: Library name: H21156

value: Control


title: H21155_Patient_NT

description: Library name: H21155

value: Patient


title: Colon, day 50

value: CD45RBhi transfer

value: no


title: Oci_AML3_4H_DMSO_r2 [A5]

value: OCI AML3


title: p2_e14_visium

description:
Library name: p2_e14_visium
visium_p2 and e14.5 sections were profiled together


title: Oci_AML3_0H_r3 [A3]

value: untreated


title: Colon, day 30


title: Oci_AML3_4H_DMSO_r1 [A4]


title: p0_visium

description:
Library name: p0_visium
visium_p0 sections


title: H21157_Control_NT

description: Library name: H21157

value: iPSC

value: No treatment


title: H21154_Patient_NT

description: Library name: H21154

value: skin fibroblasts


title: Oci_AML3_0H_r2 [A2]

value: cell line


title: Head regenerating fragment, 96hpa, repB

city: Basel

first: Panagiotis

last: Papasaikas

address: Fabrikstrasse 24

country: Switzerland

institute: Friedrich Miescher Institute

description:
Library name: 2869F2_96h
All cells, enriched for epithelial cells

data_processing:
Quantification of the generated single cell libraries was performed using the Salmon-Alevin software suite (Salmon version 1.8.0) against the NCBI Hydra vulgaris high contiguity assembly Hydra_vulgaris_105_v3  (GCF_022113875.1) and associated transcriptome. Example command: salmon alevin -l ISR -1 $R1  -2 $R2 --chromiumV3 -i $reference -p $threads -o OUTDIR --tgMap $tx2genemap --dumpFeatures --numCellBootstraps 50 --expectCells 5000
Post-alignment quality control employed alevinQC v1.8.0 within R/Bioconductor  providing barcode knee plots, mapping summaries, and other standard metrics for each sample. Gene- and cell-level quality control was carried out in R /Bioconductor  on the Hydra libraries. Cells were retained if they expressed 850–7000 genes (empirically chosen to exclude low-complexity droplets and potential multiplets).
Assembly: NCBI Hydra vulgaris Release Hydra_vulgaris_105_v3  (GCF_022113875.1)
Supplementary files format and content: tab-delimited files with raw (not normalized) UMI counts for each filtering-cleared cell (columns) and Hydra gene (row) as reported by Salmon-Alevin

organism: Hydra vulgaris

source_name: Whole tissue

growth_protocol: Animals are maintained in Hydra medium solution [1 mM CaCl2, 0.2 mM NaHCO3, 0.02 mM KCl, 0.02 mM MgCl2, and 0.2 mM tris-HCl (pH 7.4)] at 18°C and fed three times per week with freshly hatched Artemia nauplii.

extract_protocol:
Samples were incubated in Pronase E solution (7.5 mg/mL of pronase E diluted in dissociation medium [6 mM CaCI2, 1.2 mM MgSO4, 3.6 mM KCl, 12.5 mM N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid, 6 mM sodium pyruvate, 6 mM sodium citrate, 4 mM glucose; pH 6.9]) for 1h at 24°C, 300rpm, protected from light. Animals were dissociated into single cells mechanically by pipetting up and down. Cells were strained through a sterile CellTrics® 30µm cell strainer, collected in a centrifuge tube and spin 5min, 300xg at room temperature (RT). Supernatant was removed and cells were resuspended in dissociation medium + 0.01% Bovin serum albumin (BSA). Cells were centrifuged again and resuspended in dissociation medium + 0.01% BSA. Cells were strained and collected in a FACS tube. Dead cells were stained with DRAQ7 and excluded from the FACS sort. Cells were collected in a PBS + 0.04% BSA, without Cacl2 and MgCl2, solution.
FACS-sorted cells (16K) were immediately processed for scRNA-seq using 10X genomics Chromium Single Cell 3’ Reagents v3.1 with UDI indexes, according to the manufacturer’s protocol.

treatment_protocol: We bisected Hydras and collected samples at 0, 3, 6, 12, 24, 48, 72 and 96 hours after bisection separately for head and foot animal regeneration

value: Whole tissue

value: icells, ectodermal, gastrodermal

value: Body bisection

tag: time after_bisection

value: 96 hous

tag: regeneration type

value: Head


title: Oci_AML3_0H_r1 [A1]


title: e17_e11_visium

description:
Library name: e17_e11_visium
visium_e17.5 section were profiled together

data_processing:
We acquired the unfiltered feature-barcode matrix for each sample by using Space Ranger (v2. 1. 0) ‘count’ command with manually selected dots and reorient-images enabled) on the demultiplexed FASTQ files and associated image, along with the prebuilt mm10 genome reference 2020-A. After it detected tissue, aligned reads, generated feature-spot matrices, and positioned spots, we then used Seurat for all further analyses. In each slide, Seurat objects were created by Load10X_Spatial function and then normalized with natural-log transformation using log1p. Similarly, we obtained the unfiltered matrix of curioseq data by using Curio seeker (v2.0) with custom GRCm38 genome reference (add eGFP). Specifically, Curio seeker was first used to extract bead and molecular barcodes for the raw FASTQ files of each sample and filter beads obtained from sequencing data against the bead barcode whitelist. After filtering out beads with Hamming distance greater than 2 and creating new seurat object, we manually normalized counts with natural log.
We splitted out the Visium image which has more than one tissue. This process can facilitate the integration with scRNA-seq dataset in later section. We cut segments based on exact positions. After subsetting, we can visualize the certain stage cells either on the full image, or a cropped image. (Stage E11.5, P0, E14.5, E16.5 have two tissues in one image, E17_E11 and P2_E14 from second experiment have three tissues in same image.) In Curio seq samples, we first set filter range of each coordinate and then store the shrank image in a new Seurat object.
Assembly: GRCm38
Supplementary files format and content: rds
Library strategy: Spatial Transcriptomics

source_name: heart

extract_protocol:
Mouse hearts from CD1 wildtype, Wt1-CreER-mTmG, and Wt1-CreER-DTA mice were harvested and directly embeded in OCT. Then the hearts were sectioned and used for Visium or Slide-seq profiling.
The heart sections were processed by following the protocol for 10X Genomics Visium Spatial gene expression kit (1000187); For the Slide-seq experiments, we followed the updated protocol in 2023 October from Curio-Bio company.

value: heart

value: cardiac cells

value: CD1 wildtype


title: e16_visium

description:
Library name: e16_visium
visium_e16 heart sections


title: Colon, day 0

value: colon

value: Rag2 KO


title: E. coli and C. albicans  co-biofilm 48h in urine 3

status: Public on Apr 27 2026

city: South Bend

first: Ellsa

last: Wongso

address: 809 Lindenwood Dr S

institute: University of Notre Dame

description: Library name: EC-CA3

data_processing:
Sequence reads were trimmed for adapter sequence/low quality sequence using Trimmomatic on UseGalaxy (E. faecalis and E. coli) and by GeneWiz for C. albicans
HISAT2 and htseq-count were used to mapped reads to reference genome. Deseq2 was used to normalized and analyzed counts
Assembly: GCF_000013265.1 (E. coli UTI89), GCF_000172575.2 (E. faecalis OG1RF), GCF_000182965.3 (C. albicans SC5314)
Supplementary files format and content: tab delimited text files includes raw counts for each file provided by GeneWiz

organism:
Escherichia coli
Candida albicans

source_name: bacteria, fungi

growth_protocol: Bacteria and/or fungi were grown in human sterilized urine in a fibrinogen-coated flasks for 48 hours at 37℃

extract_protocol:
RNA was harvested using Direct-zol RNA miniprep kit from Zymo Research. 500 ng of total RNA was used for the construction of sequencing libraries
RNA libraries were prepared by GeneWiz

value: bacteria, fungi

value: WT

value: urine 48h


title: E. faecalis, E. coli and C. albicans  co-biofilm 48h in urine 2

description: Library name: EF-EC-CA2

organism:
Escherichia coli
Enterococcus faecalis
Candida albicans

value: OG1RF, UTI89, SC5314


title: E. faecalis, E. coli and C. albicans  co-biofilm 48h in urine 3

description: Library name: EF-EC-CA3


title: Colon, W7, Immune fraction, anti-IL-12p40-treated, Feature barcodes

library_source: other

data_processing:
Reads were analyzed using CellRanger v 6.0.2 (10X Genomics). The first run did not capture the feature barcodes of some samples due to a mistake, for which reason .tsv-files containing the feature barcode counts for those samples.
Gene expression matrices were analyzed using the Seurat 4.1.1 pipeline
Assembly: mm10
Supplementary files format and content: .h5-files for each sample and .tsv-files with feature barcode counts for some samples.

molecule: other

extract_protocol:
Colonic cells were isolated as previously described with minor alterations (Villablanca et al., 2011). Briefly, colonic tissue was cleaned from fat, opened longitudinally and cut into 1 cm pieces. Tissues from mice from the same treatment group and time point were pooled. Tissues were incubated for 30 min at 37 °C in 20 ml HBSS with 5% FCS, 5 mM EDTA, 1 mM DTT and 15 mM HEPES while shaking gently. The epithelium-enriched supernatant was then filtered through a 100 µm strainer, washed in PBS with 5% FCS and 1 mM EDTA, and cells were recovered at the interface of a 44-67% Percoll gradient. The remaining tissue was washed twice in PBS and digested in 10 ml of serum-free HBSS with Liberase TL (0.15 mg/ml, Roche) and 0.1 mg/ml DNase I (Roche) at 37 °C at 600 rpm for 60 min. After filtration through a 100 μm cell strainer, lamina propria-enriched cells were washed with PBS with 5% FCS and 1 mM EDTA and separated on a 44-67% Percoll gradient. Both epithelium-enriched and lamina propria-enriched fractions were stained with TER-119 Pacific Blue, CD45.2 PE/Cyanine7 and EpCAM FITC surface antibodies (BioLegend) for cell type assignment. Cells from the lamina propria were additionally labeled with TotalSeq antibodies (BioLegend) targeting CD90.2, CD3, CD4, KLRG1, CD127, Ly-6C, CD64, CD11b, CD11c, CD103 and Ly-6G according to manufacturer’s instructions. After additional staining with DAPI for live/dead cell identification, cells were sorted using Sony SH800 Cell Sorter into 15mL tubes filled with complete RPMI medium with 10% FCS. Epithelial cells were sorted from the epithelium-enriched fraction by gating EpCAM+/CD45- cells. Immune and stromal cells were sorted from the lamina propria-enriched fraction, by gating EpCAM-/CD45+ and EpCAM-/CD45- cells, respectively. Approximately 16000 cells per sample were loaded onto the 10X Genomics Chromium Controller and processed with the Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein (10X Genomics).
Libraries were constructed following the manufacturer’s guidelines (Chromium Next GEM Single Cell 3ʹ v3.1 (Dual Index) with Feature Barcode technology for Cell Surface Protein (10X Genomics)), with TotalSeq-derived barcodes being retained only for the immune cell fractions.
Sequencing was performed by Novogene Co. Ltd (UK) (Rag2-/- samples) or NGI Sweden (SCID samples) on NovaSeq 6000 sequencers with a targeted sequencing depth of 300M reads per gene expression sample and 50M reads per TotalSeq-derived sample. Read length was PE150 (Novogene) or 28-10-10-150 for gene expression samples and 28-10-10-25 (NGI) for TotalSeq-derived samples.

value: Immune

value: SCID

value: CD45RBhi transfer + anti-IL-12p40-treated

value: yes


title: E. coli and C. albicans  co-biofilm 48h in urine 1

description: Library name: EC-CA1


title: E. coli and C. albicans  co-biofilm 48h in urine 2

description: Library name: EC-CA2


title: HCCLM3 cells, H3K27ac, rep2, batch1

city: Zhengzhou City

first: Leixi

last: Cao

address: Zhengzhou University People's Hospital, Fengchan Road Subdistrict, Jinshui District, Zhengzhou City, Henan Province

country: China

institute: Zhengzhou University People's Hospital, Translational Medicine Research Center

description: Library name: H3K27ac_2

data_processing:
(CUT-tag)The data analysis workflow first involved adapter trimming and removal of low-quality bases from paired-end reads were conducted using Trim Galore software. Clean reads were then aligned to the hg38 reference genome using Bowtie2, followed by the removal of PCR duplicates with Picard. Genome browser tracks in bigWig format were produced from merged replicates using samtools, and peak calling was performed with MACS2 using the parameters -f BAMPE --broad -nomodel. The resulting bigWig data were visualized using the Integrative Genomics Viewer (IGV) software from the Broad Institute, while peak visualizations were prepared using Deeptools.
Assembly: hg38
Supplementary files format and content: bigwig for CUT&Tag
Library strategy: CUT&Tag

extract_protocol:
CUT&Tag experiments, cell capture was achieved using ConA-coated magnetic beads for cell enrichment.
CUT&Tag libraries were prepared according to the protocol established by Steven Henikoff's laboratory.

value: liver

value: hepatocellular carcinoma cell, epithelial cell


title: HCCLM3 cells, H3K27ac, rep1, batch1

description: Library name: H3K27ac_1


title: HCCLM3 cells, H3K4me3, rep2, batch1

description: Library name: H3K4me3_2


title: HCCLM3 cells, H3K4me2, rep2, batch1

description: Library name: H3K4me2_2


title: HCCLM3 cells, H3K4me2, rep1, batch1

description: Library name: H3K4me2_1


title: Head regenerating fragment, 96hpa, repA

description:
Library name: 2869F1_96h
All cells

value: Whole tissue

value: icells, ectodermal, gastrodermal

value: Body bisection

value: 96 hous


title: HCCLM3 cells, H3K4me1, rep2, batch1

description: Library name: H3K4me_2


title: E. faecalis, E. coli and C. albicans  co-biofilm 48h in urine 1

description: Library name: EF-EC-CA1


title: HCCLM3 cells, CDK9, rep2, batch1

description: Library name: CDK9_2


title: HCCLM3 cells, H3K4me1, rep1, batch1

description: Library name: H3K4me_1


title: HCCLM3 cells, CDK9, rep1, batch1

description: Library name: CDK9_1


title: S2-GrhScrwSD_0uM_R2

city: Madison

first: Melissa

middle: M

last: Harrison

state: WI

address: 420 Henry Mall

department: Biomolecular Chemistry

institute: University of Wisconsin Madison

description:
Library name: ATACseq_43
processed file: MF60A_0_2502_small.bw

data_processing:
Adapter sequences were trimmed from reads using Ngmerge.
Trimmed reads were aligned to the Drosophila melanogaster genome (dm6) using Bowtie2 (v2.4.4). Unmapped reads, reads aligning to the mitochondrial genome or unplaced scaffolds, reads aligning more than once or low-quality reads (MAPQ<30) were removed. Only fragments shorter than 100 bp were used for downstream analysis.
Assembly: dm6
Supplementary files format and content: bigwig files were formed from merged replicates and z-score normalized.

organism: Drosophila melanogaster

source_name: Schneider 2 cells

growth_protocol: Drosophila S2 cells were cultured in Schneider's medium with supplemented antibiotic/antimycotic and 10% FBS at 27˚C.

extract_protocol:
200,000 cells were spun down for 3min at 600g at 4˚C, washed with 1X PBS, and resuspended in 100μL ATAC lysis buffer. Lysed cells were centrifuged for 10min at 600g at 4˚C. The supernatant was replaced with 47.5μL TD buffer and 2.5μL Tn5 enzyme (Illumina) and incubated at 37˚C for exactly 30min. DNA was purified with the MinElute Reaction Cleanup kit (Qiagen).
Purified DNA was PCR amplified with IDT for Illumina Nextera DNA Unique Dual Indices in NEBNext Hi-Fi 2x PCR Master Mix (72˚C for 5min, 98˚C for 30s, followed by 12 cycles of 98˚C for 10s, 63˚C for 30s, and 72˚C for 1min). Libraries were purified with Axygen paramagentic beads (Thermo Fisher Scientific) at a ratio of 1.2x and eluted in 10 mM Tris.

treatment_protocol: S2 cells were treated with respective amounts of CuSO4 to induce expression for 48 hours.

value: Schneider 2 cells

value: 0 uM CuSO4


title: S2-GrhScr_500uM_R2

description:
Library name: ATACseq_42
processed file: MF59A_500_2502_small.bw

value: 500 uM CuSO4


title: S2-Grh_0uM_C_R2

description:
Library name: ATACseq_39
processed file: TG3A_0_2502_small.bw


title: HCCLM3 cells, H3K4me3, rep1, batch1

description: Library name: H3K4me3_1


title: S2-GrhScr_0uM_R2

description:
Library name: ATACseq_41
processed file: MF59A_0_2502_small.bw


title: S2-Grh_100uM_C_R2

description:
Library name: ATACseq_40
processed file: TG3A_100_2502_small.bw

value: 100 uM CuSO4


title: S2-GrhScr_0uM_R1

description:
Library name: ATACseq_35
processed file: MF59A_0_2502_small.bw


title: S2-GrhR806A_100uM_R2

description:
Library name: ATACseq_32
processed file: MF13A_100_2501_small.bw


title: S2-Grh_100uM_C_R1

description:
Library name: ATACseq_34
processed file: TG3A_100_2502_small.bw


title: S2-GrhScrwSD_100uM_R1

description:
Library name: ATACseq_38
processed file: MF60A_100_2502_small.bw


title: S2-GrhC800AK807A_0uM_R2

description:
Library name: ATACseq_29
processed file: MF12A_0_2501_small.bw


title: S2-GrhC800AK807A_0uM_R1

description:
Library name: ATACseq_23
processed file: MF12A_0_2501_small.bw


title: S2-Grh_100uM_B_R1

description:
Library name: ATACseq_22
processed file: TG3A_100_2501_small.bw


title: S2-Grh_0uM_B_R1

description:
Library name: ATACseq_21
processed file: TG3A_0_2501_small.bw


title: S2-GrhR806A_0uM_R2

description:
Library name: ATACseq_31
processed file: MF13A_0_2501_small.bw


title: S2-GrhR806A_100uM_R1

description:
Library name: ATACseq_26
processed file: MF13A_100_2501_small.bw


title: S2-Grh_0uM_B_R2

description:
Library name: ATACseq_27
processed file: TG3A_0_2501_small.bw


title: S2-GrhC800AK807A_100uM_R1

description:
Library name: ATACseq_24
processed file: MF12A_100_2501_small.bw


title: S2-GrhScr_500uM_R1

description:
Library name: ATACseq_36
processed file: MF59A_500_2502_small.bw


title: S2-HAGRHL2.Grh_0uM_R2

description:
Library name: ATACseq_17
processed file: MF31A_0_2406_small.bw


title: S2-Grh_100uM_B_R2

description:
Library name: ATACseq_28
processed file: TG3A_100_2501_small.bw


title: S2-GrhR806A_0uM_R1

description:
Library name: ATACseq_25
processed file: MF13A_0_2501_small.bw


title: S2-GrhC800AK807A_100uM_R2

description:
Library name: ATACseq_30
processed file: MF12A_100_2501_small.bw


title: S2-HAGrh.GRHL2_450uM_R2

description:
Library name: ATACseq_20
processed file: MF32A_450_2406_small.bw

value: 450 uM CuSO4


title: S2-HAGRHL2.Grh_450uM_R2

description:
Library name: ATACseq_18
processed file: MF31A_450_2406_small.bw


title: S2-GrhScrwSD_100uM_R2

description:
Library name: ATACseq_44
processed file: MF60A_100_2502_small.bw


title: S2-Grh_0uM_C_R1

description:
Library name: ATACseq_33
processed file: TG3A_0_2502_small.bw


title: S2-GrhScrwSD_0uM_R1

description:
Library name: ATACseq_37
processed file: MF60A_0_2502_small.bw


title: S2-HAGRHL2_450uM_R2

description:
Library name: ATACseq_16
processed file: MF30A_450_2406_small.bw


title: S2-HAGrh.GRHL2_0uM_R2

description:
Library name: ATACseq_19
processed file: MF32A_0_2406_small.bw


title: S2-HAGRHL2_0uM_R2

description:
Library name: ATACseq_15
processed file: MF30A_0_2406_small.bw


title: S2-HAGrh_200uM_R2

description:
Library name: ATACseq_14
processed file: TG14A_200_2406_small.bw

value: 200 uM CuSO4


title: S2-HAGrh_0uM_R2

description:
Library name: ATACseq_13
processed file: TG14A_0_2406_small.bw


title: S2-HAGrh.GRHL2_450uM_R1

description:
Library name: ATACseq_10
processed file: MF32A_450_2406_small.bw


title: S2-HAGrh.GRHL2_0uM_R1

description:
Library name: ATACseq_9
processed file: MF32A_0_2406_small.bw


title: S2-Grh_100uM_A_R2

description:
Library name: ATACseq_12
processed file: TG3A_100_2406_small.bw


title: S2-HAGRHL2_450uM_R1

description:
Library name: ATACseq_6
processed file: MF30A_450_2406_small.bw


title: S2-HAGRHL2.Grh_450uM_R1

description:
Library name: ATACseq_8
processed file: MF31A_450_2406_small.bw


title: S2-HAGrh_200uM_R1

description:
Library name: ATACseq_4
processed file: TG14A_200_2406_small.bw


title: S2-Grh_0uM_A_R1

description:
Library name: ATACseq_1
processed file: TG3A_0_2406_small.bw


title: S2-Grh_100uM_A_R1

description:
Library name: ATACseq_2
processed file: TG3A_100_2406_small.bw


title: S2-GrhScrwSD_100uM_aGrh_IP_R1

description: Library name: ChIPseq_43

data_processing:
Reads were aligned to the Drosophila melanogaster genome (dm6) using Bowtie2 (v2.4.4). Unmapped reads, reads aligning to the mitochondrial genome or unplaced scaffolds, reads aligning more than once or low-quality reads (MAPQ<30) were removed.
Assembly: dm6
Supplementary files format and content: bigwig files were formed from merged replicates and z-score normalized.

extract_protocol:
ChIP was performed as previously described (Gibson et al. 2024). 25x106 cells were fixed in 0.8% formaldehyde for 7 min and quenched with 125 mM gylcine. Fixed chromatin was sonicated on a Covaris S220 for five 120s rounds with 60s delay, peak power at 170, a duty factor of 10%, and 200 cycles per burst.  IPs were incubated with anti-Grh or anti-HA antibody at 4˚C overnight. Samples were purified using Dynabeads Protein A for Grh (20 uL; Thermo Fisher Scientific) or M-280 Sheep Anti-Mouse IgG for HA (60 uL; Thermo Fisher Scientific). The beads were washed, and chromatin was eluted. IPs and inputs were treated with 90ug RNaseA for 30 mins at 37˚C, and crosslinks were reversed by adding proteinase K overnight at 65˚C. DNA was isolated by phenol:chloroform extraction and concentrated overnight by ethanol precipitation.
Libraries were constructed using the NEB Next Ultra II kit.

tag: antibody

value: Grh


title: S2-HAGrh.GRHL2_450uM_aGrh_INPUT_R2

description: Library name: ChIPseq_40


title: S2-Grh_100uM_aGrh_INPUT_C_R1

description: Library name: ChIPseq_47


title: S2-GrhScr_500uM_aGrh_IP_R1

description: Library name: ChIPseq_42


title: S2-HAGRHL2_450uM_aGrh_INPUT_R2

description: Library name: ChIPseq_38


title: S2-Grh_100uM_aGrh_IP_C_R1

description: Library name: ChIPseq_41


title: S2-HAGrh_0uM_R1

description:
Library name: ATACseq_3
processed file: TG14A_0_2406_small.bw


title: S2-GrhScrwSD_100uM_aGrh_IP_R2

description: Library name: ChIPseq_46


title: S2-Grh_100uM_aGrh_IP_C_R2

description: Library name: ChIPseq_44


title: S2-Grh_100uM_aGrh_INPUT_C_R2

description: Library name: ChIPseq_50


title: S2-GrhScr_500uM_aGrh_IP_R2

description: Library name: ChIPseq_45


title: S2-GrhScrwSD_100uM_aGrh_INPUT_R2

description: Library name: ChIPseq_52


title: S2-HAGRHL2_0uM_R1

description:
Library name: ATACseq_5
processed file: MF30A_0_2406_small.bw


title: S2-HAGRHL2.Grh_450uM_aGrh_INPUT_R2

description: Library name: ChIPseq_39


title: S2-Grh_0uM_A_R2

description:
Library name: ATACseq_11
processed file: TG3A_0_2406_small.bw


title: S2-GrhScr_500uM_aGrh_INPUT_R2

description: Library name: ChIPseq_51


title: S2-HAGRHL2.Grh_0uM_R1

description:
Library name: ATACseq_7
processed file: MF31A_0_2406_small.bw


title: S2-Grh_100uM_aGrh_INPUT_B_R2

description: Library name: ChIPseq_37


title: S2-GrhScrwSD_100uM_aGrh_INPUT_R1

description: Library name: ChIPseq_49


title: S2-HAGrh.GRHL2_450uM_aGrh_IP_R2

description: Library name: ChIPseq_36

value: HA


title: S2-HAGRHL2_450uM_aGrh_IP_R2

description: Library name: ChIPseq_34


title: S2-Grh_100uM_aGrh_IP_B_R2

description: Library name: ChIPseq_33


title: S2-HAGRHL2.Grh_450uM_aGrh_IP_R2

description: Library name: ChIPseq_35


title: S2-HAGRHL2.Grh_450uM_aGrh_INPUT_R1

description: Library name: ChIPseq_31


title: S2-HAGRHL2_450uM_aGrh_INPUT_R1

description: Library name: ChIPseq_30


title: S2-GrhScr_500uM_aGrh_INPUT_R1

description: Library name: ChIPseq_48


title: S2-HAGrh.GRHL2_450uM_aHA_IP_R1

description: Library name: ChIPseq_28


title: S2-Grh_100uM_aGrh_INPUT_B_R1

description: Library name: ChIPseq_29


title: S2-HAGRHL2.Grh_450uM_aHA_IP_R1

description: Library name: ChIPseq_27


title: S2-HAGrh.GRHL2_450uM_aGrh_INPUT_R1

description: Library name: ChIPseq_32


title: S2-HAGRHL2_450uM_aHA_IP_R1

description: Library name: ChIPseq_26


title: S2-Grh_100uM_aGrh_IP_B_R1

description: Library name: ChIPseq_25


title: Pcgf5_siRNA_H2AK119ub1_rep1

city: Kyoto

first: Shinnosuke

last: Honda

address: Kitashirakawa Oiwake-cho, Sakyo-ku, Kyoto-shi

country: Japan

institute: Kyoto University

description: Library name: Sample19

data_processing:
For RNA-seq, the sequencing reads were mapped to the mouse genome (mm10) using STAR aligner software (v2.7.10.a). Gene expression levels were calculated using RSEM (ver. 1.3.3). For ChIP-seq, the sequencing reads were mapped to the mouse genome (mm10) using Bowtie2 (ver. 2.4.5) and converted to bigwig (BW) files using counts per million (CPM) normalization by bamCoverage in deepTools.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files include FPKM values for each sample generated by RSEM (v1.3.3) for RNA-seq. Bigwig files generated by banCoverage for ChIP-seq.

source_name: Morula stage embryo

growth_protocol: Superovulated mouse oocytes were in vitro fertilized and resulting embryos were cultured in KSOM up to apropriate stage (late two-cell, 36 hpi; four-cell, 48hpi; morula, 72 hpi).

extract_protocol:
RNA-seq library was generated from ten embryos per each group, by using SMART-Seq v4 PLUS Kit (Takara Bio USA) according to the manufacturer’s manual. ChIP-seq library were generated from morula-stage embryos at 72 hpi were collected as approximately 40 embryos per biological replicate. ChIP for small cell numbers was performed with a Low Cell ChIP-Seq Kit (Active Motif) according to the manufacturer’s manual (version A3) with some modifications. The morulae were freed from the zona pellucida by using pronaseK before crosslinking with formaldehyde. After crosslink-quenching, the sample was sonicated to shear chromatin using a Bioruptor UCD-250 (Cosmo Bio) for 30 x 30 s with 30-s pauses in ice-water. The sample was centrifuged for 2 min at 18,000 x g and the supernatant (200 μL) was transferred to a new tube. The 200-µL sample of sheared chromatin was processed for ChIP using anti-H2AK119ub1 antibody (8240; Cell Signaling Technology). The ChIPed DNA was decrosslinked, purified, and resuspended in 40 µL low-EDTA TE buffer. Sequencing libraries of the ChIPed DNA were constructed by using Next Gen DNA Library Kit and Next Gen Indexing Kit (Active Motif) following the manufacturer’s instruction.
SMART-Seq v4 PLUS Kit (Takara Bio USA) and Low Cell ChIP-Seq Kit (Active Motif) was used according to the manufacturer’s manual.

treatment_protocol: For KD experiment, One-cell stage embryos at 3 hpi were electroporated with non-targeting or Pcgf5-targeting siRNAs.

value: Morula stage embryo

value: in vitro produced, siPcgf5 treated from the one-cell stage


title: siRNA_Control_H2AK119ub1_rep2

description: Library name: Sample18

value: in vitro produced, siControl treated from the one-cell stage


title: Pcgf5MT2C_Mm_Homo_KO_RNA-seq_4C_rep2

description: Library name: Sample15

source_name: 4-cell stage embryo

value: 4-cell stage embryo

value: in vitro produced


title: Pcgf5_siRNA_H2AK119ub1_rep2

description: Library name: Sample20


title: Pcgf5MT2C_Mm_Homo_KO_RNA-seq_4C_rep1

description: Library name: Sample14


title: Pcgf5_siRNA_RNA-seq_Morula_rep2

description: Library name: Sample8


title: Pcgf5MT2C_Mm_Homo_KO_RNA-seq_4C_rep3

description: Library name: Sample16


title: siRNA_Control_H2AK119ub1_rep1

description: Library name: Sample17


title: WT_RNA-seq_4C_rep2

description: Library name: Sample10


title: siRNA_Control_RNA-seq_Morula_rep1

description: Library name: Sample5


title: Pcgf5_siRNA_RNA-seq_Morula_rep1

description: Library name: Sample7


title: WT_RNA-seq_4C_rep1

description: Library name: Sample9


title: siRNA_Control_RNA-seq_Morula_rep2

description: Library name: Sample6


title: Pcgf5MT2C_Mm_Hetero_KO_RNA-seq_4C_rep3

description: Library name: Sample13


title: siRNA_Control_RNA-seq_L2C_rep1

description: Library name: Sample1

source_name: Late 2-cell stage embryo

value: Late 2-cell stage embryo


title: Pcgf5MT2C_Mm_Hetero_KO_RNA-seq_4C_rep2

description: Library name: Sample12


title: Pcgf5MT2C_Mm_Hetero_KO_RNA-seq_4C_rep1

description: Library name: Sample11


title: siRNA_Control_RNA-seq_L2C_rep2

description: Library name: Sample2


title: NuTRAP;AdQCreER, PW7d-3

city: Oklahoma City

first: Lorin

middle: E.

last: Olson

state: OK

address: 825 NE 13th St,

department: Cardiovascular Biology

institute: Oklahoma Medical Research Foundation

description:
Library name: SAMPLE8
column name in raw_counts_AdQ.csv: 250918-5_AdQ_PW7d-3

data_processing:
Spliced Transcripts Alignments to a Reference (STAR, v 2.7.10b), featureCounts (v 2.0.8), and DESeq2 were used to process the seqeucning data.
Assembly: mm10
Supplementary files format and content: a csv file with raw count values for each sample

molecule: cytoplasmic RNA

source_name: skin

extract_protocol:
Pulled down the mRNA from GFP-tagged polysomes using an anti-GFP antibody and Protein G Dynabeads. Polysomal complexes were then isolated with the Nucleospin RNA kit, which included an on-column DNase digestion step.
Libraries were generated using the Takara SMART-Seq mRNA LP kit according to  the manufacturer’s instructions using 20 ng RNA

treatment_protocol: To create excisional wounds, 7-9 weeks-old mice were wounded during the telogen phase of hair cycling. Mice were administered analgesic (ketoprofen 5mg/kg) followed by inhaled anesthesia (5% isoflurane/1% oxygen). Dorsal hair was shaved and then completely removed using depilatory cream. The exposed skin was sterilized with 70% ethanol. Excisional wounding was performed using a 5mm biopsy punch to create 4 full-thickness dermal wounds.

value: skin

value: adipocyte

value: Tamoxifen,skin wound


title: NuTRAP;AdQCreER, PW7d-2

description:
Library name: SAMPLE7
column name in raw_counts_AdQ.csv: 250918-4_AdQ_PW7d-2


title: NuTRAP;AdQCreER, PW7d-1

description:
Library name: SAMPLE6
column name in raw_counts_AdQ.csv: 250918-3_AdQ_PW7d-1


title: NuTRAP;AdQCreER, PW3d-1

description:
Library name: SAMPLE4
column name in raw_counts_AdQ.csv: 251027-5_AdQ_PW3d-1


title: NuTRAP;AdQCreER, Uninjured-2

description:
Library name: SAMPLE2
column name in raw_counts_AdQ.csv: 251014-3_AdQ_Uninj2

value: Tamoxifen


title: Pcgf5_siRNA_RNA-seq_L2C_rep2

description: Library name: Sample4


title: NuTRAP;AdQCreER, Uninjured-3

description:
Library name: SAMPLE3
column name in raw_counts_AdQ.csv: 251014-5_AdQ_Uninj3


title: NuTRAP;AdQCreER, Uninjured-1

description:
Library name: SAMPLE1
column name in raw_counts_AdQ.csv: 251014-1_AdQ_Uninj1


title: WT2

city: Luzhou

first: zhenghong

last: peng

address: No. 25, Taiping Street, Jiangyang District

institute: The Affiliated Hospital of Southwest Medical University

description:
Library name: WT2
control

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

source_name: brain

extract_protocol:
RNA was extracted from tissue using TRIzol reagent. Briefly, tissue were washed with PBS, lysed in TRIzol, and incubated for 5 min. Chloroform (20% volume) was added, followed by vigorous mixing and centrifugation (12,000 ×g, 15 min, 4°C) to separate phases. The aqueous layer was collected, mixed with isopropanol, and centrifuged (12,000 ×g, 10 min) to precipitate RNA. The pellet was washed twice with 75% ethanol, air-dried, and dissolved in RNase-free water. RNA concentration and integrity (RIN >7) were assessed using Nanodrop and Bioanalyzer. Samples were stored at -80°C to prevent degradation. This method ensures high-quality RNA for transcriptomic analyses such as RNA-seq or qPCR.
Total RNA (1 µg, RIN >7) was enriched for mRNA using poly(A) selection (for eukaryotes) or rRNA depletion (for prokaryotes). The RNA was fragmented (∼200–300 nt) and reverse-transcribed into cDNA using random hexamers and SuperScript IV. Second-strand synthesis was performed with dUTP incorporation (strand-specific libraries). The cDNA was end-repaired, A-tailed, and ligated to Illumina-compatible adapters. Post-ligation cleanup (AMPure XP beads) was followed by size selection (200–500 bp) and uracil digestion (for strand specificity). Library amplification (8–12 cycles) used indexed primers, and final quantification (Qubit) and quality control (Bioanalyzer/TapeStation) ensured optimal fragment size (∼300 bp) and concentration (>10 nM). Libraries were pooled and sequenced (Illumina platforms, 150 bp paired-end).

value: brain

value: control


title: WT4

description:
Library name: WT4
control


title: WT3

description:
Library name: WT3
control


title: NuTRAP;AdQCreER, PW3d-2

description:
Library name: SAMPLE5
column name in raw_counts_AdQ.csv: 251027-6_AdQ_PW3d-2


title: AVM4

description:
Library name: AVM4
Brain arteriovenous malformation

value: Brain arteriovenous malformation


title: AVM3

description:
Library name: AVM3
Brain arteriovenous malformation


title: WT1

description:
Library name: WT1
control


title: AVM2

description:
Library name: AVM2
Brain arteriovenous malformation


title: Hyaloid blood vessels, control, SORT-seq, rep1

city: Würzburg

first: Mario

last: Vallon

address: Koellikerstr. 6

department: Institute of Anatomy and Cell Biology

institute: University of Würzburg

description: Library name: IAC-MV-s006

data_processing:
Raw reads were mapped to the mouse reference genome and unique molecular identifier (UMI) counts determined using STARsolo (version 2.7.11b).
Assembly: GRCm38
Supplementary files format and content: Standard STARsolo output files and format

source_name: Vitreous body

extract_protocol: SORT-seq PLUS (Single Cell Discoveries)

value: Vitreous body

value: Gpr124 fl/fl


title: Hyaloid blood vessels, knockout, SORT-seq, rep2

description: Library name: IAC-MV-s004

value: Gpr124 dEC/dEC


title: Hyaloid blood vessels, knockout, SORT-seq, rep1

description: Library name: IAC-MV-s003