title: ChIPseq_DMSO_HP1y_Input_rep1


title: WT1 head

status: Public on Jul 02 2026

type: SRA

city: Los Angeles

first: Lauryn

last: Higginson

state: CA

address: 1050 Childs Way

department: Biological Sciences

country: USA

institute: University of Southern California

description: Library name: Sample 10

library_source: transcriptomic

data_processing:
Raw sequencing data were basecalled in real time using MinKNOW (V6.8.11) with Dorado (v7.11.2) employing default cDNA-PCR basecalling model
Gene-level counts were quantified using featureCounts
Assembly: Reads were aligned to Drosophila melanogaster reference genome (FlyBase release r6.66) using minimap2 (v2.30).
Supplementary files format and content: csv of raw counts from each sample

molecule: total RNA

organism: Drosophila melanogaster

source_name: head

extract_protocol:
Total RNA was extracted from fly thorax using standard phenol-chloroform protocol
Total RNA samples were subjected to in vitro polyadenylation using E. coli Poly(A) polymerase (New England Biolabs, M0276S) according to the manufacturer’s instructions. Polyadenylated RNA was subsequently purified by phenol-chloroform extraction followed by ethanol precipitation. Sequencing libraries were generated from approximately 200 ng of in vitro polyadenylated RNA using Oxford Nanopore Technologies (ONT) PCR-cDNA Barcoding Kit (SQK-PCB111.24) following the manufacturer’s protocol.

tag: tissue

value: head

tag: genotype

value: WT

tag: batch


title: Rat anterior pituitary single-cell RNA-seq

city: Yokohama

first: Ken

last: Fujiwara

state: Kanagawa

department: Faculty of Science

country: Japan

institute: Kanagawa University

description:
Library name: Sample1
10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequencing data were processed using Cell Ranger (version 7.0.1). Reads were aligned to the rat reference genome (refdata-cellranger-mRatBN7.2). Gene expression matrices were generated including intronic reads. No formal cell type annotation was assigned, and cell populations were interpreted based on marker gene expression.
Assembly: mRatBN7.2
Supplementary files format and content: Processed data are provided as filtered gene expression matrices (barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz) generated by Cell Ranger. Only barcodes identified as cells are included.

organism: Rattus norvegicus

source_name: anterior pituitary

growth_protocol: Anterior pituitary glands were dissected from adult male Wistar rats and dissociated into single-cell suspensions.

extract_protocol:
Single-cell suspensions were prepared using enzymatic dissociation of anterior pituitary tissue.
Single-cell RNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (10x Genomics) according to the manufacturer's instructions.

treatment_protocol: No experimental treatment was applied.

value: anterior pituitary

tag: cell type

value: primary anterior pituitary cells


title: KPC_12.3b_35K

city: CAMBRIDGE

first: Giulia

last: Biffi

state: Cambridgeshire

address: Cancer Research UK, Robinson Way

country: United Kingdom

institute: University of Cambridge

description: Library name: SITTD1

data_processing:
CellRanger count (v8.0.1) : default parameters
Assembly: mm10-2020-A
Supplementary files format and content: raw_feature_bc_matrix.h5

organism: Mus musculus

source_name: PDAC tumors

extract_protocol:
For samples from batch 1 and 2 : Chromium Next GEM Single Cell 3' Kit v3.1, PN-1000268; Chromium Next GEM Chip G Single Cell Kit, PN-1000120; Dual Index Kit TT Set A, PN-1000215; and the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) user guide. For samples from batch 3 and 4 : Chromium GEM-X Single Cell 3' Kit v4,  PN-1000691; Chromium GEM-X Single Cell 3' Chip Kit v4, PN-1000690, PN-1000120; Dual Index Kit TT Set A, PN-1000215; and the Chromium GEM-X Single Cell 3' v4 Gene Expression User Guide (Revision B).
10x Genomics single nucleus RNA-seq

treatment_protocol: submitted 35-55-70K nuclei

value: PDAC tumors

value: KrasLSL-G12D/+; Trp53LSL-R172H/+;Cre


title: G146C3 Thorax

description: Library name: Sample 9

source_name: thorax

value: thorax


title: ChIPseq_DMSO_HP1b_IP_rep2

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

library_source: genomic

data_processing:
Raw reads in fastq format were processed with Trim-Galore tool (v0.4.4)
Reads were mapped to human reference genome (GRCh38.p12) with bwa aln, followed by bwa samse7 (v0.7.12-r1039) with -K flag set to 10000000. Samples with Drosophila melanogaster spike-in (BRD4 ChIP-seq) were mapped the the human-fly hybrid genome instead, and reads mapping to human reference were further extracted.
Duplicated reads were marked with bamsormadup tool from biobambam2 (v2.0.87) and Cross-Correlation analysis was conducted with SPP (v1.11)
Genome_build: hg38 (GRCh38.p12), dm6
Supplementary_files_format_and_content: bigwig

molecule: genomic DNA

organism: Homo sapiens

source_name: B-Lymphocyte

growth_protocol: RPMI + 15% FBS + anti/anti. BRD4 samples were grown -anti/anti

extract_protocol:
Chromatin was immunoprecipitated using the standard Covaris protocol and purified on silica columns. Samples with Drosophila melanogaster spike-in (BRD4) were processed using a common ChIP protocol and purified using phenol-chloroform extraction
Libraries were constructed using standard Illumina protocols

treatment_protocol: Samples were treated for 24 hours using indicated compounds

value: Patient Derived B-Lymphocytes

tag: cell line

tag: chip antibody

value: HP1b (Cell Signaling 8676S)

tag: treatment

value: DMSO


title: G146C2 Thorax

description: Library name: Sample 8


title: KPC_16.3b_35K

description: Library name: SITTC1


title: Apoptotic neutrophil- loaded gelatin methacryloyl (GelMA)

city: Irvine

first: Wendy

middle: F

last: Liu

email: wendy.liu@uci.edu, enriqud2@uci.edu

state: California

address: 419 S. Circle View Drive

department: Biomedical Engineering

institute: University of California Irvine

description:
Library name: Sample 3
Processed data is contained within the files Heat_barcodes.tsv.gz, Heat_features.tsv.gz, Heat_matrix.mtx.gz

data_processing:
Raw sequencing FASTQ files were processed using Cell Ranger Multi (v10.0.0) following the standard 10x Genomics Chromium Flex (single-cell gene expression with probe hybridization) workflow.Reads were aligned to the mouse reference genome GRCm39. Probe signals were filtered and quantified against the 'Chromium Mouse Transcriptome Probe Set v2.0.0'.
Cell calling and filtering were performed automatically by the Cell Ranger multi pipeline to distinguish true cell-associated barcodes from background ambient RNA.
Assembly: mm39
Supplementary files format and content: Filtered gene expression count matrices generated by Cell Ranger Multi (Flex). For each sample, the processed data consists of a sparse matrix file (matrix.mtx.gz), a feature list (features.tsv.gz), and cell barcodes (barcodes.tsv.gz).

source_name: Skin

extract_protocol:
Post-wounding day 5, wound tissue was excised with 2 mm margins encompassing both the wound bed and surrounding healthy tissue. Samples were finely minced, fixed for 24 hours, and dissociated using Liberase TH (5 mg/mL) (Roche) for 2 hours at 37°C with agitation on a shaker. Cell concentration and viability were determined using propidium iodide (Thermo Fisher Scientific) staining.
RNA libraries were prepared using the 10x Genomics GEM-X Flex v2 Mouse Kit and sequenced on the Illumina NovaSeq X.

treatment_protocol: Full-thickness skin wounding was performed on postnatal day 50 female C57BL/6J mouse strain mice. Mice were anesthetized with isoflurane, shaved, and sterilized with 70% ethanol and povidone-iodine. A 5 mm full-thickness excisional wound was created at the dorsal midline below the scapulae to reduce mechanical disruption during healing. A splint was sutured around the wound to prevent contraction. Wounds were treated with 20 μL of either GelMA or AN-loaded GelMA and crosslinked in situ using UV light for 1 minute. The wound site was covered with Tegaderm (3M) and reinforced with flexible adhesive bandages (Band-Aid). Mice were housed individually post-surgery and monitored daily. Animals were euthanized at 5 days post-wounding.

value: Skin

value: 5 mm excisional wound, treated with apoptotic neutrophil-loaded gelatin methacryloyl (GelMA)

tag: time

value: 5 days


title: Gelatin methacryloyl (GelMA)

description:
Library name: Sample 2
Processed data is contained within the files GelMa_barcodes.tsv.gz, GelMa_features.tsv.gz, GelMa_matrix.mtx.gz

value: 5 mm excisional wound, treated with GelMA


title: ChIPseq_DMSO_HP1b_IP_rep1


title: P_62_70K

description: Library name: SITTB1

source_name: Pancreatitis

value: Pancreatitis

value: Wild-type


title: ChIPseq_DMSO_HP1b_Input_rep2


title: 28472_50U-10min_9-1

city: Ithaca

first: B. Franklin

last: Pugh

state: NY

address: 465 Biotechnology Building

department: Molecular Biology & Genetics

institute: Cornell University

data_processing:
*library strategy: Benzonase-seq
Reads were aligned using BWA-MEM.
Remove duplicate reads (Picard MarkDuplicates and Samtools).
Tally coverage of read1 5' tag using deeptools
Assembly: hg19
Supplementary files format and content: BigWig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: BigWig for reverse strand -- coverage of 5' end of Read 1 across the genome

growth_protocol: K562 cells were grown in suspension at ~0.5-1.0 x 106 cell/mL in complete IMDM with ~10% FBS and ~1% PenStrep at 5% CO2 and 37oC.

extract_protocol:
Cells were poured into methanol-free formaldehyde (final 1% concentration) at room temperature with gentle mixing for 10 min. Reactions were quenched with 3M Tris (pH 8.0), with 2 moles of Tris per 1 mole of formaldehyde, for at least 5 min. Fixed cells were washed with PBS, lysed with detergent containing buffers and needle lysis. Chromatin was digested with benzonase.
Benzonase-fragmented chromatin was centrifuged at 16,363 x g for 15 min at 4˚C.  The supernatant and pellet were separately used for library preparation. The pellet was resuspended by needle lysis with increasing needle gauge to minimize clumps. In some cases, total, super, or pellet fractions underwent DNA purification before being used for library input. Depending on the preparation, typically 0.5-1.3 million cell-equivalents of Benzonase-digested chromatin was digested with ProteinaseK for approximately 16 hours. Reverse-crosslinked DNA was purified with Ampure beads at 1.8x ratio to starting material and eluted in pure water. DNA underwent end-repair, A-tailing, and ligation to fork adapters (annealed Multiplexing Read 2 Sequencing primer /Nextera Read 2 External Adapter) with 3’ Ts. Components for enzymatic reactions were added successively to the previous resulting DNA and the enzyme was then heat inactivated before adding the next master mix. The ligated DNA was purified again with Ampure beads at 1.8x ratio to the final volume of ligation reaction and then amplified by PCR using ExB2 and ExC1 primers. Amplified libraries were size selected by gel electrophoresis in the range from 200-500 bp. Libraries were sequenced with the Illumina NextSeq 550, paired-end mode.

tag: pegr id

tag: fraction

value: super

tag: benzonase digestion

tag: sonication

value: no

tag: biological replicate

tag: resequencing replicate


title: Nras+C-myc+IL-2/CD25, HCC 3

city: Hang Zhou

last: Xu

address: Huansha Roud

country: China

institute: Zhejiang University

description: Library name: Sample 6

data_processing:
Raw sequencing data were converted to FASTQ format using Illumina bcl2fastq (v5.0.1). Cell counting and gene expression profiling were performed with CellRanger (v7.0.0) and scRNA-seq data were aligned to the Ensembl reference genome.
Assembly: Ensembl mouse v105
Supplementary files format and content: matrix files with barcode、features and matrix for each sample

source_name: HCC tissue

extract_protocol:
Cells were loaded into the Chromium Controller on a Chromium Next GEM Chip G Single Cell Kit (10X Genomics, PN-1000127) and processed to generate single-cell gel beads in the emulsion (GEM) according to the manufacturer’s protocol (10X Genomics, CG000315). cDNA amplification.
library construction were performed using Chromium Next GEM Single Cell 3ʹ Kit v3.1 (10X Genomics, PN-1000268) according to the manufacturer's manual.

value: HCC tissue


title: G146C1 Thorax

description: Library name: Sample 7


title: Sham

description:
Library name: Sample 1
Processed data is contained within the files Sham_barcodes.tsv.gz, Sham_features.tsv.gz, Sham_matrix.mtx.gz

value: 5 mm excisional wound


title: P_64_55K

description: Library name: SITTH9


title: G11A3 Thorax

description: Library name: Sample 6


title: ChIPseq_DMSO_HP1b_Input_rep1


title: ChIPseq_SynTEF1_HP1y_Input_rep1


title: PDAC3

description: Library name: SITSD8

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
binned at 8um
Assembly: mm10(2020-A)
Supplementary files format and content: raw_feature_bc_matrix.h5
Supplementary files format and content: aligned_fiducials.jpg
Supplementary files format and content: detected_tissue_image.jpg
Supplementary files format and content: scalefactors_json.json
Supplementary files format and content: tissue_hires_image.png.gz
Supplementary files format and content: tissue_lowres_image.png
Supplementary files format and content: cytassist_image.tiff
Supplementary files format and content: aligned_tissue_image.jpg
Library strategy: Spatial Transcriptomics

source_name: Tumour

extract_protocol:
FFPE tissues, 5 micron-thick sections
Spatial transcriptomic Illumina-compatible libraries were prepared with 10x Genomics Visium HD Probe-based Spatial Gene Expression assay according to manfacturer's instructions. sequencer: Illumina NovaSeq X using a 25B flow cell 300 cycle kit

value: Tumour

value: KPC GEMM B6J background


title: P_63_70K

description: Library name: SITTG9


title: G11A2 Thorax

description: Library name: Sample 5


title: G11A1 Thorax

description: Library name: Sample 4


title: ChIPseq_DMSO_HP1a_IP_rep2

value: HP1a (Cell Signaling 2616S)


title: ChIPseq_DMSO_HP1a_IP_rep1


title: P_63_55K

description: Library name: SITTF9


title: P_64_70K_batch2

description: Library name: SITTA10


title: PDAC2

description: Library name: SITSC8


title: ChIPseq_DMSO_HP1a_Input_rep2


title: PDAC1

description: Library name: SITSA2


title: P_68_35K

description: Library name: SITTC9


title: WT3 Thorax

description: Library name: Sample 3

value: thorax

value: WT


title: ChIPseq_DMSO_HP1a_Input_rep1

value: Patient Derived B-Lymphocytes


title: WT2 Thorax

description: Library name: Sample 2


title: WT1 Thorax

description: Library name: Sample 1


title: P_67_35K

description: Library name: SITTB9


title: N3

description: Library name: SITSG8

source_name: Normal

value: Normal


title: ChIPseq_DMSO_H3K9me3_IP_rep2

value: H3K9me3 (Abcam Ab8898)

value: DMSO


title: cxcr6_5

city: Boston

first: The Gene Lay Institute of

last: Immunology and Inflammation

state: MA

address: 60 Fenwood Road,

institute: Brigham and Women's Hospital

description:
Library name: AH14
WT_CXCR6_CNS_m5

data_processing:
Bulk RNA-seq data were preprocessed using the SMART-Seq2 v1.3.0 workflow on Cumulus v2.4.1. The workflow aligned reads to the mm10 genome using STAR v2.7.7a and estimated expression levels using RSEM v1.3.3. The workflow then computed the TPM-normalized count for each gene, defined as TPM_i / 10**6 × c rounded to the nearest integer, where TPM_i is the TPM for gene i estimated by RSEM and c is the total number of reads achieved for the sample.
Assembly: mm10
Supplementary files format and content: CSV files containing the TPM-normalized counts for each sample.

source_name: CNS

extract_protocol:
One thousand living cells were isolated by FACS and lysed in TCL buffer (QIAGEN) supplemented with 1% b-mercaptoethanol (Sigma-Aldrich)
Full-length RNA-seq libraries were prepared following a modified SMART-Seq2 protocol. cDNA was quantified with Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) and normalized to 0.25 ng/ul prior to Nextera XT DNA Library Preparation kit (Illumina). Library size (500 bp) was verified using a Bioanalyzer (Agilent). Indexed libraries were were pooled, normalized to 2 nM, denatured using 0.1 N NaOH, and sequenced on a NextSeq 500 platform (Illumnia) using the paired-end 38 bp × 2 reads (75 cycle high output V2 kit).

value: CNS

value: T cells


title: P4

description: Library name: SITSD3

value: Pancreatitis

value: Caerulein


title: 10_GB-CP-5_mCPLT

description: Library name: SLX26264_UDP0090

data_processing:
Estimated transcript counts were counted using Salmon (version 1.9.0)
Assembly: GRCm39 (mm39) - kmer 23
Supplementary files format and content: Raw count data in tab-delimited salmon file

extract_protocol:
Samples were collected in 1 mL of TRIzol Reagent (15596018; Invitrogen). RNA was extracted using the PureLink RNA mini kit (12183018A; Invitrogen). RNA concentration was measured using a Qubit and RNA quality was assessed on a TapeStation 4200 (Agilent) using the Agilent RNA ScreenTape kit. mRNA library preparations were performed using 55 mL of 10 ng/mL per sample (RNA integrity number, RIN ≥ 8.8)
Illumina mRNA library


title: N1

description: Library name: SITSA9


title: ChIPseq_DMSO_H3K9me3_IP_rep1


title: 7_T12LOH_KPC_mCPLT

description: Library name: SLX26264_UDP0089


title: ChIPseq_DMSO_H3K9me3_Input_rep2


title: slamf6_5

description:
Library name: AH13
WT_SLAMF6_CNS_m5


title: 28390_50U-10min_5-1

value: super


title: Nras+C-myc, HCC 2

description: Library name: Sample 2

value: Control


title: 9_GB-CP-2_mCPLT

description: Library name: SLX26264_UDP0088


title: cxcr6_4

description:
Library name: AH12
WT_CXCR6_CNS_m4


title: ChIPseq_DMSO_H3K9me3_Input_rep1


title: P3

description: Library name: SITSC3


title: slamf6_4

description:
Library name: AH11
WT_SLAMF6_CNS_m4


title: 6_PSC4_KPC_Cocx

description: Library name: SLX26264_UDP0087

value: PSC


title: ChIPseq_DMSO_H3K4me3_IP_rep2

value: H3K4me3 (Abcam Ab8540)


title: 28389_50U-10min_4-1

value: no


title: P1

description: Library name: SITSA3


title: 8_GB-CP-1_mCPLT

description: Library name: SLX26264_UDP0086


title: cxcr6_3

description:
Library name: AH10
WT_CXCR6_CNS_m3


title: ChIPseq_DMSO_H3K4me3_IP_rep1


title: Terc -/- Sting gt/gt, replicate 5

city: Madrid

first: Elena

last: Piñeiro-Yáñez

address: Calle de Melchor Fernández Almagro, 3

country: Spain

institute: Spanish National Cancer Research Centre (CNIO)

description: Library name: Sample 15

data_processing:
RNA sequencing data were processed using the cluster_RNAseq pipeline [https://github.com/cnio-bu/cluster_rnaseq]. First, FASTQ files were subjected to quality control using FastQC (version 0.11.9) and FastQ Screen (version 0.15.2). Unique Molecular Identifier (UMI) barcodes were extracted from reads using UMI-tools (version 1.1.4) employing the parameter --bc-pattern=^(?P<umi_1>.{6})(?P<discard_1>.{4}).*. Subsequently, PolyA tails and adapter sequences were removed using BBDuk (BBMap version 39.01). The files used in this step included polyA.fa.gz and truseq.fa.gz from BBMap (version 38.93-0). The parameters applied were k=13, ktrim=r, useshortkmers=t, mink=5, qtrim=t, trimq=10, and minlength=20.
Reads were then aligned to the GRCm39 version of the mouse reference genome using STAR (version 2.7.11b). The alignment was performed with the following parameters: --outFilterType BySJout, --outFilterMultimapNmax 20, --alignSJoverhangMin 8, --alignSJDBoverhangMin 1, --outFilterMismatchNmax 999, --outFilterMismatchNoverLmax 0.1, --alignIntronMin 20, --alignIntronMax 1000000, --alignMatesGapMax 1000000, --outSAMattributes NH HI NM MD, --outSAMtype BAM, and SortedByCoordinate. Duplicated reads were removed using UMI-tools dedup with the option --multimapping-detection-method=NH.
Genomic feature counts were obtained using featureCounts from the subread package (version 2.1.1). Differential expression analysis was performed using DESeq2 (version 1.30.1). Differentially expressed genes were identified based on an adjusted p-value threshold of 0.05.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file including raw counts for each sample
Supplementary files format and content: tab-delimited text file including normalized counts from DESeq2 for each sample

molecule: polyA RNA

source_name: Small intestine

extract_protocol:
Total RNA was extracted with TRIzol reagent (ThermoFisher 15596026) and then purified and treated with DNAse using RNeasy Kit (QUIAGEN 74106), following manufacturer´s instructions.
Provided total RNA samples (average RIN/RQS 5.6, range 3.2-7.1) were converted into sequencing libraries using the "QuantSeq 3‘ mRNA-Seq V2 Library Prep Kit (FWD) for Illumina" (Lexogen, Cat.No. 191). Briefly, library generation is initiated by reverse transcription with oligodT priming, followed by a random-primed second strand synthesis. A UMI Second Strand Synthesis module was used, in which random primers featuring a 6 nt long Unique Molecular Identifier tag are used {to be addressed for bias correction at data analysis}. Directional cDNA libraries, stranded in the sense orientation {--library-type fr-secondstrand in TopHat, --stranded=yes in HTSeq, --rna-strandness F in HISAT}, were completed by PCR and sequenced in a single read format on an Illumina instrument.

value: Small intestine

value: Terc -/- Sting gt/gt


title: ChIPseq_DMSO_H3K4me3_Input_rep2


title: Terc -/- Sting gt/gt, replicate 4

description: Library name: Sample 14


title: 3_PSC5_mono_GM

description: Library name: SLX26264_UDP0085


title: GF Vancomycin ZT23 replicate 4

city: Safed

first: Shai

last: Bel

address: 8 Henrietta Szold St

country: Israel

institute: Bar-Ilan University

description: Library name: GF_S16

data_processing:
Data were processed using the RASflow package, DOI: 10.1186/s12859-020-3433-x
Trimming: Reads were trimmed using Trim Galore version: 0.6.2 and adapters removed using Cutadapt version: 3.5. Quality Phred score cutoff: 20. Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected). Maximum trimming error rate: 0.1 (default). Minimum required adapter overlap (stringency): 1 bp. Minimum required sequence length before a sequence gets removed: 20 bp.
Mapping: Reads were mapped to the transcriptome (Mus_musculus.GRCm39) using Salmon. The normalized values are estimated Transcripts Per Million (TPM) from Salmon and are scaled using the average transcript length over samples and then the library size by “tximport”. Any missing gene names (using mmusculus_gene_ensembl) are replaced with gene IDs. We filtered out sparse genes, which we defined as those with over 50% zero values.
Assembly: Mus_musculus.GRCm39
Supplementary files format and content: Tab-delimited text files include both ENSMUSG and gene name identifiers, and normalized expression levels per gene.

source_name: Germ Free (GF)

growth_protocol: Swiss Webster mice were bred and maintained under a 12-hour light/dark cycle and fed standard chow in either SPF or germ-free conditions at the Azrieli Faculty of Medicine of the Bar-Ilan University. 8- to 12-week-old mice were used for all experiments.

extract_protocol:
RNA from flash frozen colonic tissues was extracted using RNeasy Plus Universal mini kit (Qiagen). The integrity of the isolated RNA was analyzed using the Agilent TS HS RNA Kit and TapeStation 4200 at the Genome Technology Center at the Azrieli Faculty of Medicine, Bar-Ilan University. 1000 ng of total RNA was treated with the NEBNext poly (A) mRNA Magnetic Isolation Module (NEB, #E7490L).
RNA sequencing libraries were produced by using the NEBNext Ultra II RNA Library Prep Kit for Illumina (NEB #E7770L).  Quantification of the library was performed using a dsDNA HS Assay Kit and Qubit (Molecular Probes, Life Technologies) and qualification was done using the Agilent TS D1000 kit and TapeStation 4200. 250nM of each library was pooled together and diluted to 4nM according to the NextSeq manufacturer’s instructions. 1.6pM was loaded onto the Flow Cell with 1% PhiX library control. Libraries were sequenced with the Illumina NextSeq 550 platform with single-end reads of 75 cycles according to the manufacturer's instructions.

treatment_protocol: Mice were randomly divided into either control or antibiotic treatment groups. Mice were treated twice a day for 3 days, and once more on the 4th day, via intraperitoneal injection. Mice received 2.5mg vancomycin in 100µl of PBS. Control mice received 100µl of PBS. For treatment of germ-free mice, mice were removed from sterile isolators into Tecniplast ISOchages, where they were maintained for the duration of the treatment.

value: Whole colon

value: Vancomycin


title: cxcr6_2

description:
Library name: AH08
WT_CXCR6_CNS_m2


title: ChIPseq_DMSO_H3K4me3_Input_rep1

value: Patient Derived B-Lymphocytes


title: Terc -/- Sting gt/gt, replicate 3

description: Library name: Sample 13


title: 5_T12LOH_cocx

description: Library name: SLX26264_UDP0084V3


title: 2_PSC5_mono

description: Library name: SLX26264_UDP0083


title: slamf6_2

description:
Library name: AH07
WT_SLAMF6_CNS_m2


title: Total RNA-seq mutant grown in minimal medium supplemented with 0.25 mg/mL L-tryptophan (IAA precursor) sample 3

first: Zulema

last: Udaondo

address: Darwin 3

department: Microbial Biotechnology

institute: CNB-CSIC

description:
Library name: Sample 6
MU_T250_3

data_processing:
Raw Illumina RNA-Seq reads were first subjected to quality control and adapter trimming using Fastp v0.23.2 . This step included removal of adapter sequences, filtering of low-quality reads (phred score < 30), and exclusion of reads shorter than 50 bp. The quality of both raw and processed reads was then assessed with FastQC  to ensure the absence of adapter contamination and to evaluate per-base sequence quality. High-quality reads were aligned to the reference genome ( D. dadantii 3937, RefSeq ID = GCF_000147055) using STAR v2.7.11b  with default parameters. The resulting alignment files (sorted BAM format) were used as input for transcript assembly and quantification with StringTie2 , which generated both transcript-level and gene-level expression estimates in the form of read count matrices. Differential expression analysis was carried out in Python using pyDESeq2 , an implementation of the DESeq2 statistical model.
Assembly: D. dadantii 3937, GCF_000147055
Supplementary files format and content: tab delimited file with raw counts
Supplementary files format and content: Tab delimited file with differentially expressed genes from DESeq2

organism: Dickeya dadantii 3937

source_name: mutant sample 3

growth_protocol: Dickeya dadantii strains were grown overnight in M9 minimal medium containing 15 mM glucose. The cultures were washed twice with M9 salts and diluted to an OD600 of 0.02 in M9 minimal medium containing 15 mM glucose supplemented with different concentrations of p-hydroxybenzoic acid, indole-3-acetic acid, salicylate or benzoate. Two-hundred microliters of these cultures were transferred to microwell plates and growth (OD600) was monitored at 30 ºC over time using a Bioscreen Microbiological Growth Analyser (Oy Growth Curves Ab, Helsinki, Finland).

extract_protocol:
Total RNA was extracted by using TRI Reagent® (Invitrogen) followed by Turbo DNase treatment (Ambion) and RNA clean-up with RNeasy Mini Kit (Qiagen), according to manufacturers´ instructions. The RNA concentration was determined spectrophotometrically and RNA degradation and contamination was assessed by electrophoresis on 2% (w/vol) agarose gels. The synthesis of cDNA was performed using random hexamers (GE Healthcare) and SuperScript II reverse transcriptase (Invitrogen) in a 25 µl reaction volume with 1 µg of total RNA and incubation at 42 ºC for 2 h. RT-qPCRs were performed as described previously  using primers described in supplementary Table S2.
RNA sequencing was performed at Novogene Company Limited (United Kingdom) using samples from the wild-type D. dadantii 3937 and the ∆iaaM-km3 mutant grown in minimal medium supplemented with 0.25 mg/mL L-tryptophan (IAA precursor) and harvested at the early stationary phase of growth. Before sequencing, RNA integrity and quantification were assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). One microgram of total RNA per sample (three biological replicates per strain) was used to construct the sequencing libraries. These libraries were generated by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® (New England Biolabs; #E7530), following the manufacturer's recommendations. Prior to library construction, ribosomal RNA was depleted with Illumina Ribo-Zero Plus rRNA Depletion Kit (Illumina; Ref. 20037135), according to the manufacturer's instructions. The resulting libraries were quantified by quantitative PCR and the inserts were measured using a LabChip GX instrument, using the LabChip NGS 3K reagent kit (PerkinElmer; CLS960013). Libraries were sequenced using the NovaSeq 6000 Illumina platform and paired-end reads were generated.

value: pure culture

value: MUT


title: 4_T12LOH_mono

description: Library name: SLX26264_UDP0082


title: cxcr6_1

description:
Library name: AH06
WT_CXCR6_CNS_m1


title: Total RNA-seq mutant grown in minimal medium supplemented with 0.25 mg/mL L-tryptophan (IAA precursor) sample 2

description:
Library name: Sample 5
MU_T250_2

source_name: mutant sample 2


title: Terc -/- Sting gt/gt, replicate 1

description: Library name: Sample 11


title: 1_PSC4_mono

description: Library name: SLX26264_UDP0081


title: slamf6_1

description:
Library name: AH05
WT_SLAMF6_CNS_m1


title: Total RNA-seq mutant grown in minimal medium supplemented with 0.25 mg/mL L-tryptophan (IAA precursor) sample 1

description:
Library name: Sample 4
MU_T250_1

source_name: mutant sample 1


title: cxcr6_0

description:
Library name: AH02
KO_CXCR6_CNS_m0


title: Sting +/+ Terc -/-, replicate 3

description: Library name: Sample 10

value: Terc -/- Sting +/+


title: 59_GB-N25_mCPLT

description: Library name: SLX25210_idtUDP0287


title: Total RNA-seq wild-type D. dadantii 3937 sample 3

description:
Library name: Sample 3
WT_T250_3

source_name: wild type sample 3

value: WT


title: Sting +/+ Terc -/-, replicate 2

description: Library name: Sample 9


title: Total RNA-seq wild-type D. dadantii 3937 sample 2

description:
Library name: Sample 2
WT_T250_2

source_name: wild type sample 2


title: 15_PSC4_CP_Cocx

description: Library name: SLX25210_idtUDP0285


title: Sting +/+ Terc -/-, replicate 1

description: Library name: Sample 8


title: her4.1:dRFP_TZS

city: New York

first: Caghan

last: Kizil

institute: Columbia University Irving Medical Center

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/metrics)
The fastq files were aligned to zebrafish genome (GRCz11) and (ensemble transcripts from Ensembl Release 105) by using STAR. The BAM files were as input for Cell Ranger (10X genomics) to generate processed data files that include gene names (row names) and cell names (column names) and counts. Further analysis done by using Seurat package version 4 in R.
Assembly: GRCz11
Supplementary files format and content: filtered_bc_matrix outputs from Cell Ranger

organism: Danio rerio

source_name: telencephalon

growth_protocol: Zebrafish were kept in the re-circulating system on a 14/10-h light/dark cycle, pH7.5, at 28°C (±1°C) in groups of 20 animals per 2.8L.

extract_protocol:
Cells from zebrafish telencephalon were dissociated. Viability indicator dyes Sytox Blue (Invitrogen, Cat No. S34857) and Dycle Ruby (Invitrogen, Cat. No. V10309) were used to sort the cells by FACS. The library preparation was performed by 10X Genomics as per manufacture's protocol.
10X genomics

treatment_protocol: Double transgenic (Tg(fli1a:eGFP)/Tg(her4.1:dRFP)) zebrafish line was treated with VEGF inhibitor cocktail (TZS), and DMSO as control as described (Is et al., 2024).

value: telencephalon

value: TZS


title: Terc +/+ Sting gt/gt, replicate 3

description: Library name: Sample 7

value: Terc +/+ Sting gt/gt


title: Total RNA-seq wild-type D. dadantii 3937 sample 1

description:
Library name: Sample 1
WT_T250_1

source_name: wild type sample 1


title: WT T. pyriformis strain GL cells, vegetative growth for RNA-seq rep2

city: Hefei

first: Zhengyu

last: Luo

address: huanshang

institute: USTC

description: Library name: Sample27

data_processing:
RNA-seq library adapters were trimmed using cutadapt v4.3, then the trimmed reads were mapped to T. pyriformis reference genome using hisat v2 2.2.1.
ATAC-seq library adapters were trimmed using cutadapt v4.3. The trimmed reads were mapped to T. pyriformis reference genome using bowtie2 v2.5.0 with the following parameters: -X 2000. PCR duplication was removed using samtools v1.17. bigwig files were generated by bamCoverage in deeptools v3.5.3.
Hi-C and Micro-C library adapters were trimmed using cutadapt v4.3. The trimmed reads were mapped to MAC.v5 genome for T. thermophila or P10K-MW-000002 for T. pyriformis with HiC-Pro v3.1.0, then the validpairs were convert to .hic with hicpro2juicebox.sh in HiC-Pro and .mcool with hic2cool v0.8.3.
RNAseq raw counts were generated by featureCounts in subread v1.6.4.
Assembly: MAC.v5 for T. thermophila. P10K-MW-000002 for T. pyriformis
Supplementary files format and content: RNAseq: tsv files includes raw counts for each sample.
Supplementary files format and content: ATACseq: bigwig files. Hi-C and Micro-C: mcool files

organism: Tetrahymena pyriformis

source_name: GL

growth_protocol: T. thermophila WT strains (SB210 and Cu428) were obtained from the Tetrahymena Stock Center. Cells were cultured at 30℃ in 1x SPP medium (10 g protease peptone, 2 g dextrose, 1 g yeast extract, 0.03 g Sequestrene (Fe-EDTA), adding water to final 1 L and autoclave prior to use).

extract_protocol:
For ATAC-seq, native cells were used for lysis and Tn5 treatment. For RNA-seq, cell pellets were resuspend in TRIZOL. For FA Hi-C, cells were fixed with 1% FA, for FA+DSG Hi-C and Micro-C, cells were fixed with 1% FA and 3 mM DSG.
The RNA-seq library was generated by Sequencing company. ATAC-seq: After Tn5 treated, DNA were purified with FastPure Gel DNA Extraction Mini Kit, then amplified by PCR and purify with VAHTS DNA Clean Beads. Hi-C: after Hi-C ligation, DNA were reverse crosslink at 65C overnight, then the DNA were purified and the library was generated by sonication, biotin pull-down, end-repair, dA-tailing, adapter ligation, after adapter ligation, PCR amplification and size select were performed. Micro-C: after Micro-C ligation, DNA were reverse crosslink at 65C overnight, then the DNA were purified and size select to remove unligated DNA fragments, then biotin pull-down, end-repair, dA-tailing, adapter ligation, after adapter ligation, PCR amplification and size select were performed.

value: GL

value: wild type cells


title: 22_T6LOH_KPC_Mono

description: Library name: SLX25210_idtUDP0282


title: fli1a:eGFP_TZS_2

description: 10x Genomics


title: WT T. pyriformis strain GL cells, vegetative growth for RNA-seq rep1

description: Library name: Sample26


title: 18_PSC4_KPC_Cocx

description: Library name: SLX25210_idtUDP0281

value: PSC


title: Terc +/+ Sting gt/gt, replicate 1

description: Library name: Sample 5


title: fli1a:eGFP_TZS_1

description: 10x Genomics


title: WT T. pyriformis strain GL cells, vegetative growth for ATAC-seq rep2

description: Library name: Sample24


title: Terc +/+ Sting +/+, replicate 3

description: Library name: Sample 3

value: Terc +/+ Sting +/+


title: 13_CP3_Mono

description: Library name: SLX25210_idtUDP0276


title: fn1b-/-_ Ab42 injected

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x genomics' cellranger software version 7.1.0. (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/metrics)
The fastq files were aligned to zebrafish genome (GRCz11) and (ensemble transcripts from Ensembl Release 105) by using STAR. The BAM files were as input for Cell Ranger (10X genomics) to generate processed data files that include gene names (row names) and cell names (column names) and counts. Further analysis done by using Seurat package in R.
Assembly: GRCz11
Supplementary files format and content: filtered_bc_matrix outputs from Cell Ranger

treatment_protocol: fn1b-/- knockout zebrafish line was injected with Amyloid-beta 42 peptide, and PBS as control as descibed (Bhatatrai et al. 2016).


title: WT T. pyriformis strain GL cells, vegetative growth for ATAC-seq rep1

description: Library name: Sample23


title: 25_CP-5_Mono

description: Library name: SLX25210_idtUDP0275


title: Terc +/+ Sting +/+, replicate 1

description: Library name: Sample 1


title: fli1a:eGFP_DMSO_2

description: 10x Genomics

value: DMSO


title: WT T. pyriformis strain GL cells, vegetative growth for Micro-C rep1

description: Library name: Sample21


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag2 Rep6

first: Daniel

last: Gimenez

institute: CNIO

description: Library name: mStag2_R6

data_processing:
For each sample, three FASTQ files were generated: paired-end reads (R1 and R3) and UMI barcodes (R2). Initial quality assessment of the FASTQ files was performed using FASTQC (version 0.11.9) and FastQ Screen (version 0.14.1). Subsequently, UMI sequences were appended to the read headers of the paired-end FASTQ files.
Adapter trimming was conducted using Flexbar (version 3.5) with parameters specific to the NEBNext Single Cell/Low Input RNA Library Prep Kit. Reads were then aligned to the mouse genome (mm39) using STAR (version 2.7.11b). Gene assignment was performed using featureCounts (version 2.0.8) from the Subread package .
UMI-tools (version 1.1.6) was employed to quantify unique UMIs per gene. Differential gene expression analysis was carried out using DESeq2 with a false discovery rate FDR < 0.05.
Assembly: mm39
Supplementary files format and content: tsv, read counts

source_name: Offspring from C57BL/6.CBA.F1 mated with C57BL/6J stud males

extract_protocol:
Whole cells were processed as provided with the "NEBNext Single Cell/Low Input RNA Library Prep" kit (NEB #E6420) by following manufacturer instructions. Briefly,  cells per sample in cell lysis buffer were submitted to an oligo(dT) primed reverse transcription with a template switching reaction, and production of double stranded cDNA was performed by limited-cycle PCR
Sequencing libraries were prepared with the "NEBNext Ultra II FS DNA Library Prep Kit for Illumina" (NEB #E7805), featuring UMI adaptors from a separate "NEBNext Multiplex Oligos" module (Unique Dual Index UMI Adaptors RNA Set 1, NEB #E7416) for a more accurate profiling of the transcriptome. Libraries were analysed on an Illumina instrument by following manufacturer's protocols

treatment_protocol: Zygotes were microinjected with either buffer or 20µM Antisense Oligonucleotide (ASO). ASOs used were against Hprt, Stag1 or Stag2.After microinjection they were placed in a 30µL drop of KSOM medium, covered with mineral oil and cultured at 37oC and 5% CO2 until they reached blastocyst stage

value: Blastocyst

value: Microinjected with Stag2


title: 26_CP-5_Cocx

description: Library name: SLX25210_idtUDP0270


title: P2

description: Library name: SITSB3

value: Pancreatitis

value: Caerulein


title: WT-Ab42 injected

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x genomics' cellranger software version 6.1.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/output/metrics)
The fastq files were aligned to zebrafish genome (GRCz11) and (ensemble transcripts from Ensembl Release 105) by using STAR. The BAM files were as input for Cell Ranger (10X genomics) to generate processed data files that include gene names (row names) and cell names (column names) and counts. Further analysis done by using Seurat package in R.
Assembly: GRCz11
Supplementary files format and content: filtered_bc_matrix outputs from Cell Ranger

treatment_protocol: WT-AB line was injected with Amyloid-beta 42 peptide, and PBS as control as descibed (Bhatatrai et al. 2016).

value: WT-AB


title: Ana PHFDPCs in October, male (bio rep 3)

city: Shenyang

first: Huiling

last: Xue

address: 120 Dongling Road,110866 Shenyang,China

institute: Shenyang Agricultural University

description: Library name: Sample 24

data_processing:
Sequenced reads were trimmed for adaptor sequence, and mapped to goat (Capra hircus) transcriptomes (GCF_001704415.1_ARS1) using Kallisto (v.0.46.1) with parameters -b 100. The gene abundances were obtained by kallisto-sleuth (v.0.30.0) pipeline in TPM (transcripts per million) (Bray NL et al. 2016).
Assembly: GCF_001704415.1_ARS1
Supplementary files format and content: tab-delimited text files include TPM values for each Sample.

organism: Capra hircus

source_name: Primary hair follicle dermal papilla cells from goat skin

extract_protocol:
Total RNA was extracted from the hair follicle dermal papilla cells using RNAiso Plus (TRIzol method, TaKaRa Bio, Dalian, China).
Paired-end sequencing of the cDNA library construction for transcriptome sequencing was performed according to the operating instructions for the NEB Next® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA).

tag: Sex

value: male


title: slamf6_3

description:
Library name: AH09
WT_SLAMF6_CNS_m3

value: CNS

value: T cells


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag2 Rep5

description: Library name: mStag2_R5


title: 02_CP2_Cocx

description: Library name: SLX25210_idtUDP0269


title: Ana PHFDPCs in October, male (bio rep 2)

description: Library name: Sample 23

value: Primary hair follicle dermal papilla cells from goat skin


title: Terc -/- Sting gt/gt, replicate 2

description: Library name: Sample 12

value: Small intestine

value: Terc -/- Sting gt/gt


title: WT T. pyriformis strain GL cells, vegetative growth for Micro-C rep2

description: Library name: Sample22


title: 07_CP1_Mono

description: Library name: SLX25210_idtUDP0268


title: Ana PHFDPCs in October, male (bio rep 1)

description: Library name: Sample 22

value: Primary hair follicle dermal papilla cells


title: WT Cu428 x B2086, Refeeding 24 hours after conjugation for Micro-C rep2

description: Library name: Sample20

organism: Tetrahymena thermophila


title: 52_T6-LOH_mCPLT

description: Library name: SLX25210_idtUDP0284


title: slamf6_0

description:
Library name: AH01
KO_SLAMF6_CNS_m0


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag2 Rep3

description: Library name: mStag2_R3


title: 08_CP1_Cocx

description: Library name: SLX25210_idtUDP0267


title: Terc +/+ Sting gt/gt, replicate 2

description: Library name: Sample 6

value: Terc +/+ Sting gt/gt


title: Ana PHFDPCs in October, female (bio rep 3)

description: Library name: Sample 21

value: female


title: 49_CP3_mCPLT

description: Library name: SLX25210_idtUDP0283


title: 17_T13LOH_KPC_Cocx

description: Library name: SLX25210_idtUDP0266


title: WT Cu428 x B2086, conjugation 24 hpm for Micro-C rep2

description: Library name: Sample18

value: wild type cells


title: Terc +/+ Sting +/+, replicate 4

description: Library name: Sample 4

value: Sting +/+ Terc +/+


title: Ana PHFDPCs in October, female (bio rep 2)

description: Library name: Sample 20


title: WT T. pyriformis strain GL cells, vegetative growth for ATAC-seq rep3

description: Library name: Sample25

value: GL


title: 10_T6LOH_KPC_Mono

description: Library name: SLX25210_idtUDP0265


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag2 Rep1

description: Library name: mStag2_R1

value: Blastocyst


title: 14_CP3_Cocx

description: Library name: SLX25210_idtUDP0280


title: WT Cu428 x B2086, conjugation 24 hpm for Micro-C rep1

description: Library name: Sample17


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag2 Rep2

description: Library name: mStag2_R2

value: Microinjected with Stag2


title: her4.1:dRFP_DMSO

description: 10x Genomics

value: telencephalon

value: DMSO


title: Ana PHFDPCs in October, female (bio rep 1)

description: Library name: Sample 19


title: 51_CP5_mCPLT

description: Library name: SLX25210_idtUDP0256


title: WT Cu428 x B2086, conjugation 12 hpm for Micro-C rep2

description: Library name: Sample16


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag1-2 Rep4

description: Library name: mStag1-2_R4

value: Microinjected with Stag1 ASO2


title: fli1a:eGFP_DMSO_1

description: 10x Genomics


title: 30_PSC5_KPC_Cocx

description: Library name: SLX25210_idtUDP0255

value: PSC


title: Ana SHFDPCs in October, male (bio rep 3)

description: Library name: Sample 18

source_name: Secondary hair follicle dermal papilla cells from goat skin

value: male


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag1-2 Rep3

description: Library name: mStag1-2_R3


title: 16_T13LOH_KPC_Mono

description: Library name: SLX25210_idtUDP0253


title: Terc +/+ Sting +/+, replicate 2

description: Library name: Sample 2

value: Terc +/+ Sting +/+


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag1-2 Rep2

description: Library name: mStag1-2_R2


title: Ana SHFDPCs in October, male (bio rep 1)

description: Library name: Sample 16

value: Secondary hair follicle dermal papilla cells from goat skin


title: WT Cu428 x B2086, conjugation 8 hpm for Micro-C rep2

description: Library name: Sample14


title: fn1b-/-_ PBS injected

description: 10x Genomics

value: PBS


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag1-2 Rep1

description: Library name: mStag1-2_R1


title: 31_CP-2_Mono

description: Library name: SLX25210_idtUDP0272


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag1-1 Rep6

description: Library name: mStag1-1_R6

value: Microinjected with Stag1 ASO1


title: Ana SHFDPCs in October, male (bio rep 2)

description: Library name: Sample 17

value: Secondary hair follicle dermal papilla cells


title: WT Cu428 x B2086, conjugation 8 hpm for Micro-C rep1

description: Library name: Sample13


title: WT Cu428 x B2086, conjugation 3 hpm for Micro-C rep2

description: Library name: Sample12


title: 21_PSC5_CP_Cocx

description: Library name: SLX25210_idtUDP0249


title: 12_PSC5_KPC_Cocx

description: Library name: SLX25210_idtUDP0252V2


title: WT Cu428 x B2086, conjugation 3 hpm for Micro-C rep1

description: Library name: Sample11


title: 19_CP4_Mono

description: Library name: SLX25210_idtUDP0246


title: earlyAna PHFDPCs in June, male (bio rep 3)

description: Library name: Sample 12

value: Primary hair follicle dermal papilla cells from goat skin


title: WT Cu428 x B2086, conjugation 1.5 hpm for Micro-C rep2

description: Library name: Sample10


title: 28_T12LOH_KPC_Mono

description: Library name: SLX25210_idtUDP0245


title: WT Cu428 x B2086, conjugation 1.5 hpm for Micro-C rep1

description: Library name: Sample9


title: earlyAna PHFDPCs in June, male (bio rep 2)

description: Library name: Sample 11

value: Primary hair follicle dermal papilla cells


title: WT- PBS injected

description: 10x Genomics

value: WT-AB


title: 20_CP4_Cocx

description: Library name: SLX25210_idtUDP0242


title: WT Cu428 x B2086, conjugation 12 hpm for Micro-C rep1

description: Library name: Sample15

value: wild type cells


title: earlyAna PHFDPCs in June, male (bio rep 1)

description: Library name: Sample 10


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag2 Rep4

description: Library name: mStag2_R4


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag1-1 Rep2

description: Library name: mStag1-1_R2


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag1-1 Rep1

description: Library name: mStag1-1_R1


title: WT Cu428 cells, starvation 20 hours for Micro-C rep1

description: Library name: Sample7


title: 60_GB-N27_mCPLT

description: Library name: SLX25210_idtUDP0251


title: 29_T12LOH_KPC_Cocx

description: Library name: SLX25210_idtUDP0241


title: earlyAna PHFDPCs in June, female (bio rep 3)

description: Library name: Sample 9

value: female


title: 06_PSC4_KPC_Cocx

description: Library name: SLX25210_idtUDP0240


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Hprt Rep5

description: Library name: mHprt_R5

value: Blastocyst

value: Microinjected with Hprt ASO


title: WT Cu428 cells, vegetative growth (FA + DSG fix for Micro-C) rep2

description: Library name: Sample6


title: earlyAna PHFDPCs in June, female (bio rep 2)

description: Library name: Sample 8


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Hprt Rep4

description: Library name: mHprt_R4


title: 09_PSC5_CP_Cocx

description: Library name: SLX25210_idtUDP0239


title: WT Cu428 cells, vegetative growth (FA + DSG fix for Micro-C) rep1

description: Library name: Sample5


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Hprt Rep3

description: Library name: mHprt_R3


title: WT Cu428 cells, vegetative growth (FA + DSG fix for Hi-C) rep2

description: Library name: Sample4


title: 54_T12-LOH_mCPLT

description: Library name: SLX25210_idtUDP0238


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Hprt Rep2

description: Library name: mHprt_R2


title: earlyAna SHFDPCs in June, male (bio rep 2)

description: Library name: Sample 5


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Hprt Rep1

description: Library name: mHprt_R1

value: Microinjected with Buffer


title: 24_PSC4_KPC_Cocx

description: Library name: SLX25210_idtUDP0235


title: WT Cu428 cells, vegetative growth (FA + DSG fix for Hi-C) rep1

description: Library name: Sample3


title: WT Cu428 cells, vegetative growth (FA fix for Hi-C) rep2

description: Library name: Sample2


title: 48_CP2_mCPLT

description: Library name: SLX25210_idtUDP0231


title: Blastocyst microinjected with Buffer Rep4

description: Library name: BUF_R4


title: WT Cu428 cells, vegetative growth (FA fix for Hi-C) rep1

description: Library name: Sample1


title: Blastocyst microinjected with Buffer Rep3

description: Library name: BUF_R3


title: earlyAna SHFDPCs in June, female (bio rep 3)

description: Library name: Sample 3


title: CD4+slamf6+-6

description: Library name: rs7

data_processing:
Bulk RNA-seq data were preprocessed using the RNA-seq pipeline v2.7.4 on Via Foundry. The workflow aligned reads to mm10 genome using STAR v2.7.11a and estimated expression levels using featureCounts from Subread v1.6.4 package. Default parameters were used unless otherwise specified.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files containing gene-level read counts generated from RNA-seq analysis. Rows correspond to genes and columns correspond to samples.

extract_protocol:
One thousand living cells were isolated by FACS and lysed in TCL buffer (QIAGEN) supplemented with 1% b-mercaptoethanol (Sigma-Aldrich)
Full-length RNA-seq libraries were prepared following a modified SMART-Seq2 protocol. cDNA was quantified with Quant-iT PicoGreen dsDNA Assay Kit (Thermo Fisher Scientific) and normalized to 0.25 ng/ul prior to Nextera XT DNA Library Preparation kit (Illumina). Library size (500 bp) was verified using a Bioanalyzer (Agilent). Indexed libraries were were pooled, normalized to 2 nM, denatured using 0.1 N NaOH, and sequenced on a NextSeq 2000 platform (Illumnia) using the paired-end

value: CNS

value: T cells


title: 04_T11LOH_KPC_Mono

description: Library name: SLX25210_idtUDP0230


title: Blastocyst microinjected with Buffer Rep2

description: Library name: BUF_R2


title: CD4+cxcr6+-6

description: Library name: rc7


title: 11_T6LOH_KPC_Cocx

description: Library name: SLX25210_idtUDP0229


title: earlyAna SHFDPCs in June, female (bio rep 1)

description: Library name: Sample 1


title: Blastocyst microinjected with Buffer Rep1

description: Library name: BUF_R1


title: 58_GB-N23_mCPLT

description: Library name: SLX25210_idtUDP0228


title: CD4+slamf6+-5

description: Library name: rs5


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag1-1 Rep5

description: Library name: mStag1-1_R5


title: Parent tumor samples 74-01-66

city: Davis

first: Stephanie

last: Goldschmidt

address: one shields ave

department: VSR

institute: UC-Davis

description: Library name: GS3-74-01-66

data_processing:
Sequence reads were trimmed and aligned using canFam6 canine genome (UCSC Genome Browser assembly ID: canFam6 ;Dog Genome Sequencing Consortium Dog10K_Boxer_Tasha Oct. 2020; Accession ID: GCF_000002285.5) combined with chromosome Y obtained from canFam3.1 (UCSC Genome Browser assembly ID: canFam3; Broad Institute CanFam3.1 Sep. 2011 Accession ID: GCA_000002285.2) utilizing an Illumina DRAGEN (Dynamic Read Analysis for Genomics) Ultra-Rapid Next Generation Sequencing Data Analysis Platform
Assembly: canFam6 canine genome (UCSC Genome Browser assembly ID: canFam6 ;Dog Genome Sequencing Consortium Dog10K_Boxer_Tasha Oct. 2020; Accession ID: GCF_000002285.5) combined with chromosome Y obtained from canFam3.1 (UCSC Genome Browser assembly ID: canFam3; Broad Institute CanFam3.1 Sep. 2011 Accession ID: GCA_000002285.2)
Supplementary files format and content: DRAGEN RNA-seq pipeline with the Salmon quantification module
Supplementary files format and content: Each file contains transcript-level quantification estimates. Headers include: Name (transcript ID), Length (transcript length), EffectiveLength (bias-corrected length), TPM (Transcripts Per Million normalized abundance), and NumReads (estimated number of reads assigned to the transcript).

organism: Canis lupus familiaris

source_name: Oral tumor  - CAA

growth_protocol: Tumor samples were aseptically collected immediately following surgical excision and transported to the laboratory on ice. Collected samples (approximately 1-2 grams each) were bisected, with one section flash frozen for later sequencing and the other suspended in a 15 mL transfer media (Corning® DMEM (Dulbecco’s Modified Eagle’s Medium) (Corning, Manassas, VA) supplemented with 1% penicillin-streptomycin and fungizone (Gibco, Grand Island, NY)). Under sterile conditions, in the biosafety cabinet, the tumor sample was mechanically dissociated with a razor knife into 1-2 mm pieces and then transferred into growth medium (DMEM, 10% GenClone 25-514H GenClone™ Fetal Bovine Serum (FBS, Genessee Scientific, Morrisville, NC), 1% penicillin-streptomycin and fungizone, 1% MEM Vitamin Solution (Gibco, Grand Island, NY) and 1% Modified Eagle’s Medium Non-Essential Amino Acids (MEM NEAA, Gibco, Grand Island, NY) on 10 cm petri dishes (Fisher scientific, Waltham, MA) at 37C and 5% CO2. No genetic modifications were introduced to the cells to promote immortalization due to rapid and continued growth without intervention.

extract_protocol:
RNA was isolated from flash frozen tumor resections using Trizol reagent (ThermoFisher Scientific, Waltham, MA, USA) following manufacturer’s instructions and further purified using the RNeasy kit (Qiagen Valenica CA USA) with the optional on-column DNase step according to the manufacturer’s protocols.
Indexed, stranded mRNA-seq libraries were prepared from total RNA (1000 ng) using the KAPA Stranded mRNA-Seq Kit (Roche, Indianapolis IN USA) according to the manufacturer’s standard protocol for mRNA capture, fragmentation, random-primed first strand synthesis, second strand synthesis with dUTP marking, A-tailing, adaptor ligation, and library amplification. Libraries were pooled and multiplex sequenced on an Illumina NovaSeqX Plus System

value: Oral tumor  - CAA


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag1-1 Rep3

description: Library name: mStag1-1_R3


title: 47_CP1_mCPLT

description: Library name: SLX25210_idtUDP0227


title: 1323_Mid_Remote

city: Palo Alto

first: Yujiro

last: Kawai

address: 870 Quarry Road

department: Department of Cardiothoracic Surgery

institute: Stanford University

description: Library name: C4_1

data_processing:
Raw FASTQ reads were quality-checked using MultiQC. High-quality reads were aligned to the reference genome using standard alignment tools to generate BAM files. Gene expression levels were quantified as raw read counts. Differential expression analysis was performed using the DESeq2 package in R (generating the dds object) to identify differentially expressed genes (DEGs). Downstream functional annotation and pathway analysis were performed using GSEA (Gene Set Enrichment Analysis), GSVA (Gene Set Variation Analysis), GO (Gene Ontology), and KOBAS (KEGG pathway analysis).
Assembly: Sscrofa11.1
Supplementary files format and content: txt

organism: Sus scrofa

source_name: Heart

growth_protocol: Yorkshire pigs were housed in a temperature-controlled environment with a 12-hour light/dark cycle and provided with standard diet and water ad libitum prior to the surgery.

extract_protocol:
Total RNA was extracted from tissue samples harvested from the mid-border zone of the ischemic heart using Trizol reagent (or RNeasy Mini Kit) according to the manufacturer's instructions. RNA quality and quantity were assessed using an Agilent 2100 Bioanalyzer.
Sequencing libraries were prepared using the Novogene Messenger RNA-Seq Service. Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads (polyA selection). After fragmentation, first-strand cDNA was synthesized using random hexamer primers, followed by second-strand cDNA synthesis. The cDNA fragments went through end repair, A-tailing, and adapter ligation. The library was prepared for sequencing after size selection and PCR amplification.

treatment_protocol: orkshire pigs underwent left anterior descending (LAD) balloon occlusion for 60 minutes to induce ischemia-reperfusion injury (IRI). Starting on post-IRI day 9, animals were immunosuppressed with tacrolimus (0.75 mg/kg/day), mycophenolate mofetil (500 mg/day), and prednisolone (20 mg/day). On post-IRI day 14, animals received either topical implantation of scaffold-free EPC-SMC vascular organoids (experimental group) or fibrin glue (control group) via left thoracotomy.

value: Heart


title: CD4+cxcr6+-5

description: Library name: rc5


title: Parent tumor samples 74-88-98

description: Library name: GS2-74-88-98


title: 1323_Mid_BZ

description: Library name: C3_1


title: 03_PSC4_CP_Cocx

description: Library name: SLX25210_idtUDP0226

value: PSC


title: 1623_Mid_Remote

description: Library name: H4


title: 55_T13-LOH_mCPLT

description: Library name: SLX25210_idtUDP0225


title: CD4+cxcr6+-4

description: Library name: rc3


title: 1623_Mid_BZ

description: Library name: H3


title: 53_T11-LOH_mCPLT

description: Library name: SLX25210_idtUDP0224


title: CD4+slamf6+-3

description: Library name: rs1


title: earlyAna PHFDPCs in June, female (bio rep 1)

description: Library name: Sample 7


title: 1922_Mid_Remote

description: Library name: F4


title: 05_T11LOH_KPC_Cocx

description: Library name: SLX25210_idtUDP0223


title: CD4+cxcr6+-3

description: Library name: rc1


title: 74-88-98 cell line

description: Library name: CAA1

source_name: CAA

value: CAA


title: 1922_Mid_BZ

description: Library name: F3


title: 57_GB-N22_mCPLT

description: Library name: SLX25210_idtUDP0222


title: CD4+slamf6+-2

description: Library name: bs3

source_name: CNS


title: 1322_Mid_Remote

description: Library name: E4


title: nep_48hpi

city: 南通市

first: Guiyi

last: Zhang

state: 江苏

address: 江苏省南通市崇川区

institute: Nantong University

description:
Library name: Sample 6
singleron platform

data_processing:
Raw sequencing reads were processed using CeleScope v1.5.2 (Singleron Biotechnologies) with default parameters to generate gene expression matrices.
Assembly: The reference genome (fasta format) and gene annotation (gtf format) files were downloaded from Ensembl database (release version 94).
Supplementary files format and content: matrix files

source_name: otic vesicle

extract_protocol:
The isolated otic vesicle and inner ear organoid tissue was cut into 2–3 mm sections and rinsed with Hanks' Balanced Salt Solution (HBSS). Enzymatic digestion was performed for 15 minutes using a tissue dissociation solution (Singleron Biotechnologies, Nanjing, China). The resulting cell suspension was filtered through a sterile 40-μm filter (Corning, NY, USA) and centrifuged at 500 g for 5 minutes. Erythrocytes were removed with a lysis reagent (Singleron Biotechnologies, Nanjing, China) for 10 minutes. The cells were resuspended in phosphate-buffered saline (PBS) and stained with trypan blue (T6146, Sigma, Burlington, VT, USA). Cell viability was assessed using a TC20 automated cell counter (Bio-Rad, Hercules, CA, USA).
ScRNA-seq libraries were prepared using the GEXSCOPE® Single Cell RNA Library Kit (Singleron Biotechnologies).

value: otic vesicle

value: various cell


title: CD4+cxcr6+-2

description: Library name: bc3


title: neo_24hpi

description:
Library name: Sample 5
singleron platform


title: 23_T6LOH_KPC_Cocx

description: Library name: SLX25210_idtUDP0219


title: CD4+slamf6+-1

description: Library name: bs1


title: neo_6hpi

description:
Library name: Sample 4
singleron platform


title: 1022_Mid_Remote

description: Library name: C4


title: 50_CP4_mCPLT

description: Library name: SLX25210_idtUDP0218


title: ctrl_7dpf

description:
Library name: Sample 3
singleron platform


title: 1022_Mid_BZ

description: Library name: C3


title: 17_PSC4 mono_fibro

description: Library name: SLX24701_idtUDP0118


title: WAT - ob/ob mice treated with 100 mg/kg VE_rep3

type: RNA

city: TSUKUBA

first: ELDA NURAFNIE

last: IBNU RASID

state: IBARAKI

address: 1-1-1 TENNODAI

institute: UNIVERSITY OF TSUKUBA

description: Gene expression data of ob/ob mice that were treated with 100 mg/kg VE for 42 days

hyb_protocol: The cartridge array hybridization was performed using the Clariom cartridge array (Clariom S Array, Mouse; ThermoFisher Scientific).

scan_protocol: Scanning was performed using GeneChip Scanner (ThermoFisher Scientific).

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome Analysis Console (TAC) software. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, TAC software (CEL files) filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.1 (in linear space).
Signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4).

label: biotin

source_name: ob/ob mice were treated with 100 mg/kg VE for 42 days

label_protocol: Biotinylated cRNA were prepared according to the standard WT PLUS Reagent Kit protocol (ThermoFisher Scientific) from 100 ng/uL total RNA

extract_protocol: Total RNA was extracted using ISOGEN (Nippon Gene Co., Ltd, Tokyo, Japan) following the manufacture’s instruction.

treatment_protocol:
C57BL/6JHamSlc-+ /+ (non-obese) and C57BL/6JHamSlc-ob/ob (obese) were used in this study. Six-week-old male C57BL/6JHamSlc-+ /+ and C57BL/6JHamSlc-ob/ob (Japan SLC, Inc., Shizuoka, Japan) were maintained at room temperature in a 12 h light/dark cycle. After one week of acclimatization with standard chow diet and tap water ad libitum, on initiation day of the study (D0), all animals were randomly assigned into respective groups.
Briefly, ob/ob group mice were given vehicle, and treatment groups were given VE at 50mg/kg BW and 100mg/kg BW by oral gavage for 6 weeks. Body weight (BW) and food intake were measured on a daily and weekly basis, respectively. From the initiation of the study (D0-D42), all groups were fed with standard chow diet and tap water ad libitum. At the termination of the experiment, blood was collected by cardiac puncture after the mice were anesthetized with isoflurane inhalation.

tag: tag

value: ob/ob mice


title: CD4+slamf6+-4

description: Library name: rs3


title: Parent tumor samples 41-60-65

description: Library name: GS1-41-60-65

source_name: Oral tumor - CAA

value: Oral tumor - CAA


title: 41-60-65 cell line

description: Library name: CAA3


title: 3622_Mid_BZ

description: Library name: B4


title: ctrl_6dpf

description:
Library name: Sample 2
singleron platform


title: 06_GBT11-LOH + PSC5_tum

last: Biffi

institute: University of Cambridge

description: Library name: SLX24701_idtUDP0114


title: CD4+cxcr6+-1

description: Library name: bc1


title: WT Cu428 x B2086, Refeeding 24 hours after conjugation for Micro-C rep1

description: Library name: Sample19


title: 3622_Mid_Remote

description: Library name: B3


title: 75-01-66 cell line

description: Library name: CAA2


title: ctrl_5dpf

description:
Library name: Sample 1
singleron platform


title: 01_GBT11_LOH mono_tum

description: Library name: SLX24701_idtUDP0109


title: WAT - ob/ob mice treated with 100 mg/kg VE_rep2


title: 42077_SEM-IAA-50U-10min_2-1

description: Library name: 42077_SEM-IAA-50U-10min_2-1

data_processing:
Reads were aligned using BWA-MEM.
Remove duplicate reads (Picard MarkDuplicates and Samtools).
Tally coverage of read1 5' tag using deeptools
Assembly: hg38
Supplementary files format and content: BigWig for forward strand -- coverage of 5' end of Read 1 across the genome
Supplementary files format and content: BigWig for reverse strand -- coverage of 5' end of Read 1 across the genome

extract_protocol:
Cells were poured into methanol-free formaldehyde (final 1% concentration) at room temperature with gentle mixing for 10 min. Reactions were quenched with 3M Tris (pH 8.0), with 2 moles of Tris per 1 mole of formaldehyde, for at least 5 min. Fixed cells were washed with PBS, lysed with detergent containing buffers and needle lysis. Chromatin was digested with benzonase. Benzonase-fragmented chromatin was centrifuged at 16,363 x g for 15 min at 4˚C. The supernatant and pellet were separately used for library preparation. The pellet was resuspended by needle lysis with increasing needle gauge to minimize clumps. In some cases, total, super, or pellet fractions underwent DNA purification before being used for library input. Depending on the preparation, typically 0.5-1.3 million cell-equivalents of Benzonase-digested chromatin was digested with ProteinaseK for approximately 16 hours. Reverse-crosslinked DNA was purified with Ampure beads at 1.8x ratio to starting material and eluted in pure water. DNA underwent end-repair, A-tailing, and ligation to fork adapters (annealed Multiplexing Read 2 Sequencing primer /Nextera Read 2 External Adapter) with 3’ Ts. Components for enzymatic reactions were added successively to the previous resulting DNA and the enzyme was then heat inactivated before adding the next master mix. The ligated DNA was purified again with Ampure beads at 1.8x ratio to the final volume of ligation reaction and then amplified by PCR using ExB2 and ExC1 primers. Amplified libraries were size selected by gel electrophoresis in the range from 200-500 bp. Libraries were sequenced with the Illumina NextSeq 550, paired-end mode.
Illumina or Element library prep

tag: source

value: SEM + IAA

value: super

tag: benzonase digsetion_sonication


title: Whole lung, day 3 K3-SPG 3

city: Tokyo

first: Asuka

middle: Joy

last: Tobuse

state: Tokyo

address: 4 - 6 - 1 Shirokanedai Minato-ku

department: Microbiology and Immunology

institute: University of Tokyo, Institute of Medical Science

description:
Library name: Sample 12
10x Genomics

data_processing:
Sequencing was performed by KOTAI Biotechnologies using the DNBSEQ-G400RS high-throughput sequencing set A, on an MGI DNBSEQ-G400 instrument. Read structure were used as follows: (1) Read 1: 28 cycles, (2) i7 index: 10 cycles, (3) i5 index: 10 cycles, and (4) Read 2: 90 cycles.
Raw sequencing data were converted to FASTQ format and processed using cellranger-8.0.1. Outputs include raw FASTQ files, filtered feature_barcode matrices, and .cloupe files. The total number of recovered cells ranged from 10,214 to 20,766 cells across 12 samples.
All downstream analysis for UMAP generation, gene expression violin plots, and dot plots, were performed on Parse Biosciences Trailmaker platform based on cell ranger outputs.
Assembly: Reads were aligned to the GRCm39-2024-A reference genome.
Supplementary files format and content: Cellranger-generated filtered feature-barcode matrices, consisting of UMI count alongside corresponsing barcode and feature annotation files.

source_name: Adult lung

growth_protocol: All cells were freshly isolated on the same day and dead cell removal was performed prior to library generation.

extract_protocol:
Single-cell suspensions of lung cells were applied to the 10x Genomics Chromium Controller using the GEM-X Single Cell 3' Reagent Kits v4 according to the manufacturer's protocol. Individual cells were encapsulated into Gel Bead-in-Emulsions (GEMs), and undergo lysis and reverse transcription. Barcoded cDNA containing the cell-specific barcodes and unique molecular identifiers (UMIs) were generated. RNA extraction was not performed.
Amplification of barcoded cDNA was performed and used for library construction by Chromium Library Construction Kit C, according to the manufacturer's protocol. Sample indexing was performed using the Chromium Dual Index Kit TT Set A, and final libraries were quantified and quality-assessed prior to sequencing. Input cDNA ranged from 67.9 ng - 234 ng across 12 samples. Each sample was sequenced individually.

treatment_protocol: PBS or K3-SPG were administered via intranasal injection of 30 µL/mouse, or 15 µL/nostril, under partial anesthesia.

tag: tissue

value: Adult lung

tag: genotype

value: Wild-type

value: Day 3


title: WAT - ob/ob mice treated with 100 mg/kg VE_rep1


title: 21_GBT11-LOH + PSC5_fibro

first: Giulia

description: Library name: SLX24701_idtUDP0099

data_processing:
Estimated transcript counts were counted using Salmon (version 1.9.0)
Assembly: GRCm39 (mm39) - kmer 23
Supplementary files format and content: Raw count data in tab-delimited salmon file

tag: cell type

tag: batch


title: 42076_SEM-DMSO-50U-10min_2-1

description: Library name: 42076_SEM-DMSO-50U-10min_2-1

tag: cell line

value: SEM + DMSO


title: 36_GB_CP_2_Cocx

description: Library name: SLX22742_idtUDP0287

tag: treatment


title: Whole lung, day 3 K3-SPG 2

description:
Library name: Sample 11
10x Genomics


title: WAT - ob/ob mice treated with 50 mg/kg VE_rep3

description: Gene expression data of ob/ob mice that were treated with 50 mg/kg VE for 42 days

source_name: ob/ob mice were treated with 50 mg/kg VE for 42 days


title: Whole lung, day 3 K3-SPG 1

description:
Library name: Sample 10
10x Genomics


title: 27_PSC5_CP_Cocx

description: Library name: SLX25210_idtUDP0220


title: 41860_SEM-IAA-50U-10min_1-1

description: Library name: 41860_SEM-IAA-50U-10min_1-1


title: 1322_Mid_BZ

description: Library name: E3


title: 35_GB_CP_2_Mono

description: Library name: SLX22742_idtUDP0285


title: 41859_SEM-DMSO-50U-10min_1-1

description: Library name: 41859_SEM-DMSO-50U-10min_1-1


title: WAT - ob/ob mice treated with 50 mg/kg VE_rep2


title: WAT - ob/ob mice treated with 50 mg/kg VE_rep1


title: 42_GB_CP_1_Cocx

description: Library name: SLX22742_idtUDP0283


title: Whole lung, day 3 PBS 3

description:
Library name: Sample 9
10x Genomics

value: PBS


title: 40728_Naked-0.375U-10min_1-1

description: Library name: 40728_Naked-0.375U-10min_1-1

source_name: Naked DNA

value: Naked DNA


title: 41_GB_CP_1_Mono

description: Library name: SLX22742_idtUDP0281


title: Whole lung, day 3 PBS 2

description:
Library name: Sample 8
10x Genomics


title: Ana SHFDPCs in October, female (bio rep 3)

description: Library name: Sample 15

value: Secondary hair follicle dermal papilla cells from goat skin

value: female


title: WAT - ob/ob mice given vehicle_rep3

description: Gene expression data from ob/ob mice that were given vehicle for 42 days

source_name: ob/ob mice were given vehicle for 42 days


title: 40727_Naked-0.125U-10min_1-1

description: Library name: 40727_Naked-0.125U-10min_1-1


title: WAT - ob/ob mice given vehicle_rep2


title: 39_GB_CP_5_Cocx

description: Library name: SLX22742_idtUDP0277


title: Whole lung, day 3 PBS 1

description:
Library name: Sample 7
10x Genomics


title: Ana SHFDPCs in October, female (bio rep 2)

description: Library name: Sample 14

value: Secondary hair follicle dermal papilla cells


title: Ana SHFDPCs in October, female (bio rep 1)

description: Library name: Sample 13


title: Blastocyst microinjected with 20µM Antisense Oligonucleotide (ASO) agains Stag1-1 Rep4

description: Library name: mStag1-1_R4

value: Blastocyst

value: Microinjected with Stag1 ASO1


title: 40726_Naked-0.04U-10min_1-1

description: Library name: 40726_Naked-0.04U-10min_1-1


title: Whole lung, day 1, K3-SPG 3

description:
Library name: Sample 6
10x Genomics

value: Day 1


title: 32_GB_CP_3_Mono

description: Library name: SLX22742_idtUDP0275


title: Whole lung, day 1, K3-SPG 2

description:
Library name: Sample 5
10x Genomics


title: WAT - ob/ob mice given vehicle_rep1


title: 33_GB_CP_3_Cocx

description: Library name: SLX22742_idtUDP0273


title: WT Cu428 cells, starvation 20 hours for Micro-C rep2

description: Library name: Sample8

value: wild type cells


title: 42581_SWCK562_FOXA1_BX_rep2-1

description: Library name: 42581_SWCK562_FOXA1_BX_rep2-1

extract_protocol:
Cells were crosslinked in methanol-free formaldehyde (final 1% concentration in IMDM media) at 25 °C for 10 min. 1 mole of formaldehyde was quenched with 3 mole extra Tris (pH 8.0) at 25 °C for 5 min. Fixed cells were washed with PBS and stored at -80 oC. 25 million (M) formaldehyde crosslinked K562 were lysed by incubating with 1 mL Lysis Buffer F (20 mM Tris, pH 8.0, 85 mM KCl, 0.5% NP-40, 0.5% Triton X-100) for 20 min at 4°C, then with 1 mL RIPA Buffer M (1x PBS 1.0% NP40, 0.5% NaDeoxycholate, 0.1% SDS) for 20 min at 4°C. Nuclei (25 M) were incubated in 500 ul Benzonase Digestion Buffer (10 mM Tris, pH 8, 10 mM NaCl, 2 mM MgCl2) at a Benzonase concentration of 100 U/ml for 10 min at 25 °C. Reactions were quenched by adding 500 ul Benzonase Quench Buffer (10 mM Tris, pH 8, 800 mM NaCl, 20 mM EDTA), The quenched reactions were centrifuged at 14,000 rpm for 10 minutes to collect Benzonase-solubilized chromatin in the supernatant. Nuclei pellets were sonicated in a Bioruptor PICO model sonicator (Diagenode) for 8 cycles (30-on/ 30-off). Sonicated material was centrifuged at 13.2K rpm for 15 minutes using a Microfuge (Eppendorf 5415R). Solubilized chromatin supernatant was collected. Benzonase solubilized and sonication chromatin were collected for incubation with pAG Mag Sepharose ™ (Cytiva™) preloaded with 3 ug of antibody overnight. Following antibodies were used according to the manufacturer’s instructions to prepare ChIP-exo libraries: SMC3 (ab9263, Sigma), P300 (HPA003128, Atlas), NFIA (HPA008884, Atlas), WDR5 (HPA047182, Atlas), GABPA (HPA003258, Atlas), SP1 (HPA001853, Atlas), RAD21(HPA020044, Atlas), GTFIIB (HPA061626, Atlas), P300(A300-358A, Bethyl labs), RbBP5 (A300-109A, Bethyl labs), and CTCF (07-729, Millipore). TBP (Pugh lab). The immunoprecipitated chromatin was then processed through Lambda exonuclease digestion, first adapter ligation, cross-link reversal, second adapter ligation, and PCR for final high-throughput sequencing.
Illumina or Element library prep

tag: method

value: Benzonase ChIP-exo (v6)

tag: target

tag: antibody


title: Whole lung, day 1, K3-SPG 1

description:
Library name: Sample 4
10x Genomics


title: ob/ob mice treated with 100 mg/kg VE_rep2

data_processing:
The raw data were normalized following the signal space transformation robust multi-chip analysis (SST-RMA) algorithm. For differential expression analysis, a One-Way ANOVA followed by an empirical Bayes correction was performed. The detected above background (DABG) cutoff was set to 0.05. The positive vs negative area under the curve (AUC) value was set at greater than or equal to 0.7.
Signal intensity of all the samples derived from Transcriptome Analysis Console software (sheet 2). For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, Transcriptome Analysis Console software (CEL files) filter criteria was set as p value < 0.05 (one-way between-subjects ANOVA) and fold change > 1.1 (in linear space).
Signal space transformation robust multi-chip analysis (SST-RMA) algorithm (Transcriptome Analysis Console, version 4).

value: ob/ob mice


title: 42304_SWCK562_IgG_BX_rep1-1

description: Library name: 42304_SWCK562_IgG_BX_rep1-1

tag: pegr id

value: IgG


description: Library name: 42079_SEM-CTCFAID2-5PhIAA_CTCF_BX_rep1-2

value: SEM + IAA

value: CTCF


title: ob/ob mice treated with 100 mg/kg VE_rep3


title: Whole lung, day 1, PBS 3

description:
Library name: Sample 3
10x Genomics

value: Adult lung

value: Wild-type


title: 29_GB_CP_4_Mono

description: Library name: SLX22742_idtUDP0267


title: 43_PSC5_CP_Cocx

description: Library name: SLX22742_idtUDP0260

value: PSC


title: 42078_SEM-CTCFAID2-DMSO_CTCF_BX_rep1-2

description: Library name: 42078_SEM-CTCFAID2-DMSO_CTCF_BX_rep1-2

value: SEM + DMSO


title: Whole lung, day 1, PBS 2

description:
Library name: Sample 2
10x Genomics

value: PBS


title: ob/ob mice treated with 100 mg/kg VE_rep1


title: ob/ob mice treated with 50 mg/kg VE_rep3


title: 31_PSC4_CP_Cocx

description: Library name: SLX22742_idtUDP0257


title: 47_GB-CP-3_mCPLT

description: Library name: SLX22742_idtUDP0256


title: Whole lung, day 1, PBS 1

description:
Library name: Sample 1
10x Genomics


title: ob/ob mice treated with 50 mg/kg VE_rep2


title: 41974_KK_IgG_BX_rep1-1

description: Library name: 41974_KK_IgG_BX_rep1-1

source_name: K562 and HepG2

value: K562 and HepG2


title: HT-29 cells, treatment group3 (with 8 mM lead acetate)

first: hailiang

last: hu

address: jixi road

institute: First Affiliated Hospital of Anhui Medical University

description: Library name: Sample 6

data_processing:
Using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit) to do the total RNA sample QC: RNA concentration, RIN value, 28S/18S and the fragment length distribution. For plant and fungi samples, we use NanoDropTM to identify the purity of the RNA samples.
Firstly, we filter the low quality reads (More than 20% of the bases qualities are lower than 10), reads with adaptors and reads with unknown bases (N bases more than 5%) to get the clean reads
Then we map those clean reads onto reference genome, followed with novel gene prediction,  SNP & INDEL  calling and gene splicing detection
Finally, we identify DEGs (differentially expressed genes) between samples and do clustering analysis and functional annotations
Assembly: 6
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: csv files include FPKM values for each Sample

extract_protocol:
The concentration of total RNA was detected using Agilent 2100 Bioanalyzer (Agilent RNA 6000 Nano Kit).
The libraries were sequenced with the Illumina HiSeq 2000 sequencing platform to produce PE100 reads.

value: Colon adenocarcinoma

value: WT

value: with 8 mM lead acetate


title: 41971_KK_FOXA1_BX_rep1-1

last: Pugh

institute: Cornell University

description: Library name: 41971_KK_FOXA1_BX_rep1-1


title: 37_PSC5_CP_Cocx

address: Cancer Research UK, Robinson Way

description: Library name: SLX22742_idtUDP0255

extract_protocol:
Samples were collected in 1 mL of TRIzol Reagent (15596018; Invitrogen). RNA was extracted using the PureLink RNA mini kit (12183018A; Invitrogen). RNA concentration was measured using a Qubit and RNA quality was assessed on a TapeStation 4200 (Agilent) using the Agilent RNA ScreenTape kit. mRNA library preparations were performed using 55 mL of 10 ng/mL per sample (RNA integrity number, RIN ≥ 8.8)
Illumina mRNA library


title: 48_GB-CP-4_mCPLT

description: Library name: SLX22742_idtUDP0251


title: HT-29 cells, treatment group2 (with 8 mM lead acetate)

description: Library name: Sample 5


title: 41978_KH_IgG_BX_rep1-1

description: Library name: 41978_KH_IgG_BX_rep1-1

value: K562-SWC + HepG2-WCE


title: ob/ob mice treated with 50 mg/kg VE_rep1


title: 41965_KH_FOXA1_BX_rep1-1

description: Library name: 41965_KH_FOXA1_BX_rep1-1


title: earlyAna SHFDPCs in June, male (bio rep 3)

description: Library name: Sample 6

value: Secondary hair follicle dermal papilla cells from goat skin

value: male


title: HT-29 cells, treatment group1 (with 8 mM lead acetate)

description: Library name: Sample 4


title: 34_PSC4_CP_Cocx

description: Library name: SLX22742_idtUDP0245


title: ob/ob mice given vehicle_rep2


title: ob/ob mice given vehicle_rep3


title: HT-29 cells, Control3

description: Library name: Sample 3

value: Conventional  culture


title: Terminal Mapping (multiplexed), HIV-1/SIVmac251, Jurkat-a/b, replicate 1/2

city: Scarborough

first: Guillaume

last: Filion

state: ON

address: 1265 Military Trail

country: Canada

institute: University of Toronto

description:
Library name: all_ONT
All conditions are multiplexed in a single ONT run.

data_processing:
For Illumina reads. The ends of the LTRs were trimmed by seeq (https://github.com/ezorita/seeq) allowing 5 errors (HIV-1 target sequence: CTTGTCTTCGTTGGGAGTGAATTAGCCCTTCCA, or SIVmac251 target sequence: TCTATGTCTTCTTGCACTGTAATAAATCCCTTCCA), leaving 34 nucleotides (plus or minus errors) for mapping the read into the host genome. Mapping insertion sites in the host genome. Processed Nanopore reads were mapped using bwa  with options bwa mem `-t8 -L0 -x pacbio` in an index containing the human genome (hg38), the genome of phage PhiX174, and the sequence of the HIV and SIV constructs. The added reference sequences accelerate the mapping. Following alignment, parsed SAM files were processed to identify high-confidence integration sites. Alignments containing hard clipping (secondary alignments) or exhibiting more than 5 bp of soft clipping at the 5’ end were discarded to ensure the sequencing read began immediately at the host-virus junction.
For Oxford Nanopore Technology reads. Viral genomic segments were extracted from FASTQ files using a custom Python parser based on seeq for approximate DNA/RNA matching via Levenshtein distance (https://github.com/ezorita/seeq). Sequencing reads and their reverse complements were scanned for the so-called anchor consisting of the adapter and the added poly-A tail with a maximum tolerance of 6 errors including indels (target sequence: AAAAAAAGATCGGAAGAGCACACGTCTGAACTCCAGTCAC). Identified reads were split around the anchor, using the prefix to find an insertion site in the genome, and recursively repeating the process above on the suffix. The reason for recursively searching for insertion sites in the same read is that independent molecules are routinely ligated together to form concatemers during the adapter ligation step, so a single read may contain multiple amplicons. For each prefix, the specific viral motif from the LTR was identified with a maximum tolerance of 5 errors including indels (HIV-1 target sequence: CTTGTCTTCGTTGGGAGTGAATTAGCCCTTCCA, SIVmac251 target sequence: TCTATGTCTTCTTGCACTGTAATAAATCCCTTCCA). The sequence located between the viral LTR and the closest poly-A tract was isolated (20 As with a maximum tolerance of 3 errors including indels) and kept for further analyses.
For both Illumina and Oxford Nanopore Technology reads. Genomic coordinates were determined based on alignment orientation: for positive strand matches, the integration site was defined by the alignment start position, whereas for negative strand matches, it was defined by the alignment end (start position plus alignment length derived from the CIGAR string). To correct for sequencing or mapping imprecision, insertion sites on the same chromosome located within a 15 bp window were collapsed into a single insertion located at the mode of the cluster. Reads mapping to the internal controls (HIV, SIV, and PhiX174 genomes) were filtered out at this stage. Finally, the representative integration site for each cluster was assigned to the coordinate with the highest read count.
For Oxford Nanopore Technology reads. The number of independent capture events was estimated by quantifying unique poly-A termination sites (separated by 5 bp or more) associated with every insertion.
Assembly: hg38
Supplementary files format and content: Tab-separated values (tsv) indicating insertions with columns: chromosome, location, strand and number of reads. For Oxford Nanopore Technology reads, an additional column indicates the number of unique poly-A termination sites.

source_name: Thymus

growth_protocol: RPMI 1640 medium (Gibco, 11875-093), 10% fetal bovine serum, 1% GlutaMAX (Gibco, 35050-061), 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol:
Genomic DNA from Jurkat T cell pools was extracted 21 days post-transduction with PureLink Genomic DNA Kit (Invitrogen, K1820-01).
500 ng genomic DNA from transduced Jurkat T cells were linear-amplified using 0.02 μM of a specific primer (annealing to the HIV-1 5′ LTR and to the SIVmac251 5′ LTR, respectively) and 1.1x Red Taq DNA Polymerase Master Mix (VWR Life science, 733-2544) in a 50 μL final volume. The cycling conditions were as follows: 95°C for 5 min; 95°C for 30 s, 55°C for 1 min and 72°C for 15 s (100 cycles); and 72°C for 5 min. Following linear amplification, 25 μL single-stranded DNA product in the Taq DNA Polymerase Master Mix were mixed with 0.4 μM of a biotinylated primer annealing to HIV-1 SIVmac251 and hybridized by gradual cooling. The mixture was denatured at 95°C for 2 min, followed by slow cooling from 95°C to 15°C at a rate of 0.1°C/s. The temperature was held at 15°C for 10 min to ensure complete annealing. Biotinylated single-stranded DNA was then purified using streptavidin-coated magnetic beads (Cytiva, 30152103010350) according to the manufacturer’s instructions. Bead-bound DNA was washed thoroughly three times with 1x High salt wash buffer containing 10 mM Tris HCl pH 8.0, 1 M NaCl and 0.5 mM EDTA. The purified single-stranded DNA was eluted in 20 μL Elution Buffer (Qiagen, 19086) preheated to 95°C. The mixture was incubated at 95°C for 5 min to disrupt biotin-streptavidin interactions. The beads were then magnetically separated, and the supernatant containing the eluted DNA was collected. To catalyze the addition of poly(A) tails to the 3′ ends of DNA fragments, terminal deoxynucleotidyl transferase (TdT) reaction was performed using the 20 μL eluted DNA, 5 μL 10x  Terminal Transferase Reaction Buffer, 0.25 mM CoCl2, 1 μL 10 mM dATP, and 20 units TdT enzyme (New England Biolabs Inc., M0315) in a 50 μL final volume. The reaction mixture was incubated at 37°C for 30 min, followed by enzyme inactivation at 70°C for 10 min. For exponential amplification by PCR, 25 μL of TdT reaction products were directly added in 50 μL standard Taq DNA polymerase reaction mix (GeneBio Systems Inc., P3004) with 0.2 μM forward primer (annealing to the poly(A) tail with Illumina R2 Seq Primer overhang) and 0.2 μM reverse primer (annealing to the HIV-1 5′ LTR and to the SIVmac251 5′ LTR, respectively; with Illumina R1 Seq Primer overhang). The cycling conditions were as follows: 95°C for 5 min; 95°C for 30 s, 53°C for 1 min and 72°C for 1 min (30 cycles); and 72°C for 5 min. For each condition, at least four tubes were pooled and purified using a silica column-based purification kit (Qiagen, 28104) according to the manufacturer’s instructions and eluted in 20 μL Elution Buffer. Finally, 4 μL of the purified product were diluted to 50 μL of standard Taq DNA polymerase reaction mix with 0.2 μM of a primer annealing to the Illumina PE1.0 primer and an indexing primer annealing to the Illumina PE2.0 primer. The cycling conditions were as follows: 95°C for 5 min; 95°C for 30 s, 56°C for 1 min and 72°C for 1 min (6 cycles); and 72°C for 5 min.

treatment_protocol: Cells were transduced with viral stocks serially diluted 2-fold (from 10x to 80x) in a total volume of 1 mL of complete RPMI 1640 medium containing 8 μg of Polybrene (MilliporeSigma, TR-1003). The plates were centrifuged at 1,000 g at 32 °C for 90 min. At 48 hours post transduction, the efficiency of transduction was analyzed by the proportion of GFP (+) cells using a flow cytometer (Becton Dickinson, LSRFortessa). Following this, the RIU / mL was calculated using dilutions resulting in < 20% infection to minimize multiple infection events per cell, using the formula: RIU / mL = [cell number x ratio of GFP (+) cells x dilution factor] / volume (mL). Subsequently, the multiplicity of infection (MOI) was defined as the ratio of the RIU to the number of host cells at the time of transduction experiment (MOI = RIU / cells). For all subsequent experiments, the volume of viral supernatant required to achieve a target MOI 0.1 was adjusted based on this calculated functional titer to ensure consistent infection efficiency across replicates. Jurkat T cells were sorted two days post transduction with pseudotyped reporter viruses at an MOI of 0.1 with a cell sorter (Becton Dickinson, FACSAria III). Before sorting, cells were washed and resuspended in PBS (Gibco, 10010-023) containing 1% FBS and 5 μL of Hoechst dye (Thermo Scientific, 62249) at a concentration of 1 μg / mL. Results shown throughout the chapter correspond to representative data from experiments repeated at least twice.

value: Thymus

value: Jurkat

value: CD4+ T cell

value: Mixed

value: viral transduction


title: ob/ob mice given vehicle_rep1

value: ob/ob mice


title: GM-CSF + IL-6 + 1 nM α-MSH, biological replicate 3

city: Oldenburg

first: Anna-Galina

last: Arndt

address: Carl-von-Ossietzky-Straße 9-11

department: Department für Humanmedizin

country: Germany

institute: Carl von Ossietzky Universität Oldenburg

description:
Library name: HD_3n_MSH
Healthy donor 3, day 2 culture

data_processing:
RNA-seq was performed on an Illumina NovaSeq X Plus platform generating 150 bp paired-end reads. Raw sequencing reads were filtered to remove adapter sequences and low-quality reads using fastp. Clean reads were aligned to the human reference genome (GRCh38/hg38) using HISAT2, and the number of reads mapped to each gene was quantified using featureCounts.
Assembly: GRCh38 (hg38)
Supplementary files format and content: The file gene_count.xls provides raw read counts per gene for each sample.

source_name: Peripheral blood

growth_protocol: T and B cell depleted, myeloid enriched peripheral blood cells were cultured in MDSC medium consisting of basal cell culture medium supplemented with 10% FCS, non-essential amino acids, L-glutamine, HEPES, sodium pyruvate and penicillin/ streptomycin at 37°C in a humidified atmosphere with 5% CO₂.

extract_protocol:
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared from total RNA using poly(A) enrichment with poly-T oligo-attached magnetic beads according to the manufacturer's standard protocol (Novogene).

treatment_protocol: Cells were cultured for 2 days under three experimental conditions: MDSC medium alone (control), MDSC medium supplemented with 10 ng/ml GM-CSF and IL-6, or MDSC medium supplemented with 10 ng/ml GM-CSF and IL-6 and 1 nM α-MSH.

value: Peripheral blood

value: in vitro differentiated MDSCs

value: GM-CSF plus IL-6 plus 1 nM α-MSH


title: 30_GB_CP_4_Cocx

city: CAMBRIDGE

description: Library name: SLX22742_idtUDP0240


title: GM-CSF + IL-6 + 1 nM α-MSH, biological replicate 2

description:
Library name: HD_2n_MSH
Healthy donor 2, day 2 culture


title: 41764_SWCK562_FOXA1_BX_rep1-1

first: B. Franklin

address: 465 Biotechnology Building

description: Library name: 41764_SWCK562_FOXA1_BX_rep1-1

value: Benzonase ChIP-exo (v6)


description: Library name: 41781_SEM-CTCFAID2-5PhIAA_CTCF_BX_rep1-1

value: SEM + IAA

value: CTCF


title: 41780_SEM-CTCFAID2-DMSO_CTCF_BX_rep1-1

description: Library name: 41780_SEM-CTCFAID2-DMSO_CTCF_BX_rep1-1

value: SEM + DMSO


title: HT-29 cells, Control1

description: Library name: Sample 1

value: Colon adenocarcinoma

value: WT


title: 40_PSC5_CP_Cocx

description: Library name: SLX22742_idtUDP0235

value: PSC


title: RNAseq_SynTEF1_s45_rep3

city: Memphis

first: Wojciech

last: Rosikiewicz

address: 262 Danny Thomas Place

institute: St. Jude Childrens Research Hospital

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore
Paired-end reads were mapped by STAR(v2.7.1a) using parameters "-c -p 4 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outReadsUnmapped None --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM"
Read duplication was marked with MarkDuplicates from GATK (v4.0.4.0)
RSEM was used to quantify read counts per gene
Genome_build: hg38 (GRCh38.p12)
Supplementary_files_format_and_content: gene-based raw counts, FPKM and TPM normalized txt files

source_name: B-Lymphocyte

growth_protocol: RPMI + 15% FBS + anti/anti

extract_protocol:
RNA was extracted using Qiagen RNeasy kit
Library was constructed using standard Illumina protocols

treatment_protocol: Cells were treated with indicated compounds for 24 hours

value: Patient Derived B-Lymphocyte


title: CP-3_T12_GEM-SITTD5_NORM

description: Library name: SITTH1

data_processing:
CellRanger multi (v8.0.1) : default parameters
Assembly: mm10-2020-A
Supplementary files format and content: raw_feature_bc_matrix.h5

source_name: multi coculture

extract_protocol:
Chromium Next GEM Single Cell 3' Kit v3.1, PN-1000268; Chromium Next GEM Chip G Single Cell Kit, PN-1000120; Dual Index Kit TT Set A, PN-1000215; and the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual Index) user guide
10x Genomics single nucleus RNA-seq

value: multi coculture


title: 41762_KH_FOXA1_BX_rep2-1

city: Ithaca

description: Library name: 41762_KH_FOXA1_BX_rep2-1

value: K562 and HepG2

value: K562-SWC + HepG2-WCE


title: RNAseq_SynTEF1_s44_rep2


title: FRDA brain cells received mitochondria derived from microglia-like cells (MGLCs)

city: Stanford

first: Natalia

last: Gomez-Ospina

address: 265 Campus Drive

institute: Stanford

description: Library name: mKate2+ brain cells

data_processing:
Raw Illumina BCL sequencing files were processed through bcl2fastq (v2.20) to generate FASTQ files   (https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome)
FASTQ files were processed through Cellranger count  (v7.1.0) to obtain counts matrices
Assembly: mm10
Supplementary files format and content: Hdf5 files are provided for each sample.

source_name: Whole brain

extract_protocol:
Cells were isolated from three mice and pooled for scRNA-seq
Brain tissue dissociation was performed using a modified protocol from the Adult Brain Dissociation Kit (Miltenyi Biotec 130-107-677). Mice were deeply anesthetized with a Ketamine/Xylazine mixture and underwent rapid decapitation to minimize brain tissue damage. The extracted brains were washed three times with ice-cold Dulbecco’s phosphate-buffered saline (D-PBS) containing calcium, magnesium, glucose, and pyruvate (Thermo Fisher Scientific 14287080). Tissue pieces were collected by centrifugation at 400 g for 5 minutes and dissociated with enzyme mixes 1 and 2 in gentleMACS C Tubes (Miltenyi Biotec 130-093-237) for 30 minutes using the gentleMACS Octo Dissociator with Heaters (Miltenyi Biotec 130-096-427), according to the manufacturer’s instructions. Digested samples were quenched with ice-cold D-PBS and filtered through a 70 μm cell strainer. After debris and red blood cell removal, following the manufacturer’s instructions, the cell pellet was washed with FACs-BL and stored at 4°C for further processing.
Cells were processed using the Chromium Controller and the Chromium Next GEM Single Cell 3' Reagent Kits (10x Genomics). The libraries were sequenced via Illumina Novaseq 6000 sequencer.

value: Whole brain

value: GFP-/mKate2+ FRDA brain cells

tag: strain

value: Busulfan + PLX3397 + Bone Marrow Transplant


title: 41760_KK_FOXA1_BX_rep2-1

description: Library name: 41760_KK_FOXA1_BX_rep2-1

tag: biological replicate


title: GM-CSF + IL-6, biological replicate 2

description:
Library name: HD_2n_GI
Healthy donor 2, day 2 culture

value: Peripheral blood

value: GM-CSF plus IL-6


title: FRDA brain cells did not receive mitochondria

description: Library name: mKate2- brain cells

value: GFP-/mKate2- FRDA brain cells


title: 39899_NativeHepG2_FOXA1_BX_rep2-1

description: Library name: 39899_NativeHepG2_FOXA1_BX_rep2-1

value: Native HepG2

value: Benzonase ChIP-exo (v6)

tag: resequencing replicate


title: RNAseq_SynTEF1_RGFP109_s47_rep2


title: GM-CSF + IL-6, biological replicate 1

description:
Library name: HD_1n_GI
Healthy donor 1, day 2 culture

value: in vitro differentiated MDSCs


title: RNAseq_SynTEF1_s43_rep1