title: HSV_wildtype_bio1

value: HSV (Sigma-Aldrich, #H6030, lot 086M4845V)

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3xHA-RTF1

value: IP'd DNA from sonicated chromatin


title: HSV_rtf1_8_9A_bio4

status: Public on Aug 03 2025

type: SRA

city: Pittsburgh

first: Sarah

middle: J

last: Hainer

state: PA

address: 4249 Fifth Ave

department: Department of Biological Sciecnes

country: USA

institute: University of Pittsburgh

library_source: genomic

data_processing:
Integrity of sequencing data was verified by fastqc version 0.11.9. Fastq files were trimmed with trimmomatic version 0.38 with parameters ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 CROP:36 MINLEN:24. Reads were aligned to a combined genome containing S. cerevisiae and S. pombe using bowtie2 version 2.4.1 with parameters -q -N 1 -X 1000 for paired-end sequencing. S. cerevisiae and S. pombe reads were then separated into different bam files for each genome. Reads were counted with SAMtools version 1.12 flagstat. Normalized bigwigs were generated using deepTools version 3.3.0 bamcoverage with parameters --extendReads --binSize 10 –scaleFactor x, where the scaling factor was determined for each sample using S. pombe reads as described.[93,94] Normalized bigwigs for two to five biological replicates were averaged using WiggleTools and the ‘mean’ function.
Assembly: sacCer3, ASM294v2
Supplementary files format and content: Bigwig files contain spike-in normalized data from S. cerevisiae immunoprecipitated DNA.

molecule: genomic DNA

organism: Saccharomyces cerevisiae

growth_protocol: Yeast cultures (250 mL) were grown to log phase (OD=0.5-0.7) in YPD+Trp.

extract_protocol:
Cell pellets were resuspended in 1xFA buffer containing 0.5% SDS and 1 mM PMSF. Cells were lysed with acid-washed glass beads using 15 cycles of vortexing at maximum speed (30s on, 30s rest on ice). Lysate was separated from beads via syringe (10 mL, with P200 tip as filter), transferred to an ultracentrifuge tube (Beckman Coulter, #355603, Brea, CA), and centrifuged at 50,000 rpm for 20 min at 4°C in an ultracentrifuge (Beckman Coulter, Optima XPN-100). The supernatant was decanted, and the pellet was resuspended in 8 mL 1xFA buffer containing 0.1% SDS and 1 mM PMSF. The resuspension was spun in the ultracentrifuge as above, and the supernatant decanted. The resulting chromatin pellet was resuspended in 1.5 mL 1xFA containing 0.1% SDS and 1 mM PMSF and transferred to a 15 mL Bioruptor tube with sonication beads (Diagenode, C30010017). Chromatin  was sheared for 25 cycles (30s on and 30s off) at 4°C in a Bioruptor Pico (Diagenode, B01060010). Chromatin was transferred to an ultracentrifuge tube and 4.2 mL of 1xFA buffer containing 0.1% SDS and 1 mM PMSF was added. Chromatin was centrifuged at 50,000 rpm for 20 min at 4°C and the supernatant was retained, aliquoted, and flash frozen in liquid nitrogen. Chromatin aliquots were stored at -80°C.  S. pombe chromatin from strain KP08 was spiked-in to S. cerevisiae chromatin at a 1:9 protein ratio upon thawing of sheared chromatin. Chromatin was quantified using the Pierce BCA kit (Thermo Scientific, 23225). IPs were performed with 500 µg (for histone IPs) or 1000 µg (for all other IPs) spiked-in chromatin and samples were diluted to 700 µL or 1.4 mL in 1xFA buffer containing 0.1% SDS and 1 mM PMSF, respectively. ChIPs were performed with antibodies against the following epitopes/proteins: HSV (Sigma-Aldrich, H6030; 5 µl per 1000 µg), HA (Santa Cruz, HA-probe Antibody (F-7) AC, sc-7392; 60 µl per 1000 µg), Rpb1 (8WG16; BioLegend, 664906; 4 µL per 1000 µg), H3 (Abcam, ab1791; 1µL per 500 µg), H3K4me3 (Active Motif 39159, 39160; 2.5 µl per 500 µg), and H3K36me3 (Abcam ab9050: 6 µg per 500 µg). After overnight incubation of primary antibodies with chromatin, Protein A Sepharose beads (Cytiva, 17-5280-01) were added to HSV, 8WG16, and H3K4me3 reactions in an amount of 30 µL beads (50% slurry) per 500 µg chromatin. Protein G Sepharose beads (Cytiva, 17-0618-01) were added to H3 and H3K36me3 in an amount of 30 µL beads (50% slurry) per 500 µg chromatin. Samples with Protein A or G beads were rotated end-over-end for 2 hr at 4°C. IP reactions were performed as described above for ChIP-qPCR, with input samples performed in parallel. DNA was eluted in 100 µL 0.5X TE.
Libraries were prepared with the NEB Next II Ultra DNA library kit (NEB, E7645L) using 500 pg DNA input. Library quality was verified using fragment analysis (Fragment Analyzer, Advanced Analytical) and submitted for sequencing on an Illumina NextSeq 500 or 2000 instrument.

treatment_protocol: Cells were crosslinked with 1% formaldehyde for 20 min at room temperature with constant shaking, and quenched with a glycine-Tris solution (3 M glycine, 20 mM Tris-HCl). Cells were centrifuged at 3000 rpm for 10 min at 4°C, washed twice with 200 mL TBS (20 mM Tris-HCl pH 7.5, 150 mM NaCl), and centrifuged at 3000 rpm for 2 min at 4°C. Cells were resuspended in 1 mL 1xFA buffer containing 0.1% SDS (50 mM HEPES-KOH pH 7.5, 150 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% sodium deoxycholate, 1 mM PMSF) and transferred to 15 mL tubes to spin at 3000 rpm for 5 min at 4°C. Supernatant was removed from cell pellets and cell pellets were flash frozen in liquid nitrogen.

tag: strain

tag: cell line

tag: chip antibody

tag: genetic information

value: his3∆200 lys2-128∂ leu2∆1 ura3-52 trp1∆63 KanMx::GAL1p-FLO8-HIS3 3xHSV-CHD1 3XHA-rtf1(8-9A)

tag: molecule subtype


title: 2395B2 GPCMV

city: Minneapolis

first: Craig

middle: John

last: Bierle

state: Minnesota

address: 2001 6th Street SE

department: Pediatrics

institute: University of Minnesota

description:
Library name: 2395B2
Dam infected at 35 days gestation and euthanized at 56 days gestation

library_source: transcriptomic

data_processing:
Space Ranger (10x Genomics, version 1.3.0) was used to process the raw Illumina sequencing data.
Space Ranger outputs were uploaded to Partek® Flow® software (v10.0)
Reads that aligned to the GPCMV genome from each sample of infected placenta were visualized with Geneious (v11.1.5)
Assembly: Cavpor3.0 (GCF_000151735.1, Annotation Release 103) amended with the GPCMV genome (strain 22122, NC_020231), and a list of Guinea pig Y chromosome transcripts
Supplementary files format and content: filtered_feature_bc_matrix.h5: Filtered feature-barcode matrices
Supplementary files format and content: spatial.tar: Compressed spatial output files generated by Space Ranger.
Supplementary files format and content: .tif: High resolution slide scan images of capture areas
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

organism: Cavia porcellus

source_name: Maternal-fetal interface

growth_protocol: Guinea pigs were time mated during postpartum estrus and euthanized at 56 days gestation.

extract_protocol:
Placentas were disected, halved, and flash-frozen in OCT. Frozen placentas were trimmed to ~7X7 mm squares representing similar regions of interest and 10 μm tissue sections were prepared using a cryostat and placed onto Visium capture areas.
Sequencing libraries were prepared using Visium Spatial Gene Expression Slides (10x Genomics) and an 18 minute tissue permeabilization time according to the manufacturer's recommended protocol for fresh frozen tissue (CG000239 Rev C).

treatment_protocol: At 35 days gestation, guinea pigs were either infected with guinea pig cytomegalovirus or injected with saline.

tag: tissue

value: Maternal-fetal interface

tag: treatment

value: GPCMV-infected

tag: batch


title: 2425F Mock

description:
Library name: 2425F
Dam infected at 35 days gestation and euthanized at 56 days gestation

value: Mock-infected


title: JSA04

city: Los Angeles

first: Nils

last: Lindström

state: CA

address: 1425 San Pablo Street Lab 409

department: Stem Cell Biology and Regenerative Medicine

institute: University of Southern California (USC) -

description: Parse Biosciences SPLiT-seq

library_source: transcriptomic single cell

data_processing:
fastq files were demultiplexed and aligned to the genome using splitpipe from Parse Biosciences
Cell-gene count matricies were processed using Seurat v4 as described in the text
Assembly: Homo sapiens, hg38, Ensembl 105 annotation
Supplementary files format and content: .rds file of processed single-cells from kidney organoids from differentiation days 10 (untreated), 12, 14, and 18. Days 12, 14, and 18 include both control and proximal-biased (treated with 10 uM LY294002 from days 10-12) cells.

organism: Homo sapiens

source_name: Kidney organoid

growth_protocol: Takasato et al., 2016 Nature Protocols

extract_protocol:
6 individual organoids per timepoint were collected for FACS sorting for DRAQ5+, DAPI- single cells, and then fixed using the Parse Biosciences fixation protocol (Evercode Cell Fixation)
Parse Biosciences Evercode WT v2

treatment_protocol: Ly29-treated samples were treated with 10 uM LY294002 between days 10 and 12 of kidney organoid differentiation

value: Kidney organoid

tag: genotype

value: WT

value: Untreated, control, and Ly29-treated (10 uM between days 10-12)


title: 2425B Mock

description:
Library name: 2425B
Dam infected at 35 days gestation and euthanized at 56 days gestation


title: ChIP-seq EndoC-BH3-HNF1A-CS

city: Barcelona

first: Edgar

last: Bernardo

state: Barcelona

address: C/ del Dr. Aiguader, 88,

country: Spain

institute: CRG

data_processing:
Adapters were removed from ChIP-seq reads using cutadapt (v1.9.1)
Reads were aligned to the mouse (mm10) or human (hg19) genomes using Bowtie2 (v2.1.0)
bam files were created by filtering for multi-mapping (min MAPQ = 30) using Samtools (v1.2)
Duplicate reads and blacklisted regions were removed using Picard (v2.6.0) and Bedtools (v2.13.3)
bam files were converted into bigWig files for data visualization using Deeptools
Peaks were called using MACS2 (v.2.1.0) with the following settings: --bw=300 --keep-dup all --qvalue 0.01
Assembly: mm10
Assembly: hg19
Supplementary files format and content: bigWig files for each sample
Supplementary files format and content: bed files showing peaks for each sample

source_name: Murine β-cell line

growth_protocol:
EndoC-βH3 cells were cultured in plates coated with extracellular matrix gel from murine sarcoma and 2μg/mL fibronectin using Advanced DMEM/F12 supplemented with 2% fatty acid-free Bovine Serum Albumin Fraction V, 6.7ng/mL sodium selenite, 50μM 2-mercaptoethanol, 5.5μg/mL human transferrin, 10mM nicotinamide, 1% GlutaMAX and 100 U/mL Penicillin-Streptomycin.
MIN6 cells were cultured in DMEM High Glucose supplemented with 15% FBS, 1% GlutaMAX, 1% Penicillin-Streptomycin and 2.5μl β-mercaptoethanol.
Mouse pancreatic Islets cultured after isolation for 1-2 days in RPMI with 10% FBS and Pen-Strep (1:100) at 37ºC and 5% CO2.

extract_protocol:
~5 million cells were crosslinked in 1% formaldehyde for 10 min at RT in rotation. After quenching in 0.125 M glycine for 5 min, cells were washed in PBS and lysed in ChIP lysis buffer (2% Triton X-100, 1% SDS, 100 mM NaCl, 10 mM Tris-HCl pH 8.0, 1 mM EDTA and protease inhibitors) on ice for 30 min. Chromatin lysate was sonicated for 8 min (aiming for fragments between 150-400 bp) using a S220 Focused Ultrasonicator (Covaris)
Libraries were amplified by PCR (number of cycles were determined by qPCR using the Ct + 1 value) with KAPA HiFi Hotstart Ready mix (Kapa Biosystems) and size-selected (250–350 bp) employing Agencourt AMPure XP beads (Beckman Coulter). Bioanalyzer was used for sample QC and library pooling for multiplexing.

value: EndoC-BH3 cell line

tag: cell type

value: Human beta-cell line


title: ChIP-seq mouse_islets H3K4me3

organism: Mus musculus

source_name: Pancreatic islets

value: Pancreatic islets


title: HSV_wildtype_bio3


title: HSV_wildtype_bio2


title: 2421A GPCMV

description:
Library name: 2421A
Dam infected at 35 days gestation and euthanized at 56 days gestation


title: ChIP-seq MIN6-HNF1A-CS1

value: MIN6 cell line

value: Murine beta-cell line


title: Primary keratinocytes (strain Km), 1h culture, S2 substrate, replicate 3

status: Public on Aug 02 2025

city: London

first: Sebastiaan

last: Zijl

address: 28th Floor, Tower Wing, Guy’s Hospital, Great Maze Pond,

department: Centre for Gene Therapy and Regenerative Medicine,

country: United Kingdom

institute: King’s College London,

description: Library name: Sample 16

data_processing:
Raw RNA sequencing files were processed by GENEWIZ. To remove possible adapter sequences and poor quality nucleotides, sequencing reads were trimmed with Trimmomatic v.0.36 (Bolger et al., 2014). Quality control was performed using FastQC/0.11.8 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
Assembly: Trimmed reads were mapped to the human GRCh38 reference genome, using STAR aligner v.2.5.2b (Dobin and Gingeras, 2015). Transcript abundance was calculated using 'featureCounts' from the 'Subread' package v.1.5.2 (Liao et al., 2013). Only unique reads that fell within exon regions were counted.
Supplementary files format and content: csv files with counts for every sample

molecule: total RNA

source_name: Primary keratinocytes (strain Km), cultured for 1h culture on S2 subtrate

growth_protocol: Human keratinocytes (km) from neonatal foreskin were cultured on a feeder layer of mitotically inactivated J2 3T3 cells in 1 part Ham’s F12 medium (F12) and 3 parts Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 1.8 x 10-4M adenine (basal FAD medium). Basal FAD medium was supplemented with 10% foetal calf serum (FCS), 0.5 g/ml hydrocortisone, 5 g/ml insulin, 10–10M cholera enterotoxin and 10 ng/ml epidermal growth factor to make complete FAD medium.

extract_protocol:
RNA was isolated using the RNeasy mini kit (Qiagen). Each experiment was performed with three technical replicates per condition. Technical replicates were pooled together. The quality of the RNA was checked on a Qubit 2.0 Fluorometer (Thermo Fisher).Samples submitted for sequencing had an RNA integrity number of 9.9-10.0
Messenger RNA (mRNA) selection, library preparation and sequencing were performed by GENEWIZ Inc., as described (Cujba et al., 2022) standardized Illumina protocols.

treatment_protocol: Keratinocyte strain Km cultured on FAD media was disaggregated and seeded onto the polystyrene S1 ( circular features) and S2 substrates ( triangular features). Before seeding , the substrates were plasma cleaned and coated with 20 µg/ ml rat tail collagen 1 and the samples were collected at  1h, 4h and 12h timepoints.

value: Epidermis

value: Epidermal keratinocytes

value: S2 substrate


title: Primary keratinocytes (strain Km), 12h of culture, S2 substrate, replicate 3

description: Library name: Sample 18

source_name: Primary keratinocytes (strain Km), cultured for 12h culture on S2 subtrate


title: H7-Si-3

city: Wuhan

first: Minghe

last: Zhang

state: Hubei

address: Donghu Road

country: China

institute: WuHan University

description: Library name: Sample12

data_processing:
Paired-end reads were harvested from sequencer, and were quality controlled by Q30.
After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v4.6), the high quality clean reads were aligned to the reference genome with STAR software (v2.7.11b)
Raw read counts were extracted from the second column of the STAR output file 'ReadsPerGene.out.tab', which contained the unstranded RNA-seq read counts.
Assembly: Homo sapiens. GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample

source_name: Huh-7 cell line

extract_protocol:
Total RNA was extracted with Trizol (Invitrogen, Carlsbad, CA, USA), and subjected to ribosomal RNA (rRNA) removal using GenSeq® rRNA Removal Kit (GenSeq, Inc., Shanghai, China).
The rRNA-depleted samples were used for library construction with GenSeq® Directional RNA Library Prep Kit (GenSeq, Inc., Shanghai, China) by following manufacturer’s recommendations.

value: Huh-7 cell line

value: hepatoma cell

value: Huh-7 cells were transfected with siRNA targeting ARD1


title: Primary keratinocytes (strain Km), 4h culture, S2 substrate, replicate 3

description: Library name: Sample 17

source_name: Primary keratinocytes (strain Km), cultured for 4h culture on S2 subtrate


title: H7-Si-2

description: Library name: Sample11


title: MM-sEVs at T3

type: RNA

city: Hohhot

first: Qin

last: Si

address: Hohhot, Inner Mongolia, China

institute: Inner Mongolia International Hospital

description: Mare milk-derived small extracellular vesicles

hyb_protocol: Biotin-labeled RNA was hybridized to Affymetrix miRNA arrays at 48°C, 60 rpm for 16 hr using 100 µL (400/169 format) or 130 µL (100 format) hybridization mix containing 2X Hybridization Mix, 27.5% Formamide, DMSO, 20X Hybridization Controls, and Control Oligo B2

scan_protocol: Microarrays were scanned using Affymetrix Scanner 3000 Hybridization Oven 640

data_processing: Data were analyzed using Affymetrix default settings with global scaling as normalization method

label: biotin

organism: Equus caballus

source_name: horse milk exosomes

label_protocol: 1 µg total RNA was polyadenylated using FlashTag Biotin HSR RNA Labeling Kit (Affymetrix, 901911), followed by biotin labeling with 5X FlashTag Biotin HSR Ligation Mix and T4 DNA Ligase at 25°C for 30 min, terminated with HSR Stop Solution

growth_protocol: Horses were raised under standard farm conditions

extract_protocol: Total RNA was extracted from horse milk exosomes using TRIzol reagent according to the manufacturer's instructions

treatment_protocol: Milk samples were processed using differential ultracentrifugation to isolate exosomes. Samples were centrifuged at 3000g for 15 min at 4°C and 5000g for 30 min at 4°C to remove fat globules and cellular debris, with supernatant collected. The supernatant was filtered through a sterile filter cloth, then ultracentrifuged at 12000g for 60 min at 4°C and 70000g for 70 min at 4°C to remove casein by deposition, with supernatant collected. The supernatant was filtered through a 0.22μm filter and centrifuged at 135000g for 70 min at 4°C to obtain exosomes.


title: H7-Si-1

description: Library name: Sample10


title: MM-sEVs at T2

value: Mare milk-derived small extracellular vesicles


title: Primary keratinocytes (strain Km), 4h culture, S2 substrate, replicate 2

description: Library name: Sample 14


title: Primary keratinocytes (strain Km), 1h culture, S2 substrate, replicate 2

description: Library name: Sample 13


title: H7-NC-3

description: Library name: Sample9

value: Huh-7 cells were transfected with siRNA targeting negative control


title: H7-NC-1

description: Library name: Sample7


title: Primary keratinocytes (strain Km), 12h of culture, S2 substrate, replicate 1

description: Library name: Sample 12


title: Wound S. aureus agr mutant

city: La Jolla

first: Michelle

middle: D

last: Bagood

email: mbagood@ucsd.edu, mdbagood@gmail.com

address: 9452 Medical Center Dr.

department: Dermatology

institute: UCSD

description: 10x Genomics

data_processing:
Cell Ranger (10X Genomics) with default parameters was used to perform sample demultiplexing ,barcode processing, alignment to the mm10 reference genome, and gene counting
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: skin

extract_protocol:
Single-cell suspensions generated from mouse skin
10X Genomics 3’ V3.1

value: skin

value: whole tissue

value: S. aureus agr mutant


title: Primary keratinocytes (strain Km), 12h of culture, S2 substrate, replicate 2

description: Library name: Sample 15

value: WT


title: 3B-Si-3

description: Library name: Sample6

source_name: Hep-3B cell line

value: Hep-3B cell line

value: Hep-3B cells were transfected with siRNA targeting ARD1


title: ChIP-seq mouse islets H3K27ac

value: Pancreatic islets


title: Wound S. aureus

description: 10x Genomics

value: S. aureus


title: H7-NC-2

description: Library name: Sample8


title: 2421B GPCMV

description:
Library name: 2421B
Dam infected at 35 days gestation and euthanized at 56 days gestation

value: Maternal-fetal interface

value: GPCMV-infected


title: 3B-Si-1

description: Library name: Sample4


title: 3B-Si-2

description: Library name: Sample5


title: Primary keratinocytes (strain Km), 4h culture, S2 substrate, replicate 1

description: Library name: Sample 11

value: Epidermis

value: Epidermal keratinocytes


title: Primary keratinocytes (strain Km), 1h culture, S2 substrate, replicate 1

description: Library name: Sample 10

value: S2 substrate


title: 3B-NC-2

description: Library name: Sample2

value: hepatoma cell

value: Hep-3B cells were transfected with siRNA targeting negative control


title: MM-sEVs at T1

value: Mare milk-derived small extracellular vesicles


title: Intact S. aureus

description: 10x Genomics


title: 3B-NC-1

description: Library name: Sample1


title: Primary keratinocytes (strain Km), 12h of culture, S1 substrate, replicate 3

description: Library name: Sample 9

source_name: Primary keratinocytes (strain Km), cultured for 12h culture on S1 subtrate

value: S1 substrate


title: PLC/PRF/5 cells, oe-3

source_name: PLC/PRF/5 cell line

treatment_protocol: The control vector or ARD1-overexpressed plasmid was transfected into the PLC/PRF/5 cell line. After 48 hours, the cells were harvested for transcriptome sequencing.

value: PLC/PRF/5 cell line

value: Cells were transfected with ARD1-overexpression plasmid


title: Intact Control

description: 10x Genomics

value: skin

value: whole tissue

value: vehicle


title: PLC/PRF/5 cells, oe-2


title: Primary keratinocytes (strain Km), 4h culture, S1 substrate, replicate 3

description: Library name: Sample 8

source_name: Primary keratinocytes (strain Km), cultured for 4h culture on S1 subtrate

value: WT


title: PLC/PRF/5 cells, nc-3

value: Cells were transfected with Control vector


title: PLC/PRF/5 cells, oe-1


title: Mouse wounds

description: FFPE spatial transcriptome sequencing

data_processing:
Raw sequencing data were processed using the 10x Genomics Space Ranger 2.1.0 pipeline to generate FASTQ files
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Excange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: spatial transcriptomics

extract_protocol:
FFPE and 5 um sections
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium V5 Spatial Gene Expression Slide v2 and Reagent kit according to manufacturer's instructions

value: wound and infect


title: Primary keratinocytes (strain Km), 1h culture, S1 subtrate, replicate 3

description: Library name: Sample 7

source_name: Primary keratinocytes (strain Km), cultured for 1h culture on S1 subtrate


title: b-haSCs-PGC-D4-(scRNA)

first: Lei

last: Yang

state: Inner Mongolia Autonomous Region

address: 24 Zhaojun Rd.

department: State Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock

institute: Inner Mongolia University

description: Library name: b-haSCs-PGC-D4-(scRNA)

data_processing:
The CellRanger pipeline was used to pre-process the raw sequencing data, including demultiplexing of cellular barcodes, evaluation of the total number of cells, and applying map reads to the genome. The remaining cells and genes were used for cell clustering, and the normalization of gene expression was performed on the filtered matrix using by ‘NormalizeData’ function in Seurat.
Assembly: Bos_taurus.ARS-UCD1.2
Supplementary files format and content: rds

organism: Bos taurus

source_name: Derivation of cell lines from blastocysts

extract_protocol:
To maintain cell structure, embryo was dissociated into single-cell suspensions by enzymatic degradation of the extracellular matrix. Firstly, the tissue was washed by using icecold PBS buffer and soaked in 30 mM EDTA solution for 20 mins on ice to inhibit nuclease activity and reduce the stability of the cell membrane. The tissue was then washed again using PBS buffer, and 2 mg/ml collagenase IV (Worthington Biologicals) was used to dissociate tissue into single cells at 37°C for 20 minutes. To maintain cell viability, the single-cell suspension was put at ice and 10% FBS solution added. After dissociation, the suspension was filtered through a 40-um cell strainer (BDFalcon, BD Biosciences, San Jose, CA, USA) to remove large particles.
Single-cell barcoding and scRNA-seq library preparation were performed based on 10X Genomics single-cell RNA sequencing platform (10×Genomics, Pleasanton, CA, USA).

value: Stem-cell line

value: Formative pluripotency


title: Primary keratinocytes (strain Km), 12h of culture, S1 substrate, replicate 2

description: Library name: Sample 6

value: Epidermis


title: BATdKO KO_20344

city: Neuherberg

first: Peter

last: Weber

address: Ingolstädter Landstraße 1

country: Germany

institute: Helmholtz Zentrum München

description:
Library name: sample 23
MUC13848

data_processing:
Raw reads were trimmed by BBDuk
Read summing and quantification on gene-level was computed by Rsubread
We used the count-based expression matrix for our analysis.
The resulting count-based expression matrix was subjected to extensive quality control based on expression distribution, correlation analysis, and PCA; outliers were then removed.  Differential gene expression analysis was performed using DESeq2 standard library
Over-representation analysis was done in clusterProfiler
Assembly: mouse genome GRCm38
Supplementary files format and content: Tab delimited text
Supplementary files format and content: Expression matrix with counts

source_name: Brown fat

extract_protocol:
RNA was extracted with RNAeasy mini plus kit (Qiagen),
Lexogen‘s QuantSeqTM 3‘ mRNA-Seq Kit FWD HT

treatment_protocol: Ucp1CreERT2 positive TBLR1 fl/fl;TBL1 fl/fl and Ucp1CreERT2 negative TBLR1 fl/fl;TBL1 fl/fl control mice were housed at 30oC for 4 days and 8oC  for 6 days. Mice were born and raised at room temperature (22oC). Mice of both genotypes were moved directly to 30oC from room temperature. Mice of both genotypes were moved from room temperature to 8oC, after a gradual decrease on ambient temperature : 1day 18oC, 1day 16oC, 1day 12oC, 6 days 8oC. Mice were females. Mice were injected with tamoxifen at 5 years old and  ambient treatment protocol started 3 weeks after the last tamoxifen injection.

value: Brown fat

value: Ucp1CreERT2 positive TBRL1f/f;TBL1f/f

value: 8oC for 6 days


title: Primary keratinocytes (strain Km), 4h culture, S1 substrate, replicate 2

description: Library name: Sample 5

value: Epidermal keratinocytes


title: b-haSCs(scRNA)

description: Library name: b-haSCs(scRNA)

value: Derivation of cell lines from blastocysts


title: 3B-NC-3

description: Library name: Sample3

value: Hep-3B cell line

value: hepatoma cell

value: Hep-3B cells were transfected with siRNA targeting negative control


title: Wound Control

description: 10x Genomics

value: skin


title: PLC/PRF/5 cells, nc-1

value: PLC/PRF/5 cell line


title: BATdKO KO_20310

description:
Library name: sample 20
MUC13843


title: Primary keratinocytes (strain Km), 1h culture, S1 subtrate, replicate 2

description: Library name: Sample 4

value: S1 substrate


title: BATdKO KO_20343

description:
Library name: sample 22
MUC13847


title: BATdKO KO_20348

description:
Library name: sample 24
MUC13849


title: BATdKO KO_20321

description:
Library name: sample 21
MUC13844


title: BATdKO KO_20301

description:
Library name: sample 19
MUC13842


title: bE13(scRNA)

description: Library name: bE13(scRNA)

source_name: Cattle embryo

value: Cattle embryo

value: Peri-implantation development

tag: developmental stage

value: embryonic day 13


title: BATdKO WT_20354

description:
Library name: sample 18
MUC13852

value: Ucp1CreERT2 negative TBRL1f/f;TBL1f/f


title: bE12(scRNA)

description: Library name: bE12(scRNA)

value: embryonic day 12


title: bE11(scRNA)

description: Library name: bE11(scRNA)

value: embryonic day 11


title: Primary keratinocytes (strain Km), 12h of culture, S1 substrate, replicate 1

description: Library name: Sample 3

value: Epidermis

value: WT


title: BATdKO WT_20340

description:
Library name: sample 15
MUC13846

value: Brown fat

value: 8oC for 6 days


title: BATdKO WT_20351

description:
Library name: sample 16
MUC13850


title: Primary keratinocytes (strain Km), 1h culture, S1 subtrate, replicate 1

description: Library name: Sample 1

value: Epidermal keratinocytes


title: bE10(scRNA)

description: Library name: bE10(scRNA)

value: embryonic day 10


title: bE14(scRNA)

description: Library name: bE14(scRNA)

value: embryonic day 14


title: BATdKO WT_20291

description:
Library name: sample 13
MUC13841


title: PLC/PRF/5 cells, nc-2

value: hepatoma cell

value: Cells were transfected with Control vector


title: NHEK, scratch, ShC2, triplicate sample 3

data_processing:
Partek Flow
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Partek Flow
Trimmed sequence reads were mapped to STAR using Partek Flow
Read count extraction and normalization were performed using Partek Flow
Assembly: hg38 for human
Supplementary files format and content: tab-delimited csv file with raw counts values

source_name: primary keratinocyte

extract_protocol: ThermoFisher PureLink RNA Kit Illumina stranded mRNA or Illumina total RNA prep (ribodepletion)

value: primary keratinocyte

value: keratinocyte


title: BATdKO KO_20345

description:
Library name: sample 12
MUC13827

value: Ucp1CreERT2 positive TBRL1f/f;TBL1f/f

value: 30oC for 4 days


title: BATdKO KO_20311

description:
Library name: sample 9
MUC13820


title: NHEK, scratch, ShC2, triplicate sample 2


title: bE9(scRNA)

description: Library name: bE9(scRNA)

value: Cattle embryo

value: Peri-implantation development

value: embryonic day 9


title: BATdKO KO_20312

description:
Library name: sample 10
MUC13821


title: bE8(scRNA)

description: Library name: bE8(scRNA)

value: embryonic day 8


title: BATdKO KO_20309

description:
Library name: sample 8
MUC13819


title: BATdKO KO_20319

description:
Library name: sample 11
MUC13823


title: NHEK, scratch, ShC2, triplicate sample 1


title: BATdKO WT_20353

description:
Library name: sample 17
MUC13851

value: Ucp1CreERT2 negative TBRL1f/f;TBL1f/f


title: NHEK, scratch, USA300, triplicate sample 3


title: BATdKO KO_20303

description:
Library name: sample 7
MUC13818


title: BATdKO WT_20346

description:
Library name: sample 6
MUC13828


title: BATdKO WT_20329

description:
Library name: sample 4
MUC13825


title: Primary keratinocytes (strain Km), 4h culture, S1 substrate, replicate 1

description: Library name: Sample 2

value: Epidermis

value: WT

value: S1 substrate


title: b-ProiCHI-fetus(E75)-retarded-1

description: Library name: b-ProiCHI-fetus(E75)-retarded-1

data_processing:
Clean reads were mapped to the Cattle Bos_taurus.ARS-UCD1.2 or Sheep Ovis_aries.Oar_v3.1. genome using Tophat with default parameters.
Assembly: Cattle: Bos_taurus.ARS-UCD1.2; Sheep: Ovis_aries.Oar_v3.1
Supplementary files format and content: Tab-delimited text files include reads count.

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen) following the manufacturer's protocols, and mRNA was enriched using Oligo(dT) Magnetic Beads.
Library construction was performed following the Illumina manufacturer’s instructions, and sequencing was performed at the Frasergen (China).

value: Derivation of cell lines from blastocysts

value: Stem-cell line

value: Formative pluripotency


title: BATdKO WT_20339

description:
Library name: sample 5
MUC13826

value: Brown fat


title: NHEK, scratch, USA300, triplicate sample 2


title: b-ProiCHI-fetus(E75)-normal-2

description: Library name: b-ProiCHI-fetus(E75)-normal-2


title: BATdKO WT_20330

description:
Library name: sample 14
MUC13845

value: 8oC for 6 days


title: 1053-R2-FH

city: Columbia

first: Trupti

last: Joshi

state: Missouri

address: 103 Math Science Building

department: Department of Biomedical Informatics, Biostatistics and Medical Epidemiology (BBME)

institute: University of Missouri-Columbia

description: Library name: 1053-R2-FH

data_processing:
The trimmed sequence reads ere mapped to GRCm39 using Hisat2
fpkm files are estimted using cufflinks
Assembly: mm39
Supplementary files format and content: fpkm_tracking

source_name: Fetal-Brain

extract_protocol:
RNA was harvested using the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (Cat. No. 80224; Qiagen, MD, USA).
Raw libraries for RNA-seq were prepared using Illumina's TruSeq small RNA sample preparation kit, following manufacturer's protocol.

value: Fetal-Brain

tag: Sex

value: Male

value: Cre +


title: NHEK, scratch, USA300, triplicate sample 1

value: primary keratinocyte

value: keratinocyte


title: NHEK, scratch, TSB, triplicate sample 3

value: Control


title: 2036-L1-FH

description: Library name: 2036-L1-FH


title: b-ProiCHI-fetus(E75)-normal-1

description: Library name: b-ProiCHI-fetus(E75)-normal-1


title: b-IVF-fetus(E75)-2

description: Library name: b-IVF-fetus(E75)-2


title: NHEK, scratch, TSB, triplicate sample 2


title: BATdKO WT_20320

description:
Library name: sample 3
MUC13824

value: 30oC for 4 days


title: 1103-R2-FH

description: Library name: 1103-R2-FH


title: b-IVF-fetus(E75)-1

description: Library name: b-IVF-fetus(E75)-1


title: 2031-L1-FH

description: Library name: 2031-L1-FH

value: Female


title: 1103-L2-FH

description: Library name: 1103-L2-FH


title: 2039-L2-FH

description: Library name: 2039-L2-FH


title: b-ProiCHI-fetus(E75)-retarded-2

description: Library name: b-ProiCHI-fetus(E75)-retarded-2


title: NHEK, scratch, TSB, triplicate sample 1


title: 2039-L1-FH

description: Library name: 2039-L1-FH

value: Cre -


title: b-haSCs-PGC-D4-(buRNA)-2

description: Library name: b-haSCs-PGC-D4-(buRNA)-2


title: Non-intestinal cells, biological replicate 3

city: Utrecht

first: Matilde

last: Galli

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

description:
Library name: Sample 6
Column name in count_matrix.txt: rep3_nonint

data_processing:
Raw sequencing data from C. elegans samples were aligned to the WBcel235 reference genome (Ensembl release 108) using STARsolo (version 2.7.10a). Read alignment and count matrix generation were performed with STARsolo
Assembly: ce11
Supplementary files format and content: tab-delimited (.txt)

organism: Caenorhabditis elegans

source_name: Non-intestinal cells dividing in L1 stage

extract_protocol:
Total RNA was extracted using the standard TRIzol (Invitrogen) protocol
Libraries were prepared using an adapted version of the single-cell mRNA seq protocol of CEL-Seq. Samples were barcoded with CEL-seq primers during a reverse transcription and pooled after second strand synthesis. The resulting cDNA was amplified with an overnight In vitro transcription reaction. From this amplified RNA, sequencing libraries were prepared with Illumina Truseq small RNA primers. Paired-end sequencing was performed on the Illumina NextSeq 500 platform (read 1: 26 cycles, index read: 6 cycles, read 2: 60 cycles). Full barcode in R1, biological read in R2.


title: 1103-L1-FH

description: Library name: 1103-L1-FH


title: b-haSCs-PGC-D4-(buRNA)-1

description: Library name: b-haSCs-PGC-D4-(buRNA)-1


title: 2039-R3-FH

description: Library name: 2039-R3-FH


title: Non-intestinal cells, biological replicate 2

description:
Library name: Sample 5
Column name in count_matrix.txt: rep2_nonint

value: Non-intestinal cells dividing in L1 stage


title: Intestinal cells, biological replicate 3

description:
Library name: Sample 3
Column name in count_matrix.txt: rep3_int

source_name: Intestinal cell

value: Intestinal cell


title: 2031-R1-FH

description: Library name: 2031-R1-FH


title: BATdKO WT_20315

description:
Library name: sample 2
MUC13822

value: Ucp1CreERT2 negative TBRL1f/f;TBL1f/f


title: b-haSCs(buRNA)-3

description: Library name: b-haSCs(buRNA)-3

value: Derivation of cell lines from blastocysts


title: BATdKO WT_20293

description:
Library name: sample 1
MUC13817


title: b-haSCs-PGC-D1-(buRNA)-2

description: Library name: b-haSCs-PGC-D1-(buRNA)-2

value: Stem-cell line


title: Non-intestinal cells, biological replicate 1

description:
Library name: Sample 4
Column name in count_matrix.txt: rep1_nonint


title: 2010-R1-PRNA

description: Library name: 2010-R1-PRNA

source_name: Placenta

value: Placenta


title: Intestinal cells, biological replicate 1

description:
Library name: Sample 1
Column name in count_matrix.txt: rep1_int


title: 1083-R3-PRNA

description: Library name: 1083-R3-PRNA


title: b-haSCs-PGC-D1-(buRNA)-1

description: Library name: b-haSCs-PGC-D1-(buRNA)-1

value: Formative pluripotency


title: 2010-R5-PRNA

description: Library name: 2010-R5-PRNA


title: b-haSCs-PRM-72h-(CUT)-2

description: Library name: b-haSCs-PRM-72h-(CUT)-2

data_processing:
The sequencing reads that low quality and adapters were pre-filtered before mapping.
The cleaned data were aligned to the Bos_taurus.ARS-UCD1.2 reference with Bowtie2.
Assembly: ARS-UCD1.2
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

extract_protocol:
DNA was isolated from haESCs using the Universal CUT&Tag Assay Kit for Illumina (Vazyme, China).
Library construction was performed following the Illumina manufacturer’s instructions, and sequencing was performed at the Frasergen (China).

tag: time point


title: b-haSCs(buRNA)-1

description: Library name: b-haSCs(buRNA)-1


title: HEK293_90C_rep3

city: San Francisco

first: Daniel

last: Foyt

address: 1700 4th Street, Floor 3

department: Department of Pharmaceutical Chemistry

institute: University of California San Francisco

description: Library name: InVitro_90C_rep3

library_source: other

data_processing:
We constructed a pipeline to analyze HybriSeq data by taking raw sequencing reads and constructing a count matrix (counts per probe per cell). Briefly, we identify real barcodes, identify probe-targeting regions with correct ligation, remove duplicates using UMIs, and filter out reads not containing barcodes or probe-targeting regions. Detailed key steps were as follows:  1. To determine the location of each 7 base barcode sequence on read 1 we calculated the reverse complement of read 1, searched for the location of regions which should be common to all reads and extracted the 7 base barcode with these locations. More specifically, to determine the location of barcode 1 we searched the first 25 bases of read 1 for the sequence ATTCG, common to all barcode 1 oligos, and used the 9 bases after to determine barcode 1. To determine the location of barcode 2 we searched from base 35 to bases 56 of read 1 for the sequence TGCTTGAG, common to all barcode 2 oligos, and used the 9 bases after to determine barcode 2. To determine the location of barcode 3 we searched from base 57 to the end of read 1 for the sequence GTTTCG, common to all barcode 3 oligos, and used the 7 bases after to determine barcode 3. If the sequences ATTCG, TGCTTGAG, or GTTTCG were not found in their respective search windows, the read was excluded from analysis. 2. To determine the unique cell barcode, whitelists of each round of unique barcode sequences were constructed. We search the bases extracted from step 1 for 7 base stretches that were in the whitelists. If no match or multiple matches are found, reads were excluded. From this, a unique cell barcode was constructed. 3. To determine the targeting region from read 2 for the probe tiling experiments, a whitelist of probes was constructed including probe sequences within a hamming distance of two. Left-side probe targeting regions were determined by taking the first 30 bases of read 2 and comparing them to the probe whitelist. Similarly, right-side probe targeting regions were determined by taking the next 30 bases of read 2 and comparing them to the probe whitelist. Reads containing targeting regions not predicted to be adjacent were excluded after the percent of nonspecific ligation UMIs were calculated (Supplementary Fig. 4a). For all other experiments, the targeting region was determined by aligning read 2 to a custom index using bowtie2 with the parameters:  -L 30, and reads trimmed so that only the 60 bases of the ligated probe are aligned. The custom index included every combination of left and right side probes so that nonspecific ligation events could be calculated. The 8 bp simple UMI included on the right-side probe was extracted for both approaches. 4. We constructed a data frame of reads that included the unique cell barcode, probe targeting region, and simple 8bp UMI. We then collapsed duplicate reads by considering a combined UMI which contained the 8bp simple UMI, the unique cell barcode, and the identity of the probe targeting region. 5. We generated a count table of UMIs per probe per unique cell barcode or UMIs per gene per unique cell barcode.
Assembly: GRCh38 and GRCm39
Supplementary files format and content: cell count matrix: rows are cells, columns are probes

molecule: other

extract_protocol:
Round 3 PCR reactions were centrifuged at 500g for 1 minute to pellet cells. All round 3 PCR reaction solution was removed, pooled, and column purified with the Zymo DNA clean & concentrator kit (Zymo 11-305). Purified libraries were analyzed on an Agilent TapeStation Systems (D1000 kit) to check for the correct DNA size. If the predominate band was the correct size (252 ± 2 bp or 232 ± 2 bp depending if the left probe included a partial read 2 priming sequence) and was < 90% of the library the purified PCR product was run on a 3% agarose Tris-acetate-EDTA electrophoresis gel (200V 20 minutes) and the correct size band was cut out and extracted from the agarose with the Zymo Gel recovery kit (Zymo D4002). We observe that libraries that contained left probes containing the non-read 2 priming regions produced some nonspecific amplification requiring size selection purification. The purified pooled round 3 DNA product was placed into a final limited cycle PCR to add Illumina sequencing adaptors. The adapter addition PCR reaction was as follows: 0.5 ng DNA from pooled round 3 PCR product, 0.4 µM P7 forward primer, 0.4 µM P5 reverse primer and 1X KAPA HiFi HotStart ReadyMix. PCR thermocycling was performed as follows: 95 °C for 30 seconds, then 10 cycles at 95 °C for 30 seconds, 55 °C for 30 seconds, 72 °C for 30 seconds, followed by a final extension at 72 ºC for 30 seconds. The PCR reaction was removed and purified with a 0.8X ratio of SPRI beads to generate an Illumina-compatible sequencing library.
After probe ligation cells were counted and added to the ligase buffer (1X T4 DNA Ligase Reaction Buffer (NEB ref B0202S), 0.4 mM ATP, 40 U/mL RNasin, 0.5% Tween 20, 1% BSA, 200,000 U/mL T4 ligase) so that the final cell concentration was 22,000 cells/mL. Cells were passed through a 40 μm strainer. 22.69 µL of cells (500 cells) in ligase buffer were added to each well of a 96-well protein low bind plate, which had 2.31 µL of barcode 1 and linker 1 oligos already in each well. For the PBMC experiment, each stimulation condition was assigned to a specific set of wells, and this information was recorded. The first barcode was then used to identify the corresponding stimulation condition. Columns 1-4: Rest, columns 5-8: 6 hours, and columns 9-12: 24 hours. Cells were mixed by gently pipetting up and down. Plates were sealed and incubated at 25 ºC for 2 hours. 2 µL of 62.5 µM quenching oligo 1 (Supplementary table 6) were added to each well and mixed by pipetting. Plates were sealed and incubated at 25 ºC for 30 minutes. 25 µL of barcode wash buffer (50 mM EDTA, 0.5% Tween 20) was added to each well and incubated for 10 minutes. Cells from all 96 wells were pooled into a single 5ml low-bind Eppendorf tube. Cells were centrifuged for 3 minutes at 500 g at 4 ºC. Cells were washed two times in barcode wash buffer (+5 µM quenching oligo 1) and then washed in ligase buffer (+5 µM quenching oligo 1, -T4 ligase). Cells were resuspended in ligase buffer (+5 µM quenching oligo 1) so that the final cell concentration was 22,000 cells/mL and passed through a 40 μm strainer. 22.69 µL of cells in ligase buffer (+5 µM quenching oligo 1) were added to each well of a 96-well protein low bind plate, which had 2.31 µL of barcode 2 and linker 2 oligos already in each well. Cells were mixed by gently pipetting up and down. Plates were sealed and incubated at 25 ºC for 2 hours. 2 µL of 62.5 µM quenching oligo 2 were added to each well and mixed by pipetting. Plates were sealed and incubated at 25 ºC for 30 minutes. 25 µL of barcode wash buffer was added to each well and incubated for 10 minutes. Cells from all 96 wells were pooled into a single 5ml low-bind Eppendorf tube. Cells were centrifuged for 3 minutes at 500 g at 4 ºC. Cells were washed two times in barcode wash buffer (+5 µM each of quenching oligo 1 & 2) and then resuspended in ice-cold 1x ThermoPol reaction buffer (NEB ref B9004S) cells were passed through a 40μm strainer and counted. Cell concentration was normalized to 23,000 cells/mL in a cold ThermoPol reaction buffer. 460 cells were dispensed into 200µl PCR tubes or 96 well PCR plates. 20µL of PCR solution (1x KAPA HiFi HotStart ReadyMix (final concentration) and forward primer) with well-specific round 3 reverse primers (Supplementary Table 9) added to each well, so that the final concentration of each primer was 0.4 µM. PCR thermocycling was performed as follows: 95 °C for 30 seconds, then 20 cycles at 95 °C for 30 seconds, 55 °C for 30 seconds, 72 °C for 30 seconds, followed by a final extension at 72 ºC for 30 seconds. For the probe tiling experiment 48 wells were used in each barcoding round with the final round 3 PCR barcoding reaction containing 115 cells.


title: 1048-L1-FH

description: Library name: 1048-L1-FH


title: 2040-L2-FH

description: Library name: 2040-L2-FH


title: HEK293_90C_rep2

description: Library name: InVitro_90C_rep2


title: Intestinal cells, biological replicate 2

description:
Library name: Sample 2
Column name in count_matrix.txt: rep2_int


title: 1053-L2-FH

description: Library name: 1053-L2-FH


title: b-haSCs(buRNA)-2

description: Library name: b-haSCs(buRNA)-2


title: 1103-R1-FH

description: Library name: 1103-R1-FH


title: 1103-R2-PRNA

description: Library name: 1103-R2-PRNA


title: 1103-L2-PRNA

description: Library name: 1103-L2-PRNA


title: 2031-L1-PRNA

description: Library name: 2031-L1-PRNA


title: 2010-R4-PRNA

description: Library name: 2010-R4-PRNA


title: b-haSCs-PRM-72h-(CUT)-1

description: Library name: b-haSCs-PRM-72h-(CUT)-1


title: b-haSCs-PRM-48h-(CUT)-2

description: Library name: b-haSCs-PRM-48h-(CUT)-2


title: 1048-L1-PRNA

description: Library name: 1048-L1-PRNA


title: 2010-R3-PRNA

description: Library name: 2010-R3-PRNA


title: b-haSCs-PRM-48h-(CUT)-1

description: Library name: b-haSCs-PRM-48h-(CUT)-1


title: 1103-L1-PRNA

description: Library name: 1103-L1-PRNA


title: b-haSCs-PRM-24h-(CUT)-2

description: Library name: b-haSCs-PRM-24h-(CUT)-2


title: 38-L1-PRNA

description: Library name: 38-L1-PRNA


title: 1053-L1-FH

description: Library name: 1053-L1-FH


title: 2040-L2-PRNA

description: Library name: 2040-L2-PRNA


title: HEK293_90C_rep1

description: Library name: InVitro_90C_rep1


title: 2040-R2-PRNA

description: Library name: 2040-R2-PRNA


title: HEK293_37C_rep3

description: Library name: InVitro_37C_rep3


title: HEK293_Tile

description: Library name: Tile


title: b-haSCs-PRM-0h-(CUT)-2

description: Library name: b-haSCs-PRM-0h-(CUT)-2


title: Do-11-10_RNAseq

description: Library name: Do-11-10_RNAseq


title: 1084-R3-PRNA

description: Library name: 1084-R3-PRNA


title: HEK293_37C_rep2

description: Library name: InVitro_37C_rep2


title: 1083-R2-PRNA

description: Library name: 1083-R2-PRNA


title: Non-intestinal cells, no antibody control (ChIC), biological replicate 2

description: Library name: rep2_NoAb

data_processing:
Demultiplexing was performed with demux.py (v0.1.25) and fastq files were mapped using BWA-0.7.17(r1188) and adaptors were trimmed using cutadapt (v3.5).
Reads were mapped with bwa (0.7.17-r1188), and sorted and indexed with samtools (v1.16.1).
Reads were assigned to molecules with bamtagmultiome.py (v1.1) and deduplicated using bamFilter.py. Blacklisted genomic regions were removed with bedtools (v2.3.0).
bigWig files were generated using bamCoverage (v3.5.1) with a bin size of 20 bp, smooth length of 80 bp. Reads were extended by 100 bp.
Assembly: ce11
Supplementary files format and content: bigWig
Library strategy: ChIC-seq

source_name: Non-intestinal

extract_protocol:
Cells were lysed in 20ul stop solution (67 ul nuclease-free water (Ambion), 8ul 0.5M EGTA (Sigma Aldrich), 15ul IGEPAL CA-630 (Sigma Aldrich) and 10ul 20mg/ml Proteinase K (Invitrogen)) for six hours at 65ºC and 20 min at 80ºC and kept at 4ºC. Cells were frozen at -80ºC until further processing.
Extracted DNA fragments are blunt-ended by adding Klenow large fragment (NEB) and T4 polynucleotide kinase (NEB) in the presence of dNTP, and incubated at 37ºC for 30 min, 75ºC for 20 min and hold at 4ºC. Blunt fragments were A-tailed using AmpliTaq 360 DNA polymerase (Thermofisher) in the presence of dATP, and incubated at 72ºC for 15 min. Fragments were then ligated to T-tail forked adapters containing 8 bp cell barcodes and 3 bp UMIs with T4 DNA ligase, and incubated at 4ºC for 20 min, 16ºC for 16h, 65ºC for 10min and hold at 4ºC. Ligation products were cleaned up using Ampure XP beads (Beckman coulter). Cleaned products were linear amplified by in-vitro transcription reaction (MEGAscript T7 transcription kit, Invitrogen). Products were treated with DNAse I and RNA was cleaned using RNA clean XP beads (Beckman coulter). Cleaned RNA was fragmented by incubating it with fragmentation buffer (200 mM Tris-acetate, 500mM KOAc and 150m MgOAc) at 94ºC for 2 min, and cleaned using Ampure RNA beads. RNA was reverse transcribed using Superscript II (NEB) and amplified by PCR using Illumina smallRNA barcodes and NEBNext HF 2x PCR Master Mix, using 8-15 cycles depending on library complexity. PCR products were cleaned twice using Ampure DNA beads. Concentrations were mesured using QUBIT and fragment size distribution was analysed with a BioAnalyzer.

value: Non-intestinal


title: 2010-R7-PRNA

description: Library name: 2010-R7-PRNA


title: HEK293_37C_rep1

description: Library name: InVitro_37C_rep1


title: b-haSCs-PRM-24h-(CUT)-1

description: Library name: b-haSCs-PRM-24h-(CUT)-1


title: b-haSCs-PRM-0h-(CUT)-1

description: Library name: b-haSCs-PRM-0h-(CUT)-1


title: T24 cells, shUCHL5-3-3

first: Yuanfei

last: Cao

state: hubei province

address: 169 Donghu Road

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

data_processing:
Sequencing Platform: BGISEQ .
.Sequencing length: SE50
The raw data contains reads of low quality, reads with adaptor sequences and reads with high levels of N base. Those reads need to be filtered before the data analysis for reliability analysis results.
We used HISAT to align the clean reads to the reference genome.
We used Bowtie2 to align the clean reads to the reference genes.
Assembly: GCF_000001405.39_GRCh38.p13

growth_protocol: T24 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted from cells using trizol reagent(Invitrogen) and then reverse tran-scription was performed using the cDNA Reverse Transcription Kit (Toyobo Life Science, Shanghai China) to synthesize cDNA. 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: T24 cells were infected with lentiviral particles containing ShControl or ShUCHL5. Puromycin (600 ng/mL) was used to select transfected cells after being infected with indicated shRNA for 5 days.

value: Human bladder cancer cells

tag: condition

value: UCHL5 konckdown

value: Lentivirus-mediated stable low expression of UCHL5


title: Non-intestinal cells, H3K36me3 (ChIC), biological replicate 3

description: Library name: rep3_H3K36me3_nonint


title: Intestinal cells, H3K36me3 (ChIC), biological replicate 3

description: Library name: rep3_H3K36me3_int

source_name: Intestinal

value: Intestinal


title: T24 cells, shUCHL5-3-2


title: b-haSCs_H3K4me3_2

description:
Library name: b-haSCs_H3K4me3_2
b-haSCs_H3K4me3.bw

tag: antibody


title: Non-intestinal cells, H3K36me3 (ChIC), biological replicate 2

description: Library name: rep2_H3K36me3_nonint


title: Non-intestinal cells, no antibody control (ChIC), biological replicate 1

description: Library name: rep1_NoAb


title: T24 cells, shUCHL5-3-1


title: Non-intestinal cells, H3K36me3 (ChIC), biological replicate 1

description: Library name: rep1_H3K36me3_nonint


title: Intestinal cells, H3K36me3 (ChIC), biological replicate 1

description: Library name: rep1_H3K36me3_int


title: PBMC

description: Library name: PBMC

source_name: PBMC

value: PBMC


title: Intestinal cells, H3K27me3 (ChIC), biological replicate 3

description: Library name: rep3_H3K27me3_int


title: Intestinal cells, H3K36me3 (ChIC), biological replicate 2

description: Library name: rep2_H3K36me3_int


title: b-haSCs_H3K27me3_input

description:
Library name: b-haSCs_H3K27me3_input
b-haSCs_H3K27me3_input.bw


title: Non-intestinal cells, H3K27me3 (ChIC), biological replicate 3

description: Library name: rep3_H3K27me3_nonint


title: Non-intestinal cells, H3K27me3 (ChIC), biological replicate 2

description: Library name: rep2_H3K27me3_nonint


title: T24 cells, shUCHL5-1-1


title: b-haSCs_H3K27me3_2

description:
Library name: b-haSCs_H3K27me3_2
b-haSCs_H3K27me3.bw


title: T24 cells, shUCHL5-1-3


title: T24 cells, shUCHL5-1-2


title: b-haSCs_H3K4me3_1

description:
Library name: b-haSCs_H3K4me3_1
b-haSCs_H3K4me3.bw


title: Intestinal cells, H3K27me3 (ChIC), biological replicate 2

description: Library name: rep2_H3K27me3_int


title: Intestinal cells, H3K27me3 (ChIC), biological replicate 1

description: Library name: rep1_H3K27me3_int


title: b-haSCs_H3K27me3_1

description:
Library name: b-haSCs_H3K27me3_1
b-haSCs_H3K27me3.bw


title: Non-intestinal cells, H3K27me3 (ChIC), biological replicate 1

description: Library name: rep1_H3K27me3_nonint


title: b-haSCs_H3K4me3_input

description:
Library name: b-haSCs_H3K4me3_input
b-haSCs_H3K4me3_input.bw


title: b-haESCs(WGBS)-2

data_processing:
Clean reads were mapped to the Cattle Bos_taurus.ARS-UCD1.2 or Sheep Ovis_aries.Oar_v3.1. genome with Bismark/Bowtie2 mode
Assembly: Cattle: Bos_taurus.ARS-UCD1.2; Sheep: Ovis_aries.Oar_v3.1
Supplementary files format and content: Methylation level table

source_name: Derivation of  cell lines from  blastocysts

extract_protocol:
DNA was isolated form sperm using the Echolution Sperm DNA kit (BioEcho Life Science GmBH, Köln, Germany)
DNA was bisulfite-converted using EZ DNA Methylation-Gold^TM Kit (Zymo). Bisulfite-converted DNA was captured using AccelNGS Methyl-Seq DNA Library Kit (Swift Biosciences).


title: T24 cells 3

value: WT

value: control


title: Intestinal cells, H3K9me3 (ChIC), biological replicate 2

description: Library name: rep2_H3K9me3_int


title: T24 cells 2


title: Non-intestinal cells, H3K9me3 (ChIC), biological replicate 1

description: Library name: rep1_H3K9me3_nonint


title: b-haESCs(WGBS)-1

value: Derivation of  cell lines from  blastocysts


title: Intestinal cells, H3K9me3 (ChIC), biological replicate 1

description: Library name: rep1_H3K9me3_int


title: Non-intestinal cells, H3K4me3 (ChIC), biological replicate 3

description: Library name: rep3_H3K4me3_nonint


title: T24 cells 1


title: b-haESCs(DNA)-2

data_processing:
Clean reads were mapped to the Cattle Bos_taurus.ARS-UCD1.2 or Sheep Ovis_aries.Oar_v3.1. genome using Tophat with default parameters.
Assembly: Cattle: Bos_taurus.ARS-UCD1.2; Sheep: Ovis_aries.Oar_v3.1
Supplementary files format and content: bigWig
Library strategy: WGS

extract_protocol:
DNA was isolated form haESCs using the genomic DNA extraction kit.
Library construction was performed following the Illumina manufacturer’s instructions, and sequencing was performed at the Lc-Bio Technologies  (China).


title: High adipogenic clone 1F10

city: Québec

first: Mathieu

last: Laplante

state: Qc

address: 2725 Chemin Sainte-Foy

department: Medicine

country: Canada

institute: Université Laval

hyb_protocol: 5.5 μg of the fragmented and labeled cDNA was hybridized to Mouse Clariom S array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Pico Reagent Kit guide (Thermo Fisher).

scan_protocol: The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL. intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher).

data_processing: Probe set intensities were imported using the oligo R package (v1.70.0) [PMID: 20688976] and normalized with the Robust Multi-array Analysis (RMA) algorithm [PMID:12582260]. Differential gene expression analysis was performed using the limma R package (v3.62.2) [PMID: 25605792], and genes with an adjusted p-value < 0.1 were considered differentially expressed.

label: Biotin

source_name: High adipogenic clone 1F10

label_protocol: Microarray was performed at the GenomeQuebec in Montreal. RNA integrity was examined on a bioanalyzer (Agilent). High-quality RNA (RNA integrity number >8.5) was used for expression microarray analysis. 700 pg of total RNA was used to generate double strand cDNA, which was fragmented and biotin labeled according to Affymetrix GeneChip Pico Reagent Kit manual (Thermo Fisher).

growth_protocol: Immortalized brown preadipocytes were isolated as described (Galmozzi et al., 2014; PMID: 25466254) and kindly provided by Dr. Shingo Kajimura. The cell lines were cultured at sub-confluence in complete Dulbecco’s Modified Eagle Medium (DMEM) supplemented with Fetal Bovine Serum (FBS) (10%)

extract_protocol: Total mRNA was isolated from tissues using the RNeasy Lipid Tissue Mini Kit (Qiagen, 74104).

treatment_protocol: The cell lines were cultured at sub-confluence and RNA was extracted.

value: Immortalized brown preadipocytes


title: Intestinal cells, H3K4me3 (ChIC), biological replicate 3

description: Library name: rep3_H3K4me3_int


title: Non-intestinal cells, H3K4me3 (ChIC), biological replicate 2

description: Library name: rep2_H3K4me3_nonint


title: High adipogenic clone 1H8

source_name: High adipogenic clone 1H8


title: Intestinal cells, H3K4me3 (ChIC), biological replicate 1

description: Library name: rep1_H3K4me3_int


title: Non-intestinal cells, H3K4me3 (ChIC), biological replicate 1

description: Library name: rep1_H3K4me3_nonint


title: b-haESCs(DNA)-1


title: High adipogenic clone 2D5

source_name: High adipogenic clone 2D5


title: Intestinal cells, H3K4me3 (ChIC), biological replicate 2

description: Library name: rep2_H3K4me3_int


title: Cavia porcellus UnInfected 1

city: Bangalore

first: madavan

last: vasudevan

state: Karnataka

address: Kasturi Nagar

country: India

institute: Theomics International Private Limited

data_processing:
CASAVA Pipeline for BCL to FASTq conversion
FASTQC for raw data QC
NFCORE-RNASEQ pipeline for data processing
Assembly: Cavpor3.0
Supplementary files format and content: Complete_ReadCount_File.xlsx contains the raw read counts of all the genes identified to be expressed

source_name: Lung

growth_protocol: Dunken Hartley guinea pigs were infected with 10-30 bacilli per group (Mtb H37Rv/ MtbΔnagA/ MtbΔnagA.comp) by aerosol route of infection or left uninfected. Animals were kept in individual ventilated cages and were given food and water ad libitum. Animals were euthanized at 10 weeks post infection by CO2 asphyxiation and lungs were aseptically removed and used for total RNA isolation.

extract_protocol: Lung tissue samples were homogenized for 30 seconds in Trizol reagent. For lysis, bead beating was performed using 0.5 mm glass beads. QIAGEN RNeasy Kit was used for total RNA isolation by using manufacturer’s instructions. ..µg RNA was used for library preparation.

treatment_protocol: Guinea pig lung tissue samples were stored in RNA later reagent at -80°C until use.

value: Lung

value: uninfected


title: HEK293_Do-11-10_Rep1

description: Library name: Rep1

organism:
Homo sapiens
Mus musculus

value: Mix


title: Non-intestinal cells, H3K9me3 (ChIC), biological replicate 2

description: Library name: rep2_H3K9me3_nonint


title: Cavia porcellus UnInfected 3


title: Cavia porcellus UnInfected 2


title: HEK293_Do-11-10_mix

description: Library name: Cell_mixing


title: Cavia porcellus Infected with wild type Mtb H37Rv 1

value: wild type Mtb H37Rv


title: Cavia porcellus Infected with wild type Mtb H37Rv 3


title: High adipogenic clone 3E10

source_name: High adipogenic clone 3E10


title: High adipogenic clone 3B1

source_name: High adipogenic clone 3B1


title: HEK293_Do-11-10_Rep2

description: Library name: Rep2


title: Cavia porcellus Infected with wild type Mtb H37Rv 2


title: o-ProiCHI-fetus(E65)-retarded-1

description: Library name: o-ProiCHI-fetus(E65)-retarded-1

organism: Ovis aries

source_name: Derivation of cell lines from blastocysts

value: Stem-cell line


title: Cavia porcellus infected with nagA geneknockoutofMtb 3

value: nagA geneknockoutofMtb


title: High adipogenic clone 4E8

source_name: High adipogenic clone 4E8


title: Cavia porcellus infected with nagA geneknockoutofMtb 2


title: Cavia porcellus infected with nagA geneknockoutofMtb 1


title: o-IVF-fetus(E65)-2

description: Library name: o-IVF-fetus(E65)-2

value: Derivation of cell lines from blastocysts

value: Formative pluripotency


title: High adipogenic clone 4H10

source_name: High adipogenic clone 4H10


title: H3K4me3_GCB cells, Cfp1fl/flAcidaCre _rep3

city: guang zhou

first: yanan

last: Zhao

state: guang dong

address: No. 74 Zhongshan 2nd Road

institute: SunYat-sen University

description: Library name: K4_KO3

data_processing:
RNA: The clean reads were mapped to the mouse genome mm10/GRCm38 using Hisat2 (version 2.1.0),CUT&Tag: Alignments against the mm10 reference genome using BWA (version 0.7.17) and sorted BAM files were generated using samtools.
RNA: FeatureCount was used to generate featureCounts data,Differential gene expression analysis of raw featurecounts was performed using R package DESeq2. CUT&Tag: R package DiffBind was used for calculating differential peaks, and R package ChipSeeker was employed for annotating the peaks.
Sorted BAM files were generated using samtools (version 1.10.2) and then density bigWig files were generated by using the deepTools (version 3.5.1) with a normalizing scale factor to calculate RPKM.
IGV (version 2.18.2) was used to display specialized features among genomic regions with BigWig files as the input.
Assembly: mm10
Supplementary files format and content: Featurecounts  for each sample,bigWig
Library strategy: CUT&Tag

source_name: Spleen

growth_protocol: For immunization with MnJ adjuvant, mice were immunized intraperitoneally with 60 μg of NP (27-28)-KLH mixed with 300 μg MnJ (MS0001, MnStarter Biotechnology) and boosted with 60 μg NP (27-28)-KLH at day 8 for analysis at day 14

extract_protocol:
,Total RNA extraction and purification were performed using Trizol and chloroform. CUT&Tag was conducted as previously described (Kaya-Okur et al., 2019)
purified RNA (100 ng) was subsequently utilized to prepare RNA-sequencing libraries with the VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina kit (NR605-02, Vazyme) with dNTP standard method according to the provided protocol. And CUT&Tag performed PCR using the primers listed in Supplementary Table 1 , libraries were purified with 1.3 × DNA clean beads (N411, Vazyme) to get fragments larger than 250bp.

value: Spleen

value: B cells

value: Germinal center B cells

value: CFP1 knockout

value: mice were immunized intraperitoneally with NP-KLH


title: H3K4me3_GCB cells, Cfp1fl/flAcidaCre_ rep2

description: Library name: K4_KO2


title: o-IVF-fetus(E65)-1

description: Library name: o-IVF-fetus(E65)-1


title: High adipogenic clone 2G2

source_name: High adipogenic clone 2G2


title: Low adipogenic clone 1A12

source_name: Low adipogenic clone 1A12


title: Low adipogenic clone 1A10

source_name: Low adipogenic clone 1A10


title: o-haSCs(buRNA)-3

description: Library name: o-haSCs(buRNA)-3


title: o-ProiCHI-fetus(E65)-retarded-2

description: Library name: o-ProiCHI-fetus(E65)-retarded-2


title: H3K4me3_GCB cells, Cfp1fl/fl _ rep2

description: Library name: K4_WT2

value: WT


title: Low adipogenic clone 1C2

source_name: Low adipogenic clone 1C2


title: BSO-3

data_processing:
Merge paired-end data obtained from sequencing using the flash software (with parameters: flash R1 R2 -m 20 -d WorkDir -o Prefix -M 1000 --allow-outies -q). Utilize in-house scripts to extract target sgRNAs from both merged and unmerged R1, R2 data, based on the upstream and downstream 5bp bases. Then, conduct data quantity statistics and quality assessment on the extracted sgRNAs. Utilize MAGeCK software to align the extracted sgRNAs to the sgRNA library (with parameters: mageck count --trim-5 0 -l Library -n Prefix --sample-label Sample1, Sample2,… --fastq Sample1.fq, Sample2.fq,… --sgrna-len len --unmapped-to-file --norm-method control --control-sgrna control sgrna.txt), aggregate alignment data for all samples, and evaluate alignment rate, gRNA sequencing depth, and gRNA and gene coverage. Count the reads for each gRNA in every sample, annotate them to their corresponding target genes, and normalize the counting results. Perform principal component analysis and cluster analysis on the samples to demonstrate clustering relationships. Then RRA algorithm of MAGeCK software was used for differential gene screening (with parameters: mageck mle -k CountFile -d DesignMatrix -n OutputPrefix --norm-method control --control-sgrna control sgrna.txt), and visualize the results.
Assembly: Homo sapiens. GRCh38
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Library strategy: CRISPR screen

organism: synthetic construct

source_name: Huh-7 cell line

extract_protocol:
5 × 10^7 cells were collected by centrifugation at 500 × g for 10 minutes at 4°C and then genomic DNA was extracted with a genomic DNA extraction kit (TIANGEN, DP403).
The construction process of the CRISPR Screen library were as follows: two-step PCR method was used to build the library, and the number of PCR reactions was determined according to different templates. Design universal primers (with bridging sequences) in the pre and post sequence of the sgRNA region, and construct a reaction system using high fidelity enzyme (NEB Q5) . The first step is to obtain the target fragment through PCR. After amplification, each reaction section is merged and enriched, and purified using magnetic beads; The second step of PCR is to amplify the purified PCR product 15ul with a primer (index). After the two-step PCR is completed, magnetic beads are used for recycling to obtain a single target band. After purification, the library was subjected to agarose electrophoresis to confirm the bands (fragment size of about 280bp), quantified using Qubit, and diluted to 3ng/ul. The library was then placed on the machine according to the QC standard of the library.For each sample, >20ng purified PCR fragment was used for library preparation. These PCR productswere treated with End Prep Enzyme Mix for end repairing, 5’ Phosphorylation and dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Adaptor-ligated DNA was then performed using DNA Clean Beads. A second PCR reaction was carried out with P5 and P7 primers carrying sequences which can anneal with flowcell to perform bridge PCR and index allowing for multiplexing. The final library product for sequencing were then purified by beads and was qualified.The qualified libraries were sequenced pair end 150bp on the illumina HiseqXten System.

treatment_protocol: The CRISPER-PoolTM KOUT human library containing 123,441 sgRNAs targeting 19,050 genes and 1,864 miRNAs was purchased from Genechem Co., Ltd. (Shanghai, China). After Huh-7 cells were transduced with various concentrations of the lentiviral library (2.5%-60%) for 72 hours, 2.5 μg/ml puromycin (Biosharp, China) was added to the medium, and the functional multiplicities of infection (MOIs) were assessed via a CCK-8 assay. A total of 2 × 108 Huh-7 cells were transduced with the corresponding amounts of lentiviral particles at functional MOIs to ensure 500-fold coverage and subjected to selection for cells stably infected for 72 hours with 2.5 μg/ml puromycin. The transduced cells were then divided into two groups and treated with or without the glutathione synthesis inhibitor buthionine sulfoximine (BSO; MCE, USA) at the IC20. Following 24 days of selection, at least 5 × 107 cells were collected and subjecred to  DNA extraction, PCR amplification and sgRNA sequencing.

tag: host cell_type

value: hepatoma cell

tag: host cell_treatment

value: Cells were treated with BSO of IC20 for 24 days.

tag: crispr screen_library

value: CRISPER-PoolTM KOUT


title: o-haSCs(buRNA)-1

description: Library name: o-haSCs(buRNA)-1

tag: cell line


title: o-haSCs(buRNA)-2

description: Library name: o-haSCs(buRNA)-2


title: Low adipogenic clone 2C4

source_name: Low adipogenic clone 2C4

value: Immortalized brown preadipocytes


title: BSO-2


title: o-haESCs(WGBS)-2

source_name: Derivation of  cell lines from  blastocysts


title: RNA_GCB cells, Cfp1fl/flAcidaCre _rep3

description: Library name: RNA_KO3

data_processing:
RNA: The clean reads were mapped to the mouse genome mm10/GRCm38 using Hisat2 (version 2.1.0),CUT&Tag: Alignments against the mm10 reference genome using BWA (version 0.7.17) and sorted BAM files were generated using samtools.
RNA: FeatureCount was used to generate featureCounts data,Differential gene expression analysis of raw featurecounts was performed using R package DESeq2. CUT&Tag: R package DiffBind was used for calculating differential peaks, and R package ChipSeeker was employed for annotating the peaks.
Sorted BAM files were generated using samtools (version 1.10.2) and then density bigWig files were generated by using the deepTools (version 3.5.1) with a normalizing scale factor to calculate RPKM.
IGV (version 2.18.2) was used to display specialized features among genomic regions with BigWig files as the input.
Assembly: mm10
Supplementary files format and content: Featurecounts  for each sample,bigWig


title: BSO-1


title: Low adipogenic clone 3E5

source_name: Low adipogenic clone 3E5


title: RNA_GCB cells, Cfp1fl/flAcidaCre _rep1

description: Library name: RNA_KO1


title: Low adipogenic clone 2G5

source_name: Low adipogenic clone 2G5


title: o-haESCs(WGBS)-1

value: Derivation of  cell lines from  blastocysts


title: o-haESCs(DNA)-2


title: RNA_GCB cells, Cfp1fl/fl _ rep2

description: Library name: RNA_WT2


title: Do-11-10_HybriSeq

description: Library name: Do-11-10_HybriSeq


title: o-haESCs(DNA)-1


title: H3K4me3_GCB cells, Cfp1fl/fl _rep3

description: Library name: K4_WT3


title: control-2

value: Cells were treated with 0.02% DMSO for 24 days.


title: control-1


title: Low adipogenic clone 4H3

source_name: Low adipogenic clone 4H3


title: H3K4me3_GCB cells, Cfp1fl/flAcidaCre _rep1

description: Library name: K4_KO1


title: H3K4me3_GCB cells, Cfp1fl/fl _rep1

description: Library name: K4_WT1


title: Pad 207879870093_R05C01

status: Public on Aug 01 2025

type: genomic

city: Lebanon

first: Irma

last: Vlasac

state: NH

address: 1 Medical Center Drive.

department: Epidemiology

institute: Dartmouth College

description: Pad

hyb_protocol: none provided

scan_protocol: none provided

data_processing: MethylationEPICv2 Intensity data (IDATs) were preprocessed for normal exponential out-of-band (Noob) correction using Minfi10. Quality control was performed using a detection P, CpG, and sample threshold of 5%, with zero samples demonstrating a percentage of low quality CpG values greater than 5%. Beta value technical replicates were collapsed by averaging probes with common probe ID prefixes using SeSAMe11.Beta values were normalized using beta mixture quantile normalization (BMIQ).

label: Cy3 and Cy5

label_protocol: none provided

extract_protocol: none provided


title: Swab 207879870093_R06C01

description: Swab


title: RNA_GCB cells, Cfp1fl/fl _rep1

description: Library name: RNA_WT1


title: Cup 207879870093_R08C01

description: Cup


title: Multiome 207879870093_R07C01

description: Multiome


title: RNA_GCB cells, Cfp1fl/flAcidaCre_ rep2

description: Library name: RNA_KO2


title: Cup 207879870093_R02C01

description: Cup


title: Swab 207879870093_R04C01

description: Swab


title: Low adipogenic clone 4H7

source_name: Low adipogenic clone 4H7


title: Swab 207879870093_R01C01

description: Swab


title: Swab 207879870083_R06C01

description: Swab


title: Cup 207879870083_R08C01

description: Cup


title: Pad 207879870083_R04C01

description: Pad


title: RNA_GCB cells, Cfp1fl/fl _rep3

description: Library name: RNA_WT3


title: Pad 207879870083_R07C01

description: Pad


title: Cup 207879870083_R05C01

description: Cup


title: Multiome 207879870074_R07C01

description: Multiome


title: Pad 207879870064_R07C01

description: Pad


title: Pad 207879870064_R04C01

description: Pad


title: Pad 207879870083_R01C01

description: Pad


title: Cup 207879870074_R01C01

description: Cup


title: Swab 207879870064_R05C01

description: Swab


title: Swab 207879870074_R04C01

description: Swab


title: Pad 207879870074_R05C01

description: Pad


title: Swab 207879870064_R03C01

description: Swab


title: Cup 207879870064_R02C01

description: Cup


title: Multiome 207879870064_R01C01

description: Multiome


title: Pad 207879870029_R08C01

description: Pad


title: Cup 207879870029_R05C01

description: Cup


title: Pad 207879870029_R04C01

description: Pad


title: Pad 207879870074_R03C01

description: Pad


title: SRSF12KO_5nt_testis_rep1

city: Cambridge

first: Jimmy

last: Ly

state: Massachusetts

address: 455 main street

department: Biology

institute: Whitehead Institute

description: Library name: SRSF12KO_5nt_testis_rep1

data_processing:
Samples were demultiplexed with bcl2fastq v2.20 to generate fastq files.
Reads were aligned using STAR v2.7.1.a with options ---runThreadN 6 --runMode alignReads --outFilterMultimapNmax 1 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate for RIP-seq; --runThreadN 2 --limitBAMsortRAM 10000000000 --runMode alignReads --outFilterMultimapNmax 5000 --winAnchorMultimapNmax 1000 --outFilterType BySJout --outSAMattributes All --outSAMtype BAM SortedByCoordinate for rRNA analysis.
Transcript counts were quantified using Htseq-count
Dfferential expression analysis was performed using DEseq2
Assembly: Human genome: hg38 (gencode v25) and Mouse genome: m38 (gencode v24)
Supplementary files format and content: Transcript counts are stored in tab-delimited files with one row per transcript, quantification done using Htseq-count.

source_name: Testis

growth_protocol: HeLa cells were maintained in DMEM supplemented with 10% fetal bovine serum, 2 mM L-glutamine, and 100 U/mL penicillin/streptomycin

extract_protocol:
Cells in 6 well plates were washed once with 1x PBS then lysed in 400uL Trizol on plate. To the TRI Reagent lysate, 120 µL of chloroform was added, followed by shaking and centrifugation at 21,000 x g for 15 minutes at 4°C to achieve phase separation. The upper aqueous phase, was carefully transferred to a new tube, mixed with an equal volume of chloroform, and centrifuged again at 21,000 x g for 1 minute at 4°C. RNA was then precipitated by adding 300 mM NaCl and 30 µg of GlycoBlue (AM9516), along with an equal volume of isopropanol, and incubating the mixture overnight at -20°C. The RNA pellet was centrifuged at 21,000 x g for 15 minutes at 4°C, washed with 70% ethanol, and resuspended in RNase-free water. For the last replicate of SRSF12 overexpression analysis, we used Phasemaker tubes to extract RNA.
With one exeption (below), all RNA was prepped with the Watchmaker genomics kit with rRNA depletion according to manufacturer's instructions. For the third replicate of SRSF12 overexpression transcriptome analysis, rRNA depletion and library preparation were carried out with the KAPA RNA HyperPrep Kit with RiboErase (HMR) (Roche KK8560) according to manufacturer’s instructions.

treatment_protocol: GFP transgene expression was induced with 1 ug/mL doxycycline for 2 days and cells were harvested for RNA-sequencing

value: Testis

value: C57BL/6, SRSF12 5nt deletion


title: Swab 207879870083_R03C01

description: Swab


title: Multiome 207879870083_R02C01

description: Multiome


title: SRSF12KO_2nt_testis_rep1

description: Library name: SRSF12KO_2nt_testis_rep1

value: C57BL/6, SRSF12 2nt insertion


title: SRSF12KO_2nt_brain_rep2

description: Library name: SRSF12KO_2nt_brain_rep2

source_name: Brain

value: Brain


title: Swab 207879870074_R08C01

description: Swab


title: BL6_testis_rep2

description: Library name: BL6_testis_rep2


title: Cup 207879870074_R06C01

description: Cup


title: BL6_brain_rep1

description: Library name: BL6_brain_rep1


title: RNA-seq of P. ostreatus treated with BBP and PB replicate 2

city: Changsha

first: Rui

last: Zhuo

state: Hunan

address: Tianma 2nd Street , Yuelu District, Changsha, Hunan 410082, P.R.China

institute: GEMB

description:
Library name: BBP_PB_2
2×150bp paired-end sequencing

data_processing:
Raw sequencing data in FASTQ format were first quality-checked and filtered using fastp (https://github.com/OpenGene/fastp) to remove adapter contamination, low-quality reads, and undetermined bases. Clean reads were then aligned to the reference genome (Pleurotus ostreatus PC15 v2.0, JGI database) using HISAT2 (https://ccb.jhu.edu/software/hisat2). Transcript assembly and quantification were performed with StringTie (https://ccb.jhu.edu/software/stringtie), and expression levels were calculated as FPKM values.
Assembly: Pleurotus ostreatus PC15 v2.0 (JGI database)
Supplementary files format and content: normalized expression values for all 9 samples. Each value represents count, FPKM per gene.

organism: Pleurotus ostreatus

source_name: mycelium

growth_protocol: Pleurotus ostreatus GEMB-PO1 was cultured in GYP medium (20 g/L glucose, 5 g/L yeast extract, 5 g/L peptone) at 28 °C and 180 rpm

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen) following the manufacturer’s instructions. RNA quality was confirmed using NanoDrop and Bioanalyzer 2100 (RIN > 7.0).
Poly(A) mRNA was enriched using Dynabeads Oligo(dT) and fragmented at 94 °C for 5–7 min. Libraries were prepared using SuperScript II, dUTP-based second-strand synthesis, and UDG digestion. Libraries were size-selected (~300 bp), PCR-amplified (8 cycles), and sequenced on an Illumina NovaSeq 6000 using 2×150 bp paired-end mode.

treatment_protocol: Cultures were treated with 200 mg/L butyl benzyl phthalate (BBP) or 200 mg/L BBP + 1 mM piperonyl butoxide (PB), while the control group received no chemical addition.

value: mycelium

value: fungal

value: treated with BBP and PB


title: RNA-seq of P. ostreatus treated with BBP and PB replicate 1

description:
Library name: BBP_PB_1
2×150bp paired-end sequencing


title: RNA-seq of P. ostreatus treated with BBP replicate 3

description:
Library name: BBP_3
2×150bp paired-end sequencing

value: treated with BBP


title: Cup 207879870064_R08C01

description: Cup


title: RNA-seq of P. ostreatus treated with BBP replicate 2

description:
Library name: BBP_2
2×150bp paired-end sequencing


title: Cup 207879870064_R06C01

description: Cup


title: Cup 207879870029_R07C01

description: Cup


title: Swab 207879870029_R06C01

description: Swab


title: Cup 207879870029_R03C01

description: Cup


title: triticum_lrm_180_2

city: Seville

first: Francisco

middle: José

last: Romero-Campero

address: Americo Vespucio 49

department: Institute for Plant Biochemistry and Photosynthesis

institute: University of Sevilla

data_processing:
Quality control was performed with FASTQC.
Short read mapping to the reference genome (Triticum 4.0 assembly GenBank accession: GCA_002220415.3) (Alonge et al. 2020) was carried out with HISAT2 (Kim et al. 2019).
Transcripts assembly and gene expression estimation based on discrete mapped read counts was performed using StringTie (Kovaka et al. 2019).
Differential gene expression was determined using the Bioconductor R package DESeq2 (Love et al. 2014) using a fold-change of 2 and an adjusted p-value of 0.05.
Assembly: Triticum 4.0 assembly GenBank accession: GCA_002220415.3
Supplementary files format and content: Tab separated value containing gene expression measured as FPKM
Supplementary files format and content: Comma separated value containing read counts for each gene.

organism: Triticum aestivum

source_name: Leaves

growth_protocol: Triticum aestivum seeds variety ‘Chinese Spring L42’ (WBCDB0017) were acquired from the Germplasm Resource Unit (GRU) at the John Innes Center, Norwich (UK). Seeds were stratified for 4 days at 4ºC in the dark and  subsequently germinated on plates in growth chambers under long summer day conditions (16h light : 8h dark) at 24ºC. Seedlings were then planted in pots in the greenhouse, which had been pre-irragated to their maximum retention volume of 180 ml. Plants were divided into four groups: fully irrigated control plants, fully irrigated treated plants, drought-stressed control plants and drought-stressed treated plants. Fully irrigated plants were watered twice a week with 180ml and drought-stressed plants with 30 ml. The greenhouse conditions were long summer days, with 22ºC during the day and 20ºC during the night.

extract_protocol:
For RNA extraction, plant samples were ground to a fine powder in liquid N2 and TRIsure™ (BIOLINE, Memphis, TN, USA) was used following manufacturer's instructions. RNA purification was carried out using ISOLATE II RNA Plant Kit (BIOLINE) and RNA integrity was assessed with a Bioanalyzer Agilent 2100 system.
Illumina's instructions were followed for mRNA libraries preparation and sequencing was performed on a NextSeq500 Illumina sequencer (Illumina, San Diego, CA, USA)

treatment_protocol: The microalgae-based biostimulant LRM™ was provided by AlgaEnergy (Madrid, Spain). Following  manufacturer's instructions, LRM™ was diluted at 0.5% in water and was applied by foliar spraying over treated plants on the next day after planting and every 14 days there after. Control plants were sprayed with water.

value: Leaves

tag: variety

value: Chinese Spring L42 (WBCDB0017)

value: Wild type

tag: irrigation

value: Full Irrigation (180ml)

value: Foliar spary with LRMTM


title: Pad 207879870093_R03C01

description: Pad


title: triticum_lrm_180_1


title: triticum_h2o_30_3

value: Drought (30 ml)

value: Foliar spray with water


title: triticum_h2o_30_2


title: Pad 207879870029_R02C01

description: Pad


title: triticum_h2o_180_1


title: Swab 207879870029_R01C01

description: Swab


title: Spleen, TNFdARE, anti-LTa3, TCR-seq

city: New York

first: Emma

middle: Claire

last: Erlich

state: NY

address: 417 E 68th St

institute: Memorial Sloan Kettering

description: Library name: sample 21

data_processing:
Illumina base call (BCL) files were converted to FASTQ using Cell Ranger "mkfastq"
Expression data was processed using Cell Ranger "multi", pipeline version cellranger-8.0.1
Assembly: mm10 (refdata-gex-mm10-2020-A for GEX)
Assembly: GRCm38 (vdj-GRCm38-alts-ensembl-7.0.0 for VDJ)
Supplementary files format and content: Tab-seperated values files and matrix files for the 5' RNA data
Supplementary files format and content: filtered_contig_annotations.csv analyzed by Cell Ranger 8.0.1 for the BCR and TCR data
Library strategy: TCR-seq

extract_protocol:
Lymph nodes and spleens were harvested from mice and placed in RPMI-1640 media with 2% fetal bovine serum (FBS). The organs were gently crushed against a 100-micron filter before digestion in collagenase IV (1 mg/ml) and DNAse I (0.2 mg/ml) for 30 minutes at 37C in 5% CO2 to obtain a single cell suspension. Cells were strained through a 100-micron filter, washed with 5 ml of cold FACS buffer consisting of 1% FBS, 2 mM EDTA, and 0.2% sodium azide in HBSS. For the spleen, red blood cell lysis was performed for five minutes. Live photoconverted red+Cd45+ cells were selected by flow sorting. Sorted cells were pooled from 3 mice for each of the 4 experimental cohorts
The 10x Genomics Chromium Single Cell 5' Library and Gel Bead Kit was used. We sequenced 5' RNA expression, TCR sequencing, and BCR sequencing as per the manufacturer's protocol.

treatment_protocol: TNFdARE or wild-type (WT) KikGR+ (a photoconvertible protein) bone marrow chimera mice were treated with either anti-LTa3 mAb S5H3 LTa.Fc-MT (0.6 mg/kg)9 or isotype control (0.6 mg/kg (Clone C1.18.4; Leinco Technologies). Treatments were administered before surgery to allow adequate systemic absorption. Mice were anesthetized using inhaled isoflurane to effect and placed on a heating pad. A midline incision was made through the skin and linea alba to expose the intestines. A 365-nm fiber optic light source was used to photoconvert 15 discrete intestinal regions, beginning at the ileum. Each spot was exposed to light for 10 seconds, followed by a 30-second rest, repeated for three cycles per site. The peritoneum was closed with continuous absorbable 4-0 vicryl sutures, and the skin was closed with non-absorbable nylon surgical knots. Mice were placed on a heating pad until active. A second dose of anti-LTa3 or isotype control (0.6 mg/kg) was administered hours before tissue harvest. Mice were sacrificed in the same order as they were photoconverted.

value: Spleen

value: TCR+ cells

tag: recipient genotype

value: WT

tag: donor genotype

value: TNFdARE


title: Spleen, TNFdARE, anti-LTa3, BCR-seq

description: Library name: sample 20

data_processing:
Illumina base call (BCL) files were converted to FASTQ using Cell Ranger "mkfastq"
Expression data was processed using Cell Ranger "multi", pipeline version cellranger-8.0.1
Assembly: mm10 (refdata-gex-mm10-2020-A for GEX)
Assembly: GRCm38 (vdj-GRCm38-alts-ensembl-7.0.0 for VDJ)
Supplementary files format and content: Tab-seperated values files and matrix files for the 5' RNA data
Supplementary files format and content: filtered_contig_annotations.csv analyzed by Cell Ranger 8.0.1 for the BCR and TCR data
Library strategy: BCR-seq

tag: tissue

value: BCR+ cells

tag: treatment


title: SRSF12KO_5nt_testis_rep2

description: Library name: SRSF12KO_5nt_testis_rep2

value: Testis

tag: genotype

value: C57BL/6, SRSF12 5nt deletion


title: Spleen, TNFdARE, anti-LTa3, scRNA-seq

description: Library name: sample 19

data_processing:
Illumina base call (BCL) files were converted to FASTQ using Cell Ranger "mkfastq"
Expression data was processed using Cell Ranger "multi", pipeline version cellranger-8.0.1
Assembly: mm10 (refdata-gex-mm10-2020-A for GEX)
Assembly: GRCm38 (vdj-GRCm38-alts-ensembl-7.0.0 for VDJ)
Supplementary files format and content: Tab-seperated values files and matrix files for the 5' RNA data
Supplementary files format and content: filtered_contig_annotations.csv analyzed by Cell Ranger 8.0.1 for the BCR and TCR data

tag: cell type

value: CD45+ immune cells


title: Swab 207879870074_R02C01

description: Swab


title: Spleen, TNFdARE, Isotype, TCR-seq

description: Library name: sample 18

value: Isotype


title: SRSF12KO_5nt_brain_rep2

description: Library name: SRSF12KO_5nt_brain_rep2

value: Brain


title: SRSF12KO_5nt_brain_rep1

description: Library name: SRSF12KO_5nt_brain_rep1


title: SRSF12KO_2nt_testis_rep2

description: Library name: SRSF12KO_2nt_testis_rep2

value: C57BL/6, SRSF12 2nt insertion


title: BL6_testis_rep1

description: Library name: BL6_testis_rep1


title: BL6_brain_rep2

description: Library name: BL6_brain_rep2


title: Mesenteric Lymph Node, TNFdARE, Isotype, BCR-seq

description: Library name: sample 8

source_name: Mesenteric Lymph Node

value: Mesenteric Lymph Node


title: Mesenteric Lymph Node, TNFdARE, Isotype, scRNA-seq

description: Library name: sample 7


title: RNA-seq of P. ostreatus treated with BBP and PB replicate 3

description:
Library name: BBP_PB_3
2×150bp paired-end sequencing

value: mycelium

value: fungal

value: treated with BBP and PB

tag: batch


title: Mesenteric Lymph Node, WT, anti-LTa3, BCR-seq

description: Library name: sample 5


title: RNA-seq of P. ostreatus treated with BBP replicate 1

description:
Library name: BBP_1
2×150bp paired-end sequencing

value: treated with BBP


title: RNA-seq of P. ostreatus CK replicate 3

description:
Library name: CK_3
2×150bp paired-end sequencing

value: control


title: Mesenteric Lymph Node, WT, anti-LTa3, scRNA-seq

description: Library name: sample 4


title: Mesenteric Lymph Node, WT, Isotype, scRNA-seq

description: Library name: sample 1


title: SRSF12KO_2nt_brain_rep1

description: Library name: SRSF12KO_2nt_brain_rep1


title: RNA-seq of P. ostreatus CK replicate 1

description:
Library name: CK_1
2×150bp paired-end sequencing


title: RNA-seq of P. ostreatus CK replicate 2

description:
Library name: CK_2
2×150bp paired-end sequencing


title: RNAseq heterozygous Apobec3-humanized mouse-331 lung

city: Minato

first: Manabu

last: Ozawa

state: Tokyo

address: 4-6-1, Shirokanedai

department: Institute of Medical Science

country: Japan

institute: The University of Tokyo

description: Library name: Hu_Lu_331

data_processing:
For RNA-seq, the genomic regions spanning certain positions were extracted from the GRCh38.p14 reference genome to build an index with HISAT2 (version 2.2.1). The following genome sequences were used: 54650015 to 54746557 on chromosome 4 for c-KIT gene, and 38,927,609 to 39,128,836 on chromosome 22 for the APOBEC3 gene cluster. Paired-end RNA sequencing reads were mapped to this index using HISAT2. The resulting SAM alignment files were converted into sorted BAM files using SAMtools (version 1.21).
Assembly: GRCh38.p14
Supplementary files format and content: .txt formatted TPM values

source_name: Lungs

extract_protocol:
NucleoSpin RNA plus (TaKaRa) or RNeasy Fibrous Tissue Mini Kit (QIAGEN) for RNA.
For mRNA-seq in spermatogonia of c-Kit-humanized mice, libraries were generated using a Hieff NGS Ultima Dual-mode mRNA Library Prep Kit for Illumina (Yeasen) and subjected to paired-end sequencing (150bp) with NovaSeq X plus (Illumina). For total RNA-seq in Apobec3-humanized BALB/c mice,　libraries were generated using an Illumina Stranded Total RNA Prep with Ribo-Zero Plus (NEB) and subjected to paired-end sequencing (100bp) with NovaSeq X plus (Illumina).

value: Lungs

value: Heterozygous hAPOBEC3 gene cluster


title: RNAseq heterozygous Apobec3-humanized mouse-324 lung

description: Library name: Hu_Lu_324


title: triticum_lrm_30_1

value: Leaves

value: Chinese Spring L42 (WBCDB0017)

value: Wild type

value: Drought (30 ml)

value: Foliar spary with LRMTM


title: RNAseq WT BALBc mouse lung

description: Library name: WT_Lu_1

value: WT


title: triticum_lrm_30_2


title: triticum_lrm_30_3


title: triticum_lrm_180_3

value: Full Irrigation (180ml)


title: RNAseq heterozygous Apobec3-humanized mouse-331 spleen

description: Library name: Hu_Sp_331

source_name: Spleen

value: Spleen


title: Mesenteric Lymph Node, WT, Isotype, TCR-seq

description: Library name: sample 3

value: TCR+ cells

value: Isotype


title: RNAseq heterozygous c-Kit-humanized mouse-2 c-Kit-positive spermatogonia

description: Library name: hKIT2

source_name: Spermatogonia

value: Spermatogonia

value: Heterozygous hKIT


title: RNAseq heterozygous c-Kit-humanized mouse-1 c-Kit-positive spermatogonia

description: Library name: hKIT1


title: RNAseq WT C57BL6 mouse c-Kit-positive spermatogonia

description: Library name: WT


title: triticum_h2o_30_1

value: Foliar spray with water


title: triticum_h2o_180_2


title: triticum_h2o_180_3


title: RAW264.7 cells, oxLDL and tirzepatide 3

city: shenyang

first: mengjie

last: kang

state: 辽宁省

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

institute: Shenyang Medical College

description:
Library name: Sample15
OandT-3_tpm

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by fastp (version 0.18.0).
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome RNA (rRNA) database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.
The mapped reads of each sample were assembled by using StringTie v1.3.1[4][5] in a referencebased approach. For each transcription region, a FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: GRCm39/mm39
Supplementary files format and content: processed data.xlsx

growth_protocol: Murine macrophage RAW264.7 cells were cultured in high-glucose DEME medium supplemented with 10% fetal bovine serum and the 1% penicillin-streptomycin antibiotics at 37 °C and 5% CO2.

extract_protocol:
Total RNA was extracted from the macrophages using Trizol reagent kit following the manufacturer’s protocols.
The extracted mRNA is enriched using mRNA Capture Beads. After purification with beads, the mRNA is fragmented using high temperatures. The fragmented mRNA is then used as a template to synthesize the first strand of cDNA in a reverse transcription enzyme mixture system. While synthesizing the second strand of cDNA, end repair and A-tailing are completed. Next, adapters are ligated, and Hieff NGS® DNA Selection Beads are used for purification to select target fragments. PCR library amplification is then performed, and finally, detection is carried out using the Illumina Novaseq X Plus.

treatment_protocol: For macrophage phenotype studies, cells were treated with vehicle (culture medium), oxLDL (50 μg/ml), Tirzepatide (100 nmol/ml) or a combination of oxLDL and Tirzepatide

value: mononuclear macrophage leukemia cells

value: O and T-3

value: oxLDL and Tirzepatide


title: RAW264.7 cells, oxLDL and tirzepatide 4

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample16
OandT-4_tpm

value: O and T-4


title: Spleen, WT, Isotype, TCR-seq

description: Library name: sample 15


title: Spleen, TNFdARE, Isotype, BCR-seq

description: Library name: sample 17

value: BCR+ cells

value: TNFdARE


title: Day 3 cells cultured in TSCM with Dox (cDNA)

city: Ithaca

first: Weiyu

last: Zhang

address: 215 Tower Rd, Biotechnology Building

department: MBG

institute: Cornell University

data_processing:
DNBC4tools (v2.1.3) was employed to align the reads from the scRNA-seq data and quantify gene counts. Seurat (5.1.0) was then utilized for downstream analysis, with cells displaying low gene counts and high mitochondrial expression excluded from the dataset. Gene expression was normalized using scran (v1.28.1), and DoubletFinder (v2.0.4) was applied to identify and filter out potential doublets. For further analysis, up to 30 principal components (PCs) were selected, and a clustering resolution of 0.2 was used. Outlier clusters were filtered out to optimize downstream analysis.
Assembly: hg38
Supplementary files format and content: RDS file containing a Seurat object.

extract_protocol:
Total RNA was extracted with TRIzol reagent.
scRNA-seq libraries were prepared using a DNBelab C Series High-throughput Single-cell RNA Library Preparation set (MGI).

value: Expanded Potential Stem Cells

value: DOX


title: Spleen, WT, Isotype, BCR-seq

description: Library name: sample 14


title: RAW264.7 cells, oxLDL and tirzepatide 1

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample13
OandT-1_tpm

value: O and T-1


title: P2 hEPSC without DOX (cDNA)

value: METTL3 iKO


title: RAW264.7 cells, tirzepatide 4

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample12
T-4_tpm

value: Tirzepatide


title: Spleen, WT, Isotype, scRNA-seq

description: Library name: sample 13

value: Spleen

value: CD45+ immune cells

value: WT


title: Mesenteric Lymph Node, TNFdARE, anti-LTa3, TCR-seq

description: Library name: sample 12

value: Mesenteric Lymph Node

value: TCR+ cells


title: Mesenteric Lymph Node, TNFdARE, anti-LTa3, BCR-seq

description: Library name: sample 11


title: RAW264.7 cells, tirzepatide 3

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample11
T-3_tpm


title: P0 hEPSC (cDNA)


title: Spleen, TNFdARE, Isotype, scRNA-seq

description: Library name: sample 16

value: Isotype


title: Mesenteric Lymph Node, WT, anti-LTa3, TCR-seq

description: Library name: sample 6


title: Mesenteric Lymph Node, TNFdARE, Isotype, TCR-seq

description: Library name: sample 9


title: Mesenteric Lymph Node, TNFdARE, anti-LTa3, scRNA-seq

description: Library name: sample 10


title: Mesenteric Lymph Node, WT, Isotype, BCR-seq

description: Library name: sample 2


title: RAW264.7 cells, oxLDL 4

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample8
O-4_tpm

value: mononuclear macrophage leukemia cells

value: oxLDL


title: RAW264.7 cells, oxLDL 3

address: 辽宁省沈阳市于洪区黄河北大街沈阳医学院

description:
Library name: Sample7
O-3_tpm


title: RNAseq heterozygous Apobec3-humanized mouse-324 spleen

description: Library name: Hu_Sp_324

value: Heterozygous hAPOBEC3 gene cluster


title: RNAseq WT BALBc mouse spleen

description: Library name: WT_Sp_1