title: IgG + BTKi 1


title: AL7232, GEX

status: Public on Nov 08 2024

type: SRA

city: New York

first: Amaia

last: Lujambio

state: New York

address: 1470 Madison Avenue

country: USA

institute: Icahn School of Medicine at Mount Sinai

description:
10x Genomics
srt_obj.rds

library_source: transcriptomic single cell

data_processing:
Raw features by cells matrices were generated with CellRanger > v.5.0.1
Assembly: mm10
Supplementary files format and content: seurat objects including raw count matrices, represents all data (15 total samples RNA(15) + TCR(15))
Supplementary files format and content: contig files of TCR-seq

molecule: total RNA

organism: Mus musculus

source_name: Hepatocellular carcinoma

extract_protocol:
Mice were sacrificed and then the liver was perfused with PBS+EDTA 2mM through the inferior cava vein. Individual tumor nodules were visually inspected and selected to avoid healthy adjacent tissue and normalize for both size and level of expected necrosis across all samples. The selected tumor was then extracted from the liver using a sterile scalpel, weighed, and manually minced with sterile instruments. Minced tumor nodules were then enzymatically digested with 2.5mL enzymatic digestion mix (Miltenyi Biotech,Tumor dissociation Kit) in DMEM medium in a gentleMACS C Tube (Miltenyi Biotech) and then placed on gentleMACS Octo Dissociator (Miltenyi Biotech) for enzymatic and further mechanical dissociation with the “37°C_m_TDK1” program. Lysates were strained through a 70-µm cell strainer (Miltenyi) and resultant single cells were pelleted at 300g for 5 min at 4°C. From this point onward, cells were kept at 4°C. Elimination of red blood cells using “Red blood cell lysis solution” (Miltenyi Biotech) for 2 min on ice followed by elimination of dead cells using the “Dead Cell Removal” kit (Miltenyi Biotech) was performed according to manufacturer protocols. CD45 positive cells (immune cells) were separated from CD45 negative cells (tumor and non-immune stromal cells) using the CD45 microbeads mouse kit (Miltenyi Biotech) and each fractions were counted manually using a hemacytometer, then recombined at 1:1 ratio. This step was performed to ensure sufficient numbers of immune cells were sequenced from the bulk tumor samples. Only samples with a viability >80% were used.
Single-cell RNA sequencing (scRNA-seq) sample processing was immediately performed after cell extraction/isolation by the HIMC core facility at the Icahn School of Medicine at Mount Sinai. Two single-cell suspensions were counted (Nexcelom Cellometer Auto 2000) and each loaded on one lane of the 10x Genomics NextGem 5’v2.0 assay as per the manufacturer’s protocol with a targeted cell recovery of 10,000 cells per lane. Gene expression (5’Gex) and TCR libraries were generated as per the 10x Genomics demonstrated protocol (https://assets.ctfassets.net/an68im79xiti/57JaTECQNBPSpyDz8 oucdi/ced6aa8eaf73d6ee18dea8fdbd945faa/CG000331_Chromium_Next_GEM_Single_Cell_5-v2_UserGuide_RevD.pdf). All libraries were quantified via Agilent Technologies 4200 Tapestation and KAPA library quantification kit (Roche). Gene expression libraries were sequenced at a targeted depth of 25,000 reads per cell and TCR libraries at a targeted read depth of 5,000 reads per cell. Libraries were sequenced on the Illumina NovaSeq S2 100 cycle kit with run parameters set to 26x10x10x90 (R1xi7xi5xR2).

tag: tissue

value: Hepatocellular carcinoma

tag: Sex

value: F

tag: genotype

value: MycLucOS, NICD

tag: library type

value: GEX


title: 4MDLZ

city: Newark

first: Jason

last: Weinstein

state: NJ

address: New Jersey Medical School Cancer Center 205 South Orange Ave

department: Center for Immunity and Inflmmation

institute: Rutgers New Jersey Medical School

description: 4M DZ1

library_source: transcriptomic

data_processing:
Base calling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and Alignment (Cutadapt v2.5, STAR vSTAR_2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Assembly: Genome_build: GRCm38
Supplementary files format and content: Comma delimited file (csv) for differential gene expression counts via DESeq2.

source_name: Spleen

extract_protocol:
RNA was extracted using the RNAeasy plus mini kit (Qiagen)
Paired end strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols at Genewiz.

value: Spleen

tag: treatment


title: Psoriasis 017

type: RNA

city: Lausanne

first: JEREMY

last: DI DOMIZIO

state: Vaud

address: Av Boveresses 155, 1066 Epalinges

country: Switzerland

institute: CHUV

description:
internal positive and negative controls were used
PsO_017

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Data were normalized and log2 transformed using nSolver® 4.0 (Nanostring Technologies). Basically, housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library

label: NanoString indexing

organism: Homo sapiens

source_name: skin biopsy

label_protocol: NanoString indexing

extract_protocol: mRNA expression of 600 targets was analysed with the nCounter Human Immunology V2 panel including 20 customized probes (Nanostring Technologies, Seattle, WA, USA) on the nCounter® platform (Nanostring Technologies) using 100 ng of RNA per skin sample.

treatment_protocol: samples were snap-frozen without any treatment

tag: disease

value: Psoriasis


title: Psoriasis 018

description:
internal positive and negative controls were used
PsO_018


title: IgG 3

city: Cambridge

first: Timothy

middle: R

last: Hammond

state: MA

address: 350 Water Street

institute: Sanofi

data_processing:
Quantification was performed at gene level to obtain count-level information using the Expectation-Maximization (EM) algorithm54. Differential expression. Analysis was performed using DESeq2 (version 1.30.1) in RStudio (R 4.0.2).
Assembly: Human B38 reference genome, GenCode.V24
Supplementary files format and content: Counts matrix

molecule: polyA RNA

source_name: iPSC-derived microglia

extract_protocol:
RLT buffer (Qiagen)
Illumina Stranded mRNA Prep Ligation

tag: cell type

value: iPSC-derived microglia

value: IgG


title: AL7122, GEX

description:
10x Genomics
srt_obj.rds

value: MycLucOS, sgp53


title: AL7237, GEX

description:
10x Genomics
srt_obj.rds


title: 2M1DZ

description: 2M DZ1


title: Psoriasis 016

description:
internal positive and negative controls were used
PsO_016


title: IgG 2


title: L23

city: Coralville

first: Amanda

last: Bullert

state: Iowa

address: 2501 Crosspark Rd

department: Occupational and Environmental Health

institute: UNIVERSITY OF IOWA

data_processing:
cDNA library was constructed using the ribosomal depletion methods, and reads were sequenced in 120 bp paired-end sequences per the Illumina 1.9 encoding Novogene protocols
Sample data integrity was examined using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, version 0.11.9) for quality control of fastq files.
Sequence reads were then mapped to the UCSC mm10 reference genome using HISAT2
Gene counts were generated from the BAM files using SummarizedExperiments (version 1.28.0) with the UCSC mus musculus (mm10) reference genome
Assembly: mm10
Supplementary files format and content: CSV file includes raw counts for each sample

source_name: liver

extract_protocol:
Tissue punches collected from brain regions of interest were rinsed with PBS and placed in a lysing matrix tube containing 1 mL of TRIzol. Sample solutions were then aliquoted to RNeasy spin columns, followed by the QIAGEN RNeasy Kits protocol to clean and isolate RNA from the tissue samples.
mRNA enrichment: poly (A) capture or rRNA removal

value: liver

value: Female

tag: strain


title: 6M2LZ

description: 6M LZ2


title: Psoriasis 015

description:
internal positive and negative controls were used
PsO_015


title: IgG 1


title: L25


title: 6M1LZ

description: 6M LZ1


title: L28


title: Psoriasis 014

description:
internal positive and negative controls were used
PsO_014


title: 4M2DZ

description: 4M DZ2


title: Psoriasis 013

description:
internal positive and negative controls were used
PsO_013


title: 4M2LZ

description: 4M LZ2


title: BTKi 3

value: BTKi


title: 4M1LZ

description: 4M LZ1


title: BTKi 4


title: IgG 4


title: Psoriasis 012

description:
internal positive and negative controls were used
PsO_012


title: L29


title: BTKi 2


title: 2M2LZ

description: 2M LZ2


title: BTKi 1


title: L3

value: Vehicle


title: 2M2DZ

description: 2M DZ2


title: L4


title: Control 4

value: Control


title: 2M1LZ

description: 2M LZ1


title: Psoriasis 011

description:
internal positive and negative controls were used
PsO_011


title: L41


title: PM510-Healthyliver

data_processing:
Reads were aligned to the transcriptome derived from UCSC genome assembly mm10 using Tophat2 with default parameters. Read counts for each transcript were measured using featureCounts (2). Differentially expressed genes were determined using DESeq2 (3) and a cut-off of 0.05 on adjusted p-value (corrected for multiple hypotheses testing) was used for creating gene lists.
Assembly: mm10
Supplementary files format and content: ALLsamples_normalized_TPM.txt

source_name: Healthy liver

growth_protocol: hydrodynamic tail vein delivery

extract_protocol:
Trizol® (Invitrogen) followed by digestion with DNase I (Roche) and purification with the RNeasy Kit (Qiagen).
TruSeq RNA Sample Preparation

treatment_protocol: no treatment

tag: method

value: Hydrodynamic tail-vein injection method

value: Healthy liver


title: Control 3


title: L42


title: Psoriasis 009

description:
internal positive and negative controls were used
PsO_009


title: L45


title: Psoriasis 008

description:
internal positive and negative controls were used
PsO_008


title: Control 1


title: PM508-Healthyliver


title: Psoriasis 007

description:
internal positive and negative controls were used
PsO_007


title: L46


title: Psoriasis 006

description:
internal positive and negative controls were used
PsO_006


title: AL1560-Healthyliver


title: L48


title: Psoriasis 005

description:
internal positive and negative controls were used
PsO_005


title: Oligodendrocytes_WM_A2B5_Negative_AC27

city: Montreal

first: Alyson

last: Fournier

state: QC

address: 3801 Rue University

department: Department of Neurology and Neurosurgery

country: Canada

institute: McGill University

description: NS.2188.001.UDP0343_i7---UDP0343_i5.AC27

data_processing:
Raw FastQ files were aligned to the GRCh38 genome reference using the STAR aligner with default parameters
Assembly: GRCh38 genome
Supplementary files format and content: CSV contains raw read counts

source_name: Brain

extract_protocol:
RNA extracted from four distinct cell groups (GM A2B5-positive, WM A2B5-positive, GM 23 A2B5-negative and WM A2B5-negative cells) immediately after A2B5 selection. GM and WM 24 microglia RNA was extracted after 4 days in culture.
polyA-enriched RNA (stranded)

value: Brain

tag: cell line

value: Primary oligodendrocytes

value: Oligodendrocyte


title: Oligodendrocytes_GM_A2B5_Positive_AC24

description: NS.2188.001.UDP0342_i7---UDP0342_i5.AC24


title: L52


title: AL1558-Healthyliver


title: L50


title: Psoriasis 010

description:
internal positive and negative controls were used
PsO_010


title: AL1559-Healthyliver


title: L53


title: AL7539-MYC-lucOS-nicd-males

source_name: Liver tumors

value: Liver tumors


title: Psoriasis 004

description:
internal positive and negative controls were used
PsO_004


title: Oligodendrocytes_GM_A2B5_Negative_AC6


title: Psoriasis 003

description:
internal positive and negative controls were used
PsO_003


title: Psoriasis 002

description:
internal positive and negative controls were used
PsO_002


title: PM509-Healthyliver


title: AL7545-MYC-lucOS-nicd-males


title: Oligodendrocytes_WM_A2B5_Negative_AC4


title: L54


title: AL7534-MYC-lucOS-nicd-males


title: Psoriasis 001

description:
internal positive and negative controls were used
PsO_001


title: Oligodendrocytes_GM_A2B5_Positive_AC35

description: NS.2188.001.UDP0344_i7---UDP0344_i5.AC35


title: Microglia_WM_A46

value: Microglia


title: Control 2


title: L55


title: AL7533-MYC-lucOS-nicd-males


title: Microglia_GM_A45


title: AL7532-MYC-luc-nicd-males


title: Microglia_WM_A44


title: Pyoderma Gangrenosum 004

description:
internal positive and negative controls were used
PG_004

value: Pyoderma Gangrenosum


title: L58


title: AL7530-MYC-luc-nicd-males


title: AL7524-MYC-luc-nicd-males


title: Microglia_GM_A43


title: Pyoderma Gangrenosum 002

description:
internal positive and negative controls were used
PG_002


title: Pyoderma Gangrenosum 001

description:
internal positive and negative controls were used
PG_001


title: AL7523-MYC-luc-nicd-males


title: Microglia_WM_A42


title: AL5424-MYC-lucOS-nicd


title: L7


title: L8


title: Pyoderma Gangrenosum 005

description:
internal positive and negative controls were used
PG_005


title: S23

source_name: striatum

value: striatum


title: Non Responder 017

description:
internal positive and negative controls were used
NR_017

value: Non Responder


title: Microglia_WM_A40


title: S24


title: Microglia_GM_A39


title: Non Responder 016

description:
internal positive and negative controls were used
NR_016


title: L56


title: S25


title: Pyoderma Gangrenosum 003

description:
internal positive and negative controls were used
PG_003


title: Oligodendrocytes_WM_A2B5_Negative_AC38

description: NS.2188.001.UDP0035_i7---UDP0035_i5.AC38


title: Non Responder 015

description:
internal positive and negative controls were used
NR_015


title: S28


title: AL5421-MYC-lucOS-nicd


title: Oligodendrocytes_WM_A2B5_Positive_AC37

description: NS.2188.001.UDP0034_i7---UDP0034_i5.AC37


title: Microglia_GM_A41


title: Non Responder 013

description:
internal positive and negative controls were used
NR_013


title: Oligodendrocytes_WM_A2B5_Positive_AC34

description: NS.2188.001.UDP0031_i7---UDP0031_i5.AC34


title: AL5160-MYC-lucOS-nicd


title: AL5420-MYC-lucOS-nicd


title: S29


title: AL5154-MYC-lucOS-nicd


title: S3


title: AL5430-MYC-lucOS-nicd


title: Non Responder 012

description:
internal positive and negative controls were used
NR_012


title: Oligodendrocytes_WM_A2B5_Positive_AC33

description: NS.2188.001.UDP0030_i7---UDP0030_i5.AC33


title: AL5407-MYC-luc-nicd


title: Oligodendrocytes_GM_A2B5_Positive_AC32

description: NS.2188.001.UDP0029_i7---UDP0029_i5.AC32


title: S4


title: Non Responder 010

description:
internal positive and negative controls were used
NR_010


title: Non Responder 011

description:
internal positive and negative controls were used
NR_011


title: S42


title: Non Responder 009

description:
internal positive and negative controls were used
NR_009


title: Oligodendrocytes_GM_A2B5_Negative_AC29

description: NS.2188.001.UDP0026_i7---UDP0026_i5.AC29


title: AL5415-MYC-luc-nicd


title: S45


title: Non Responder 014

description:
internal positive and negative controls were used
NR_014


title: S46


title: Non Responder 008

description:
internal positive and negative controls were used
NR_008


title: Oligodendrocytes_GM_A2B5_Positive_AC31

description: NS.2188.001.UDP0028_i7---UDP0028_i5.AC31


title: Oligodendrocytes_GM_A2B5_Positive_AC28

description: NS.2188.001.UDP0025_i7---UDP0025_i5.AC28


title: Non Responder 007

description:
internal positive and negative controls were used
NR_007


title: Oligodendrocytes_WM_A2B5_Positive_AC26

description: NS.2188.001.UDP0023_i7---UDP0023_i5.AC26


title: AL5412-MYC-luc-nicd


title: AL5129-MYC-luc-nicd


title: Oligodendrocytes_GM_A2B5_Positive_AC20

description: NS.2188.001.UDP0019_i7---UDP0019_i5.AC20


title: S48


title: AL5122-MYC-luc-nicd


title: Non Responder 006

description:
internal positive and negative controls were used
NR_006


title: S41


title: AL5124-MYC-luc-nicd


title: IPIKID029.T1.rna.live

city: San Francisco

first: Bushra

last: Samad

state: CA

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

data_processing:
The remaining reads were aligned to the Ensembl GRCh38.85 transcriptome build using STAR
Assembly: GRCh38
Supplementary files format and content: FASTQ files

source_name: Primary tumor

extract_protocol:
The mRNA was isolated via DinaBead Direct, then converted into amplified
The dsDNA went through tagmentation, amplification and clean up with  AMPure XP beads steps, using the Illumina Nextera XT DNA Library Prep Kit. Quality control analysis was performed on the resulting pooled libraries with the Agilent Bioanalyzer HS DNA chip to assess fragment size distribution and concentration
RNAseq reads were first aligned to reference of rRNA and mitochondrial rRNA using BWA-mem

value: Primary tumor


title: S50


title: Oligodendrocytes_WM_A2B5_Negative_AC19

description: NS.2188.001.UDP0018_i7---UDP0018_i5.AC19


title: S52


title: Non Responder 005

description:
internal positive and negative controls were used
NR_005


title: IPIHNSC072.T1.rna.live


title: Non Responder 004

description:
internal positive and negative controls were used
NR_004


title: IPIGYN012.T1.rna.live


title: Oligodendrocytes_WM_A2B5_Positive_AC18

description: NS.2188.001.UDP0017_i7---UDP0017_i5.AC18


title: S53


title: S54


title: Oligodendrocytes_GM_A2B5_Positive_AC16

description: NS.2188.001.UDP0015_i7---UDP0015_i5.AC16


title: IPILUNG087.T1.rna.myeloid


title: Non Responder 002

description:
internal positive and negative controls were used
NR_002


title: S55


title: Non Responder 001

description:
internal positive and negative controls were used
NR_001


title: Oligodendrocytes_GM_A2B5_Positive_AC13

description: NS.2188.001.UDP0012_i7---UDP0012_i5.AC13


title: IPILUNG080.T1.rna.myeloid


title: IPILUNG081.T1.rna.myeloid


title: Oligodendrocytes_GM_A2B5_Negative_AC10

description: NS.2188.001.UDP0009_i7---UDP0009_i5.AC10


title: Lichen Planus 018

description:
internal positive and negative controls were used
LP_018

value: Lichen Planus


title: S56


title: Lichen Planus 017

description:
internal positive and negative controls were used
LP_017


title: S58


title: IPILUNG077.T1.rna.myeloid


title: S7


title: S8


title: Oligodendrocytes_GM_A2B5_Positive_AC5


title: IPILUNG074.T1.rna.myeloid


title: Non Responder 003

description:
internal positive and negative controls were used
NR_003


title: IPILUNG076.T1.rna.myeloid


title: Lichen Planus 015

description:
internal positive and negative controls were used
LP_015


title: Oligodendrocytes_WM_A2B5_Positive_AC7


title: Oligodendrocytes_WM_A2B5_Positive_AC3


title: K562 cell, Hyperoside, rep3

city: hangzhou

first: junyi

last: wei

state: zhejiang

address: Yuhangtang Road

country: China

institute: zhejiang university

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.
Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. Then clean reads for each sample were retained for subsequent analyses.
The clean reads were mapped to the reference genome using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count.
Assembly: hg38
Supplementary files format and content: text files include RPKM values and some annotations for each Sample
Supplementary files format and content: text files include raw counts and some annotations for each Sample

source_name: Bone

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Bone

tag: disease state

value: leukemia

value: Hyperoside


title: Oligodendrocytes_GM_A2B5_Negative_AC17

description: NS.2188.001.UDP0016_i7---UDP0016_i5.AC17


title: P24

source_name: prefrontal cortex

value: prefrontal cortex

value: Female


title: P23


title: IPILUNG070.T1.rna.myeloid


title: Lichen Planus 014

description:
internal positive and negative controls were used
LP_014


title: IPILUNG069.T1.rna.myeloid


title: Lichen Planus 013

description:
internal positive and negative controls were used
LP_013


title: P25


title: Lichen Planus 016

description:
internal positive and negative controls were used
LP_016


title: K562 cell, Hyperoside, rep1


title: Lichen Planus 012

description:
internal positive and negative controls were used
LP_012


title: P28


title: IPIKID112.T1.rna.myeloid


title: Lichen Planus 011

description:
internal positive and negative controls were used
LP_011


title: IPIKID111.T1.rna.myeloid


title: K562 cell, Control, rep3

value: Control


title: P29


title: K562 cell, Control, rep2


title: Lichen Planus 010

description:
internal positive and negative controls were used
LP_010


title: P3

value: Vehicle


title: P4


title: IPIKID097.T1.rna.myeloid


title: K562 cell, Control, rep1


title: K562 cell, Hyperoside, rep2


title: Lichen Planus 007

description:
internal positive and negative controls were used
LP_007


title: Z11_12Z374C2

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

data_processing:
Bioinformatic analyses were performed using Partek Flow Genomic Analysis Software (Partek, St. Louis, Missouri, USA), And R
Sequenced raw FASTQ files were trimmed for Nextera transposase adapters.
Trimmed reads were mapped to the reference genome mus musculus mm10 using STAR aligner.
Mapped reads were further filtered and quantified to transcripts and genes using mm10 assembly and GENCODE Genes- release M25.
Assembly: hg38
Supplementary files format and content: txt file with deseq2 normalised values for each sample

source_name: 12Z cell line

extract_protocol:
RNA extraction from tissues and cell lines was performed using the Zymo quick RNA-microprep kit (Zymo Research, Cat.R1501) according to the manufacturer's instructions.
cDNA library was constructed using well established Smart-seq2 protocol (Picelli et al. 2013, Picelli et al. 2014)
mRNA sequencing with 2x150bp setup

value: 12Z cell line

value: Epithelial cell


title: IPIKID073.T1.rna.myeloid


title: P41


title: P42


title: Lichen Planus 009

description:
internal positive and negative controls were used
LP_009


title: IPILUNG057.T1.rna.myeloid


title: Z10_CY_12Z374C1


title: Lichen Planus 008

description:
internal positive and negative controls were used
LP_008


title: Z12_12Z374C3


title: P45


title: Lichen Planus 006

description:
internal positive and negative controls were used
LP_006


title: Lichen Planus 005

description:
internal positive and negative controls were used
LP_005


title: IPIKID066.T1.rna.myeloid


title: Z9_12Z374M3


title: Lichen Planus 004

description:
internal positive and negative controls were used
LP_004


title: Z8_12Z374M2


title: IPIKID110.T1.rna.myeloid


title: IPIKID059.T1.rna.myeloid


title: IPIKID101.T1.rna.myeloid


title: P46


title: IPIKID054.T1.rna.myeloid


title: P48


title: Z7_12Z374M1


title: Lichen Planus 003

description:
internal positive and negative controls were used
LP_003


title: P50


title: IPIKID032.T1.rna.myeloid


title: Z6_12Z193C3


title: P52


title: Lichen Planus 002

description:
internal positive and negative controls were used
LP_002


title: IPIKID029.T1.rna.myeloid


title: Lichen Planus 001

description:
internal positive and negative controls were used
LP_001


title: P53


title: Hidradenitis Suppurativa 005

description:
internal positive and negative controls were used
HS_005

value: Hidradenitis Suppurativa


title: Z5_12Z193C2


title: P54


title: Z4_12Z193C1


title: IPIKID025.T1.rna.myeloid


title: IPIHNSC072.T1.rna.myeloid


title: Hidradenitis Suppurativa 004

description:
internal positive and negative controls were used
HS_004


title: Z2_12Z193M2


title: Hidradenitis Suppurativa 003

description:
internal positive and negative controls were used
HS_003


title: P55


title: IPIHNSC059.T1.rna.myeloid


title: Hidradenitis Suppurativa 002

description:
internal positive and negative controls were used
HS_002


title: P56


title: Z1_12Z193M1


title: IPIHNSC005.T1.rna.myeloid


title: P58


title: IPIHNSC017.T1.rna.myeloid


title: Hidradenitis Suppurativa 001

description:
internal positive and negative controls were used
HS_001


title: P7


title: IPIGYN095.T1.rna.myeloid


title: H11_HESC374C2

source_name: HESC cell line

value: HESC cell line

value: Stromal cell


title: P8


title: Healthy Donor 007

description:
internal positive and negative controls were used
HD_007

value: Healthy Donor


title: H10_HESC374C1


title: IPIGYN083.T1.rna.myeloid


title: Healthy Donor 006

description:
internal positive and negative controls were used
HD_006


title: H9_HESC374M3


title: Z3_12Z193M3


title: IPIGYN066.T1.rna.myeloid


title: H8_HESC374M2


title: homozygous male mouse, white adipocytes  Mettl14 KO, m6A IP, biol rep 1

city: Chicago

first: Cheng-Wei

last: Ju

state: Illinois

address: 929 East 57th Street, GCIS, Room E313

institute: The University of Chicago

description:
M14.iWAT.Adipoq.RADAR.csv
CF61IP

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (4.2)
Trimmed sequence reads were mapped to mm10 using HISAT2 (2.2.1).
Read count extraction and differential expression levels of exons and genes were analyzed using RADAR (0.2.4) followed by DEseq2 (1.36.0).
For differential m6A regions of mRNA, RADAR software (0.2.4) was used as well.
Assembly: mm10 (GRCm38.102), hg38 (GRCh38.107)
Supplementary files format and content: DESeq2 results with normalized reads for each sample and m6A analysis results from RADAR

source_name: white adipocytes

growth_protocol:
All mice were fed with chow-diet for twenty-four weeks from four week of age. At the end of the experiment, mice were euthanized after overnight fasting, followed by serum and tissue sample collection.
Cells were differentiated for 21 days, washed with PBS and cultured in 1% BSA containing high-glucose DMEM medium for 24 hours, and then collected cell pallet for RNA extraction.

extract_protocol:
Total RNA was then extracted from iBAT/iWAT by TRIzol. 1 μg of mRNAs was isolated from total RNA using a Dynabeads mRNA DIRECT purification kit (Thermo Fisher). Then, mRNA was adjusted to about 10 ng μl−1 in 100 μl and fragmented using a Bioruptor ultrasonicator (Diagenode) with 30 s on/off for 30 cycles. m6A immunoprecipitation (m6A-IP) and library preparation were performed using the EpiMark N6-Methyladenosine enrichment kit (NEB).
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's protocols.

value: Mettl 14 knockout

value: white adipocytes


title: Healthy Donor 005

description:
internal positive and negative controls were used
HD_005


title: IPIGYN032.T1.rna.myeloid

value: Primary tumor


title: homozygous male mouse, white adipocytes  Control, m6A IP, biol rep 4

description:
M14.iWAT.Adipoq.RADAR.csv
CF60IP

value: WT


title: H12_HESC374C3


title: IPIGYN027.T1.rna.myeloid


title: Healthy Donor 004

description:
internal positive and negative controls were used
HD_004


title: H6_HESC193C3


title: Healthy Donor 003

description:
internal positive and negative controls were used
HD_003


title: IPIGYN012.T1.rna.myeloid


title: homozygous male mouse, white adipocytes  Control, m6A IP, biol rep 3

description:
M14.iWAT.Adipoq.RADAR.csv
CF59IP


title: IPICRC053.T1.rna.myeloid


title: Healthy Donor 002

description:
internal positive and negative controls were used
HD_002


title: homozygous male mouse, white adipocytes  Mettl14 KO, m6A IP, biol rep 2

description:
M14.iWAT.Adipoq.RADAR.csv
CF62IP


title: H4_HESC193C1


title: IPICRC032.T1.rna.myeloid2


title: Healthy Donor 001

description:
internal positive and negative controls were used
HD_001


title: H5_HESC193C2


title: homozygous male mouse, white adipocytes  Control, m6A IP, biol rep 1

description:
M14.iWAT.Adipoq.RADAR.csv
CF57IP


title: homozygous male mouse, white adipocytes  Mettl14 KO, input, biol rep 2

description:
M14.iWAT.Adipoq.RADAR.csv
M14.iWAT.Adipoq.Deseq2.csv
CF62C


title: Healthy Donor 008

description:
internal positive and negative controls were used
HD_008


title: homozygous male mouse, white adipocytes  Control, m6A IP, biol rep 2

description:
M14.iWAT.Adipoq.RADAR.csv
CF58IP


title: homozygous male mouse, white adipocytes  Mettl14 KO, input, biol rep 1

description:
M14.iWAT.Adipoq.RADAR.csv
M14.iWAT.Adipoq.Deseq2.csv
CF61C


title: Erythroderma 030

description:
internal positive and negative controls were used
Eryth_030

value: Erythroderma


title: H1_HESC193M1


title: H3_HESC193M3


title: homozygous male mouse, white adipocytes  Control, input, biol rep 4

description:
M14.iWAT.Adipoq.RADAR.csv
M14.iWAT.Adipoq.Deseq2.csv
CF60C


title: H2_HESC193M2


title: H7_HESC374M1


title: homozygous male mouse, white adipocytes  Control, input, biol rep 3

description:
M14.iWAT.Adipoq.RADAR.csv
M14.iWAT.Adipoq.Deseq2.csv
CF59C


title: homozygous male mouse, white adipocytes  Control, input, biol rep 2

description:
M14.iWAT.Adipoq.RADAR.csv
M14.iWAT.Adipoq.Deseq2.csv
CF58C


title: Erythroderma 026

description:
internal positive and negative controls were used
Eryth_026


title: E9_CY_endometrioma155

source_name: Endometrioma

value: Endometrioma

value: endometriosis


title: Erythroderma 027

description:
internal positive and negative controls were used
Eryth_027


title: homozygous male mouse, white adipocytes, Control, input, biol rep 1

description:
M14.iWAT.Adipoq.RADAR.csv
M14.iWAT.Adipoq.Deseq2.csv
CF57C


title: E8_CY_endometrioma47


title: Erythroderma 025

description:
internal positive and negative controls were used
Eryth_025


title: Erythroderma 024

description:
internal positive and negative controls were used
Eryth_024


title: homozygous male mouse, brown adipocytes  Mettl14 KO, m6A IP, biol rep 4

description:
M14.iBAT.Ucp1.RADAR.csv
CF36IP

source_name: brown adipocytes

value: brown adipocytes


title: Erythroderma 023

description:
internal positive and negative controls were used
Eryth_023


title: IPICRC003.T1.rna.myeloid


title: E5_CY_endometrioma436


title: E4_CY_endometrioma432


title: homozygous male mouse, brown adipocytes  Mettl14 KO, m6A IP, biol rep 3

description:
M14.iBAT.Ucp1.RADAR.csv
CF35IP


title: homozygous male mouse, brown adipocytes  Mettl14 KO, m6A IP, biol rep 1

description:
M14.iBAT.Ucp1.RADAR.csv
CF33IP


title: Erythroderma 022

description:
internal positive and negative controls were used
Eryth_022


title: Erythroderma 029

description:
internal positive and negative controls were used
Eryth_029


title: E10_CY_endometrioma170


title: homozygous male mouse, brown adipocytes  Mettl14 KO, m6A IP, biol rep 2

description:
M14.iBAT.Ucp1.RADAR.csv
CF34IP


title: E6_CY_endometrioma446


title: E3_CY_endometrioma386


title: Erythroderma 021

description:
internal positive and negative controls were used
Eryth_021


title: homozygous male mouse, brown adipocytes  Control, m6A IP, biol rep 4

description:
M14.iBAT.Ucp1.RADAR.csv
CF32IP


title: homozygous male mouse, brown adipocytes  Control, m6A IP, biol rep 3

description:
M14.iBAT.Ucp1.RADAR.csv
CF31IP


title: Erythroderma 020

description:
internal positive and negative controls were used
Eryth_020


title: Erythroderma 019

description:
internal positive and negative controls were used
Eryth_019


title: E1_CY_endometrioma302


title: E2_CY_endometrioma304


title: Erythroderma 018

description:
internal positive and negative controls were used
Eryth_018


title: homozygous male mouse, brown adipocytes  Control, m6A IP, biol rep 2

description:
M14.iBAT.Ucp1.RADAR.csv
CF30IP


title: homozygous male mouse, brown adipocytes  Control, m6A IP, biol rep 1

description:
M14.iBAT.Ucp1.RADAR.csv
CF29IP


title: C10_CY_endometriosis170

source_name: Endometrium

value: Endometrium

value: non-endometriosis control


title: Erythroderma 017

description:
internal positive and negative controls were used
Eryth_017


title: E7_CY_endometrioma454


title: homozygous male mouse, brown adipocytes  Mettl14 KO, input, biol rep 4

description:
M14.iBAT.Ucp1.RADAR.csv
M14.iBAT.Ucp1.Deseq2.csv
CF36C


title: C9_CY_endometriosis155


title: homozygous male mouse, brown adipocytes  Mettl14 KO, input, biol rep 3

description:
M14.iBAT.Ucp1.RADAR.csv
M14.iBAT.Ucp1.Deseq2.csv
CF35C


title: Erythroderma 016

description:
internal positive and negative controls were used
Eryth_016


title: Erythroderma 015

description:
internal positive and negative controls were used
Eryth_015


title: C8_CY_endometriosis47


title: Erythroderma 014

description:
internal positive and negative controls were used
Eryth_014


title: homozygous male mouse, brown adipocytes  Mettl14 KO, input, biol rep 2

description:
M14.iBAT.Ucp1.RADAR.csv
M14.iBAT.Ucp1.Deseq2.csv
CF34C


title: homozygous male mouse, brown adipocytes  Mettl14 KO, input, biol rep 1

description:
M14.iBAT.Ucp1.RADAR.csv
M14.iBAT.Ucp1.Deseq2.csv
CF33C


title: C6_CY_endometriosis446


title: homozygous male mouse, brown adipocytes  Control, input, biol rep 4

description:
M14.iBAT.Ucp1.RADAR.csv
M14.iBAT.Ucp1.Deseq2.csv
CF32C


title: Erythroderma 013

description:
internal positive and negative controls were used
Eryth_013


title: Erythroderma 012

description:
internal positive and negative controls were used
Eryth_012


title: Erythroderma 011

description:
internal positive and negative controls were used
Eryth_011


title: C4_CY_endometriosis432


title: homozygous male mouse, brown adipocytes  Control, input, biol rep 2

description:
M14.iBAT.Ucp1.RADAR.csv
M14.iBAT.Ucp1.Deseq2.csv
CF30C


title: Erythroderma 010

description:
internal positive and negative controls were used
Eryth_010


title: homozygous male mouse, brown adipocytes  Control, input, biol rep 3

description:
M14.iBAT.Ucp1.RADAR.csv
M14.iBAT.Ucp1.Deseq2.csv
CF31C


title: homozygous male mouse, brown adipocytes, Control, input, biol rep 1

description:
M14.iBAT.Ucp1.RADAR.csv
M14.iBAT.Ucp1.Deseq2.csv
CF29C


title: C3_CY_endometriosis386


title: Erythroderma 008

description:
internal positive and negative controls were used
Eryth_008


title: C2_CY_endometriosis304


title: C1_CY_endometriosis302


title: C57BL/6 mice, NSP12 vaccine, VDJ

city: Los Angeles

first: Owen

last: Witte

state: California

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California, Los Angeles

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, aggregation, and paired clonotype calling were made using the Cell Ranger software v4.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: scVDJ-seq

source_name: spleen

extract_protocol:
Spleen single cells were isolated from  immunized C57BL/6 mice (n=5). For red blood cell lysis, cell suspensions were centrifuged at 300xg for 2 minutes at 4C, decanted, and cell pellets were resuspended in 3 mL of ACK lysis buffer and incubated for 3 minutes at room temperature. ACK was quenched by adding 10 mL of scRNAseq buffer (PBS without Ca/Mg +0.04% BSA). CD8+ cells were positively selected using magnetic separation per manufacturer instructions using anti-CD8 (Ly-2) mouse microbeads. Enriched CD8+ cells were centrifuged and washed twice with scRNAseq buffer. 5 samples from each treatment group were pooled 1:1:1:1:1 at 1000 cells / µL in 1 mL of scRNAseq buffer and viability was confirmed to be > 70% using trypan blue exclusion. Single cell capture and library construction was performed at the UCLA Technology Center for Genomics and Bioinformatics (TCGB) core facility using the 10x Genomics 5’GEX kit alongside V(D)J enrichment. Libraries were sequenced by Novaseq SP at 2x50 read length.
Single cell gene expression libraries (GEX) were created using Chromium Next GEM Single Cell 5' (v2 Chemistry) (10X Genomics #PN-1000263), the TCR V(D)J amplification was performed using 10X Chromium Single Cell mouse TCR amplification kit (10X Genomics #PN-1000254), Chromium Next GEM Chip G Single Cell Kit (10X Genomics #PN-1000127), and Chromium i7 Multiplex Kit (10X Genomics PN-120262) according to the manufacturer’s instructions. Briefly, cells were loaded to target 10,000 cells to form GEMs and barcode individual cells. GEMs were then cleaned cDNA and libraries were also created according to manufacturer’s instructions. Library quality was assessed using 4200 TapeStation System with both D1000 and D5000 ScreenTapes (Agilent) and Qubit 2.0 (Invitrogen) for size distribution and concentration. Samples were sequenced using Paired End sequencing (91+19+24+91) Novaseq 6000 (Illumina). Fastq.gz files were trimmed and generated 10X Genomics specifications using bcl2fastq (Illumina). 200 M reads (GEX) and 50M reads (TCR V(D)J) were targeted for each sample, targeting 20,000 reads per cell.

value: spleen

value: CD8+ splenocytes

value: female

value: RdRp mRNA vaccine immunization


title: Erythroderma 009

description:
internal positive and negative controls were used
Eryth_009

source_name: skin biopsy


title: C57BL/6 mice, NSP12 vaccine, GEX

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting, aggregation, and paired clonotype calling were made using the Cell Ranger software v4.0.0
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files


title: HYST114 HIV

city: Detroit

first: Marta

last: Rodriguez-Garcia

state: MI

address: 275 E Hancock St

institute: Wayne State University

description: Raw files contain poly A tail, protein and sample multiplexing libraries. References for protein (AbSeq) sequences and sample multiplexing (SampleTag) are provided in supplementary file  "HYST114_Control_feature_reference.csv". Sample multiplexing annotations are provided in supplementary file "HYST114_HIV_SampleTagCalls.csv"

data_processing:
FASTQ files containing unaligned reads were generated on NovaSeq6000 sequencing system (Illumina). Gene counts were generated by aligning and annotating reads to the human genome on Seven Bridges using BD Rhapsody WTA Analysis Pipeline to generate processed data.
Assembly: GRCh38.p12v29
Supplementary files format and content: BD Rhapsody WTA Analysis Pipeline output file: HYST64_Control_RSEC_mols.csv
Supplementary files format and content: BD Rhapsody WTA Analysis Pipeline output file: HYST64_HIV_RSEC_mols.csv
Supplementary files format and content: BD Rhapsody WTA Analysis Pipeline output file: HYST114_Control_RSEC_mols.csv
Supplementary files format and content: BD Rhapsody WTA Analysis Pipeline output file: HYST114_HIV_RSEC_mols.csv
Library strategy: CITE-seq

source_name: Female genital tract tissue

extract_protocol:
Tissues from the endometrium and ectocervix were obtained after hysterectomy. Tissues were minced into 1-2 mm fragments in Roswell Park Memorial Institute (RPMI) medium (Gibco) containing enzymes from Tumor Dissociation Kit, human (Miltenyi Biotec) and 0.01% DNAse (Worthington Biochemical) and transfered into sterile gentleMACSTM C Tubes (Miltenyi Biotec). Enzymatic digestion was performed on genlteMACSTM Dissociator (Miltenyi Biotec) using “37C_h_TDK_1” program. Digested tissue was filtered through 100um, 70um and 30um MACSTM SmartStrainers (Miltenyi Biotec) to generate stromal single cells suspensions. Single-cell suspensions were enriched for immune cells by magnetic bead removal of CD235a+ (CD235a (Glycophorin A) MicroBeads, human; Miltenyi Biotec) red blood cells and fibroblasts (Anti-fibroblast MicroBeads, human; Miltenyi Biotec). Purified cells were washed thoroughly with PBS containing 0.5% HS to remove any excess magnetic beads. The cells were incubated with HIV-BaL (MOI = 0.5) in XVIVO-15 or media alone for 30 minutes at 37C after which they were washed to remove excess unbound virus. Subsequently, the cells were incubated with oligo-conjugated antibodies (AbSeq) and barcoded sample tags (BD Hu Single Cell Sample Multiplexing Kit; BD Biosciences), to differentiate between tissue sites, for 20 minutes at room temperature in PBS containing 0.5% HS. Single cells from control and HIV treated samples were subsequently captured on separate cartridges, followed by synthesis of cDNA on BD Rhapsody Express system according to manufacturer's protocol https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/Protocol-Enh-Bead-WTA-%2B-AbSeq-%2B-SMK-RUO.pdf
Libraries containing whole transcriptome, protein (AbSeq) and sample multiplexing (SampleTag) were constructed from generated cDNA according to manufacturer's protocol. https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/Protocol-Enh-Bead-WTA-%2B-AbSeq-%2B-SMK-RUO.pdf

value: Female genital tract tissue

value: HIV


title: Erythroderma 007

description:
internal positive and negative controls were used
Eryth_007


title: Control-adherent3

city: Saint Louis

first: Pavle

last: Boskovic

state: MO

address: 4515 McKinley Ave

institute: Washington University in Saint Louis

data_processing:
Paired sequencing was done on NovaSeq 6000 according to Illumina instructions, adapters removed by STAR –clip3pAdapterSeq
Alignment STAR Version 2.5.3a --twopassMode Basic --twopass1readsN -1 --genomeLoad NoSharedMemory --outSAMtype BAM Unsorted SortedByCoordinate --limitBAMsortRAM 100000000000 --outBAMsortingThreadN=1 --outSAMstrandField intronMotif --outSAMunmapped Within KeepPairs --outFilterMultimapNmax 1 --outFilterMismatchNmax 5 --outFilterMismatchNoverLmax 0.3 --chimSegmentMin 15 --chimScoreMin 1 --chimScoreJunctionNonGTAG 0 --chimJunctionOverhangMin 15  --chimSegmentReadGapMax 3 --alignSJstitchMismatchNmax 5 -1 5 5 --alignIntronMax 1100000 --alignMatesGapMax 1100000 --alignSJDBoverhangMin 3 --alignIntronMin 20
duplication marking was done with sambamba 0.6.5
FeatureCounts was used for gene counting using Gencode.vM12 annotation
Assembly: mm10
Supplementary files format and content: tab delimited text files containing raw counts and FPKM/TPM values for each sample

source_name: mGB2 cell line

growth_protocol: Prior to RNA extraction, the cells were grown adherentlly on a Ecm marix-coated plate in full glioblastoma stem cell medium (DMEM:F12 containing N2, B27, EGF, FGF)

extract_protocol:
Total RNA was extracted using the Rneasy QIAGEN kit according to manufacturer's instructions. Genomic DNA was digested on-column using DNase I as recommended by the protocol
Libraries were prepared with the Illumina TruSeq Stranded mRNA Kit

value: mGB2 cell line

value: glioblastoma stem cell

value: Control

value: untreated


title: IPICRC090.T1.rna.tcell

value: Primary tumor


title: HYST114 Control

description: Raw files contain poly A tail, protein and sample multiplexing libraries. References for protein (AbSeq) sequences and sample multiplexing (SampleTag) are provided in supplementary file  "HYST114_Control_feature_reference.csv". Sample multiplexing annotations are provided in supplementary file "HYST114_Control_SampleTagCalls.csv"

value: Media/Control


title: Erythroderma 006

description:
internal positive and negative controls were used
Eryth_006

value: Erythroderma


title: Control-adherent2


title: C5_CY_endometriosis436


title: HYST64 HIV

description: Raw files contain poly A tail, protein and sample multiplexing libraries. References for protein (AbSeq) sequences and sample multiplexing (SampleTag) are provided in supplementary file  "HYST64_HIV_feature_reference.csv". Sample multiplexing annotations are provided in supplementary file "HYST64_HIV_SampleTagCalls.csv"


title: Erythroderma 004

description:
internal positive and negative controls were used
Eryth_004


title: C7_CY_endometriosis454


title: Control-adherent1


title: Erythroderma 003

description:
internal positive and negative controls were used
Eryth_003


title: Bko-adherent2


title: Bko-adherent3


title: HYST22 CITEseq

description: Raw files contain poly A tail, protein and sample multiplexing libraries. References for protein (AbSeq) sequences and sample multiplexing (SampleTag) are provided in supplementary file  "feature_reference.csv". Sample multiplexing annotations are provided in supplementary file "HYST22_SampleTagCalls.csv"

data_processing:
FASTQ files containing unaligned reads were generated on NovaSeq6000 sequencing system (Illumina). Gene counts were generated by aligning and annotating reads to the human genome on Seven Bridges using BD Rhapsody WTA Analysis Pipeline to generate processed data.
Assembly: GRCh38.p12v29
Supplementary files format and content: BD Rhapsody WTA Analysis Pipeline output file: HYST22_RSEC_mols.csv
Library strategy: CITE-seq

extract_protocol:
Tissues from the endometrium and ectocervix were obtained after hysterectomy. Tissues were minced into 1-2 mm fragments in Roswell Park Memorial Institute (RPMI) medium (Gibco) containing enzymes from Tumor Dissociation Kit, human (Miltenyi Biotec) and 0.01% DNAse (Worthington Biochemical) and transfered into sterile gentleMACSTM C Tubes (Miltenyi Biotec). Enzymatic digestion was performed on genlteMACSTM Dissociator (Miltenyi Biotec) using “37C_h_TDK_1” program. Digested tissue was filtered through 100um, 70um and 30um MACSTM SmartStrainers (Miltenyi Biotec) to generate stromal single cells suspensions. Single-cell suspensions were enriched for immune cells by magnetic bead removal of CD235a+ (CD235a (Glycophorin A) MicroBeads, human; Miltenyi Biotec) red blood cells and fibroblasts (Anti-fibroblast MicroBeads, human; Miltenyi Biotec). Purified cells were washed thoroughly with PBS containing 0.5% HS to remove any excess magnetic beads. The cells were incubated with oligo-conjugated antibodies (AbSeq) and barcoded sample tags (BD Hu Single Cell Sample Multiplexing Kit; BD Biosciences), to differentiate between tissue sites, for 20 minutes at room temperature in PBS containing 0.5% HS. Single cells were subsequently captured, followed by synthesis of cDNA on BD Rhapsody Express system according to manufacturer's protocol  https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/Single-Cell-Capture-cDNA-Synthesis-BD-Rhapsody-Express-Single-Cell-Analysis-System-User-Guide.pdf
Libraries containing whole transcriptome, protein (AbSeq) and sample multiplexing (SampleTag) were constructed from generated cDNA according to manufacturer's protocol. https://www.bdbiosciences.com/content/dam/bdb/marketing-documents/Protocol-Enh-Bead-WTA-%2B-AbSeq-%2B-SMK-RUO.pdf


title: Erythroderma 002

description:
internal positive and negative controls were used
Eryth_002


title: HYST35_Homeostatic

description: Raw files contain poly A tail, protein and sample multiplexing libraries. References for protein (AbSeq) sequences and sample multiplexing (SampleTag) are provided in supplementary file  "feature_reference.csv". Sample multiplexing annotations are provided in supplementary file "HYST35_SampleTagCalls.csv"

data_processing:
FASTQ files containing unaligned reads were generated on NovaSeq6000 sequencing system (Illumina). Gene counts were generated by aligning and annotating reads to the human genome on Seven Bridges using BD Rhapsody WTA Analysis Pipeline to generate processed data.
Assembly: GRCh38.p12v29
Supplementary files format and content: BD Rhapsody WTA Analysis Pipeline output file: HYST35_RSEC_mols.csv
Library strategy: CITE-seq


title: Bko-adherent1


title: Erythroderma 001

description:
internal positive and negative controls were used
Eryth_001


title: Drug Hypersensitivity Reaction 010

description:
internal positive and negative controls were used
DHR_010

value: Drug Hypersensitivity Reaction


title: SkMel28_1ug_Dox_R3

city: Oxford

first: Pakavarin

last: Louphrasitthiphol

address: Old Road Campus Research Building (off Roosevelt Drive)

department: Nuffield Department of Clinical Medicine

country: United Kingdom

institute: Ludwig Institute for Cancer Research

data_processing:
Basecalling, demultiplexing were carried out by the Wellcome Trust Genomic Service, Oxford
Quality of the raw sequencing data was evaluated using FastQC (v.0.11.7)
Adapter contamination removed using CutAdapt (v.2.8) and mapped to the human reference genome (hg38) with STAR (version 2.5.1b)
Normalisation and differential gene expression analyses were performed as previously described (PMID: 31207090, 31733993, 31595650) using edgeR glmQLFTest.
Assembly: hg38
Supplementary files format and content: .txt (normalised gene expression)

source_name: SkMel 28 (CVCL_0526)

growth_protocol: MeWo cells were maintained in EMEM with 10% FBS while SkMel28 cells were maintained in RPMI with 10% FBS. Both were grown in humidified incubator with 10% CO2

extract_protocol:
Total RNA samplewere prepared using RNeasy Mini Kit (QIAGEN #74106)  according to manufacturer protocol
3' end RNA-seq; 500ng Total RNA was used to generate sequencing library using QuantSeq Forward kit (LEXOGEN #0.15.96) according to the supplier protocol

treatment_protocol: Media with or without 1µg/ml Doxycycline were changed every other day.

value: SkMel 28 (CVCL_0526)

value: Cutaneous melanoma

value: 1µg/ml Doxycycline


title: DBD_machine_B.PRE_A39

city: Barcelona

first: Juanjo

last: Lozano

address: C/ Rosselló 153

department: Plataforma de Bioinformatica

country: Spain

institute: CIBEREHD

description: Liver tissue from DBD_machine_B.PRE_A39

data_processing:
raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and eventually filtered using skewer v0.2.2 (Jiang et al., 2014) for removing the low quality reads and trimming the Illumina adapter if necessary.
Mapping of the reads were obtained using the STAR program against human genome (GRCh38) and the quantification of genes and transcripts were done with the RSEM program using  GENCODE.v26 database .
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: RSEM output (txt)

source_name: Liver

extract_protocol:
For total RNA extraction, cryopreserved liver tissue samples were homogenized in TRIzol reagent (Invitrogen) using bead-beating technology (Tissuelyser, Qiagen) in 1.5 ml reaction tubes (Eppendorf). Total RNA was then extracted following the manufacture’s guidelines. The concentration, purity and quality of the RNA were measured and assessed using Nanodrop (ThermoScientific).
RNA libraries were prepared and amplified using TruSeq stranded mRNA sample preparation with the corresponding kit (Illumina Inc, USA).

value: Liver

value: machine

tag: time

value: PRE


title: sciatic nerve mpzNedd4cKO mouse 4

city: Zurich

first: Jorge

middle: A.

last: Pereira

address: Otto-Stern-Weg 7

department: Dep. of Biology

institute: ETH Zurich

data_processing:
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20) using Trimmomatic (Version 0.36).
Sequence pseudoalignment of the resulting high-quality reads to the Mouse reference genome (build GRCm38.p6 with the gene annotations downloaded on 2019-11-05 from GENCODE M23) and quantification of transcript level expression was carried out using Kallisto (Version 0.44).
The Kallisto options were "--bias --bootstrap-samples 10 --seed 42 --single --rf-stranded --fragment-length 150 --sd 70".
Assembly: mm10/GRCm38.p6
Supplementary files format and content: tab-delimited txt-file including Raw and normalized Transcript Counts from Kallisto

source_name: Schwan cells

extract_protocol:
Immediately after dissection, sciatic nerves were placed in ice-cold PBS, the epineurium and perineurium were removed as much as possible, and nerves were snap-frozen in 1.5ml microcentrifugation tubes using liquid nitrogen. Prior to RNA purificaton, the endoneurium-enriched nerves were mechanically grinded to a powder while frozen using an RNAse free pestle. Total RNA was extracted using Qiazol, for as per manufacturer’s instructions.
RNA libraries were prepared for sequencing using Illumina's TruSeq Stranded mRNA

value: Schwan cells

tag: age


title: SkMel28_1ug_Dox_R2


title: DBD_machine_B.PRE_A31

description: Liver tissue from DBD_machine_B.PRE_A31


title: sciatic nerve mpzNedd4cKO mouse 3


title: sciatic nerve mpzNedd4cKO mouse 2


title: SkMel28_0ug_Dox_R3


title: SkMel28_1ug_Dox_R1


title: Drug Hypersensitivity Reaction 009

description:
internal positive and negative controls were used
DHR_009

data_processing: Data were normalized and log2 transformed using nSolver® 4.0 (Nanostring Technologies). Basically, housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library


title: Erythroderma 005

description:
internal positive and negative controls were used
Eryth_005


title: Drug Hypersensitivity Reaction 008

description:
internal positive and negative controls were used
DHR_008


title: HYST64 Control

description: Raw files contain poly A tail, protein and sample multiplexing libraries. References for protein (AbSeq) sequences and sample multiplexing (SampleTag) are provided in supplementary file  "HYST64_Control_feature_reference.csv". Sample multiplexing annotations are provided in supplementary file "HYST64_Control_SampleTagCalls.csv"

value: Female genital tract tissue


title: DBD_machine_B.PRE_A13

description: Liver tissue from DBD_machine_B.PRE_A13


title: DBD_machine_B.PRE_A11

description: Liver tissue from DBD_machine_B.PRE_A11


title: sciatic nerve Control mouse 4


title: SkMel28_0ug_Dox_R2


title: sciatic nerve mpzNedd4cKO mouse 1


title: Drug Hypersensitivity Reaction 007

description:
internal positive and negative controls were used
DHR_007


title: Drug Hypersensitivity Reaction 006

description:
internal positive and negative controls were used
DHR_006


title: DBD_machine_B.PRE_A09

description: Liver tissue from DBD_machine_B.PRE_A09


title: MeWo_1ug_Dox_R3

source_name: MeWo (CVCL_0445)

value: MeWo (CVCL_0445)


title: DBD_machine_B.PRE_A05

description: Liver tissue from DBD_machine_B.PRE_A05


title: sciatic nerve Control mouse 2


title: Drug Hypersensitivity Reaction 004

description:
internal positive and negative controls were used
DHR_004


title: DBD_machine_B.POST_A40

description: Liver tissue from DBD_machine_B.POST_A40

value: POST


title: sciatic nerve Control mouse 1


title: MeWo_1ug_Dox_R1


title: Drug Hypersensitivity Reaction 003

description:
internal positive and negative controls were used
DHR_003


title: DBD_machine_B.PRE_A21

description: Liver tissue from DBD_machine_B.PRE_A21


title: DBD_machine_B.POST_A32

description: Liver tissue from DBD_machine_B.POST_A32


title: MeWo_0ug_Dox_R3


title: TR2

city: Shen Zhen

first: Shu

last: Chen

address: Nanshan

institute: Tsinghua University

data_processing:
The sequencing data were filtered with SOAPnuke (v1.5.2) followed by mapping to the reference genome using HISAT2 (v2.0.4). Differential expression analysis was performed using the DESeq2 (v1.4.5) with Q value ≤0.05.
Assembly: NCBI: GCF_000001405.39_GRCh38.p13

source_name: Tumor

extract_protocol:
Cells were washed with cold PBS and collected in TRIzol reagent (Thermo Fisher) on ice. > 2 µg of total RNA was used for the construction of sequencing libraries
RNA-sequencing libraries was subsequently constructed by BGI (Shenzhen, China).

value: Tumor

value: epithelial cells

value: WT

value: tamoxifen


title: MeWo_0ug_Dox_R2

value: Control


title: DBD_machine_B.POST_A14

description: Liver tissue from DBD_machine_B.POST_A14


title: DBD_machine_B.POST_A22

description: Liver tissue from DBD_machine_B.POST_A22


title: Drug Hypersensitivity Reaction 001

description:
internal positive and negative controls were used
DHR_001

extract_protocol: mRNA expression of 600 targets was analysed with the nCounter Human Immunology V2 panel including 20 customized probes (Nanostring Technologies, Seattle, WA, USA) on the nCounter® platform (Nanostring Technologies) using 100 ng of RNA per skin sample.


title: MeWo_0ug_Dox_R1


title: TD2


title: Dissecant Cellulitis 003

description:
internal positive and negative controls were used
DC_003

value: Dissecant Cellulitis


title: SkMel28_0ug_Dox_R1


title: TD1


title: sciatic nerve Control mouse 3


title: Drug Hypersensitivity Reaction 005

description:
internal positive and negative controls were used
DHR_005

value: Drug Hypersensitivity Reaction


title: TR1


title: Dissecant Cellulitis 002

description:
internal positive and negative controls were used
DC_002


title: CHDControl

city: Helsinki

first: Martin

last: Broberg

address: Viikinkaari 5D

department: Biosciences

country: Finland

institute: University of Helsinki

description:
Pluripotent cardiomyocytes
Control
Single-cell RNA sequencing

data_processing:
Data processing and analysis were performed using 10X Genomics Cell Ranger v2.1.1 pipelines.
The “cellranger mkfastq” pipeline was used to produce FASTQ (raw data) files.
The “cellranger count” was used to perform alignment, filtering and UMI counting.
Mkfastq was run using the Illumina bcl2fastq v2.2.0 and alignment was done against human genome GRCh38.
Cellranger “aggr” pipeline was used to combine data from multiple samples into an experiment-wide gene-barcode matrix and analysis.
Genome_build: GRCh38
Supplementary_files_format_and_content: *_possorted_genome_RNAcounts.txt: RNA abundances tables for identified cells.

source_name: Human induced pluripotent stem cell

extract_protocol:
The cell lines were differentiated to hiPS-CMs as previously described (Helle et al., 2021). Briefly, Wnt-pathway activation and inactivation were used to induce differentiation, and metabolic selection with media containing lactate instead of glucose was used to ensure purity of the CM culture. The cells were processed for single-cell sequencing as described previously (Helle et al., 2021). The cells were detached using Multi Tissue Dissociation Kit 3 (130-110-204, Miltenyi Biotec), according to the manufacturer’s instructions. The cells were washed once with PBS containing 0.04% BSA, and then resuspended in PBS with 0.04% BSA to a concentration of 2.0 × 10^6 cells/ml. The cells were passed through a 35 μm strainer (352235, Corning) and combined into two samples (one containing cells from healthy individuals, one containing patient cells) and placed on ice until continuation of the 10× Genomics Single Cell Protocol.
The Chromium Single Cell 3′ RNAseq run and library preparation were made using the Chromium Single Cell 3′ Reagent version 3 chemistry.

tag: diagnosis

value: Healthy control

value: hiPSC-CM


title: TC2

value: vehicle


title: MeWo_1ug_Dox_R2

value: Cutaneous melanoma

value: 1µg/ml Doxycycline


title: DBD_machine_B.POST_A10

description: Liver tissue from DBD_machine_B.POST_A10

value: Liver

value: machine


title: Dissecant Cellulitis 001

description:
internal positive and negative controls were used
DC_001


title: CHDCases

description:
Pluripotent cardiomyocytes
Cases
Single-cell RNA sequencing

value: Congenital heart disease


title: DBD_machine_B.POST_A06

description: Liver tissue from DBD_machine_B.POST_A06


title: TC1


title: Cutaneous Lupus Erythematosus 019

description:
internal positive and negative controls were used
CLE_019

value: Cutaneous Lupus Erythematosus


title: FR2

value: fulvestrant


title: DBD_cold_B.PRE_A47

description: Liver tissue from DBD_cold_B.PRE_A47

value: cold

value: PRE


title: Drug Hypersensitivity Reaction 002

description:
internal positive and negative controls were used
DHR_002


title: STN23_334

data_processing:
cDNA library was constructed using the ribosomal depletion methods, and reads were sequenced in 120 bp paired-end sequences per the Illumina 1.9 encoding Novogene protocols
Sample data integrity was examined using FASTQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/, version 0.11.9) for quality control of fastq files.
Sequence reads were then mapped to the UCSC rn6 rat reference genome using HISAT2
Gene counts were generated from the BAM files using SummarizedExperiments (version 1.28.0) with the UCSC Rattus Norvegicus (rn6) reference genome
Assembly: Rn6
Supplementary files format and content: CSV file includes raw counts for each sample

organism: Rattus norvegicus

source_name: striatum

growth_protocol: 28-day-old male and female Sprague-Dawley rats (Charles River, Wilmington, MA) were allowed to acclimate for 8 days, followed by a 30 min and a 2 h training day in the nose-only apparatus. All rats were provided food (sterile Teklad 5% stock diet, Harlan, Madison, WI) and water ad libitum. 24 Rats were weighed and assigned to the sham or PCB52 exposure groups using a random number generator at 39 days of age for males and 42 days of age for females to begin PCB52 exposure

extract_protocol:
Tissue punches collected from brain regions of interest were rinsed with PBS and placed in a lysing matrix tube containing 1 mL of TRIzol. Sample solutions were then aliquoted to RNeasy spin columns, followed by the QIAGEN RNeasy Kits protocol to clean and isolate RNA from the tissue samples.
mRNA enrichment: poly (A) capture or rRNA removal

treatment_protocol: Animals were exposed for 4 h daily for 28 days to PCB52 using a nose-only inhalation system by passing dried, high-efficiency particulate air (HEPA)-filtered air through the PCB52-coated glass beads at a flow rate of 12 L/min,

value: striatum

value: Male

value: Sprague-Dawley


title: STN22_359

value: Female


title: DBD_machine_B.POST_A12

description: Liver tissue from DBD_machine_B.POST_A12

value: POST


title: DBD_cold_B.PRE_A41

description: Liver tissue from DBD_cold_B.PRE_A41


title: DBD_cold_B.PRE_A33

description: Liver tissue from DBD_cold_B.PRE_A33


title: Cutaneous Lupus Erythematosus 016

description:
internal positive and negative controls were used
CLE_016


title: Cutaneous Lupus Erythematosus 018

description:
internal positive and negative controls were used
CLE_018


title: FD2

value: Tumor

value: epithelial cells

value: WT


title: STN21_087


title: Cutaneous Lupus Erythematosus 017

description:
internal positive and negative controls were used
CLE_017


title: FR1


title: DBD_cold_B.PRE_A27

description: Liver tissue from DBD_cold_B.PRE_A27


title: DBD_cold_B.PRE_A25

description: Liver tissue from DBD_cold_B.PRE_A25


title: STN20_591


title: FD1


title: FC2

value: vehicle


title: DBD_cold_B.PRE_A19

description: Liver tissue from DBD_cold_B.PRE_A19


title: Cutaneous Lupus Erythematosus 015

description:
internal positive and negative controls were used
CLE_015


title: Cutaneous Lupus Erythematosus 014

description:
internal positive and negative controls were used
CLE_014


title: STN24_332


title: Cutaneous Lupus Erythematosus 013

description:
internal positive and negative controls were used
CLE_013


title: DBD_cold_B.PRE_A07

description: Liver tissue from DBD_cold_B.PRE_A07


title: FC1


title: Cutaneous Lupus Erythematosus 012

description:
internal positive and negative controls were used
CLE_012


title: DBD_cold_B.PRE_A03

description: Liver tissue from DBD_cold_B.PRE_A03


title: STN17_768


title: STN18_771


title: Erythroderma 028

description:
internal positive and negative controls were used
Eryth_028

value: Erythroderma


title: 202312794_06

type: genomic

city: Miami

first: Lily

last: Wang

address: 1120 NW 14th St

institute: University of Miami

description: study sample

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridized to Illumina MethylationEPIC v2.0 BeadChip using standard Illumina protocol.

scan_protocol: Standard recommended Illumina scanner setting.

data_processing:
idat files were read using minfi::read.metharray.exp, converted to beta values with minfi::getBeta
The beta.csv contains beta values

label: Cy3 and Cy5

molecule: genomic DNA

label_protocol: Standard Illumina Protocol.

extract_protocol: Bisulfite conversion of genomic DNA from peripheral blood was performed using the EZ DNA methylation kit according to manufacturer's instructions (Zymo Research).


title: 202312793_06

description: study sample


title: STN16_873


title: DBD_cold_B.PRE_A01

description: Liver tissue from DBD_cold_B.PRE_A01

value: Liver


title: 202312792_11

description: study sample


title: Cutaneous Lupus Erythematosus 011

city: Lausanne

first: JEREMY

last: DI DOMIZIO

address: Av Boveresses 155, 1066 Epalinges

institute: CHUV

description:
internal positive and negative controls were used
CLE_011


title: 202312790_12

description: study sample


title: Cutaneous Lupus Erythematosus 010

description:
internal positive and negative controls were used
CLE_010


title: STN15_052


title: 202312789_12

description: study sample


title: STN19_067


title: Cutaneous Lupus Erythematosus 009

description:
internal positive and negative controls were used
CLE_009


title: STN14_338


title: DBD_cold_B.POST_A42

description: Liver tissue from DBD_cold_B.POST_A42


title: DBD_cold_B.POST_A34

description: Liver tissue from DBD_cold_B.POST_A34


title: Cutaneous Lupus Erythematosus 008

description:
internal positive and negative controls were used
CLE_008


title: STN12_637

value: Sham


title: STN13_79


title: Cutaneous Lupus Erythematosus 007

description:
internal positive and negative controls were used
CLE_007


title: 202312787_12

description: study sample


title: DBD_cold_B.POST_A28

description: Liver tissue from DBD_cold_B.POST_A28


title: STN11_288


title: 202312788_12

description: study sample


title: 202312785_12

description: study sample


title: Cutaneous Lupus Erythematosus 005

description:
internal positive and negative controls were used
CLE_005


title: Cutaneous Lupus Erythematosus 006

description:
internal positive and negative controls were used
CLE_006


title: 202312786_12

description: study sample


title: DBD_cold_B.POST_A20

description: Liver tissue from DBD_cold_B.POST_A20


title: STN9_341


title: 202312783_12

description: study sample


title: DBD_cold_B.POST_A08

description: Liver tissue from DBD_cold_B.POST_A08


title: Cutaneous Lupus Erythematosus 004

description:
internal positive and negative controls were used
CLE_004


title: DBD_cold_B.POST_A48

description: Liver tissue from DBD_cold_B.POST_A48


title: STN8_012


title: Cutaneous Lupus Erythematosus 003

description:
internal positive and negative controls were used
CLE_003


title: DBD_cold_B.POST_A04

description: Liver tissue from DBD_cold_B.POST_A04


title: 202312782_13

description: study sample


title: 202312781_12

description: study sample


title: DBD_cold_B.POST_A02

description: Liver tissue from DBD_cold_B.POST_A02


title: Cutaneous Lupus Erythematosus 002

description:
internal positive and negative controls were used
CLE_002


title: STN7_347


title: STN6_367


title: PDX-M2 tumor (J000111056, 6th generation)

city: Taichung

first: Tzu-Chun

last: Cheng

state: --- Select One ---

address: Address: No. 100, Section 1, Jingmao Road, Beitun District

country: Taiwan

institute: China Medical University

data_processing:
processing:trimmomatic v0.39
reading map:bowtie2 v2.3.4.1
quantification:RSEM v1.2.28
differential expression analysis:EBSeq v1.16.0
enrichment analysis:clusterprofiler v3.6.0
Assembly: reference genome hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: breast cancer tumor tissue

growth_protocol: PDX tumors were transplanted into the mammary gland of NSG mice.

extract_protocol:
RNA was harvested using a TRIzol reagent. One mg of total RNA was used to construct the sequencing library.
following TruSeq Stranded mRNA Library Prep Kit protocol

treatment_protocol: No treatment

value: breast cancer tumor tissue

value: Mammary Epithelial Cells

value: Control

value: No

tag: generation

value: 6th generation


title: 202312780_12

description: study sample


title: DBD_cold_B.POST_A26

description: Liver tissue from DBD_cold_B.POST_A26

value: cold


title: PDX-M1 tumor (J000100674, 6th generation)


title: Cutaneous Lupus Erythematosus 001

description:
internal positive and negative controls were used
CLE_001

value: Cutaneous Lupus Erythematosus


title: Bullous Pemphigoid 017

description:
internal positive and negative controls were used
BP_017

value: Bullous Pemphigoid


title: control_BIOT.021_CTR_72hrs_3

city: Brno

first: Martina

last: Zapletalová

address: Kamenice 5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

data_processing:
FastQC
Trim Galore
Rbowtie2
Rsamtools
DeSeq2
Assembly: hg38
Supplementary files format and content: tab-delimited file includes raw count for each sample

source_name: iPSC-derived astrocyte

growth_protocol: The hiPSC-derived neural progenitor cells (NPCs) were propagated for at least 10 days in a completed neural maintenance medium. Cells were passaged with Accutase upon reaching confluence, and they were plated into poly-ornithine-laminin (POL)-coated plates with a seeding density of 50.000-150.000 cells/cm2. NPCs were seeded into matrigel-coated plates on day 14. To initiate the generation of astroglial progenitor cells (APCs), the culture medium was changed to medium into astrocyte growth medium the next day. The medium was changed every other day until the 21st day of differentiation. At the 21st day of astrocyte induction, APCs were seeded into matrigel-coated plates in an astrocyte induction medium with a density of 25.000-50.000 cells/cm2. The next day the medium was switched to astrocyte maturation medium, which was changed every other day until day 42.

extract_protocol:
Total RNA from cellular pellet samples was isolated using TRI Reagent (Merck, USA) with RapidOutput DNA removal kit (ThermoFisher Scientific, USA).
The quantity and quality of RNA extracts were analyzed by using a Qubit 4 fluorometer (ThermoFisher Scientific, USA) and Fragment Analyzer (Agilent, USA). Complementary DNA (cDNA) libraries were synthesized using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, UK). RNA sequencing was performed on the Illumina NovaSeq 6000 platform with the NovaSeq S4 300 kit generating 150 bp pair-end reads (Illumina, USA).

value: female

value: iPSC-derived astrocyte

value: control, healthy

value: non-treated

tag: donor

value: healthy, 70-years old, female


title: Bullous Pemphigoid 016

description:
internal positive and negative controls were used
BP_016


title: STN10_638

city: Coralville

first: Amanda

last: Bullert

address: 2501 Crosspark Rd

institute: UNIVERSITY OF IOWA

value: striatum

value: Female

value: Sprague-Dawley


title: STN5_115

value: Male

value: Sham


title: STN3_818


title: Bullous Pemphigoid 015

description:
internal positive and negative controls were used
BP_015


title: 202312777_12

description: study sample


title: control_BIOT.021_CTR_72hrs_1


title: STN2_797


title: Bullous Pemphigoid 014

description:
internal positive and negative controls were used
BP_014


title: 202312776_11

description: study sample


title: control_BIOT.009_CTR_72hrs_3

value: healthy, 35-years old, female


title: CBLM24_332

source_name: cerebellum

value: cerebellum


title: control_BIOT.009_CTR_72hrs_2


title: Bullous Pemphigoid 012

description:
internal positive and negative controls were used
BP_012


title: Bullous Pemphigoid 013

description:
internal positive and negative controls were used
BP_013


title: 202312774_12

description: study sample


title: 202312775_12

description: study sample


title: CBLM23_334


title: control_BIOT.009_CTR_72hrs_1


title: 202312773_12

description: study sample


title: 202312778_12

description: study sample


title: 202312779_12

description: study sample


title: human white adipocyte cell line, Mettl14 KD, m6A IP, biol rep 3

description:
hWAT.siKD.RADAR.csv
CF10IP

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Cutadapt (4.2)
Trimmed sequence reads were mapped to mm10 using HISAT2 (2.2.1).
Read count extraction and differential expression levels of exons and genes were analyzed using RADAR (0.2.4) followed by DEseq2 (1.36.0).
For differential m6A regions of mRNA, RADAR software (0.2.4) was used as well.
Assembly: mm10 (GRCm38.102), hg38 (GRCh38.107)
Supplementary files format and content: DESeq2 results with normalized reads for each sample and m6A analysis results from RADAR

source_name: white adipocyte cell

value: METTL 14 knockdown

value: white adipocyte cell


title: Bullous Pemphigoid 010

description:
internal positive and negative controls were used
BP_010


title: 202312772_12

description: study sample


title: Bullous Pemphigoid 009

description:
internal positive and negative controls were used
BP_009


title: human white adipocyte cell line, Mettl14 KD, m6A IP, biol rep 2

description:
hWAT.siKD.RADAR.csv
CF09IP


title: STN4_308


title: CBLM21_087


title: 202312771_12

description: study sample


title: Bullous Pemphigoid 011

description:
internal positive and negative controls were used
BP_011


title: control_BIOT.021_CTR_72hrs_2


title: STN1_022


title: CBLM20_591


title: Bullous Pemphigoid 008

description:
internal positive and negative controls were used
BP_008


title: CBLM22_359


title: human white adipocyte cell line, Mettl14 KD, m6A IP, biol rep 1

description:
hWAT.siKD.RADAR.csv
CF08IP


title: 202312770_12

description: study sample


title: CBLM19_067


title: human white adipocyte cell line, Mettl14 KD, input, biol rep 3

description:
hWAT.siKD.RADAR.csv
hWAT.siKD.Deseq2.csv
CF10C


title: Bullous Pemphigoid 007

description:
internal positive and negative controls were used
BP_007


title: 202312769_12

description: study sample


title: CBLM18_771


title: Bullous Pemphigoid 006

description:
internal positive and negative controls were used
BP_006


title: 202312768_12

description: study sample


title: human white adipocyte cell line, Mettl14 KD, input, biol rep 2

description:
hWAT.siKD.RADAR.csv
hWAT.siKD.Deseq2.csv
CF09C


title: CBLM16_873


title: human white adipocyte cell line, Mettl14 KD, input, biol rep 1

description:
hWAT.siKD.RADAR.csv
hWAT.siKD.Deseq2.csv
CF08C


title: Bullous Pemphigoid 005

description:
internal positive and negative controls were used
BP_005


title: 202312767_12

description: study sample


title: human white adipocyte cell line, Mettl14 KO, m6A IP, biol rep 4

description:
hWAT.RADAR.csv
CF07IP

value: METTL 14 knockout


title: Bullous Pemphigoid 004

description:
internal positive and negative controls were used
BP_004


title: Bullous Pemphigoid 003

description:
internal positive and negative controls were used
BP_003


title: CBLM14_338


title: 202312765_12

description: study sample


title: human white adipocyte cell line, Mettl14 KO, m6A IP, biol rep 3

description:
hWAT.RADAR.csv
CF06IP


title: CBLM15_052


title: 202312764_12

description: study sample


title: CBLM13_79


title: human white adipocyte cell line, Mettl14 KO, m6A IP, biol rep 2

description:
hWAT.RADAR.csv
CF05IP


title: Bullous Pemphigoid 002

description:
internal positive and negative controls were used
BP_002


title: CBLM12_637


title: Bullous Pemphigoid 001

description:
internal positive and negative controls were used
BP_001


title: human white adipocyte cell line, Control, m6A IP, biol rep 3

description:
hWAT.RADAR.csv
hWAT.siKD.RADAR.csv
hWAT_hBAT.RADAR.csv
CF03IP

value: WT


title: Atopic Dermatitis 058

description:
internal positive and negative controls were used
AD_058

value: Atopic Dermatitis


title: 202312762_13

description: study sample


title: 202312763_12

description: study sample


title: CBLM10_638


title: Atopic Dermatitis 057

description:
internal positive and negative controls were used
AD_057


title: 202312766_12

description: study sample


title: 202312760_12

description: study sample


title: 202312761_12

description: study sample


title: Atopic Dermatitis 056

description:
internal positive and negative controls were used
AD_056


title: human white adipocyte cell line, Control, m6A IP, biol rep 1

description:
hWAT.RADAR.csv
hWAT.siKD.RADAR.csv
hWAT_hBAT.RADAR.csv
CF01IP


title: CBLM9_341


title: human white adipocyte cell line, Mettl14 KO, input, biol rep 4

description:
hWAT.RADAR.csv
hWAT.Deseq2.csv
CF07C


title: CBLM8_012


title: 202312759_12

description: study sample


title: Atopic Dermatitis 055

description:
internal positive and negative controls were used
AD_055


title: CBLM7_347


title: 202312750_06

description: study sample

source_name: Blood:Buffy Coat

value: Blood:Buffy Coat


title: Atopic Dermatitis 054

description:
internal positive and negative controls were used
AD_054


title: human white adipocyte cell line, Mettl14 KO, input, biol rep 3

description:
hWAT.RADAR.csv
hWAT.Deseq2.csv
CF06C


title: Atopic Dermatitis 053

description:
internal positive and negative controls were used
AD_053


title: human white adipocyte cell line, Mettl14 KO, input, biol rep 2

description:
hWAT.RADAR.csv
hWAT.Deseq2.csv
CF05C


title: 202312749_06

description: study sample


title: CBLM11_288


title: human white adipocyte cell line, Mettl14 KO, input, biol rep 1

description:
hWAT.RADAR.csv
hWAT.Deseq2.csv
CF04C


title: CBLM6_367


title: CBLM4_308


title: human white adipocyte cell line, Mettl14 KO, m6A IP, biol rep 1

description:
hWAT.RADAR.csv
CF04IP


title: Atopic Dermatitis 052

description:
internal positive and negative controls were used
AD_052


title: Atopic Dermatitis 051

description:
internal positive and negative controls were used
AD_051


title: human white adipocyte cell line, Control, m6A IP, biol rep 2

description:
hWAT.RADAR.csv
hWAT.siKD.RADAR.csv
hWAT_hBAT.RADAR.csv
CF02IP


title: human white adipocyte cell line, Control, input, biol rep 3

description:
hWAT.RADAR.csv
hWAT.Deseq2.csv
hWAT.siKD.RADAR.csv
hWAT.siKD.Deseq2.csv
hWAT_hBAT.RADAR.csv
hWAT_hBAT.Deseq2.csv
CF03C


title: CBLM3_818


title: 202312746_06

description: study sample


title: human white adipocyte cell line, Control, input, biol rep 2

description:
hWAT.RADAR.csv
hWAT.Deseq2.csv
hWAT.siKD.RADAR.csv
hWAT.siKD.Deseq2.csv
hWAT_hBAT.RADAR.csv
hWAT_hBAT.Deseq2.csv
CF02C


title: Atopic Dermatitis 050

description:
internal positive and negative controls were used
AD_050


title: CBLM2_797


title: human white adipocyte cell line, Control, input, biol rep 1

description:
hWAT.RADAR.csv
hWAT.Deseq2.csv
hWAT.siKD.RADAR.csv
hWAT.siKD.Deseq2.csv
hWAT_hBAT.RADAR.csv
hWAT_hBAT.Deseq2.csv
CF01C


title: 202312745_06

description: study sample


title: Atopic Dermatitis 049

description:
internal positive and negative controls were used
AD_049


title: Atopic Dermatitis 048

description:
internal positive and negative controls were used
AD_048


title: CBLM1_022


title: 202312744_06

description: study sample


title: MHCC97H cells, shUBXN1 .R2

city: Shanghai

first: Kun

last: Jiao

address: No. 800 Dongchuan Road, Shanghai

institute: Shanghai Jiaotong University

data_processing:
Clean data was generated by trimming the adaptor and filtering rRNAs using Seqtk (https://github.com/lh3/seqtk)
Clean reads were mapped to homo genome (GRCh37) with Hisat2(version:2.0.4)
The uniquely mapped fragments of genes were counted by Stringtie(version:1.3.0).
Assembly: GRCh37
Supplementary files format and content: tab-delimited text file includes counts for each gene in each sample

extract_protocol:
Total RNA was extracted using TRIZOL Reagent (Cat#15596-018，Life technologies, Carlsbad, CA, US)following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
RNA libraries were prepared for sequencing using VAHTS mRNA-seq V2 Library Prep Kit for Illumina

value: Liver

value: Hepatocellular carcinoma

value: UBXN1 knockdown


title: 202312748_06

description: study sample


title: Atopic Dermatitis 046

description:
internal positive and negative controls were used
AD_046


title: MHCC97H cells, shUBXN1 .R1


title: 202312747_06

description: study sample


title: 202312742_06

description: study sample


title: CBLM5_115


title: human brown adipocyte cell line, Mettl14 KO, m6A IP, biol rep 1

description:
hBAT.RADAR.csv
CF14IP

source_name: brown adipocyte cell

value: brown adipocyte cell


title: MHCC97H cells, shCon .R2

value: control


title: Atopic Dermatitis 047

description:
internal positive and negative controls were used
AD_047


title: human brown adipocyte cell line, Control, m6A IP, biol rep 3

description:
hBAT.RADAR.csv
hWAT_hBAT.RADAR.csv
CF13IP


title: 202312743_06

description: study sample


title: human brown adipocyte cell line, Control, m6A IP, biol rep 2

description:
hBAT.RADAR.csv
hWAT_hBAT.RADAR.csv
CF12IP


title: MHCC97H cells, shCon .R1


title: Atopic Dermatitis 045

description:
internal positive and negative controls were used
AD_045


title: human brown adipocyte cell line, Control, m6A IP, biol rep 1

description:
hBAT.RADAR.csv
hWAT_hBAT.RADAR.csv
CF11IP


title: Atopic Dermatitis 044

description:
internal positive and negative controls were used
AD_044


title: 202312740_06

description: study sample


title: K195765

city: Lexington

first: Barry

last: Ball

state: Kentucky

address: 108 Gluck Equine Research Center,

department: Veterinary Scinece

institute: University of Kentucky

data_processing:
The Fastq files were evaluated for read quality using FastQC 0.11.8
Trim Galore 0.4.3 was used for adapter and read quality trimming (Phred score threshold of 30).
Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using STAR 2.7.2a (Dobin, Davis et al. 2013)
Reads were annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1
Fragments per kilobase per million (FPKM) were used to determine the expression level of genes
Based on fragments per kilobase of exon (FPKM), all 37 samples were divided into four groups using k-means clustering (R Ver 3.1)
Cuffdiff 2.2.1 was used to calculate differentially expressed genes (DEGs) between samples from theprepartum and postpartum groups
Significance level was set at FDR-adjusted p-value of the test statistic < 0.05 using a Benjamini-Hochberg correction
Genome_build: EquCab 3.0
Supplementary_files_format_and_content: Normalized abundance measurements- Cufflink Gene.FPKM.Tracking

organism: Equus caballus

source_name: Chorioallantois

extract_protocol:
Total RNA was isolated from tissue samples using RNeasy Mini Kit (#74104: Qiagen). RNA concentrations and quantities were confirmed using the Nanodrop 2000 spectrophotometer (ThermoFisher Scientific, MA, USA). Then, RNA integrity was assessed using the Bioanalyzer 2100 system (Agilent Technologies, CA, USA). All samples had a 260/280 ratio >2.0 and RNA integrity number (RIN) >7.0.
A total of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following the manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer (5X). First-strand cDNA was synthesized using random hexamer primer and M- MuLV Reverse Transcriptase (RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, NEBNext Adaptor with hairpin loop structure was ligated to prepare for hybridization. To select cDNA fragments of preferentially 150~200 bp in length, the library fragments were purified with the AMPure XP system (Beckman Coulter, Beverly, USA). Then 3 µl USER Enzyme (NEB, USA) was used with size-selected, adaptor-ligated cDNA at 37 °C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. Finally, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: Chorioallantois

tag: development stage

value: Postpartum


title: human brown adipocyte cell line, Mettl14 KO, input, biol rep 2

description:
hBAT.RADAR.csv
hBAT.Deseq2.csv
CF15C

extract_protocol:
Total RNA was then extracted from iBAT/iWAT by TRIzol. 1 μg of mRNAs was isolated from total RNA using a Dynabeads mRNA DIRECT purification kit (Thermo Fisher). Then, mRNA was adjusted to about 10 ng μl−1 in 100 μl and fragmented using a Bioruptor ultrasonicator (Diagenode) with 30 s on/off for 30 cycles. m6A immunoprecipitation (m6A-IP) and library preparation were performed using the EpiMark N6-Methyladenosine enrichment kit (NEB).
RNA libraries for RNA-seq were prepared using TruSeq RNA Library Prep Kit following manufacturer's protocols.


title: Atopic Dermatitis 043

description:
internal positive and negative controls were used
AD_043

source_name: skin biopsy


title: human brown adipocyte cell line, Mettl14 KO, m6A IP, biol rep 2

description:
hBAT.RADAR.csv
CF15IP


title: 202312739_07

description: study sample

tag: tissue


title: 202312738_06

description: study sample


title: Atopic Dermatitis 042

description:
internal positive and negative controls were used
AD_042


title: human brown adipocyte cell line, Mettl14 KO, input, biol rep 1

description:
hBAT.RADAR.csv
hBAT.Deseq2.csv
CF14C


title: K195691


title: 202312737_06

description: study sample


title: human brown adipocyte cell line, Control, input, biol rep 3

description:
hBAT.RADAR.csv
hBAT.Deseq2.csv
hWAT_hBAT.RADAR.csv
hWAT_hBAT.Deseq2.csv
CF13C


title: Atopic Dermatitis 040

description:
internal positive and negative controls were used
AD_040


title: 202312741_06

description: study sample


title: K194844


title: human brown adipocyte cell line, Control, input, biol rep 1

description:
hBAT.RADAR.csv
hBAT.Deseq2.csv
hWAT_hBAT.RADAR.csv
hWAT_hBAT.Deseq2.csv
CF11C


title: Atopic Dermatitis 038

description:
internal positive and negative controls were used
AD_038


title: human brown adipocyte cell line, Control, input, biol rep 2

description:
hBAT.RADAR.csv
hBAT.Deseq2.csv
hWAT_hBAT.RADAR.csv
hWAT_hBAT.Deseq2.csv
CF12C


title: 202312735_06

description: study sample


title: RPE1_PEBP1_KO_oligomycin_3

city: Haining

first: Mikael

last: Bjorklund

address: International Campus

institute: Zhejiang University-University of Edinburgh Institute

data_processing:
After removal of poor-quality reads, the remaining reads were mapped against human transcriptome (Ensembl v100) using Salmon to obtain transcript abundances. Gene level summaries were generated by tximport. Differential gene expression analysis was done using DESeq2 from vst normalized counts.
Assembly: human transcriptome (Ensembl v100)
Supplementary files format and content: Vst normalized counts from DESeq2 output

growth_protocol: RPE1 control KO and PEBP1 KO cells were seeded at the density of 0.6x105 cells/ml in a 10cm dish. Cells were incubated at 37℃ 5% CO2 for 42h to reach ~90% confluence.

extract_protocol:
Cells were washed twice with PBS and lysed in 1 ml TRIzol on ice. Lysates were frozen in liquid nitrogen and stored at -80℃.
RNA library preparation and sequencing was performed at Novogene (Beijing). Briefly, sequencing libraries were generated from total RNA using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, Cat.No. E7530L) following manufacturer’s recommendations. After random fragmentation, 370~420 bp cDNA fragments were selected for paired end sequencing of 150bp.

treatment_protocol: Three dishes of control and PEBP1 KO cells were treated with 1uM Oligomycin A or equal volume of DMSO as control for 6 hours.

value: PEBP1 knockout

value: Oligomycin (1microM)


title: Atopic Dermatitis 041

description:
internal positive and negative controls were used
AD_041


title: 202312734_06

description: study sample


title: L061

value: Prepartum (330 d GA)


title: Atopic Dermatitis 039

description:
internal positive and negative controls were used
AD_039


title: Atopic Dermatitis 037

description:
internal positive and negative controls were used
AD_037


title: 202312733_06

description: study sample


title: 202312736_06

description: study sample


title: K069


title: K193967


title: L045


title: Atopic Dermatitis 036

description:
internal positive and negative controls were used
AD_036


title: RPE1_PEBP1_KO_oligomycin_2


title: 202312732_06

description: study sample


title: RPE1_PEBP1_KO_oligomycin_1


title: 202312731_06

description: study sample


title: RPE1_PEBP1_KO_3

value: DMSO


title: Atopic Dermatitis 035

description:
internal positive and negative controls were used
AD_035


title: CMT2 with V1200R mutation in ddcc Line3

city: St Louis

first: Xuehua

last: Zhong

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

library_source: genomic

data_processing:
For all samples in Col-0 background, sequencing raw reads were trimmed using FASTP and aligned to the Arabidopsis thaliana TAIR10 genome using bsmap version 2.9; allowing 4% mismatches, trimmed anything with a quality score of 33 or less, and removed any reads with more than five N's. Methylation at every cytosine was determined by bsmap's methratio.py script, processing only unique reads and removing duplicates. Differentially methylated regions (DMRs) were identified using methylKit with the cutoffs: 40% difference for CG, 20% for CHG and 10% difference for CHH DMRs, and a p-value <0.01.
For Lhasa-0 BS-seq, reads were filtered for < 5 N, quality trimmed (Phred score >= 30) and alignment was allowed proceed with up to 8% read mismatch. Methylation tracks were created by calling cytosine methylation in all contexts via the methratio.py script removing duplicated reads and including zeros. After alignment via BSMap, 100 bp DMRs were called against 54 wildtype high confidence Arabidopsis libraries via hcDMR caller, accepting only unique mappings and using the -Steve filter.
Assembly: TAIR10
Supplementary files format and content: bigwig file of DNA methylation

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Seedlings were grown on 1/2 MS medium containing 1% sucrose for 10 days in long-day growth conditions (16 hrs light: 8 hours dark) at 22°C. For leaf tissues in Lhasa-0 sample, plants were grown 4 weeks in long-day growth conditions.

extract_protocol:
DNA was extracted using conventional CTAB method.
For bisulfite sequencing, the genomic DNA was fragmented to a mean size of 100-300 bp by sonication using a Covaris S220 focused-ultrasonicator, followed by end-repair, 3'-end adenylation and methylated adaptor ligation using Illumina TruSeq DNA kit. Then, bisulfite conversion was performed using a Zymo EZ DNA Methylation-Lightning kit, and the bisulfite-converted, adaptor-ligated DNA was enriched by PCR for 12 cycles using KAPA HiFi HotStart Uracil+ Kit, purified with Agencourt beads and quantified by Qubit HS dsDNA kit.

value: whole seedling


title: RPE1_PEBP1_KO_2


title: Atopic Dermatitis 034

description:
internal positive and negative controls were used
AD_034


title: 202312730_06

description: study sample


title: RPE1_PEBP1_KO_1


title: Atopic Dermatitis 033

description:
internal positive and negative controls were used
AD_033


title: CMT2 in ddcc Line28


title: 202312728_06

description: study sample


title: Atopic Dermatitis 032

description:
internal positive and negative controls were used
AD_032


title: RPE1_CTRL_KO_oligomycin_3


title: CMT2 in ddcc Line27


title: 202312726_06

description: study sample


title: RPE1_CTRL_KO_oligomycin_2


title: Atopic Dermatitis 031

description:
internal positive and negative controls were used
AD_031


title: 202312725_06

description: study sample


title: drm1 drm2 cmt3 cmt2 mutant in Col-0


title: CMT2 with V1200R mutation in cc Line15


title: RPE1_CTRL_KO_oligomycin_1


title: 202312724_06

description: study sample


title: Atopic Dermatitis 030

description:
internal positive and negative controls were used
AD_030


title: Atopic Dermatitis 029

description:
internal positive and negative controls were used
AD_029


title: CMT2 with V1200R mutation in ddcc Line11


title: H034


title: CMT2 with V1200R mutation in cc Line9


title: 202312723_06

description: study sample


title: Atopic Dermatitis 028

description:
internal positive and negative controls were used
AD_028


title: RPE1_CTRL_KO_2


title: CMT2 in cc Line19


title: Atopic Dermatitis 027

description:
internal positive and negative controls were used
AD_027


title: CMT2 in cc Line1


title: RPE1_CTRL_KO_1


title: 202312721_06

description: study sample


title: Atopic Dermatitis 026

description:
internal positive and negative controls were used
AD_026


title: cmt2 cmt3 mutant in Col-0


title: 202312720_06

description: study sample


title: day 2

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

country: Japan

institute: Kyoto University, Graduate school of medicine

description: human primordial germ cell-like cell (PGCLC) induction from human iPSC 585B1-868 cell line, day 2

data_processing:
Raw data were demultiplexed with the mkfastq command in Cell Ranger (v XXXX) with default setting to generate fastq files. The fastq files were processed with count command in Cell Ranger v5.0.0 with or without "--include-intron" option to map to the reference genome for human GRCh38.p12 (hard masked PAR of chrY).
Resulting "possorted_genome_bam.bam" files were processed with dropEst (v0.8.6) with "-L eiEBA" option and configuration file for 10X data, 10x.xml with modification at “<umi_length>” from 10 to 12 for Chromium Single Cell Kits v3.1 data.
The output .rds files for each sample, including UMI counts for both exon and intron of genes, were imported into R and used for following analysis.
Assembly: GRCh38.p12 (hard masked PAR of chrY)
Supplementary files format and content: csv file containing dropEst output,read count matrix within exonic regions
Supplementary files format and content: csv file containing dropEst output,read count matrix within intronic regions
Supplementary files format and content: R data in h5ad format countaining all file timepoint data
Supplementary files format and content: cellranger output CSV files including UMI counts per genes

source_name: PGCLC

extract_protocol:
All protocols are same as in GSE175525.  The suspension of cells were generated as the same manner with passage or the induction of differentiation.
For the aggregates of PGCLC induction at day 0.5, 1, 1.5 and 2, the aggregates were collected, washed once in PBS, and dissociated with 0.25% Trypsin–EDTA for 10–15 min at 37°C with gentle pipetting every 5 min. Trypsin was neutralized with a 5× volume of 10% FBS in DMEM and washed once with 0.1% BSA in PBS.  Prior to proceeding the scRNA-seq analysis, the live single cells were sorted using FACS Aria III system (BD Biosciences) by FSC-SSC and DRAQ7 (ab109202) staining for iMeLC, or FSC-SSC and EGFP-tdTomato gating with DRAQ7 staining for day 0.5, 1, 1.5 and 2 PGCLCs.
Single-cell RNA-seq libraries of 10X data were generated using the 10X Genomics Chromium Controller (10X Genomics) and Chromium Single Cell 39 Reagent Kits v3.1 according to the manufacturer’s instructions.  The final libraries were quantified using a KAPA library quantification kit (KK4824), and the fragment size distribution of the libraries was determined using a LabChip GX DNA high sensitivity kit (Perkin Elmer).  Pooled libraries were then sequenced using a NovaSeq 6000 Illumina Sequencer with a NovaSeq 6000 S1 Reagent Kit (100 Cycles, 20012865).

value: PGCLC

tag: transgene

value: PRDM1-tdTomato, TFAP2C-EGFP

tag: time point

value: day 2


title: 202312719_06

description: study sample


title: Atopic Dermatitis 025

description:
internal positive and negative controls were used
AD_025

value: Atopic Dermatitis


title: Atopic Dermatitis 024

description:
internal positive and negative controls were used
AD_024


title: day 1.5

description: human primordial germ cell-like cell (PGCLC) induction from human iPSC 585B1-868 cell line, day 1.5

value: day 1.5