title: 4476-JJ-6

city: Nashville

first: Lance

last: Riley

state: TN

address: 9445 MRB4, 2213 Garland Ave

department: Biomedical Engineering

institute: Vanderbilt University

data_processing:
Sequenced reads were mapped and gene counts were quantified using Illumina DRAGEN RNA pipeline v. 3.6.3
Gene count data was compiled using htseq-count
Differential gene expression was determined using DESeq2 using Cook's outliers to filter out low expression and alpha = 0.05 to for significance.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw counts for every gene and every sample.
Supplementary_files_format_and_content: Matrix table with DEseq2 counts for every gene and every sample.

source_name: Aortic root

growth_protocol: C57BL6/J background mice with wild-type or double knockout  of the Sost gene were aged to 4 months on standard chow and then transferred to high-cholesterol diet (TestDiet 5TJT) for 8 months. Food and water was provided ad libitum. Mice lived largely undistrubed except for echocardiography imaging performed at 4, 9, and 12 months of age.

extract_protocol:
Aortic roots were submerged in Trizol reagent and carefully homogenized on ice. RNA samples were isolated using the Zymo Direct-zol RNA Microprep Kit with DNAase treatment without deviation from manufacturer protocols.
Libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kits according to standard protocols.

treatment_protocol: N=3 aortic roots from each experimental group were used for the analysis. Aortic roots were quickly snap frozen in liquid nitrogen after dissection in sterile conditions.

value: Sost-/-

value: 12 mo


title: Myometrial Arteries_4

status: Public on Dec 01 2024

type: SRA

city: Newcastle Upon Tyne

first: Michael

last: Taggart

state: Tyne And Wear

address: International Centre for Life,

department: Biosciences Institute,

country: United Kingdom

institute: Newcastle University

description:
sample_18_S18
MA_4

library_source: transcriptomic

data_processing:
QC checks with FastQC v0.11.9 and FastQ Screen v0.14.1, adapter contamination <0.1% across all samples.
Sequence reads aligned to Homo_sapiens.GRCh38.104 genome using hisat2 v2.2.1
Quantified raw read counts per gene using HTSeq-count version 1.99.2 and Homo_sapiens.GRCh38.104.gtf (genome feature file)
Pre-filter row with at least read count of 21.
Regularised logarithm (rlog) normalisation using DESeq2.
Assembly: Homo_sapiens.GRCh38.104
Supplementary files format and content: normalised_counts.csv-  Comma-seperated text file consists of normalised counts of each samples
Supplementary files format and content: rawCountsTable.csv- Comma-sperated text file consists of un-normalised raw counts of each samples

molecule: total RNA

organism: Homo sapiens

source_name: myometrial arteries

extract_protocol:
Tissue pieces weighed about 3.5mg to 5mg was used for RNA extraction. RNA was extracted using Rneasy Micro Kit (QIAGEN 74004) according to the manufacturer's instructions.
RNA library was prepared  using standard illumina protocols.

tag: tissue

value: myometrial arteries


title: M_PH7.15_bio_rep_2

city: Memphis

middle: A

last: Dyer

state: Tennessee

address: 262 Danny Thomas

department: DNB

country: USA

institute: St. Jude Children's Research Hospital

data_processing:
Read alignment to the reference genome was performed with STAR (version 2.7; PMID: 23104886) software. Gene level quantification was determined using RSEM (version 1.3.1 ; PMID: 21816040).
Assembly: mm10-mouse / GRCh38 – human
Supplementary files format and content: tab delimited text file with raw counts for each sample

organism: Mus musculus

source_name: retina

extract_protocol:
Retinal punches were dissolved in 800uL Trizol Reagent (Invitrogen #15596026). 200uL chloroform was added to each sample, inverted, incubated at room temperature for 3 minutes. Samples were then spun down at 12,000 3 g at 4 C for 15 min. The aqueous later was transferred to a new tube and 1uL glycogen and 500 uL isopropanol was added to each sample and mixed by vortex. Samples were incubated at room temperature for 10 minutes and spun down at 12,000 3 g at 4 C for 15 min. The isopropanol was removed and the pellet was washed twice with ice-cold 80% EtOH. The washed pellet was resuspened in water.
Libraries were constructed using Illumina library prep acording to manufacturer protocols

treatment_protocol: Retina were dissected from the eye cup in Retinal Explant Media (REM). 1.5mm punches were taken from each eye using a biopsy punchand were placed on a Nuclepore 1.0uM membrane floating on 2mL of REM in a 12-well dish. The retinal punches were incubated for 24 hours (37C, 5% CO2) for culture control retina. Punches were harvested after 24 hours.

value: retina

tag: strain

tag: treatment

value: 24 hour culture in REM at pH 7.15


title: hWJ EV 2

city: Tsukuba shi

first: Neni

last: Anggraeni

state: Ibaraki

address: 1-1-1 Tennodai

country: Japan

institute: University of Tsukuba

data_processing:
FASTQ files were imported to CLC Genomics Workbench (Ver.10.1.1, Qiagen).
Reads were grouped by sequence then matched to miR-base annotated microRNAs (miRbase v21)
Total counts were normalized by adjusting total counts to 1x10^6.
Assembly: mirbase 21
Supplementary files format and content: Microsoft Excel file format, containing gene name, raw read counts and normalized read counts

source_name: Wharton's Jelly

growth_protocol: The cells were culture using EV-depleted medium at 37°C under 5% CO2  for 24 hr and under a hypoxic condition (1%O2)

extract_protocol:
The cell samples were collected, and RNA was purified using Trizol reagent according to the standard protocol. 500 ng of total RNA was applied for sequencing. The NEBNext Small RNA Library Prep Kit was used to build a sequencing small RNA library, which was selected according to size using AMPure beads and verified using a Bioanalyzer DNA High-sensitivity Kit.
NEBNext Small RNA Library Prep Kit, small RNA library

treatment_protocol: Hypoxic condition (1%O2)

value: Wharton's Jelly

tag: cell type

value: Mesenchmal Stem cell

tag: genotype

value: Wild Type

value: treated


title: 4476-JJ-5

tag: age


title: hWJ EV 1


title: Myometrial Arteries_3

description:
sample_17_S17
MA_3


title: M_ Glut _bio_rep_2

value: 24 hour culture in REM + 1mM Glutamate


title: WJ EV 2

value: untreated


title: Myometrial Arteries_2

description:
sample_16_S16
MA_2


title: 4476-JJ-3

value: Sost+/+


title: M_ 40pct _bio_rep_1

value: 24 hour culture in REM at 40% Oxygen


title: WJ EV 1

value: Wild type


title: Myometrial Arteries_1

description:
sample_15_S15
MA_1


title: OA chondrocytes, mitochondrial_3

city: Shanghai

first: Junjie

last: Gao

address: 600 Yishan Road

country: China

institute: Shanghai Sixth People’s Hospital Affiliated to Shanghai Jiao Tong University School of Medicine

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (FPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Data filtering steps.Prior to assembly, the low quality reads(1,reads containing sequencing adaptors; 2,reads containing sequencing primer;3, nucleotide with q quality score lower than 20 )were removed .software CutAdapter,parameters -o 5 -p 100
Read alignment software,software HISAT ,version 2.0 ,parameters -l fr-firststrand -mi 20 -mx 500000 -p 2 -b dta -q phred33-quals -x 9
perform expression level for mRNAs by calculating FPKM.stimate the expression levels of all transcripts.software StringTie ,version 1.3.0,parameters -b dta -q phred33-quals.
Assembly: mmu10
Supplementary files format and content: tab-delimited text file includes FPKM and count values for each Sample

source_name: chondrocytes

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 10 ug of total RNA representing a specific adipose type was subjected to isolate Poly (A) mRNA with poly-T oligoattached magnetic beads (Invitrogen). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (Illumina, San Diego, USA), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Novaseq™ 6000 at the (lc-bio, China) following the vendor's recommended protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: disease state

value: OA

value: chondrocytes

value: wt

value: IL-1β, mitochondria


title: Myometrium_7

description:
sample_14_S14
M_7

source_name: myometrial strips

value: myometrial strips


title: 4476-JJ-2

value: 12 mo


title: OA chondrocytes, mitochondrial_1


title: sample19_24h_infected_RMC113

city: Stanford

first: Halise Busra

last: Cagirici

state: California

address: 300 Pasteur Drive

institute: Stanford University

description: Parse Biosciences

library_source: transcriptomic single cell

data_processing:
The demultiplexing, alignment of raw reads to reference genome, and gene counting were performed using the Parse Biosciences processing pipeline (split-spipe v1.0.3a).
Assembly: GRCh38
Supplementary files format and content: h5ad

source_name: lung

growth_protocol: Lung-organoid-derived monolayers (ALOs) were prepared as outlined in (PMID: 37581931 and PMID: 34463615) and plated in Pneumacult Ex-Plus Medium (StemCell Technologies)

extract_protocol:
ALOs were seeded in 96-well plates at 1x105 cells per well and infected with SARS-CoV-2 (MOI=1) in the presence of 5 μM RMC-113 or 0.1% DMSO. After a 4-hour incubation, the viral inoculum was removed, and cells were washed thoroughly and supplemented with fresh medium with or without the compound. At 4 and 24 hpi, ALOs were washed and then detached via 5-min incubation with TrypLE followed by centrifuguation at 300 g for 10 minutes.
Library was performed according to the manufacturers instructions (Parse Biosciences). Briefly, the pellets were suspended and fixed with Cell fixation solution (Parse, Evercode Fixation, cat: ECF2001, Part number WF303) for 10 minutes followed by incubation with Cell permeabilization Solution (Parse, Evercode Fixation, cat: ECF2001, Part number WF305) for 3 minutes at RT. ALOs were then taken out from BSL3 for single-cell sequencing according to the manufacturer’s instructions (Parse, EvercodeTM WT mini Mega v2). Please find the protocol here- https://support.parsebiosciences.com/hc/en-us/article_attachments/24507636161940

treatment_protocol: ALOs were seeded in 96-well plates at 1x105 cells per well and infected with SARS-CoV-2 (MOI=1) in the presence of 5 μM RMC-113 or 0.1% DMSO for 4 hours and 24 hours.

value: lung

value: AT2, AT1, Basal and NGFR-HOPX-CEACAM6+

tag: time post_infection_(h)

tag: infection

value: SARS-CoV-2 infected

tag: library prep

value: EvercodeTM WT mega v2


title: sample18_24h_infected_DMSO

description: Parse Biosciences

value: DMSO


title: 4476-JJ-1


title: OA chondrocytes, mitochondrial_2


title: OA chondrocytes, vehicle_3

value: IL-1β, vehicle


title: Qpct-ko-placenta-E15-point-5

first: jihong

last: zheng

state: Shanghai

address: Siping Road, Yangpu District

institute: Tongji University

data_processing:
Construction of fastq files were done by sequencing company
Alignment of files to reference genome using cellranger (v5.0.1) count
Converting feature-barcode matrices from sparse format to dense   CSV format using cellranger(v5.0.1) mat2csv
Genome_build: mm10
Supplementary_files_format_and_content: matrix.mtx.gz contains the counts of cells called by cellranger;barcodes.tsv.gz contains the barcode name associated with each cell. The order is the same as the order of entries in matrix.mtx.gz;features.tsv.gz contains the gene name. The order is the same as the order of entries in matrix.mtx.gz

molecule: polyA RNA

source_name: Placenta

growth_protocol: Mice were normally fed individually before sampling

extract_protocol:
Placenta was dissected from freshly prepared placenta tisstue, dissociated into single-cell suspension via protease treatement, FACS sorted to enrich live cells, and then followed by  the 10X Chromium protocols.
Libraries were constructed following the instructions of the 10xGenomics Chromium platform

treatment_protocol: Mice were maintained following the guidelines of  Animal Care and Use at Tongji University

value: Placenta

value: Qpct -/-


title: Myometrium_6

description:
sample_13_S13
M_6


title: sample8_4h_infected_RMC113

description: Parse Biosciences

value: EvercodeTM WT mini v2


title: sample7_4h_infected_DMSO

description: Parse Biosciences


title: Myometrium_5

description:
sample_12_S12
M_5


title: Myometrial Arteries_5

description:
sample_19_S19
MA_5

value: myometrial arteries


title: Myometrium_4

description:
sample_11_S11
M_4


title: WT-placenta-E15-point-5

value: Qpct +/+


title: WJ EV 3

value: Wharton's Jelly

value: Mesenchmal Stem cell

value: Wild Type

value: untreated


title: HeLa,HC10,3

city: Beijing

first: Min

last: Tan

address: XueYuan Road No.37,HaiDian District

institute: Beihang University

data_processing:
SOAPnuke [1](V2.1.0) was used to filter the sequencing data.HISAT2[1] (V2.1.0) was used to compare clean reads with the reference genome, and Bowtie2 [2] (V2.3.5) was used to align the quality controlled sequence to the reference transcription sequence.
Assembly: Using RSEM[1], the bowtie2[2] comparison results were used for statistics, and the number of Reads compared to each transcript of each sample was obtained, and FPKM[3] (Fragments Per Kilobase Per Million bases) conversion was performed.
Supplementary files format and content: CSV

source_name: cervix

extract_protocol:
Total RNA was extracted using the Trizol(Invitrogen, CA, USA), RNA purity and integrity was monitored by NanoDrop 2000 spectrophotometer (NanoDrop Technologies, Wilmington, DE, USA) and a Bioanalyzer 2100 system (Agilent Technologies, CA, USA). RNA contamination was assessed by 1.5% agarose gel
The mRNA was purified from the total RNA using poly-T oligo - attachedmagnetic beads. Sequencing libraries were generated from the purified mRNA usingthe V AHTS Universal V6 RNA-seq Library Kit for MGI (V azyme, Nanjing, China)following the manufacturer's recommendations with unique index codes. The LibraryQubit 3.0 Fluorometer (Lifequantification and size was assessed usingTechnologies, Carlsbad, CA, USA) and Bioanalyzer 2100 system (AgilentTechnologies, CA, USA).

value: cervix

tag: cell line

value: HeLa

value: human cervical cancer cells


title: 4476-JJ-4

value: Sost-/-

value: 12 mo


title: OA chondrocytes, vehicle_2

value: OA

value: chondrocytes

value: wt


title: Myometrium_3

description:
sample_10_S10
M_3

value: myometrial strips


title: M_ Glut _bio_rep_1

value: retina

value: 24 hour culture in REM + 1mM Glutamate


title: sample6_4h_uninfected_RMC113

description: Parse Biosciences

value: lung

value: AT2, AT1, Basal and NGFR-HOPX-CEACAM6+

value: uninfected

value: EvercodeTM WT mini v2


title: OA chondrocytes, vehicle_1

value: IL-1β, vehicle


title: Myometrium_2

description:
sample_09_S09
M_2


title: sample5_4h_uninfected_DMSO

description: Parse Biosciences

value: DMSO


title: HeLa,HC10,1

value: cervix


title: AT2 cells, KO, rep2

first: Lian

last: Li

address: No.1158, Gongyuan East Road, Shanghai

department: Department of Respiratory and Critical Care Medicine

institute: QingPu Branch of Zhongshan Hospital Affiliated to Fudan University

data_processing:
paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30.
3’ adaptor-trimming and low-quality reads removing by cutadapt software (v1.9.3)
The high-quality clean reads were aligned to the mouse reference genome (UCSC MM10) with hisat2 software (v2.0.4).
Guided by the Ensembl gtf gene annotation file, cuffdiff software (v2.2.1, part of cufflinks) was used to get the gene level FPKM as the expression profiles of LncRNA and mRNA, and fold change and p-value were calculated based on FPKM, differentially expressed LncRNA and mRNA were identified.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FKPM values for each Sample

source_name: Lung

growth_protocol: Primary alveolar epithelial type II cells (AT2) were isolated from lungs of 6-month-old WT, Fbxo45-cKO mice by flow cytometry

extract_protocol:
Total RNA (1 μg) was used for removing the rRNAs using Ribo-Zero rRNA Removal Kits (Illumina, San Diego, CA, USA) following the manufacturer's instructions and then was used for the construction of sequencing libraries.
RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).
10 pM libraries were denatured as single-stranded DNA molecules, captured on Illumina flow cells, amplified in situ as clusters and finally sequenced for 150 cycles on Illumina HiSeq Sequencer according to the manufacturer’s instructions.

treatment_protocol: Untreated

value: Lung

value: Fbxo46 knockout

tag: time


title: sample2_24h_uninfected_RMC113

description: Parse Biosciences

value: EvercodeTM WT mini v1


title: Myometrium_1

description:
sample_08_S08
M_1


title: AT2 cells, WT, rep2

value: Primary alveolar epithelial type II cells

value: WT


title: AT2 cells, KO, rep1

value: Fbxo45 knockout


title: HeLa,HC3,2

value: HeLa

value: human cervical cancer cells


title: Placental Arteries_7

description:
sample_07_S07
PA_7

source_name: placental chorionic plate arteries

value: placental chorionic plate arteries


title: sample1_24h_uninfected_DMSO

description: Parse Biosciences


title: HeLa,HC3,3


title: Placental Arteries_6

description:
sample_06_S06
PA_6


title: AT2 cells, WT, rep1


title: HeLa,HC3,1


title: Optimally activated CAR Her2 transduced T cells bio rep 3

city: Tel Aviv

first: Alon

last: Richter

address: Ramat Aviv

department: Pathology

country: Israel

institute: Tel Aviv University

data_processing:
Gene count matrix was analyzed for differential expression using DESeq2 1.24.0
Enrichment analysis was performed on differentially expressed genes (adjusted p-value < 0.05)
using clusterProfiler 3.12.0
KEGG pathway enrichment analysis was performed using GAGE 2.42.0 (27), and visualized with Pathview 1.32.0
Assembly: mm10
Supplementary files format and content: DEoutput_all_07092023.xlsx
Supplementary files format and content: raw counts.csv
Supplementary files format and content: normalized counts.csv

source_name: T cells

extract_protocol:
Qiagene Rneasy micro kit
INCPM mRNA-seq
Illumina NextSeq mid output 150 cycles

value: T cells

tag: transduction

value: CAR Her2

value: Optimally activated


title: HeLa,HC1,2


title: Placental Arteries_5

description:
sample_05_S05
PA_5


title: Optimally activated CAR Her2 transduced T cells bio rep 2


title: Placental Arteries_4

description:
sample_04_S04
PA_4


title: Optimally activated CAR Her2 transduced T cells bio rep 1


title: HeLa,HC10,2


title: Placental Arteries_3

description:
sample_03_S03
PA_3


title: WT_PBS_muscle 2

city: shanghai

first: meng

last: liu

address: 1239,SiPing Road

institute: TongJi University

data_processing:
Sequenced reads were trimmed for adaptor sequence, low quality and low complexity reads, then mapped to mm10 reference genome using hisat2 (v2.1.0) (parameters: --no-discordant --no-mixed --no-unal).
Gene expression for each sample was quantified to read count using GFOLD(v1.1.4).
Genome_build: mm10
Supplementary_files_format_and_content: Tab-delimited text files include read count values for each transcript.

source_name: muscle

extract_protocol:
Total RNA was extracted by TRIzol(Invitrogen).
The RNA sequencing libraries were constructed from the extracted RNA using standard Illumina libraries prep protocols.

tag: status

value: Wild Type

value: admimnistrate PBS


title: Not activated CAR Her2 transduced T cells bio rep 3

value: Not activated


title: beta-arrestin_ko_PBS_muscle


title: WT_DKK1_muscle

value: admimnistrate DKK1


title: beta-arrestin_ko_DKK1_muscle


title: HeLa,HC1,1

value: cervix


title: Placental Arteries_2

description:
sample_02_S02
PA_2


title: HeLa,HC0,3


title: Not activated CAR Her2 transduced T cells bio rep 2


title: Placental Arteries_1

description:
sample_01_S01
PA_1


title: Not activated CAR Her2 transduced T cells bio rep 1


title: Optimally activated Sham transduced T cells bio rep 3

value: Sham


title: HeLa,HC0,1


title: Tumor_PBS_muscle

value: Tumor


title: Tumor_MDC_muscle

value: admimnistrate MDC


title: No treatment_2

city: Kawasaki

first: Tatsuto

last: Kageyama

state: Kanagawa

address: Life Innovation Center, 3-25-22 Tonomachi

institute: Kanagawa Institute of Industrial Science and Technology

data_processing:
Data processing were conducted using NovaSeq Control Software v1.7.5, Real Time Analysis (RTA) v3.4.4, bcl2fastq2 v2.20, and DRAGEN Bio-IT Platform v3.9.3
Assembly: hg18
Supplementary files format and content: tab-delimited text file includes RPKM values for each sample

source_name: hair follicle

growth_protocol: Adult human DP cells were obtained from PromoCell (Heidelberg, Germany), passaged up to passage four with R-STEM in hMSC high-growth medium (EM1; Roto, Japan), and used for 2D culture.

extract_protocol:
Total RNA was extracted using an RNeasy Mini Kit (Qiagen) from DP cells with/without 10 μM OXT treatment for 6 days.
RNA library for RNA-seq were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit for Sequencing and Nextera XT DNA Library Prep Kit

treatment_protocol: Dermal papilla cells (2 × 10^4 cells) were suspended in 0.5 mL EM1 medium supplemented with 0 or 10 μM OXT (Peptide Institute Inc., Japan) and seeded into the wells of a 24-well cell culture plate (Corning Inc., Corning, NY, USA). Gene expression in DP cells was assessed  after 6 days of culture.

value: hair follicle

value: dermal papilla cells

value: control


title: WT_PBS_muscle 1


title: HeLa,HC1,3

value: HeLa


title: No treatment_1


title: HeLa,LC0,3

value: human cervical cancer cells


title: WT_PBS_kindey

source_name: kindney


title: Optimally activated Sham transduced T cells bio rep 2


title: HeLa,LC0,2


title: Oxytocin treatment_2

value: Oxytocin


title: Tumor_PBS_kindey


title: Optimally activated Sham transduced T cells bio rep 1

value: T cells


title: HeLa,LC0,1


title: Sub-optimally activated Sham transduced T cells bio rep 3

value: Sub-optimally activated


title: Oxytocin treatment_1


title: HeLa,HC0,2


title: PBMC, Atopic Dermatitis, PBMC, rep 18

city: Taipei

first: Chen-Hsin

last: Wang

address: Zhongshan S. Rd

country: Taiwan

institute: National Taiwan University Hospital and College of Medicine

data_processing:
CLC Genomics Workbench v 10.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.01)
Trimmed sequence reads were mapped to Human/hg38 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.5 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Supplementary files format and content: Hg38
Supplementary files format and content: tab-delimited text files include FPKM and read count values for each Sample

source_name: PBMC

extract_protocol:
Biopsy sample collection: Lesional and nonlesional (>10cm from active lesions) truncal skin biopsies were obtained from AD patients, while healthy skin samples were taken from healthy controls using either a punch biopsy or a simple fusiform biopsy under Institutional Review Board-approved protocols. The samples were collected and stored in RNA protect Tissue Reagent (Qiagen Mat. No.1017980) before being frozen at -80°C. The biopsy sites showed no signs of infection.
Blood protein quantification: 18 ml of serum were collected individually from each patient and healthy control using two Vacuette tubes (#455051) containing 9 ml of NH Sodium Heparin. The collected samples were centrifuged at 12000 rpm for 10 minutes at room temperature with a slow deceleration. The top layer of plasma was collected and then diluted with HBSS (Corning #21-020-CV) at a ratio of 1:1. The diluted blood was added above the Ficoll layer (4 ml, Cytiva #1714403), and centrifuged at 3000 rpm for 20 minutes at room temperature with a slow deceleration, which separated the PBMC. The PBMC was collected, diluted 2-fold with RPMI (Cytiva #SH30027.02), and then underwent another centrifugation at 2000 rpm for 10 minutes at room temperature. After resuspending the cells, 10% DMSO (Cell Signaling #12611S) was added to the sample, which was then frozen. To extract the RNA, the samples were thawed in a water bath, centrifuged to remove the supernatant, and then processed using the RiboPure Kit (Invitrogen). Finally, 1 μl of the sample was analyzed using the Agilent 2100 Bioanalyzer and RNA 6000 nano assay.
1000 ng of each sample was used to construct a library with Universal Plus mRNA 243 Seq and NuQuant (TECAN). The library was then tested for quality and concentration using two systems: Qubit® 2.0 Fluorometer with its dsDNA High Sensitivity Kit and Agilent 2100 Bioanalyzer with its DNA 1000 assay.

value: PBMC

value: Disease


title: PBMC, Atopic Dermatitis, PBMC, rep 19


title: Not activated Sham transduced T cells bio rep 3


title: Sub-optimally activated Sham transduced T cells bio rep 2


title: PBMC, Atopic Dermatitis, PBMC, rep 16


title: YM4

first: Zunpeng

last: Liu

address: Beichen West Road

department: Institute of Zoology, Chinese Academy of Sciences

institute: State Key Laboratory of Stem Cell and Reproductive Biology

description: RNA sequencing of lung tissue of cynomolgus monkey

data_processing:
Reads were trimmed to remove the adapter sequences and low quality bases.
Clean reads were aligned to macFas5 Macaca fascicularis refference genome using histat2 software.
Genome_build: macFas5 for Macaca fascicularis.
Supplementary_files_format_and_content: Txt file of read count for RNA-seq.

organism: Macaca fascicularis

source_name: Lung tissue of young male cynomolgus monkey

extract_protocol:
For RNA-seq, total RNA was extracted using TRIzol (Thermo Fisher Scientific).
For RNA-seq, sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: Lung

tag: gender

value: male

value: young


title: Scc1-PK wt_Glu WCE

city: Tokyo

first: Sao

middle: Anh

last: Nguyen

address: 1-1-1 Yayoi, Bunkyo-ku

department: Institute for Quantitative Biosciences

institute: University of Tokyo

library_source: genomic

data_processing:
Raw sequencing reads were mapped to S.cerevisiae and C.glabrata reference genomes by Bowtie (v.1.2.3) using default parameter.
Reads mapped to each reference genome were qualified using parse2wig in the DROMPAplus package (v.1.17.2). Number of non-redundant reads uniquely mapped to each reference genome in IP and input was used to calculate the Occupancy Ratio and Normalization Factor as described previously.
Non-redandunt reads mapped to S.cer were processed to bin data by parse2wig using the normalization factors calculated above, to produce bigwig files of read count per bin.
Fold-enrichment (FE) of ChIP/input ratio was executed using DROMPA peakcall PC_ENRICH, which produced bigwig file of FE per bin, and bed file of enriched peaks with enrichment threshold set to 2.
Assembly: Saccharomyces Genome Database (SGD), identical with sacCer3 Candida Genome Database (CGD)
Supplementary files format and content: bigwig (read counts): both IP and input
Supplementary files format and content: bigwig (fold enrichment): IP only
Supplementary files format and content: bed (peaks)

molecule: genomic DNA

organism: Saccharomyces cerevisiae BY4741

source_name: G2/M, input

growth_protocol: Budding yeast was cultured in YEPD supplemented with specific treatments as described in Method session of the manuscript.

extract_protocol:
S.cer and C.gla cells mixture  was crosslinked in 1% formaldehyde for 30min, then incubated at 4oC overnight. Cells were broken in lysis buffer using multi-beads shocker (Yasui-kikai). Cell extract was then processed to chromatin shearing by sonication (Sonifier Branson, 2508).
Sequencing library was prepared using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645). Library was processed to double-sided size selection using AMPure XP Reagent (Beckman Coulter, A63881). Library was validated by Agilent High Sensitivity DNA kit and quantified by KAPA Library Quantification Kits.

tag: spike in

value: Candida glabrata [NCYC No.388; SN50; SCC1-PK:NatMX]

tag: strain no

value: Scer:MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 SCC1-9PK:KanMX6


title: YM1

tag: tissue


title: Scc1-PK gal-ub-eco1_Glu IP

source_name: G2/M, IP

tag: strain

value: Scer:MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 SCC2-9PK:TRP1 Pgal-ub-rECO1::KanMX6


title: Scc1-PK wt_Glu IP


title: Sub-optimally activated Sham transduced T cells bio rep 1

value: Sham

tag: treatment


title: PBMC, Atopic Dermatitis, PBMC, rep 15

tag: cell type


title: Pds5-PK ∆wpl1 ∆eco1 IP

tag: genotype

value: Scer:MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 wpl1{delta}::TRP1 eco1{delta}::LEU2 PDS5-9PK:HIS3MX6


title: YM2

tag: age


title: PBMC, Atopic Dermatitis, PBMC, rep 17


title: Scc1-PK gal-ub-eco1_Glu WCE


title: Optimally activated AG2G transduced T cells bio rep 3

value: Optimally activated


title: YF3

source_name: Lung tissue of young female cynomolgus monkey

value: female


title: Optimally activated AG2G transduced T cells bio rep 2


title: YF2


title: Not activated Sham transduced T cells bio rep 2

value: Not activated


title: YM3


title: Pds5-PK ∆wpl1 ∆eco1 WCE


title: YF4


title: Pds5-PK wt WCE

value: Scer:MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 PDS5-9PK:HIS3MX6


title: PBMC, Atopic Dermatitis, PBMC, rep 13


title: PBMC, Atopic Dermatitis, PBMC, rep 11


title: YF1


title: PBMC, Atopic Dermatitis, PBMC, rep 12


title: Pds5-PK wt IP


title: Rpo21 ∆eco1 ∆wpl1_WCE

tag: spike-in

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 wpl1{delta}::TRP1 eco1{delta}::LEU2

value: G2/M, input


title: Not activated Sham transduced T cells bio rep 1

value: T cells


title: PBMC, Atopic Dermatitis, PBMC, rep 10

value: PBMC


title: Sub-optimally activated AG2G transduced T cells bio rep 2

value: Sub-optimally activated


title: OM3

source_name: Lung tissue of old male cynomolgus monkey

value: Lung

value: old


title: Rpo21_wt_IP

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0

value: G2/M, IP


title: OM4

value: male


title: Rpo21 ∆eco1 ∆wpl1_IP


title: OM2


title: Sub-optimally activated AG2G transduced T cells bio rep 3


title: Not activated AG2G transduced T cells bio rep 3


title: PBMC, Atopic Dermatitis, PBMC, rep 8

value: Disease


title: OM1


title: Scc1-PK ∆eco1 ∆wpl1 Scc2-AID_S IP

source_name: S, IAA, IP

value: Candida glabrata [NCYC No.388; SN50; SCC1-PK:NatMX]

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 BY4741 wpl1{delta}::TRP1 eco1{delta}::LEU2 TIR1-9Myc:Aur1 SCC2-AID:KanMX6 SCC1-9PK:HIS3MX6Cgla:SCC1-PK:NatMX

value: S, IAA


title: Optimally activated AG2G transduced T cells bio rep 1

value: Optimally activated


title: OF4

source_name: Lung tissue of old female cynomolgus monkey

value: female


title: PBMC, Atopic Dermatitis, PBMC, rep 14


title: Sub-optimally activated AG2G transduced T cells bio rep 1


title: Scc1-PK ∆eco1 ∆wpl1 Scc2-AID_S WCE

source_name: S, IAA, input


title: PBMC, Atopic Dermatitis, PBMC, rep 9


title: Not activated AG2G transduced T cells bio rep 2

value: Not activated


title: PBMC, Atopic Dermatitis, PBMC, rep 7


title: Not activated AG2G transduced T cells bio rep 1


title: OF3


title: Scc1-PK Scc2-AID_S IP

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 TIR1-9Myc:Aur1 SCC2-AID:KanMX6 SCC1-9PK:HIS3MX6Cgla:SCC1-PK:NatMX


title: Scc1-PK Scc2-AID_S WCE


title: Scc1-PK Scc2-AID_G2/M WCE

source_name: G2/M, IAA, input

value: G2/M, IAA


title: IOMM-Lee, 78 nM digitoxin + 2 nM torin 2, 24h, rep2

city: Evanston

first: Thomas

middle: P

last: Wytock

state: IL

address: 633 Clark St

department: Physics

institute: Northwestern University

data_processing:
Raw sequencing data were processed according to the Uniform Processing Pipeline developed by the ENCODE project (https://github.com/ENCODE-DCC/long-rna-seq-pipeline/tree/master/dnanexus/small-rna).
Alignment was performed using the STAR alignment program with parameters --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000
--outSAMheaderCommentFile COfile.txt --outSAMheaderHD @HD VN:1.4 SO:coordinate --outSAMunmapped Within --outFilterType BySJout --outSAMattributes NH HI AS NM MD --outSAMstrandField intronMotif --outSAMtype BAM SortedByCoordinate --quantMode TranscriptomeSAM --sjdbScore 1 --limitBAMsortRAM 200000000000
The resulting BAM files were converted to bigwig files using STAR with arguments (--runMode inputAlignmentsFromBAM --outWigType bedGraph --outWigStrand Unstranded --outWigReferencesPrefix chr)
BAM files were converted to counts using RSEM (rsem-calculate-expression --bam --estimate-rspd --calc-ci --seed 12345 -p 15 --no-bam-output --ci-memory 200000 --forward-prob 1)
yielding the processed data files.
Assembly: GRCh38 v24
Supplementary files format and content: tab-delimited text files include the expected count, TPM, FPKM, as well as their posterior mean estimates (posterior_mean_count, pme_TPM, pme_FPKM), confidence intervals (TPM_ci_lower_bound, TPM_ci_upper_bound, FPKM_ci_lower_bound, FPKM_ci_upper_bound),
Supplementary files format and content: coefficients of quartile variation (TPM_coefficient_of_quartile_variation, FPKM_coefficient_of_quartile_variation), and posterior standard deviation (posterior_standard_deviation_of_count).

source_name: Meninges

growth_protocol: Cells were maintained in DMEM (GIBco) with 10% Fetal Bovine Serum (Gibco) and Primocin antibiotic (InvivoGen).

extract_protocol:
RNA was harvested using the Rneasy kit (Qiagen). RNA yields of ranging from 270-870 ng were used for the construction of sequencing libraries.
RNA libraries for RNA-Seq were prepared using the Illumina Stranded RNA Library Preparation kit from 100ng of high-quality RNA samples (RIN > 7) according to the manufacturer's instructions. This procedure includes mRNA purification and fragmentation,   cDNA synthesis, 3’ end adenylation, Illumina adapter ligation, library PCR   amplification and validation. Illumina sequencer was used to sequence the   libraries with the production of single-end, 50 bp reads at the depth of   20-25 M reads per sample.

treatment_protocol: Cells were treated with the specified drugs (DMSO, digitoxin, torin 2, digitoxin + torin 2) and the specified concentrations (respectively: 0.2%, 78 nM, 2 nM, 78 nM + 2 nM) for 24 hours.

value: Meninges

value: IOMM-Lee

value: Meningioma

value: 24 hours

value: 78 nM digitoxin, 2 nM torin 2


title: Scc1-PK Scc2-AID_G2/M IP

source_name: G2/M, IAA, IP


title: PBMC, Atopic Dermatitis, PBMC, rep 4

value: PBMC


title: PBMC, Atopic Dermatitis, PBMC, rep 5


title: IOMM-Lee, 78 nM digitoxin + 2 nM torin 2, 24h, rep3


title: IOMM-Lee, 2 nM torin 2, 24h, rep3

value: 2 nM torin 2


title: PBMC, Atopic Dermatitis, PBMC, rep 2


title: OF1

value: Lung

value: old


title: human iPSC, neurons, MDD patient 3, rep3

city: beijing

first: xinyu

last: She

address: shuangqing road, haidian district

department: school of life sciences

institute: Tsinghua university

description:
Library name: MDD_neurons_3_1
Neuron_gene_FPKM.xlsx

data_processing:
Primary sequencing data, called as raw reads, is subjected to quality control (QC)to determine if a resequencing step is needed. After QC, raw reads are filtered into clean reads which will be aligned to the reference sequences, QC of alignment is performed to determine if resequencing is needed. The alignment data is utilized to calculate distribution of reads on reference genes and mapping ratio. If alignment result passes QC, we will proceed with downstream analysis including gene expression and deep analysis based on gene expression (PCA/correlation/screening differentially expressed genes and so on). Further, we also can perform deep analysis based on DEGs, including Gene Ontology (GO) enrichment analysis, KEGG pathway enrichment analysis, cluster analysis, protein-protein interaction network analysis and finding transcription factor.
Assembly: https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.25
Supplementary files format and content: Excel spreadsheet, gene count of all samples
Supplementary files format and content: Excel spreadsheet, FPKM for each sample

source_name: human iPSC

growth_protocol: Quick-freeze samples immediately after collection and store at –80°C or in liquid nitrogen until RNA isolation.

extract_protocol:
1. Add 1 mL of TRIzol™ Reagent per 30 mg of ipsc derived neurons and islet-like organoids to the sample. 2. Pipet the lysate up and down several times to homogenize. 3. Incubate for 5 minutes to permit complete dissociation of the nucleoproteins complex. 4. Add 0.2 mL of chloroform per 1 mL of TRIzol™ Reagent used for lysis, then securely cap the tube. 5. Incubate on ice for 2–3 minutes. 6. Centrifuge the sample for 30 minutes at 12,000 × g at 4°C. The mixture separates into a lower red phenol-chloroform, and interphase, and a colorless upper aqueous phase. 7. Transfer the aqueous phase containing the RNA to a new tube. 8. Add 0.5 mL of isopropanol to the aqueous phase, per 1 mL of TRIzol™ Reagent used for lysis. 9. Incubate at -80 ℃ for 30 mins. 10. Centrifuge for 30 minutes at 12,000 × g at 4°C. Total RNA precipitate forms a white gel-like pellet at the bottom of the tube. 10. Discard the supernatant with a micropipettor. 11. Resuspend the pellet in 1 mL of 75% ethanol per 1 mL of TRIzol™ Reagent used for lysis. 12. Vortex the sample briefly, then centrifuge for 5 minutes at 7500 × g at 4°C. 13. Discard the supernatant with a micropipettor. 14. Air dry the RNA pellet for 5–10 minutes. 15. Resuspend the pellet in 20–50 µL of RNase-free water.16. Deliver the samples to the company using dry ice.
1)There are two methods to treat total RNA. Oligo(dT)magnetic beads are used to select mRNA with poly A tail, or hybridize the rRNA with DNA probe and digest the DNA / RNA hybrid strand, followed by DNase I reaction to remove DNA probe. Then obtain the target RNA after purification. 2) Fragment the target RNA and reverse transcription to double-strand cDNA (dscDNA) by N6 random primer. 3) End repair the dscDNA with phosphate at5' end and stickiness 'A'at3'end, then ligate and adaptor with stickiness 'T'at3' end to the dscDNA. 4) Two specific primers are used to amplify the ligation product. 5) Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase. 6)Perform sequencing on prepared library.

value: human iPSC

value: ipsc-derived neurons

value: Major depressive disorder

value: Female

tag: batch


title: Scc1-PK wt IP_rep1

source_name: G2/M, IP, rep1

value: Candida glabrata [NCYC No.388; SN50; SCC1-PK:NatMX]

value: EtOH


title: OF2

value: female


title: PBMC, Atopic Dermatitis, PBMC, rep 3

value: Disease


title: human iPSC, neurons, MDD patient 1, rep1

description:
Library name: MDD_neurons_1_1
Neuron_gene_FPKM.xlsx


title: PBMC, Atopic Dermatitis, PBMC, rep 6


title: IOMM-Lee, 2 nM torin 2, 24h, rep2

value: Meninges


title: human iPSC, neurons, MDD patient 2, rep2

description:
Library name: MDD_neurons_2_1
Neuron_gene_FPKM.xlsx


title: Scc1-PK wt WCE_rep1

source_name: G2/M, input, rep1

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 TIR1-9Myc:Aur1 SCC2-AID:KanMX6 SCC1-9PK:HIS3MX6Cgla:SCC1-PK:NatMX


title: PBMC, Atopic Dermatitis, PBMC, rep 1


title: Scc2-PK gal-ub-eco1_Glu WCE

source_name: G2/M, Glucose, input

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 SCC2-9PK:TRP1 PGal-ub-rECO1:KanMX6Cgla:SCC1-PK:NatMX

value: (-)Gal


title: IOMM-Lee, 2 nM torin 2, 24h, rep1

value: IOMM-Lee

value: Meningioma

value: 24 hours


title: PBMC, Normal, rep5

value: PBMC

value: Normal


title: PBMC, Normal, rep4


title: IOMM-Lee, 78 nM digitoxin, 24h, rep3

value: 78 nM digitoxin


title: human iPSC, neurons, healthy contro 5, rep5

description:
Library name: Ctrl_neurons_5_1
Neuron_gene_FPKM.xlsx

value: human iPSC

value: ipsc-derived neurons

value: Healthy control


title: Scc2-PK wt_Glu WCE

source_name: G2/M, Glucose, WCE

value: S.cer:BY4741; C.gla:NCYC No.388

value: Scer:SN40; C.gla:SN50

value: Scer:MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 SCC2-9PK:TRP1; Cgla:SCC1-PK:NatMX


title: PBMC, Normal, rep3

source_name: PBMC


title: human iPSC, neurons, MDD patient 4, rep4

description:
Library name: MDD_neurons_4_1
Neuron_gene_FPKM.xlsx

value: Major depressive disorder

value: Female


title: human iPSC, neurons, healthy contro 4, rep4

description:
Library name: Ctrl_neurons_4_1
Neuron_gene_FPKM.xlsx


title: Scc2-PK wt_Glu IP

source_name: G2/M, Glucose, IP


title: PBMC, Normal, rep2


title: IOMM-Lee, 78 nM digitoxin + 2 nM torin 2, 24h, rep1

value: Meninges

value: 78 nM digitoxin, 2 nM torin 2


title: IOMM-Lee, 78 nM digitoxin, 24h, rep2


title: Scc2-PK ∆eco1 ∆wpl1_S WCE

source_name: S phase, input

value: Candida glabrata [NCYC No.388; SN50; SCC1-PK:NatMX]

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 SCC2-9PK:TRP1Cgla:SCC1-PK:NatMX


title: human iPSC, neurons, healthy contro 3, rep3

description:
Library name: Ctrl_neurons_3_1
Neuron_gene_FPKM.xlsx


title: IOMM-Lee, 78 nM digitoxin, 24h, rep1

value: IOMM-Lee

value: Meningioma


title: PBMC, Normal, rep1

value: PBMC


title: human iPSC, neurons, healthy contro 2, rep2

description:
Library name: Ctrl_neurons_2_1
Neuron_gene_FPKM.xlsx


title: IOMM-Lee, 0.2% DMSO, 24h, rep3

value: 24 hours

value: 0.2percent DMSO


title: Scc2-PK ∆eco1 ∆wpl1_S  IP

source_name: S phase, IP


title: IOMM-Lee, 0.2% DMSO, 24h, rep2


title: human iPSC, neurons, healthy control 1, rep1

description:
Library name: Ctrl_neurons_1_1
Neuron_gene_FPKM.xlsx

value: human iPSC


title: Scc2-PK wt_S WCE


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 21

source_name: Skin

value: Skin

value: Non Lesion region

value: Disease


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 20


title: Scc2-PK gal-ub-eco1_Glu IP

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 SCC2-9PK:TRP1 PGal-ub-rECO1:KanMX6Cgla:SCC1-PK:NatMX

value: (-)Gal


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 19


title: IOMM-Lee, 0.2% DMSO, 24h, rep1


title: Scc2-PK Pds5-AID WCE

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 SCC2-9PK:TRP1 TIR1-9Myc:Aur1 PDS5-AID:KanMX6Cgla:SCC1-PK:NatMX

value: IAA


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 18


title: human iPSC, neurons, BDII patient 2, rep2

description:
Library name: BDII_neurons_2_1
Neuron_gene_FPKM.xlsx

value: ipsc-derived neurons

value: Bipolar II disorder

value: Female


title: CH-157MN, 78 nM digitoxin + 2 nM torin 2, 24h, rep2

value: Meninges

value: 78 nM digitoxin, 2 nM torin 2


title: Scc2-PK wt_S IP

value: Candida glabrata [NCYC No.388; SN50; SCC1-PK:NatMX]

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 SCC2-9PK:TRP1Cgla:SCC1-PK:NatMX


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 17


title: Scc2-PK Pds5-AID IP


title: Scc2-PK_Pds5-AID_EtOH WCE

source_name: G2/M, EtOH, input

value: EtOH


title: human iPSC, neurons, BDII patient 1, rep1

description:
Library name: BDII_neurons_1_1
Neuron_gene_FPKM.xlsx


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 16


title: CH-157MN, 78 nM digitoxin + 2 nM torin 2, 24h, rep1

value: Meningioma

value: 24 hours


title: CH-157MN, 2 nM torin 2, 24h, rep3

value: 2 nM torin 2


title: Scc2-PK_Pds5-AID_EtOH IP

source_name: G2/M, EtOH, IP


title: SU-DHL-8 cells,Beta-ST 15μM,24h,rep3

city: Tianjin

first: Minghan

last: Qiu

state: Tianjin

address: Department of Oncology, Tianjin Union Medical Center of Nankai Univercity, 190 Jieyuan Street, Hongqiao District, Tianjin, China.

department: Department of Oncology

data_processing:
Raw reads were filtered and cleaned by fastp software (v0.23.2).
Gene expression levels were quantified with featureCounts v2.0.1,referencing the GENCODE28 annotations.
Sequences were then aligned to the GRCh38 reference genome using STAR v2.7.10.
Transcript assembly and abundance estimation were performed using StringTie v2.2.1.
R was used for visualization.
Assembly: hg38
Supplementary files format and content: table-delimited text file includes raw counts for each sample
Supplementary files format and content: table-delimited text file includes TPM values for each sample

source_name: cell line

growth_protocol: SU-DHL-8 cells were maintained  in RPMI 1640, all with 10% FBS, penicillin (100 IU/ml), and streptomycin (100 μg/ml) in a 5% CO2 atmosphere at 37°C.

extract_protocol:
Total RNA was extracted using TRIzol reagent
RNA libraries were prepared using standard Illumina protocols.

treatment_protocol: SU-DHL-8 cells were treated with 15μM β-ST for 24 hours, with an equal concentration of DMSO as the control

value: cell line

value: DLBCL cell

value: WT

value: β-ST 15μM,24h


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 15

value: Skin

value: Non Lesion region

value: Disease


title: SU-DHL-8 cells,Beta-ST 15μM,24h,rep2

institute: Tianjin Union Medical Center of Nankai Univercity


title: human iPSC, neurons, BDII patient 4, rep4

description:
Library name: BDII_neurons_4_1
Neuron_gene_FPKM.xlsx

value: human iPSC

value: ipsc-derived neurons

value: Bipolar II disorder


title: SU-DHL-8 cells,Beta-ST 15μM,24h,rep1


title: CH-157MN, 78 nM digitoxin + 2 nM torin 2, 24h, rep3

value: Meninges

value: 78 nM digitoxin, 2 nM torin 2


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 13


title: CH-157MN, 2 nM torin 2, 24h, rep1


title: CH-157MN, 78 nM digitoxin, 24h, rep3

value: 78 nM digitoxin


title: Scc2-PK ∆wpl1 IP

source_name: G2/M, IP

value: Candida glabrata [NCYC No.388; SN50; SCC1-PK:NatMX]

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 wpl1{delta}::TRP1 SCC2-9PK:HIS3MX6Cgla:SCC1-PK:NatMX


title: SU-DHL-8 cells,DMSO,24h,rep3


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 14


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 12


title: Scc2-PK wt WCE_rep2

source_name: G2/M, input, rep2

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 SCC2-9PK:TRP1Cgla:SCC1-PK:NatMX


title: human iPSC, neurons, BDII patient 3, rep3

description:
Library name: BDII_neurons_3_1
Neuron_gene_FPKM.xlsx

value: Female


title: CH-157MN, 78 nM digitoxin, 24h, rep2

source_name: Meninges

value: Meningioma

value: 24 hours


title: SU-DHL-8 cells,DMSO,24h,rep1

value: cell line

value: DLBCL cell

value: WT


title: SU-DHL-8 cells,DMSO,24h,rep2


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 10

value: Skin

value: Non Lesion region


title: Scc2-PK wt IP_rep2

source_name: G2/M, IP, rep2


title: Scc2-PK ∆eco1 ∆wpl1 WCE_rep1

value: MATa his3{delta}1 leu2{delta}0 met15{delta}0 ura3{delta}0 wpl1{delta}::TRP1 eco1{delta}::LEU2 SCC2-9PK:HIS3MX6Cgla:SCC1-PK:NatMX


title: CH-157MN, 0.2% DMSO, 24h, rep3

value: 0.2percent DMSO


title: Scc2-PK ∆wpl1 WCE

source_name: G2/M, input


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 9

value: Disease


title: CH-157MN, 2 nM torin 2, 24h, rep2

value: Meninges

value: 2 nM torin 2


title: CH-157MN, 0.2% DMSO, 24h, rep2


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 8


title: Scc2-PK wt WCE_rep1


title: MT_SOD1_PSPC_treat5_rep2

type: RNA

city: Amsterdam

first: Andreia

last: Duarte

state: Select a State

address: Science Park 408

country: Netherlands

institute: VectorY

description: nCounter Neuropathology Panel

hyb_protocol: Samples for the nCounter assay were treated as described in the nanoString technologies Gene expression hybridization protocol (Gene Expression CodeSet RNA Hybridization Protocol; MAN-10056-05) and 5 µL of sample (20 ng/ul) was used in each hybridization reaction. The entire hybridization reaction was used as input for the nCounter prep station and run on an nCounter MAX cartridge. Each nCounter cartridge was read on the nanostring digital analyzer (nCounter MAX/FLEX) with 280 fields of view (FOV). Finally, digital count files were generated for each sample run.

data_processing: All samples were verified regarding quality control (QC) parameters using Basic nSolver analysis software (101), applying default settings recommended by nanoString for binding density, mRNA content, mRNA positive normalization factor, mRNA content normalization facto and fields of view (FOV). Only transcripts with average counts ≥ 80 reads were considered as suitable housekeeping genes. Negative control probe reads were used to define minimum expression threshold (≥ 15 reads). Therefore, all transcripts with expression levels (Max counts) below the negative control limit were excluded from further analysis. Following QC, samples were clustered into the respective experiment groups. Pairwise ratios comparisons were applied to datasets on both panels to compare experimental groups. Fold-change (FC) was used as a readout for each possible combination.  Regression analysis (Coefficient of determination, R2) was used to analyze independent replicates, that showed R2 ≥ 0.95 across all datasets. Detailed information about the software, including the recommended ranges of values for the different QC parameters, creating experiments, normalization, and analyzing data, can be found at nSolver 4.0 Analysis Software User Manual (nanostring.com).

source_name: motor neurons, SOD1 mutation, exposed to PSPC treated with AAV6

growth_protocol: Human iPS-derived cell lines (iCell Motor Neurons and Astrocytes) were purchased from FujiFilm Cellular Dynamics International (FCDI, Madison, WI). Frozen vials were thawed and seeded according to manufacturer's instructions at a recommended of 100.000 live cells/cm2. iCell Motor neurons were cultured in a volume of 500 on a 12- (3513, Corning).

extract_protocol: Cell lysates were collected in QIAzol lysis reagent (79306, Qiagen). RNA isolation was performed using the miRNeasy Mini kit (217004, Qiagen) according to the manufacturer’s protocol for samples containing <1 μg total RNA. RNA concentrations were determined using NanoDrop ONEC (Thermo Scientific). Quality control analysis was executed with Bioanalyzer (Agilent RNA 6000 Nano), according to manufacturer's instructions. All the analyzed samples contained high quality RNA, with RNA integrity number (RIN) above 8.5, and clear ribosomal RNA (rRNA) 18/28S peaks.

treatment_protocol: PSPC/PONPC: Cells were treated with 25 µM and incubated for 24 hr. // AAV: Human iPS-derived cultures were transduced with different AAV constructs at a multiplicity of infection (MOI) of 10E6 and 107 in culturing media at seven days post-seeding. Half of the medium was removed from the wells before adding the AAV mixture. The same volume of fresh media was added to the cells 4 h post-transduction.

tag: phenotype

value: SOD1 (G93A) point mutation


title: CH-157MN, 0.2% DMSO, 24h, rep1


title: MT_SOD1_PSPC_treat5_rep1

description: nCounter Neuropathology Panel

source_name: motor neurons, SOD1 mutation, exposed to PSPC treated with AAV5


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 7


title: Scc2-PK wt IP_rep1

source_name: G2/M, IP, rep1

value: Candida glabrata [NCYC No.388; SN50; SCC1-PK:NatMX]


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 6


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 11


title: humanpbmc2

first: Zhaoqi

last: Zhang

state: Beijing

address: Beijing China Institute of Zoology，Chinese Academy of Sciences

institute: University of Chinese Academy of Sciences

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Supplementary files format and content: GRCh38 and susScr11_genome_10.2
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: blood

extract_protocol:
The pig is a promising candidate for xenotransplantation. Understanding the differences between human and swine immune systems is critical for addressing xeno-transplant rejection and hematopoietic reconstitution. We performed single-cell RNA-seq on human and pig immune cells. High oxidative phosphorylation, HIF-1, glycolysis, and lysosome-related gene expressions in pig CD14+ monocytes were observed, whereas pig CD14+ monocytes exhibited lower levels of cytokine receptors and JAK-STAT-related genes. Pig activated CD4+T cells decreased cell adhesion and inflammation, while enriched for migration and activation processes. Porcine GNLY+CD8+T cells reduced cytotoxicity and increased proliferation compared with human GNLY+CD8+T cells. Pig CD2+CD8+γδT cells were functionally homologous to human CD2+CD4+ γδT cells. Pig CD2-CD8-γδT cells expressed genes with quiescent and precursor characteristics, while CD2-CD8+γδT cells expressed migration and memory-related molecules. Pig CD24+ and CD5+B cells are associated with inflammatory responses. Our research with integrated scRNA-seq enables a deeper understanding of the development and function of porcine immune cells.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: blood

value: PBMC


title: WG194_RNA_YPG-90min_rep1

city: Brighton

first: William

last: Gittens

state: I am not in the U.S. or Canada

address: Science Park Road

department: Genome Damage and Stability Centre

institute: University of Sussex

data_processing:
Data were aligned to the Cer3 (R64-1-1) genome using STAR. Briefly, the genome indexes were first generated using STAR –runMode genomeGenerate, in combination with the Saccharomyces_cerevisiae.R64-1-1.107.gtf gene coordinate file, and settings --sjdbOverhang 41 and --genomeSAindexNbases 10. Then RNA-seq paired-end FASTQ files were aligned with STAR, with the settings –runThreadN 7 and –alignIntronMax 2500. Sense RNA-seq counts per gene were outputted directly by STAR and are tabulated in the supplementary file “Sense_RNA_Counts.txt”. SAM files generated by STAR alignment were sorted and converted to BAM format, using samtools-sort and samtools-view. The genome-wide coverage on each strand was computed using deepTools-bamCoverage, with the options –extendReads and –binSize 10. The resulting BedGraph files on each strand were converted to FullMap format, for ease of plotting alongside our CC-seq data within our bespoke CCTools R package (https://github.com/WHG1990/CCTools). For in-house compatibility purposes, the FullMap data were converted from Cer3 coordinates to Cer3H4L2 coordinates by increasing the Pos coordinate by the known insert sizes, at the known insert coordinates on chromosome III.
Assembly: Cer3H4L2
Supplementary files format and content: FullMap files containing 10bp histograms detailing the total of Watson (+) and Crick (-) coverage outputed by bamCoverage. 4-column format (Chr, Pos, Watson, Crick).

organism: Saccharomyces cerevisiae

growth_protocol: For all experiments, cells were grown overnight to saturation in 4 mL YPD medium at 30 °C with shaking at 250 rpm, then diluted to OD600 0.5 in 500 mL YPD, or YP-Raffinose (for galactose induction experiments), and grown until OD600 2.0 in a 2 L baffled flask with antifoam 204 (Sigma A8311) added to 0.0001%. Alpha mating factor was added to a concentration of 20 µg/mL, and the cultures were incubated for a further 90 min. A second dose of alpha factor was added to a final total concentration of 26.6 µg/mL (including first dose), and the cultures were incubated for a further 30 min. At this point >99% of the cells were arrested in G1.

extract_protocol:
Total RNA was extracted using the Monarch Total RNA Miniprep Kit, coupled with bead-beating based cell wall disruption using a Fastprep-24 ribolyser (4 x 30s at 6 m/s velocity, with 1 min on ice slurry between pulses). RNA integrity was checked by TBE-agarose gel electrophoresis, whereupon no significant degradation of the ribosomal RNA bands was observed.
Total stranded RNA-seq was performed using the NEBNext Ultra™ II Directional RNA Library Prep Kit for Illumina, coupled with the QIAseq FastSelect –rRNA Yeast Kit, all according to the manufacturer’s instructions. cDNA Libraries were quantified by Bioanalyzer (Agilent), prior to sequencing on the Nextseq 500 (Illumina).


title: MT_SOD1_PSPC_rep2

description: nCounter Neuropathology Panel

source_name: motor neurons, SOD1 mutation, exposed to PSPC


title: WG195_RNA_YPG-90min_rep2


title: CH-157MN, 78 nM digitoxin, 24h, rep1

value: 78 nM digitoxin


title: MT_SOD1_PSPC_rep1

description: nCounter Neuropathology Panel


title: WG193_RNA_YPG-60min_rep2


title: WT_SOD1_PONPC_treat5_rep2

description: nCounter Neuropathology Panel

source_name: motor neurons, wild-type, exposed to PONPC treated with AAV6

value: Apparently Healthy Neurons (AHN)


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 4


title: Scc2-PK ∆eco1 ∆wpl1 IP_rep1


title: Hep3B, A4368

city: Incheon

first: Kwang Won

last: Jeong

address: 191 Hambakmoe-ro, Yeonsu-gu

department: College of Pharmacy

country: South Korea

institute: Gachon University

data_processing:
Illumina Casava1.8.2 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 whole genome using TopHat v2.0.12(with bowtie v2.2.3) with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon per Megabase of library size (FPKM) were calculated using Cufflinks from Trapnell, et al. 2012, Nature Biotechnology, 2012. In short, exons from all isoforms of a gene were merged to create one meta-transcript.
The number of fragments falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Assembly: Genome_build: hg19

source_name: Liver

growth_protocol: Hep3B cells were grown in DMEM supplemented with 10% FBS.

extract_protocol: Total RNA was isolated using the RNeasy mini kit (Qiagen)

treatment_protocol: Cells were treated with A4368 (25 microM) for 24 h.

value: hepatocellular carcinoma

value: Liver

tag: source

value: ATCC


title: Hep3B, Control

tag: cell line

value: no treatment control


title: WT_SOD1_PONPC_treat5_rep1

description: nCounter Neuropathology Panel

source_name: motor neurons, wild-type, exposed to PONPC treated with AAV5


title: humanpbmc1

description: 10x Genomics


title: WG192_RNA_YPG-60min_rep1


title: D14Macrophage rep2

city: Minatoku

first: Shunsuke

last: Tabe

address: 4-6-1 shirokanedai

department: Regenetive medicine

institute: Institute of medical and science,the university of Tokyo

data_processing:
The sequencing reads were aligned to hg19_AmpliSeq_Transcriptome_ERCC_v1 using Torrent Mapping Alignment Program. The data were analyzed on AmpliSeqRNA plug-in v5.2.0.3 of the Torrent Suite Software v5.2.2 (Thermo Fisher Scientific).
Assembly: hg19
Supplementary files format and content: Csv file include RPM value in each sample
Supplementary files format and content: Csv file include sample barcode and related sample information

source_name: macrophages cocultured in FPCO

extract_protocol:
RNA-Seq libraries were generated using 40 ng and 80 ng of total RNA from cancer cells and THP-1, M0-macrophages, M1/M2 macrophages,FPCO-macrophage respectively
RNA-seq library was prepared using Ion Ampliseq Transcriptome Human Gene Expression kit (Thermo Fisher Scientific, Carlsbad, CA), according to the manufacturer’s protocol.

value: macrophages cocultured in FPCO


title: WG191_RNA_YPG-30min_rep2


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 2

source_name: Skin

value: Skin

value: Non Lesion region


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 3


title: WG190_RNA_YPG-30min_rep1


title: WT_SOD1_PONPC_rep1

description: nCounter Neuropathology Panel

source_name: motor neurons, wild-type, exposed to PONPC


title: WT_SOD1_PSPC_rep2

description: nCounter Neuropathology Panel

source_name: motor neurons, wild-type, exposed to PSPC


title: D14Macrophage rep1


title: WG188_RNA_YPR-0min_rep1


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 1


title: WG189_RNA_YPR-0min_rep2


title: D14M0FPCO_cancer rep2

source_name: Cancer cells derived PDAC patient

value: Cancer cells derived PDAC patient


title: Skin tissue, Atopic Dermatitis, Lesion, rep 21

value: Lesion region

value: Disease


title: Skin tissue, Atopic Dermatitis, Lesion, rep 19


title: D14Macrophage rep3


title: WT_SOD1_PSPC_rep1

description: nCounter Neuropathology Panel


title: WT_SOD1_PONPC_rep2

description: nCounter Neuropathology Panel


title: WG185_RNA_YPD_rep2


title: D14 FPCO_cancer rep3


title: Skin tissue, Atopic Dermatitis, Lesion, rep 18


title: D14 FPCO_cancer rep2


title: Skin tissue, Atopic Dermatitis, Lesion, rep 17


title: MT_TDP-43 M337V__treat4_rep2

description: nCounter Neuropathology Panel

source_name: motor neurons, TDP-43 mutation treated with AAV4

value: TDP-43 (M337V) point mutation


title: WG221_YPG-60min_rep1

data_processing:
Multiplexed library pools were sequenced on the Illumina NextSeq 500 (Kit v2–75 cycles) or Illumina NextSeq 1000 (Kit P2–100 cycles), with paired-end read lengths of 42, or 51 bp, respectively. Paired-end reads that passed filter were aligned using bowtie2 (options: -X 1000 –no-discordant –very-sensitive –mp 5,1 –np 0), using MAPQ0 settings, then SAM files processed via terminalMapper (Perl, v5.22.1; https://github.com/Neale-Lab) that computes the coordinates of the protein-linked 5′-terminal nucleotide. The reference genome used in this study is our in-house Cer3H4L2 (S. cerevisiae) build, which we generated by inclusion of the his4::LEU2 and leu2::hisG loci into the Cer3 yeast genome build. Specifically, Cer3H4L2 is identical to the sacCer3 reference genome (R64-1-1), with the addition of two ectopic insertions: 1,173 bp of hisG sequence inserted at the LEU2 locus at position 91,965, and 3,077 bp of LEU2 sequence including 77 bp of associated unidentified bacterial sequence at position 65,684. All subsequent analyses were performed in R (Version 4.4) using RStudio (Version 2024.04.2+764), unless indicated otherwise. Yeast data sets were filtered to exclude the rDNA, the CUP1-2 locus, the mitochondrial genome and the 2-micron plasmid. Final averaged datasets used for generating figures are included in the supplementary files for the series accession.
Assembly: Cer3H4L2
Supplementary files format and content: FullMap files containing sparsely-formatted, 1bp histograms detailing the total number of Watson (+) and Crick (-) hits for all mapped base-pairs. 4-column format (Chr, Pos, Watson, Crick).
Library strategy: Top2 CC-seq

extract_protocol:
CC-seq-v2 is an update of our prior published method that improves sensitivity by several orders of magnitude, enabling the detection of physiological Top2ccs in etoposide-unchallenged cells. Transient physiological Top2ccs were rapidly fixed by denaturation via the direct addition of 70 mL of culture to 150 mL of ethanol (-20˚C) in a 250 mL centrifuge vessel (NALGENE), which had been pre-chilled overnight at -20˚C. Mixtures were immediately vigorously shaken, resulting in a final concentration of 70% ethanol at ~0˚C, prior to incubation at -20˚C for 15 min. Tubes were centrifuged at 3500g for 3 min (4˚C) and the supernatant was aspirated fully. Cell pellets were resuspended in 1.2 mL spheroplasting buffer (1 M sorbitol, 50 mM NaHPO4 buffer pH 7.2, 10 mM EDTA) containing 400 μg/mL Zymolyase 100 T (AMS Biotech) and 1% β-mercaptoethanol (Sigma) for 20 min at 37 °C. The entire spheroplast suspension was transferred to 5 mL eppendorfs containing 3.773 ml of ethanol (-20˚C), shaken vigorously to mix, and pelleted by centrifugation at 1000g for 2 min. The ethanolic supernatant of each sample was fully aspirated prior to addition of 800 µL 1× STE buffer (2% SDS, 0.5 M Tris pH 8.1, 10 mM EDTA, 0.05% bromophenol blue). Cells were lysed using a small plastic pestle (VWR) before addition of a further 1600 µL 1× STE buffer, with mixing by inversion and incubation for 10 min at 65 °C. Samples were cooled on ice and 1250 µL Phenol-Chloroform-isoamyl alcohol (25:24:1; Sigma) was added. The mixtures were emulsified by shaking vigorously 30 times, prior to incubation at room temperature (RT) for 5 min. The mixtures were re-emulsified by shaking vigorously 30 times, prior to phase separation by centrifugation at 20,000 × g for 5 min. 2 mL of the aqueous phase was removed to a clean microcentrifuge tube, taking care not to disturb the interphase, and nucleic acids were precipitated with 3.5 mL ice-cold ethanol, pelleted by centrifugation, washed with 5 mL ice-cold 70% ethanol, and dissolved in 1 mL 1x TE buffer pH 7.5 overnight at 4 °C. 1 mL aliquots of nonproteolysed DNA (prepared as above) were fully resuspended by heavy vortexing and inversion on a rotation wheel for 15 min (RT), prior to sonication to an average fragment size of 300–400 bp with Covaris (duty cycle: 10%, intensity/peak power incidence: 75 W, cycles/burst: 200, time: 21 min). A sample of 12 uL was removed and incubated at 37˚C for 45 min with 3 uL of RNAse A (50 mg/mL). DNA shearing was checked by 1% agarose gel electrophoresis, and DNA was quantified in technical triplicate with the Qubit (ThermoFisher) and High Sensitivity reagents. Human-Lambda DNA spike was added to 950 uL of sample, then the total volume was made up to 1 mL with 1x TE (pH 7.5). Triton-X100, N-Lauroylsarcosine sodium salt and NaCl were then added to complete the binding buffer (final concentrations: 0.3 M NaCl, 0.2% Triton-X100, 0.1% N-Lauroylsarcosine sodium salt). Each sample was divided over two QIAquick silica fibre membrane spin columns (QIAGEN). Under these conditions, protein, but not nucleic acids, bind to the silica membrane, leading to selective retention of any CCs. The flowthrough was reapplied to the column to improve yield. Columns were washed six times with 600 µL of TEN (10 mM Tris pH 7.5, 1 mM EDTA, 0.3 M NaCl) per 1 min wash to remove any residual non-CC DNA fragments, prior to elution twice with 125 µL TES (10 mM Tris pH 7.5, 1 mM EDTA, 0.5% SDS). The SDS detergent in the elution buffer releases interactions between protein and silica, thereby releasing bound CCs.
Eluted products were pooled to 500 µL in TES and incubated with 1 mg/mL Proteinase K (Sigma) for 60 min at 50 °C, prior to overnight ethanol precipitation at −20 °C with 1.41 mL ethanol, 0.2 mg/mL glycogen and 200 mM NaOAc. The DNA-glycogen precipitate was pelleted by centrifugation at 20,000 × g for 1 h at 4 °C, washed once with 1.5 mL 70% ethanol without disturbing the pellet, and re-centrifuged for 15 min. The supernatant was aspirated, and the pellet was air-dried for 10 min at room temperature, prior to solubilisation in 26 µL 10 mM Tris-HCl pH 7.5. DNA concentration was measured in a 1 µL sample using a Qubit (ThermoFisher) and High Sensitivity reagents. The remaining 25 µL was used as input for one round of end repair and adapter ligation with NEBNext Ultra II DNA Library Preparation kit (NEB), according to manufacturer’s instructions, except all steps were conducted at half-scale and a custom P7 adapter was used. The use of custom adapters is to allow differentiation of the sheared end (P7 adapter) from the Top2cc end (P5 adapter). After ligation of the P7 adapter, TE was added to a final volume of 90 uL. DNA was isolated with AMPure XP beads (Beckman Coulter) according to manufacturer’s instructions (beads:input of 78:90 uL) and eluted in 85 µL water. Next, 10 uL of 10X Cutsmart buffer and 5 uL Shrimp Alkaline Phosphatase (rSAP; NEB) were added before incubation for 30 min at 37˚C. DNA was isolated again with AMPure XP beads (Beckman Coulter) according to manufacturer’s instructions (beads:input of 83:100 uL) and eluted in 50 µL 10 mM Tris-HCl. Samples were diluted twofold with 50 µL TDP2 reaction buffer (100 mM TrisOAc, 100 mM NaOAc, 2 mM MgOAc, 2 mM DTT, 200 µg/mL BSA) and incubated with 3 µL of 10 µM recombinant zebrafish TDP2 catalytic domain (Addgene plasmid #200512)  for 1 h at 37 °C. DNA was isolated again with AMPure XP beads (beads:input of 83:103) and eluted in 26 µL 10 mM Tris-HCl. Next, a second round of adapter ligation was conducted using a new custom adapter dp-P5 without prior end repair in order to prevent dephosphorylation of DNA 3′-phosphate termini which may be generated by TDP2 activity on 3′-CCs. After ligation of the dp-P5 adapter to the Top2-cleaved end, sample volume was adjusted to 90 uL with Tris-HCl, DNA was isolated with AMPure XP beads (beads:input of 78:90) and eluted in 16 µL 10 mM Tris-HCl. DNA concentration was measured in 1 µL using a Qubit. The remaining 15 µL was used as template for the NEBNext Ultra II PCR step using universal primer (P5 end) and indexed primers for multiplexing (P7 end), according to manufacturer’s instructions (12–15 cycles). PCR reactions were diluted with 50 µL 10 mM Tris-HCl, DNA was isolated with AMPure XP beads (beads:input of 83:100) and eluted in 30 µL 1 mM Tris-HCl pH 8.1, 100 uM EDTA. Sample DNA molarities were quantified using the Bioanalyzer or Tapestation (Agilent).


title: MT_TDP-43 M337V__treat3_rep1

description: nCounter Neuropathology Panel

source_name: motor neurons, TDP-43 mutation treated with AAV3


title: Skin tissue, Atopic Dermatitis, Lesion, rep 20


title: MT_TDP-43 M337V__treat3_rep2

description: nCounter Neuropathology Panel


title: D14M0FPCO_cancer rep3


title: D14M0FPCO_cancer rep1


title: MT_TDP-43 M337V__treat4_rep1

description: nCounter Neuropathology Panel


title: Skin tissue, Atopic Dermatitis, Lesion, rep 15


title: MT_TDP-43 M337V__treat2_rep1

description: nCounter Neuropathology Panel

source_name: motor neurons, TDP-43 mutation treated with AAV2


title: Skin tissue, Atopic Dermatitis, Lesion, rep 16


title: MT_TDP-43 M337V__treat2_rep2

description: nCounter Neuropathology Panel


title: Skin tissue, Atopic Dermatitis, NonLesion, rep 5


title: Skin tissue, Atopic Dermatitis, Lesion, rep 12


title: D14 FPCO_cancer rep1


title: M0FPCO-cancer rep3


title: FPCO-cancer rep2


title: Skin tissue, Atopic Dermatitis, Lesion, rep 11


title: MT_TDP-43 M337V_rep2

description: nCounter Neuropathology Panel

source_name: motor neurons, TDP-43 mutation


title: WG214_YPG-90min_OS-2min_rep4


title: WG184_RNA_YPD_rep1


title: MT_TDP-43 M337V_rep1

description: nCounter Neuropathology Panel


title: M0FPCO-cancer rep2


title: WG219_YPR-90min_rep1


title: Skin tissue, Atopic Dermatitis, Lesion, rep 14


title: WG218_YPR-60min_rep1


title: WG222_YPG-90min_rep1


title: FPCO-cancer rep1


title: Skin tissue, Atopic Dermatitis, Lesion, rep 13


title: MT_TDP-43 M337V__treat1_rep2

description: nCounter Neuropathology Panel

source_name: motor neurons, TDP-43 mutation treated with AAV1


title: M0FPCO-cancer rep1


title: MT_TDP-43 M337V__treat1_rep1

description: nCounter Neuropathology Panel


title: WT_TDP-43_rep2

description: nCounter Neuropathology Panel

source_name: motor neurons, wild-type


title: WG213_YPG-60min_OS-2min_rep4


title: FPCO-cancer rep3


title: FPCO-Mac rep3


title: MT_TDP-43 M337V_rep3

description: nCounter Neuropathology Panel


title: WG216_YPR-0min_rep1


title: WG220_YPG-30min_rep1


title: WT_TDP-43_rep1

description: nCounter Neuropathology Panel


title: Skin tissue, Atopic Dermatitis, Lesion, rep 10


title: M2 rep3

source_name: macrophages exposed IL4 and IL13

value: macrophages exposed IL4 and IL13


title: Skin tissue, Atopic Dermatitis, Lesion, rep 6


title: Skin tissue, Atopic Dermatitis, Lesion, rep 5


title: WG209_YPR-30min_OS-2min_rep1


title: WG217_YPR-30min_rep1


title: M2 rep1


title: Skin tissue, Atopic Dermatitis, Lesion, rep 9


title: Skin tissue, Atopic Dermatitis, Lesion, rep 8


title: WG212_YPG-30min_OS-2min_rep4


title: Skin tissue, Atopic Dermatitis, Lesion, rep 7


title: WG210_YPR-60min_OS-2min_rep1


title: FPCO-Mac rep2


title: M2 rep2


title: WG208_YPR-0min_OS-2min_rep4


title: WG203_YPR-90min_OS-2min_rep3


title: M1 rep3

source_name: macrophages exposed LPS and IFNgamma

value: macrophages exposed LPS and IFNgamma


title: lens_hom_rep3

city: Neuherberg

first: Martin

last: Irmler

state: Bayern

address: Ingolstaedter Landstrasse 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum München GmbH

description: SAMPLE 6

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol using HiScan

data_processing: The data were normalised using cubic spline normalisation with Illumina Genomestudio 2011.1

label: biotin

source_name: lens

label_protocol: Biotinylated cRNA were prepared with the Ambion MessageAmp kit for Illumina arrays

extract_protocol: RNA was extracted with Trizol reagent, followed by clean-up with QIAGEN RNeasy midi kit in accordance with the prescribed protocol provided with the kit. Quality control was performed with gel electrophoreses.

value: lens

value: homozygous Fgf9Y162C mutant

value: 18 weeks

tag: mouse id

tag: Sex

value: male


title: WG211_YPR-90min_OS-2min_rep4


title: M1 rep2


title: WG202_YPG-90min_OS-2min_rep3


title: Skin tissue, Atopic Dermatitis, Lesion, rep 2


title: FPCO-Mac rep1


title: M1 rep1


title: WG200_YPG-30min_OS-2min_rep3


title: WG201_YPG-60min_OS-2min_rep3


title: Skin tissue, Atopic Dermatitis, Lesion, rep 1


title: M0_D7 rep3

source_name: Macrophages derived from THP-1 cultured in FPCO medium


title: Skin tissue, Atopic Dermatitis, Lesion, rep 4


title: lens_hom_rep2

description: SAMPLE 5

value: female


title: lens_wt_rep3

description: SAMPLE 3

value: wild type


title: lens_hom_rep1

description: SAMPLE 4


title: lens_wt_rep2

description: SAMPLE 2


title: lens_wt_rep1

description: SAMPLE 1


title: Skin tissue, Normal, rep 9

value: Normal


title: WG199_YPR-0min_OS-2min_rep3


title: Skin tissue, Normal, rep 8


title: M0_D7 rep2

value: Macrophages derived from THP-1 cultured in FPCO medium


title: WG179_YPR-90min_OS-2min_rep2


title: Skin tissue, Normal, rep 7


title: M0_D7 rep1


title: WG178_YPR-90min_OS-2min_rep1


title: Skin tissue, Normal, rep 6


title: M0pre rep2

source_name: Macrophages derived from THP-1

value: Macrophages derived from THP-1


title: Skin tissue, Normal, rep 5

value: Skin


title: M0pre rep3


title: Skin tissue, Atopic Dermatitis, Lesion, rep 3


title: M0pre rep1


title: WG176_YPG-90min_OS-2min_rep1


title: WG177_YPG-90min_OS-2min_rep2


title: THP-1 rep3


title: Skin tissue, Normal, rep 4


title: WG175_YPG-60min_OS-2min_rep2


title: Skin tissue, Normal, rep 2


title: Skin tissue, Normal, rep 3


title: WG173_YPG-30min_OS-2min_rep2


title: WG174_YPG-60min_OS-2min_rep1


title: heart_homozygous_rep3

description: replicate 3

value: homozygous ABCB5 mutant

value: 17 weeks

value: heart


title: heart_homozygous_rep1

description: replicate 1


title: heart_wildtype_rep3

description: replicate 3


title: heart_homozygous_rep4

description: replicate 4


title: heart_wildtype_rep4

description: replicate 4


title: THP-1 rep1


title: Skin tissue, Normal, rep 1


title: heart_wildtype_rep2

description: replicate 2


title: WG172_YPG-30min_OS-2min_rep1


title: RORc+_Cells_Experiment_cDNA

city: Jerusalem

first: Oren

last: Parnas

address: Faculty of Medicine, Ein-Kerem medical center

department: Immunology

institute: The Hebrew University of Jerusalem

data_processing:
cDNA Fastq files were aligned to mm10 library (Ensembl v98) using Cellranger (v8.0).
Seurat (v4.3.1) was used to create an object that combined all samples. Cells with low cDNA counts or with a high percentage of mitochondrial genes were filtered out.
Normalization of individual assays and other downstream analysis was performed as detailed in methods in the paper.
Assembly: MM10
Supplementary files format and content: scRNA-seq 10X output format

source_name: liver

extract_protocol:
GFP+ Immune cells were isolated from 6 months old DEN-injected mice. Immune cells were isolated from 5 IKK RORc Het mice (cells were pooled after isolation). Livers were cut to small pieces in 5 ml liver digest medium, squashed with a syringe piston, and incubated at 37⁰c for 30 min. PBS was added and cells were centrifuged at 350g for 5 min at 4⁰c. Suspension was passed through a 70 µm mesh filter. Two centrifugations at 30g for 5 min at 4⁰c were performed to reduce hepatocytes content. Supernatant was then centrifuged at 350g at 4⁰c to precipitate the immune cells, and the pellet was resuspended in 6ml of 35% Percoll and gently placed on top of 3ml of 75% Percoll. Cells were centrifuged for 20 min at 900g without brake, and the ring of immune cells between the 2 Percoll concentrations was taken out into PBS and centrifuged for 8 min at 350g. Red blood cell lysis was performed for 2 min at RT and cells were resuspended in PBS+2%FBS (FACS buffer). Cells were counted using Trypan blue.  GFP+ cells were sorted using a BD FACSAria™ III sorter. Sorting was performed using a 85-micron nozzle and threshold was kept in the range of 3000 events/second. Cells were sorted into Eppendorf tubes containing 1ml FACS buffer, and then centrifuged without brake. Cells were counted and brought to a concentration of 1000 cells/µl.
Cells were loaded onto a Chromium single-cell 3′ v2 chip (10x Genomics) and libraries were prepared according to the manufacturer’s protocol.
Libraries were sequenced by Illumina HiSeq 2500 and the reads were mapped to mm10 library (ensembl v98).

value: liver

value: GFP+ immune cells

value: Alb-IKKBeta(EE)Hep;RORctm2Litt +/-  (termed:IKK RORc Het)


title: heart_homozygous_rep2

description: replicate 2


title: HULEC, ACRE-DEP, 24hr  exposure, biological replicate 3

city: College Station

first: Eva

last: Vitucci

state: TX

address: 212 Adriance Lab Road

institute: Texas A&M University

data_processing:
Mapping of sequence reads to the human genome (GRCh38) was performed by STAR (version 2.5) with the following parameters: -- outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 -- outMultimapperOrder Random (other parameters at default settings).
Mapped read counts per gene were collected by Subread feature Counts (version 1.5.0-0-p1).
Genes with a minimum average of normalized mapped read counts > 50 in at least one category were selected for differential gene expression analysis.
Differential gene expression analysis was conducted using DESeq2 (v1.34.0) with filtering thresholds of FDR < 0.01 and |fold change| > 2 to normalize gene expression and identify differentially expressed genes.
Assembly: human genome (GRCh38)
Supplementary files format and content: tab-delimited text files include the average, of 3 biological replicates, baseMean, log2FoldChange, lfcSE, stat, pvalue, and padj values for each exposure condition (cell type, exposure timepoint, exposure material)

source_name: HULEC

extract_protocol:
Total RNA was extracted from the H441 and HULEC using the Zymo Quick-RNA Miniprep Kit (Zymo Research, #R1055) and quantified using a Nanodrop OneC nanospectrophotometer (ThermoFisher). Total RNA concentration and quality was validated by running an RNA broad range Qubit (Thermo Fisher Scientific, #Q10211) and from an Agilent Tapestation 4200 (Agilent, Model #G2991BA), respectively, at the UNC High Throughput Sequencing core.
cDNA libraries for the H441 and HULEC RNA-seq analysis were generated at the UNC High Throughput Sequencing core using the KAPA Stranded mRNA-Seq Kit, with KAPA mRNA Capture Beads (Roche Sequencing and Life Science, #07962207001) to enrich for polyadenylated species

tag: time

value: HULEC

value: lung microvascular endothelial cell

value: WT

value: ACRE-DEP


title: WG171_YPR-0min_OS-2min_rep2


title: WG170_YPR-0min_OS-2min_rep1


title: liver_homozygous_rep1

description: replicate 1

value: male


title: HULEC, ACRE-DEP, 24hr  exposure, biological replicate 2


title: Control_cDNA

description:
Combined_cDNA_AllCellTypes.tar.gz
Combined_cDNA_TCells.tar.gz
Combined_cDNA_BCells.tar.gz

data_processing:
cDNA Fastq files were aligned to mm10 library (Ensembl v98) using Cellranger (v4.0.6). Each GEM was processed separately.
Seurat (v4.0.2) was used to create an object that combined all samples. Cells with low cDNA counts or with a high percentage of mitochondrial genes were filtered out.
Normalization of individual assays and other downstream analysis was performed as detailed in methods in the paper.
Subanalysis of T-Cell and B-Cell populations was performed as well.
Assembly: mm10
Supplementary files format and content: Matrices containing cDNA UMIs for all cells and selected subpopulations of cells:  Combined_cDNA_AllCellTypes.tar.gz (in barcodes.tsv: 1k - Experiment_1, 2k - Experiment_2, 3k - Control), Combined_cDNA_TCells.tar.gz, Combined_cDNA_BCells.tar.gz.

extract_protocol:
Livers were cut to small pieces in 5 ml liver digest medium, squashed, and incubated at 37⁰c for 30 min. PBS was added and cells were centrifuged at 350g for 5 min at 4⁰c. Further digestion was done with Accumax+DNAse for 10 min at 37⁰c followed by neutralization with FBS and PBS. Suspension was filtered through a 70 µm mesh. Two centrifugations at 30g for 5 min at 4⁰c were performed to reduce hepatocytes content. Supernatant was then centrifuged at 350g at 4⁰c to precipitate the immune cells, and the pellet was resuspended in 6ml of 35% Percoll and gently placed on top of 3ml of 75% Percoll. Cells were centrifuged for 20 min at 900g without brake, and the ring of immune cells between the 2 Percoll concentrations was taken into PBS and centrifuged for 8 min at 350g. Red blood cell lysis was performed and three million cells were taken for antibody staining. Before staining, blocking (FACS buffer, 1%Rat Serum, 1%Fc Blocker) was done for 10 min at 4⁰c. Cells were incubated with primary antibodies (Pacific Blue-CD45 and APC-F4/80) for 20 minutes at 4⁰c. Cells were washed and filtered. Viable CD45+F4/80-  cells were sorted using a BD FACSAria™ III sorter.
Cells were loaded onto a Chromium single-cell 3′v2 chip (10x Genomics) and libraries were prepared according to the manufacturer’s protocol.
Libraries were sequenced by Illumina HiSeq 2500 and the reads were mapped tomm10library (ensembl v98).

value: CD45+ immune cells

value: Alb-IKKbeta(EE)Hep;RORctm2Litt +/- (termed:IKK RORc Het)


title: HULEC, ACRE-DEP, 24hr  exposure, biological replicate 1


title: HULEC, vehicle control, 24hr  exposure, biological replicate 3

value: Vehicle


title: THP-1 rep2


title: heart_wildtype_rep1

description: replicate 1

value: wild type


title: WG246_OS-30min_rep2


title: WG245_OS-10min_rep2


title: Experiment_1_cDNA

value: Alb-IKKbeta(EE)Hep;RORctm2Litt -/- (termed:IKK RORc KO)


title: HULEC, vehicle control, 24hr  exposure, biological replicate 2


title: liver_homozygous_rep3

description: replicate 3


title: liver_wildtype_rep3

description: replicate 3


title: liver_wildtype_rep4

description: replicate 4


title: KO_DS_3

city: Shanghai

first: Jianghong

last: Yu

state: State...

address: Dong'an Road

institute: Fudan University

description:
gene_sample_log2normalized_count_with_symbol
gene_sample_log2FPKM_with_symbol

data_processing:
The raw data was handled by Skewer and data quality was checked by fastq.gzC v0.11.2 (http:// www.bioinformatics.babraham.ac.uk/projects/fastq.gzc/ ).
Clean reads were aligned to the  GrCM38/mm10 using STAR.
The expression of the transcript was calculated by FPKM (Fragments Per Kilobase of exon model per Million mapped reads) using Perl.
Assembly: mm10
Supplementary files format and content: gene_sample_log2normalized_count_with_symbol
Supplementary files format and content: gene_sample_log2FPKM_with_symbol

source_name: colon

extract_protocol:
Total RNA from mouse colon tissues was extracted using the TRIzol reagent, according to the manufacturer’s instructions.
Preparation of library and sequencing of transcriptome were implemented with Illumina HiSeq 2500 system.

treatment_protocol: Expression changes of genes in colon tissues from Glul∆Lyz2 mice and Glul f/f littermates treated with H2O or DSS

value: colon

value: tissue

value: Glul KO

value: DSS


title: KO_DS_2


title: HULEC, vehicle control, 24hr exposure, biological replicate 1


title: WG243_OS-3min_rep2


title: HULEC, ACRE-DEP, 6hr exposure, biological replicate 3

value: 6 h


title: KO_DS_1


title: liver_wildtype_rep1

description: replicate 1

value: 17 weeks

value: liver


title: WG242_OS-2min_rep2


title: DS4


title: WG241_OS-1min_rep2


title: HULEC, ACRE-DEP, 6hr exposure, biological replicate 2

value: HULEC


title: Experiment_2_cDNA


title: HULEC, ACRE-DEP, 6hr exposure, biological replicate 1

value: lung microvascular endothelial cell


title: WG240_OS-30s_rep2


title: HULEC, vehicle control, 6hr exposure, biological replicate 3

value: WT


title: DS1


title: WG244_OS-5min_rep2


title: DS2


title: WG239_UT_rep2


title: HULEC, vehicle control, 6hr exposure, biological replicate 2


title: KO2


title: NCI-H441 cells, ACRE-DEP, 24hr  exposure, biological replicate 3

value: alveolar-like epithelial cell

value: ACRE-DEP


title: KO1


title: KO3


title: WG229_OS-10min_rep1


title: WG227_OS-3min_rep1


title: WT3


title: WG228_OS-5min_rep1


title: WG226_OS-2min_rep1


title: NCI-H441 cells, ACRE-DEP, 24hr  exposure, biological replicate 2


title: liver_wildtype_rep2

description: replicate 2

value: male


title: WT2


title: WG225_OS-1min_rep1


title: HULEC, vehicle control, 6hr exposure, biological replicate 1


title: NCI-H441 cells, ACRE-DEP, 24hr  exposure, biological replicate 1


title: liver_homozygous_rep2

description: replicate 2

value: homozygous ABCB5 mutant


title: NCI-H441 cells, vehicle control, 24hr  exposure, biological replicate 3

value: Vehicle


title: WG223_UT_rep1


title: DN-FAPs

city: Chengdu

first: Xia

last: Kang

address: Rongdu Avenue, #270

institute: General Hospital of Western Theater Command

library_source: other

data_processing:
The raw data were processed using an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA) to remove adapter dimers, junk, low complexities, common RNA families (rRNA, tRNA, snRNA, snoRNA) (http://rfam.sanger.ac.uk/), repeats (http://www.girinst.org/repbase), and sequences <18 nt or >26 nt in length.
The unique sequences that aligned to the known miRNAs sequences in miRBase 22.0 were identified as known miRNA. Secondary structure of pre-miRNAs was presented as a hairpin, including 5p- and 3p- derived miRNA.
all the obtained miRNAs were used to predict the secondary structures using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAWebSuite/RNAfold.cgi).
miRNA differential expression based on normalized deep-sequencing counts was analyzed by selectively using Student t test. The significance threshold was set to be 0.05 in the test.
Assembly: The mapped reads of each sample were assembled using StringTie.
Supplementary files format and content: Matrix table with raw gene counts for differentially expressed genes

molecule: other

source_name: muscle

growth_protocol: Primary FAPs were directly isolated from muscles without culture in vitro.

extract_protocol:
Total RNA was extracted using an Total RNA Purification Kit (LC Sciences, Houston, USA)
Sequencing libraries were generated using a TruSeq Small RNA Sample Prep Kits(Illumina, San Diego, USA)

treatment_protocol: Muscles were injured with injection of cardiotoxin, or performed sciatic denervation or without injury

value: muscle

value: primary cells

value: sciatic denervation


title: IsoA stimulated rep4

description: replicate 6

source_name: t cells

treatment_protocol: MALT1-deficient CD4-positive T cells of four individual mice were purified and retrovirally resonstituted with either MALT1 isoform A, MALT1 isoform B or mock. The cells were stimulated with CD3/CD28 for 2,5 h and then lysed, giving rise to four samples per mouse: MALT1 isoform A unstimulated, mock stimulated, MALT1 isoform A stimulated, MALT1 isoform B stimulated.

value: MALT1 deficient

value: MALT1 IsoA transfected, stimulated with CD3/CD28

value: CD4+ T cell

tag: genetic background


title: IsoB stimulated rep4

description: replicate 1

value: MALT1 IsoB transfected, stimulated with CD3/CD28


title: IsoB stimulated rep3

description: replicate 3


title: WT1

value: colon

value: tissue


title: WG136_top2td_Degron_rep1

source_name: W303-1a top2-td

value: W303-1a top2-td


title: NCI-H441 cells, ACRE-DEP, 6hr exposure, biological replicate 3

value: 6 h


title: CTXD5-FAPs

value: WT

value: cardiotoxin


title: WG134_wtdgb_Degron_rep1

source_name: W303-1a degron background control

value: W303-1a degron background control


title: IsoA unstimulated rep4

description: replicate 5

value: MALT1 IsoA transfected, unstimulated with CD3/CD28


title: IsoB stimulated rep2

description: replicate 3


title: IsoA unstimulated rep3

description: replicate 1


title: IsoA stimulated rep3

description: replicate 2


title: NCI-H441 cells, vehicle control, 24hr  exposure, biological replicate 2

value: alveolar-like epithelial cell


title: WG224_OS-30s_rep1


title: IsoA stimulated rep2

description: replicate 2


title: NCI-H441 cells, ACRE-DEP, 6hr exposure, biological replicate 2

value: ACRE-DEP


title: Normal-FAPs

value: muscle

value: normal


title: Mock stimulated rep4

description: replicate 2

value: Mock transfected, stimulated with CD3/CD28


title: Mock stimulated rep2

description: replicate 4

value: MALT1 deficient


title: NCI-H441 cells, ACRE-DEP, 6hr exposure, biological replicate 1


title: WG215_YPD_rep2


title: WG206_YPD_rep1c


title: NCI-H441 cells, vehicle control, 6hr exposure, biological replicate 3

value: Vehicle


title: Mock stimulated rep3

description: replicate 4

value: CD4+ T cell


title: control muscle, 10 days old_rep2

city: Vienna

first: Maria

last: Novatchkova

address: Dr Bohrgasse

country: Austria

institute: IMP/IMBA

data_processing:
Reads were trimmed using trim-galore v0.5.0, and reads mapping to abundant sequences included in the iGenomes UCSC GRCm38 reference (mouse rDNA, mouse mitochondrial chromosome, phiX174 genome, adapter) were removed using bowtie2 v2.3.4.1 alignment. Remaining reads were aligned to the mouse genome (Ensembl GRCm38 release 94) using star v2.6.0c, and reads in genes were counted with featureCounts (subread v1.6.2; -s 2).
Assembly: mm10
Supplementary files format and content: tab-delimited text files of readcounts per sample per gene

source_name: skeletal muscle/quadriceps

growth_protocol: Control Pcyt2 flox/flox and Myf5Cre-Pcyt2 mice were fed chow diet and maintained at standard housing conditions

extract_protocol: RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: Skeletal muscle (quadriceps) was surgicaly removed from terminally sacrificed P10 old pups and frozen in LN2.

value: skeletal muscle/quadriceps

value: Pcyt2 flox/flox


title: Myf5Cre-Pcyt2 muscle, 10 days old_rep3

value: Myf5Cre-Pcyt2 flox/flox


title: Myf5Cre-Pcyt2 muscle, 10 days old_rep1


title: NCI-H441 cells, vehicle control, 6hr exposure, biological replicate 2


title: control muscle, 10 days old_rep3


title: KYSE410 Hypoxia rep3

city: Changchun

first: Tongjian

last: Zhao

address: 1266 Fujin Road

institute: School of Pharmaceutical Sciences, Jilin University

description:
K410expression_matrix.txt
K410H3_S58

data_processing:
bcl2fastq,v2.20
fastp,0.22.0
HISAT2,2.2.1
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

extract_protocol:
RNA was harvested using TRIzol™ Reagent (ThermoFisher). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using VAHTS VAHTS mRNA Capture Beads and VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina  following manufacturer's protocols.

value: esophageal cancer cell line

value: ambient o2 concentration:0.50percent duration of hypoxia

tag: time point

value: 48 hours


title: control muscle, 10 days old_rep1


title: NCI-H441 cells, vehicle control, 24hr exposure, biological replicate 1

value: WT


title: WG204_YPD_rep1a


title: Mock stimulated rep1

description: replicate 4


title: Myf5Cre-Pcyt2 muscle, 10 days old_rep2


title: POI1

city: Guangzhou

first: Xiaofei

address: 1838 North Guangzhou Avenue

department: Department of Gynecology and Obstetrics

institute: Nanfang Hospital, Southern Medical University

data_processing:
Raw reads obtained by Illumina HiSeq2500 sequencing are filtered first: remove the adapters at both ends of reads, remove reads with fragment length <17nt and low-quality reads, etc. complete the preliminary filtering of data and obtain high-quality data (clean reads).  Genome-wide reads distribution map was obtained by aligning clean reads with reference genome, and ncRNA classification annotation was performed on clean reads.  The miRNA expression was calculated, miRNA expression clustering and miRNA differential expression analysis among samples.
Assembly: hg38
Supplementary files format and content: Microsoft Excel  Worksheet (.xls) file includes counts for each sample

source_name: Follicular fluid exosomes

extract_protocol:
Follicular fluid from POI patients and control group patients were collected. Exosomes from follicular fluid were extracted by ultracentfugation method, total RNA from exosomes was extracted by trizol method, and sRNA of 18-30nt was screened for high throughput sequencing
The library construction process mainly includes the following steps: extraction of total RNA or purified sRNA fragments of the sample, connection of connector successively, reverse transcription into cDNA, and then PCR amplification. Then the target fragment library was recovered by cutting glue, and the qualified library was sequenced.

value: Follicular fluid exosomes

value: Premature ovarian insufficiency


title: IsoB stimulated rep1

description: replicate 3

value: MALT1 IsoB transfected, stimulated with CD3/CD28


title: POI2


title: IsoA unstimulated rep2

description: replicate 1

value: MALT1 IsoA transfected, unstimulated with CD3/CD28


title: IsoA unstimulated rep1

description: replicate 1


title: WG205_YPD_rep1b


title: IsoA stimulated rep1

description: replicate 2

value: MALT1 IsoA transfected, stimulated with CD3/CD28


title: Con3

value: Normal ovarian reserve


title: HC618110940

city: Beijing

first: Yin

last: Wu

state: -- select

address: No. 8 Gongti south street road, Chaoyang district

department: Heamotologic department

institute: Capital Medical University Beijing Chaoyang Hospital

description: see next sheet

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Primeview Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 7G.

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

source_name: NDMM bone marrow plasmacells, CD138 magnetic beads sorted

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: primary plasmacells were sortted from bone marrow of newly diagnosed multiple myeloma patients using CD138 magnetic beads according to the manufacturer's instructions.

extract_protocol: Trizol extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: no

value: Batch 4

tag: gender

value: M

tag: time at diagnosis

tag: type

value: IgG-K

tag: riss

value: II

tag: treatment strategy

tag: best respose

value: VGPR

tag: chromosome

value: complicated

tag: FISH


title: HC618110946

description: see next sheet

tag: batch

tag: age

value: IgG-Lambda

value: PR MRD+

value: negtive

tag: os(months)


title: HC618110938

description: see next sheet

value: CR

value: ND


title: NCI-H441 cells, vehicle control, 6hr exposure, biological replicate 1

value: 6 h

tag: cell line

tag: cell type

value: alveolar-like epithelial cell

tag: genotype

value: WT

tag: treatment

value: Vehicle


title: POI3

tag: tissue

value: Follicular fluid exosomes

value: Premature ovarian insufficiency


title: HC618110937

description: see next sheet

value: Batch 4

value: F

value: IgA-k

value: III

value: BCD*2, BTD*1, RD maintenance