title: Blood plasma EVs, EoE.Basal ID 29


title: Blood plasma EVs, EoE.Pos.tx ID 50

status: Public on Oct 15 2024

type: SRA

first: Elena

last: Grueso-Navarro

state: Ciudad Real

address: Vereda de Socuéllamos s/n

department: Gastroenterology

country: Spain

institute: Hospital General de Tomelloso

library_source: transcriptomic

data_processing:
raw reads processing included quality control analysis with multiQC v1.6 tool
trimming for Illumina adapters, and alignment to human genome using BWA (Burrow-Wheeler aligner)
Gene quantification by means HTseq software(3) was performed using gencode v.26 as annotation database
To determine the overall microRNA (miRNA) and transfer RNA-Related Fragments (tRFs) composition for each sample, miRge3.0 pipeline(5) from processed reads from no outliers against a set of sRNA annotation libraries was used to obtain their tabulated counts.
Assembly: gencode v.26
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

molecule: total RNA

organism: Homo sapiens

source_name: Blood plasma

extract_protocol:
Total RNA was isolated from EV samples using Total RNA Purification Kit (Norgen Biotek, Ontario, Canada) and treated with DNAse with RNAse-free DNAse I Kit (Norgen Biotek) to eliminate contaminant DNA according to manufacturer’s protocol.
Sequencing libraries were prepared following the manufacturer’s protocol for “NEXTflex™ Small RNA-Seq Kit v3” (Bioo Scientific Corporation, Austin, TX, USA).

tag: tissue

value: Blood plasma


title: Blood plasma EVs, EoE.Basal ID 10


title: Blood plasma EVs, EoE.Basal ID 11


title: Blood plasma EVs, EoE.Basal ID 18


title: Blood plasma EVs, EoE.Basal ID 5


title: Blood plasma EVs, EoE.Pos.tx ID 1


title: Drosophila_simulans_testes_G_87_87c_S11

city: Davis

first: Ben

last: Hopkins

state: CA

address: One Shields Avenue

department: Evolution & Ecology

country: USA

institute: UC Davis

data_processing:
After quality filtering with trimmomatic, we obtained 10, 22, 38, and 54 million reads for each of the 4 or five libraries.
Mapped paired-end reads to the genome and annotation from each species using STAR v. 2.5.3 (Dobin et al. 2013).
Assemlbed reference-only transcripts using Stringtie v. 1.3.4 (Pertea et al. 2015) to estimate expression in Transcrpts per million (TPM).
Assembly: Flybase: Dmel_r6.12, Dsim_r2.02, Dyak_r1.05, Dana_r1.05  NCBI: Dbia_2.0, Dbip_2.0, Dele_2.0, Deug_2.0, Dfic_2.0, Dkik_2.0, Dtak_2.0
Supplementary files format and content: Tab delimmited TPM files. One column for each biological replicate

molecule: polyA RNA

organism: Drosophila simulans

source_name: testes

extract_protocol:
We isolated mRNA from total RNA using NEBNext Poly(A) mRNA magnetic isolation.
Constructed RNA-seq directional paired-end libraries using NEBNext Ultra Directional RNA Library prep kit. We quantified library size using NEBNext Library Quant Kit (New England BioLabs, Ipswich, MA)

value: testes

tag: sample id

tag: library name

tag: strain information


title: Blood plasma EVs, Control, ID 3


title: Blood plasma EVs, EoE.Basal ID 4


title: Drosophila_simulans_ag_NG_64_64c_S7

source_name: accessory glands

value: accessory glands


title: Drosophila_simulans_ag_NG_91_91b_S19


title: Drosophila_simulans_testes_NG_81_81b_S36


title: B6_D0, RNA-seq

city: dallas

first: Shaheen

last: Khan

state: texas

address: 5323 Harry Hines Blvd

institute: UT Southwestern Medical Center

description: RNA-seq data

data_processing:
Reads with phred quality scores less than 20 and less than 35 bp after trimming were removed from further analysis using trimgalore version 0.4.1
Quality-filtered reads were then aligned to the mouse reference genome GRCm38 (mm10) using the HISAT (v 2.0.1) (Kim, Langmead, & Salzberg, 2015) aligner using default settings and marked duplicates using Sambamba version 0.6.6 (Tarasov et al., 2015).
Aligned reads were quantified using ‘featurecount’ (v1.4.6) (Liao et al., 2013) per gene ID against mouse Gencode version 20 (Frankish et al., 2018).
RNA-seq data was also analyzed using CLC Biosystems Genomic Workbench software (CLC Bio, a Qiagen company. Location: Waltham, MA).
Assembly: GRCm38
Supplementary files format and content: text files FPKM/RPKM

organism: Mus musculus

source_name: BMDCs

growth_protocol: Naive T cells were purified from splenic cell suspensions using EasySep mouse naive CD4+ T Cell Isolation Kit (StemCell Technologies) and cultured with or without anti-CD3 and anti-CD28 antibodies for different time points. Single-cell suspensions of Bone marrow were cultured with macrophage colony-stimulating factor (M-CSF) to generate BMDMs, or interleukin-4 (IL-4) plus granulocyte-macrophage-CSF (GM-CSF) to generate BMDCs (10 ng/ml for all cytokines; R&D Systems). All cells were cultured in RPMI-1640 with 10% FBS, 2 mM L-glutamine, 10 mM HEPES, 1 mM sodium pyruvate, 100 U/ml penicillin, 100 µg/mL streptomycin at 37ºC in a humidified CO2 incubator

extract_protocol:
RNA was isolated from CD4 T cells, BMDMs, and BMDCs using TRIzol reagent (Life Technologies) and RNAeasy kit per the manufacturer’s protocol (Qiagen Corp. Valencia, CA). RNA quality was verified using Agilent Bioanalyzer 2100 (Agilent Technologies).
One μg of total RNA was used to perform RNA-SEQ using TruSeq RNA Sample Preparation kit v2 (Illumina) as per the manufacturer’s instructions. The library from each sample was sequenced on Illumina Hiseq 2000 or NextSeq 550 using 50-bp or 36-bp single-end protocol

treatment_protocol: BMDMs or BMDCs were stimulated with 1 ug/ml R848 or 1µM ODN18206 or 10 ng/ml of LPS for all the experiments.

tag: age

value: 8-12 wk old

tag: timepoint

value: 0 h

tag: cell type

value: BMDCs

tag: genotype

tag: treatment


title: Sle3_D0, RNA-seq

description: RNA-seq data


title: B6_D1, RNA-seq

description: RNA-seq data

value: 6 h


title: Sle3_D1, RNA-seq

description: RNA-seq data


title: Blood plasma EVs, EoE.Basal ID 24


title: KLF13-/-_D3, replicate 2, ATAC-seq

description: ATAC-seq data

library_source: genomic

data_processing:
Reads were mapped to the B6 mouse reference genome mm10 using BWA (Burrows-Wheeler transformation)
Paired-end reads were adapter and quality trimmed using Trim Galore, then mapped to the mouse genome (GRCm38) using bwa.
Duplicates were remarked and proceeded with filtering to remove: reads mapping to mitochondrial DNA, mapping to blacklisted regions, reads marked as duplicates, secondary alignment reads, unmapped reads, multimapping reads, reads containing greater than 4 mismatches, soft-clipped reads, reads with a calculated insert size over 2kb, read pairs mapping to a different chromosome, reads not in the FR orientation, reads where only one read of a pair fails any of the previous filters.
Broad peaks were called with MACS2, peaks were annotated relative to gene features using HOMER, and consensus peaks across replicates were detected.
Bedgraphs were converted to Bigwig files
Assembly: GRCm38
Supplementary files format and content: Bigwig/Bedgraphs

molecule: genomic DNA

extract_protocol:
ATAC-seq library preparations were performed as described in Buenostro et al., 2015. 40,000-60,000 cells were used with 10 cycles of PCR amplification
All the libraries were sequenced using NextSeq 550 using 75-bp paired-end protocol.


title: WT_D2, replicate 2, ATAC-seq

description: ATAC-seq data

value: Wild type


title: WT_D2, replicate 1, ATAC-seq

description: ATAC-seq data


title: KLF13-/-_D1, replicate 2, ATAC-seq

description: ATAC-seq data


title: KLF13-/-_D1, replicate 1, ATAC-seq

description: ATAC-seq data


title: WT_D1, replicate 1, ATAC-seq

description: ATAC-seq data


title: Blood plasma EVs, EoE.Basal ID 13


title: KLF13-/-_D3, replicate 1, ATAC-seq

description: ATAC-seq data


title: KLF13-/-_M, replicate 1, ATAC-seq

description: ATAC-seq data

source_name: BMDM

value: BMDM


title: WT_D1, replicate 2, ATAC-seq

description: ATAC-seq data


title: KLF13-/-_T1, replicate 2, ATAC-seq

description: ATAC-seq data

source_name: CD4 T cell

value: CD4 T cell


title: WT_M, replicate 2, ATAC-seq

description: ATAC-seq data


title: KLF13-/-_M, replicate 2, ATAC-seq

description: ATAC-seq data


title: KLF13-/-_T1, replicate 1, ATAC-seq

description: ATAC-seq data


title: WT_T1, replicate 2, ATAC-seq

description: ATAC-seq data


title: WT_T1, replicate 1, ATAC-seq

description: ATAC-seq data


title: WT_M, replicate 1, ATAC-seq

description: ATAC-seq data


title: WT_T, replicate 2, ATAC-seq

description: ATAC-seq data


title: KLF13-/-_T, replicate 2, ATAC-seq

description: ATAC-seq data


title: Sle3k_M, replicate 1, ATAC-seq

description: ATAC-seq data


title: B6_M, replicate 2, ATAC-seq

description: ATAC-seq data


title: B6_M, replicate 1, ATAC-seq

description: ATAC-seq data


title: Sle3k_M, replicate 2, ATAC-seq

description: ATAC-seq data


title: Sle3k_T, replicate 2 ATAC-seq

description: ATAC-seq data


title: B6_T, replicate 2, ATAC-seq

description: ATAC-seq data


title: B6_T, replicate 1, ATAC-seq

description: ATAC-seq data


title: Mouse lung cells, Saline, Day2, rep3

city: Omaha

first: Aaron

middle: D

last: Schwab

state: NE

address: 42nd and Emile St.

institute: University of Nebraska Medical Center

data_processing:
The original fastq format reads were trimmed by fqtirm tool (https://ccb.jhu.edu/software/fqtrim) to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30).
The trimmed fastq files were processed by FastQC (Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data; available online at:http://www.bioinformatics.babraham.ac.uk/projects/fastqc) for quality control.
The trimmed fastq files were processed by a standard pipeline utilizing STAR as the aligner and RSEM as the tool for annotation and quantification at gene level.
The trimmed fastq files were mapped to mm10 (GRCm38) mouse reference genome
Assembly: mm10 (GRCm38)
Supplementary files format and content: Excel spreadsheet that gives raw read counts and normalized expression abundance in TPM and FPKM values for all the available genes.

source_name: Primary mouse lung

extract_protocol:
RNA was harvested using Rneasy mini kit (Qiagen).
Sequencing libraries were generated by the UNMC NGS Core using the NuGEN Universal Plus mRNA-Seq library kit from TECAN following the manufacturers recommended procedure (TECAN, USA Redwood City, CA 94063).

treatment_protocol: C57BL/6J (WT) mice were intratracheally instilled with either 10 ug of LPS (O55:B5; Sigma, St. Louis, MO) or saline in a 50 ul volume. Animals were euthanized 48 hours post-exposure, lungs were perfused, harvested, and homogenized in a collagenase solution. RNA was extracted from single cell suspension of resultant lung homogenate.

value: Primary mouse lung

tag: strain

value: Collagenase treated lung homogenate

value: WT

tag: Sex

value: male

value: Intratracheal Saline


title: Mouse lung cells, LPS, Day2, rep2

value: Intratracheal 10ug LPS


title: Mouse lung cells, LPS, Day2, rep3


title: Mouse lung cells, Saline, Day2, rep1


title: ApoA1 positive MG from ApoA1 KO mouse 4

city: Stanford

first: Tony

last: Wyss-Coray

address: 290 Jane Stanford way, RM E365 TWC-Neurology

institute: Stanford University

data_processing:
Adapter sequences and low-quality base calls (Phred score < 30 at ends) were trimmed using Cutadapt v1.8.1. Trimmed reads were aligned to the reference genome using STAR 2.7.10b with comprehensive gene annotations from GENCODE release vM30. Gene-level transcript abundances were quantified with RSEM v1.3.1. RNA-Seq read counts and Transcripts Per Million (TPM) values were obtained from RSEM output and imported into R software for further analysis
Assembly: mm10
Supplementary files format and content: gene count (Rdata)
Supplementary files format and content: gene Tpm (Rdata)

source_name: isolated cells

extract_protocol:
RNA was extracted using Rneasy plus micro kit (Qiagen)
Libraries were prepared using a SMART-Seq mRNA LP and a SMART-Seq Library Prep Kit following manufacturer's protocols

tag: cell line

value: isolated cells

value: microglia


title: Mouse lung cells, Saline, Day2, rep2


title: ApoA1 positive MG from ApoA1 KO mouse 3


title: ApoA1 positive MG from ApoA1 KO mouse 2


title: Mouse lung cells, LPS, Day2, rep1


title: ApoA1 negative MG from ApoA1 KO mouse 4


title: WT_T, replicate 1, ATAC-seq

description: ATAC-seq data


title: ApoA1 negative MG from ApoA1 KO mouse 3


title: ApoA1 positive MG from WT mouse 2


title: ApoA1 positive MG from ApoA1 KO mouse 1


title: KLF13-/-_T, replicate 1, ATAC-seq

description: ATAC-seq data


title: ApoA1 positive MG from WT mouse 4


title: ApoA1 negative MG from ApoA1 KO mouse 2


title: Sle3k_T, replicate 1 ATAC-seq

description: ATAC-seq data


title: ApoA1 positive MG from WT mouse 1


title: ApoA1 negative MG from WT mouse 2


title: ApoA1 negative MG from WT mouse 4


title: ApoA1 positive MG from WT mouse 3


title: ApoA1 negative MG from WT mouse 1


title: ApoA1 negative MG from WT mouse 3


title: P22-TH-3-plasma intensity high

description: smart-seq 2

data_processing:
raw sequencing files in blc format were demultiplexed with bcl2fastq to generate fastq files and were trimmed to remove adaptor contamination and poor-quality reads using Trim Galore!. Trimmed reads were aligned using STAR (v.2.5.3a) GeneCounts function, multi-mapped reads were filtered, and gene expression matrices were generated using SeqMonk. Seurat package was used to perform all downstream analysis.
Assembly: mm10
Supplementary files format and content: counttable (Text file)

source_name: Brain

extract_protocol:
cells were lysed in the lysis buffer and follow the smart-seq2 pipeline to generate cDNA
smart-seq2 in house pipeline

value: Brain


title: P21-TH-3-plasma intensity high

description: smart-seq 2


title: P23-TH-3-plasma intensity high

description: smart-seq 2


title: P19-TH-3-plasma intensity high

description: smart-seq 2


title: P18-TH-3-plasma intensity high

description: smart-seq 2


title: P14-TH-3-plasma intensity low

description: smart-seq 2


title: P16-TH-3-plasma intensity low

description: smart-seq 2


title: P17-TH-3-plasma intensity high

description: smart-seq 2


title: ApoA1 negative MG from ApoA1 KO mouse 1


title: P15-TH-3-plasma intensity low

description: smart-seq 2


title: P12-TH-3-plasma intensity low

description: smart-seq 2


title: P10-TH-3-plasma intensity low

description: smart-seq 2


title: P13-TH-3-plasma intensity low

description: smart-seq 2


title: P11-TH-3-plasma intensity low

description: smart-seq 2


title: P7-TH-3-plasma intensity none

description: smart-seq 2


title: P4-TH-3-plasma intensity none

description: smart-seq 2


title: P6-TH-3-plasma intensity none

description: smart-seq 2


title: P2-TH-3-plasma intensity none

description: smart-seq 2


title: P8-TH-3-plasma intensity none

description: smart-seq 2


title: P1-TH-3-plasma intensity none

description: smart-seq 2


title: O23-TH-3-plasma intensity high

description: smart-seq 2


title: O24-TH-3-plasma intensity high

description: smart-seq 2


title: O22-TH-3-plasma intensity high

description: smart-seq 2


title: P20-TH-3-plasma intensity high

description: smart-seq 2


title: P5-TH-3-plasma intensity none

description: smart-seq 2


title: P9-TH-3-plasma intensity low

description: smart-seq 2


title: O17-TH-3-plasma intensity high

description: smart-seq 2


title: P3-TH-3-plasma intensity none

description: smart-seq 2


title: O19-TH-3-plasma intensity high

description: smart-seq 2


title: O16-TH-3-plasma intensity low

description: smart-seq 2


title: O20-TH-3-plasma intensity high

description: smart-seq 2


title: O15-TH-3-plasma intensity low

description: smart-seq 2


title: O21-TH-3-plasma intensity high

description: smart-seq 2


title: O18-TH-3-plasma intensity high

description: smart-seq 2


title: O14-TH-3-plasma intensity low

description: smart-seq 2


title: O13-TH-3-plasma intensity low

description: smart-seq 2


title: O11-TH-3-plasma intensity low

description: smart-seq 2


title: O12-TH-3-plasma intensity low

description: smart-seq 2


title: O10-TH-3-plasma intensity low

description: smart-seq 2


title: O8-TH-3-plasma intensity none

description: smart-seq 2


title: O6-TH-3-plasma intensity none

description: smart-seq 2


title: O9-TH-3-plasma intensity low

description: smart-seq 2


title: O5-TH-3-plasma intensity none

description: smart-seq 2


title: O7-TH-3-plasma intensity none

description: smart-seq 2


title: O4-TH-3-plasma intensity none

description: smart-seq 2


title: O3-TH-3-plasma intensity none

description: smart-seq 2


title: N22-TH-3-plasma intensity high

description: smart-seq 2


title: O2-TH-3-plasma intensity none

description: smart-seq 2


title: N21-TH-3-plasma intensity high

description: smart-seq 2


title: O1-TH-3-plasma intensity none

description: smart-seq 2


title: N23-TH-3-plasma intensity high

description: smart-seq 2


title: N14-TH-3-plasma intensity low

description: smart-seq 2


title: N15-TH-3-plasma intensity low

description: smart-seq 2


title: N19-TH-3-plasma intensity high

description: smart-seq 2


title: N16-TH-3-plasma intensity low

description: smart-seq 2


title: N10-TH-3-plasma intensity low

description: smart-seq 2


title: N18-TH-3-plasma intensity high

description: smart-seq 2


title: N12-TH-3-plasma intensity low

description: smart-seq 2


title: N11-TH-3-plasma intensity low

description: smart-seq 2


title: N20-TH-3-plasma intensity high

description: smart-seq 2


title: N9-TH-3-plasma intensity low

description: smart-seq 2


title: N13-TH-3-plasma intensity low

description: smart-seq 2


title: N7-TH-3-plasma intensity none

description: smart-seq 2


title: N3-TH-3-plasma intensity none

description: smart-seq 2


title: N2-TH-3-plasma intensity none

description: smart-seq 2


title: N6-TH-3-plasma intensity none

description: smart-seq 2


title: M21-TH-3-plasma intensity high

description: smart-seq 2


title: M20-TH-3-plasma intensity high

description: smart-seq 2


title: N1-TH-3-plasma intensity none

description: smart-seq 2


title: N4-TH-3-plasma intensity none

description: smart-seq 2


title: M23-TH-3-plasma intensity high

description: smart-seq 2


title: N17-TH-3-plasma intensity high

description: smart-seq 2


title: M24-TH-3-plasma intensity high

description: smart-seq 2


title: M22-TH-3-plasma intensity high

description: smart-seq 2


title: N5-TH-3-plasma intensity none

description: smart-seq 2


title: M17-TH-3-plasma intensity high

description: smart-seq 2


title: M18-TH-3-plasma intensity high

description: smart-seq 2


title: N8-TH-3-plasma intensity none

description: smart-seq 2


title: M19-TH-3-plasma intensity high

description: smart-seq 2


title: M15-TH-3-plasma intensity low

description: smart-seq 2


title: M11-TH-3-plasma intensity low

description: smart-seq 2


title: M14-TH-3-plasma intensity low

description: smart-seq 2


title: M8-TH-3-plasma intensity none

description: smart-seq 2


title: M9-TH-3-plasma intensity low

description: smart-seq 2


title: M5-TH-3-plasma intensity none

description: smart-seq 2


title: M10-TH-3-plasma intensity low

description: smart-seq 2


title: M16-TH-3-plasma intensity low

description: smart-seq 2


title: M7-TH-3-plasma intensity none

description: smart-seq 2


title: M6-TH-3-plasma intensity none

description: smart-seq 2


title: M3-TH-3-plasma intensity none

description: smart-seq 2


title: M4-TH-3-plasma intensity none

description: smart-seq 2


title: L24-TH-3-plasma intensity high

description: smart-seq 2


title: M2-TH-3-plasma intensity none

description: smart-seq 2


title: L22-TH-3-plasma intensity high

description: smart-seq 2


title: L23-TH-3-plasma intensity high

description: smart-seq 2


title: L19-TH-3-plasma intensity high

description: smart-seq 2


title: L21-TH-3-plasma intensity high

description: smart-seq 2


title: L20-TH-3-plasma intensity high

description: smart-seq 2


title: M1-TH-3-plasma intensity none

description: smart-seq 2


title: L16-TH-3-plasma intensity low

description: smart-seq 2


title: L18-TH-3-plasma intensity high

description: smart-seq 2


title: L17-TH-3-plasma intensity high

description: smart-seq 2


title: L14-TH-3-plasma intensity low

description: smart-seq 2


title: M12-TH-3-plasma intensity low

description: smart-seq 2


title: M13-TH-3-plasma intensity low

description: smart-seq 2


title: L13-TH-3-plasma intensity low

description: smart-seq 2


title: L12-TH-3-plasma intensity low

description: smart-seq 2


title: L11-TH-3-plasma intensity low

description: smart-seq 2


title: L7-TH-3-plasma intensity none

description: smart-seq 2


title: L5-TH-3-plasma intensity none

description: smart-seq 2


title: L10-TH-3-plasma intensity low

description: smart-seq 2


title: L6-TH-3-plasma intensity none

description: smart-seq 2


title: L9-TH-3-plasma intensity low

description: smart-seq 2


title: L2-TH-3-plasma intensity none

description: smart-seq 2


title: L4-TH-3-plasma intensity none

description: smart-seq 2


title: K21-TH-3-plasma intensity high

description: smart-seq 2


title: K23-TH-3-plasma intensity high

description: smart-seq 2


title: K20-TH-3-plasma intensity high

description: smart-seq 2


title: K22-TH-3-plasma intensity high

description: smart-seq 2


title: K19-TH-3-plasma intensity high

description: smart-seq 2


title: K18-TH-3-plasma intensity high

description: smart-seq 2


title: L15-TH-3-plasma intensity low

description: smart-seq 2


title: K16-TH-3-plasma intensity low

description: smart-seq 2


title: K13-TH-3-plasma intensity low

description: smart-seq 2


title: K14-TH-3-plasma intensity low

description: smart-seq 2


title: K10-TH-3-plasma intensity low

description: smart-seq 2


title: K15-TH-3-plasma intensity low

description: smart-seq 2


title: K12-TH-3-plasma intensity low

description: smart-seq 2


title: K8-TH-3-plasma intensity none

description: smart-seq 2


title: K6-TH-3-plasma intensity none

description: smart-seq 2


title: L8-TH-3-plasma intensity none

description: smart-seq 2


title: K9-TH-3-plasma intensity low

description: smart-seq 2


title: L1-TH-3-plasma intensity none

description: smart-seq 2


title: K5-TH-3-plasma intensity none

description: smart-seq 2


title: K4-TH-3-plasma intensity none

description: smart-seq 2


title: K1-TH-3-plasma intensity none

description: smart-seq 2


title: K2-TH-3-plasma intensity none

description: smart-seq 2


title: J24-TH-3-plasma intensity high

description: smart-seq 2


title: J22-TH-3-plasma intensity high

description: smart-seq 2


title: L3-TH-3-plasma intensity none

description: smart-seq 2


title: K17-TH-3-plasma intensity high

description: smart-seq 2


title: J21-TH-3-plasma intensity high

description: smart-seq 2


title: K11-TH-3-plasma intensity low

description: smart-seq 2


title: J18-TH-3-plasma intensity high

description: smart-seq 2


title: J19-TH-3-plasma intensity high

description: smart-seq 2


title: J23-TH-3-plasma intensity high

description: smart-seq 2


title: J14-TH-3-plasma intensity low

description: smart-seq 2


title: J16-TH-3-plasma intensity low

description: smart-seq 2


title: J20-TH-3-plasma intensity high

description: smart-seq 2


title: K7-TH-3-plasma intensity none

description: smart-seq 2


title: J15-TH-3-plasma intensity low

description: smart-seq 2


title: J17-TH-3-plasma intensity high

description: smart-seq 2


title: J12-TH-3-plasma intensity low

description: smart-seq 2


title: J9-TH-3-plasma intensity low

description: smart-seq 2


title: J13-TH-3-plasma intensity low

description: smart-seq 2


title: J10-TH-3-plasma intensity low

description: smart-seq 2


title: J11-TH-3-plasma intensity low

description: smart-seq 2


title: K3-TH-3-plasma intensity none

description: smart-seq 2


title: J8-TH-3-plasma intensity none

description: smart-seq 2


title: J4-TH-3-plasma intensity none

description: smart-seq 2


title: J6-TH-3-plasma intensity none

description: smart-seq 2


title: J5-TH-3-plasma intensity none

description: smart-seq 2


title: J7-TH-3-plasma intensity none

description: smart-seq 2


title: J1-TH-3-plasma intensity none

description: smart-seq 2


title: J2-TH-3-plasma intensity none

description: smart-seq 2


title: I22-TH-3-plasma intensity high

description: smart-seq 2


title: I21-TH-3-plasma intensity high

description: smart-seq 2


title: I23-TH-3-plasma intensity high

description: smart-seq 2


title: J3-TH-3-plasma intensity none

description: smart-seq 2


title: I19-TH-3-plasma intensity high

description: smart-seq 2


title: I20-TH-3-plasma intensity high

description: smart-seq 2


title: I17-TH-3-plasma intensity high

description: smart-seq 2


title: I12-TH-3-plasma intensity low

description: smart-seq 2


title: I15-TH-3-plasma intensity low

description: smart-seq 2


title: I13-TH-3-plasma intensity low

description: smart-seq 2


title: I11-TH-3-plasma intensity low

description: smart-seq 2


title: I10-TH-3-plasma intensity low

description: smart-seq 2


title: I9-TH-3-plasma intensity low

description: smart-seq 2


title: I8-TH-3-plasma intensity none

description: smart-seq 2


title: I6-TH-3-plasma intensity none

description: smart-seq 2


title: I7-TH-3-plasma intensity none

description: smart-seq 2


title: I5-TH-3-plasma intensity none

description: smart-seq 2


title: I3-TH-3-plasma intensity none

description: smart-seq 2


title: I2-TH-3-plasma intensity none

description: smart-seq 2


title: I1-TH-3-plasma intensity none

description: smart-seq 2


title: H23-TH-3-plasma intensity high

description: smart-seq 2


title: H22-TH-3-plasma intensity high

description: smart-seq 2


title: H21-TH-3-plasma intensity high

description: smart-seq 2


title: H20-TH-3-plasma intensity high

description: smart-seq 2


title: H19-TH-3-plasma intensity high

description: smart-seq 2


title: H14-TH-3-plasma intensity low

description: smart-seq 2


title: H15-TH-3-plasma intensity low

description: smart-seq 2


title: I18-TH-3-plasma intensity high

description: smart-seq 2


title: H13-TH-3-plasma intensity low

description: smart-seq 2


title: I16-TH-3-plasma intensity low

description: smart-seq 2


title: I14-TH-3-plasma intensity low

description: smart-seq 2


title: H12-TH-3-plasma intensity low

description: smart-seq 2


title: H11-TH-3-plasma intensity low

description: smart-seq 2


title: H9-TH-3-plasma intensity low

description: smart-seq 2


title: H8-TH-3-plasma intensity none

description: smart-seq 2


title: H10-TH-3-plasma intensity low

description: smart-seq 2


title: H7-TH-3-plasma intensity none

description: smart-seq 2


title: I4-TH-3-plasma intensity none

description: smart-seq 2


title: H6-TH-3-plasma intensity none

description: smart-seq 2


title: H5-TH-3-plasma intensity none

description: smart-seq 2


title: H4-TH-3-plasma intensity none

description: smart-seq 2


title: H3-TH-3-plasma intensity none

description: smart-seq 2


title: H2-TH-3-plasma intensity none

description: smart-seq 2


title: H18-TH-3-plasma intensity high

description: smart-seq 2


title: H17-TH-3-plasma intensity high

description: smart-seq 2


title: H16-TH-3-plasma intensity low

description: smart-seq 2


title: G22-TH-3-plasma intensity high

description: smart-seq 2


title: G17-TH-3-plasma intensity high

description: smart-seq 2


title: G21-TH-3-plasma intensity high

description: smart-seq 2


title: G18-TH-3-plasma intensity high

description: smart-seq 2


title: G16-TH-3-plasma intensity low

description: smart-seq 2


title: G12-TH-3-plasma intensity low

description: smart-seq 2


title: G11-TH-3-plasma intensity low

description: smart-seq 2


title: G13-TH-3-plasma intensity low

description: smart-seq 2


title: G20-TH-3-plasma intensity high

description: smart-seq 2


title: G10-TH-3-plasma intensity low

description: smart-seq 2


title: G19-TH-3-plasma intensity high

description: smart-seq 2


title: G9-TH-3-plasma intensity low

description: smart-seq 2


title: G15-TH-3-plasma intensity low

description: smart-seq 2


title: G8-TH-3-plasma intensity none

description: smart-seq 2


title: H1-TH-3-plasma intensity none

description: smart-seq 2


title: G7-TH-3-plasma intensity none

description: smart-seq 2


title: G3-TH-3-plasma intensity none

description: smart-seq 2


title: G4-TH-3-plasma intensity none

description: smart-seq 2


title: G23-TH-3-plasma intensity high

description: smart-seq 2


title: G2-TH-3-plasma intensity none

description: smart-seq 2


title: F23-TH-3-plasma intensity high

description: smart-seq 2


title: G1-TH-3-plasma intensity none

description: smart-seq 2


title: F21-TH-3-plasma intensity high

description: smart-seq 2


title: G14-TH-3-plasma intensity low

description: smart-seq 2


title: F22-TH-3-plasma intensity high

description: smart-seq 2


title: F19-TH-3-plasma intensity high

description: smart-seq 2


title: F20-TH-3-plasma intensity high

description: smart-seq 2


title: F18-TH-3-plasma intensity high

description: smart-seq 2


title: F14-TH-3-plasma intensity low

description: smart-seq 2


title: F17-TH-3-plasma intensity high

description: smart-seq 2


title: F15-TH-3-plasma intensity low

description: smart-seq 2


title: F13-TH-3-plasma intensity low

description: smart-seq 2


title: F16-TH-3-plasma intensity low

description: smart-seq 2


title: G6-TH-3-plasma intensity none

description: smart-seq 2


title: F10-TH-3-plasma intensity low

description: smart-seq 2


title: F12-TH-3-plasma intensity low

description: smart-seq 2


title: F9-TH-3-plasma intensity low

description: smart-seq 2


title: F11-TH-3-plasma intensity low

description: smart-seq 2


title: G5-TH-3-plasma intensity none

description: smart-seq 2


title: F7-TH-3-plasma intensity none

description: smart-seq 2


title: F8-TH-3-plasma intensity none

description: smart-seq 2


title: F4-TH-3-plasma intensity none

description: smart-seq 2


title: F6-TH-3-plasma intensity none

description: smart-seq 2


title: F3-TH-3-plasma intensity none

description: smart-seq 2


title: F1-TH-3-plasma intensity none

description: smart-seq 2


title: F5-TH-3-plasma intensity none

description: smart-seq 2


title: F2-TH-3-plasma intensity none

description: smart-seq 2


title: E22-TH-3-plasma intensity high

description: smart-seq 2


title: E19-TH-3-plasma intensity high

description: smart-seq 2


title: E21-TH-3-plasma intensity high

description: smart-seq 2


title: E20-TH-3-plasma intensity high

description: smart-seq 2


title: E17-TH-3-plasma intensity high

description: smart-seq 2


title: E15-TH-3-plasma intensity low

description: smart-seq 2


title: E16-TH-3-plasma intensity low

description: smart-seq 2


title: E13-TH-3-plasma intensity low

description: smart-seq 2


title: E14-TH-3-plasma intensity low

description: smart-seq 2


title: E10-TH-3-plasma intensity low

description: smart-seq 2


title: E11-TH-3-plasma intensity low

description: smart-seq 2


title: E8-TH-3-plasma intensity none

description: smart-seq 2


title: E9-TH-3-plasma intensity low

description: smart-seq 2


title: E6-TH-3-plasma intensity none

description: smart-seq 2


title: E7-TH-3-plasma intensity none

description: smart-seq 2


title: E12-TH-3-plasma intensity low

description: smart-seq 2


title: E5-TH-3-plasma intensity none

description: smart-seq 2


title: E4-TH-3-plasma intensity none

description: smart-seq 2


title: E3-TH-3-plasma intensity none

description: smart-seq 2


title: D24-TH-3-plasma intensity high

description: smart-seq 2


title: E23-TH-3-plasma intensity high

description: smart-seq 2


title: D23-TH-3-plasma intensity high

description: smart-seq 2


title: E2-TH-3-plasma intensity none

description: smart-seq 2


title: D20-TH-3-plasma intensity high

description: smart-seq 2


title: E1-TH-3-plasma intensity none

description: smart-seq 2


title: D22-TH-3-plasma intensity high

description: smart-seq 2


title: D21-TH-3-plasma intensity high

description: smart-seq 2


title: E18-TH-3-plasma intensity high

description: smart-seq 2


title: D19-TH-3-plasma intensity high

description: smart-seq 2


title: D17-TH-3-plasma intensity high

description: smart-seq 2


title: D18-TH-3-plasma intensity high

description: smart-seq 2


title: D16-TH-3-plasma intensity low

description: smart-seq 2


title: D15-TH-3-plasma intensity low

description: smart-seq 2


title: D12-TH-3-plasma intensity low

description: smart-seq 2


title: D13-TH-3-plasma intensity low

description: smart-seq 2


title: H011-NileO

type: genomic

city: HongKong

first: Suetyi

last: Leung

address: Queen Mary Hospital, Pokfulam Road

department: Department of Pathology

country: China

institute: The University of Hong Kong

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing:
Illumina GenomeStudio V2011.1
matrix processed value definition: Average Beta

label: cy3, cy5

source_name: Human normal ileum organoid

label_protocol: standard protocol

growth_protocol: IM and normal gastric organoids were cultured in a standard gastric organoid medium containing Wnt-3A, R-spondin1, Noggin, B27, A83-01, EGF, N-acetylcysteine, Gastrin and FGF10. Normal intestianl organoids were cultured in a standard intestinal organoid medium containing Wnt-3A, R-spondin1, Noggin, B27, A83-01, EGF, N-acetylcysteine, Gastrin and SB202190.

extract_protocol: DNA of each sample was extracted using AllPrep® DNA/RNA/miRNA Universal Kit and an average of 500ng of genomic DNA per sample was input for bisulfite conversion using the EZ DNA Methylation kit, according to manufacturers' instructions.

treatment_protocol: IM and normal gastric organoids were cultured in a standard gastric organoid medium, while normal intestinal organoids were cultured in a standard intestinal organoid medium.

tag: tissue/cell type

value: Human normal ileum organoid

tag: gender

value: Female

tag: culture condition

value: Standard gastric organoid medium


title: H007-NileO

value: Male


title: D11-TH-3-plasma intensity low

description: smart-seq 2


title: D10-TH-3-plasma intensity low

description: smart-seq 2


title: H007-NCaeO

source_name: Human normal colon organoid

value: Human normal colon organoid


title: D9-TH-3-plasma intensity low

description: smart-seq 2


title: H007-NAsCO


title: GX094-BfO

source_name: Human normal gastric organoid

value: Human normal gastric organoid


title: GX091-BgO


title: GX089-BlO


title: D7-TH-3-plasma intensity none

description: smart-seq 2


title: D8-TH-3-plasma intensity none

description: smart-seq 2


title: D6-TH-3-plasma intensity none

description: smart-seq 2


title: GX077-BO


title: D4-TH-3-plasma intensity none

description: smart-seq 2


title: GX076-BO


title: D3-TH-3-plasma intensity none

description: smart-seq 2


title: GX066-BO


title: D5-TH-3-plasma intensity none

description: smart-seq 2


title: D1-TH-3-plasma intensity none

description: smart-seq 2


title: D2-TH-3-plasma intensity none

description: smart-seq 2


title: D14-TH-3-plasma intensity low

description: smart-seq 2


title: GX059-BO


title: GX039-BO


title: C23-TH-3-plasma intensity high

description: smart-seq 2


title: C22-TH-3-plasma intensity high

description: smart-seq 2


title: GX026-BO


title: C21-TH-3-plasma intensity high

description: smart-seq 2


title: GX023-BO


title: C20-TH-3-plasma intensity high

description: smart-seq 2


title: GX024-BO


title: C19-TH-3-plasma intensity high

description: smart-seq 2


title: C18-TH-3-plasma intensity high

description: smart-seq 2


title: GX012-BO


title: C16-TH-3-plasma intensity low

description: smart-seq 2


title: GX093-IM2O

tag: subtype reclassification

value: Reclassify as normal gastric organoid based on transcriptome data


title: GX001-BO


title: GX092-AO


title: C15-TH-3-plasma intensity low

description: smart-seq 2


title: C14-TH-3-plasma intensity low

description: smart-seq 2


title: GX041-BO


title: GX089-AlO


title: C13-TH-3-plasma intensity low

description: smart-seq 2


title: GX056-BO


title: GX090-AO


title: C12-TH-3-plasma intensity low

description: smart-seq 2


title: GX089-AgO


title: GX035-BO


title: C11-TH-3-plasma intensity low

description: smart-seq 2


title: GX087-IM2O


title: C10-TH-3-plasma intensity low

description: smart-seq 2


title: C9-TH-3-plasma intensity low

description: smart-seq 2


title: GX082-AO


title: GX080-IMO


title: C8-TH-3-plasma intensity none

description: smart-seq 2


title: GX069-AO


title: C17-TH-3-plasma intensity high

description: smart-seq 2


title: C7-TH-3-plasma intensity none

description: smart-seq 2


title: C5-TH-3-plasma intensity none

description: smart-seq 2


title: C6-TH-3-plasma intensity none

description: smart-seq 2


title: GX072-AO


title: GX086-IM2O


title: GX068-AO


title: C3-TH-3-plasma intensity none

description: smart-seq 2


title: GX058-AO


title: C1-TH-3-plasma intensity none

description: smart-seq 2


title: B24-TH-3-plasma intensity high

description: smart-seq 2


title: GX044-AO


title: GX025-AO


title: GX022-AO


title: GX052-AO


title: B23-TH-3-plasma intensity high

description: smart-seq 2


title: B21-TH-3-plasma intensity high

description: smart-seq 2


title: GX036-AO


title: B22-TH-3-plasma intensity high

description: smart-seq 2


title: GX099-IMO

source_name: Human IM organoid

value: Human IM organoid


title: C4-TH-3-plasma intensity none

description: smart-seq 2


title: GX099-IM2O


title: B20-TH-3-plasma intensity high

description: smart-seq 2


title: GX098-IMO


title: B19-TH-3-plasma intensity high

description: smart-seq 2


title: B16-TH-3-plasma intensity low

description: smart-seq 2


title: B17-TH-3-plasma intensity high

description: smart-seq 2


title: GX094-IMO


title: GX092-BO

value: Reclassify as IM organoid based on transcriptome data


title: B18-TH-3-plasma intensity high

description: smart-seq 2


title: GX091-AgO


title: B13-TH-3-plasma intensity low

description: smart-seq 2


title: B15-TH-3-plasma intensity low

description: smart-seq 2


title: B12-TH-3-plasma intensity low

description: smart-seq 2


title: GX088-IMO


title: GX085-IMO


title: B11-TH-3-plasma intensity low

description: smart-seq 2


title: C2-TH-3-plasma intensity none

description: smart-seq 2


title: GX078-IM2O


title: GX076-IM2O


title: B10-TH-3-plasma intensity low

description: smart-seq 2


title: GX072-IMO


title: GX072-IM3O


title: B9-TH-3-plasma intensity low

description: smart-seq 2


title: B8-TH-3-plasma intensity none

description: smart-seq 2


title: GX076-IMO


title: GX091-BlO


title: GX062-IM2O


title: B14-TH-3-plasma intensity low

description: smart-seq 2


title: B5-TH-3-plasma intensity none

description: smart-seq 2


title: B4-TH-3-plasma intensity none

description: smart-seq 2


title: B6-TH-3-plasma intensity none

description: smart-seq 2


title: GX054-IM2O


title: B3-TH-3-plasma intensity none

description: smart-seq 2


title: B2-TH-3-plasma intensity none

description: smart-seq 2


title: GX060-IMO


title: B7-TH-3-plasma intensity none

description: smart-seq 2


title: GX062-IMO


title: B1-TH-3-plasma intensity none

description: smart-seq 2


title: GX040-IMO


title: A23-TH-3-plasma intensity high

description: smart-seq 2


title: GX031-IMO


title: A22-TH-3-plasma intensity high

description: smart-seq 2


title: A21-TH-3-plasma intensity high

description: smart-seq 2


title: GX006-IM3O


title: GX014-IM2O


title: GX023-IM3dysO


title: A19-TH-3-plasma intensity high

description: smart-seq 2


title: GX049-IMO


title: GX059-IMO


title: GX023-IM2O


title: A18-TH-3-plasma intensity high

description: smart-seq 2


title: A20-TH-3-plasma intensity high

description: smart-seq 2


title: A17-TH-3-plasma intensity high

description: smart-seq 2


title: S. pombe 3' READS Replicate A

city: Boston

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

description: 3' READS library from wild-type S. pombe

data_processing:
Prep fastq files for mapping (discard reads with ambiguous base calls, remove of library adapters, count/remove of initial Ts in each read) python
Map to S. pombe genome, using first 17 nt after adapter and initial T removal; no mismatches allowed, keeping only uniquely mapped reads, Bowtie
Discard reads for which the number of initial Ts could be explained by A residues in the genome adjacent to the mapped position, python
Tally remaining read starts by strand and genomic position, scaling each replicate to 50M total reads (merged replicates scaled to 100M), python
Assembly: May 2023 genome version from Pombase
Supplementary files format and content: Tab-delimited text files giving relative 3' isoform end frequencies by coordinate in the 400nt downstream of each CDS
Supplementary files format and content: Tab-delimited text files of merged A and B replicates giving relative isoform frequencies by genomic coordinate  in the 400nt downstream of each CDS
Library strategy: 3'READS

organism: Schizosaccharomyces pombe

growth_protocol: Exponential growth at 30°C in YPD medium

extract_protocol:
Total RNA extracted with hot acid phenol and subjected to Qiagen RNEasy purification with DNase treatment
3' READS (Jin, Y. et al., 2015 Curr Protoc Mol Biol 110, 4.23.21-24.23.17)

value: Exponential growth in YPD medium


title: A15-TH-3-plasma intensity low

description: smart-seq 2


title: A13-TH-3-plasma intensity low

description: smart-seq 2


title: S. pombe 3' READS Replicate B


title: GX001-IM3O


title: A24-TH-3-plasma intensity high

description: smart-seq 2


title: GX035-AO


title: A16-TH-3-plasma intensity low

description: smart-seq 2


title: A11-TH-3-plasma intensity low

description: smart-seq 2


title: A12-TH-3-plasma intensity low

description: smart-seq 2


title: A9-TH-3-plasma intensity low

description: smart-seq 2


title: A8-TH-3-plasma intensity none

description: smart-seq 2


title: A6-TH-3-plasma intensity none

description: smart-seq 2


title: WT_D2, replicate 2, RNA-seq

description: RNA-seq data

value: 8-12 wk old

value: 6 h

value: BMDCs

value: Wild type


title: WT_D2, replicate 1, RNA-seq

description: RNA-seq data


title: A14-TH-3-plasma intensity low

description: smart-seq 2

value: isolated cells


title: KLF13-/-_D1, replicate 2, RNA-seq

description: RNA-seq data

value: LPS


title: A5-TH-3-plasma intensity none

description: smart-seq 2

value: Brain

value: microglia


title: KLF13-/-_D2, replicate 1, RNA-seq

description: RNA-seq data


title: A3-TH-3-plasma intensity none

description: smart-seq 2


title: KLF13-/-_D1, replicate 1, RNA-seq

description: RNA-seq data


title: A2-TH-3-plasma intensity none

description: smart-seq 2


title: WT_D1, replicate 1, RNA-seq

description: RNA-seq data


title: A1-TH-3-plasma intensity none

description: smart-seq 2


title: A4-TH-3-plasma intensity none

description: smart-seq 2


title: KLF13-/-_D0, replicate 2, RNA-seq

description: RNA-seq data

value: 0 h


title: GX048-AO

value: Standard gastric organoid medium


title: A10-TH-3-plasma intensity low

description: smart-seq 2


title: KLF13-/-_D2, replicate 2, RNA-seq

description: RNA-seq data


title: A7-TH-3-plasma intensity none

description: smart-seq 2


title: WT_D0, replicate 2, RNA-seq

description: RNA-seq data


title: P23-TH-2-plasma intensity high

description: smart-seq 2


title: P21-TH-2-plasma intensity high

description: smart-seq 2


title: KLF13-/-_D0, replicate 1, RNA-seq

description: RNA-seq data


title: P20-TH-2-plasma intensity high

description: smart-seq 2


title: WT_D0, replicate 1, RNA-seq

description: RNA-seq data


title: P19-TH-2-plasma intensity high

description: smart-seq 2


title: KLF13-/-_M3, RNA-seq

description: RNA-seq data

value: BMDM


title: WT_M3, RNA-seq

description: RNA-seq data


title: WT_D1, replicate 2, RNA-seq

description: RNA-seq data


title: P18-TH-2-plasma intensity high

description: smart-seq 2


title: KLF13-/-_M2, RNA-seq

description: RNA-seq data


title: P17-TH-2-plasma intensity high

description: smart-seq 2


title: P22-TH-2-plasma intensity high

description: smart-seq 2


title: P16-TH-2-plasma intensity low

description: smart-seq 2


title: P15-TH-2-plasma intensity low

description: smart-seq 2


title: KLF13-/-_M1, RNA-seq

description: RNA-seq data


title: P14-TH-2-plasma intensity low

description: smart-seq 2


title: KLF13-/-_M0, RNA-seq

description: RNA-seq data


title: WT_M0, RNA-seq

description: RNA-seq data


title: WT_M1, RNA-seq

description: RNA-seq data


title: P11-TH-2-plasma intensity low

description: smart-seq 2


title: KLF13-/-_T2, replicate 2, RNA-seq

description: RNA-seq data

value: CD4 T cell


title: KLF13-/-_T2, replicate 1, RNA-seq

description: RNA-seq data


title: P10-TH-2-plasma intensity low

description: smart-seq 2


title: P13-TH-2-plasma intensity low

description: smart-seq 2


title: WT_M2, RNA-seq

description: RNA-seq data


title: P12-TH-2-plasma intensity low

description: smart-seq 2


title: WT_T2, replicate 2, RNA-seq

description: RNA-seq data


title: P9-TH-2-plasma intensity low

description: smart-seq 2


title: WT_T2, replicate 1, RNA-seq

description: RNA-seq data


title: P8-TH-2-plasma intensity none

description: smart-seq 2


title: KLF13-/-_T1, replicate 2, RNA-seq

description: RNA-seq data


title: P7-TH-2-plasma intensity none

description: smart-seq 2


title: P6-TH-2-plasma intensity none

description: smart-seq 2


title: WT_T1, replicate 2, RNA-seq

description: RNA-seq data


title: KLF13-/-_T1, replicate 1, RNA-seq

description: RNA-seq data


title: P5-TH-2-plasma intensity none

description: smart-seq 2


title: P4-TH-2-plasma intensity none

description: smart-seq 2


title: WT_T1, replicate 1, RNA-seq

description: RNA-seq data


title: P2-TH-2-plasma intensity none

description: smart-seq 2


title: WT_T0, replicate 2, RNA-seq

description: RNA-seq data


title: Sle3_T2, RNA-seq

description: RNA-seq data


title: O23-TH-2-plasma intensity high

description: smart-seq 2


title: O22-TH-2-plasma intensity high

description: smart-seq 2


title: O21-TH-2-plasma intensity high

description: smart-seq 2


title: O20-TH-2-plasma intensity high

description: smart-seq 2


title: B6_T2, RNA-seq

description: RNA-seq data


title: P3-TH-2-plasma intensity none

description: smart-seq 2


title: KLF13-/-_T0, replicate 2, RNA-seq

description: RNA-seq data


title: Sle3_T1, RNA-seq

description: RNA-seq data


title: KLF13-/-_T0, replicate 1, RNA-seq

description: RNA-seq data


title: B6_T1, RNA-seq

description: RNA-seq data


title: WT_T0, replicate 1, RNA-seq

description: RNA-seq data


title: KLF13_B6_T0,  RNA-seq

description: RNA-seq data


title: O18-TH-2-plasma intensity high

description: smart-seq 2


title: P1-TH-2-plasma intensity none

description: smart-seq 2


title: Drosophila_ananassae_testes_G_z2_130917_I1135

organism: Drosophila ananassae

value: testes


title: O16-TH-2-plasma intensity low

description: smart-seq 2


title: Drosophila_ananassae_testes_G_z2_131017_I1125


title: O15-TH-2-plasma intensity low

description: smart-seq 2


title: KLF13_NZW_T0, RNA-seq

description: RNA-seq data


title: O19-TH-2-plasma intensity high

description: smart-seq 2


title: O14-TH-2-plasma intensity low

description: smart-seq 2


title: Drosophila_ananassae_ag_G_z1_131017_I1125

value: accessory glands


title: Drosophila_ananassae_ag_G_z1_130917_I1135


title: O13-TH-2-plasma intensity low

description: smart-seq 2


title: O12-TH-2-plasma intensity low

description: smart-seq 2


title: O11-TH-2-plasma intensity low

description: smart-seq 2


title: O9-TH-2-plasma intensity low

description: smart-seq 2


title: O6-TH-2-plasma intensity none

description: smart-seq 2


title: Mycelium - KO_VeA - Rep5

type: RNA

city: TOULOUSE

first: Olivier

last: PUEL

address: 180 chemin de Tournefeuille

department: TOXALIM UMR 1331

country: France

institute: INRAE

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >6 pmol Cy3/µg cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 µl containing 10x Agilent fragmentation buffer and 25x Agilent blocking agent following the manufacturer's instructions (Agilent Technologies, Santa Clara, CA). On completion of the fragmentation reaction, 25 µl of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to SurePrint G3 Custom GE microarray (8X60K, Design 085497  enclosed in Agilent SureHyb-enabled hybridization chambers for 17 hours at 65°C in a rotating Agilent hybridization oven. After hybridization, microarrays were washed sequentially in Wash buffer 1 (Agilent Technologies, 1 min) and Wash buffer 2 (Agilent Technologies, 37°C, 1 min).

scan_protocol: Slides were scanned immediately after washing on a Agilent G2505C Microarray Scanner with Agilent Scan Control A.8.5.1 software

data_processing:
The scanned images were analyzed with Feature Extraction Software 10.10.1.1 (Agilent Technologies, Santa Clara, CA) using default parameters (protocol GE1_1010_Sep10 and Grid: 085497_D_F_20180419). All subsequent data analyses were done under R (www.r-project.org) using packages of Bioconductor (www.bioconductor.org). Raw data (median of pixels intensity) were imported into R using the read.maimages function from the limma package with the following weight function (assigning a weight of 1 or 0 to each spot): myfunw<-function(x) {okType<-x$ControlType==0; okFoundGreen<-x$gIsFound==1; okPos=x$gIsPosAndSignif==1; okWellAbove<- x$gIsWellAboveBG==1; as.numeric(okType & okFoundGreen & okPos & okWellAbove);}.
We firstly selected control probes and probes targeting Penicillium expansum PEXP transcripts (GeneNames begining by 'PEXP_') giving a dataset with 12341 entries. We next selected the spots with a minimal weight of 1 for 16 out of 11 microarrays or with a minimal weight of 3 per group from at least one experimental group. At this step, 10255 spots out of 12341 were selected. Data were then stored in an ExpressionSet object and normalized by the qsmooth method using the qsmooth function from the qsmooth R library. The resulting matrix has 10255 rows each corresponding to a unique ProbeName (provided as data Matrix).

organism: Penicillium expansum

source_name: Mycelium

label_protocol: For each sample, Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng of total RNA using the One-Color Quick Amp Labeling kit (Agilent Technologies, Santa Clara, CA) according to the manufacturer's instructions, followed by Agencourt RNAClean XP (Agencourt Bioscience Corporation, Beverly, Massachusetts) purification. Dye incorporation and cRNA yield were checked using Dropsense™ 96 UV/VIS droplet reader (Trinean, Belgium).

growth_protocol: Six, four, five and five MEA Petri dishes were inoculated with PeΔlaeA  (KO_LaeA),  PeΔVelB (KO_VelB), PeΔVeA  (KO_VeA)and Wild Type (WT) strains, respectively. Before the inoculation, Petri dishes were overlaid with a sterile cellophane layer. Then, the cultures were incubated at 25°C for 5 days in the dark.

extract_protocol: At the end of the incubation period, mycelia were removed from cellophane layer and RNAs were extracted as described by Tannous et al ( 2014). Tannous J, El Khoury R, Snini SP, Lippi Y, El Khoury A, Atoui A, Lteif R, Oswald IP, Puel O. Sequencing, physical organization and kinetic expression of the patulin biosynthetic gene cluster from Penicillium expansum. Int J Food Microbiol. 2014 Oct 17;189:51-60

value: Mycelium


title: O10-TH-2-plasma intensity low

description: smart-seq 2


title: O7-TH-2-plasma intensity none

description: smart-seq 2


title: Mycelium - KO_LaeA - Rep6


title: O8-TH-2-plasma intensity none

description: smart-seq 2


title: O3-TH-2-plasma intensity none

description: smart-seq 2


title: O5-TH-2-plasma intensity none

description: smart-seq 2


title: Mycelium - KO_LaeA - Rep5


title: O1-TH-2-plasma intensity none

description: smart-seq 2


title: Mycelium - KO_VelB - Rep3


title: Mycelium - WT - Rep5

value: WT


title: Mycelium - WT - Rep4


title: Mycelium - KO_VelB - Rep4


title: Mycelium - KO_VeA - Rep3


title: Mycelium - KO_VeA - Rep2


title: Mycelium - KO_VeA - Rep4


title: O4-TH-2-plasma intensity none

description: smart-seq 2


title: N22-TH-2-plasma intensity high

description: smart-seq 2


title: N20-TH-2-plasma intensity high

description: smart-seq 2


title: Mycelium - KO_LaeA - Rep3


title: N21-TH-2-plasma intensity high

description: smart-seq 2


title: N18-TH-2-plasma intensity high

description: smart-seq 2


title: Mycelium - WT - Rep3


title: High grade 23 [CytoScanHD_Array]

city: Barcelona

first: Itziar

last: Salaverria

address: Rossello 153

institute: Hospital Clínic

description: Cytoscan HD

hyb_protocol: Samples were hybridized onto Cytoscan arrays Cytoscan HD and were washed and stained with GeneChip Fluidics Station 450 (Affymetrix)

scan_protocol: GeneChip Scanner 3000 7G (Affymetrix)

data_processing:
Nexus biodiscovery 9.0 edition Software
primary data description: Gains and losses were evaluated with visual inspection by 2 different observers using Nexus Biodiscovery software (Biodiscovery, Hawthorne CA, USA). The CNAs with a minimum size of 100kb were considered real. Loss of heterozigosity regions where considered when size was >5Mb.

label: Biotin

source_name: abdominal mass

label_protocol: CytoScan™ Reagent Kit / 901808,t

extract_protocol: DNAs from frozen tissues samples were extracted using the QIAamp DNA Mini Kit.

tag: type of sample

value: B-NHL with intermediate features between BL and DLBCL

value: male

tag: tissue type

value: frozen tissue

value: abdominal mass


title: N19-TH-2-plasma intensity high

description: smart-seq 2

tag: tissue


title: N16-TH-2-plasma intensity low

description: smart-seq 2


title: MXD3562, Adeno-GFP

city: Madrid

first: Vasiliki

last: Liaki

address: Melchor Fernandez Almagro 3

institute: CNIO

hyb_protocol: Illumina Infinium Mouse Methylation BreadChip arrays

scan_protocol: Illumina HIIScanSQ with Autoloader system

data_processing:
Data was processed using sesame package pipeline in R environment
Processed_bVals.csv (.csv format containing Average Beta value and detection P.value)

label: Cy3 and Cy5

source_name: pancreas

label_protocol: Standard illumina Protocol

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

extract_protocol: Genomic DNA was extracted and purified from the different cell lines using Qiagen DNeasy Kit according to standard instructions

treatment_protocol: Cells were infected with Adeno-GFP viral particles.

value: pancreas

value: adenocarcinoma

value: single


title: High grade 34 [CytoScanHD_Array]

description: Cytoscan HD

source_name: cervical LN

value: cervical LN


title: High grade 6 [CytoScanHD_Array]

description: Cytoscan HD

source_name: kidney

value: female

value: kidney


title: Mycelium - WT - Rep2


title: Mycelium - KO_LaeA - Rep2


title: Mycelium - KO_VeA - Rep1


title: Mycelium - KO_LaeA - Rep1


title: High grade 11 [CytoScanHD_Array]

description: Cytoscan HD

source_name: intestine

value: intestine


title: Mycelium - KO_VelB - Rep1


title: MPL1071, Adeno-GFP


title: N14-TH-2-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: N17-TH-2-plasma intensity high

description: smart-seq 2


title: Mycelium - KO_VelB - Rep2


title: MXD1803, Adeno-GFP


title: MPL1540, Adeno-GFP


title: MXD2365,Adeno-GFP


title: N11-TH-2-plasma intensity low

description: smart-seq 2


title: N12-TH-2-plasma intensity low

description: smart-seq 2


title: MPL337, Adeno-GFP


title: N15-TH-2-plasma intensity low

description: smart-seq 2


title: MXD2401, Adeno-GFP


title: N10-TH-2-plasma intensity low

description: smart-seq 2


title: MXD1078, Adeno-GFP


title: MPL474, Adeno-GFP


title: N7-TH-2-plasma intensity none

description: smart-seq 2


title: N8-TH-2-plasma intensity none

description: smart-seq 2


title: MXD2696, Adeno-GFP


title: N6-TH-2-plasma intensity none

description: smart-seq 2


title: MXD1439, Adeno-GFP


title: N5-TH-2-plasma intensity none

description: smart-seq 2


title: DCD2257, Adeno-GFP


title: High grade 17 [CytoScanHD_Array]

description: Cytoscan HD

source_name: tonsil

value: tonsil


title: N13-TH-2-plasma intensity low

description: smart-seq 2


title: N4-TH-2-plasma intensity none

description: smart-seq 2


title: N3-TH-2-plasma intensity none

description: smart-seq 2


title: Mycelium - WT - Rep1

value: Mycelium


title: N2-TH-2-plasma intensity none

description: smart-seq 2


title: N9-TH-2-plasma intensity low

description: smart-seq 2


title: BF_Control2 8hrs

city: Cambridge

first: Punam

last: Bisht

state: Massachusetts

address: 455 Main St

institute: Whitehead Institute

data_processing:
Reads were mapped with STAR (39) using a genome index made with either the human genome sequence version hg38 or the bat genome sequence version mRhiFer1_v1.p, concatenated to the SARS-CoV-2 sequence from National Center for Biotechnology Information (NCBI) reference sequence NC_045512.2. We used the following STAR parameters: “--outFilterMultimapNmax 100, --alignSJoverhangMin 8, --alignSJDBoverhangMin 3, --outSJfilterOverhangMin 12 12 12 12, --outSJfilterCountUniqueMin 1 1 1 1,  --outSJfilterCountTotalMin 1 1 1 1, --outSJfilterDistToOtherSJmin 0 0 0 0, --outFilterMismatchNmax 999, --outFilterMismatchNoverReadLmax 0.04,  --scoreGapNoncan -4, --scoreGapATAC -4, --chimOutType Junctions WithinBAM HardClip, --chimScoreJunctionNonGTAG 0, --alignSJstitchMismatchNmax -1 -1 -1 -1, --alignIntronMin 10, --alignIntronMax 95000, --alignMatesGapMax 95000, --chimSegmentMin 5 ".
Gene counts were obtained with featureCounts (40) using parameters “-p -s 2 -d 10 -D 30000”.  For the human samples we also used the parameter “-M” to be able to count the reads mapping the identical endogenous and inserted copies of “ACE2”.
Assembly: hg38  or mRhiFer1_v1.p
Supplementary files format and content: Text files containing gene counts.

organism: Rhinolophus ferrumequinum

source_name: Primary cells

growth_protocol: Cells were grown in their specific media and kept at 37°C with 5% CO2

extract_protocol:
RNA is extracted using RNeasy Plus Mini Kit (QIAGEN), according to manufacturer’s directions
Libraries were prepared using the NEBNext Ultra II RNA Library Prep Kit (NEB), according to the manufacturer’s directions

treatment_protocol: Cells were either not treated,  infected with lentiviral vector containing the human ACE2 gene 24 hours prior to mock infection, or infected with lentiviral vector containing the human ACE2 gene 24 hours prior to SARS CoV-2 infection for either 8 or 48 hours.

value: Primary cells

tag: replicate

value: Replicate 2

value: Fibroblast cells

tag: infection

value: hACE2 Lenti infected


title: N1-TH-2-plasma intensity none

description: smart-seq 2


title: BF_Infected2 8hrs

value: hACE2 Lenti infected+SARS CoV-2 infected


title: BF_Control1 8hrs

value: Replicate 1


title: M23-TH-2-plasma intensity high

description: smart-seq 2


title: M22-TH-2-plasma intensity high

description: smart-seq 2


title: BF_Infected1 8hrs


title: BF_Uninfected 1 8hrs


title: M21-TH-2-plasma intensity high

description: smart-seq 2


title: M20-TH-2-plasma intensity high

description: smart-seq 2


title: O17-TH-2-plasma intensity high

description: smart-seq 2


title: Bat_iPSCs_hACE2_Inf_2 48hrs

source_name: iPSCs reprogrammed from fibroblast

value: iPSCs reprogrammed from fibroblast

value: Stem cell


title: Bat_iPSCs_hACE2_Inf_1 48hrs


title: M18-TH-2-plasma intensity high

description: smart-seq 2


title: M19-TH-2-plasma intensity high

description: smart-seq 2


title: Bat_iPSCs_Uninfected_1 48hrs


title: Bat_iPSCs_hACE2_contr_1 48hrs


title: M16-TH-2-plasma intensity low

description: smart-seq 2


title: M15-TH-2-plasma intensity low

description: smart-seq 2


title: Bat_Fib_Uninfected_2 48hrs


title: M14-TH-2-plasma intensity low

description: smart-seq 2


title: M12-TH-2-plasma intensity low

description: smart-seq 2


title: Bat_Fib_Uninfected_1 48hrs


title: Bat_Fib_hACE2_INF_1 48hrs


title: M13-TH-2-plasma intensity low

description: smart-seq 2


title: M11-TH-2-plasma intensity low

description: smart-seq 2


title: BF_Uninfected 2 8hrs


title: Bat_Fib_hACE2_contr_1 48hrs


title: Bat_Fib_hACE2_contr_2 48hrs


title: Bat_iPSCs_Uninfected_2 48hrs


title: M9-TH-2-plasma intensity low

description: smart-seq 2


title: M10-TH-2-plasma intensity low

description: smart-seq 2


title: M17-TH-2-plasma intensity high

description: smart-seq 2


title: M7-TH-2-plasma intensity none

description: smart-seq 2


title: M6-TH-2-plasma intensity none

description: smart-seq 2


title: BRF33.C1,scRNAseq

city: MILAN

first: Luca

last: Agnelli

address: Venezian 1

department: Department of Advanced Diagnostics

country: Italy

institute: IRCCS Istituto Nazionale dei Tumori

library_source: transcriptomic single cell

data_processing:
Cellranger v 7.1.0 has been used to demultiplex FASTQ files output and perform alignment, filtering, barcode and UMI counting to obtain feature and barcode count matrices. The following steps have been performed using a modified version of Satja’s lab Seurat v5.0.1 pipeline 62 in R software version 4.3.1. To ensure high-quality data analysis, low-quality cells identified by the low number of expressed genes (<200) or high mitochondrial gene content (higher than 10% of the whole expression) have been filtered out. Similarly, lowly expressed genes (in less than 3 cells) have been removed. Cells expressing any amount (higher than 0.1% of the whole expression) of the following genes: HBA1, HBA2, HBB, HBD, HBG2, HBM, AHSP, PPBP, and PF4 were removed to avoid erythrocytes and platelets contamination. Normalization and integration steps were carried out following the sctransform v0.4.1 R package pipeline. DoubletFinder v 2.0.4 has been used to remove doublets, whose estimates were computed according to the proportions outlined by the manufacturer. The integration was performed with harmony v1.2.0 R package, using the 5000 most variable genes in each dataset (SelectIntegrationFeatures function). The dimensionality of the data was calculated using the Elbow method, which determines 26 as the optimal number of dimensions to represent the dataset variability. Cell clusters were determined using Uniform Manifold Approximation and Projection (UMAP), a technique allowing non-linear dimension reduction run under Seurat function findClusters. We preliminarily annotated cell clusters using the SingleR package and the HumanPrimaryCellAtlas data. To reduce classification biases induced by “pan-cell-atlas” approaches, we subsequently proceeded to refine the classification using known cellular markers using the AUCell R package. To identify putative cancer cells, we assessed chromosomal changes in epithelial and myoepithelial cells with the inferCNV package (v1.11.3), using stromal cells and lymphocytes as a reference. To evaluate transcriptomic modulations across different conditions, we employed GSVA, thus allowing the estimation of gene set activity at the single-cell level. We calculated single-cell enrichment scores for predefined metabolic gene sets, and then subjected to statistical analysis to ascertain significant differences (adj p-value < 0,05; log2FC >0,25 or <-0.25) in gene set activity, providing insights into the modification induced by systemic treatment.
Assembly: GRCh38
Supplementary files format and content: Barcodes tsv matrix
Supplementary files format and content: Features tsv matrix
Supplementary files format and content: Expression tsv matrix

source_name: Breast cancer

extract_protocol:
Fresh tumor was minced into cubes <1mm3 and digested using LiberaseTM (Roche, Besel, Switzerland) and TrypLE™ Express Enzyme (Thermo Fisher Scientific, Walthman, MA, USA). After filtration and centrifugation, the obtained cell pellet was resuspended in PBS + 0.04% BSA at 1000 cells/µL. Cancer cell viability was microscopically assessed by Trypan blue staining. Single cell suspensions were diluted (cell number target: 10.000 per sample), loaded on a Chromium Single Cell 5' Chip (10X Genomics) and run in the Chromium Controller of the 10x Genomics Chromium X platform to generate single cell gel beads emulsions, following manufacturer's instructions. Obtained libraries were sequenced on Illumina NovaSeq 6000 platform.
Chromium Next GEM Single Cell 5' Kit v2

value: Breast cancer


title: BRF33,scRNAseq


title: BRF5,scRNAseq


title: M5-TH-2-plasma intensity none

description: smart-seq 2


title: BRF32.C1,scRNAseq


title: BRF4,scRNAseq


title: M4-TH-2-plasma intensity none

description: smart-seq 2


title: Bat_Fib_hACE2_INF_2 48hrs


title: BRF31.C1,scRNAseq


title: M2-TH-2-plasma intensity none

description: smart-seq 2


title: BRF32,scRNAseq


title: Bat_iPSCs_hACE2_contr_2 48hrs


title: BRF3,scRNAseq


title: L23-TH-2-plasma intensity high

description: smart-seq 2


title: L22-TH-2-plasma intensity high

description: smart-seq 2


title: BRF24.C1,scRNAseq


title: BRF3.C1,scRNAseq


title: M8-TH-2-plasma intensity none

description: smart-seq 2


title: L21-TH-2-plasma intensity high

description: smart-seq 2


title: L20-TH-2-plasma intensity high

description: smart-seq 2


title: BRF23.C1,scRNAseq


title: L19-TH-2-plasma intensity high

description: smart-seq 2


title: BRF23,scRNAseq


title: L18-TH-2-plasma intensity high

description: smart-seq 2


title: L16-TH-2-plasma intensity low

description: smart-seq 2


title: L15-TH-2-plasma intensity low

description: smart-seq 2


title: BRF22,scRNAseq


title: M3-TH-2-plasma intensity none

description: smart-seq 2


title: BRF18.C1,scRNAseq


title: BRF24,scRNAseq


title: BRF16,scRNAseq


title: BRF18,scRNAseq


title: L14-TH-2-plasma intensity low

description: smart-seq 2


title: L12-TH-2-plasma intensity low

description: smart-seq 2


title: L11-TH-2-plasma intensity low

description: smart-seq 2


title: BRF15.C1,scRNAseq


title: L10-TH-2-plasma intensity low

description: smart-seq 2


title: L13-TH-2-plasma intensity low

description: smart-seq 2


title: O2-TH-2-plasma intensity none

description: smart-seq 2


title: BRF15,scRNAseq


title: L9-TH-2-plasma intensity low

description: smart-seq 2


title: BRF22.C1,scRNAseq


title: L8-TH-2-plasma intensity none

description: smart-seq 2


title: L7-TH-2-plasma intensity none

description: smart-seq 2


title: L6-TH-2-plasma intensity none

description: smart-seq 2


title: BRF19.C1,scRNAseq


title: Ad-NNMT transfected HUVECs, H3K27me3

city: Beijing

first: Jun

last: Guo

address: Dahua Road

institute: Beijing Hospital

description: Cut&Tag followed by methylation sequencing to investigate H3K27me3 histone modifications in Ad-NNMT transfected HUVECs

data_processing:
Raw sequencing reads were quality-checked using FastQC, and adapters were trimmed with Trim Galore. The resulting clean reads were aligned to the human reference genome (hg38) using Bismark. Methylation calls were extracted using Bismark's methylation extractor.
Assembly: hg38 (Human Genome Version 38)
Supplementary files format and content: Processed data files include methylation calls in the form of BED or bigWig files, containing coordinates of methylated cytosines along with their methylation percentages.

source_name: Umbilical vein

growth_protocol: Human umbilical vein endothelial cells (HUVECs) were cultured in endothelial cell growth medium (EGM) supplemented with growth factors and antibiotics at 37°C in a 5% CO2 atmosphere.

extract_protocol:
After transfection, cells were harvested, and protein was extracted using lysis buffer suitable for subsequent Cut&Tag analysis with H3K4me3 and H3K27me3 antibodies. DNA was extracted following the standard protocols for methylation sequencing.
Methylation sequencing libraries were prepared using a standard bisulfite conversion method, followed by adapter ligation and PCR amplification, optimized for paired-end sequencing.

treatment_protocol: HUVECs were transfected with either Ad-NC or Ad-NNMT for 48 h.

value: Umbilical vein

value: HUVECs

value: Endothelial Cells

value: Ad-NNMT transfection


title: Ad-NC transfected HUVECs, H3K27me3

description: Cut&Tag followed by methylation sequencing to investigate H3K27me3 histone modifications in Ad-NC transfected HUVECs

value: Ad-NC transfection


title: BRF31,scRNAseq


title: Ad-NC transfected HUVECs, H3K4me3

description: Cut&Tag followed by methylation sequencing to investigate H3K4me3 histone modifications in Ad-NC transfected HUVECs


title: L4-TH-2-plasma intensity none

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: BRF16.C1,scRNAseq


title: M1-TH-2-plasma intensity none

description: smart-seq 2


title: L5-TH-2-plasma intensity none

description: smart-seq 2


title: BRF14,scRNAseq


title: N23-TH-2-plasma intensity high

description: smart-seq 2


title: L17-TH-2-plasma intensity high

description: smart-seq 2


title: HZ12_ATAC

city: Palo Alto

first: Yu

last: Liu

address: 1215 Welch Road

department: CVI

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore. Trimmed data was mapped to hg19 whole genome using bowtie2.Peaks were called against sequenced input chromatin using MACS2. Differences in peaks between conditions were detected by using Manorm2.
Assembly: hg19
Supplementary files format and content: .bw

source_name: heart

extract_protocol:
Primary fibroblasts were isolated from heart tissues of healthy donors. The genomic DNA was extracted using ATAC-Seq Kit from ACTIVE MOTIF.
Illumina NovaSeq 6000

value: heart

value: Line 3

value: primary fibroblast

value: TGFβ+ART


title: L3-TH-2-plasma intensity none

description: smart-seq 2

source_name: Brain


title: HZ11_ATAC

value: TGFβ


title: L2-TH-2-plasma intensity none

description: smart-seq 2


title: K23-TH-2-plasma intensity high

description: smart-seq 2


title: HZ10_ATAC

value: ART


title: HZ9_ATAC

value: Vehicle control (DMSO)


title: HZ7_ATAC

value: Line 2


title: K22-TH-2-plasma intensity high

description: smart-seq 2


title: K21-TH-2-plasma intensity high

description: smart-seq 2


title: Ad-NNMT-H3K4me3

description: Cut&Tag followed by methylation sequencing to investigate H3K4me3 histone modifications in Ad-NNMT transfected HUVECs


title: K20-TH-2-plasma intensity high

description: smart-seq 2


title: HZ4_ATAC

value: Line 1


title: HZ5_ATAC


title: K19-TH-2-plasma intensity high

description: smart-seq 2


title: K16-TH-2-plasma intensity low

description: smart-seq 2


title: K17-TH-2-plasma intensity high

description: smart-seq 2


title: HZ3_ATAC


title: HZ2_ATAC


title: HZ1_ATAC


title: HZ8_ATAC


title: TGFβ_Sample6

data_processing:
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence by TrimGalore. Then Trimmed data was mapped to hg38 whole genome using STAR.The raw read counts was counted by using Featurecounts
Assembly: hg38
Supplementary files format and content: TPM value.csv

source_name: Heart

extract_protocol: The primary fibroblasts were extracted from heart tissue of healthy donors. RNA was extracted in Trizol and further processed according to the manufacturer's instructions (Qiagen, Cat. No. / ID: 217084).

value: Heart

value: Primary fibroblasts


title: K11-TH-2-plasma intensity low

description: smart-seq 2


title: K10-TH-2-plasma intensity low

description: smart-seq 2


title: K14-TH-2-plasma intensity low

description: smart-seq 2


title: K12-TH-2-plasma intensity low

description: smart-seq 2


title: K13-TH-2-plasma intensity low

description: smart-seq 2


title: TGFβ_Sample5


title: K18-TH-2-plasma intensity high

description: smart-seq 2


title: HZ6_ATAC


title: TGFβ+ART_Sample5


title: K9-TH-2-plasma intensity low

description: smart-seq 2


title: K8-TH-2-plasma intensity none

description: smart-seq 2


title: L1-TH-2-plasma intensity none

description: smart-seq 2


title: TGFβ_Sample4


title: K7-TH-2-plasma intensity none

description: smart-seq 2


title: TGFβ+ART_Sample3


title: TGFβ+ART_Sample4


title: TGFβ+ART_Sample6


title: Ctrl_Sample4

value: DMSO (Ctrl)


title: K6-TH-2-plasma intensity none

description: smart-seq 2


title: K5-TH-2-plasma intensity none

description: smart-seq 2


title: Mycelium - KO_LaeA - Rep4

value: Mycelium


title: Ctrl_Sample3


title: K15-TH-2-plasma intensity low

description: smart-seq 2


title: K2-TH-2-plasma intensity none

description: smart-seq 2


title: TGFβ_Sample2


title: K1-TH-2-plasma intensity none

description: smart-seq 2


title: TGFβ+ART_Sample1


title: J22-TH-2-plasma intensity high

description: smart-seq 2


title: TGFβ+ART_Sample2


title: J21-TH-2-plasma intensity high

description: smart-seq 2


title: Ctrl_Sample2


title: Ctrl_Sample5


title: J20-TH-2-plasma intensity high

description: smart-seq 2


title: TGFβ_Sample3


title: J18-TH-2-plasma intensity high

description: smart-seq 2


title: IMR_Control1 8hrs

value: Primary cells

value: Replicate 1

value: Fibroblast cells

value: hACE2 Lenti infected


title: IMR_Control2 8hrs

value: Replicate 2


title: IMR_Infected1 8hrs

value: hACE2 Lenti infected+SARS CoV-2 infected


title: J16-TH-2-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: J17-TH-2-plasma intensity high

description: smart-seq 2


title: IMR_Infected2 8hrs


title: K4-TH-2-plasma intensity none

description: smart-seq 2


title: IMR_Uninfected_2  8hrs


title: J15-TH-2-plasma intensity low

description: smart-seq 2


title: K3-TH-2-plasma intensity none

description: smart-seq 2


title: IMR_Uninfected_1 8hrs


title: Human_Fib_Uninfected_2 48hrs


title: J14-TH-2-plasma intensity low

description: smart-seq 2


title: TGFβ_Sample1

value: TGFβ


title: J23-TH-2-plasma intensity high

description: smart-seq 2


title: J13-TH-2-plasma intensity low

description: smart-seq 2


title: Ctrl_Sample1


title: J19-TH-2-plasma intensity high

description: smart-seq 2


title: Human_Fib_Uninfected_1 48hrs


title: J11-TH-2-plasma intensity low

description: smart-seq 2


title: Human_Fib_hACE2_Inf_2  48hrs


title: J9-TH-2-plasma intensity low

description: smart-seq 2


title: Human_Fib_hACE2_Inf_1  48hrs


title: Human_Fib_hACE2_contr_1 48hrs


title: J12-TH-2-plasma intensity low

description: smart-seq 2


title: J10-TH-2-plasma intensity low

description: smart-seq 2


title: Human_Fib_hACE2_contr_2 48hrs


title: J8-TH-2-plasma intensity none

description: smart-seq 2


title: J7-TH-2-plasma intensity none

description: smart-seq 2


title: Human_ES_Uninfected_1 48hrs

source_name: Cell line

value: Cell line

value: Stem cell


title: Human_ES_Uninfected_2 48hrs


title: J6-TH-2-plasma intensity none

description: smart-seq 2


title: J5-TH-2-plasma intensity none

description: smart-seq 2


title: Human_ES_hACE2_Inf_2 48hrs


title: J3-TH-2-plasma intensity none

description: smart-seq 2


title: Human_ES_hACE2_control_2 48hrs


title: J4-TH-2-plasma intensity none

description: smart-seq 2


title: Human_ES_hACE2_control_1 48hrs


title: J2-TH-2-plasma intensity none

description: smart-seq 2


title: J1-TH-2-plasma intensity none

description: smart-seq 2


title: I23-TH-2-plasma intensity high

description: smart-seq 2


title: LIP.16 beefore weight loss, SAAT

city: Saint Louis

first: Silvia

last: Gonzalez-Nieves

state: Missouri

department: Pharmacology & Physiology

institute: Saint Louis University

data_processing:
Sequence reads were aligned to Homo_sapiens.GRCh38.110  using the STAR (version 2.5.2b)(average mapped length: 199.67 bp; Mismatch rate per base: 0.0026%; deletion rate per base: 0.0001.)
Counts were generated using Featurecounts (version 2.0.6).
Assembly: Homo_sapiens.GRCh38.110
Supplementary files format and content: tab-delimited text file icnludes raw counts for all the samples.

source_name: Adipose tissue

extract_protocol:
Total RNA was isolated from frozen SAAT and SFAT samples by using QIAzol lysis reagent and a RNeasy mini kit (Qiagen, Valencia, CA) in combination with a RNase-free DNase Set (Qiagen) .
Library preparation was performed with total RNA and cDNA fragments sequenced on an Illumina NovaSeq 6000 (Illumina, San Diego, CA) with all samples sequenced on the same instrument and analyzed during the same run to avoid batch effects.

value: Adipose tissue

tag: time

value: Pre weight-loss

value: SAAT


title: I22-TH-2-plasma intensity high

description: smart-seq 2


title: LIP.16 beefore weight loss, SFAT

value: SFAT


title: LIP.16 after weight loss, SAAT

value: Post weight-loss


title: I21-TH-2-plasma intensity high

description: smart-seq 2


title: LIP.16 after weight loss, SFAT


title: I19-TH-2-plasma intensity high

description: smart-seq 2


title: LIP.12 after weight loss, SFAT


title: Ctrl_Sample6

value: Heart

value: Primary fibroblasts

value: DMSO (Ctrl)


title: I18-TH-2-plasma intensity high

description: smart-seq 2


title: LIP.12 beefore weight loss, SFAT


title: LIP.12 beefore weight loss, SAAT


title: I17-TH-2-plasma intensity high

description: smart-seq 2


title: LIP.11 beefore weight loss, SAAT


title: Human_ES_hACE2_Inf_1 48hrs

value: Replicate 1


title: I15-TH-2-plasma intensity low

description: smart-seq 2


title: I16-TH-2-plasma intensity low

description: smart-seq 2


title: LIP.12 after weight loss, SAAT


title: LIP.10 beefore weight loss, SFAT


title: I14-TH-2-plasma intensity low

description: smart-seq 2


title: LIP.10 beefore weight loss, SAAT


title: LIP.11 beefore weight loss, SFAT


title: LIP.10 after weight loss, SAAT


title: I12-TH-2-plasma intensity low

description: smart-seq 2


title: I13-TH-2-plasma intensity low

description: smart-seq 2


title: I11-TH-2-plasma intensity low

description: smart-seq 2


title: LIP.09 beefore weight loss, SFAT


title: I20-TH-2-plasma intensity high

description: smart-seq 2


title: I10-TH-2-plasma intensity low

description: smart-seq 2


title: I9-TH-2-plasma intensity low

description: smart-seq 2


title: LIP.09 beefore weight loss, SAAT


title: LIP.09 after weight loss, SFAT


title: I6-TH-2-plasma intensity none

description: smart-seq 2


title: LIP.07 after weight loss, SFAT


title: LIP.07 beefore weight loss, SFAT


title: LIP.07 beefore weight loss, SAAT


title: I5-TH-2-plasma intensity none

description: smart-seq 2


title: I4-TH-2-plasma intensity none

description: smart-seq 2


title: LIP.05 beefore weight loss, SAAT


title: LIP.07 after weight loss, SAAT


title: I3-TH-2-plasma intensity none

description: smart-seq 2


title: LIP.05 after weight loss, SFAT


title: I2-TH-2-plasma intensity none

description: smart-seq 2


title: I1-TH-2-plasma intensity none

description: smart-seq 2


title: LIP.10 after weight loss, SFAT


title: LIP.05 beefore weight loss, SFAT


title: LIP.02 beefore weight loss, SFAT


title: LIP.05 after weight loss, SAAT


title: LIP.02 beefore weight loss, SAAT


title: H23-TH-2-plasma intensity high

description: smart-seq 2


title: H21-TH-2-plasma intensity high

description: smart-seq 2


title: H20-TH-2-plasma intensity high

description: smart-seq 2


title: LIP.02 after weight loss, SFAT


title: LIP.09 after weight loss, SAAT


title: I7-TH-2-plasma intensity none

description: smart-seq 2


title: I8-TH-2-plasma intensity none

description: smart-seq 2


title: H19-TH-2-plasma intensity high

description: smart-seq 2


title: LIP.02 after weight loss, SAAT


title: H18-TH-2-plasma intensity high

description: smart-seq 2


title: H17-TH-2-plasma intensity high

description: smart-seq 2


title: LIP.01 beefore weight loss, SAAT


title: LIP.01 beefore weight loss, SFAT


title: H16-TH-2-plasma intensity low

description: smart-seq 2


title: H15-TH-2-plasma intensity low

description: smart-seq 2


title: LIP.01 after weight loss, SAAT


title: H14-TH-2-plasma intensity low

description: smart-seq 2


title: LIP.01 after weight loss, SFAT


title: H13-TH-2-plasma intensity low

description: smart-seq 2


title: H22-TH-2-plasma intensity high

description: smart-seq 2


title: Dermal Lymphatic Endothelial Cells,METTL3 shRNA transfected,rep1

city: Nanjing

first: Lianjun

last: Shi

state: Jiangsu

address: No.138 Hanzhong Road

institute: Eye Hospital, Nanjing Medical University

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
We aligned reads of all samples to the Homo_sapiens (ftp://ftp.ensembl.org/pub/release-101/fasta/homo_sapiens/dna/) reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome. And then by removing sequence-dependent bias and amplification noise using UMI-tools.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample ...
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: HDLEC

extract_protocol:
Total RNA was extracted usingTrizol reagent following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit, high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters, which including custom Unique Molecular Identifiers for minimizing sequence-dependent bias and amplification noise according to (Shiroguchi et al. 2012). Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 following the vendor's recommended protocol.

value: HDLEC

value: Primary Human Dermal Lymphatic Endothelial Cells

value: METTL3 shRNA transfected


title: Dermal Lymphatic Endothelial Cells,METTL3 shRNA transfected,rep2


title: Dermal Lymphatic Endothelial Cells,negative control shRNA transfected,rep3

value: negative control shRNA transfected


title: H9-TH-2-plasma intensity low

description: smart-seq 2

value: Brain

value: isolated cells

value: microglia


title: H8-TH-2-plasma intensity none

description: smart-seq 2


title: H12-TH-2-plasma intensity low

description: smart-seq 2


title: Dermal Lymphatic Endothelial Cells,negative control shRNA transfected,rep2


title: Dermal Lymphatic Endothelial Cells,METTL3 shRNA transfected,rep3


title: Dermal Lymphatic Endothelial Cells,negative control shRNA transfected,rep1


title: MOLT4, LDB1, CUT&Tag

city: Suzhou

first: Zimu

last: Zhang

address: Zhongnan Street

institute: Children’s Hospital of Soochow University

data_processing:
Basecalls were performed using bcl2fastq v2.17 for Novaseq output. CUT&Tag reads were trimmed using Fastp v0.23.2 with default settings, and were aligned to the UCSC hg38 genome using Bowtie2 version v2.4.4 with parameter --end-to-end --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Peaks were identified using MACS3 (v3.0.0a6) with the significance cut-off FDR<0.01
bigWig files were generated using bedGraphToBigWig tool.
Assembly: hg38
Supplementary files format and content: bigwig files
Library strategy: CUT&Tag

source_name: cell line

extract_protocol:
CUT&Tag was performed with Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme) according to the manufacturer’s protocol.
Library construction was performed using TruePrep® DNA Library Prep Kit V2 for Illumina (Vazyme) and TruePrep® Index Kit V2 for Illumina (Vazyme).

value: cell line

value: T-ALL cells

value: LDB1(Abcam, #ab96799)


title: H10-TH-2-plasma intensity low

description: smart-seq 2


title: H11-TH-2-plasma intensity low

description: smart-seq 2


title: H7-TH-2-plasma intensity none

description: smart-seq 2


title: H5-TH-2-plasma intensity none

description: smart-seq 2


title: hand2 FLD+/? 20 hpf CMs_rep3

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

country: Germany

institute: MPI for heart and lung research

description:
WT-Het_3
ExpB_counts.matrix.norm_anno

data_processing:
Trimmomatic version 0.39 was employed to trim reads after a quality drop below a mean of Q20 in a window of 20 nucleotides. Only reads between 15 and 75 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned vs. the Ensembl zebrafish genome version danRer11 (ensemble release 104) using STAR 2.7.10a with the parameter “–outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 2.0.2. tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
Differentially expressed genes were identified using DESeq2 version 1.30.1. Only genes with a minimum fold change of ±1.5 (log2 ± 0.59), a maximum Benjamini–Hochberg corrected p-value of 0.05, and a minimum combined mean of 5 reads were deemed to be significantly differentially expressed.
Assembly: danRer11
Supplementary files format and content: library size normalized counts

organism: Danio rerio

source_name: embryonic heart

extract_protocol:
miRNeasy micro Kit (Qiagen), using low input DNase protocol
Approximately 1ng of total RNA was used as starting material for SMART®-Seq HT Kit (Takara Bio).

value: embryonic heart

value: cardiomyocytes

value: sibling WT of hand2 mutants

value: sorted cells by FACS


title: Loucy, LDB1, CUT&Tag

value: Loucy


title: H6-TH-2-plasma intensity none

description: smart-seq 2


title: H4-TH-2-plasma intensity none

description: smart-seq 2


title: hand2 FLD+/? 20 hpf CMs_rep2

description:
WT-Het_2
ExpB_counts.matrix.norm_anno


title: H3-TH-2-plasma intensity none

description: smart-seq 2


title: Loucy, IgG, CUT&Tag

value: IgG(Abcam, #ab172730)


title: H1-TH-2-plasma intensity none

description: smart-seq 2


title: H2-TH-2-plasma intensity none

description: smart-seq 2


title: WT 20 hpf CMs_rep3

description:
CMs-WT_3
ExpA_counts.matrix.norm_anno

value: sibling WT of hand2 OE


title: H2O2_BIOT.009_3

city: Brno

first: Martina

last: Zapletalová

address: Kamenice 5

department: Department of Biochemistry

country: Czech Republic

institute: Masaryk University

data_processing:
Raw sequencing reads were quality-checked using FastQC and were subsequently trimmed using Trim Galore. Following this, the reads were aligned to the human genome sequence hg38, employing the R packages Rbowtie2 and Rsamtools. Differential analysis of count data was performed using the R package DeSeq2. Transcripts exhibiting |log2 fold change| > 1 and q < 0.01 (FDR-adjusted P-values) were identified as differentially expressed genes (DEGs). Cluster analysis was conducted using the R packages pvclust and dendextend. To determine the cell type, the R package clustifyr was employed against the scRNA-seq human cortex database. Cellular deconvolution was carried out using BrainDeconvShiny with the assistance of dtangle and the NG database. Heatmaps were constructed using R package ComplexHeatmap.
Assembly: hg38
Supplementary files format and content: tab-delimited file includes raw count for each sample

source_name: iPSC-derived astrocyte

growth_protocol:
NPCs were thawed in completed neural maintenance medium (NMM) (containing 50% DMEM/F12 with glutamine, 50% Neurobasal medium, 1X B27 supplement, 1X N2 supplement, 1% Penicillin/Streptomycin, 1% GlutaMax (all purchased from Gibco), non-essential amino-acids (Sigma), completed with 10 ng/mL recombinant human epidermal growth factor, and 10 ng/mL basic fibroblast growth factor) supplemented with Rhock-inhibitor at a final concentration of 10 µM and plated into poly-L-ornithine/laminin-coated dishes. On the next day, the medium was changed to completed NMM. The cell culture medium was changed every two days. Thawed NPC lines were propagated for the next passage (with a density of 100.000 cells/cm2) and seeded into Matrigel-coated dishes for astrocyte differentiation at day 10, upon reaching confluence again, (with a cell-density of 50.000/cm2).
LSFP method of Astrocyte differentiation: NPCs at day 10 were seeded into poly-L-ornithine/laminin-coated plates at a density of 50.000 cells/cm2 and maintained in GPC expansion medium (containing DMEM/F12 Glutamax, 1X B27-A supplement, 1X N2 supplement completed with 10 ng/ml recombinant human epidermal growth factor (EGF) and 10 ng/ml basic fibroblast growth factor (FGF2)) for 2 weeks. The medium was changed every two days. At day 24, cells were seeded into Matrigel-coated plates at a density of 50.000 cells/cm2 and maintained in astrocyte induction medium (containing DMEM/F12 Glutamax with 1X B27-A supplement, 1X N2 supplement completed with 10 ng/ml recombinant human epidermal growth factor (EGF), and 10 ng/ml leukemia inhibitory factor (LIF)) for 2 weeks. The medium was changed every two days. At day 36, cells were plated into Matrigel (50.000 cells/cm2) in astrocyte maturation medium, which was DMEM/F12 Glutamax medium containing 1X B27-A supplement, 1X N2 supplement, and 20 ng/ml recombinant human ciliary neurotrophic factor (CNTF, by Peprotech). Cells were kept in maturation medium for 4 more weeks with medium changes every two days and cultures were inspected by light microscopic imaging.
SSFP method of Astrocyte differentiation: NPCs at day 10 were seeded into Matrigel-coated plates at a density of 50.000 cells/cm2 and maintained in astrocyte induction medium (containing DMEM/F12 Glutamax with 1X B27-A supplement, 1X N2 supplement completed with 10 ng/ml recombinant human epidermal growth factor (EGF), and 10 ng/ml leukemia inhibitory factor (LIF)) for 2 weeks. Medium was changed every two days. When the culture reached confluence, cells were passaged using Accutase for cell-dissociation and seeded into Matrigel-coated 6-well plates with 50.000 cells/cm2. At day 24, cells were plated into Matrigel (50.000 cells/cm2) in astrocyte maturation medium, which was DMEM/F12 Glutamax medium containing 1X B27-A supplement, 1X N2 supplement and 20 ng/ml recombinant human ciliary neurotrophic factor (CNTF, by Peprotech). Cells were kept in maturation medium for 4 more weeks with medium changes every two days and cultures were inspected by light microscopic imaging.
TUSP method of Astrocyte differentiation and treatment: The NPCs at day 10 were seeded into Matrigel-coated plates at a density of 50.000 cells/cm2 and maintained in the astrocyte induction medium (ScienceCell’s astrocyte growth medium supplemented with 2% FBS) for 4 weeks. The medium was changed every two days. When the culture reached confluence, cells were passaged using Accutase for cell dissociation and seeded into Matrigel-coated 6-well plates with 50.000 cells/cm2. At day 42, cells were plated into Matrigel (50.000 cells/cm2) in astrocyte maturation medium, which was serum-free astrocyte growth medium containing 20 ng/ml recombinant human ciliary neurotrophic factor (CNTF, by Peprotech). Cells were kept in maturation medium for 4 more weeks with medium changes every two days and cultures were inspected by light microscopic imaging. On day 70 after the end of maturation phase the cells were treated in triplicates with 500 nM A42 (Biotalentum, HU) or 150 uM H2O2 for 2 hours. Cellular pellets for RNAseq and cellular media for IL-6 analysis were collected 72 hours after the treatment.

extract_protocol: The cellular pellet samples were used to isolate total RNA with TRI Reagent (Merck, USA) and RapidOutput DNA removal kit (ThermoFisher Scientific, USA). A Qubit 4 fluorometer (ThermoFisher Scientific, USA) and Fragment Analyzer (Agilent, USA) were used to analyse the isolated RNA for quantity and quality, respectively. Complementary DNA (cDNA) libraries were synthesized using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, UK). The concentration and quality of cDNA libraries were assessed using a Qubit 4 fluorometer (ThermoFisher Scientific, USA) and Fragment Analyzer (Agilent, USA). The cDNA samples were then diluted to 4 nM and sequenced on the Illumina NextSeq® platform with NextSeq® 500/550 High Output Kit v2.5 (150 cycles) (Illumina, USA), generating 75 bp pair-end reads, and on the Illumina NovaSeq® 6000 platform with NovaSeq® S4 300 kit (Illumina, USA), generating 150 bp pair-end reads.

treatment_protocol: On day 70 after the end of maturation phase the cells were treated in triplicates with 500 nM AB42 (Biotalentum, HU) or 150 uM H2O2 for 2 hours. Cellular pellets for RNAseq were collected 72 hours after the treatment.

tag: differentiation protocol

value: TUSP method

value: iPSC-derived astrocyte

value: control, healthy

value: 150 uM H2O2 for 2 hours

tag: donor

value: healthy, 35-years old, female


title: G23-TH-2-plasma intensity high

description: smart-seq 2

value: Brain

value: isolated cells

tag: cell type


title: G20-TH-2-plasma intensity high

description: smart-seq 2

value: microglia


title: G18-TH-2-plasma intensity high

description: smart-seq 2


title: G21-TH-2-plasma intensity high

description: smart-seq 2


title: H2O2_BIOT.009_1

tag: genotype

tag: treatment


title: WT 20 hpf CMs_rep1

description:
CMs-WT_1
ExpA_counts.matrix.norm_anno


title: AB_BIOT.009_3

value: 500 nM Ab42 for 2 hours


title: G17-TH-2-plasma intensity high

description: smart-seq 2


title: WT 20 hpf CMs_rep2

description:
CMs-WT_2
ExpA_counts.matrix.norm_anno


title: AB_BIOT.009_2


title: H2O2_BIOT.009_2


title: hand2 OE 20 hpf CMs_rep3

description:
CMs-OE_3
ExpA_counts.matrix.norm_anno

value: overexpression hand2 in myocardium


title: G15-TH-2-plasma intensity low

description: smart-seq 2


title: MOLT4, IgG, CUT&Tag

value: cell line

value: T-ALL cells


title: G16-TH-2-plasma intensity low

description: smart-seq 2


title: G14-TH-2-plasma intensity low

description: smart-seq 2


title: hand2 OE 20 hpf CMs_rep2

description:
CMs-OE_2
ExpA_counts.matrix.norm_anno

value: embryonic heart

value: cardiomyocytes


title: AB_BIOT.009_1


title: G13-TH-2-plasma intensity low

description: smart-seq 2


title: hand2 OE 20 hpf CMs_rep1

description:
CMs-OE_1
ExpA_counts.matrix.norm_anno

value: sorted cells by FACS


title: G12-TH-2-plasma intensity low

description: smart-seq 2


title: hand2 FLD+/? 20 hpf CMs_rep1

description:
WT-Het_1
ExpB_counts.matrix.norm_anno

value: sibling WT of hand2 mutants


title: control_BIOT.009_3

value: non-treated


title: G22-TH-2-plasma intensity high

description: smart-seq 2


title: G11-TH-2-plasma intensity low

description: smart-seq 2


title: control_BIOT.009_2

value: TUSP method


title: G10-TH-2-plasma intensity low

description: smart-seq 2


title: G19-TH-2-plasma intensity high

description: smart-seq 2


title: G8-TH-2-plasma intensity none

description: smart-seq 2


title: G6-TH-2-plasma intensity none

description: smart-seq 2


title: hand2 FLD-/- 20 hpf CMs_rep2

description:
Mut_2
ExpB_counts.matrix.norm_anno

value: hand2 mutant


title: hand2 FLD-/- 20 hpf CMs_rep1

description:
Mut_1
ExpB_counts.matrix.norm_anno