title: HS-SY-II Cas9 cellline in vivo in mouse (CDX), replicate1

data_processing:
MAGeCK (Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout) pipeline was used for mapping reads (paired end fastqs) to sgRNA custom library (Manuscript Supplemental Table S1)designed using DepMap (DepMap repository version 21Q3 https://depmap.org/portal/), normalization using 10% of non-trageting controls (Manuscript Supplemental Table S1), and quality control. Identification of positively and negatively selected genes/hits comparing Day14_in_vitro vs Day0 and CDX vs Day0 was performed used MAGeCK RRA (Robust Rank Aggregation).
Assembly: hg38
Supplementary files format and content: Tab-delimted counts for sgRNAs
Supplementary files format and content: Tab-delimted normalized counts for sgRNA

source_name: HS-SY-II Cas9

growth_protocol: Cells were cultured in DMEM supplemented with 10% FBS, 1 % penicillin-streptomycin and 1% L-glutamine. HS-SY-II cells were additionally supplemented with 0.5% Sodium Pyruvate.

extract_protocol:
Genomic DNA was extracted from collected cell pellets using a Zymo Quick DNA miniprep kit (#D3024).
The sgRNA were PCR amplified by NEBNext Ultra II Q5 Master Mix (NEB #M0544) from the genomic DNA using the indexed PCR primers with next-generation sequencing adapters compatible with Illumina's NEXTERA kit. PCR products were size-selected by gel electrophoresis, quantified byQubit(Thermo Fisher Scientific) and sequenced using HiSeq (Illumina).
CRISPR Screening

treatment_protocol: Screens were performed in duplicates. HS-SY-II Cas9 cells were transduced with the screen library in the presence of 0.8 mg/ml polybrene with an efficiency of 30% or lower to ensure most cells received a single sgRNA. After selection with puromycin (1μg/mL) for 2-4days, a cell aliquot containing 5 million cells (~1,000X coverage of library) was frozen as the day 0 or input reference sample. The remaining cells were divided into 2 arms for thein vivoandin vitroscreens. For thein vivoscreen, 2 million cells in 50% Matrigel were transplanted subcutaneously into the flanks of 4 athymic nude mice per replicate. The resultant tumor was monitored, and mice were sacrificed when the tumor volume reached 1 cm3. The tumor was dissociated into single cell suspension36 using collagenase II (20 mg/mL) along with Dnase I (10,000 Kunitz/mL) and used for further experiments. For thein vitroscreens, at least 5 million cells were maintained throughout the 14-day culture period and collected at the end of the screen.

value: HS-SY-II Cas9

value: Synovial sarcoma

value: CRISPR transfection of lentiviral sgRNAs


title: Runx3 E12.5 TrkC Cut&Run rep2

status: Public on Nov 06 2024

type: SRA

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

country: Israel

institute: The Weizmann Institute

library_source: genomic

data_processing:
Sequence reads were trimmed for adaptor with cutadapt
Trimmed sequence reads were mapped to GrCM38/mm10 using bowtie with ‘--no-mixed --no-discordant’
After alignment, fragments with size ≤ 90 bp were selected for peak calling of Runx3/Brn3a/Islet1 samples. No size selection was applied to the H3K27Ac.
Peak calling was performed with MACS2 against the control samples (NRS) using ‘--keep-dup all’. For the Runx3 samples we also used '-p e-5'.
Assembly: mm10
Supplementary files format and content: bed file for every experiment with the genomic regions of the consensus peaks.
Supplementary files format and content: Peak calling was performed with MACS2 against the control samples using ‘--keep-dup all’, For the Brn3a samples we also used '-p e-5'

molecule: genomic DNA

organism: Mus musculus

source_name: dorsal root ganglia (DRG)

extract_protocol:
DRG were dissected from E12.5 BacE-GFP expressing embryos (Appel et al 2016) and dissociated with Trypsin B/Collagenase H.  GFP positive cells were FACS isolated and 300,000-600,000 cells were used for Cut&Run analysis with anti-Brn3a (1:200) (kindly provided by E.Turner), home made anti-Runx3 (1:200), anti-H3K27Ac (1:50) (Abcam 4729) antibodies or Normal Rabbit Serum (NRS, 1:200). GFP positive TrkC neurons were bound to ConA beads, permeabilized, incubated with anti-Brn3a, anti-Runx3, anti-H3K27Ac or NRS and targeted by MNase cleavege. Antibody bound DNA was extracted by phenol chloroform.
Library was prepared using NEBNEXT Ultra II DNA Library Prep Kit for Illumina (#E7645). DNA fragments were PCR amplified with Illumina primers for no more than 15 cycles and library fragments up to ~250 bp (insert plus adaptor and PCR primer sequences) were SPRI (x0.8) purified. Libraries were sequenced on the Illumina NextSeq 500/550 following the manufacturer's protocols.

tag: tissue

value: dorsal root ganglia (DRG)

tag: cell type

value: TrkC proprioceptive neurons

tag: genotype

value: Runx3-BAC-GFP-CB6 transgenic mice


title: HS-SY-II Cas9 cellline in vivo in mouse (CDX), replicate2

city: La Jolla

first: Aniruddha

middle: J.

last: Deshpande

state: CA

address: 10901 North Torrey Pines Road

department: Cancer Genome and Epigenetics Program

country: USA

institute: Sanford Burnham Prebys Medical Discovery Institute

library_source: other

molecule: other

organism: Homo sapiens

tag: cell line

tag: treatment


title: H3K9ac, Kat6b-/-, sample 3

city: Parkville

first: Waruni

last: Abeysekera

state: Victoria

address: 1G Royal Parade

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the Mus musculus (mm39) and Drosophila melanogaster (Dme1R6.32) genomes by Rsubread version 2.12.3.
Read counts were summarized by genomic regions - Promoters (TSS - 1 kb to TSS), Gene body and Transcription end sites (TES to TES + 1 kb) of protein coding genes, and H3K4me1+/H3K27ac+ enhancer enriched regions - using the Rsubread's featureCounts function and Rsubread's inbuilt mm39 NCBI annotation.
Assembly: mm39 and Dme1R6.32
Supplementary files format and content: Tab-delimited text files for Promoter region counts of protein coding genes; columns represent Entrez Gene ID, region length in base counts, and the number of sequence reads mapping to that region.
Supplementary files format and content: Tab-delimited text files for Gene body counts of protein coding genes; columns represent Entrez Gene ID, gene length in base counts, and the number of reads mapping to that gene.
Supplementary files format and content: Tab-delimited text files for Transcription end site region counts of protein coding genes; columns represent Entrez Gene ID, region length in base counts, and the number of reads mapping to that region.
Supplementary files format and content: Tab-delimited text files for H3K4me1+/H3K27ac+ enhancer enriched regions; columns represent region ID, region length in base counts, and the number of reads mapping to that region.
Supplementary files format and content: Supplementary file containing sequence read counts for all samples in matrix form are also provided.
Library strategy: CUT&Tag

source_name: Dorsal telencephalon

growth_protocol: Neural stem and progenitor cells were isolated from the dorsal telencephalon of E12.5 mouse embryos and cultured as free-floating neurosphere colonies as described in Rietze et al. (Nature 2001).

extract_protocol:
All NSPCs were primary cells, derived from freshly dissected tissue. All molecular assays were performed at passages 3-5.
CUT&Tag sequencing was performed using 50,000 NSPCs combined with 50,000 Drosophila melonagaster S2 cells, as described in Kaya-Okur et al. (Nature Communications 2019), with minor modifications as described in Wichmann et al. (Cell Death and Disease 2022).

tag: strain

value: Dorsal telencephalon

value: Neural stem and progenitor cells

tag: cut&tag antibody


title: HS-SY-II Cas9 cellline cultured in vitro for 14 days, replicate2


title: Runx3 E12.5 TrkC Cut&Run rep1


title: HS-SY-II Cas9 cellline cultured in vitro for 0 days, replicate2


title: H3K9ac, Kat6b-/-, sample 1


title: HS-SY-II Cas9 cellline cultured in vitro for 0 days, replicate1


title: HS-SY-II Cas9 cellline cultured in vitro for 14 days, replicate1


title: HFD + C2, biol rep 3

city: Cheongju

first: Gun-Hwa

last: Kim

address: 162 Yeongudanji-ro

country: South Korea

institute: Korea Basic Science Institute

library_source: transcriptomic

data_processing:
Sequence reads of the raw FASTQ files were trimmed using Trimmomatic 0.39.
Trimmed sequence reads were mapped and counted with STAR 2.7.
Read counts were extracted and normalized using DESeq2.
Assembly: mm10
Supplementary files format and content: *.txt: Tab-delimited output files (normalized abundance measurements for each sample).

molecule: total RNA

source_name: Liver

extract_protocol:
Total RNA was extracted from mouse liver tissues using Tri Reagent (Molecular Research Center Inc.), according to the manufacturer’s instructions. RNA quality was evaluated by analyzing the RNA integrity number determined using a 2100 bioanalyzer (Agilent RNA 6000 Nano kit, Agilent Technologies).
Library preparation was performed using Advanta RNA-seq XT NGS Library Prep kits for Fluidigm JUNO.

treatment_protocol: C57BL/6N mice were fed a normal chow diet (NCD) or HFD (60% of energy derived from fat) for 12 weeks, mice were injected intraperitoneally with C1 and C2 (5 mg/kg/day) for 12 weeks.

value: Liver


title: H3K9ac, C57BL/6 Wildtype, sample 4

value: Wildtype


title: tamoxifen-resistant MDA-MB-231 cells (replicate 3)

city: Ribeirao PReto

first: Patrick

last: Santos

address: 3900 Bandeirantes Ave

country: Brazil

institute: USP

data_processing:
Data were initially processed in UNIX based cluster. Further analysis were performed in R-Studio, using the DeSeq2 Package
A quality control test was performed before alignment using FastQC software (17). All low-quality reads and Illumina adapters were removed by the 0.39 version of the Trimmomatic tool
Reads that passed the quality filter were aligned to the reference genome index (Homo sapiens Ensembl GRCh38, release 109) using STAR 2.7.0a alignment software
The DESeq2 package was used to detect differentially expressed genes (DEGs) by using negative binomial generalized linear models
The comparison between sensitive EVs vs. resistant EVs treatment for each cell line was estimated by the logarithmic fold-change log2 (sensitive vs. resistant). The lists with the DEGs of each condition were filtered using a 5% false discovery rate (FDR) cutoff and an absolute fold change > 1.5 for upregulated and downregulated genes.
Assembly: Homo sapiens Ensembl GRCh38, release 109
Supplementary files format and content: tab-limited text includes raw counts for each sample

growth_protocol: Cells were cultivated in RPMI 1640 media with 10% fetal bovine serum and 1% antibiotics in a humidified CO2 (5%) incubator

extract_protocol:
RNA was extracted from MCF-7 and MDA-MB-231 cell lysates using a spin column supplied with the RNeasy kit
The mRNA capture and construction of 150 base pair double-stranded mRNA-Seq libraries were performed using Zymo-Seq RiboFree Total RNA (Zymo Research, USA). The protocol included the capture, elution, and fragmentation of mRNA, followed by synthesis of the first and second 150 strands. Illumina adapters were ligated to the ends of the mRNA-derived cDNA fragments, followed by library PCR amplification. The libraries were sequenced in the SP lane of an Illumina NovaSeq6000 sequencer.

treatment_protocol: Sensitive MCF-7 and MDA-MB-231 cells were exposed to tamoxifen- and doxoruibicin-resistant EVs for 24 h

value: breast cancer

value: cells exposed to tamoxifen-resistant EVs


title: H3K9ac, C57BL/6 Wildtype, sample 3


title: HFD + C2, biol rep 2


title: tamoxifen-resistant MDA-MB-231 cells (replicate 1)


title: H3K9ac, C57BL/6 Wildtype, sample 2


title: doxorubicin-resistant MDA-MB-231cells (replicate 2)

value: cells exposed to doxorubicin-resistant EVs


title: HFD + C2, biol rep 1


title: doxorubicin-resistant MDA-MB-231 cells (replicate 3)


title: HFD + C1, biol rep 3


title: H3K9ac, C57BL/6 Wildtype, sample 1


title: Sensitive MDA-MB-231 cells (replicate 3)

value: no treatment


title: doxorubicin-resistant MDA-MB-231 cells (replicate 1)


title: Sensitive MDA-MB-231 cells (replicate 2)


title: HFD + C1, biol rep 2


title: Sensitive MDA-MB-231 cells (replicate 1)


title: MCF-7 cells (replicate 2)


title: H3K23ac, Kat6b-/-, sample 3


title: MCF-7 cells (replicate 3)


title: MCF-7 cells (replicate 1)


title: HFD + C1, biol rep 1


title: H3K23ac, Kat6b-/-, sample 2


title: HFD, biol rep 3

value: HFD


title: HFD, biol rep 2


title: H3K23ac, Kat6b-/-, sample 1


title: H1755 cells, treated by birinapant and cocultured with PBMC, replicate2

city: Atlanta

first: Changfa

last: Shu

state: GA

address: 1510 Clifton Rd

department: Pharmacology and Chemical Biology

institute: Emory University

data_processing:
Htseq v0.6.1 was used to count the read numbers mapped of each gene
FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: hg38
Supplementary files format and content: txt file includesFPKM value for each samples
Supplementary files format and content: txt file includes read counts for each samples

source_name: cell line

growth_protocol: H1755 lung cancer cells were maintained in RPMI1640 medium supplemented with 10% FBS and antibiotics in humidified conditions with 5% CO2 at 37°C

extract_protocol:
The total RNA was isolated using E.Z.N.A.® Total RNA Kit I(Omega)
Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina following manufacturer's intructions

treatment_protocol: H1755 cells were treated with birinapant (50 nM) in cancer cells alone culture or co-cultured with PBMC (E:T=1:1).

value: cell line

value: Lung adenocarcinoma cells

value: WT

value: birinapant+PBMC


title: H3K23ac, C57BL/6 Wildtype, sample 4


title: H1755 cells, treated by birinapant and cocultured with PBMC, replicate1


title: H1755 cells, treated by birinapant and cocultured with PBMC, replicate3


title: HFD, biol rep 1


title: H1755 cells, treated by birinapant, replicate3

value: birinapant


title: tamoxifen-resistant MDA-MB-231 cells (replicate 2)


title: H3K23ac, C57BL/6 Wildtype, sample 3


title: H1755 cells, treated by birinapant, replicate2


title: H1755 cells, treated by birinapant, replicate1


title: NCD, biol rep 2

value: NCD


title: NCD, biol rep 3


title: H3K23ac, Kat6b-/-, sample 4


title: H3K23ac, C57BL/6 Wildtype, sample 2


title: PBMC, DBLET01_Hu_M2, scTCR-seq: 317, 392, 403, 405, 428

first: Ningxin

last: Kang

state: California

address: 9420 Athena Cir

institute: La Jolla Institute for Immunology

description: 10x Genomics

data_processing:
The sequencing results were put into the 10X Genomics Cell Ranger (v7.0.0)function multi for alignment (to GRCh38 v2020-A, GENCODE v32/Ensembl 98), and demultiplexing (using 3’ cell multiplexing pipeline). A Seurat object was built with Cell Ranger outputs using R package Seurat (v4.9.9) and R (v4.2.2). Quality check is taken to remove low-quality cells.
Assembly: GRCh38 v2020-A
Supplementary files format and content: Cell Ranger output files: filtered_contig.fasta, filtered_contig_annotations.csv, metrics_summary.csv

source_name: PBMC

extract_protocol:
Cells were sorted by flow cytometry into a low retention 1.5 ml collection tubes, containing 500 μl of a sorting buffer of PBS:FBS (1:1) supplemented with RNase inhibitor (1:100). After sorting, ice-cold PBS was added, then cells were spun down, and single-cell libraries were prepared as per the manufacturer’s instructions (10x Genomics). Samples were processed using 10x 5'v2 chemistry as per the manufacturer’s recommendations.
10x Chromium Next GEM Single cell Standard 5V2 (Dual index)with feature Barcode technology

treatment_protocol: PBMC

value: PBMC

value: T cell, Monocyte

tag: run id

tag: lane id

tag: assay

value: scTCR


title: PBMC, DBLT02_Hu_M1, scTCR-seq: 528, 453, 507, 520, 517

description: 10x Genomics


title: PBMC, 517, Convalescent, Doublet, scRNA-seq

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The sequencing results were put into the 10X Genomics Cell Ranger (v7.0.0)function multi for alignment (to GRCh38 v2020-A, GENCODE v32/Ensembl 98), and demultiplexing (using 3’ cell multiplexing pipeline). A Seurat object was built with Cell Ranger outputs using R package Seurat (v4.9.9) and R (v4.2.2). Quality check is taken to remove low-quality cells.
Assembly: GRCh38 v2020-A
Supplementary files format and content: Cell Ranger output files: features.tsv, barcodes.tsv, matrix.mtx

tag: category

value: Doublet

tag: visit

value: Convalescent

tag: Sex

value: Male

tag: donorid

tag: cells detected

value: scGEX


title: H3K23ac, C57BL/6 Wildtype, sample 1

value: Wildtype

value: Dorsal telencephalon

value: Neural stem and progenitor cells


title: NCD, biol rep 1

value: Liver


title: IgE+BSA+Luteolin, rep3

city: Gangneung

first: Myungsuk

address: 679, Saimdang-ro, Gangneung-si, Gangwon-do, Republic of Korea

institute: KIST

data_processing:
Raw reads were filtered to remove contaminants, adaptor sequences, and low-quality reads using HTStream (v1.1.0). The processed data were aligned to the reference genome using STAR (version 2.7.0f)15. Custom R scripts were used to assess read and alignment quality, compile counts, and filter transcripts with a median CPM > 1 across samples
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes FPKM values for each Sample

source_name: Primary cells

growth_protocol: Bone marrow cells were isolated from C57BL/6 mice and subsequently cultured in DMEM that was enriched with 30% WEHI-3-conditioned medium and 20% heat-inactivated FBS. To support cell growth and prevent contamination, the medium also contained 100 U/mL of penicillin and streptomycin. The medium was replaced with fresh solution twice a week to maintain optimal growth conditions. The cell cultures were maintained in a controlled environment at a temperature of 37°C and a CO2 concentration of 5%. This setup was sustained for at least four weeks to facilitate the maturation and achieve a high purity of BMMCs.

extract_protocol:
Total RNA was extracted using the HybridR RNA Isolation Kit (GeneAll, Seoul, Korea), following the manufacturer's protocol. RNA quality and quantity were assessed using the 2100 Bioanalyzer System (Agilent Technologies, Amstelveen, Netherlands) and the NanoDrop™ 2000 Spectrophotometer (Thermo Fisher).
RNA libraries were prepared using the TruSeq Stranded mRNA Library Prep Kit (Illumina, CA, USA) and sequenced on a NovaSeq 6000 instrument (Illumina, CA, USA).

treatment_protocol: cells were seeded in the 6-well plate and treated with Luteolin 10 uM for 24 hours.

value: Primary cells

value: BMMCs

value: IgE+BSA+Luteolin


title: PBMC, 517, Acute, Doublet, scRNA-seq

description: 10x Genomics

value: Acute


title: IgE+BSA+Luteolin, rep2


title: PBMC, 520, Convalescent, Doublet, scRNA-seq

description: 10x Genomics


title: RNA.Pol.II, Tg(Kat6b), sample 4

value: FVB x BALB/c


title: msEpiCRISPRi_NPC_Upf2KO_50_GFP

city: duarte

first: LU

last: YANG

address: 1500 duarte rd

institute: city of hope

description:
PCR amplified CRISPR sgRNA
SE75 by NextSeq550

data_processing:
Illumina RTA was used to create .bcl files, and bcl2fastq v2.20.0.422 software was used for base calling (for samples split between flowcells and later merged per run)
Raw reads were mapped against sgRNA library and raw counts table of sgRNA was generated using MAGeCK v0.5.9.3
Supplementary files format and content: raw counts table in txt format of every sample in CRISPR sgRNA project

source_name: Neuronal progenitor cells (NPCs)

growth_protocol: dCas9-Krab-expressing mouse NPCs were harvested from Upf2(f/f) mice.

extract_protocol:
The integrated sgRNA were amplified from each sample using DCF01 5’-CTTGTGGAAAGGACGAAACACCG-3’ and DCR03 5’- CCTAGGAACAGCGGTTTAAAAAAGC-3’.
https://media.addgene.org/cms/filer_public/61/16/611619f4-0926-4a07-b5c7-e286a8ecf7f5/broadgpp-sequencing-protocol.pdf

treatment_protocol: The epigenetic CRISPRi library (3630 sgRNAs) were delivered into the NPCs via lentiviral infection. The Upf2 gene knockout was induced by a Cre construct, and a GFP construct is used as a control condition.

value: Neuronal progenitor cells (NPCs)

tag: sequencing type

value: CRISPR sequencing


title: msEpiCRISPRi_NPC_Upf2KO_50_sgRNA


title: RNA.Pol.II, Tg(Kat6b), sample 2


title: msEpiCRISPRi_NPC_Upf2KO_50_Cre


title: PBMC, DBLT02_Hu_M2, scTCR-seq: 528, 453, 507, 520, 517

description: 10x Genomics

value: PBMC

value: T cell, Monocyte


title: RNA.Pol.II, Tg(Kat6b), sample 1


title: IgE+BSA, rep2

value: IgE+BSA


title: msEpiCRISPRi_NPC_Upf2KO_05_sgRNA


title: PBMC, 453, Convalescent, Singlet, scRNA-seq

description: 10x Genomics

value: Singlet

value: Convalescent


title: PBMC, 507, Acute, Singlet, scRNA-seq

description: 10x Genomics

value: Male

value: scGEX


title: IgE+BSA, rep3


title: RNA.Pol.II, FVB x BALB/c Wildtype, sample 4

value: Wildtype

value: Dorsal telencephalon


title: msEpiCRISPRi_NPC_Upf2KO_05_GFP


title: IgE+BSA, rep1


title: PBMC, 453, Acute, Singlet, scRNA-seq

description: 10x Genomics


title: RNA.Pol.II, FVB x BALB/c Wildtype, sample 3

value: Neural stem and progenitor cells


title: msEpiCRISPRi_NPC_Upf2KO_05_Cre


title: RNA.Pol.II, FVB x BALB/c Wildtype, sample 2


title: RNA.Pol.II, Tg(Kat6b), sample 3


title: RNA.Pol.II, FVB x BALB/c Wildtype, sample 1


title: PBMC, 520, Acute, Singlet, scRNA-seq

description: 10x Genomics


title: PBMC, 520, Acute, Doublet, scRNA-seq

description: 10x Genomics

value: Doublet


title: Control, rep2

value: Primary cells

value: BMMCs

value: Control


title: Control, rep1


title: ko2

city: Shanghai

first: Jialei

last: Sun

address: 180 Fenglin Road

country: China

institute: Zhongshan Hospital, Fudan University

data_processing:
Paired-end sequence files (fastq) were mapped to the reference genome using Hisat2 (Hierarchical Indexing for Spliced Alignment of Transcripts, version 2.0.5).
The output SAM (sequencing alignment/map) files were converted to BAM (binary alignment/map) files and sorted using SAMtools (version 1.3.1).
Gene abundance was expressed as fragments per kilobase of exon per million reads mapped (FPKM).
Stringtie software was used to count the fragment within each gene, and TMM algorithm was used for normalization.
Differential expression analysis for mRNA was performed using R package edgeR. Differentially expressed RNAs with |log2(FC)| value >1 and q value <0.05, considered as significantly modulated, were retained for further analysis.
Assembly: mm10
Supplementary files format and content: Tab-delimited txt file include raw counts for each sample.
Supplementary files format and content: Tab-delimited txt file include FPKM values for each sample.

source_name: HCC tissue

growth_protocol: All animal care and experimental protocols were carried out in accordance with guidelines approved by the Institutional Animal Care and Use Committee of Zhongshan Hospital, Fudan University.

extract_protocol:
RNA was obtained by RNeasy mini kit (Qiagen, Germany). 1.3μg of total RNA was used for construction of sequencing libararies.
RNA libraries for RNA-seq were prepared using VAHTSTM mRNA-seq V2 Library Prep Kit following manufacturer's protocols.

treatment_protocol: no

value: HCC tissue


title: Immunized with  PBS_3

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

data_processing:
Sequencing was carried out on a DNBseq (2 × 150 bp paired end reads).
RNA-Seq analysis Sequencing reads were mapped against the Mus musculus reference genome mm10.
Reads were mapped and aligned with Hisat2 and counted using the R package Rsubread, featureCounts
Assembly: GRCm39
Supplementary files format and content: Differentially expressed genes

source_name: macrophage

growth_protocol: F4/80+ liver-associated macrophages were isolated from liver

extract_protocol:
RNA was harvested using RNeasy Mini Kit (Qiagen, USA) The quality and concentrations of RNA were measured by a NanoDropTM 2000 spectrophotometer (Thermo Fisher Scientific).
RNA libraries were prepared using a DNBSEQ Eukaryotic Strand-specific mRNA library kit (BGI Genomics, Shenzhen, China).

treatment_protocol: Mice were randomly divided into 2 groups for OVA mRNA/LNP  vaccinated groups and placebo groups (PBS)

value: macrophage

value: PBS


title: Immunized with  OVA  mRNA/LNP_3

data_processing:
Sequencing was carried out on a DNBseq (2 × 150 bp paired end reads).
RNA-Seq analysis Sequencing reads were mapped against the Mus musculus reference genome mm10.
Reads were mapped and aligned with Hisat2 and counted using the R package Rsubread, featureCounts
Assembly: mm10
Supplementary files format and content: Differentially expressed genes

source_name: tissue

value: tissue

value: OVA mRNA/LNP


title: PBMC, 507, Acute, Doublet, scRNA-seq

description: 10x Genomics

value: PBMC

value: T cell, Monocyte

value: Acute


title: H3K9ac, Tg(Kat6b), sample 3

value: FVB x BALB/c


title: ko1


title: PBMC, 453, Convalescent, Doublet, scRNA-seq

description: 10x Genomics

value: Convalescent

value: Male

value: scGEX


title: IgE+BSA+Luteolin, rep1

value: IgE+BSA+Luteolin


title: Immunized with  PBS_2


title: PBMC, 528, Acute, Singlet, scRNA-seq

description: 10x Genomics

value: Singlet


title: PBMC, 453, Acute, Doublet, scRNA-seq

description: 10x Genomics

value: Doublet


title: Control, rep3

value: Primary cells

value: BMMCs


title: H3K9ac, Tg(Kat6b), sample 1

value: Dorsal telencephalon

value: Neural stem and progenitor cells


title: wt2

value: HCC tissue


title: H3K9ac, Tg(Kat6b), sample 2


title: wt1


title: PBMC, 528, Acute, Doublet, scRNA-seq

description: 10x Genomics


title: H3K9ac, FVB x BALB/c Wildtype, sample 4

value: Wildtype


title: Immunized with  OVA  mRNA/LNP_1

value: macrophage

value: OVA mRNA/LNP


title: PBMC, 517, Acute, Singlet, scRNA-seq

description: 10x Genomics

value: PBMC

value: T cell, Monocyte


title: Lactate

first: Hong

last: Zhang

address: 600 Yishan Road

department: Shanghai Diabetes Institute

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

data_processing:
The reads were then aligned to the mouse mm10 reference genome using the BWA. To visualize read coverage across the genome, bigWig files were generated from the bam files using deepTools.Peaks were called using MACS2, and the resulting narrowPeak files were used for downstream analysis.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag

growth_protocol: Neuro2a cells were seeded in collagen I conjugated 6-well plates (2.5 x 10 ^ 6 cells/well) and cultured cultured at 37 °C with 5% CO2 in DMEM with 10% fetal bovine serum.

extract_protocol:
NaCl or lactate (25 mM) treated neuro2a cells were collected and bounded to Concanavalin A–coated beads. Subsequently, cells were resuspended in antibody buffer and incubated with primary antibodies against H4K12la and secondary antibodies in order. The samples were incubated with pA-Tn5 transposase. After transposon activation and tagmentation, DNA was isolated, amplified, and purified to construct library.
The library for sequencing was constructed and VAHTS DNA Clean Beads (N411, Vazyme Biotech) were used for purification steps. The library was quantified with VAHTS Library Quantification Kit for Illumina (Vazyme Biotech) and sequenced on an Illumina Novaseq 150PE system.

value: Mouse Brain Tumor Cells

tag: chip antibody

value: Lactate 25mM


title: H3K9ac, Tg(Kat6b), sample 4

value: FVB x BALB/c

tag: tissue


title: H3K9ac, FVB x BALB/c Wildtype, sample 3

tag: cell type


title: PBMC, 428, Convalescent, Doublet, scRNA-seq

description: 10x Genomics

value: Convalescent

value: Male

value: scGEX


title: OVA-2_H3K4me3_ChIP

data_processing:
Reads were aligned to Mus musculus reference genome mm10 using bowtie2
The SAM files were converted and sorted to the BAM format using Samtools. PCR duplicates were removed by Picardtools.
The BAM files were converted to bigwig files by deepTools for visualization and heatmaps.
For comparison across samples with a spike-in genome, the bigwig files were normalized to spike-in genome coverage (Saccharomyces cerevisiae R64-1-1).
Genome browser tracks were visualized by Integrative Genomics Viewer (IGV) and pyGenomeTracks.
Assembly: mm10
Supplementary files format and content: Peak enrichment

extract_protocol:
Cells were harvested, washed, and fixed with 37% formaldehyde to achieve the final concentration of 0.1% Cells were then bound with the activated concanavalin A-coated magnetic beads and permeabilized with digitonin. The complex of bead-bound-cells were incubated with antibodies (rabbit anti-H3K4me3 and normal rabbit IgG as negative control). DNA was purified using DNA purification kit.
DNBSEQ ChIP-Seq

value: tissue


title: Immunized with  OVA  mRNA/LNP_2


title: H3K9ac, FVB x BALB/c Wildtype, sample 2

tag: genotype


title: Ctrl

tag: cell line

value: NaCl


title: OVA-1_Input

tag: treatment


title: ADV-shFam172a-3

data_processing:
The cleaned reads were aligned to the index file of the mm10 genome generated by HISAT2 version 2.0.5. Read counts for each gene were calculated by HTSeq-count
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

extract_protocol:
Total RNA was extracted from Neuro2a cells via TRIzol reagent (Thermo Fisher).
RNA libraries were constructed using VAHTS® Universal V6 RNA-seq Library Prep Kit for Illumina Vazyme, according to the manufacturer’s protocol, and paired-end reads were obtained on the NovaSeq 6000 platform.

treatment_protocol: Neuro2a cells were transfected with ADV-shCtrl and ADV-shFam172a virus at 37℃ for 48 h, and then harvested.

value: WT


title: H3K9ac, FVB x BALB/c Wildtype, sample 1

tag: strain

value: Dorsal telencephalon


title: OVA-1_H3K4me3_ChIP


title: Immunized with  PBS_1

value: PBS


title: PBMC, 403, Acute, Singlet, scRNA-seq

description: 10x Genomics

value: Singlet

value: Acute


title: H3K23ac, Tg(Kat6b), sample 4

value: Neural stem and progenitor cells

tag: cut&tag antibody


title: PBS-2_Input

value: macrophage


title: ADV-shFam172a-2


title: PBMC, 392, Convalescent, Singlet, scRNA-seq

description: 10x Genomics

value: PBMC


title: ADV-shFam172a-1


title: OVA-2_Input

value: OVA mRNA/LNP


title: PBMC, 317, Convalescent, Singlet, scRNA-seq

description: 10x Genomics

value: T cell, Monocyte


title: PBS-2_H3K4me3_ChIP


title: H3K23ac, Tg(Kat6b), sample 3


title: PBS-1_Input


title: H3K23ac, Tg(Kat6b), sample 2


title: ADV-shCtrl-2

value: Mouse Brain Tumor Cells

value: ADV-shCtrl


title: PBMC, 317, Acute, Singlet, scRNA-seq

description: 10x Genomics


title: PBS-1_H3K4me3_ChIP


title: PBMC, 405, Acute, Doublet, scRNA-seq

description: 10x Genomics

value: Doublet


title: H3K23ac, Tg(Kat6b), sample 1

value: FVB x BALB/c


title: ADV-shCtrl-1


title: H3K23ac, FVB x BALB/c Wildtype, sample 4

value: Wildtype


title: PBMC, HaHi04_Hu_M2, scTCR-seq: TT0105, TT0106, TT0109, TT0108

extract_protocol:
Cells were sorted by flow cytometry into a low retention 1.5 ml collection tubes, containing 500 μl of a sorting buffer of PBS:FBS (1:1) supplemented with RNase inhibitor (1:100). After sorting, ice-cold PBS was added, then cells were spun down, and single-cell libraries were prepared as per the manufacturer’s instructions (10x Genomics). Samples were processed using 10x 5'v2 chemistry as per the manufacturer’s recommendations.
10x Chromium Next GEM Single cell Standard 5V2 (Dual index) with feature Barcode technology.

tag: run id

value: scTCR


title: PBMC, HaHi05_Hu_M1, scTCR-seq: TT0105, TT0106, TT0109, TT0108

tag: lane id


title: WT_BR3

city: New York

first: Tarmo

last: Äijö

address: 162 5th Avenue

department: Center for Computational Biology

institute: Flatiron Institute

data_processing:
Adapter trimming and quality filtering of the sequencing libraries was done using fastp (0.21.0).
The sequencing libraries were mapped against mm10 and the GRCm38.100 transcriptome using STAR (2.7.5a).
The differential expression analysis was done using DESeq2 based on the read counts per gene produced by STAR.
The TCR repertoire extraction was done using MiXCR (3.0.13) from RNA-seq data using the “-p rna-seq” mode
Genome_build: mm10
Supplementary_files_format_and_content: STAR produced gene read counts and MixCR produced clone count information.

source_name: spleen

growth_protocol: All mice were bred and maintained under specific pathogen-free conditions at University of North Carolina (UNC) Genetic Medicine building, in a facility managed by the Division of Comparative Medicine at UNC Chapel Hill. The experimental procedures were approved by the UNC Institutional Animal Care and Use Committee.

extract_protocol:
Total RNA was isolated using the RNeasy Plus Mini Kit (Qiagen). RNA was quantified using HS RNA kit (Invitrogen) in a Qubit 4 Fluorometer (Invitrogen).
RNA integrity was assessed in a Bionalyzer (Agilent) using RNA 6000 pico kit (Agilent, cat no 5067-1513) or a Tapestation 4150 (Agilent) using Agilent High sensitivity RNA screen tape (Agilent, cat no: 5067-5579) and accompanying reagents such as high sensitivity RNA screen tape ladder (Agilent, cat no: 5067-5579) and high sensitivity RNA screen tape sample buffer (Agilent, cat no:5067-5581). RNA with RIN value higher than 9 was used for library preparation. RNAseq library preparation and sequencing were performed by Beijing Genomics Institute (BGI).

treatment_protocol: Live CD4+CD25- TCRb+, aGalCerCd1d tetramer- cells were sorted wit purity of 98% or higher.  For transplanted Tet2/3 DKO CD4 cells (1st or 2nd transplantation)  live, Cd45.2+, CD45.1- cells were sorted by Flow cytometry (purity>98%).

value: CD4+CD25- TCRb+, aGalCerCd1d tetramer-

value: wild type

value: male


title: PBMC, 403, Convalescent, Doublet, scRNA-seq

description: 10x Genomics

value: Convalescent

value: Male

tag: assay

value: scGEX


title: H3K23ac, FVB x BALB/c Wildtype, sample 3

value: Dorsal telencephalon

value: Neural stem and progenitor cells


title: WT_BR2


title: Inv_SmoM2_SurvivinGOF

city: Bruxelles

first: Yura

last: Song

address: 808, route de Lennik

country: Belgium

institute: Université Libre de Bruxelles

data_processing:
Demultiplexing of samples from the raw datasets are done by CellRanger (v6.1.1) with multi module.
Sequencing reads were aligned and annotated with the mm10-2020-A reference dataset as provided by 10X and CellRanger with default parameters.
Further downstream analyses were carried out individually for each of the three samples.
Quality control and downstream analysis were performed on R (version 4.3.0), using the Seurat R package (v.4.2.0)
For each sample, all the cells passed the following criteria: showed expression of more than 1500 and less than 6000 unique genes and had less than 10% UMI counts belonging to mitochondrial sequences.
Read counts were normalized by NormalizeData function of Seurat, with parameter ‘normalization.method = "LogNormalize" and scale.factor=10000’.
A PCA for each sample was calculated using the scaled expression data of the most variable genes (identified as outliers on a mean/variability plot, implemented in the FindVariableGenes).
UMAP calculation and graph-based clustering were done for each sample using the appropriate functions from Seurat (default parameters) with the respective PCA results as input.
Assembly: mm10-2020-A
Supplementary files format and content: .tsv.gz / cell barcode and features
Supplementary files format and content: .mtx.gz / count matrix

source_name: Skin epidermis

extract_protocol:
We sorted cells for α6High/CD34-/YFP+ from INV-SmoM2 (n=8046) and INV-SmoM2-SurvivinGOF mice. Total10,000 cells were loaded onto each channel of the Chromium Single Cell 3′ microfluidic chips (V2-chemistry, PN-120232, 10X Genomics) and barcoded with a 10X Chromium controller according to the manufacturer’s recommendations (10X Genomics).
RNA from the barcoded cells was subsequently reverse transcribed, followed by amplification, shearing 5′ adaptor and sample index attachment. The libraries were prepared using the Chromium Single Cell 3′ Library Kit (V3-chemistry, PN-120233, 10X Genomics).

value: Skin epidermis

value: Epithelial


title: PBMC, HaHi04_Hu_M2, scTCR-seq: TT0033, TT0069, TT0124

value: PBMC

value: T cell, Monocyte


title: Inv_SmoM2


title: ADV-shCtrl-3

value: Mouse Brain Tumor Cells

value: WT

value: ADV-shCtrl


title: H3K23ac, FVB x BALB/c Wildtype, sample 2

value: FVB x BALB/c

value: Wildtype


title: Krt14-CREER/Rosa-SmoM2 8w TAM. Sample 2

data_processing:
Reads were mapped against the mouse reference genome (Grcm38/mm10) using STAR software to generate read alignments for each sample.
After transcripts assembling, gene level counts were obtained using HTseq-count and normalized to 20 millions of aligned reads.
Genes with individual sample expression levels lower than 10 and replicate average expression levels lower than 20 were filtered out.
The fold changes of average gene expression for the replicates were used to calculate the level of differential gene expression between different cell populations.
Genes with an expression fold change greater or equal to 2 were considered as up-regulated and those with an expression fold change lower or equal to 0.5 were considered down-regulated.
Assembly: mm10/Grcm38.87
Supplementary files format and content: .csv / normalized count

molecule: polyA RNA

extract_protocol:
10.000-200.000 FACS cells were collected directly in the lysis buffer provided by the manufacturer (RNAeasy Microkit, Quiagen) and RNA extraction was then carried out according to the manufacturer’s protocol.
Indexed cDNA libraries were obtained using the Ovation Solo RNA-seq Systems (NuGen) following manufacturer’s recommendations.

value: Krt14-CREER/Rosa- SmoM2


title: PBMC, HaHi04_Hu_M1, scTCR-seq: TT0033, TT0069, TT0124

value: scTCR


title: H3K23ac, FVB x BALB/c Wildtype, sample 1

data_processing:
FASTQ files were output using standard Illumina protocols and software.
Reads were aligned to the Mus musculus (mm39) and Drosophila melanogaster (Dme1R6.32) genomes by Rsubread version 2.12.3.
Read counts were summarized by genomic regions - Promoters (TSS - 1 kb to TSS), Gene body and Transcription end sites (TES to TES + 1 kb) of protein coding genes, and H3K4me1+/H3K27ac+ enhancer enriched regions - using the Rsubread's featureCounts function and Rsubread's inbuilt mm39 NCBI annotation.
Assembly: mm39 and Dme1R6.32
Supplementary files format and content: Tab-delimited text files for Promoter region counts of protein coding genes; columns represent Entrez Gene ID, region length in base counts, and the number of sequence reads mapping to that region.
Supplementary files format and content: Tab-delimited text files for Gene body counts of protein coding genes; columns represent Entrez Gene ID, gene length in base counts, and the number of reads mapping to that gene.
Supplementary files format and content: Tab-delimited text files for Transcription end site region counts of protein coding genes; columns represent Entrez Gene ID, region length in base counts, and the number of reads mapping to that region.
Supplementary files format and content: Tab-delimited text files for H3K4me1+/H3K27ac+ enhancer enriched regions; columns represent region ID, region length in base counts, and the number of reads mapping to that region.
Supplementary files format and content: Supplementary file containing sequence read counts for all samples in matrix form are also provided.
Library strategy: CUT&Tag


title: Inv-CREER/Rosa-SmoM2 8w TAM.Sample 1


title: PBMC, HaHi03_Hu_M2, scTCR-seq: TT0003, TT0027, TT0119


title: Prx1-EV-9

city: Rochester

first: Gabriela

last: Mendez-Pacheco

state: MN

address: 200 1st St SW

department: Quantitative Health Sciences

institute: Mayo Clinic

data_processing:
Sequenced miRNA reads were analyzed using the CAP-miRSeq (v1.4) workflow.
Sequencing adapters were trimmed using Cutadapt (v1.18).
The trimmed reads were aligned to the reference genome and miRNAs were quantified using mirDeep2 (v2.0.0.8).
Assembly: mm10
Supplementary files format and content: Microsoft Excel file including raw counts for each mature miRNA.

source_name: EVs from mouse bone marrow plasma

extract_protocol:
RNA was isolated using the RNeasy Plus Kit (Qiagen) and 1 ng of total RNA used in making the miRNA sequencing libraries.
Total RNA concentration and quality were determined using Qubit fluorometry (ThermoFisher Scientific, Waltham, MA) and the Agilent Fragment Analyzer (Santa Clara, CA). miRNA libraries were then prepared from 1 ng of total RNA according to Qiagen’s protocol for the QIAseq miRNA Library Kit (Germantown, MD). Briefly, specific adaptors were ligated to the 3’ and 5’ ends of the miRNAs. A complementary primer was annealed to the 3’ adaptor sequences and reverse transcription was performed to generate a cDNA library of miRNAs. The cDNA libraries were purified followed by an enrichment step in which a unique index was added to each sample. After a final purification step, the completed libraries were quantified using the Agilent Bioanalyzer and Qubit fluorometry.

value: EVs from mouse bone marrow plasma

tag: strain background


title: WT_BR1

value: CD4+CD25- TCRb+, aGalCerCd1d tetramer-

value: wild type

value: male


title: 1st transplantation BR3

description: 1st transplantation (received cd4 cells from DKO mice)

value: transferred ex CD4, CD45.2+,TCRb+

value: female


title: Inv-CREER/Rosa-SmoM2 8w TAM.Sample 2

value: Skin epidermis


title: Prx1-EV-8


title: PBMC, HaHi03_Hu_M1, scTCR-seq: TT0003, TT0027, TT0119


title: 1st transplantation BR1


title: Prx1-EV-7


title: PBMC, TT0109, Diagnosis, Other doublets, scRNA-seq

description: 10x Genomics

tag: category

value: Other doublets

tag: visit

value: Diagnosis

value: Female

tag: donor id

value: scGEX


title: Krt14-CREER/Rosa-SmoM2/Survivin LOF 6w TAM.Sample 2

value: Epithelial

value: Krt14-CREER/Rosa-SmoM2/Survivin LOF


title: Tet2/3 DKO peripheral CD4 cells BR3

description: dko CD4

tag: Sex


title: Prx1-EV-6


title: PBMC, TT0108, End-treatment, Doublet, scRNA-seq

description: 10x Genomics

value: PBMC

value: T cell, Monocyte

value: Doublet

value: End-treatment

value: Male

tag: cells detected


title: Krt14-CREER/Rosa-SmoM2/Survivin LOF 6w TAM.Sample 1


title: Prx1-EV-5

value: EVs from mouse bone marrow plasma


title: PBMC, TT0108, Diagnosis, Doublet, scRNA-seq

description: 10x Genomics


title: Krt14-CREER/Rosa-SmoM2 6w TAM. Sample1

value: Krt14-CREER/Rosa- SmoM2


title: Tet2/3 DKO peripheral CD4 cells BR1

description: dko CD4

value: CD4+CD25- TCRb+, aGalCerCd1d tetramer-

value: male


title: Krt14-CREER/Rosa-SmoM2 6w TAM. Sample2


title: PBMC, TT0109, End-treatment, Doublet, scRNA-seq

description: 10x Genomics


title: WT_BR5

value: wild type


title: Prx1-EV-4


title: Inv-CREER/Rosa-SmoM2/Krt14rtTA/Survivin-GOF 8w TAM. Sample 2

value: Skin epidermis


title: Prx1-EV-3


title: PBMC, TT0109, Diagnosis, Singlet, scRNA-seq

description: 10x Genomics

value: Singlet


title: PBMC, TT0105, End-treatment, Singlet, scRNA-seq

description: 10x Genomics


title: 1st transplantation BR2

value: transferred ex CD4, CD45.2+,TCRb+


title: WT_BR4


title: Krt14-CREER/Rosa-SmoM2 8w TAM. Sample1


title: Inv-CREER/Rosa-SmoM2/Krt14rtTA/Survivin-GOF 8w TAM. Sample 1


title: 1st transplantation BR4


title: Prx1-EV-2


title: Prx1-EV-10


title: 2nd transplantation BR7

description: 2d transplantation

value: female


title: PDE 2 ChIP

city: Shenzhen

first: Yongheng

last: Xie

address: 1017 Dongmen North Road, Luohu District, Shenzhen

institute: Shenzhen People’s Hospital

data_processing:
Raw data (raw reads) of fastq format were firstly processed using fastp (version 0.19.11) software. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using BWA (v 0.7.12) and clean reads were aligned to the reference genome using BWA mem (v 0.7.12).
We used the MACS2 (version 2.1.0) peak calling software to identify regions of IP enrichment over background. A q-value threshold of 0.05 was used for all data sets.
The position of peak summit around transcript start sites of genes can predict the interaction sites between protein and gene. ChIPseeker was used to retrieve the nearest genes around the peak and annotate genomic region of the peak.
Assembly: mm39
Supplementary files format and content: BigWig

source_name: Bone marrow

growth_protocol: αMEM with 15% FBS, 1% glutamine, 0.1% β-mercaptoethanol, 100 IU/ml penicillin and 100 µg/ml streptomycin. Cells were cultured  in a incubator at 37℃ with 5% CO2.

extract_protocol:
Cells were treated with 1% formaldehyde for 10 minutes at room temperature to crosslink proteins to DNA. Sonicate up to 500 μl of lysate with several pulses to disrupt the nuclear membrane.
The library was constructed by Novogene Corporation (Beijing, China). Subsequently, pair-end sequencing of sample was performed on Illumina platform (Illumina, CA, USA). Library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Pregnant mice were serially numbered: odd-numbered mice were assigned to the PDE group and received repeated dexamethasone exposure (1.2 mg/Kg/day, #HY-14648, MedChemExpress, New Jersey, USA), while even-numbered mice were assigned to the control group and received the same volume of vehicle (normal saline) by subcutaneous injection during gestational days 12-14 (GD 12-14). Bone mesenchymal progenitors were isolated from the long bones of PDE and control mice offspring and cultured for 2 weeks.

value: Bone marrow

value: Bone mesenchymal progenitors

value: MSC

tag: chip antibody

value: dexamethasone


title: Prx1-EV-1

tag: tissue


title: Tet2/3 DKO peripheral CD4 cells BR2

description: dko CD4

tag: cell type


title: 2nd transplantation BR6

description: 2d transplantation

tag: genotype


title: PBMC, TT0108, End-treatment, Singlet, scRNA-seq

description: 10x Genomics

value: PBMC

value: T cell, Monocyte

value: scGEX


title: Ocn-EV-6

value: CAGS-Snorkel//Ocn-Cre


title: PDE 1 ChIP

tag: cell line


title: PBMC, TT0108, Diagnosis, Singlet, scRNA-seq

description: 10x Genomics

value: Diagnosis

value: Male


title: PDE input

tag: treatment


title: PBMC, TT0109, End-treatment, Singlet, scRNA-seq

description: 10x Genomics

value: End-treatment

value: Female


title: sham 2 ChIP

value: normal saline


title: Ocn-EV-5

value: EVs from mouse bone marrow plasma


title: 2nd transplantation BR4

description: 2nd transplantation (received cells that have already been expanded to another recipient)

value: male


title: PBMC, TT0109, Diagnosis, Doublet, scRNA-seq

description: 10x Genomics

value: Doublet


title: Ocn-EV-4


title: 2nd transplantation BR3

value: transferred ex CD4, CD45.2+,TCRb+


title: Ocn-EV-3


title: PBMC, TT0106, Diagnosis, Singlet, scRNA-seq

description: 10x Genomics

value: Singlet


title: sham input

value: Bone marrow

value: Bone mesenchymal progenitors


title: PBMC, TT0105, End-treatment, Doublet, scRNA-seq

description: 10x Genomics


title: 2nd transplantation BR2


title: sham 1 ChIP

value: MSC


title: Ocn-EV-1


title: Sample_108969

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

data_processing:
For RNA-seq, STAR was used for alignment, and HTSeq was used for gene quantification
For ATAC-seq, BWA was used for alignment, and Macs2 for peak calling.
Assembly: GRCh37
Supplementary files format and content: read counts

source_name: mouse macrophage

growth_protocol: All mice were maintained at the University of Michigan Biomedical Sciences and Research Building in the Unit for Laboratory and Animal Medicine (ULAM). Mouse experiments were conducted with approval from our Institutional Animal Care and Use Committee (IACUC) (Protocol no. PRO00009811). C57BL/6 mice (RRID: IMSR_JAX:000664) were obtained at 6-7 weeks age from Jackson Laboratory (Bar Harbor, ME) maintained in breeding pairs in the ULAM facilities.

extract_protocol:
For ATAC-seq, wound macrophages were harvested from mice at day 5 as described above using MACS and nuclei were isolated as described previously (45). For RNA-seq, day 5 wounds were harvested from Setdb2flox/floxLyz2Cre, Stat3flox/floxLyz2Cre, and cre-negative littermate control mice, digested, and underwent negative selection for CD3, CD19, and Ly6G lineage markers. Remaining cells were surface stained and sorted by FACs into CD11b+Ly6CHi and CD11b+Ly6CLo populations. RNA isolation was performed using a RNeasy Kit (Qiagen) with DNase digestion.
Library construction and analysis of reads was performed as described previously (41). Briefly, reads were trimmed using Trimmomatic and mapped using HiSAT2 (47, 48). Read counts were performed using the feature-counts option from the subRead package followed by the elimination of low reads, normalization and differential gene expression using edgeR (49, 50). Differential expression was performed on mapped reads using the taqwise dispersion algorithm in edgeR.

value: mouse macrophage

value: macrophage

value: LyzCrePos

value: Lo


title: PBMC, TT0124, End-treatment, Doublet, scRNA-seq

description: 10x Genomics

value: PBMC

value: T cell, Monocyte

value: scGEX


title: PBMC, TT0106, Diagnosis, Doublet, scRNA-seq

description: 10x Genomics

value: Diagnosis

value: Female


title: Sample_108968

value: Hi


title: Ocn-EV-2

value: EVs from mouse bone marrow plasma

value: CAGS-Snorkel//Ocn-Cre


title: Tet2/3 DKO peripheral CD4 cells BR5

description: dko young CD4

value: CD4+CD25- TCRb+, aGalCerCd1d tetramer-

value: male


title: PBMC, TT0069, End-treatment, Doublet, scRNA-seq

description: 10x Genomics

value: Doublet

value: End-treatment

value: Male


title: 2nd transplantation BR1

value: transferred ex CD4, CD45.2+,TCRb+


title: 2nd transplantation BR5

value: female


title: Sample_108967

value: mouse macrophage

value: macrophage

value: LyzCrePos


title: Tet2/3 DKO peripheral CD4 cells BR4

description: dko young CD4


title: PBMC, TT0069, Diagnosis, Singlet, scRNA-seq

description: 10x Genomics

value: PBMC

value: T cell, Monocyte

value: Singlet


title: Sample_108966


title: smRNA hda6ldl12 rep3

city: Taipei

first: Pao-Yang

last: Chen

address: 128 Sec. 2, Academia Rd, Nankang,

department: Institute of Plant and Microbial Biology

country: Taiwan

institute: Academia Sinica

data_processing:
smRNA-seq reads were trimmed (removing sequencing adapter and low-quality reads) by using Cutadapt.
The clean reads were aligned to the Arabidopsis genome using Bowtie2, and sequences that did not perfectly align and those mapped to rRNAs, miRNAs, snRNAs, and tRNAs were discarded. The 24nt-siRNA sequences were extracted and normalized by calculating the 24nt-siRNA reads per million based on the total abundance of genome-matched 24nt-siRNA reads
Genome browser tracks were generated using deeptools (v 3.4.3) bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM)
Assembly: TAIR10
Supplementary files format and content: Processed data files are sequencing depth tracks (bigWig) obtained using bamCoverage (deepTools)

organism: Arabidopsis thaliana

source_name: seedling

growth_protocol: Arabidopsis was grown in growth chambers under 12/12 h light/dark conditions at 22°C and harvested after 14 days.

extract_protocol:
For small RNA-seq, cells were lysed in Trizol and RNA extracted using standard methods.
Small RNA libraries were made using the Illumina TruSeq Small RNA Library kit according to the manufacturer’s protocol.

tag: developmental stage

value: 14 days seedling

tag: ecotype

value: seedling


title: PBMC, TT0033, End-treatment, Singlet, scRNA-seq

description: 10x Genomics

data_processing:
The sequencing results were put into the 10X Genomics Cell Ranger (v7.0.0)function multi for alignment (to GRCh38 v2020-A, GENCODE v32/Ensembl 98), and demultiplexing (using 3’ cell multiplexing pipeline). A Seurat object was built with Cell Ranger outputs using R package Seurat (v4.9.9) and R (v4.2.2). Quality check is taken to remove low-quality cells.
Assembly: GRCh38 v2020-A
Supplementary files format and content: Cell Ranger output files: features.tsv, barcodes.tsv, matrix.mtx

value: Female

tag: run id

value: scGEX


title: PBMC, TT0033, Diagnosis, Singlet, scRNA-seq

description: 10x Genomics

value: Diagnosis

tag: lane id


title: smRNA hda6ldl12 rep1


title: Sample_108964

value: Hi


title: PBMC, TT0124, End-treatment, Singlet, scRNA-seq

description: 10x Genomics

tag: assay


title: NPC_Euploid_Sample9

type: RNA

city: Bethesda

first: Laura

middle: L

last: Baxter

state: MD

address: 35A Convent Drive

department: NHGRI

institute: NIH

description: Gene expression data from neural progenitor cells

hyb_protocol: Arrays were washed and stained using the GeneTitan Hybridization, Wash, and Stain kit with streptavidin-phycoerythrin protocol according to the manufacturer's instructions.

scan_protocol: Arrays were scanned using the GeneTitan automated microarray system.

data_processing: Data were processed with Partek Genomics Suite using robust multiarray average (RMA) background correction with quantile normalization and log2 transformation.

label: biotin

source_name: Cultured human neural progenitor cells

label_protocol: Samples were labeled with Biotin Allonamide Triphosphate using Human Clariom S HT arrays (Cat. No. 902970, Thermo Fisher Scientific) and the GeneTitan automated microarray system.

growth_protocol: Fibroblasts were maintained in DMEM high glucose with GlutaMAX, pyruvate, 10% FBS, and 100 U penicillin/ 100 µg streptomycin / ml. iPSCs were maintained on Vitronectin-XF-coated plates in StemFlex medium (A3349401, ThermoFisher Scientific). Neural progenitor cells were maintained on Matrigel-coated plates in STEMdiff Neural Progenitor Medium (05833, StemCell Technologies).

extract_protocol: RNA samples were extracted from 5 x 10^5 cells per line for each fibroblast, iPSC, and NPC line using NucleoSpin RNA XS Plus kits (Macherey-Nagel). RNA concentrations and quality were measured using a Nanodrop (ThermoFisher Scientific). RNA was converted to cDNA with GeneChip HT WT PLUS Reagent Kits (ThermoFisher Scientific).

value: Euploid

value: male


title: Sample_108963

value: LyzCreNeg

value: Lo


title: PBMC, TT0124, Diagnosis, Singlet, scRNA-seq

description: 10x Genomics


title: Sample_108962


title: smRNA hda6ldl12 rep2


title: smRNA ldl12 rep1


title: Sample_108961


title: PBMC, TT0069, End-treatment, Singlet, scRNA-seq

description: 10x Genomics

value: End-treatment

value: Male


title: NPC_Euploid_Sample6


title: PBMC, TT0069, Diagnosis, Doublet, scRNA-seq

description: 10x Genomics

value: Doublet


title: smRNA hda6 rep3


title: Sample_108960

value: mouse macrophage

value: macrophage


title: smRNA hda6 rep2


title: PBMC, TT0033, End-treatment, Doublet, scRNA-seq

description: 10x Genomics

value: PBMC

value: T cell, Monocyte


title: Sample_108959


title: Sample_108965

value: LyzCrePos


title: PBMC, TT0033, Diagnosis, Doublet, scRNA-seq

description: 10x Genomics


title: Sample_108958


title: smRNA ldl12 rep2

value: 14 days seedling

value: seedling


title: smRNA ldl12 rep3


title: NPC_T21_Sample7


title: NPC_Euploid_Sample7


title: PBMC, TT0027, Diagnosis, Other doublets, scRNA-seq

description: 10x Genomics

value: Other doublets

value: scGEX


title: smRNA WT rep3

value: WT


title: 1306-AD-1_CGTACTAG_S2


title: NPC_Euploid_Sample8

value: Euploid

value: female


title: NPC_Euploid_Sample4


title: NPC_Euploid_Sample2


title: NPC_Euploid_Sample3

value: male


title: PBMC, TT0119, End-treatment, Doublet, scRNA-seq

description: 10x Genomics


title: smRNA WT rep2


title: 1306-AD-1_TAAGGCGA_S1


title: NPC_T21_Sample5


title: PBMC, TT0119, Diagnosis, Doublet, scRNA-seq

description: 10x Genomics

value: Diagnosis


title: smRNA WT rep1


title: PBMC, TT0027, End-treatment, Doublet, scRNA-seq

description: 10x Genomics

value: End-treatment


title: NPC_Euploid_Sample5


title: 1306-AD-1_TAGGCATG_S6


title: NPC_T21_Sample6


title: PBMC, TT0027, Diagnosis, Singlet, scRNA-seq

description: 10x Genomics

value: Singlet

value: Male


title: NPC_T21_Sample3


title: 1306-AD-1_GGACTCCT_S5

value: mouse macrophage


title: WGBS hda6/ldl1/2 rep1

data_processing:
BS-seq reads were trimmed (removing sequencing adapter and low-quality reads) by using Trimmomatic.
High-quality clean BS-seq reads were aligned to the Arabidopsis reference genome (TAIR10) using BS-Seeker2.
Assembly: TAIR10
Supplementary files format and content: Processed data (CGmap) is in text format. column 1=chromosome id; column 2=C/G (G stands for C on the opposite strand); column 3= chromosomal location; column 4=sequence context (CG/CHG/CHH); column 5=sequence context (CA/CT/CC/CG); column 6=methylation fraction #C/(#C+#T); column 7=number of C (#C); column 8 #C+#T.

extract_protocol:
Total DNA were extracted by grinding in liquid nitrogen followed by purification with Dneasy Plant Mini Kit (Qiagen)
Genomic DNA was extracted from 14-d-old seedlings of Col-0, hda6, ldl1/2, and hda6/ldl1/2 using a DNeasy Plant Mini Kit (Qiagen). After quality assessment, 200 ng genomic DNA was sheared using Covaris and used to make libraries  using Nugen Ultralow Methyl-seq kit (Ovation) according to the manufacturer’s protocol.


title: 1306-AD-1_CTCTCTAC_S7

value: macrophage


title: WGBS ldl1/2 rep2


title: PBMC, TT0003, End-treatment, Singlet, scRNA-seq

description: 10x Genomics

value: PBMC

value: Female


title: 1306-AD-1_CAGAGAGG_S8


title: smRNA hda6 rep1


title: NPC_T21_Sample2


title: 1306-AD-1_AGGCAGAA_S3


title: WGBS ldl1/2 rep1


title: NPC_T21_Sample4


title: PBMC, TT0119, End-treatment, Singlet, scRNA-seq

description: 10x Genomics

value: T cell, Monocyte


title: 7589-KM-9_TGGATCGA-TATCGCAC_S21

value: CreNeg

value: Lo


title: iPSC_Euploid_Sample9

description: Gene expression data from iPSCs

source_name: Cultured human induced pluripotent stem cells


title: iPSC_Euploid_Sample10

description: Gene expression data from iPSCs


title: PBMC, TT0119, Diagnosis, Singlet, scRNA-seq

description: 10x Genomics


title: NPC_T21_Sample1


title: WGBS hda6 rep1

value: 14 days seedling

value: seedling


title: 7589-KM-8_CAAGCTAG-CGCTATGT_S20

value: CrePos

value: Hi


title: PBMC, TT0027, End-treatment, Singlet, scRNA-seq

description: 10x Genomics

value: scGEX


title: WGBS WT rep2

value: WT


title: 1306-AD-1_TCCTGAGC_S4


title: 7589-KM-7_GCTTGTCA-GTATGTTC_S19


title: PBMC, TT0003, Diagnosis, Singlet, scRNA-seq

description: 10x Genomics

value: Diagnosis


title: WGBS hda6/ldl1/2 rep2


title: iPSC_Euploid_Sample7

description: Gene expression data from iPSCs

value: Euploid

value: male


title: iPSC_Euploid_Sample8

description: Gene expression data from iPSCs


title: PBMC, TT0027, Diagnosis, Doublet, scRNA-seq

description: 10x Genomics

value: Doublet

value: Male


title: WGBS hda6 rep2


title: NPC_Euploid_Sample1

value: female


title: WGBS WT rep1


title: ATAC hda6/ldl1/2 rep2

data_processing:
ATAC-seq reads were trimmed (removing sequencing adapter and low-quality reads) by using Trimmomatic.
Raw reads were aligned to the Arabidopsis genome TAIR10 using Bowtie2 with default parameters.
Reads mapped with mitochondria and plastid and fragment length greater than 150 bp were removed
Genome browser tracks were generated using deeptools (v 3.4.3) bamCoverage (deepTools, options --binSize 10 --normalizeUsing RPKM)
Supplementary files format and content: Processed data files are sequencing depth tracks (bigWig) obtained using bamCoverage (deepTools)

extract_protocol:
2 g of 14-day-old Arabidopsis seedlings were collected immediately before the nuclear extraction procedure. Seedlings were sequentially chopped using a sharp razor blade with 5 ml cold NEB buffer on ice. The slurry was filtered through 4 layers of Miracloth and a 20-μm CellTrics twice to remove large debris, followed by centrifugation at 800g for 10 min at 4°C. The supernatant was removed without disturbing the green pellet and gently resuspended by 200 μl ORB (with 1% Triton X-100). The nuclei suspension was filtered through a 10-μm CellTrics twice to remove aggregate nuclei and debris and transferred to the top of the Sucrose-Percoll gradient (400 μl 60% Percoll in ORB and 200 μl SCB buffer), followed by centrifuging at 1,000g for 15 min at 4°C for nuclei enrichment. The nuclei located at the Sucrose-Percoll interface were collected. Some nuclei were taken and stained with DAPI (0.3 μg/ml) to examine the integrity under microscopy using excitation wavelength at 353 nm and emission wavelength at 465 nm for DAPI. The nuclei number was estimated by a hemocytometer.
The Tn5 transposition was carried out by Nextera DNA Library Preparation Kit (Illumina) according to the manufacturer’s manual. The 5,000 nuclei were suspended in the transposition reaction mix and incubated at 37°C for 30 min in an Eppendorf Thermo Mixer Comfort (Eppendorf) with agitation at 1,000 rpm for 2 min and resting for 2 min. The transposed DNA fragments were purified immediately after with a MinElute PCR Purification Kit (Qiagen). The purified transposed DNA fragments were amplified by Nextera Index Kit (Illumina) and NEBNext High-Fidelity 2x PCR Master Mix (New England Biolabs) for the first PCR amplification with 5 cycles. The KAPA Library Quantification Kit is used for the quantitative PCR to estimate the secondary PCR amplification. The libraries were purified with AMPure XP beads (Beckman Coulter)


title: PBMC, TT0003, Diagnosis, Doublet, scRNA-seq

description: 10x Genomics

value: PBMC


title: 7589-KM-6_ATCCACTG-ACGCACCT_S18

value: mouse macrophage

value: macrophage


title: 7589-KM-5_AAGTCCAA-TACTCATA_S17


title: ATAC hda6/ldl1/2 rep1


title: 7589-KM-4_GGACTTGG-CGTCTGCG_S16


title: ATAC ldl1/2 rep1


title: 7589-KM-3_TTATAACC-TCGATATC_S15


title: iPSC_Euploid_Sample6

description: Gene expression data from iPSCs


title: PBMC, TT0003, End-treatment, Doublet, scRNA-seq

description: 10x Genomics

value: T cell, Monocyte

value: End-treatment

value: Female


title: ATAC hda6 rep2

value: 14 days seedling

value: seedling


title: iPSC_Euploid_Sample4

description: Gene expression data from iPSCs


title: MCF7, non-ATF6α overexpression, rep3

city: Incheon

first: So-Hyun

last: Bae

state: Yeonsu-gu

address: 119, Academy-ro

department: Division of Life Sciences, College of Life Sciences and Bioengineering

institute: Incheon National University

data_processing:
Quality assessment of raw sequences was performed by FastQC (v.0.11.9)
Low-quality and adapter sequences were eliminated with trimgalore (v.0.6.5-1) before the analysis.
The remaining sequences were aligned to the human GRCh38 reference genome using the 2-pass method of STAR (v2.7.3a)
Sequence reads were assigned to genes and the count table was generated by featureCounts (v.2.0.0)
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RNA-seq counts for each Sample

source_name: Breast; Mammary gland

growth_protocol: Human breast cancer MCF-7 cells were obtained from the Korean Cell Line Bank (Seoul, Korea) and cultured in DMEM supplemented with 10% FBS (Gibco) and 1% Anti-Anti (antibiotic-antimycotic) (Gibco). Cells were grown at 37°C in a humidified atmosphere of 5% CO2 and frequently tested for mycoplasma infection using a mycoplasma detection kit (iNtRON, Korea).

extract_protocol:
RNA quantification was achieved with the ND-2000 Spectrophotometer (Thermo Inc., DE, USA).
RNA libraries for RNA-seq were prepared using NEBNext Ultra II Directional RNA-Seq Kit (NEB Inc., UK)

treatment_protocol: To examine the genes involved in significant expression changes through ATF6a ectopic expression in MCF-7 cells, the p3´Flag-ATF6 plasmid (Addgene) was transfected into MCF-7 cells, which were plated in 100 mm culture dishes (SPL Life Sciences, Korea) at 1 ´ 106 cells/dish and grown for 24 hrs, using Lipofectamine 2000 (Invitrogen). For the whole transcriptome sequencing from MCF-7cells overexpressing ATF6a (MCF-7/ATF6a) at three distinct time points (baseline, 6 hrs, and 9 hrs), MCF-7/ATF6a cells were harvested at 0, 6, and 9 hours after ATF6a overexpression.

value: Breast; Mammary gland

value: epithelial cell

value: non-ATF6alpha overexpression


title: iPSC_T21_Sample8

description: Gene expression data from iPSCs


title: ATAC hda6 rep1


title: ATAC ldl1/2 rep2


title: iPSC_Euploid_Sample5

description: Gene expression data from iPSCs


title: MCF7, ATF6α overexpression for 6 hours, rep3

value: WT

value: ATF6alpha overexpression for 6 hours


title: iPSC_T21_Sample7

description: Gene expression data from iPSCs

value: male


title: MCF7, ATF6α overexpression for 9 hours, rep3

value: ATF6alpha overexpression for 9 hours


title: 7589-KM-16_CTCTCGTC-AGGTTATA_S28

value: CreNeg

value: Hi


title: 7589-KM-2_CCGCGGTT-CTAGCGCT_S14

value: CrePos

value: Lo


title: 7589-KM-1_CCAAGTCT-TCATCCTT_S13

value: mouse macrophage

value: macrophage


title: Rich 10

city: Nashville

first: Jessica

last: Blackburn

address: 1611 21st Ave MCN

institute: VUMC

description: 10x Genomics

data_processing:
Cellranger version-6.1.2
Assembly: GRCh38-2020-A
Supplementary files format and content: TSV and Matrix; barcodes, features, and matrix

source_name: Distal lung tissue

extract_protocol:
Each lung sample was digested in an enzymatic cocktail (Miltenyi Multi Tissue Dissociation Kit 1) using a gentleMACS Octo Dissociator (Miltenyi, Inc.). Tissue homogenates were serial filtered through sterile gauze, then 100 μm, and  40-μm sterile cell strainers. Single-cell suspensions then were treated with ACK buffer to lyse blood cells and then underwent cell sorting using EPCAM magnetic bead based selection. The EPCAM enriched fraction was used as the input for the single cell libraries.
Followed manufacturer insructions for Single Cell 5' PE kit (10x Genomics) Sequenced by VANTAGE at VUMC

value: Distal lung tissue

tag: disease state

value: COPD explant

value: Male

tag: age


title: Rich 7

description: 10x Genomics

value: Female


title: Rich 9

description: 10x Genomics


title: ATAC WT rep2

value: 14 days seedling

value: seedling


title: Rich 3

description: 10x Genomics


title: Rich 1

description: 10x Genomics


title: ATAC WT rep1


title: 7589-KM-15_AATCCGGA-AACTGTAG_S27


title: VU COPD 49

description: 10x Genomics


title: 7589-KM-14_GGCTTAAG-GGTCACGA_S26


title: 7589-KM-12_TCTCTACT-GAACCGCG_S24


title: 7589-KM-13_TTGGACTC-CTGCTTCC_S25


title: BO_BACE_AD4_4

city: Groningen

first: Alejandro

last: Marmolejo

state: Groningen

address: Antonius Deusinglaan 2

country: Netherlands

institute: University of Groningen

data_processing:
GenomeScan delivers the alignment (BAM with index), feature counts, and differential expression analysis using the RNA-Seq pipeline that was developed in-house and described in standard operating procedure SOP 70 (RNA-Seq Analysis). The workflow includes library prep QC (INS 74), raw data quality control (INS 92), UMI processing (INS 78), adapter trimming (INS 88), alignment of short reads (INS 61), feature counting and differential expression (INS 79).
The reads were mapped to the reference sequence using a short read aligner based on Burrows—Wheeler Transform (Tophat v2.0.14) with default settings. The aligner is a splice-aware mapper that detects splice junctions and incorporates them to help align the entire read. The statistics of mapping the reads to the reference genome are shown in Fig. 4 and Table 5. Samples are comparable is there is uniformity of the mapping result for each sample.
BAM files were generated as a result of this step. The alignment files (BAM files sorted on coordinates and indexed with the samtools v2.0.14 package) containing the mapping information are provided in the Mapping folder.
Based on the mapped locations in the alignment file the frequency of how often a read was mapped on a transcript was determined with HTSeq v0.11.0. The hit counts were summarised and reported using the gene_id feature inthe annotation file. Only unique reads that fall within exon regions were counted. The counts were savedto count files, which serve as input for downstream RNA-Seq differential expression analysis
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited count files include count values for each Sample

source_name: Brain Organoid

growth_protocol: Human induced pluripotent stem cells (iPSCs:AD4 harbouring the PSEN1-ΔE9 mutation, isogenic control corrected for the PSEN1-ΔE9 mutation and healthy control stem cell lines were kindly provided by Dr. Šárka Lehtonen and Prof. Jari Koistinaho. iPSCs were maintained on 6-well plates coated with Matrigel (Corning, USA #356234) in Essential 8TM flex medium (E8F; GibcoTM, Thermo Fisher Scientific, Netherlands # A2858501) at 37 °C, 5% CO2. The human brain organoids were generated from the above mentioned iPSCs (AD4 harbouring PSEN1-ΔE9 mutation, isogenic control corrected for PSEN1-ΔE9 mutation and healthy control stem cell lines). At 80-90% confluency, a day before spheroid formation, iPSCs were pre-treated with 1% dimethyl sulfoxide (DMSO; Merck Life Science N.V, Sigma, Netherlands #S002D) to improve spheroid differentiation capacity (30). Cells were first washed with phosphate buffer saline (PBS; Gibco, Thermo Fisher Scientific, Netherlands #70011044) and detached with Accutase® (Stemcell Technologies, USA #07920) for 5 minutes at 37 °C. The dissociated single cells were seeded on AggreWellTM800 plates (Stemcell Technologies, USA #34850) containing 300 microwells per well, pre-treated with AggreWell™ rinsing solution (Stemcell Technologies, USA #07010), according to user’s manual. Cells were spun down at 100 rcf for 3 min and each single microwell contained at least 5,000 cells, cultured in E8F medium (without antibiotic) containing 10 μM ROCK inhibitor Y-27632 (10 mM stock, Stemcell Technologies, USA #72304). After 24 hrs of incubation, spheroids were collected from the microwells using cut 1000 μL pipette tip and transferred into a sterile 10 cm petri dishes in cortical differentiation medium [E8F with 10 μM dorsomorphin (DM; 25 mM stock, Stemcell Technologies, USA #72102), 10 μM SB-431542 (10 mM stock, Stemcell Technologies, USA #72234) and 10 μM XAV-939 (10 mM stock, Stemcell Technologies, USA #72674)]. Medium was changed every day for 6 days. At day 6, medium was changed into neuronal maintenance medium consisting of: Neurobasal (GibcoTM, Thermo Fisher Scientific, Netherlands #21103049) containing 1:50 B-27 supplement without vitamin A (GibcoTM, Thermo Fisher Scientific, Netherlands #12587010) and 1:100 GlutaMax (GibcoTM, Thermo Fisher Scientific, Netherlands #35050061). This medium was supplemented with 20 ng/mL epidermal growth factor (EGF; 100 μg/mL stock, Stemcell Technologies, USA #780061) and 20 ng/mL fibroblast growth factor 2 (FGF2; 100 μg/mL stock, Stemcell Technologies, USA #781341) from day 6 to day 16 with daily medium change. From day 16 to day 24, medium was changed every other day with fresh EGF and FGF2 added every time. At day 24, neuronal maintenance medium was supplemented with 20 ng/mL brain-derived neurotrophic factor (BDNF; 100 μg/mL stock, Stemcell Technologies, USA #78133) and 20 ng/mL Neurotrophin-3 (NT3; 100 μg/mL stock, Stemcell Technologies, USA #78074) until day 43, with media change every other day. cBOs were maintained in neuronal maintenance medium without growth factors from day 43 with media change every other day.

extract_protocol:
Isolation of RNA was performed using the Nucleospin® RNA isolation Kit (Macherey-Nagel). The samples were stored at -80°C until they were sent for transcriptomic analysis.
The quality of the samples, the construction and the sequencing of the RNA-libraries were performed by GenomeScan Bv. Data obtained from the transcriptomic analysis: quality control data, raw count files, FPKMs, RPMs and CPMs.

treatment_protocol: We treated brain organoids for 25 days with BACE inhibitor or co-cultured them with iMGLs. From day 25 of the protocol of differentiation until Day 50, when they were collected for RNAseq experiments.

value: Brain Organoid

value: Isogenic Control

value: BACE


title: iPSC_T21_Sample6

description: Gene expression data from iPSCs

value: female


title: iPSC_T21_Sample5

description: Gene expression data from iPSCs

value: male


title: 7589-KM-11_GACCTGAA-CTCACCAA_S23

value: CreNeg


title: BO_BACE_AD4_3


title: iPSC_Euploid_Sample2

description: Gene expression data from iPSCs

value: Euploid


title: iPSC_Euploid_Sample3

description: Gene expression data from iPSCs


title: BO_BACE_AD4_2


title: iPSC_T21_Sample4

description: Gene expression data from iPSCs


title: 7589-KM-10_AGTTCAGG-TCTGTTGG_S22


title: siPHD2/AIP1_5

middle: A

last: Ferreyra

address: 9000 Rockville Pike - Building 10 room 4D03

department: CCMD

institute: Clinical Center

description: Both KD Gene expression data

hyb_protocol: 2 ug of labeld and fragmented sscDNA per samples was used for hybridized using Clariom S human chips ( applied Biosystems) following manufaturer protocols.

scan_protocol: Arrays were scanned using the Affymetrix GeneChip Scanner 7G.

data_processing: Raw data were normalized using SST-RMA in Transcription Analysis 4.0 Version 2 Console and presented as log2 transformed signal intensity. The probe set results were all within bounds.

label: Biotin

source_name: Human LMVECs

label_protocol: WT Plus reagents ( Applied Biosystem) were used for the amplification and labeing of 150 ng of tRNA following manufaturer protocols

growth_protocol: Human lung vascular endothelial cells were cultured in complete medium comprising of endothelial basal medium-2 (EBM-2) and supplement EGMTM-2 MV (LONZA).

extract_protocol: Total RNA was then extracted using RNeasy miniprep kits (Qiagen). Total RNA was quantified and assessed for quality (RIN 8.6 to 10)

treatment_protocol: Cells were transfected with either scrambled pool non-targeting control siRNA, specific PHD2 (siPHD2, 15 nM), AIP1 (siAIP1, 15 nM), or both (siBoth) siRNA for 48 hours

value: lung vascular endothelial cells

tag: knockdown


title: iPSC_T21_Sample3

description: Gene expression data from iPSCs


title: KO-MZB3

city: shihezi

first: XT

last: Z

address: shihezi

institute: Shihezi 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 research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) 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.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) 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: Mus musculus GRCm38 ensembl_V101
Supplementary files format and content: tab-delimited text files include gene counts for each Sample

extract_protocol:
SMARTer cDNA synthesis starts with 0. 50 ng total RNA/sample. A modified oligo(dT) primer (the SMART CDS Primer) primes the first-strand synthesis reaction. When SMARTScribeTMReverse Transcriptase reaches the 5' end of the mRNA, the enzyme's terminal transferase activity adds a few additional nucleotides to the 3' end of the cDNA. The carefully-designed SMARTer Oligonucleotide base-pairs with the non-template nucleotide stretch, creating an extended template to enable SMARTScribe RT continue replicating to the end of the oligonucleotide. The resulting full-length, single-stranded (ss) cDNA contains the complete 5' end of the mRNA, as well as sequences that are complementary to the SMARTer Oligonucleotide. Amplify sscDNA by LD PCR and get enough dscDNA for library construction.
cDNA was fragmented by dsDNA Fragmentase (NEB, M0348S) by incubate at 37°C for 30min. Library construction begins with fragmented cDNA. Blunt-end DNA fragments are generated using a combination of fill-in reactions and exonuclease activity, and size selection is performed with provided sample purification beads. An A-base is then added to the blunt ends of each strand, indexed Y adapters are ligated to the fragments, and the ligated products are amplified with PCR. And then we performed the paired-end sequencing on an Illumina NovaseqTM6000 at the (LC Sceiences, USA) following the vendor's recommended protocol.

value: spleen

value: Rack1 knockdown

value: Flow sorting


title: siPHD2_5

description: PHD2 KD Gene expression data


title: iPSC_T21_Sample2

description: Gene expression data from iPSCs


title: iPSC_Euploid_Sample1

description: Gene expression data from iPSCs


title: BO+MG_AD4_4

source_name: Brain Organoid/iMGL co-culture

value: Brain Organoid/iMGL co-culture

value: iMGL co-culture


title: siPHD2/AIP1_4

description: Both KD Gene expression data


title: siControl_5

description: Control KD Gene expression data

value: siControl


title: iPSC_T21_Sample1

description: Gene expression data from iPSCs


title: Fibroblast_Euploid_Sample9

description: Gene expression data from fibroblasts

source_name: Cultured primary human fibroblasts


title: siAIP1_5

description: AIP1 KD Gene expression data


title: siPHD2_4

description: PHD2 KD Gene expression data


title: Fibroblast_Euploid_Sample7

description: Gene expression data from fibroblasts


title: siAIP1_4

description: AIP1 KD Gene expression data


title: BO_BACE_AD4_1

value: Male


title: BO+MG_AD4_2


title: KO-MZB2


title: WT-MZB1

value: WT


title: Fibroblast_Euploid_Sample8

description: Gene expression data from fibroblasts


title: Fibroblast_Euploid_Sample5

description: Gene expression data from fibroblasts


title: siControl_4

description: Control KD Gene expression data


title: siPHD2/AIP1_3

description: Both KD Gene expression data


title: siAIP1_3

description: AIP1 KD Gene expression data


title: KO-MZB1


title: BO_AD4_4

value: Untreated


title: KO-FOB3


title: Fibroblast_Euploid_Sample4

description: Gene expression data from fibroblasts


title: Fibroblast_Euploid_Sample6

description: Gene expression data from fibroblasts


title: WT-MZB3


title: BO+MG_AD4_3


title: KO-FOB2


title: BO_AD4_2

value: Brain Organoid


title: Fibroblasts_T21_Sample8

description: Gene expression data from fibroblasts


title: BO+MG_AD4_1

value: Isogenic Control


title: siPHD2_3

description: PHD2 KD Gene expression data


title: siControl_3

description: Control KD Gene expression data


title: KO-FOB1


title: BO_AD4_1


title: WT-MZB2


title: WT-FOB3


title: Fibroblast_Euploid_Sample3

description: Gene expression data from fibroblasts


title: siPHD2/AIP1_2

description: Both KD Gene expression data


title: Fibroblast_Euploid_Sample2

description: Gene expression data from fibroblasts


title: WT-FOB1


title: iPSC_AD4_3

source_name: iPSC

value: iPSC


title: Control-ASO BMDM

first: Xingguang

last: Liu

address: Xiangyin road 800

department: National Key Laboratory of Immunity & Inflammation

institute: Naval medical university

data_processing:
For each sample, RNA-seq clean reads were obtained that mapped to Genome mm10 using HISAT2 (hierarchical indexing for spliced alignment of transcripts) v2.0.477. Sequencing read counts were calculated using Stringtie (v.1.3.0). Then expression levels from different samples were normalized by the Trimmed Mean of M values (TMM) method. The normalized expression levels of different samples were converted to FPKM (Fragments Per Kilobase of transcript per Million mapped fragments).
The edgeR package of R was used to analyze the difference between intergroup gene expression, the P-values were calculated, and the multiple hypothesis test was performed. The P-value threshold was determined by controlling the FDR (False Discovery Rate) with the Benjamini algorithm. The corrected P-value is called the q-value. Differentially expressed genes (DEGs) were defined as transcripts with a fold change in expression level (according to the FPKM value) greater than 2.0 and a q-value less than 0.05.
GO enrichment analysis was performed with the clusterProfiler package of R and the enrichment criteria including a q-value < 0.05. Heatmaps of specific genes were generated using the pheatmap package of R. PCA analysis was visualized using the scatterplot3d package of R.
Assembly: mm10
Supplementary files format and content: raw counts and PFKM value for every sample

source_name: bone marrow

extract_protocol:
Total RNA was isolated using RNeasy mini kit (Qiagen, Germany). Strand-specific libraries were prepared using the TruSeq Stranded Total RNA Sample Preparation kit (Illumina, USA) following the manufacturer’s instructions.
Library construction was perfromed following the steps of mRNA isolation, fragmentation, first strand cDNA synthesis, second strand cDNA synthesis, end repair, adding A at the 3 'end, connecting connectors, enrichment, using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® (Vazyme), AHTS® mRNA Capure Beads (Human/Mouse/Rat) (Vazyme), VAHTS DNA Clean Beads (Vazyme), Qubit™ dsDNA HS Assay Kit (Invitrogen) and Agilent High Sensitivity DNA Kit (Aligent).

value: bone marrow

value: BMDM

value: Mouse primary bone marrow-derived macrophages

value: Control-ASO transfection and LPS treatment


title: Fibroblast_Euploid_Sample1

description: Gene expression data from fibroblasts

value: Euploid

value: female


title: siAIP1_2

description: AIP1 KD Gene expression data

value: lung vascular endothelial cells


title: siPHD2_2

description: PHD2 KD Gene expression data


title: AclyE14-ASO BMDM

value: AclyE14-ASO transfection and LPS treatment


title: iPSC_AD4_2


title: iPSC_AD4_1

value: PSEN1 Mutation DeltaE9


title: BO+BACE_AD4Isogenic_4

value: BACE


title: Fabp7 KO MEST, rep5

city: Spokane

first: Jason

middle: Robert

last: Gerstner

state: WA

address: 412 E Spokane Falls BLVD

department: Translational Medicine and Physiology

institute: Washington State Univ. Spokane

description:
columns for KO_vs_KO_S_2_diffexpr_results.xlxs are: Gene , baseMean , log2FoldChange , lfcSE , stat , pvalue , padj , KO1-M , KO2-M , KO3-M , KO4-M , KO5-M , KO2 , KO3 , KO4 , KO5
KO_vs_KO_S_2_diffexpr_results.xlxs

data_processing:
DNA was sequenced from both ends (paired-end) with a read length of 150 bp.  The raw bcl files were converted to fastq files using the software program bcl2fastq, and adaptors were trimmed from the fastq files during the conversion.
Sequence data (FASTQ files) were processed by trimming low-quality reads using Trimmomatic (version 0.39) (PMID:24695404) and removing rRNA sequences using SortMeRNA (version 4.3.5) (PMID:23071270).
The remaining reads were aligned to the Mus musculus reference genome (mm10, UCSC) using HISAT2 (version 2.2.1) (PMID: 25751142).
Gene expression quantification was analyzed using featureCounts (part of the Subread package, version 2.0.3) (PMID: 24227677).
Differential expression was analyzed using DESeq2 (version 1.36.0) (PMID: 25516281).
Assembly: Mus musculus reference genome (mm10, UCSC)
Supplementary files format and content: Excel .xlsx files with rows are gene symbols. columns: Gene, baseMean, log2FoldChange, lfcSE, stat, pvalue, padj, normalized reads for each smaple

source_name: Hippocampus + cortex segment

growth_protocol: 12h ligh:12h dark. Food and water ad libitum

extract_protocol:
Total RNA was purified using an RNeasy Mini Kit (Qiagen). The integrity of total RNA was assessed using Fragment Analyzer (Advanced Analytical Technologies, Ankeny, IA) with the High Sensitivity RNA Analysis Kit. RNA Quality Numbers (RQNs) from 1 to 10 were assigned to each sample to indicate its integrity or quality. “10” stands for a perfect RNA sample without any degradation, whereas “1” marks a completely degraded sample.
RNA samples with RQNs ranging from 8 to 10 were used for RNA library preparation with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA). Briefly, mRNA was isolated from 1-2.5 µg of total RNA using poly-T oligo attached to magnetic beads and then subjected to fragmentation, followed by cDNA synthesis, dA-tailing, adaptor ligation and PCR enrichment. The sizes of RNA libraries were assessed by Fragment Analyzer with the High Sensitivity NGS Fragment Analysis Kit. The concentrations of RNA libraries were measured using the StepOnePlus Real-Time PCR System (ThermoFisher Scientific, San Jose, CA) with the KAPA Library Quantification Kit (Kapabiosystems, Wilmington, MA).

treatment_protocol: At ZT20, Eight hours after lights-out, wild-type (WT) mice and FABP7 knockout (Fabp7KO) mice were teted for seizure threshold. Mice were tested with a single electric shock delivered via ear clip electrodes once per day. Sham mice received the same handling, but did not receive the shock. We used a constant current electroshock unit (model No. 7801, Ugo Basile, Varese, Italy) in which the initial current level was set at 20 mA and increased by 2 mA with each successive daily trial until a maximal seizure was observed. Other parameters of the stimulus were held constant (60 Hz, 0.4 ms pulse width, 0.2 s duration). Upon maximal electroshock seizure threshold (MEST) defined by bilateral tonic hind limb extension, mice were euthanized and a block of brain tissue was collected from one hemisphere encompassing the hippocampus and cortex from about Bregma 0 to -4 sagittal and about 2.5 horizontal.

value: Hippocampus + cortex segment

tag: strain

tag: age (weeks)

value: male

tag: time

value: Fabp7 KO

value: electroshock


title: BO+BACE_AD4Isogenic_3

tag: Sex

value: Male

value: Brain Organoid


title: Fabp7 KO MEST, rep4

tag: tissue


title: Fibroblasts_T21_Sample6

description: Gene expression data from fibroblasts


title: Phase I 4C × Phase II 4C, 69 day_rep3

city: Geneva

first: Hongrui

last: Wang

state: NY

address: 630 W. North Street

department: School of Integrative Plant Science, Horticulture section

institute: Cornell University

description:
Second_H10_N172_T8_4_TTCCGC
ControlAcclimation_gene_count_geo.csv

data_processing:
FastQC for quality control
BBDuk for removing adaptors and poly-A following the pipeline suggested by the manufacturer (https://www.lexogen.com/quantseq-data-analysis/)
STAR for gene level quantification using ‘-quantMode GeneCounts’
Low count gene filterig based on 'total gene count greater than sample number'
DESeq2 for variance stabilization transformation and gene expression normalization
WGCNA for gene co-expression analysis, noise gene filtering, module eigengene visualization and contrast generation
GSEA for pathway enrichment analysis
Assembly: Vitis vinifera 12X.v2 genome with VCost.v3 annotation
Supplementary files format and content: One matrix table with raw gene counts for every gene and every sample without any filtering

organism: Vitis vinifera

source_name: bud

extract_protocol:
Total RNA was extracted using SpectrumTM Plant Total RNA Kit (Sigma Aldrich, St Louis, MO, USA) following the protocol suggested by the manufacturer
Libraries were constructed with Lexogen QuantSeq 3’mRNA-Seq Prep Kit (Lexogen, Greenland, NH, USA) following standard practices as a service provided by Cornell University Institute of Genomic Diversity (Ithaca, NY, USA). Sequencing of the libraries was accomplished using NextSeq500 (Illumina, Inc., San Diego, CA, USA) with 95 samples per lane at Cornell University Institute of Biotechnology (Ithaca, NY, USA). The read length was 85 bp.

value: bud

tag: cultivar

value: Cabernet Sauvignon

tag: time in_treatment_(day)

tag: phase

value: Phase II

tag: phase i_treatment_(°c)

tag: phase ii_treatment_(°c)

tag: replication


title: iPSC_AD4_4

tag: cell type

value: iPSC

tag: genotype

value: Isogenic Control

tag: treatment

value: Untreated


title: Fibroblasts_T21_Sample7

description: Gene expression data from fibroblasts


title: siAIP1_1

description: AIP1 KD Gene expression data

value: female


title: Fabp7 KO MEST, rep3


title: Fibroblasts_T21_Sample4

description: Gene expression data from fibroblasts


title: BO+BACE_AD4Isogenic_2


title: Fibroblasts_T21_Sample5

description: Gene expression data from fibroblasts


title: siPHD2_1

description: PHD2 KD Gene expression data

value: lung vascular endothelial cells


title: heart, CGRP_05

city: Fuzhou City

first: Shaodan

last: Feng

state: Fujian Province

address: Taijiang District

department: Emergency Department

institute: First Affiliated Hospital of Fujian Medical University

data_processing:
Trimmomatic (version 0.36)
Raw sequencing data was filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed.
Clean data were mapped to the reference genome of Rattus norvegicus using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKMs were calculated.
Assembly: Rattus_norvegicus.Rnor_6.0
Supplementary files format and content: Complete raw counts: All_reads_counts.xls
Supplementary files format and content: Normalized abundance measurements for all samples: All_samples_rpkm.txt
Supplementary files format and content: Diff-expressed data file: RPKM_of_all_diff_genes.xls

organism: Rattus norvegicus

source_name: heart

growth_protocol: Each of sprague-dawley male rats, was maintained at 21±2 °C and a cycle of 12 hours of light followed by 12 hours of darkness. Rats received access to food and water ad libitum.

extract_protocol:
TRIzol reagent (Invitrogen, China) was used to extract total RNA from the myocardial tissue. Then, a wide range of RNA was measured and assayed using the QubitTM RNA Wide Range Assay Kit (Life Technologies, Q10210) and Qubit 3.0.
Total RNAs (2 μg) were utilized for library construction with a KCTM Stranded mRNA Library Prep Kit for Illumina®. High-quality total RNA was used to construct cDNA libraries.

treatment_protocol: Following one week of adaptation, rats were given an intraperitoneal dose of 10 mg/kg LPS to cause SCM. Further, they were injected intraperitoneally with or without a dose of 50 μg/kg CGRP or a body weight-matched 0.3 mL/100 g dose of saline 1 hour before LPS injection.

value: heart


title: siPHD2/AIP1_1

description: Both KD Gene expression data


title: Fabp7 KO MEST, rep1


title: Fibroblasts_T21_Sample2

description: Gene expression data from fibroblasts


title: Phase I 4C × Phase II 4C, 20 day_rep3

description:
Second_H08_N156_T3_4_CCTGCT
ControlAcclimation_gene_count_geo.csv

value: Phase I


title: heart, CGRP_04


title: siControl_2

description: Control KD Gene expression data

value: siControl


title: Fibroblasts_T21_Sample3

description: Gene expression data from fibroblasts


title: Fibroblasts_T21_Sample1

description: Gene expression data from fibroblasts


title: BO+MG_AD4Isogenic_4

value: Brain Organoid/iMGL co-culture

value: PSEN1 Mutation DeltaE9

value: iMGL co-culture


title: heart, CGRP_03


title: Phase I 7C × Phase II 7±5C, 41 day_rep3

description:
Second_H04_N124_T6_7V_GGAGGT
ControlAcclimation_gene_count_geo.csv


title: Phase I 11C × Phase II 7±5C, 55 day_rep3

description:
Second_H06_N140_T7_11V_GGCCAA
ControlAcclimation_gene_count_geo.csv


title: BO+MG_AD4Isogenic_3


title: WT MEST, rep5

description:
columns for WT-M vs WT diffexpr_results.xlsx are: Gene , baseMean , log2FoldChange , lfcSE , stat , pvalue , padj , WT1-M , WT2-M , WT3-M , WT4-M , WT5-M , WT1 , WT2 , WT3 , WT4 , WT5
WT-M vs WT diffexpr_results.xlsx

value: Hippocampus + cortex segment

value: male

value: WT

value: electroshock


title: siControl_1

description: Control KD Gene expression data


title: WT MEST, rep4


title: heart, CGRP_02


title: BO+MG_AD4Isogenic_2

value: Male


title: Phase I 2C × Phase II 7±5C, 41 day_rep3

description:
Second_H02_N109_T6_2V_CAACAG
ControlAcclimation_gene_count_geo.csv

value: bud

value: Cabernet Sauvignon

value: Phase II


title: Phase I 4C × Phase II 4C, 41 day_rep3

description:
Second_H09_N164_T6_4_GGTATA
ControlAcclimation_gene_count_geo.csv


title: Phase I 22C × Phase II 22C, 55 day_rep3

description:
Second_H01_N101_T7_22_TTGGTA
ControlAcclimation_gene_count_geo.csv


title: BO+BACE_AD4Isogenic_1

value: Brain Organoid

value: BACE


title: heart, CGRP_01


title: WT MEST, rep2


title: BO+MG_AD4Isogenic_1


title: heart, LPS_05


title: heart, LPS_04


title: BO_AD4Isogenic_3

value: Untreated


title: Phase I 4C × Phase II 4C, 34 day_rep3

description:
Second_G09_N163_T5_4_GTGTAG
ControlAcclimation_gene_count_geo.csv


title: Fabp7 KO sham, rep5

value: Fabp7 KO

value: sham handling


title: Phase I 4C × Phase II 4C, 20 day_rep2

description:
Second_G08_N155_T3_4_AATCCG
ControlAcclimation_gene_count_geo.csv

value: Phase I


title: BO_AD4Isogenic_2


title: Phase I 4C × Phase II 4C, 69 day_rep2

description:
Second_G10_N171_T8_4_ACTCTT
ControlAcclimation_gene_count_geo.csv


title: Fabp7 KO sham, rep4


title: heart, LPS_02

value: heart


title: Fabp7 KO sham, rep3


title: heart, LPS_01


title: BO_AD4Isogenic_1

value: PSEN1 Mutation DeltaE9


title: Phase I 11C × Phase II 7±5C, 41 day_rep3

description:
Second_G06_N139_T6_11V_TACCTT
ControlAcclimation_gene_count_geo.csv


title: Phase I 7C × Phase II 7±5C, 41 day_rep2

description:
Second_G04_N123_T6_7V_CACTAA
ControlAcclimation_gene_count_geo.csv


title: iPSC_AD4Isogenic_4

value: iPSC


title: WT MEST, rep3

value: Hippocampus + cortex segment


title: Fabp7 KO sham, rep2

value: male


title: iPSC_AD4Isogenic_3


title: Phase I 2C × Phase II 7±5C, 41 day_rep2

description:
Second_G02_N108_T6_2V_AACCGA
ControlAcclimation_gene_count_geo.csv


title: WT sham, rep5

description:
columns for WT-M vs WT diffexpr_results.xlsx are: Gene , baseMean , log2FoldChange , lfcSE , stat , pvalue , padj , WT1-M , WT2-M , WT4-M , WT4-M , WT5-M , WT1 , WT2 , WT3 , WT4 , WT5
WT-M vs WT diffexpr_results.xlsx

value: WT


title: heart, Control_04


title: WT MEST, rep1

value: electroshock


title: BO_AD4Isogenic_4

value: Male


title: heart, LPS_03


title: iPSC_AD4Isogenic_2


title: Phase I 22C × Phase II 22C, 41 day_rep3

description:
Second_G01_N100_T6_22_AACAAG
ControlAcclimation_gene_count_geo.csv

value: bud


title: WT sham, rep4


title: heart, Control_03


title: iPSC_AD4Isogenic_1


title: Phase I 4C × Phase II 4C, 69 day_rep1

description:
Second_F10_N170_T8_4_GTAGAA
ControlAcclimation_gene_count_geo.csv

value: Cabernet Sauvignon


title: heart, Control_02


title: HK-2 cells,  DMEM medium containing 5mg/mL recombinant S100A8/S100A9-3, 48h

city: Guiyang

first: Qing

state: Guizhou

address: Zhongshan Road 83

department: Department of Urology

institute: Guizhou Provincial People's Hospital

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: Ensembl_release100
Supplementary files format and content: tab-delimited text files include RPKM values for all Samples

source_name: Kidney

growth_protocol: In a humidified atmosphere of 37°C and 5% CO2, HK-2 cells were cultured with DMEM medium (HyClone, USA)  containing 10% fetal bovine serum (Gibico, USA).

extract_protocol:
Total RNA was extracted using Trizol reagent kit (Invitrogen, USA) according to the manufacturer’s protocol.
Eukaryotic mRNA was enriched by Oligo(dT) beads. Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reverse transcripted into cDNA with random primers. Second-strand cDNA were synthesized by DNA polymerase I, RNase H, dNTP and buffer. Then the cDNA fragments were purified with QiaQuick PCR extraction kit(Qiagen, Venlo, The Netherlands), end repaired, poly(A) added, and ligated to Illumina sequencing  adapters. The ligation products were size selected by agarose gel electrophoresis, PCR amplified, and sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. (Guangzhou, China)

treatment_protocol: We cultured the HK-2 cells with 5mg/mL recombinant S100A8, recombinant S100A9, or recombinant S100A8/S100A9 protein for 48h and then sequenced the total cellular mRNAS. mRNAS from HK-2 cells cultured with DMEM medium containing corresponding amount of PBS was set as the control group.

value: Kidney

tag: cell line

value: Epithelial Cells

tag: time point


title: Phase I 4C × Phase II 4C, 34 day_rep2

description:
Second_F09_N162_T5_4_ACACGC
ControlAcclimation_gene_count_geo.csv

value: Phase II


title: WT sham, rep2


title: heart, Control_01


title: HK-2 cells,  DMEM medium containing 5mg/mL recombinant S100A8/S100A9-2, 48h


title: Phase I 4C × Phase II 4C, 13 day_rep3

description:
Second_F08_N154_T2_4_TCGTTC
ControlAcclimation_gene_count_geo.csv


title: WT sham, rep1