title: LPS 3.5h biol rep 4


title: LPS 3.5h biol rep 3

status: Public on Sep 18 2022

type: SRA

city: Dublin

first: Karsten

last: Hokamp

address: College Green

department: Smurfit Institute of Genetics

country: Ireland

institute: Trinity College Dublin

library_source: transcriptomic

data_processing:
paired reads of 150 bp length were mapped against GRCm38 (mm10) using STAR with the following options: --outFilterType BySJout  --outFilterMultimapNmax 20  --outFilterMismatchNmax 2  --alignIntronMin 20  --alignIntronMax 1000000  --alignMatesGapMax 1000000  --alignSJoverhangMin 8  --alignSJDBoverhangMin 1  --alignSJstitchMismatchNmax 5  -1   5   5    --chimSegmentMin 12  --chimJunctionOverhangMin 12  --chimSegmentReadGapMax 3  --chimOutJunctionFormat 1   --quantMode GeneCounts  --twopassMode Basic
quantification was carried out during STAR mapping through the option --quantMode GeneCounts
Assembly: mm10
Supplementary files format and content: readcount.txt

molecule: total RNA

organism: Mus musculus

source_name: Bone marrow derived macrophages

growth_protocol: BMDM were seeded in 12 well plates, 1 million cells per well, and incubated overnight in RPMI GlutMax supplemented with 10% FBS, penicillin (100 IU/ml), streptomycin (100ug/ml) and recombinant murine (M-CSF, 25μg/ml).

extract_protocol:
RNA was extracted with the RNeasy Kit (QIAGEN)
Samples frozen at -80℃ before shipping on dry ice to Novogene who performed RNA sequencing analysis.

treatment_protocol: Cells were washed with PBS and replenished with fresh media containing 1 mM CaCl2, then incubated with pd-VWF (10μg/ml) or LPS (100ng/ml) for 3.5 hours (T1) or 16 hours (T2) respectively.

tag: cell type

value: Bone marrow derived macrophages

tag: treatment

value: incubation with LPS

tag: time

value: 3.5 hours


title: SLP eGFP ZT0.5 HY replicate 1

city: Beijing

first: Rui

last: Zhou

address: NIBS

country: China

institute: NIBS

data_processing:
Basecalls performed using CASAVA version 1.9
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped with STAR (version 2.6.1a) to the GRCm38 mouse reference genome with default parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using featureCounts function from Rsubread (v2.0.1) and rpkm function of edgeR (v3.28.1). In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.

molecule: polyA RNA

source_name: mouse hypothalamus

growth_protocol: Mice were bred and maintained under a controlled temperature (22-25ºC) with a 12 h-light/12 h-dark cycle (light on from 9 am to 9 pm), and ad libitum access to water and a standard chow diet.

extract_protocol:
Total RNA was isolated from the brain tissues using RNAprep Pure Tissue Kit (TIANGEN).
Libraries were constructed with the NEBNext Ultra II DNA Library Prep Kit for Illumina (E7645L, NEB).

treatment_protocol: Mice were retro-obital injected with AAV viruses 3 weeks before dissection.

tag: strain

tag: genotype

tag: overexpression

value: eGFP

tag: zt time


title: LPS 3.5h biol rep 2


title: SLP eGFP ZT0.5 TH replicate 4

source_name: mouse thalamus


title: LPS 3.5h biol rep 1


title: SLP eGFP ZT0.5 TH replicate 3


title: Ctrl 16h biol rep 3

value: incubation with PBS

value: 16 hours


title: SLP eGFP ZT0.5 TH replicate 2


title: SLP eGFP ZT0.5 CTX replicate 4

source_name: mouse cortex


title: SLP eGFP ZT0.5 TH replicate 1


title: Ctrl 16h biol rep 4


title: SLP eGFP ZT0.5 CTX replicate 3


title: Ctrl 16h biol rep 1


title: SLP eGFP ZT0.5 HY replicate 2


title: Ctrl 3.5h biol rep 3


title: Ctrl 3.5h biol rep 4


title: SLP HDAC4CA ZT0.5 CTX replicate 3


title: WT eGFP ZT0.5 HY replicate 2

description: WT

value: WT


title: Ctrl 3.5h biol rep 5


title: WT eGFP ZT0.5 HY replicate 3

description: WT


title: Ctrl 3.5h biol rep 1


title: WT eGFP ZT0.5 HY replicate 4

description: WT


title: Ctrl 3.5h biol rep 2


title: Ctrl 16h biol rep 5


title: WT eGFP ZT0.5 HY replicate 1

description: WT


title: WT eGFP ZT0.5 TH replicate 4

description: WT


title: RNAseq_DMSO_2

city: Chengdu, China

first: Ailing

last: Zhong

state: Sichuan

address: No.17 Renmin road section3

department: State Key Laboratory of Biotherapy, West China Hospital, Sichuan University.

institute: Sichuan University

data_processing:
Illumina sequencing workflow
STAR was performed for RNAseq alignment. Bowtie2 was performed for CUT&Tag and ATACseq data alignment. The mouse genome (mm10) was the reference genome.
Normalized data were generated from DESeq2 .
Assembly: mm10
Supplementary files format and content: csv files include DESeq2 normalized values for each sample.

source_name: bone marrow cells

extract_protocol:
HSPCs isolated from bone marrow cells of Trp53-/- mice were transfected with retroviruses encoding shKmt2d or shRen. 48 hours later, GFP-positive cells were sorted by a BD FACSAria™ III Cell Sorter (BD Biosciences) for RNA-seq. Kmt2d knockdown and Kmt2d restored AML cells with doxycycline withdrawal for 4 days were harvested for RNA-seq. RNA libraries were prepared using standard Illumina protocols. Transcriptome sequencing was performed by an Illumina NovaSeq 6000 sequencing platform with 150 bp paired-end sequencing.Kmt2d knockdown and Kmt2d restored AML cells with doxycycline withdrawal for 4 days were harvested for ATAC-seq. Genome sequencing was performed using an Illumina NovaSeq 6000 sequencing platform.
RNA-seq library construction HSPCs isolated from bone marrow cells of Trp53-/- mice were transfected with retroviruses encoding shKmt2d or shRen. 48 hours later GFP-positive cells were sorted by the BD FACSAria™ III Cell Sorter (BD Biosciences, San Jose, CA) for RNA-seq. Kmt2d knockdown and Kmt2d restored AML cells with doxycycline withdrawal for 4 days were harvested for RNA-seq. RNA libraries were prepared using standard Illumina protocols.

tag: tissue

value: Bone marrow cells

value: DMSO treated AML cells


title: RNAseq_DMSO_3


title: SLP HDAC4CA ZT0.5 TH replicate 1


title: WT eGFP ZT0.5 TH replicate 3

description: WT


title: Ctrl 16h biol rep 2


title: SLP eGFP ZT0.5 CTX replicate 2


title: RNAseq_DMSO_1


title: WT eGFP ZT0.5 TH replicate 2

description: WT


title: SLP eGFP ZT0.5 CTX replicate 1


title: RNAseq_DZNeP_1

value: DZNeP treated AML cells


title: RNAseq_DZNeP_2


title: WT eGFP ZT0.5 CTX replicate 4

description: WT


title: WT eGFP ZT0.5 TH replicate 1

description: WT


title: WT eGFP ZT0.5 CTX replicate 2

description: WT


title: WT eGFP ZT0.5 CTX replicate 3

description: WT


title: CUTTag_H3K27me3_ON_3

description: CUTTag_H3K27me3_Kmt2d-restoration_VS_KD_processed.csv

library_source: genomic

data_processing:
Illumina sequencing workflow
STAR was performed for RNAseq alignment. Bowtie2 was performed for CUT&Tag and ATACseq data alignment. The mouse genome (mm10) was the reference genome.
Normalized data were generated from DESeq2 .
Assembly: mm10
Supplementary files format and content: csv files include DESeq2 normalized values for each sample.
Library strategy: CUT&TAG

molecule: genomic DNA

extract_protocol:
HSPCs isolated from bone marrow cells of Trp53-/- mice were transfected with retroviruses encoding shKmt2d or shRen. 48 hours later, GFP-positive cells were sorted by a BD FACSAria™ III Cell Sorter (BD Biosciences).  Genome sequencing was performed using an Illumina NovaSeq 6000 sequencing platform.
CUT&Tag library construction Kmt2d knockdown and Kmt2d restored AML cells with doxycycline withdrawal for 4 days were harvested for CUT&Tag assay using NovoNGS® CUT&Tag 3.0 High-Sensitivity Kit (N259-YH01-01A, NovoProtein, Suzhou, China).

value: Kmt2d knockdown

tag: antibody

value: H3K27me3 (Cell Signaling Technology,Polyclonal,9733S)


title: CUTTag_H3K27me3_ON_1


title: CUTTag_H3K27me3_ON_2


title: CUTTag_H3K27me3_OFF_3

value: Kmt2d restoration


title: CUTTag_H3K27ac_ON_2

description: CUTTag_H3K27ac_Kmt2d_restoration_VS_KD_processed.csv

value: H3K27ac (Abcam,Polyclonal,ab4729)


title: CUTTag_H3K27me3_OFF_1


title: WT eGFP ZT0.5 CTX replicate 1

description: WT


title: SLP CREB ZT12.5 HY replicate 3

value: CREB


title: SLP CREB ZT12.5 HY replicate 1


title: SLP CREB ZT12.5 HY replicate 4


title: SLP CREB ZT12.5 TH replicate 4


title: RNAseq_DZNeP_3


title: CUTTag_H3K27me3_OFF_2


title: CUTTag_H3K27ac_OFF_2


title: SLP CREB ZT12.5 TH replicate 2


title: SLP CREB ZT12.5 TH replicate 3


title: SLP CREB ZT12.5 TH replicate 1


title: CUTTag_H3K4me2_ON_2

description: CUTTag_H3K4me2_Kmt2d_restoration_VS_KD_processed.csv

value: H3K4me2 (Abcam,Polyclonal,ab7766)


title: SLP CREB ZT12.5 CTX replicate 4


title: SLP CREB ZT12.5 CTX replicate 3


title: SLP CREB ZT12.5 HY replicate 2


title: CUTTag_H3K27ac_OFF_1


title: SLP CREB ZT12.5 CTX replicate 1


title: CUTTag_H3K4me1_ON_1

description: CUTTag_H3K4me1_Kmt2d_restoration_VS_KD_processed.csv

value: H3K4me1 (Abcam,Polyclonal,ab8895)


title: SLP CREB ZT12.5 CTX replicate 2


title: CUTTag_H3K4me2_ON_1


title: SLP HDAC4CA ZT12.5 HY replicate 4


title: CUTTag_H3K4me2_OFF_1


title: CUTTag_H3K4me2_OFF_2


title: CUTTag_H3K27ac_ON_1


title: SLP HDAC4CA ZT12.5 HY replicate 2


title: CUTTag_H3K4me1_OFF_2


title: CUTTag_H3K4me1_ON_2


title: Aged, WT,  lung infected 5dpi rep1

city: London

first: Andreas

last: Wack

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Read alingment and gene count was done using the nf-core/rnaseq v 3.0
Differential gene expression was done using DESeq2
Genome_build: Mus musculus Ensembl release 95
Supplementary_files_format_and_content: Table of log transformed normalized counts per gene per sample

source_name: total lung

extract_protocol: Total RNA was isolated from lungs using the Qiagen RNeasy mini kit

value: wild-type

tag: developmental stage

value: aged

tag: infection

value: SARS-CoV-2 variant (SARS-CoV-2 MA20), 5 days post infection

tag: alternative sample name


title: SLP HDAC4CA ZT12.5 HY replicate 3


title: Aged, WT,  lung infected 5dpi rep3


title: Aged, WT,  lung infected 4dpi rep4

value: SARS-CoV-2 variant (SARS-CoV-2 MA20), 4 days post infection


title: SLP HDAC4CA ZT12.5 TH replicate 4


title: CUTTag_H3K4me1_OFF_1


title: SLP HDAC4CA ZT12.5 TH replicate 3


title: SLP HDAC4CA ZT12.5 HY replicate 1


title: SLP HDAC4CA ZT12.5 TH replicate 2


title: SLP HDAC4CA ZT12.5 CTX replicate 4


title: Aged, WT,  lung infected 4dpi rep3


title: Aged, WT,  lung infected 4dpi rep2


title: SLP HDAC4CA ZT12.5 CTX replicate 3


title: SLP HDAC4CA ZT12.5 TH replicate 1


title: Aged, WT,  lung infected 4dpi rep1


title: Aged, WT,  lung infected 5dpi rep2


title: Aged, WT,  lung infected 3dpi rep3

value: SARS-CoV-2 variant (SARS-CoV-2 MA20), 3 days post infection


title: Aged, WT,  lung infected 3dpi rep5


title: Aged, WT,  lung infected 3dpi rep4


title: Aged, WT,  lung infected 3dpi rep2


title: SLP eGFP ZT12.5 HY replicate 2

value: eGFP


title: Aged, WT,  lung mock rep4

value: mock


title: Aged, WT,  lung mock rep5


title: SLP HDAC4CA ZT12.5 CTX replicate 2


title: Aged, WT,  lung mock rep2


title: SLP eGFP ZT12.5 TH replicate 3


title: Aged, WT,  lung infected 3dpi rep1


title: SLP eGFP ZT12.5 HY replicate 3


title: SLP eGFP ZT12.5 TH replicate 4


title: SLP eGFP ZT12.5 TH replicate 1


title: SLP eGFP ZT12.5 HY replicate 1


title: Aged, WT,  lung mock rep1


title: SLP eGFP ZT12.5 TH replicate 2


title: Aged, WT,  lung mock rep3


title: SLP eGFP ZT12.5 CTX replicate 4


title: Adult, WT,  lung infected 5 dpi rep5

value: adult


title: SLP HDAC4CA ZT12.5 CTX replicate 1


title: SLP eGFP ZT12.5 HY replicate 4


title: SLP eGFP ZT12.5 CTX replicate 2


title: Adult, WT,  lung infected 5 dpi rep4


title: SLP eGFP ZT12.5 CTX replicate 3


title: Adult, WT,  lung infected 5 dpi rep3


title: SLP eGFP ZT12.5 CTX replicate 1


title: Adult, WT,  lung infected 5 dpi rep1


title: WT eGFP ZT12.5 HY replicate 3

description: WT

value: WT


title: Adult, WT,  lung infected 4 dpi rep4


title: Adult, WT,  lung infected 4 dpi rep5


title: WT eGFP ZT12.5 HY replicate 1

description: WT


title: Adult, WT,  lung infected 4 dpi rep1


title: Adult, WT,  lung infected 3 dpi rep5


title: Adult, WT,  lung infected 4 dpi rep3


title: WT eGFP ZT12.5 HY replicate 2

description: WT


title: WT eGFP ZT12.5 TH replicate 1

description: WT


title: WT eGFP ZT12.5 TH replicate 4

description: WT


title: WT eGFP ZT12.5 CTX replicate 4

description: WT


title: WT eGFP ZT12.5 TH replicate 3

description: WT


title: Adult, WT,  lung infected 4 dpi rep2


title: Adult, WT,  lung infected 3 dpi rep4


title: Adult, WT,  lung infected 3 dpi rep3


title: WT eGFP ZT12.5 TH replicate 2

description: WT


title: Adult, WT,  lung infected 3 dpi rep2


title: WT eGFP ZT12.5 CTX replicate 3

description: WT


title: Adult, WT,  lung infected 3 dpi rep1


title: WT eGFP ZT12.5 CTX replicate 1

description: WT


title: WT eGFP ZT12.5 CTX replicate 2

description: WT


title: WT eGFP ZT12.5 HY replicate 4

description: WT


title: Adult, WT,  lung infected 5 dpi rep2


title: Adult, WT,  lung mock rep5


title: CREB HY replicate 4

description: WT


title: CREB HY replicate 3

description: WT


title: CREB HY replicate 2

description: WT


title: Adult, WT,  lung mock rep4


title: 0.04X, replicate 4, CITE-seq

city: La Jolla

first: Klaus

last: Ley

state: California

address: 9420 Athena Cir

country: USA

institute: La Jolla Institute for Immunology

description:
barcodes.tsv.gz
features.tsv.gz
matrix.mtx
metadata.csv.zip

data_processing:
Cellranger v3.0 was used to map the sequencing reads to the genome
Doublets were removed using DoubletFinder v3 and cells expressing >10% of mitochondrial genes were removed
Seurat v4 used to nomalize and perform dimentaionality reduction on the data
Immune cell subtypes were called based on thresholded andibody expression
Downstream plots were generated using the R package ggplot2
Assembly: GRCh38-3.0.0
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, genes.tsv.gz, matrix.mtx.gz
Library strategy: CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing)

organism: Homo sapiens

source_name: PBMCs

extract_protocol:
Library was prepared using Chromium Single Cell 3ʹ v2 protocol (10x Genomics). Cellular mRNA and antibody-derived oligos were reverse-transcribed and indexed with a shared cellular barcode. Indexed cDNAs were then pooled and amplified by PCR according to the Chromium Single Cell 3’ v2 protocol (10x Genomics) and with specific primers amplifying the antibody-derived tags. SPRI bead size selection was performed in order to separate both the mRNA-derived cDNA (>300bp) and the antibody-derived tagged cDNAs (180bp). For the mRNA derived cDNA library preparation, we further proceeded according to the manufacturer’s instructions for Single Cell 3’ v2 protocol (10x Genomics). For antibody-derived tagged library, we used the KAPA HiFI HotStart Library Amplification Kit (Roche) with the following primers and amplification program:
-CITE-seq library: amplification was performed at 95°C for 3’ followed by ten cycles at 95°C f¬¬or 20’’; 60°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGTGATGTGACTGGAGTTCCTTGGCACCCGAGAATTCCA-3’ Small RNA RPI1 primer as i7 primer (Illumina).
-HASH-seq library: amplification was performed at 95°C for 3’ followed by ten cycles 95°C for 20’’; 64°C for 30’’; 72°C for 20’’ and final elongation 72°C for 5’ with 5’-CAAGCAGAAGACGGCATACGAGATCGAGTAATGTGACTGGAGTTCAGACGTGTGC-3’ TruSeq D701_s primer as i7 primer (Illumina).
The following 5’- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ SI-PCR primer as i5 primer (Illumina) was used for both CITE- and HASH- seq library amplification.
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.

value: PBMCs


title: 0.2X, replicate 3, CITE-seq


title: CREB TH replicate 4

description: WT


title: Adult, WT,  lung mock rep3


title: 1X, replicate 2, CITE-seq


title: Adult, WT,  lung mock rep2


title: CREB TH replicate 3

description: WT


title: CREB TH replicate 2

description: WT


title: Adult, WT,  lung mock rep1


title: 2X, replicate 1, CITE-seq


title: CREB CTX replicate 4

description: WT


title: 0.04X, replicate 4, scRNAseq

library_source: transcriptomic single cell

data_processing:
Cellranger v3.0 was used to map the sequencing reads to the genome
Doublets were removed using DoubletFinder v3 and cells expressing >10% of mitochondrial genes were removed
Seurat v4 used to nomalize and perform dimentaionality reduction on the data
Immune cell subtypes were called based on thresholded andibody expression
Downstream plots were generated using the R package ggplot2
Assembly: GRCh38-3.0.0
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, genes.tsv.gz, matrix.mtx.gz

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.


title: 0.2X, replicate 3, scRNAseq


title: Aged, Ifnar1 KO, lung infected rep5

value: Ifnar1 KO

value: SARS-CoV-2 variant (SARS-CoV-2 MA), 3 days post infection

value: lung


title: CREB CTX replicate 1

description: WT


title: CREB CTX replicate 2

description: WT


title: HDAC4CA HY replicate 4

description: WT


title: CREB CTX replicate 3

description: WT


title: HDAC4CA HY replicate 3

description: WT


title: Aged, Ifnar1 KO, lung infected rep4


title: 1X, replicate 2, scRNAseq


title: Aged, Ifnar1 KO, lung infected rep3


title: HDAC4CA HY replicate 1

description: WT


title: HDAC4CA HY replicate 2

description: WT


title: CREB HY replicate 1

description: WT


title: HDAC4CA TH replicate 4

description: WT


title: HDAC4CA TH replicate 3

description: WT


title: Het-1A 5% Pgsupernatant rep3

first: Xueting

last: Jia

address: No. 95 Yong'an Road, Xicheng District

institute: Beijing Friendship Hospital, Capital Medical University

data_processing:
RNA degradation and contamination was monitored on agarose gels. RNA purity was checked using the spectrophotometer. RNA concentration was measured using Qubit. RNA integrity was assessed using the Agilent 2100.
A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using VAHTS mRNA-seq v2 Library Prep Kit for Illumina following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using fragmentation buffer. First strand cDNA was synthesized and second strand cDNA synthesis was subsequently performed. Remaining overhangs were converted into blunt ends. After adenylation of 3’ ends of DNA fragments, adaptor with hairpin loop structure were ligated. Then the PCR was performed. At last, Qubit HS quantification, Agilent 2100 Bioanalyzer/Fragment Analyzer 5300 quality control, the final library size of about 350bp.
The libraries were sequenced on an Illumina NovaSeq platform to generate 150 bp paired-end reads, according to the manufacturer’s instructions.
Raw data (raw reads) of fastq format were firstly processed through primary quality control. In this step, clean data (clean reads) were obtained by removing read pairs that contain N more than 3 or the proportion of base with quality value below 5 is more than 20%, in any end,or adapter sequence was founded. All the downstream analyses were based on the clean data with high quality.
Paired-end clean reads were aligned to the reference genome using TopHat. We selected TopHat as the mapping tool for that TopHat can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools.
HTSeq was used to count the reads numbers mapped to each gene.
Differential expression analysis between two conditions was performed using the DEGSeq R package (1.20.0). Differentially expressed genes were defined as those for which the adjusted P-value below 0.05 and the log2(Fold change) more than 1.
GO and KEGG enrichment analysis of differentially expressed gene sets were implemented in the GOseq R and KOBAS 3.0 package, respectively. GO terms with adjusted P-value below 0.05 were considered as significantly enriched by differential expressed genes.
The Retrieval of Interacting Genes (STRING, http://string.embl.de/) database was used to construct a protein-protein interaction (PPI) network based on the differentially expressed gene sets and the names of all the interacting proteins and the protein-coding genes were extracted from the network. A confidence score of ≥700 was set as the parameter for significance. After obtaining the PPI relationship, a network diagram was constructed with Cytoscape3.4.0.
The differentially expressed gene sets were used as candidate genes, and transcription factors (TFs) were predicted with iTAK by hmmscan for plants and with TFDB 2.0 database by hmmsearch for animal and human.
Alternative splicing events were detected and quantified using the rMATS software. The number of AS events in each sample was estimated, separately.
Picard-tools and samtools were used to sort, mark duplicated reads and reorder the bam alignment results of each sample. SNPs were identified with GATK2 software.
The Cufflinks Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from TopHat alignment results.
Fusion Genes were detected using the STAR-Fusion software.
Assembly: The Cufflinks Reference Annotation Based Transcript (RABT) assembly method was used to construct and identify both known and novel transcripts from TopHat alignment results.
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: esophagus

extract_protocol:
RNA was extracted using Trizol reagent according to the manufacturer's instructions. A total amount of 2 μg RNA per sample was used as input material for the RNA sample preparations.
Sequencing libraries were generated using VAHTS mRNA-seq v2 Library Prep Kit for Illumina following manufacturer’s recommendations

tag: cell line

value: esophagus

value: 5% P.g supernatant present medium, culture for 24h


title: CREB TH replicate 1

description: WT

value: CREB


title: Aged, Ifnar1 KO, lung infected rep1


title: Aged, Ifnar1 KO, lung infected rep2


title: HDAC4CA TH replicate 1

description: WT


title: HDAC4CA TH replicate 2

description: WT


title: HDAC4CA CTX replicate 4

description: WT


title: Aged, Ifnar1 KO, lung mock rep5


title: Aged, Ifnar1 KO, lung mock rep4


title: mCherry HY replicate 4

description: WT

value: mCherry


title: HDAC4CA CTX replicate 1

description: WT


title: HDAC4CA CTX replicate 3

description: WT


title: Het-1A 5% Pgsupernatant rep1


title: Aged, Ifnar1 KO, lung mock rep2


title: mCherry HY replicate 2

description: WT


title: mCherry HY replicate 3

description: WT


title: HDAC4CA CTX replicate 2

description: WT


title: Aged, Ifnar1 KO, lung mock rep3


title: mCherry HY replicate 1

description: WT


title: Het-1A control rep3

value: 5% P.g supernatant blank medium, culture for 24 h


title: Het-1A control rep1


title: Het-1A control rep2


title: mCherry TH replicate 3

description: WT


title: Aged, Ifnar1 KO, lung mock rep1

value: aged


title: mCherry TH replicate 4

description: WT


title: Adult, Ifnar1 KO, lung infected rep5


title: 7119

city: Ithaca

first: Charles

middle: G

last: Danko

state: NY

address: Hungerford Hill Rd

department: Baker Institute

institute: Cornell University

description: ChRO-seq

data_processing:
Data were processed using the PRO-seq 2.0 pipeline (https://github.com/Danko-Lab/proseq2.0).
We used dREG web Gateway (https://dreg.dnasequence.org/) to  identify the location of promoters and enhancers.
Assembly: mm10
Supplementary files format and content: Mapped, de-duplicated ChRO-seq data representing raw counts (default) or reads-per-million normalized counts (files ending in .rpm.bw) are provided. The location of promtoers/ enhancers obtained using dREG on merged count files is included in a BED file (Kurpios_heart_10.dREG.peak.score.bed.gz).
Library strategy: ChRO-seq

source_name: Whole heart tissue

growth_protocol: Whole heart grew in living mice.

extract_protocol:
Heart tissue was obtained, cryopulverized, and chromatin extracted using Chu et. al. (2018) Nature Genetics (PMID: 30349114).
The library prep was performed as described in Chu et. al. (2018) Nature Genetics (PMID: 30349114).

tag: individual

value: PHDHET


title: mCherry TH replicate 2

description: WT


title: Adult, Ifnar1 KO, lung infected rep4


title: 7114

description: ChRO-seq


title: mCherry TH replicate 1

description: WT


title: mCherry CTX replicate 4

description: WT


title: 4595

description: ChRO-seq

value: Wild-type


title: Adult, Ifnar1 KO, lung infected rep3


title: Adult, Ifnar1 KO, lung infected rep2


title: mCherry CTX replicate 3

description: WT


title: 4594

description: ChRO-seq


title: 4590

description: ChRO-seq


title: Adult, Ifnar1 KO, lung mock rep4


title: 4581

description: ChRO-seq


title: Het-1A 5% Pgsupernatant rep2

value: 5% P.g supernatant present medium, culture for 24 h


title: 2183

description: ChRO-seq

value: Playrr mutant


title: mCherry CTX replicate 1

description: WT


title: mCherry CTX replicate 2

description: WT


title: DKO-thymus_rep3

city: Seoul

first: Jae Seok

last: Roe

address: Yonsei-ro, 50

country: South Korea

institute: Yonsei University

data_processing:
RNA-Seq samples were analyzed using TopHat–Cufflinks pipeline. Reads were mapped to the mm10 genome with TopHat v2.1.1. Transcripts were assembled using Cufflinks v2.2.1. Final transcriptome assembly was performed with cuffmerge v1.0.0, and differential expression was identified with cuffdiff v2.2.1.
Assembly: mm10
Supplementary files format and content: Differentially expressed genes were analyzed using Cufflinks tools (Trapnell et al, 2012; PMID: 22383036)

source_name: thymus

extract_protocol:
Total RNAs were extracted from excised thymus using Qiaizol reagent
Libraries were prepared using the NEXTflex Rapid Directional mRNA-seq kit (Cat# NOVA-5138-11; PerkinElmer) according to the manufacturer's instructions.

tag: biological replicate


title: Adult, Ifnar1 KO, lung mock rep3

value: mock


title: 2182

description: ChRO-seq


title: 2181

description: ChRO-seq


title: DKO-thymus_rep1


title: p53KO-thymus_rep3


title: DKO-thymus_rep2


title: Adult, Ifnar1 KO, lung mock rep1

value: adult


title: Adult, Ifnar1 KO, lung mock rep2


title: ATACseq_Kmt2d_ON_2

description: bulkATACseq_Kmt2d_OFF_VS_ON_processed.csv

data_processing:
Illumina sequencing workflow
we used NGmerge to remove adapters, Bowtie2 for sequence alignment, MarkDuplicates tools of Picard for duplicates removal.
The standard workflow of HMMRATAC was utilized for ATAC-seq peak calling step.
DESeq2 normalized data were calculated .
Genome_build: mm10
Supplementary_files_format_and_content: csv files include DESeq2 normalized values for each Sample ...

extract_protocol:
HSPCs isolated from bone marrow cells of Trp53-/- mice were transfected with retroviruses encoding shKmt2d or shRen. 48 hours later, GFP-positive cells were sorted by a BD FACSAria™ III Cell Sorter (BD Biosciences) for RNA-seq. Kmt2d knockdown and Kmt2d restored AML cells with doxycycline withdrawal for 4 days were harvested for RNA-seq. RNA libraries were prepared using standard Illumina protocols. Transcriptome sequencing was performed by an Illumina NovaSeq 6000 sequencing platform with 150 bp paired-end sequencing.Kmt2d knockdown and Kmt2d restored AML cells with doxycycline withdrawal for 4 days were harvested for ATAC-seq. Genome sequencing was performed using an Illumina NovaSeq 6000 sequencing platform.
libraries were prepared for sequencing using standard Illumina protocols
Bulk RNA-Seq and Bulk ATAC-seq

value: Bone marrow cells

value: Kmt2d knockdown


title: ATACseq_Kmt2d_ON_1


title: Adult, Ifnar1 KO, lung infected rep1

value: Ifnar1 KO


title: p53KO-thymus_rep1


title: ATACseq_Kmt2d_OFF_2

value: Kmt2d restoration


title: Adult, Ifnar1 KO, lung mock rep5

value: lung


title: CD3-CD56+ NK cells from PBMC of obese donor 3

city: Houston

first: Haoqiang

last: Ying

state: Texas

address: 1515 Holcombe Blvd

institute: M. D. Anderson Cancer Center

description:
obese_3
OB70301NK

data_processing:
Sequence reads were trimmed for adaptor sequence (using cutadapt) low-quality sequences removed (using fastp).
Trimmed sequence reads were mapped to hg38 transcriptome using STAR2 v2.6.0b.
Raw counts were collected using htseq v0.11.0 and TPM calculated using gencode reported gene lengths.
Assembly: hg38
Supplementary files format and content: *.txt: Tab-delimited text files include TPM and raw count values for each Sample.

source_name: Blood

extract_protocol:
RNA was harvested using QIAzol Lysis Reagent. 1.0 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were generated from cDNA using the Illumina Nextera XT DNA Sample Preparation Kit. cDNA library quality was assessed using an Agilent 2100 Bioanalyzer.

value: Blood

value: CD3-CD56+ NK Cells

value: wild type

tag: weight

value: obese


title: CD3-CD56+ NK cells from PBMC of obese donor 5

description:
obese_5
OB82703NK


title: CD3-CD56+ NK cells from PBMC of obese donor 4

description:
obese_4
OB72802NK


title: 2177

description: ChRO-seq


title: CD3-CD56+ NK cells from PBMC of obese donor 2

description:
obese_2
OB01183NK


title: CD3-CD56+ NK cells from PBMC of normal weight donor 4

description:
normal_weight_4
NW70801

value: normal


title: RNAseq_Kmt2d_ON_2

description: bulkRNAseq_Kmt2d_OFF_VS_ON_processed.csv

data_processing:
Illumina sequencing workflow
Sequenced reads were mapped to mm10 whole genome using STAR v2.6.0 .
DESeq2 normalized data were calculated .
Genome_build: mm10
Supplementary_files_format_and_content: csv files include DESeq2 normalized values for each Sample ...


title: RNAseq_Kmt2d_ON_1


title: MJ rep3

city: seoul

first: jiah

last: yeom

address: Anamro 145

institute: Korea university

data_processing:
Illumina Casava1.8 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence(using fastx_trimmer), then mapped to mm10 (UCSC) whole genome using Bowtie2
Read count extraction using bedtools.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count values for each Sample

source_name: macrophage

growth_protocol: Raw 264.7 cells were seeded at the concentration of 1 x 10^5 cells/mL on 6-mm dish and incubated in DMEM containing 10% fetal bovine serum and 1% penicillin and streptomycin at 37℃ with the atmosphere of 5% CO₂ for overnight.

extract_protocol:
RNA was harvested using Trizol reagent (Invitrogen). 500 ng of total RNA was used for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using LEXOGEN Quant-Seq Library Prep Kit (Cat#001.24) standard protocols.

treatment_protocol: RANKL (50 ng/mL), heat-killed P. freudenreichii MJ2 (1 x 10^7 cells/mL), and surface protein extracted from P. frudenreichii MJ2 (10 μg/mL) were treated for 4 days.

value: BALB/c

value: Blood lymph

tag: passages


title: SF rep2


title: SF rep3


title: CD3-CD56+ NK cells from PBMC of normal weight donor 3

description:
normal_weight_3
NW70702NK

tag: cell type


title: NC rep2


title: RNAseq_Kmt2d_OFF_3


title: CD3-CD56+ NK cells from PBMC of normal weight donor 2

description:
normal_weight_2
NW401NK


title: MJ rep2


title: CD3-CD56+ NK cells from PBMC of normal weight donor 1

description:
normal_weight_1
NW100127NK


title: RNAseq_Kmt2d_OFF_2


title: SF rep1


title: RNAseq_Kmt2d_OFF_1


title: RNAseq_Kmt2d_ON_3


title: ATACseq_Kmt2d_OFF_1

data_processing:
Illumina sequencing workflow
we used NGmerge to remove adapters, Bowtie2 for sequence alignment, MarkDuplicates tools of Picard for duplicates removal.
The standard workflow of HMMRATAC was utilized for ATAC-seq peak calling step.
DESeq2 normalized data were calculated .
we used NGmerge to remove adapters, Bowtie2 for sequence
Genome_build: mm10
Supplementary_files_format_and_content: csv files include DESeq2 normalized values for each Sample ...


title: NC rep3


title: NC rep1


title: CD3-CD56+ NK cells from PBMC of obese donor 1

description:
obese_1
OB01003NK


title: RNAseq_shRen_3

description: bulkRNAseq_shKmt2d_VS_shRen_processed.csv

source_name: Hematopoietic stem and progenitor cells

value: Hematopoietic stem and progenitor cells

value: Kmt2d WT


title: MJ rep1


title: RNAseq_shRen_2


title: EPI

city: Belvaux

first: Jens

middle: Christian

last: Schwamborn

address: 6, Avenue du Swing

country: Luxembourg

institute: LCSB

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2  https://www.10xgenomics.com/support
Assembly: Cell Ranger 4.0.0 software and human reference GRCh38 3.0.0
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Midbrain (from iPSCs)

extract_protocol:
Organoids and assembloids were gently  dissociated using 500 ml of 0.1  Lysis Buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% Tween- 20, 0.1% Nonidet P40 Substitute, 0.01% digitonin, 1% BSA, nucleasefree water) by pipetting 10X with a wide-pore 1000 μl pipette, followed by a 10-min incubation period on ice. This was repeated for two cycles. To reduce batch effects and increase the number of nuclei per experiment, material from four different organoids or assembloids were pooled for each group. Cells were filtered through a 40-μM strainer using 300 μl at a time, using a new 40-μM strainer. The same procedure was done with 20-μM (Sysmex, AN777717) and 10-μM (Sysmex, AP275603) strainers, followed by centrifugation for 5 min at 500g, at 4 C. Nuclei were then stained using Hoechst 33342 (1:2000) for 5 min at room temperature and counted on the Countess II.
Using Diluted Nuclei Buffer (10x Genomics, 2,000,153) each sample was adjusted to a concentration of 4000 nuclei/μl. We generated one library for each sample, aiming for 6000 nuclei. Single-nuclei experiments were performed using the 10x Genomics Next GEM  Single Cell 50 Library Kit v1.1 (1000168) to encapsulate nuclei and amplify cDNA, to generate sequencing libraries. Each library was barcoded using i7 barcodes provided by 10x Genomics. cDNA and sequencing library quality and quantity were determined using Agilent's High Sensitivity DNA Assay (5067-4626) and KAPA (KK4824). Final libraries were pooled, loaded on two lanes of the Illumina's HiSeq X, and sequenced in 150PE mode.

value: Midbrain (from iPSCs)

value: Neural cells - with microglia

value: WT


title: 163

description: 10x Genomics


title: RNAseq_shKmt2d_3


title: K7

description: 10x Genomics


title: RNAseq_shKmt2d_2


title: LX2 cells, DMSO, 48 h 2

city: Wuhan

first: Huanzhang

last: Niu

address: Jiefang Avenue 1277#

institute: Wuhan Union 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
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: hepatic stellate cells

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

value: hepatic stellate cells

tag: treatment

value: DMSO


title: Wildtype

description: 10x Genomics

value: Neural cells - without microglia


title: LX2 cells, Ginkgetin, 48h 1

value: Ginkgetin (5microM)


title: LX2 cells, DMSO, 48 h 1


title: LX2 cells, DMSO, 48 h 3


title: LX2 cells, Ginkgetin, 48h 3


title: RNAseq_shKmt2d_1

value: Kmt2d knockdown


title: LX2 cells, Ginkgetin, 48h 2


title: RNAseq_shRen_1


title: HBV-POS2-LOD5-20200922

status: Public on Sep 17 2022

city: Basel

first: Jitao David

last: Zhang

address: Grenzacherstrasse 124

department: Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel

country: Switzerland

institute: F. Hoffmann-La Roche

data_processing:
Linker tags were removed from RNA sequencing by the FASTX Toolkit, v0.0.13 (http://hannonlab.cshl.edu/fastx_toolkit/).
Reads mapped to the human genome are removed. The STAR aligner (version 2.6.1d) and the human reference genome GRch38.p12 is used.
The remaining reads were analyzed with HBVouroboros.
Assembly: HBV genomes in HBVdb are used as part of the HBVouroboros
Supplementary files format and content: vcf files: variant calling

organism: Hepatitis B virus

source_name: A plasmid containing cloned HBV genome

extract_protocol: A pair of primers (forward primer sequence: ccggaaagcttgagctcttcTTTTTCACCTCTGCCTAATCA; reverse primer sequence: ccggaaagcttgagctcttcAAAAAGTTGCATGGTGCTGG) were designed based on the open loop region for long fragment amplification to cover the whole length of HBV DNA with PCR buffer of 2 × Vazyme LAmp® Master Mix (Vazyme Biotech Co. Ltd, Nanjing, China). After purification of the PCR product, long fragment HBV DNA were performed the random fragmentation via ultrasound fragmentation instrument of LE220 (Covaris, Woburn, Massachusetts) and utilized the NEXTflex Rapid DNA-Seq Kit for Illumina (Bioo Scientific, Austin, Texas) to obtain the DNA libraries. Quality of long fragment amplification products were assessed by gel electrophoresis while quality of amplified libraries was assessed by capillary electrophoresis with a DNA chip on a 2100 Bioanalyzer

tag: sample type

value: A plasmid containing cloned HBV genome

value: U95551 (WT), with modifications:C669A, A681G, C682G, G736T, A741G, G743T


title: HBV-WT-20200924


title: HBV-POS2-LOD6-20200924


title: HBV-WT-20200922


title: HBV-POS2-LOD6-20200923


title: HBV-POS2-LOD6-20200922


title: HBV-WT-20200923


title: HBV-POS2-LOD5-20200924


title: HBV-POS2-LOD4-20200924


title: HBV-POS2-LOD5-20200923


title: HBV-POS2-LOD4-20200923


title: HBV-POS2-LOD3-20200924


title: HBV-POS2-LOD4-20200922


title: HBV-POS2-LOD3-20200923


title: HBV-POS2-LOD3-20200922


title: HBV-POS2-LOD2-20200924


title: HBV-POS2-LOD2-20200923


title: HBV-POS2-LOD2-20200922


title: HBV-POS2-LOD1-20200922


title: HBV-POS1-LOD6-20200922

value: U95551 (WT), with modifications:C673T and A838C


title: HBV-POS1-LOD6-20200924


title: HBV-POS1-LOD5-20200924


title: HBV-POS1-LOD5-20200923


title: HBV-POS1-LOD5-20200922


title: HBV-POS1-LOD4-20200923


title: HBV-POS1-LOD2-20200923


title: HBV-POS1-LOD3-20200922


title: HBV-POS1-LOD3-20200924


title: HBV-POS1-LOD2-20200924


title: HBV-POS1-LOD4-20200924


title: HBV-POS1-LOD2-20200922


title: Coculture rep3

city: Philadelphia

first: Joseph

last: Zackular

state: Pennsylvania

address: 3615 Civic Center Blvd

institute: University of Pennsylvania

data_processing:
RNA-eq reads were aligned to the CD196 and OG1RF genome assemblies using STAR version 2.7.6a with the following configurations --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 1500000000 --outSAMmapqUnique 255 --outFilterMultimapNmax 1 --alignIntronMax 1
Reads count on each gene was calculated at the same time of mapping with the parameter --quantMode GeneCounts.
Differential expression analysis between Coculture vs C.difficile alone was done using R package DESeq2 (version 1.30.0)
Genome_build: CD196
Supplementary_files_format_and_content: bigwig files were generated using genomeCoverageBed program from bedtools v2.29.2; Scores represent normalized read counts
Genome_build: OG1RF

organism:
Enterococcus faecalis
Clostridioides difficile

source_name: Clostridioides difficile, Enterococcus faecalis

growth_protocol: OD normalized cultures of C. difficile strain CD196, E. faecalis strain OG1RF, and mixed co-cultures were grown anaerobically in biological triplicate in BHIS + L-cysteine at 37 °C for 4 hours (exponential phase). For co-cultures, C. difficile was seeded at a 2:1 ratio to E. faecalis to account for differences in growth rates between species.

extract_protocol:
Samples were stored at -80 °C until used for RNA extraction. Samples were thawed on ice, pelleted, and resuspended in 750 µL of LETS buffer (1 M LiCl, 0.5 M EDTA, 1 M Tris pH7.4). Cells were transferred to tubes containing lysing matrix B beads (MP Biomedicals) and lysed by a FastPrep-24 (MP Biomedicals) bead beater for 45 s at 6 m/s. Lysed samples were heated for 5 min at 55 °C and pelleted by centrifugation for 10 min. The supernatant was transferred to a fresh tube and 1 mL TRIzol (Thermo Scientific) was added. Chloroform (200 µL) was added to each sample and vortexed prior to separation of the aqueous and organic layers by centrifugation for 15 min. The aqueous (upper) layer was transferred to a fresh tube and the RNA was precipitated through the addition of 1 mL isopropyl alcohol. Samples were incubated for 10 min and RNA was pelleted by centrifugation for 10 min. Supernatant was removed and the RNA pellet was washed with 200 µL of 70% ethanol. Samples were air dried for 1 min, then resuspended in 100 µL RNase free water. DNA contamination was removed through the addition of 8 µL RQ1 DNase, 12 µL 10x RQ1 buffer, and 2 µL RNase inhibitor (Promega) to the purified RNA. Samples were DNase treated for 2 h and purified using the RNeasy miniprep RNA cleanup kit (Qiagen). RNA was quantified and either used for RNA sequencing or quantitative PCR (qPCR) as described below.
RNA-seq library construction and sequencing were performed by HudsonAlpha Institute for Biotechnology (Huntsville, AL). The concentration and integrity of extracted total RNA were estimated by a Qubit 2.0 Fluorometer (Invitrogen) and an Agilent 2100 Bioanalyzer (Applied Biosystems), and 500 ng of RNA was utilized for downstream applications. rRNA was removed using the Ribo-Zero Gold (Epidemiology) kit (Illumina) according to the manufacturer’s instructions. RNA was fragmented and primed for first-strand synthesis using the NEBNext first strand synthesis module (New England BioLabs). Directional second-strand synthesis was performed using the NEBNext Ultra Directional second strand synthesis kit. Libraries were then prepared from samples using the NEBNext DNA Library Prep master mix set (Illumina) with the following slight modifications. End repair was performed and followed by polyadenylic acid (poly[A]) addition and custom adapter ligation. Ligated samples were individually barcoded with unique in-house Genomic Services Lab (GSL) primers and amplified through 12 cycles of PCR. Library quantity was assessed by a Qubit 2.0 Fluorometer, and the library quality was assessed by utilizing a DNA High Sensitivity Chip on a Caliper GX (PerkinElmer). The quantitative PCR (qPCR)-based Kapa Biosystems library quantification kit (Kapa Biosystems) was used for final accurate quantification of libraries prior to sequencing. Each library was diluted to a final concentration of 12.5 nM and pooled equimolar prior to clustering. Paired-end sequencing was performed on an Illumina HiSeq2500 sequencer (Illumina).

treatment_protocol: Mono-cultures vs. co-cultures

tag: strain

value: CD196, OG1RF

tag: media

value: BHIS


title: Coculture rep2


title: HBV-POS2-LOD1-20200923

tag: genotype


title: 2X, replicate 1, scRNAseq

value: PBMCs


title: HBV-POS1-LOD3-20200923


title: HBV-POS1-LOD1-20200922


title: HBV-POS2-LOD1-20200924


title: Coculture rep1


title: HBV-POS1-LOD1-20200923


title: HBV-POS1-LOD1-20200924


title: HBV-POS1-LOD6-20200923


title: HBV-POS1-LOD4-20200922


title: 2uMButyroside D 2

type: RNA

city: Tsukuba,

first: Meriem

last: Bejaoui

state: Ibaraki

address: 1 Chome-1-1 Tennodai

country: Japan

institute: University of Tsukuba

description: Gene expression data from 2 μM Butyroside D for 48 h

hyb_protocol: Following fragmentation, 2.3 μg of cRNA were hybridized for 16 hr at 45C on Clariom S Array, mouse . GeneChips were washed and stained in the GeneChip® Fluidic station 450

scan_protocol: GeneChips were scanned using the GeneChip® Scanner 3000

data_processing:
The raw data were normalized using Expression Console Software provided by the Affymetrix following robust multichip average (RMA) algorithm (http://www.affymetrix.com). Subsequent analysis of the gene expression data was carried out in the freely available Transcriptome Analysis Console (TAC) version 4 (Thermofisher inc.). Further analysis was conducted using an online data mining tool DAVID (Database for Annotation, Visualization and Integrated Discovery, ver. 6.8). We used 'Functional Annotation' tool of DAVID to identify the most relevant biological terms, including gene ontology (GO) terms, biological pathways. We also performed gene set enrichment analysis (GSEA) for the top DEGs.
Expression console signal intensity. For calculating average value, standard deviation, fold change, and Anova p-value of signal intensity of replicates, we used freely available Transcriptome Analysis Console software (CHP files ).

label: biotin

organism: Mus

source_name: cell treated with 2 μM Butyroside D

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 100 ng total RNA

growth_protocol: Murine B16F10 melanoma cell lines were obtained from Riken Cell Bank (Tsukuba, Japan) and maintained in Roswell Park Memorial Institute medium (RPMI 1640) (Gibco, MA, United States,)

extract_protocol: For RNA extraction, Isogen (Nippon Gene Co. Ltd., Toyama, Japan) was added and the cell suspensions were centrifuged for 5 minutes at 500 g and the pellet was stored at -80oC until use.

treatment_protocol: After the initial 24 hour seeding  in 6-well plates.  The medium was changed with 0 (Control) and 2 μM Butyroside D (2uMButyrosideD) for 48 h.

value: B16F10 cells


title: 0.2uMButyroside D 2

description: Gene expression data from 0.2 μM Butyroside D for 48 h

source_name: cell treated with 0.2 μM Butyroside D

treatment_protocol: After the initial 24 hour seeding  in 6-well plates.  The medium was changed with 0 (Control) and 0.2 μM Butyroside D (0.2uMButyrosideD) for 48 h.


title: 0.2uMButyroside D 4


title: METTL3 Overexpressed BGC-823 Cell replicate1

city: 蚌埠

first: 癸森

last: 彭

address: F座

institute: 蚌埠医学院

description: Biological replicate 1 of 3. Lentiviral Stable Transfection for METTL3 Overexpression.

hyb_protocol: 50 μL hybridization solution was dispensed into the gasket slide and assembled to the m6A-mRNA&lncRNA Epitranscriptomic Microarray slide.

scan_protocol: 2.5 μg of Cy3 and Cy5 labeled cRNAs were mixed.

data_processing:
Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images.
Raw intensities of IP (immunoprecipitated, Cy5-labelled) and Sup (supernatant, Cy3-labelled) were normalized with average of log2-scaled Spike-in RNA intensities.

source_name: Gastric cancer epithelial METTL3 overexpressing cells

label_protocol: The “IP” RNAs and “Sup” RNAs were added with equal amount of calibration spike-in control RNA, separately amplified and labeled with Cy3 (for “Sup”) and Cy5 (for “IP”) using Arraystar Super RNA Labeling Kit. The synthesized cRNAs were purified by RNeasy Mini Kit. The concentration and specific actitity (pmol dye/μg cRNA) were measured with NanoDrop ND-1000.

growth_protocol: The human GC cell line BGC-823 was purchased from the Institute of Cell Research of the Chinese Academy of Sciences in Shanghai. The BGC-823 cells are supplemented with 10% fetal bovine serum (FBS; Gibco) and 1% penicillin/streptomycin (HuaXiao gene Technology) in DMEM (Procell Life Science&Technology Co.,Ltd) in a 37 °C, 5% CO2 incubator with a humidified atmosphere. Lentivirus-mediated METTL3-overexpressing and control were purchased from Jikai Gene Chemical Technology Co.,Ltd (Shanghai, China).

extract_protocol: The total RNA the control and METTL3 overexpression group were extracted by Trizol for m6A-tagged mRNA quantification.

treatment_protocol: Establishment and screening of METTL3-overexpressing stable cell models according to the instructions of Jikai Gene Technology Co., Ltd. Briefly, when the cells in the logarithmic growth phase, the control (NC group) and METTL3 overexpressing lentivirus were added in BGC-823 cells, puromycin (4 μg/mL) was used to screen the successfully transfected cells for the subsequent experiments.

tag: age

value: 62 years old

value: m6A IP

value: control (SUP)


title: Control BGC-823 Cell replicate2

description: Biological replicate 2 of 3. Control gastric cancer epithelial cells, untreated.

source_name: gastric cancer epithelial cells

value: gastric cancer epithelial cells


title: 2uMButyroside D 3


title: 0.2uMButyroside D 1


title: 0.2uMButyroside D 3


title: Control 3

description: Gene expression data from meduim treated for 48 h

source_name: cell treated with meduim


title: 2uMButyroside D 4


title: Control BGC-823 Cell replicate1

description: Biological replicate 1 of 3. Control gastric cancer epithelial cells, untreated.


title: Control BGC-823 Cell replicate3

description: Biological replicate 3 of 3. Control gastric cancer epithelial cells, untreated.


title: Brain_cuprizone 3wks + Siponimod_mouse 5

city: Aachen

first: Tim

last: Clarner

state: Germany

address: Wendlingweg 2

country: Germany

institute: Neuroanatomie

description:
0.25% cuprizone (w/w)
DEA_Siponimod_vs_Control.xlsx

data_processing:
Generation of the fastq files and removal of adapters were completed using the Illumina demultiplexing and conversion software bcl2fastq
Subsequently, RNA-Seq primary analysis was performed with the RNA-Seq pipeline of nf.core v3.0 using standard parameters.
library complexity was measured with preseq v2.0.3 (61).
Adapter and quality trimming was performed using TrimGalore v.0.6.6
reads were aligned to the mm10 reference genome sequence using STAR v2.6.1d (62) with default parameters. For quantification, reads were counted with the quasi-mapping quantification tool salmon v1.4.0 (63).
Assembly: mm10
Supplementary files format and content: Excel files including TPM

source_name: corpus callosum + neocortex

extract_protocol:
RNA isolation was performed using the RNeasy Lipid Tissue Mini Kit (Qiagen, Germany) strictly following the manufacturer’s instructions
all cDNA libraries were generated from 1 μg total RNA using the TrueSeq Stranded Total Library Preparation Kit with the Ribo-Zero Gold Kit (Illumina Inc. USA)

tag: tissue

value: corpus callosum + neocortex

value: wild type

value: 3 weeks cuprizone plus siponimod


title: Brain_cuprizone 3wks + Siponimod_mouse 4


title: Control 4


title: Brain_cuprizone 3wks + Siponimod_mouse 3


title: p53KO-thymus_rep2


title: Brain_cuprizone 3wks_mouse 4

description:
0.25% cuprizone (w/w)
DEA_Vehicle_vs_Control.xlsx

value: 3 weeks cuprizon plus vehicle


title: 2uMButyroside D 1


title: Brain_cuprizone 3wks + Siponimod_mouse 1


title: Brain_cuprizone 3wks_mouse 5


title: Brain_cuprizone 3wks_mouse 2


title: Control 1


title: Brain_cuprizone 3wks_mouse 3


title: METTL3 Overexpressed BGC-823 Cell replicate2

description: Biological replicate 2 of 3. Lentiviral Stable Transfection for METTL3 Overexpression.

value: Gastric cancer epithelial METTL3 overexpressing cells


title: METTL3 Overexpressed BGC-823 Cell replicate3

description: Biological replicate 3 of 3. Lentiviral Stable Transfection for METTL3 Overexpression.


title: Brain_cuprizone 3wks_mouse 1


title: Control 2


title: Brain_control_mouse 5

description:
standart chow
DEA_Vehicle_vs_Control.xlsx

value: no treatment


title: Brain_cuprizone 3wks + Siponimod_mouse 2


title: Brain_control_mouse 3


title: Brain_control_mouse 4


title: Brain_control_mouse 2


title: Brain_control_mouse 1


title: Transcriptome of P. falciparum 3D7 untreated (for PRQ 3D7 Bioreplicate 2 experiments). Technical replicate 2

city: Singapore

first: Zbynek

last: Bozdech

state: Singapore

address: 50 Nanyang Avenue

country: Singapore

institute: Nanyang Technological University

hyb_protocol: Equal amounts of labelled sample and reference cDNA were hybridized on the microarray chip using the Agilent hybridization system. Hybridizations were performed for 20 hours at 70°C in a rotating hybridization oven at 10rpm as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923:

scan_protocol: Microarray scanning was done using PowerScanner (Tecan) at 10uM resolution and with autogain PMT adjustments for both channels. Data was acquired using GenePix Pro v6.0 software (Axon Instruments) as described in Mok, S., M. Imwong et al (2011) Artemisinin resistance in Plasmodium falciparum is associated with an altered temporal pattern of transcription. BMC Genomics 12: 391.

data_processing:
Features with flag>0 and with median foreground intensity greater than 1.5 fold median background intensity for either channel passed quality control and were accepted.
Local  background correction using normexp, followed by lowess normalization across all features within array and quantile normalization between arrays were carried out to generate the normalized Log2 gene expression ratios.
Background corrected and normalized log2 transformed ratios (Cy5/Cy3) of the RNA sample/3D7 RNA reference pool.

organism: Plasmodium falciparum

source_name: In vitro culture, asexual blood stage, laboratory strain 3D7, treated with antimalarial

label_protocol: Reverse transcription and cDNA synthesis were done following modifed Smart-Seq2 protocol (Picelli, S., Faridani, O., Björklund, Å. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat Protoc 9, 171–181 (2014)). Synthesis of aminoallyl-coupled cDNA and labeling of samples with Cy fluorophore (GE Healthcare) were carried out as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

growth_protocol: P. falciparum strain 3D7 and Dd2 strains was obtained from BEI Resources and cultured under standard conditions in RPMI1640 media. Prior to drug treatment, parasites were double-synchronized with 5% sorbitol solution to achieve a synchrony of +/- 6 hours and cultured under constant agitation

extract_protocol: Total RNA was extracted using Trizol following manufacturer's instructions and as described in Bozdech, Z., S. Mok & A. P. Gupta, (2013) DNA microarray-based genome-wide analyses of Plasmodium parasites. Methods in molecular biology 923: 189-211.

treatment_protocol: Parasite culture was divided into 10 well in two 6-well plates with each well containing 6 mL of culture at 3% parasitaemia and 2% hematocrit and treated with 4-fold dilution series of CQ (10 µM top concentration), MK4815 (20 µM top concentration), MFQ (10 µM top concentration), primaquine (50 µM), and an equivalent volume of DMSO at 0.1% concentration and incubated for 6 hours at 37°C with 5% CO2, 3% O2, and 92% N2. Following incubation, the samples were harvested and centrifuged at 2,500 rpm for 5 minutes. Supernatant was removed and 1 mL of trizol was added the the pellets

tag: treatmant

value: PRQ Control

source_name: In vitro culture, asexual blood stage, laboratory strain 3D7, mixture of equal amounts of RNA harvested every 6 hours over the 48-hour parasite's intraerythrocytic life cycle

tag: condition

value: RNA reference pool


title: Transcriptome of P. falciparum 3D7 treated with 781 nM PRQ for 6 hours. Bioreplicate 2

value: PRQ 781 nM


title: Transcriptome of P. falciparum 3D7 untreated (for PRQ 3D7 Bioreplicate 2 experiments). Technical replicate 1


title: Transcriptome of P. falciparum 3D7 treated with 48 nM PRQ for 6 hours. Bioreplicate 2

value: PRQ 48 nM


title: Transcriptome of P. falciparum 3D7 treated with 195 nM PRQ for 6 hours. Bioreplicate 2

value: PRQ 195 nM


title: Transcriptome of P. falciparum 3D7 treated with 12 nM PRQ for 6 hours. Bioreplicate 2

value: PRQ 12 nM


title: Transcriptome of P. falciparum 3D7 treated with 3125 nM PRQ for 6 hours. Bioreplicate 2

value: PRQ 3125 nM


title: Transcriptome of P. falciparum 3D7 untreated (for PRQ 3D7 Bioreplicate 1 experiments). Technical replicate 1


title: Transcriptome of P. falciparum 3D7 untreated (for PRQ 3D7 Bioreplicate 1 experiments). Technical replicate 3


title: Transcriptome of P. falciparum 3D7 treated with 48 nM PRQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 0.8 nM PRQ for 6 hours. Bioreplicate 2

value: PRQ 0.8 nM


title: Transcriptome of P. falciparum 3D7 treated with 781 nM PRQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 untreated (for PRQ 3D7 Bioreplicate 1 experiments). Technical replicate 2


title: Transcriptome of P. falciparum 3D7 treated with 3 nM PRQ for 6 hours. Bioreplicate 1

value: PRQ 3 nM


title: Transcriptome of P. falciparum 3D7 treated with 50000 nM PRQ for 6 hours. Bioreplicate 1

value: PRQ 50000 nM


title: Transcriptome of P. falciparum 3D7 treated with 195 nM PRQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 12500 nM PRQ for 6 hours. Bioreplicate 1

value: PRQ 12500 nM


title: Transcriptome of P. falciparum 3D7 treated with 3125 nM PRQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 0.8 nM PRQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 12 nM PRQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 untreated (for MFQ 3D7 Bioreplicate 2 experiments). Technical replicate 3

value: MFQ Control


title: Transcriptome of P. falciparum 3D7 untreated (for MFQ 3D7 Bioreplicate 2 experiments). Technical replicate 2


title: Transcriptome of P. falciparum 3D7 untreated (for MFQ 3D7 Bioreplicate 2 experiments). Technical replicate 1


title: Transcriptome of P. falciparum 3D7 treated with 50000 nM PRQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 9.8 nM MFQ for 6 hours. Bioreplicate 2

value: MFQ 9.8 nM


title: Transcriptome of P. falciparum 3D7 treated with 12500 nM PRQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 625 nM MFQ for 6 hours. Bioreplicate 2

value: MFQ 625 nM


title: Transcriptome of P. falciparum 3D7 treated with 39 nM MFQ for 6 hours. Bioreplicate 2

value: MFQ 39 nM


title: Transcriptome of P. falciparum 3D7 treated with 2500 nM MFQ for 6 hours. Bioreplicate 2

value: MFQ 2500 nM


title: Transcriptome of P. falciparum 3D7 treated with 3 nM PRQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 2.5 nM MFQ for 6 hours. Bioreplicate 2

value: MFQ 2.5 nM


title: Transcriptome of P. falciparum 3D7 treated with 156 nM MFQ for 6 hours. Bioreplicate 2

value: MFQ 156 nM


title: Transcriptome of P. falciparum 3D7 treated with 0.6 nM MFQ for 6 hours. Bioreplicate 2

value: MFQ 0.6 nM

value: RNA reference pool


title: Transcriptome of P. falciparum 3D7 untreated (for MFQ 3D7 Bioreplicate 1 experiments). Technical replicate 3


title: Transcriptome of P. falciparum 3D7 treated with 0.2 nM MFQ for 6 hours. Bioreplicate 2

value: MFQ 0.2 nM


title: Transcriptome of P. falciparum 3D7 treated with 9.8 nM MFQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 625 nM MFQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 156 nM MFQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 39 nM MFQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 0.2 nM MFQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 2500 nM MFQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 untreated (for MK4815 Dd2 Bioreplicate 2 experiments). Technical replicate 3

source_name: In vitro culture, asexual blood stage, laboratory strain Dd2, treated with antimalarial

value: MK4815 Control


title: Transcriptome of P. falciparum Dd2 untreated (for MK4815 Dd2 Bioreplicate 2 experiments). Technical replicate 2


title: Transcriptome of P. falciparum 3D7 treated with 2.5 nM MFQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 0.6 nM MFQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 untreated (for MK4815 Dd2 Bioreplicate 2 experiments). Technical replicate 1


title: Transcriptome of P. falciparum Dd2 treated with 78 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 10000 nM MFQ for 6 hours. Bioreplicate 1

value: MFQ 10000 nM


title: Transcriptome of P. falciparum Dd2 treated with 5000 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum Dd2 treated with 4.9 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum Dd2 treated with 20000 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum Dd2 treated with 312 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum Dd2 treated with 19 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum Dd2 treated with 1.2 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 untreated (for MFQ 3D7 Bioreplicate 1 experiments). Technical replicate 1


title: Transcriptome of P. falciparum Dd2 treated with 0.3 nM MK-4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum Dd2 untreated (for MK4815 Dd2 Bioreplicate 1 experiments). Technical replicate 2


title: Transcriptome of P. falciparum 3D7 untreated (for MFQ 3D7 Bioreplicate 1 experiments). Technical replicate 2


title: Transcriptome of P. falciparum Dd2 untreated (for MK4815 Dd2 Bioreplicate 1 experiments). Technical replicate 3


title: Transcriptome of P. falciparum Dd2 untreated (for MK4815 Dd2 Bioreplicate 1 experiments). Technical replicate 1


title: Transcriptome of P. falciparum Dd2 treated with 5000 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 78 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 312 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 1250 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 19 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 20000 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 1250 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 untreated (for MK4815 3D7 Bioreplicate 2 experiments). Technical replicate 2


title: Transcriptome of P. falciparum Dd2 treated with 0.3 nM MK-4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 4.9 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 1.2 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 untreated (for MK4815 3D7 Bioreplicate 2 experiments). Technical replicate 3


title: Transcriptome of P. falciparum 3D7 treated with 78 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 5000 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 untreated (for MK4815 3D7 Bioreplicate 2 experiments). Technical replicate 1


title: Transcriptome of P. falciparum 3D7 treated with 312 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 1.2 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 1250 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 4.9 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 19 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 20000 nM MK4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 0.3 nM MK-4815 for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 4.9 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 untreated (for MK4815 3D7 Bioreplicate 1 experiments). Technical replicate 1


title: Transcriptome of P. falciparum 3D7 treated with 78 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 untreated (for MK4815 3D7 Bioreplicate 1 experiments). Technical replicate 2


title: Transcriptome of P. falciparum 3D7 treated with 312 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 5000 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 20000 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 19 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 1250 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 untreated (for CQ Dd2 Bioreplicate 2 experiments). Technical replicate 2

value: CQ Control


title: Transcriptome of P. falciparum Dd2 untreated (for CQ Dd2 Bioreplicate 2 experiments). Technical replicate 3


title: Transcriptome of P. falciparum Dd2 treated with 625 nM CQ for 6 hours. Bioreplicate 2

value: CQ 625 nM


title: Transcriptome of P. falciparum Dd2 untreated (for CQ Dd2 Bioreplicate 2 experiments). Technical replicate 1


title: Transcriptome of P. falciparum 3D7 treated with 0.3 nM MK-4815 for 6 hours. Bioreplicate 1


title: P45

city: Chongqing

first: He

last: Xiao

state: Chongqing

address: No. 10, Changjiang Branch Road, Yuzhong District, Chongqing 400042, China

department: Department of Cancer Center

institute: Daping Hospital, Army Medical University

description: Resected tissue after nCRT without complete pathological response

data_processing:
Raw fastq files were assessed by FastQC (v0.11.5).
The adapters and low-quality sequence were trimmed by cutadapt (v-1.13).
The gene expression quantification analysis was performed by Salmon (v-0.9.1) based on the reference genome hg38 (GRCh38) with gene annotation from GENCODE (release 28).
The raw counts of reads mapped to each gene were extracted and used for subsequent analysis.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Tissue sample

extract_protocol:
Total RNA was extracted from 27 locally advanced rectal cancer tissues. Ribosomal RNA were further removed.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Tissue sample

tag: disease state

value: LARC

tag: group

value: npCR


title: P38


title: Transcriptome of P. falciparum Dd2 treated with 39 nM CQ for 6 hours. Bioreplicate 2

value: CQ 39 nM


title: Transcriptome of P. falciparum Dd2 treated with 9.8 nM CQ for 6 hours. Bioreplicate 2

value: CQ 9.8 nM


title: Transcriptome of P. falciparum 3D7 untreated (for MK4815 3D7 Bioreplicate 1 experiments). Technical replicate 3


title: P36


title: P25


title: P22


title: Transcriptome of P. falciparum Dd2 treated with 2.5 nM CQ for 6 hours. Bioreplicate 2

value: CQ 2.5 nM


title: P14


title: P18


title: Transcriptome of P. falciparum Dd2 treated with 10000 nM CQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum Dd2 treated with 156 nM CQ for 6 hours. Bioreplicate 2

value: CQ 156 nM


title: P5


title: P34

description: Resected tissue after nCRT with complete pathological response

value: pCR


title: Transcriptome of P. falciparum Dd2 treated with 0.6 nM CQ for 6 hours. Bioreplicate 2

value: CQ 0.6 nM


title: Transcriptome of P. falciparum Dd2 treated with 0.2 nM CQ for 6 hours. Bioreplicate 2

value: CQ 0.2 nM


title: Transcriptome of P. falciparum 3D7 treated with 1.2 nM MK4815 for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 untreated (for CQ Dd2 Bioreplicate 1 experiments). Technical replicate 3


title: Transcriptome of P. falciparum Dd2 untreated (for CQ Dd2 Bioreplicate 1 experiments). Technical replicate 2


title: P33


title: Transcriptome of P. falciparum Dd2 treated with 2500 nM CQ for 6 hours. Bioreplicate 2

value: CQ 2500 nM


title: P32


title: Transcriptome of P. falciparum Dd2 untreated (for CQ Dd2 Bioreplicate 1 experiments). Technical replicate 1

value: RNA reference pool


title: Transcriptome of P. falciparum Dd2 treated with 9.8 nM CQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 625 nM CQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 39 nM CQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 2500 nM CQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 2.5 nM CQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 156 nM CQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 10000 nM CQ for 6 hours. Bioreplicate 1


title: P6


title: Transcriptome of P. falciparum Dd2 treated with 0.2 nM CQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum Dd2 treated with 0.6 nM CQ for 6 hours. Bioreplicate 1


title: P35

description: Biopsy tissue prior to nCRT

value: Pre


title: P30

description: Biopsy tissue prior to nCRT


title: P26

description: Biopsy tissue prior to nCRT


title: Transcriptome of P. falciparum 3D7 treated with 10000 nM MFQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 untreated (for CQ 3D7 Bioreplicate 2 experiments). Technical replicate 2


title: Transcriptome of P. falciparum 3D7 treated with 9.8 nM CQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 untreated (for CQ 3D7 Bioreplicate 2 experiments). Technical replicate 1


title: Transcriptome of P. falciparum 3D7 untreated (for CQ 3D7 Bioreplicate 2 experiments). Technical replicate 3


title: P1


title: P40

description: Biopsy tissue prior to nCRT


title: P13


title: P42

description: Biopsy tissue prior to nCRT


title: P27


title: P46

description: Biopsy tissue prior to nCRT


title: P43

description: Biopsy tissue prior to nCRT


title: P21


title: P47

description: Biopsy tissue prior to nCRT


title: P11


title: P41

description: Biopsy tissue prior to nCRT


title: P17


title: Transcriptome of P. falciparum 3D7 treated with 10000 nM CQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 625 nM CQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 39 nM CQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 156 nM CQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 2.5 nM CQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 2500 nM CQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 untreated (for CQ 3D7 Bioreplicate 1 experiments). Technical replicate 2


title: Transcriptome of P. falciparum 3D7 untreated (for CQ 3D7 Bioreplicate 1 experiments). Technical replicate 3


title: Transcriptome of P. falciparum 3D7 treated with 0.6 nM CQ for 6 hours. Bioreplicate 2


title: Transcriptome of P. falciparum 3D7 treated with 0.2 nM CQ for 6 hours. Bioreplicate 2


title: Liver, tissue resident memory, mouse E

city: Davis

first: Claire

last: Depew

state: CA

address: 4115 Primate Drive

institute: University of California Davis

description: ELT

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using htstream
Trimmed sequence reads were mapped to GrCM39 reference genome using star with default parameters
Quantification of gene expression was generated using htseq-count with "-s yes -m union -nonunique=none" parameter
Assembly: mm10
Supplementary files format and content: normalized counts in text document

source_name: Liver

extract_protocol:
Infection protocol: IFNy-YFP reporter mice were infected with 5E5 CFU of Salmonella enterica serovar Typhimurium ΔaorA intravenously. Livers and spleens were collected at 45 days post infection
sort protocol: CD4 T cells were enriched by MACs magnetic beads. Memory population was sorted with a BD FACS Aria and TRM were defined as CD69+ YFP+ CD4 T cells, TEM were defined as CD69- YFP+ CD4 T cells
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using QuantSeq FWD kit following manufacturers protocol

value: Liver

value: tissue resident memory CD4 T cell

tag: time

value: day 45 post infection


title: Liver, effector memory, mouse E

description: ELE

value: effector memory CD4 T cell


title: Spleen, effector memory, mouse E

description: ESE

source_name: Spleen

value: Spleen


title: Transcriptome of P. falciparum 3D7 treated with 156 nM CQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 9.8 nM CQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 untreated (for CQ 3D7 Bioreplicate 1 experiments). Technical replicate 1

value: CQ Control


title: Transcriptome of P. falciparum 3D7 treated with 2.5 nM CQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 39 nM CQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 2500 nM CQ for 6 hours. Bioreplicate 1


title: Transcriptome of P. falciparum 3D7 treated with 625 nM CQ for 6 hours. Bioreplicate 1

value: CQ 625 nM


title: Transcriptome of P. falciparum 3D7 treated with 10000 nM CQ for 6 hours. Bioreplicate 1


title: K562THZ531_chase6h_rep1

city: Ann Arbor

first: Brian

last: Magnuson

state: MI

address: 1500 East Medical Center Drive

institute: University of Michigan

description:
bru-labeled RNA
K562THZ531 bruChase-seq 6h replicate 1

data_processing:
Illumina Casava v1.8.2 software used for basecalling.
Reads were trimmed using BBDuk (BB Tools v38.46). The bundled adapter sequences and following parameters were used. Single-end reads: ktrim=r, mink=5, minlength=20, hdist=1.  The k parameter was set to 30 or the length of the smallest adapter sequence, whichever is larger.  Paired-end reads: ktrim=r, mink=11, hdist=1, k=31.
Reads were pre-mapped to the ribosomal RNA (rRNA) repeating unit (GenBank U13369.1) and the mitochondrial and EBV genomes (from the hg38 analysis set) using Bowtie2 (2.3.3).
Reads that did not align with rRNA, mitochondrial and EBV genomes were subsequently mapped to human genome build hg38/GRCh38 using STAR (v 2.5.3a) and a STAR index created from GENCODE annotation version 27.
Coverages were determined using bedtools 2 v2.28.0 as (1 / read length) for each base in the genome. These base coverages were used to obtain pseudo-read counts in strand-specific regions of interest using bedtools intersect. Reads Per Kilobase per Megabase of library size (RPKM) were calculated for meta-transcripts ("genes") defined by merging exons and intervening intronic spaces from all isoforms of a gene in the GENCODE v27 "basic" annotation. Genes were quantified by summing pseudo-counts falling within the features (exons and intronic spaces) and normalized by the effective gene length (sum of feature lengths) and by the size of the library (uniquely mapped read count).
Genome_build: hg38
Supplementary_files_format_and_content: The columns of the genes.bed indicate: (1) chromosome; (2) start; (3) end; (4) name; (5) strand; (6) effective gene length (7) read count (8) RPKM

growth_protocol: hTERT immortalized human diploid foreskin fibroblasts (HF1) (a gift from Dr. Mary Davis, Department of Radiation Oncology, University of Michigan, Ann Arbor) were grown in MEM growth media (Minimal Essential Medium, 10% FBS, 1x MEM Amino Acids (ThermoFisher Scientific), 1x Non-Essential Amino Acids (ThermoFisher Scientific), 2 mM l-glutamine, 1X antibiotic–antimycotic (Invitrogen), 1x MEM vitamin mixture, 0.15% (w/v) sodium bicarbonate. K562 cells (ATCC) were grown in suspension in IMDM with 10% FBS. HeLa cells (Millipore-SIGMA) DMEM, 10% FBS, 100 U/mL penicillin and 100 U/mL streptomycin. HeLa-AS cells were grown in DMEM. THZ531 (MedChemExpress) and 1-NM-PP1 (Axon Medchem) were dissolved in DMSO.

extract_protocol:
Cells were lysed directly in TRIzol followed by isolation of total RNA. For experiments involving HF1, K562, and HeLa treated with THZ531 (including controls), the isolated total RNA was further treated with DNAse (TURBO DNA-free Kit; Invitrogen) and a spike-in cocktail of Bru-labeled and unlabeled RNA was mixed in with total RNA. Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences).
Strand-specific libraries for the HeLa-AS experiments were prepared from a modified protocol using the TruSeq Kit (Illumina) as previously described (Paulsen et al., 2014; Paulsen et al., 2013). This protocol used single-index barcoded ligation adapters and universal primers for PCR. For the experiments in HF1, K562, and HeLa cells involving THZ531 treatment, a spike-in cocktail of Bru-labeled and unlabeled RNA (described below) was mixed in with total RNA prior to Bru-RNA IP.  Ribosomal RNA was reduced via QiaSeq FastSelect (Qiagen) prior to first strand synthesis. These strand-specific libraries were made using a universal ligation adapter and dual-index, barcoded primers for PCR. Size selection for all libraries was via agarose gel excision.
Bru-seq

treatment_protocol: For the Bru-seq experiments, cells were mock-treated or treated in conditioned media with 400 nM THZ531 (HF1, K562 and HeLa) or 10 µM 1-NM-PP1 (HeLa-AS) for 60 min where bromouridine (Bru) (Aldrich) was included during the last 30 minutes at a final concentration of 2 mM to label nascent RNA. For BruChase-Seq experiments, cells were treated as for Bru-seq above but then at the conclusion of the Bru-labeling, cells were washed in PBS and conditioned media containing 20 mM uridine were added back together with either 400 nM THZ531, 10 µM 1-NM-PP1 or no drug during the chase for 2 hours in HeLa and HeLa-AS cells and 6 hours in HF1 and K562 cells.

tag: bru labeling time

value: 0.5 hours

tag: assay

value: bruChase-seq

tag: time between end of bru labeling and rna extraction

value: 6 hours

tag: labeling agent

value: Bromouridine (Bru)

tag: spike-ins

value: Bru-seq spike-in cocktail 0.25x


title: Spleen, effector memory, mouse D

description: DSE

tag: cell type


title: Transcriptome of P. falciparum 3D7 treated with 0.2 nM CQ for 6 hours. Bioreplicate 1


title: K562THZ531_bruseq_rep1

description:
bru-labeled RNA
K562THZ531 bruseq replicate 1

tag: treatment

value: bruseq

value: 0 hours

value: Bru-seq spike-in cocktail 1x


title: Liver, tissue resident memory, mouse D

description: DLT


title: K562_bruseq_rep1

description:
bru-labeled RNA
K562 bruseq replicate 1

value: DMSO


title: Transcriptome of P. falciparum 3D7 treated with 0.6 nM CQ for 6 hours. Bioreplicate 1

tag: strain

value: CQ 0.6 nM

value: RNA reference pool


title: K562_chase6h_rep1

description:
bru-labeled RNA
K562 bruChase-seq 6h replicate 1


title: HF1THZ531_chase6h_rep1

description:
bru-labeled RNA
HF1THZ531 bruChase-seq 6h replicate 1


title: Spleen, effector memory, mouse C

description: CSE


title: HF1_chase6h_rep1

description:
bru-labeled RNA
HF1 bruChase-seq 6h replicate 1


title: HF1THZ531_bruseq_rep1

description:
bru-labeled RNA
HF1THZ531 bruseq replicate 1


title: helaASDMSO_chase2h_rep3

description:
bru-labeled RNA
HeLaASDMSO bruChase-seq 2h replicate 3

source_name: HeLa

value: 2 hours


title: Clostridioides difficile monoculture rep2

organism: Clostridioides difficile

source_name: Clostridioides difficile

tag: media

value: BHIS


title: Liver, effector memory, mouse D

description: DLE

value: Liver

value: effector memory CD4 T cell

value: day 45 post infection


title: Clostridioides difficile monoculture rep3


title: Clostridioides difficile monoculture rep1


title: Liver, tissue resident memory, mouse C

description: CLT

value: tissue resident memory CD4 T cell


title: helaASDMSO_chase2h_rep2

description:
bru-labeled RNA
HeLaASDMSO bruChase-seq 2h replicate 2

value: 0.5 hours


title: Phb1 WT 1

city: Rockville

first: Bin

last: Gao

state: MD

address: 5625 Fishers Lane, Room 2S-33

institute: NIAAA

data_processing:
FASTQC
TRIMMOMATIC
hisat2
samtools
featureCounts
DEseq2
Assembly: Mus_musculus.GRCm38.102.gtf
Supplementary files format and content: tab-delimited text file representing counts

extract_protocol:
Trizol
PolyA selection for mRNA species (eukaryotic)

tag: Sex

value: male

tag: genotype

value: WT

value: HFD 3 months


title: Phb1 WT 6

tag: tissue


title: Phb1 WT 4


title: Phb1 WT 5


title: Phb1 KO 5

value: Phb1 KO


title: Phb1 WT 3


title: Phb1 KO 2


title: Phb1 WT 2


title: Phb1 KO 6


title: Phb1 KO 4


title: Phb1 KO 1


title: Phb1 KO 3


title: helaASDMSO_chase2h_rep1

description:
bru-labeled RNA
HeLaASDMSO bruChase-seq 2h replicate 1

value: bruChase-seq

value: Bromouridine (Bru)


title: HF1_bruseq_rep1

description:
bru-labeled RNA
HF1 bruseq replicate 1

value: bruseq

value: 0 hours

value: Bru-seq spike-in cocktail 1x


title: NTC-20200924

organism: blank sample

source_name: No tmeplate control

tag: sample type

value: No tmeplate control


title: helaTHZ531_chase2h_rep1

description:
bru-labeled RNA
HeLaTHZ531 bruChase-seq 2h replicate 1

value: 2 hours


title: helaASDMSO_bruseq_rep2

description:
bru-labeled RNA
HeLaASDMSO bruseq replicate 2

value: DMSO


title: NTC-20200923


title: helaTHZ531_bruseq_rep1

description:
bru-labeled RNA
HeLaTHZ531 bruseq replicate 1


title: Spleen, effector memory, mouse B

description: BSE

value: Spleen


title: Liver, effector memory, mouse C

description: CLE

value: Liver

value: effector memory CD4 T cell


title: helaASDMSO_bruseq_rep1

description:
bru-labeled RNA
HeLaASDMSO bruseq replicate 1


title: hela_chase2h_rep1

description:
bru-labeled RNA
HeLa bruChase-seq 2h replicate 1


title: Enterococcus faecalis monoculture rep3

organism: Enterococcus faecalis

source_name: Enterococcus faecalis

value: BHIS


title: Liver, tissue resident memory, mouse B

description: BLT

value: tissue resident memory CD4 T cell

value: day 45 post infection


title: hela_bruseq_rep1

description:
bru-labeled RNA
HeLa bruseq replicate 1

value: 0.5 hours


title: Spleen, effector memory, mouse A

description: ASE


title: Liver, effector memory, mouse B

description: BLE


title: Liver, tissue resident memory, mouse A

description: ALT


title: helaAS1NMPP1_bruseq_rep2

description:
bru-labeled RNA
HeLaAS1NMPP1 bruseq replicate 2


title: Enterococcus faecalis monoculture rep2


title: Liver, effector memory, mouse A

description: ALE


title: helaAS1NMPP1_chase2h_rep3

description:
bru-labeled RNA
HeLaAS1NMPP1 bruChase-seq 2h replicate 3


title: helaAS1NMPP1_chase2h_rep2

description:
bru-labeled RNA
HeLaAS1NMPP1 bruChase-seq 2h replicate 2


title: helaAS1NMPP1_chase2h_rep1

description:
bru-labeled RNA
HeLaAS1NMPP1 bruChase-seq 2h replicate 1


title: Enterococcus faecalis monoculture rep1


title: helaAS1NMPP1_bruseq_rep1

description:
bru-labeled RNA
HeLaAS1NMPP1 bruseq replicate 1


title: KO-1

first: Neha

last: Shrestha

address: 1000 Wall Street

data_processing:
Cell ranger (v.3.0.0)  was used to QC and generate filtered gene matrices
Single-cell RNA seq data was processed by Seurat package (v.2.3.4).
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files contain UMI count matrices from single cell RNA-seq.

source_name: Islet

growth_protocol: Following isolation, islets were recovered in 11mM RPMI overnight.

extract_protocol:
To dissociate islets into single cells, islets were incubated in trypsin for 15 minutes at 37 degree celcius.
RNA libraries were prepared for sequencing using standard 10X genomics protocols

tag: age

value: 7 weeks

value: Sel1L knockout


title: KO-2


title: WT-2

value: wild type


title: WT-1


title: NTC-20200922


title: 1016A h-ASTROs, replicate 1, scRNAseq

city: Cambridge

first: Matthew

middle: Thomas

last: Tegtmeyer

state: MA

address: 75 Ames St

department: Stanley Center

institute: Broad Institute

description: 10x Genomics

data_processing:
Raw sequence data was demultiplexed and aligned following the standard Drop-Seq protocol (Macosko et al., 2015)
Human experiments were aligned to the GRCh38 reference and Ensembl v89 gene models. Sequencing reads were then filtered to reads that mapped at high quality (MQ>=10) to the human genome
Matrices were built from 10X Chromium Single Cell 3’ Reagents V3 as described above. Any barcode with less than 200 genes and combined UMI matrices were used for downstream analysis using Seurat (v4.0.2) (Stuart et al., 2019).
The matrix was then processed via the Seurat pipeline by using SCTransform on a merged object running the PreSCTIntegration() function according to the sctransform integration pipeline (Hafemeister and Satija, 2019)
Assembly: GRCh38 reference and Ensembl v89 gene models

growth_protocol: Astrocytes differentiated using the protocol described in Rapino et. al, Stem Cell Reports 2022 were plated on PLL coated 6 wells and culture in complete astrocytes media (AM scienCell Catalogue number 1801)

extract_protocol:
Cells were washed once with PBS1X and incubated with Tripsin 0.25% for 5 minutes. After cells were detached they were colleced in faclon tube, pun down at 300g for 3 minutes and resuspended in PBS
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

treatment_protocol: No treatment

value: stem cell derived astrocytes

tag: cell line


title: H1 h-ASTROs, replicate2, scRNAseq

description: 10x Genomics


title: H1 h-ASTROs, replicate1, scRNAseq

description: 10x Genomics


title: 1016A h-ASTROs, replicate 3, scRNAseq

description: 10x Genomics


title: Hues8  h-ASTROs, replicate 2, scRNAseq

description: 10x Genomics


title: 1016A h-ASTROs, replicate 2, scRNAseq

description: 10x Genomics


title: Hues8  h-ASTROs, replicate 1, scRNAseq

description: 10x Genomics


title: Hues8  h-ASTROs, replicate 3, scRNAseq

description: 10x Genomics


title: BCG_LysateStimulated3

status: Public on Sep 16 2022

city: Hamilton

first: Zhou

last: Xing

state: Ontario

address: MDCL building, 1280 Main St W

department: Division of Respirology

country: Canada

institute: McMaster University

data_processing:
Raw sequence data were exported to FASTQ format and were filtered based on quality scores.
Next the reads were mapped to  the UCSC/mm10 reference version using HISAT2.
The counts were obtained by using ht-seq count with the “intersection-strict” option.
Counts were transformed with TMM transformation and then normalized with VOOM.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing log2 normalized values for each Sample
Supplementary files format and content: Zhou_RNAseq_Jun2019_VOOM-TMM.csv

source_name: BCG (S)

extract_protocol: RNA extraction protocol not provided.

treatment_protocol: Mice were vaccinated sub cutaneously with BCG (BCG) or carrier (PBS). At 5 weeks post-vaccination, airway alveolar macrophages isolated by bronchoalveolar lavage (BAL) was cultured in the presence (S) or absence (US) of stimulation with M. tuberculosis whole cell lysate for 16 h. Isolated RNA from the cultured cells were subjected to transcriptional analysis.

value: Alveolar macrophage

value: BCG (stimulated)


title: BCG_LysateStimulated1


title: BCG_LysateStimulated2


title: Naive_LysateStimulatedi3

source_name: PBS (S)

value: PBS (stimulated)


title: Naive_LysateStimulatedi2


title: BCG_Unstimulated1

source_name: BCG (US)

value: BCG (unstimulated)


title: BCG_Unstimulated3


title: Naive_LysateStimulatedi1


title: Naive_Unstimulated1

source_name: PBS (US)

value: PBS (unstimulated)


title: Naive_Unstimulated2


title: Naive_Unstimulated3


title: anti-CD40L treated LNSC scRNA-seq

city: BALTIMORE

first: yang

last: song

address: 670 W. Baltimore St.

institute: UNIVERSITY OF MARYLAND IN BALTIMORE

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.1.0.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: lymph nodes

extract_protocol:
C57BL/6 mice received one dose of 250 ug anti-CD40L i.v. for one day. After enzymatic digestion of the lymph nodes (LNs)from  C57BL/6 mice received one dose of 250 ug anti-CD40L i.v. for one day, CD45- cells were purified with the CD45 negative selection beads and were stained with anti-mouse CD45 before sorting for viable CD45- cells.
C57BL/6 mice received one dose of 250 ug anti-CD40L i.v. for one day lymph node stromal cells were isolated for scRNA-seq, more than 2x104 cells were run on the 10X Chromium Controller (10X Genomics) to partition single cells with uniquely barcoded beads and processed for sequencing library preparation using the Chromium Single Cell 3’ Reagent Kit. cDNA libraries were sequenced on a NovaSeq 6000 sequencing system.

value: lymph nodes

value: stromal cells


title: MV.RV1.NI.4_S4

data_processing:
Raw sequence data were exported to FASTQ format and were filtered based on quality scores.
Next the reads were mapped to  the UCSC/mm10 reference version using HISAT2.
The counts were obtained by using ht-seq count with the “intersection-strict” option.
Counts were transformed with TMM transformation and then normalized with VOOM.
Assembly: mm10
Supplementary files format and content: tab-delimited text file containing log2 normalized values for each Sample
Supplementary files format and content: Zhou_RNAseq_Apr2022_VOOM-TMM.csv

source_name: DW (S)

treatment_protocol: A mix of L-carnitine and butyrate hydrochloride was introduced to the drinking water (DW+M) of a group of naïve animals for a period of 3 weeks and as control, other animals received drinking water without supplements (DW). Alveolar macrophages were obtained by bronchoalveolar lavage and cultured in the presence (S) or absence (US) of stimulation with M. tuberculosis whole cell lysate for 16 h. Isolated RNA from the cultured cells were subjected to transcriptional analysis.

value: Regular drinking water (stimulated)


title: MV.RV1.NI.12_S12

source_name: DW+M (S)

value: Metabolite supplemented drinking water  (stimulated)


title: MV.RV1.NI.8_S8

source_name: DW+M (US)

value: Metabolite supplemented drinking water  (unstimulated)


title: MV.RV1.NI.11_S11


title: MV.RV1.NI.7_S7


title: MV.RV1.NI.10_S10


title: MV.RV1.NI.5_S5


title: MV.RV1.NI.3_S3

source_name: DW (US)

value: Regular drinking water (unstimulated)


title: MV.RV1.NI.1_S1


title: MV.RV1.NI.6_S6


title: HCC-T

city: Kanagawa

first: Satoko

last: Takizawa

state: Kamakura

institute: Toray Industries, Inc.

hyb_protocol: Hybridization solution of the Agilent SurePrint G3 Human Gene Expression v3 8×60K Microarray Kit was added and hybridized for 17 h at 65°C in an Agilent hybridization oven. Hybridization buffer and washing protocol was attached in the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (V 6.5, 2010, Agilent Technology, Inc.).

scan_protocol: Agilent Microarray Scanner D (Agilent Technologies, Inc.) was used for scanning.

data_processing:
Fluorescent value gProcessedSignal is degitalized as the data using Agilent Feature Extraction software v11.0 (Agilent Technologies, Inc.).
Each fluorescent raw value was run in batches from standardization (in the sample direction by Z-score) to principal component analysis.

source_name: Primary hepatobiliary tumor

label_protocol: 200 ng of total RNA from each sample was linearly amplified and labeled with Cy3-dCTP.

extract_protocol: Mean 28.2 ul of total RNA from tissue samples was extracted and purified using an RNeasy mini kit (Qiagen, Inc.).

tag: histology

value: Hepatocellular carcinoma, tumor part

tag: mean age

tag: male/female


title: HCC-NT

value: Hepatocellular carcinoma, non-tumor part


title: YCC-T

value: Cholangiocarcinoma (younger than 40s), tumor part


title: Be-T

value: Inflammatory pseudotumor (benign), Angiomyolipoma (benign), Adenomyomatous hyperplasia of gallbladder (benign), Focal nodular hyperplasia of liver (benign); tumor part


title: MV.RV1.NI.2_S2


title: Ascl1-Hnf1a-Myod1-Oct4, 48h biol rep 2

city: Planegg-Martinsried

first: Bob

last: Hersbach

address: Großhaderner Str. 9

department: Institute of Stem Cell Research

institute: Helmholtz Zentrum Munich

description: 10x Genomics v2

data_processing:
For the alignment of reads we used the sequences and annotation files for the Mouse genome (GRCm38) from Ensembl (release 97).
The synthetic transcription factors and reporter sequences and a custom generated annotation were appended to the genome sequence and annotation. The Cell Ranger software (version 3.1.0) run with the command ‘cellranger mkref’ created an index of the genome.
The Cell Ranger pipeline run with the command ‘cellranger count’ aligned the reads, generated QC metrics, estimated the number of valid barcodes and created the count matrices.
The command was executed with standard parameters, except that we adjusted the number of expected cells and the chemistry parameter accordingly
AnnData objects of the raw and filtered count matrices were created using the Python package Scanpy (Wolf, Angerer and Theis, 2018), version 1.4.4).
The alignment files (bam) were sorted by barcode using samtools (Li et al., 2009), version 1.10) and Velocyto ((la Manno et al., 2018), version 0.17.17) was run using the ‘velocyto run’ command with the filtered barcodes list from the Cell Ranger run.
Assembly: GRCm38
Supplementary files format and content: Raw and filtered CellRanger output in .h5 file format
Supplementary files format and content: Velocyto ouput containing spliced and unspliced read information in .loom format
Supplementary files format and content: Processed scRNA-seq data in .h5ad format

source_name: Skin

growth_protocol: DMEM (High Glucose), 10% fetal bovine serum,1x Sodium Pyruvate, 1 mM HEPES, 1x penicillin/streptomycin. Cells were cultured at 37C at 5% CO2.

extract_protocol: Library was performed according to the manufacter’s instructions (single cell 3’ v2/3.1 protocol, 10x Genomics). Briefly, MEFs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Skin

value: Mouse Embryonic fibroblasts

value: Doxycyline


title: Be-NT

value: Inflammatory pseudotumor (benign), Angiomyolipoma (benign), Adenomyomatous hyperplasia of gallbladder (benign), Focal nodular hyperplasia of liver (benign); non-tumor part


title: YCC-NT

value: Cholangiocarcinoma (younger than 40s), non-tumor part


title: CC-NT

value: Cholangiocarcinoma, non-tumor part


title: AF8368

city: Madrid

first: Jose Maria

middle: Moreno

last: Navarrete

state: (None)

address: Calle de Monforte de Lemos nº 5

country: Spain

institute: CIBER

data_processing:
RNA-seq reads mapped with STAR software v2.5.3a with ENCODE parameters.
Annotated genes quantified with RSEM v1.3.0
Assembly: GRCh38
Supplementary files format and content: Matrix with samples as columns and raw gene counts as rows

source_name: Small intestine - Jejunum

extract_protocol:
RNA purification was performed using RNeasy Lipid Tissue Mini Kit (QIAgen, Izasa SA, Barcelona, Spain)
RNA libraries were prepared using TruSeq Stranded total RNA kit (Ribozero)

value: Small intestine - Jejunum

tag: condition

value: morbidly obese


title: AF8367


title: AF8366


title: AF8365


title: BCG_Unstimulated2

value: Alveolar macrophage

value: BCG (unstimulated)


title: MV.RV1.NI.9_S9


title: AF8361


title: AF8359