title: KoD3-3

status: Public on Oct 13 2021

city: Greenville

first: Weihua

last: Huang

state: North Carolina

address: 600 Moye Blvd, Brody 7S-24

department: Pathology

institute: East Carolina University

data_processing:
Salmon (v0.8.1) for pseudo-alignment to Ensembl mouse reference transcriptome GRCm38
DESeq2 (v1.16.1) for differential gene expression
Genome_build: GRCm38 transcriptome
Supplementary_files_format_and_content: TPM in an Excel file

source_name: KO Day 3 Lungs

growth_protocol: Francisella tularensis Live Vaccine Strain (F. tularensis LVS) cultures were grown on Mueller-Hinton (MH) chocolate agar plates (BD Biosciences, San Jose, CA) supplemented with IsoVitaleX at 37°C with 5% CO2 or in MH broth (BD Biosciences, San Jose, CA) supplemented with ferric pyrophosphate and IsoVitaleX (BD Biosciences, San Jose, CA) at 37°C with shaking (160 rpm). A o.2 OD bacterial suspension was diluted to achieve 1x10(4)/20 microliter concentration and was used to infect mice.

extract_protocol:
Total RNA was extracted from the clarified supernatants using the Invitrogen PureLink RNA mini kit. DNA was eliminated from the samples by DNase treatment using Qiagen RNase-Free DNase.
TruSeq Stranded Total RNA Library Prep Kit with polyadenylation pull-down

treatment_protocol: Wild type C57BL/6 and Nlrp3-/- mice infected with 1 × 104 F. tularensis LVS were sacrificed on days 3 and 7 post-infection. Lungs were harvested aseptically from these mice and placed in excess of trizol.

tag: genotype

value: NLRP3 KO

tag: strain

tag: agent

value: infected by F. tularensis LVS

tag: time point

value: Day 3


title: E2F1 siRNA 0.1nM R1881 1 [R20-022; SBS20-004]

status: Public on Oct 14 2021

type: SRA

city: BUFFALO

first: Eduardo

last: Cortes

state: NY

address: ELM AND CARLTON STREETS

department: Biostatistics and Bioinformatics

country: USA

institute: ROSWELL PARK CANCER INSTITUTE

library_source: transcriptomic

data_processing:
Basecalls performed using CASAVA version 1.8.2
Sequenced reads were mapped to GRCh38 reference GENCODE annotation (p7) using tophat 2.0.13
TopHat aligned BAMs were merged using MergeSamFiles from Picard v1.97
Reads counts are obtained using featureCounts from SubRead (v1.6.4)
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

molecule: total RNA

organism: Homo sapiens

source_name: LNCaP_E2F1 siRNA_0.1nM R1881

growth_protocol: LNCaP prostate cancer cells were seeded in  androgen-deprived media (9% charcoal-stripped serum), next day cells were transfected with siRNA SmartPools targeting E2F1, or E2F2 or a non-targeting siRNA SmartPool using Lipofectamine 2000.

extract_protocol:
Cells were harvested 48h after treatment, RNA was isolated using Trizol and purified using RNAeasy columns.
RNA Libraries are prepared using the Illumina NextSeqTruSeq RNA Exome protocol and kit reagents.

treatment_protocol: 48h post transfection, cells were treated with 0.1nM of synthetic androgen R1881 or vehicle.

tag: cell line

value: LNCaP

tag: cell type

value: prostate cancer cells

tag: genotype/varaition

value: E2F1 siRNA

tag: treatment


title: KoD3-2

molecule: polyA RNA

organism: Mus musculus


title: KoD3-1


title: ICM-1-NMIN scRNA-seq

city: Beijing

first: Shengshou

last: Hu

address: No.167 North Lish Road

country: China

institute: Fuwai Hospital

data_processing:
scRNA-seq sequencing reads were aligned to human genome reference build hg38 with cellranger 3.0
bulk RNA-seq sequencing reads were aligned to human genome reference build hg38,  transcript per million (TPM) were calculated with RSEM software.
Genome_build: hg38
Supplementary_files_format_and_content: scRNA-seq expression matrix were uploaded as zipped file. In each zipped file, it contains barcodes.tsv.gz, features.tsv.gz and matrix.mtx.gz. T cell receptor sequencing had additional clonotype file and metrics_summary.csv files.

source_name: primary human-derived cells

growth_protocol: ACKR1+ endothelial cells derived from human explanted hearts were sorted by FACS and cultured in 0.1% gelatin-coated dishes with an endothelial cell medium complete kit (Sciencell, 1001).

extract_protocol:
cell pellete was collected and RNA was extracted using an RNeasy Mini kit (QIAGEN, 74104) by following the manufacturer’s protocol.
Libraries were prepared with an NEBNext Poly(A) mRNA Magnetic Isolation Module kit (NEB) and an NEBNext Ultra RNA Library Prep Kit for Illumina Paired-end Multiplexed Sequencing Library (NEB).

treatment_protocol: Human CXCL8 protein (R&D, 208-I-050) was added to stimulate ACKR1+ ECs at a final concentration of 8 ng/ml. Seventy-two hours after stimulation, the cells were harvested and washed twice with PBS.

value: CD45- cells

tag: tissue

value: heart

tag: tissue type

value: left ventricle, non-infarcted myocardium

tag: other

value: 3' scRNA-seq


title: WtD7-2

source_name: WT Day 7 Lungs

value: Wild Type

value: Day 7


title: WtD7-3


title: control siRNA vehicle 1 [R20-013; SBS20-001]

source_name: LNCaP_control siRNA_ETOH

value: control siRNA

value: ETOH


title: WtD3-2

source_name: WT Day 3 Lungs


title: WtD3-1


title: WtD3-3


title: enzalutamide_6hr_rep2

type: RNA

city: Darlinghurst

first: Hui-Ming

last: Lin

state: NSW

address: 384 Victoria Street

country: Australia

institute: Garvan Institute of Medical Research

description: Gene expression data from C42B cells after 6 hour treatment with drug(s) or vehicle control

hyb_protocol: Following fragmentation, 2.3 ug of cRNA were hybridized on Clariom S arrays for 17 hr at 45C and 60 rpm as per Affymetrix Hybridisation Protocol. Arrays were washed and stained in the Affymetrix GeneChip Fluidics Station 450 ( Fluidics protocol FS450_0007).

scan_protocol: Arrays were scanned using the Affymetrix GCS3000 scanner, and Affymetrix GeneChip Command Console (AGCC) Scan Control software (version 4.0.0.1567).

data_processing: The data were analysed with Transcriptome Analysis Console software (version 4.02) with RMA as the normalisation method.

label: biotin

source_name: C42B cells treated with 10uM enzalutamide for 6 hours

label_protocol: Biotinylated cRNA were prepared from 100 ng total RNA with GeneChip WT PLUS Reagent Kit P/N (GeneChip WT Plus Reagent Kit Manual Target Preparation for GeneChip Whole Transcript (WT) Expression Arrays P/N 703174 Rev.2

growth_protocol: C42B cell were cultured in RPMI media with 10% fetal bovine serum at a seeding density of 140000 cells in 2ml per well of 6-well plates.

extract_protocol: Total RNA was extracted with the Qiagen RNAeasy mini kit according to the manufacturer's instructions.

treatment_protocol: After 3 days of culture, drug(s) or DMSO vehicle control were added to each well. After 6 hours of treatment, cells were lysed with lysis buffer from the RNA extraction kit (Qiagen RNAeasy mini kit) and the lysates were frozen at minus 70C. Total RNA extraction was completed on another day.

tag: disease

value: human prostate cancer


title: enzalutamide_6hr_rep1


title: N-1-Bld scRNA-seq

value: CD45+ cells

value: blood


title: CD8_neg_pos_NYBC265_run1_67

city: Ithaca

first: Colleen

last: Lau

state: New York

address: 930 Campus Road

department: Microbiology & Immunology

institute: Cornell University

description: Sample_HD-265T-NKG2C-SP_IGO_08801_D_67_run1

data_processing:
BCL files were converted to fastq using bcl2fastq2 (v2.17.1.14, v2.18.0,  or v2.20.0.422).
RNA-seq reads were trimmed for quality and adaptors using Trimmomatic (v.0.38).
Transcript quantification was performed by salmon (v0.13.1) using arguments '-l IU --gcBias --validateMappings --rangeFactorizationBins 4 --useVBOpt --numBootstraps 30' and tximport (v0.10.1) using the UCSC Known Gene transcript assembly.
Please note that some biological samples were sequenced twice (designated as 'run1' and 'run2').
Genome_build: hg38
Supplementary_files_format_and_content: Text files are raw estimated gene-level counts (1 count = 1 read pair) as quantified by salmon (v0.13.1) and imported by tximport (v1.10.1). Also provided are gene IDs (Entrez and Ensembl), gene names, gene descriptions, and chromosome.

source_name: peripheral blood NK cells

extract_protocol:
RNA was isolated from sorted cell populations using TRIzol (Invitrogen).
After RiboGreen quantification and quality control by Agilent BioAnalyzer, 0.27-2.0ng total RNA with RNA integrity numbers ranging from 3.3 to 10 underwent amplification using the SMART-Seq v4 Ultra Low Input RNA Kit (Clonetech catalog # 63488), with 12 cycles of amplification. Subsequently, 5.7-7.0ng of amplified cDNA was used to prepare libraries with the KAPA Hyper Prep Kit (Kapa Biosystems KK8504) using 8 cycles of PCR. Samples were barcoded and run on a NovaSeq 6000 in a PE50 run, using the NovaSeq 6000 S1 or S2 Reagent Kit (100 Cycles) (Illumina).  An average of 71 million paired reads were generated per sample and the percent of mRNA bases per sample ranged from 29% to 65%.

tag: celltype

value: neg

value: pos

tag: donor

tag: run

tag: sampleID


title: N-1-RVN scRNA-seq

value: right ventricle


title: E2F1 siRNA vehicle 1 [R20-019; SBS20-003]

source_name: LNCaP_E2F1 siRNA_ETOH

value: LNCaP


title: SKNFI_FOXR2 shRNA (3)

city: Heidelberg

first: Marcel

last: Kool

address: Im Neuenheimer Feld 280

department: Pediatric Neurooncology

country: Germany

institute: German Cancer Research Center DKFZ

hyb_protocol: Affymetrix protocol

scan_protocol: Affymetrix protocol

data_processing: For normalization of the expression data we used the MAS5.0 algorithm of the GCOS program (Affymetrix Inc). Target intensity was set to 100 (α1= 0.04 and α2 = 0.06). Detection p-values were assigned to each probe set using the MAS5.0 algorithm (trimmed mean 96 = 100). Quality of the arrays was ensured by inspection of the ß-actin and GAPDH 5′-3′ ratios as well as the percentage of present calls generated by the MAS5.0 algorithm (Affymetrix Inc).

label: Biotin

source_name: SK-N-FI

label_protocol: Affymetrix protocol

extract_protocol: Total RNA from cells was isolated with the Maxwell® RSC Instrument using simplyRNA Tissue Kit according to the manufacturer’s protocol

tag: shRNA

value: FOXR2 shRNA


title: SKNFI_FOXR2 shRNA (1)


title: SKNFI_Scrambled shRNA (1)

value: Scrambled shRNA


title: SKNFI_FOXR2 shRNA (2)


title: MSL2-Metafemale 1

first: Lin

last: Sun

address: Xinjiekouwai Street

institute: Beijing Normal University

description:
msl2metafemale1
Drosophila_Sex_Chromosome_Aneuploidy_Data.txt.gz

data_processing:
Basecalls performed using CASAVA.
Mapping using HISAT2 with the default parameters.
SAMtools was used to convert data format.
Transcripts were assembled and quantitated using StringTie.
The 'male' and 'female' samples data in the processed data files are from GSE46354 and GSE41679.
Genome_build: GCF_000001215.4_Release_6_plus_ISO1_MT_genomic.fna
Supplementary_files_format_and_content: *_Data.txt: Matrix table of average expression and ratio.

organism: Drosophila melanogaster

source_name: third-instar larvae

growth_protocol: All the stocks are incubated at 25 degrees.

extract_protocol:
Total RNA was isolated using TRIZOL Reagent.
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: biological replicate

tag: genotype

value: XXX,AA

tag: Sex

value: female

tag: over-expression

tag: developmental stage

value: third-instar larvae

value: whole body


title: SKNAS_FOXR2 shRNA (3)

source_name: SK-N-AS


title: MSL2-Metafemale 2

description:
msl2metafemale2
Drosophila_Sex_Chromosome_Aneuploidy_Data.txt.gz


title: SKNAS_FOXR2 shRNA (2)


title: KoD7-1

source_name: KO Day 7 Lungs

value: NLRP3 KO

tag: strain

tag: agent

value: infected by F. tularensis LVS

tag: time point


title: MSL2-2L male 1

description:
mslc2Lmale1
Drosophila_Autosomal_Aneuploidy_Data.txt.gz

value: XY,AAA

value: male

tag: tissue


title: SKNAS_Scrambled shRNA (2)


title: MM

city: wuhan

first: han

middle: shao

last: qing

address: whu

institute: school

data_processing:
Library strategy: SLIM-m6A-seq/RNA-seq/m6A-seq
According to the principle of library construction, the raw data is split by custom scripts.
Adapter seqeucnes were trimmed by using trim galore.
fastuniq is used to remove PCR duplication. Then use seqtk trimfq remove random sequences added in library construction.
Clean reads were mapped to genome by using STAR; with parameter "--outFilterMultimapNmax 20 --outFilterMismatchNmax 10". Only the proper pair and uniquely mapped alignments was persisted for the downstream pipelines.
Aligned reads were used for peak calling and enriched regions comparing by exomePeak.
HOMER was used for peak annotation and detection of the sequence motif.
Genome_build: hg38 and mm10

source_name: murine model heart tissue

growth_protocol: HEK293T (ATCC) cells were cultured in T25 cell culture flask using DMEM (Dulbecco's modified Eagle's medium, high glucose, Gibco) supplemented with 10% fetal bovine serum (FBS, Gibco), and 1% penicillin/streptomycin (Beijing Dingguo changsheng Biotechnology Co.,Ltd, GA3502).

extract_protocol:
Total RNA was isolated from cell lines, peripheral blood or Murine heart tissue with TRIzol (Invitrogen) according to the manufacture’s protocol. The mRNA was isolated by subjecting total RNA to oligo(dT) enrichment using Dynabeads Oligo(dT)25 (NEB)
for No.1-SING &No. 1-SING-IP: Fragmented mRNAs from Hek293T cells were first treated with T4 PNK. Then the samples were ligated with 3'-linker (5'- rApp-NNNNNNTGGAATTCTCGGGTGCCAAGG-SpC3 -3', Italic N represents for 6-nt random sequences). Extra 3'-linker were removed by 5′-deadenylase and RecJf digestion. The reaction mixtures were subsequently purified. 1/50 of the purified sample was retained as input control while the remaining sample was applied to m6A antibody immunoprecipitation (IP). The input control sample and the IP sample were reverse transcripted using RT primer (5'-ACACGACGCTCTTCCGATCT-3') to obtain cDNA samples. The cDNA samples were then ligated with 5'-adaptor (5'-Phos-NNNNNNNNNNAGATCGGAAGAGCACACGTCTG-SpC3-3'), followed by determination of PCR cycle number by RT-qPCR. Finally, library PCR amplification was performed using the NEB primers and the products were purified by magnetic beads or agarose gel electrophoresis.
for samples other than No.1-SING &No. 1-SING-IP: Fragmented mRNAs from different samples were first treated with T4 PNK. Then the samples were ligated with pre-adenylated 3'-linkerLs (5'-NNNNNNNNNNNNAGATCGGAAGAGCGTCGTG-3', Bold N represnts for designed 6-nt barcode sequences, Italic N represents for 6-nt random sequences). Extra 3'-linkerLs were removed by 5′-deadenylase and RecJf digestion. The reaction mixtures were subsequently pooled together and purified. 1/50 of the purified sample was retained as input control while the remaining sample was applied to m6A antibody immunoprecipitation (IP). The input control sample and the IP sample were reverse transcripted using RT primer (5'-ACACGACGCTCTTCCGATCT-3') to obtain cDNA samples. The cDNA samples were then ligated with 5'-adaptor (5'-Phos-NNNNNNNNNNAGATCGGAAGAGCACACGTCTG-SpC3-3'),followed by determination of PCR cycle number by RT-qPCR. Finally, library PCR amplification was performed using the NEB primers and the products were purified by magnetic beads or agarose gel electrophoresis.

value: Murine Heart

tag: treatment

value: Murine （Type 2 diabetes/Type 2 diabetic myocardial infarction/healthy control）


title: KoD7-2

value: Day 7


title: ABC294640_6hr

source_name: C42B cells treated with 15uM ABC294640 for 6 hours

tag: cell line

value: human prostate cancer


title: MSL2-2L female 2

description:
mslc2Lfemale2
Drosophila_Autosomal_Aneuploidy_Data.txt.gz

value: XX,AAA


title: DMSO_6hr_rep2

source_name: C42B cells treated with 0.125% DMSO vehicle control for 6 hours

tag: disease


title: 2L female 1

description:
c2Lfemale1
Drosophila_Autosomal_Aneuploidy_Data.txt.gz


title: 2L female 2

description:
c2Lfemale2
Drosophila_Autosomal_Aneuploidy_Data.txt.gz


title: ATAC_KO_unwounded

city: Irvine

first: Ghaidaa

last: Kashgari

address: 250 sprague Hall

institute: University of California Irvine

library_source: genomic

data_processing:
FastqC for sequencing quality
Kallisto for alignemnt and mapping
Edgar for differentially expressed genes
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...

molecule: genomic DNA

source_name: keratinocytes

extract_protocol:
RNeasy Micro Kit-QIAGEN
Libraries were prepared according to Illumina's instructions

tag: cell type

value: sorted epidermal keratinocytes

value: GRHL3 KO

value: unwounded


title: KO1_wounded

value: wounded


title: ATAC_WT_unwounded

value: WT


title: MSL2-2L female 3

description:
mslc2Lfemale3
Drosophila_Autosomal_Aneuploidy_Data.txt.gz

value: female


title: KoD7-3


title: KO2_unwounded


title: WT2_wounded


title: Metafemale 1

description:
metafemale1
Drosophila_Sex_Chromosome_Aneuploidy_Data.txt.gz

value: XXX,AA

value: third-instar larvae


title: DMSO_6hr_rep1


title: SKNAS_FOXR2 shRNA (1)

value: FOXR2 shRNA


title: WT2_unwounded


title: SKNAS_Scrambled shRNA (3)

value: Scrambled shRNA


title: SKNFI_Scrambled shRNA (2)


title: SKNFI_Scrambled shRNA (3)


title: Control ChIP-seq rep2

city: Baltimore

first: Zhibin

last: Wang

state: MD

address: 615 N Wolf Steet

department: Environmental Health and Engineering

institute: Johns Hopkins University

data_processing:
The adapter sequences were removed from the raw sequencing data and the individual libraries were converted to the FASTA format.
Sequence reads were aligned to the rat genome (rn6) with HISAT2 (v2.1.0) and the resulting alignment files were reconstructed with the EdgeR3 package.  RefSeq database (Build 37.3) was chosen as the annotation references for mRNA analysis.
The read counts of each transcript were normalized to the length of the individual transcript and to the total mapped fragment counts in each sample and expressed as reads per kilobase of exon per million fragments mapped (RPKM) of mRNAs in each sample.
ChIP-seq reads were mapped to the rat genome (rn6) using Bowtie aliger allowing up to two mismatches (Langmead, 2010). Only the uniquely mapped reads were used for further analysis. The EdgeR3 program was used to identify the differential peaks between treatment and control groups (cutoff: FC>2 and FDR<0.01).
SICER call peak program was used to call the peaks with a window size of 200 bp and a gap size of 400 bp, and an E value of 1.
The EdgeR3 program was used to identify the differential peaks between treatment and control groups (cutoff: FC>2 and FDR<0.01).
Genome_build: rn6
Supplementary_files_format_and_content: Tab-delimited text file include RPKM(Reads Per Kilobase Million) values were generated for RNA-seq samples and bigwig (.bw) files were generated for ChIP-seq samples.

organism: Rattus norvegicus

source_name: N27_Control ChIP-seq

growth_protocol: N27 cells were routinely cultured in T175 flasks in RPMI medium (Gibco) supplemented with fetal bocine serum (FBS), L-glutamine, penicillin and streptomycin.

extract_protocol:
Total RNAs from treatment and control groups were isolated and quality controlled according to the Illumina protocols. A total of 2 μg RNA per sample was used as initial material for library construction. Chromatin immunoprecipitation (ChIP) was performed as described previously (Wang et al., 2 009b; Wang et al., 2 008). In brief, cells were crosslinked with 1% formaldehyde for 10 min at room temperature and the reaction was quenched with 125 mM glycine. After chromatin fragmented to 100 to 1000bp by sonication, chromatin templates from 20 million cells were used for ChIP experiment. Samples were immunoprecipitated with 2- 4μg of H3K27ac antibody overnight at 4 °C followed by washing steps.
For RNAseq library construction, Poly-A containing mRNA molecules was purified by using poly-T oligo-attached magnetic beads and fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using reverse transcriptase and random primers. Strand specificity is achieved by replacing dTTP with dUTP, followed by second strand cDNA synthesis. These cDNA fragments then have the addition of a single ‘A’ base and subsequent ligation of the adapter. The products are then purified and enriched with PCR to create the final cDNA library. For ChIPseq library construction, after reverse cross-linking, ChIP-DNA fragments were purified and constructed into libraries by using the ThruPLEX DNA-seq Kit (Rubicon Genomics, Takara, Japan). Amplified libraries around 300 – 500 bp were isolated from agarose gel prior to sequencing.

treatment_protocol: Cells were treated with rotenone or crispr knockout TFAM gene.

value: dopaminergic neuronal cells

tag: genotype/variation

value: wild type

tag: chip antibody


title: Rotenone ChIP-seq rep3

source_name: N27_Rotenone ChIP-seq


title: Rotenone ChIP-seq rep1


title: Crispr Control ChIP-seq rep2

source_name: N27_Crispr Control ChIP-seq


title: Metafemale 2

description:
metafemale2
Drosophila_Sex_Chromosome_Aneuploidy_Data.txt.gz

value: whole body


title: Crispr Control ChIP-seq rep1


title: WtD7-1

source_name: WT Day 7 Lungs

value: Wild Type

value: infected by F. tularensis LVS


title: Crispr TFAM ChIPseq rep3

source_name: N27_Crispr TFAM ChIPseq

value: Tfam-/-


title: MSL2-2L female 1

description:
mslc2Lfemale1
Drosophila_Autosomal_Aneuploidy_Data.txt.gz

value: XX,AAA


title: 2L male 1

description:
c2Lmale1
Drosophila_Autosomal_Aneuploidy_Data.txt.gz

value: XY,AAA

value: male


title: 2L male 3

description:
c2Lmale3
Drosophila_Autosomal_Aneuploidy_Data.txt.gz


title: ATAC_KO_wounded

value: sorted epidermal keratinocytes

value: GRHL3 KO


title: MSL2-2L male 3

description:
mslc2Lmale3
Drosophila_Autosomal_Aneuploidy_Data.txt.gz


title: Rotenone RNAseq rep3

description:
processed data file: N27_Ctrl_vs_Rote_rpkm.txt
Rote_RNAseq_rep3

source_name: N27_Rotenone RNAseq


title: SKNAS_Scrambled shRNA (1)


title: Control ChIP-seq rep3


title: Crispr Control RNAseq rep3

description:
processed data file: N27_Ctrl_vs_TFAMKO_rpkm.txt
TFAMCK_RNAseq_rep3

source_name: N27_Crispr Control RNAseq


title: 2L female 3

description:
c2Lfemale3
Drosophila_Autosomal_Aneuploidy_Data.txt.gz


title: MSL2-2L male 2

description:
mslc2Lmale2
Drosophila_Autosomal_Aneuploidy_Data.txt.gz


title: KO2_wounded

value: wounded


title: 2L male 2

description:
c2Lmale2
Drosophila_Autosomal_Aneuploidy_Data.txt.gz


title: Control ChIP-seq rep1


title: Control RNAseq rep3

description:
processed data file: N27_Ctrl_vs_Rote_rpkm.txt
CK_RNAseq_rep3

source_name: N27_Control RNAseq


title: WT1_wounded

value: WT


title: Crispr TFAM ChIPseq rep1


title: Crispr TFAM ChIPseq rep2


title: Crispr Control ChIP-seq rep3


title: Crispr Control RNAseq rep1

description:
processed data file: N27_Ctrl_vs_TFAMKO_rpkm.txt
TFAMCK_RNAseq_rep1


title: Rotenone RNAseq rep1

description:
processed data file: N27_Ctrl_vs_Rote_rpkm.txt
Rote_RNAseq_rep1


title: Control RNAseq rep2

description:
processed data file: N27_Ctrl_vs_Rote_rpkm.txt
CK_RNAseq_rep2


title: Rotenone ChIP-seq rep2


title: Crispr TFAM RNAseq rep1

description:
processed data file: N27_Ctrl_vs_TFAMKO_rpkm.txt
TFAMKO_RNAseq_rep1

source_name: N27_Crispr TFAM RNAseq


title: WT1_unwounded

value: unwounded


title: CACO_JAMA_2

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

country: Switzerland

institute: IOR

hyb_protocol: RNA was hybridized to capture probes and detection probes using the NanoString nCounter system according to the manufacturer's protocol. Detection probes were provided by the manufacturer and were labeled with a proprietary fluorescent barcode system.

scan_protocol: Scanning was conducted using the NanoString confocal microscope scanner/Digital Analyzer according to manufacturer's instructions.

data_processing: Data were collected as NanoString RCC files and provided as an Excel spreadsheet.

label_protocol: RNA was not labeled; instead, RNA (33 ng/ul) was pre-processed following the NanoString manufacturer's protocol.

extract_protocol: RNA was isolated from FFPE tissue using Recover ALL kit (Ambion)

value: CACO

value: JAM-A silencing


title: Crispr TFAM RNAseq rep2

description:
processed data file: N27_Ctrl_vs_TFAMKO_rpkm.txt
TFAMKO_RNAseq_rep2


title: Rotenone RNAseq rep2

description:
processed data file: N27_Ctrl_vs_Rote_rpkm.txt
Rote_RNAseq_rep2


title: Crispr TFAM RNAseq rep3

description:
processed data file: N27_Ctrl_vs_TFAMKO_rpkm.txt
TFAMKO_RNAseq_rep3


title: Crispr Control RNAseq rep2

description:
processed data file: N27_Ctrl_vs_TFAMKO_rpkm.txt
TFAMCK_RNAseq_rep2


title: JL_JAMA_1

value: JL


title: Macrophage_normal_rep3

city: Tsukuba

first: Hirohide

last: Uenishi

state: Ibaraki

address: 2-1-2 Kannondai

country: Japan

institute: National Institute of Agrobiological Sciences

hyb_protocol: The mixed labelled cRNAs were hybridized overnight to each array at 65 °C under constant rotation in the hybridization buffer supplied with the Gene Expression Hybridization Kit (Agilent).

scan_protocol: Arrays were washed by using a Gene Expression Wash Pack (Agilent) and scanned with a G2505B DNA microarray scanner (Agilent) in accordance with the manufacturer’s protocol.

data_processing: Agilent Feature Extraction Software (v 9.5.3.1) was used for background subtraction and LOWESS normalization. Cy5 and Cy3 intensities were linearly normalized independently based on the 75 percentile value. Intensities less than 100 or background in the raw data were disregarded.

organism: Sus scrofa

source_name: Macrophages from a normal pig (3), unstimulated

label_protocol: Each total RNA (400 ng) was used to synthesize fluorescence-labelled complementary RNA (cRNA) by using a Low RNA Input Fluorescent Linear Amplification Kit (Agilent) in accordance with the manufacturer’s protocol. Total RNAs from the cells with or without stimulation were labelled with cyanine-5 (Cy5) and cyanine-3 (Cy3), respectively. The labelled cRNA was purified by using a QIAGEN RNeasy Mini Kit (Qiagen).

growth_protocol: Cells were plated at a density of 1 x 10^6 cells per well in a 24-well plate format. After stimulation with 10 ng/ml lipid A for 4 h, the cells were collected by centrifugation.

extract_protocol: Total RNA was extracted from the cells by using RNeasy Mini Kit (Qiagen) in accordance with the manufacturer's protocol.

value: macrophage

tag: animal

value: normal pig (3)

tag: stimulant

source_name: Macrophages from a normal pig (3) stimulated by lipid A

value: lipid A


title: JL_JAMA_3


title: ATAC_WT_wounded


title: CACO_JAMA_3


title: hLFSCs-N-MS-N1

city: Xining

first: Liu

last: Chenhao

state: Qinghai

address: Xinqiao Street

department: Orthopedic

institute: Qinghai Provincial People's Hospital

data_processing:
Differential expression analysis of two sample types was performed using the DEGseq (2010) R package.
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts or FPKM values for each Sample

source_name: Human ligament flavum stem cells

extract_protocol:
Total RNA was extracted from cells with Tripure Isolation Reagent (Roche, Mannheim, Germany).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Human ligament flavum stem cells

tag: stress

value: no


title: Control RNAseq rep1

description:
processed data file: N27_Ctrl_vs_Rote_rpkm.txt
CK_RNAseq_rep1

value: dopaminergic neuronal cells

value: wild type


title: JL_Ctrl_1

tag: genotype

value: control


title: hLFSCs-N-MS-N0


title: JL_Ctrl_3


title: hLFSCs-MS-S4

value: Mechanical stress


title: hLFSCs-MS-S2


title: hLFSCs-MS-S1


title: JL_Ctrl_2


title: CACO_Ctrl_3


title: JL_JAMA_2


title: CACO_JAMA_1


title: Patient_1

city: Utrecht

first: Balthasar

middle: Adrianus

last: Heesters

state: Utrecht

address: Universiteitsweg 99

department: Pharmaceutical Sciences

country: Netherlands

institute: Utrecht University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using STARSolo v2.7.8a
fastq files alligned to genome
Genome_build: GRCh38
Supplementary_files_format_and_content: Sparse Matrix  with raw gene counts, features and barcodes for every gene and every cell

source_name: Gut

extract_protocol:
Guts removed in surgeries were washed in PBS, disected,minced and digested with Collagenase D and Dnase. Cells were sorted in 384-wells plates by FACS. CD127+ ILC and NK cells were selected.
RNA libraries were prepared for sequencing using standard CEL-seq2 protocols
RNA-Seq: CEL-seq2 [scdiscoveries]

value: gut

tag: disease state

value: Crohn's disease


title: PROSER1KO1D3_RNA-seq_rep2

city: Memphis

first: Wojciech

last: Rosikiewicz

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St. Jude Childrens Research Hospital

description:
RNA was isolated from 3 x 106 cells with the RNeasy Mini Kit (Qiagen, 74106) following the manufacturer’s instructions with the minor alterations.
1858628_SJNORM059110_C19-HEK293_PROSER1KO1D3_rep2

data_processing:
Quality control filtering and adapter trimming of fastq files was performed with trim_galore
Paired-end reads were mapped by STAR(v2.7.1a) using parameters "-c -p 4 --outFilterType BySJout --outFilterMultimapNmax 20 --alignSJoverhangMin 8 --alignSJstitchMismatchNmax 5 -1 5 5 --alignSJDBoverhangMin 10 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 100000 --alignMatesGapMax 100000 --outSAMmapqUnique 60 --outSAMmultNmax 1 --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM NM MD --outSAMunmapped Within --outSAMtype BAM SortedByCoordinate --outReadsUnmapped None --chimJunctionOverhangMin 12 --chimSegmentReadGapMax 3 --chimMultimapNmax 10 --chimMultimapScoreRange 10 --chimNonchimScoreDropMin 10 --chimOutJunctionFormat 1 --quantMode TranscriptomeSAM GeneCounts --twopassMode Basic --peOverlapNbasesMin 12 --peOverlapMMp 0.1 --outWigType wiggle --outWigStrand Stranded --outWigNorm RPM"
Read duplication was marked with MarkDuplicates from GATK (v4.0.4.0)
RSEM was used to quantify read counts per gene
Genome_build: hg38 (GRCh38.p12)
Supplementary_files_format_and_content: gene-based raw counts and FPKM normalized txt files

source_name: HEK293 cells

growth_protocol: Cells were grown in Gibco DMEM medium plus 10% FBS with Pen-Strep, Zeocin and Blasticidin under 37 degree.

extract_protocol:
RNA was isolated from 3 x 10^6 cells with the RNeasy Mini Kit (Qiagen, 74106) following the manufacturer’s instructions with the following alterations. Cells were homogenized in 600 μL RLT buffer (with 2-Mercaptoethanol) and passed through a QIAshredder column (Qiagen, 79656) by centrifugation in a table top centrifuge for 2 min at full speed at room temperature. The optional step after the second wash with RPE buffer was applied to dry the membrane. For DNA digestion, RNA was eluted with 85 μL H2O and mixed with 10 μL10 x DNAase buffer and 5 μL DNAse I (NEB, M0303S), then incubated at room temperature for 20 min. After incubation, RNA was purified by following the ‘RNA Cleanup’ protocol in the RNeasy Mini Handbook. RNA was finally eluted in 50 μL H2O and concentration determined with a NanoDrop 8000 Spectrophotometer.
RNA was quantified using the Quant-iT RiboGreen RNA Assay Kit (Thermo Fisher Scientific, R11490) and quality-checked with the RNA 6000 Nano Kit (Agilent, 5067–1511) on a 2100 Bioanalyzer (Agilent, G2939BA) or High Sensitivity RNA ScreenTape Assay (Agilent, 5067–5579, 5067–5580, 5067–5581) on a 4200 TapeStation (Agilent, G2991AA) prior to library generation. Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Gold Kit (Illumina, 20020599) according to the manufacturer’s instructions. Libraries were analyzed for insert size distribution with the High Sensitivity DNA Kit (Agilent, 5067–4626) on a 2100 Bioanalyzer or the High Sensitivity D1000 ScreenTape Assay (Agilent, 5067–5584, 5067–5585, 5067–5587, 5067–5603) on a 4200 TapeStation. Libraries were quantified using the Quant-iT PicoGreen dsDNA Assay (Thermo Fisher Scientific, P11496).

tag: cell line full name

value: Flp-In T-REx HEK293 (Invitrogen, R78007)

value: human embryonic kidney cells

value: PROSER1 KO


title: PROSER1KO1D3_RNA-seq_rep1

description:
RNA was isolated from 3 x 106 cells with the RNeasy Mini Kit (Qiagen, 74106) following the manufacturer’s instructions with the minor alterations.
1858627_SJNORM059110_C18-HEK293_PROSER1KO1D3_rep1


title: CACO_Ctrl_2

value: CACO


title: Macrophage_normal_rep2

source_name: Macrophages from a normal pig (2), unstimulated

value: normal pig (2)

source_name: Macrophages from a normal pig (2) stimulated by lipid A


title: hLFSCs-N-MS-N2


title: hLFSCs-N-MS-N3


title: Macrophage_normal_rep4

source_name: Macrophages from a normal pig (4), unstimulated

value: normal pig (4)

source_name: Macrophages from a normal pig (4) stimulated by lipid A


title: CACO_Ctrl_1


title: Macrophage_immune-selected_rep2

source_name: Macrophages from an immune-selected pig (2), unstimulated

value: macrophage

value: immune-selected pig (2)

source_name: Macrophages from an immune-selected pig (2) stimulated by lipid A


title: Macrophage_normal_rep1

source_name: Macrophages from a normal pig (1), unstimulated

value: normal pig (1)

source_name: Macrophages from a normal pig (1) stimulated by lipid A

value: lipid A


title: PB169 Sample 61

city: New York

first: Aarthi

last: Ramakrishnan

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

description: gender 0

data_processing:
We first performed quality control using FastQC. The script Trim Galore! was used to trim adapter sequences and raw RNA-sequencing reads from the human genome were aligned to hg38 Ensembl v90 using HISAT2.
Counts of reads mapped to genes were obtained using HTSeq. Threshold for filtering out low expressed genes was set to at least 5 reads across 60% of the samples.
Differential gene expression analysis was carried out using DESeq2
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text file

source_name: Blood

extract_protocol:
RNA was extracted using the PAXgene Blood RNA Kit (Qiagen) according to the manufacturer instructions. RNA quality, RNA integrity number (RIN) and RNA concentrations were assessed using Nanodrop (Thermo Fischer Scientific) and Bionalyzer (Agilent).
750 ng of purified RNA was used for library preparation, which was performed using the TruSeq Stranded mRNA kit (Illumina). Libraries were barcoded for multiplexing. Before sequencing, library quality and concentration were measured using Bioanalyzer (Agilent). Libraries were sequenced (2x150 base pair, paired-end reads configuration) on an Illumina HiSeq machine at a minimum of 40 million reads per sample.

tag: rin

tag: timepoint

value: CON

tag: response

tag: race

tag: bmi

tag: age

tag: group


title: Macrophage_immune-selected_rep3

source_name: Macrophages from an immune-selected pig (3), unstimulated

value: immune-selected pig (3)

source_name: Macrophages from an immune-selected pig (3) stimulated by lipid A


title: Macrophage_immune-selected_rep1

source_name: Macrophages from an immune-selected pig (1), unstimulated

value: immune-selected pig (1)

source_name: Macrophages from an immune-selected pig (1) stimulated by lipid A


title: PB092 Sample 57

description: gender 1

value: control


title: PB237 Sample 58

description: gender 1

value: Pre

value: nonresponder

value: MDD


title: Macrophage_immune-selected_rep4

source_name: Macrophages from an immune-selected pig (4), unstimulated

value: immune-selected pig (4)

source_name: Macrophages from an immune-selected pig (4) stimulated by lipid A


title: Patient_6

source_name: Gut

tag: tissue

value: gut

value: Crohn's disease


title: PB207 Sample 55

description: gender 1

value: responder


title: PB215 Sample 53

description: gender 1


title: Patient_3


title: Patient_2


title: Patient_4


title: PB230 Sample 66

description: gender 1


title: FlpInTREx_control_RNA-seq_rep1

description:
RNA was isolated from 3 x 106 cells with the RNeasy Mini Kit (Qiagen, 74106) following the manufacturer’s instructions with the minor alterations.
1858625_SJNORM059110_C16-HEK293_FlpInTREx_control_rep1

source_name: HEK293 cells

value: Flp-In T-REx HEK293 (Invitrogen, R78007)

tag: cell type

value: human embryonic kidney cells

tag: treatment

value: Mock treated


title: hLFSCs-MS-S3

source_name: Human ligament flavum stem cells

value: Human ligament flavum stem cells

value: Mechanical stress


title: PB154 Sample 50

description: gender 0


title: PB144 Sample 51

description: gender 0


title: Patient_5


title: PB198 Sample 47

description: gender 1

value: Post


title: PB198 Sample 46

description: gender 1


title: FlpInTREx_control_RNA-seq_rep2

description:
RNA was isolated from 3 x 106 cells with the RNeasy Mini Kit (Qiagen, 74106) following the manufacturer’s instructions with the minor alterations.
1858626_SJNORM059110_C17-HEK293_FlpInTREx_control_rep2


title: PB195 Sample 69

description: gender 0

value: CON


title: PB173 Sample 63

description: gender 1


title: PB212 Sample 64

description: gender 0


title: PB230 Sample 67

description: gender 1


title: PB100 Sample 44

description: gender 0


title: PB172 Sample 68

description: gender 0


title: PB100 Sample 45

description: gender 0


title: PB153 Sample 41

description: gender 0


title: PB147 Sample 39

description: gender 1


title: PB219 Sample 60

description: gender 1


title: PB237 Sample 59

description: gender 1


title: PB082 Sample 36

description: gender 1


title: PB179 Sample 35

description: gender 1


title: PB122 Sample 62

description: gender 1


title: PB069 Sample 31

description: gender 1


title: PB186 Sample 28

description: gender 0


title: PB188 Sample 32

description: gender 1


title: PB158 Sample 56

description: gender 0


title: PB186 Sample 27

description: gender 0


title: PB212 Sample 65

description: gender 0


title: PB085 Sample 42

description: gender 1


title: PB183 Sample 24

description: gender 0


title: PB191 Sample 22

description: gender 1


title: PB084 Sample 21

description: gender 0


title: PB234 Sample 19

description: gender 1


title: PB215 Sample 54

description: gender 1


title: PB059 Sample 18

description: gender 1


title: PB144 Sample 52

description: gender 0


title: PB188 Sample 33

description: gender 1


title: PB087 Sample 43

description: gender 1


title: PB234 Sample 20

description: gender 1


title: PB179 Sample 34

description: gender 1


title: PB197 Sample 37

description: gender 0


title: PB205 Sample 48

description: gender 0


title: PB183 Sample 23

description: gender 0


title: PB176 Sample 9

description: gender 1


title: PB076 Sample 14

description: gender 1


title: PB176 Sample 10

description: gender 1


title: PB098 Sample 26

description: gender 1


title: PB182 Sample 15

description: gender 0


title: PB045 Sample 8

description: gender 0


title: PB147 Sample 38

description: gender 1


title: PB182 Sample 16

description: gender 0


title: PB205 Sample 49

description: gender 0


title: EMCN+ cells, Ctnnb1(Ex3)fl/wt biological replicate 5

city: Mannheim

first: Carolina

last: Delatorre

address: Theodor-Kutzer-Ufer 1-3

institute: University Heidelberg

description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 5, EMCN+ cells

hyb_protocol: Hybridization (16h x 45°C) was processed according to the standard Affymetrix protocol.

scan_protocol: Affymetrix GeneArray Scanner3000

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 10, from SAS. Gene expression profiling was performed using arrays of human MoGene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Primary bone marrow endothelial cells of Ctrl

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol.

growth_protocol: RNA was extracted from primary bone marrow endothelial cells immediately after isolation

extract_protocol: RNA was extracted using InnuPrep RNA Mini Kit (Analytik Jena AG, Jena, Germany)

treatment_protocol: Murine EMCN+ cells from different groups were isolated and purified using EMCN antibody coated MicroBeads. Enrichment of endothelial cells was assesed by comparative qPCR of endothelial genes using flow through cells as a reference.

value: Ctrl

value: Primary bone marrow endothelial cells


title: EMCN+ cells, Ctnnb1(Ex3)fl/wt biological replicate 1

description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 1, EMCN+ cells


title: PB062 Sample 6

description: gender 1

value: control


title: PB150 Sample 40

description: gender 0


title: PB093 Sample 29

description: gender 0


title: PB080 Sample 30

description: gender 1


title: PB106 Sample 1

description: gender 0

value: Pre


title: PB174 Sample 12

description: gender 0


title: PB174 Sample 11

description: gender 0


title: PB098 Sample 25

description: gender 1


title: EMCN+ cells, Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 1

description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 1, EMCN+ cells

source_name: Primary bone marrow endothelial cells of Ctnnb1OE-SEC


title: PB059 Sample 17

description: gender 1


description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 3, Population PIV

data_processing: The data were analyzed with a commercial software called JMP Genomics, version 10, from SAS. Gene expression profiling was performed using arrays of mouse MoGene-2_0-type from Affymetrix. A Custom CDF Version 22 with Entrez based gene definitions was used to annotate the arrays. The Raw fluorescence intensity values were normalized applying quantile normalization, RMA background correction and Medianpolish Probeset Summary

source_name: Orthochromatic erythroblasts and reticulocztes from WT

growth_protocol: Cells were lysed immediately after sorting.

value: WT

value: PIV (orthochromatic erythroblasts and reticulocytes)


title: EMCN+ cells, Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 5

description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 5, EMCN+ cells


description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 4, Population PIV

treatment_protocol: Cells were lysed immediately after sorting.


title: PB134 Sample 3

description: gender 0

value: MDD


title: EMCN+ cells, Ctnnb1(Ex3)fl/wt biological replicate 3

description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 3, EMCN+ cells


title: PB075 Sample 13

description: gender 0


title: EMCN+ cells, Ctnnb1(Ex3)fl/wt biological replicate 2

description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 2, EMCN+ cells


title: PB045 Sample 7

description: gender 0

value: nonresponder


title: PB134 Sample 4

description: gender 0


title: EMCN+ cells, Ctnnb1(Ex3)fl/wt biological replicate 4

description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 4, EMCN+ cells


description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 2, Population PIV


title: PB023 Sample 2

description: gender 1


title: PB065 Sample 5

description: gender 0


description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 5, Population PIV


title: EMCN+ cells, Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 2

description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 2, EMCN+ cells


title: Single nuclei (TST) Donor 3

city: Toronto

first: Tallulah

middle: Suzanne

last: Andrews

state: Ontario

address: MARS Building

country: Canada

institute: UHN Research

data_processing:
Reads were QCed, mapped, and UMIs were quantilfied using cell-ranger (v3).
Viable cells were identified using EmptyDrops (v1.2.0), and ambient RNA was removed using SoupX (v1.2.2) with known markers
Feature selection, and dimensionality reduction was done with Seurat (v3)
Samples were integrated using Harmony (v1.0), and clustered using Seurat (v3)
Clusters were manually annotated.
Genome_build: GRCh38
Supplementary_files_format_and_content: Processed files contain compressed folders of the raw count matrices from cell ranger, and the final metadata table for the retained cells with their complete manual annotation and sample metadata.

source_name: Liver Caudate Lobe

extract_protocol:
During organ retrieval, donor liver grafts were perfused in situ with cold (HTK) solution (Methapharm) to thoroughly flush circulating cells, leaving only tissue resident cells that are then used to prepare a single-cell suspension for scRNA-seq analysis. At our institute, the caudate lobe (segment 1) of the liver is often removed in preparation of the organ for implantation. The removed caudate lobe was then dissociated using the protocol as fully described in [https://doi.org/10.17504/protocols.io.m9sc96e] and detailed below.
Samples were prepared as outlined by the 10x Genomics Single Cell 3′ v2 Reagent Kit user guide. Briefly, the samples were washed twice in PBS (Life Technologies) + 0.04% BSA (Sigma) and re-suspended in PBS + 0.04% BSA. Sample viability was assessed via Trypan Blue (Thermo Fisher) and using a haemocytometer (Thermo Fisher). Following counting, the appropriate volume for each sample was calculated for a target capture of 6000 cells. Samples below the required cell concentration as defined by the user guide (i.e., <400 cells/µl) were pelleted and re-suspended in a reduced volume and counted again using a haemocytometer prior to loading onto the 10x Genomics single-cell-A chip. After droplet generation, samples were transferred onto a pre-chilled 96-well plate (Eppendorf), heat-sealed and reverse transcription was performed using a Veriti 96-well thermal cycler (Thermo Fisher). After the reverse transcription, cDNA was recovered using Recovery Agent provided by 10x followed by a Silane DynaBead clean-up (Thermo Fisher) as outlined in the user guide. Purified cDNA was amplified for 12 cycles before being cleaned up using SPRIselect beads (Beckman). Samples were diluted 4:1 (elution buffer (Qiagen):cDNA) and run on a Bioanalyzer (Agilent Technologies) to determine cDNA concentration. cDNA libraries were prepared as outlined by the Single Cell 3′ Reagent Kits v2 user guide with appropriate modifications to the PCR cycles based on the calculated cDNA concentration (as recommended by 10X Genomics).
The molarity of each library was calculated based on library size as measured using a bioanalyzer (Agilent Technologies) and qPCR amplification data (Kappa/Roche). Samples were pooled and normalized to 10 nM, then diluted to 2 nM using elution buffer (Qiagen) with 0.1% Tween20 (Sigma). Each 2 nM pool was denatured using 0.1 N NaOH at equal volumes for 5 min at room temperature. Library pools were further diluted to 20 pM using HT-1 (Illumina) before being diluted to a final loading concentration of 14 pM. 150 μl from the 14 pM pool was loaded into each well of an 8-well strip tube and loaded onto a cBot (Illumina) for cluster generation. Samples were sequenced on a HiSeq 2500 with the following run parameters: Read 1—26 cycles, read 2—98 cycles, index 1—8 cycles. A median sequencing depth of 60,000 reads/cell was targeted for each sample.

tag: Sex

value: F

tag: time frozen

value: 1 year

tag: age (years)


title: Single cell Donor 3


title: Single nuclei (NST) Donor 1

value: 1 year 8 months


title: Single cell Donor 4


title: Single nuclei (TST) Donor 4

value: 5 months


title: Single nuclei (TST) Donor 1


title: EMCN+ cells, Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 3

description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 3, EMCN+ cells


description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 1, Population PIV


description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 5, Population PIV

source_name: Orthochromatic erythroblasts and reticulocztes from Ctnnb1OE-SEC


description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 1, Population PIV


description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 4, Population PIV


title: Subject_23_AlcoholUseDisorder

city: Boston

first: Huiping

last: Zhang

state: Massachusetts

address: 72 East Concord Street

department: Psychiatry

institute: Boston University School of Medicine

description:
Sample_191
miRNA transcriptome data

data_processing:
The bulk RNA-seq processing pipeline Pipeliner [Federico et al. Front Genet 2019; 10, 614] was utilized to quantitate gene expression.
Genome_build: hg19
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Human postmortem ventral tegmental area

growth_protocol: Not applicable

extract_protocol:
RNA was extracted with the Trizol reagent using the QIAGEN RNeasy mini kit and followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyzer System.
The KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, Wilmington, MA, USA) was used to deplete ribosomal RNAs (rRNAs) and construct RNA-seq libraries with 1 ug of total RNAs as the starting material.
Ribosomal RNA depletion RNA-seq

treatment_protocol: Not applicable

tag: aud status

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

value: Female

tag: batch

tag: brainweight

tag: brainph

tag: pmi

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Toxicity

tag: smoking

value: Never

tag: liverclass

value: Steatosis


title: Single nuclei (TST) Donor 2

value: M

value: 11 months


description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 2, Population PIV

tag: genotype


title: Subject_21_AlcoholUseDisorder

description:
Sample_189
miRNA transcriptome data

value: Male

tag: rin

value: Left

value: Current

value: Cirrhosis


description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 3, Population PIV

tag: cell type

value: PIV (orthochromatic erythroblasts and reticulocytes)


title: Single nuclei (CST) Donor 1

value: F


title: Subject_22_Control

description:
Sample_190
miRNA transcriptome data

value: Control

value: Cardiac

value: Normal


title: Subject_17_Control

description:
Sample_185
miRNA transcriptome data

value: Vascular


title: Subject_16_AlcoholUseDisorder

description:
Sample_184
miRNA transcriptome data

value: AlcoholUseDisorder


title: Subject_14_AlcoholUseDisorder

description:
Sample_182
miRNA transcriptome data

value: Female


title: Single cell Donor 2


description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 4, Population PIII

source_name: Polychromatic erythroblasts from WT

value: WT

value: PIII (polychromatic erythroblasts)


description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 4, Population PIII

source_name: Polychromatic erythroblasts from Ctnnb1OE-SEC


description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 1, Population PIII


description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 2, Population PIII


description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 5, Population PIII


description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 5, Population PIII


description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 1, Population PIII


description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 2, Population PIII


title: Subject_13_Control

description:
Sample_181
miRNA transcriptome data

value: Never


description: Gene expression data from Ctnnb1(Ex3)fl/wt biological replicate 3, Population PIII


description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 3, Population PIII


title: Subject_11_Control

description:
Sample_179
miRNA transcriptome data

value: Congestion


title: Subject_20_Control

description:
Sample_188
miRNA transcriptome data

value: Toxicity

value: Unknown


title: Subject_24_AlcoholUseDisorder

description:
Sample_192
miRNA transcriptome data

value: Male

value: Left

value: Cardiovascular

value: Steatosis


title: Subject_3_Control

description:
Sample_171
miRNA transcriptome data

value: Current


title: Subject_19_Control

description:
Sample_187
miRNA transcriptome data

value: Control

value: Right


title: Subject_1_Control

description:
Sample_169
miRNA transcriptome data

value: Cardiac

value: MildSteatosis


title: Sample_164_Subject_20_Control

description:
miRNA transcriptome data
793_PUT_041_152_S46_L001

source_name: Human postmortem putamen_Control

extract_protocol:
RNA was extracted with the Trizol reagent using the QIAGEN RNeasy mini kit and followed by clean-up and DNase I treatment in accordance with the prescribed protocol provided with the kit. Quality control was performed with the Agilent Bioanalyzer System.
The KAPA RNA HyperPrep Kit with RiboErase (KAPA Biosystems, Wilmington, MA, USA) was used to deplete ribosomal RNAs (rRNAs) and construct RNA-seq libraries with 1 ug of total RNAs as the starting material.

tag: alcoholdailyuse (gram/day)


title: Sample_166_Subject_22_Control

description:
miRNA transcriptome data
PUT_804_S49_L002

tag: Sex

value: Normal


title: Sample_167_Subject_23_AlcoholUseDisorder

description:
miRNA transcriptome data
810_PUT_029_164_S47_L001

value: AlcoholUseDisorder

value: Female


title: EMCN+ cells, Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 4

description: Gene expression data from Stab2-iCreF3 Ctnnb1(Ex3)fl/wt biological replicate 4, EMCN+ cells

value: Primary bone marrow endothelial cells


title: Subject_10_Control

description:
Sample_178
miRNA transcriptome data


title: Subject_15_Control

description:
Sample_183
miRNA transcriptome data


title: Subject_18_AlcoholUseDisorder

description:
Sample_186
miRNA transcriptome data

value: Hepatic


title: Sample_163_Subject_19_Control

description:
miRNA transcriptome data
787_PUT_053_140_S45_L001

value: Congestion


title: 8 NIH/3T3 ctrl2

city: Freiburg

first: Justus

last: Duyster

address: Hugstetter Str. 55

department: Department of Hematology and Oncology

institute: Freiburg University Medical Center

hyb_protocol: Labeled fragments were hybridized to Affymetrix Clariom S arrays for 16h at 45°C with 60 rpm in an Affymetrix Hybridization oven 645

scan_protocol: After washing and staining, the arrays were scanned with the Affymetrix GeneChip Scanner 3000 7G. CEL-files were produced from the raw data with Affymetrix GeneChip Command Console Software.

data_processing: CHP data were generated using Transcriptome analysis software.

source_name: connective tissue

label_protocol: We used the Affymetrix WT Plus kit for cDNA synthesis, amplification, and second-cycle cDNA synthesis, as well as fragmentation and labeling with Biotin, as described by the manufacturer.

extract_protocol: RNA was isolated using RNeasy Mini Kit (Qiagen)

treatment_protocol: Cells were starved overnight and treated with 10 ng/mL of murine OSM for 6 hours.

tag: cell line

tag: agent

value: fibroblast


title: 10 NIH/3T3 OSM1

value: 10 ng/mL of OSM


title: 4 OP9 OSM1

source_name: bone marrow

value: stroma


title: 12 NIH/3T3 OSM3


title: Sample_161_Subject_17_Control

description:
miRNA transcriptome data
PUT_741_S46_L002

tag: aud status

value: Male

value: Vascular


title: Sample_160_Subject_16_AlcoholUseDisorder

description:
miRNA transcriptome data
732_PUT_065_128_S44_L001

value: Left

value: Cirrhosis


title: Subject_4_AlcoholUseDisorder

description:
Sample_172
miRNA transcriptome data

tag: alcoholdailyuse(gram/day)

value: Toxicity

value: Current


title: Sample_159_Subject_15_Control

description:
miRNA transcriptome data
PUT_723_S45_L002

value: Control

tag: batch

value: Cardiac


title: Subject_5_AlcoholUseDisorder

description:
Sample_173
miRNA transcriptome data

tag: brainweight

value: Right

value: Respiratory


title: 3 OP9 ctrl3


title: 2B2

city: Greenville

first: Weihua

last: Huang

address: 600 Moye Blvd, Brody 7S-24

institute: East Carolina University

description: RiboZero bacterial rRNA depletion

data_processing:
gene expression levels were estimated with EDGE-pro (v1.3.1) using Bowtie2 (v2.3.5.1) alignment to F. tularensis reference
differential gene expression was analyzed by DESeq2 (v1.16.1)
Genome_build: NC_007880
Supplementary_files_format_and_content: reads of each gene in an Excel file as used for DESeq2

organism: Francisella tularensis subsp. holarctica LVS

source_name: F. tularensis LVS osrR Mutant

growth_protocol: The Francisella strains were cultured on Mueller-Hinton (MH) chocolate agar plates (BD Life Sciences) and incubated for 48 hours at 37οC and 5% CO2. Individual colonies were selected and inoculated in MH broth (MHB) enhanced with Isovitalex (BD Biosciences), Ferric Pyrophosphate, Glucose, Anhydrous Calcium Chloride, and Hydrous Magnesium Chloride. The bacterial cultures were incubated at 37οC with constant shaking until the bacterial growth reached the mid-log phase (0.2OD).

extract_protocol:
Total RNA was extracted with Invitrogen PureLink RNA mini kit and treated with DNase using Invitrogen TURBO DNA-free Kit
Illumina TruSeq Stranded Total RNA Library Prep kit with RiboZero bacterial rRNA depletion

treatment_protocol: To determine the role of OsrR as a global transcriptional regulator, we profiled the whole transcriptome of the DosrR mutant in the absence or the presence of oxidative stress. The superoxide-generating compound, menadione (final concentration of 1.25mM), was used as an oxidative stress inducer. This concentration of menadione equally affects the viability of wild type F. tularensis LVS or the DosrR mutant. For untreated control, an equal volume of MHB was added, and bacteria were incubated for 1 hour at 37οC with 5% CO2.

value: Treated with Menadione

value: osrR Mutant

tag: experiment

value: 2B2 Expt. 2


title: Subject_9_AlcoholUseDisorder

description:
Sample_177
miRNA transcriptome data

value: AlcoholUseDisorder

tag: brainph

tag: pmi

value: Steatosis


title: 2B1

description: RiboZero bacterial rRNA depletion

value: 2B1 Expt. 1


title: Subject_2_Control

description:
Sample_170
miRNA transcriptome data

value: Female

tag: leftrightbrain

tag: causeofdeathcategory

value: Unknown

value: Normal


title: Subject_6_AlcoholUseDisorder

description:
Sample_174
miRNA transcriptome data

tag: smoking

tag: liverclass


title: Sample_155_Subject_11_Control

description:
miRNA transcriptome data
649_PUT_089_104_S41_L001

value: Male

tag: rin

value: Left

value: Congestion


title: Sample_168_Subject_24_AlcoholUseDisorder

description:
miRNA transcriptome data
853_PUT_017_176_S48_L001

value: Cardiovascular

value: Current


title: Subject_7_AlcoholUseDisorder

description:
Sample_175
miRNA transcriptome data

value: Cardiac

value: Cirrhosis


title: 2A1

description: RiboZero bacterial rRNA depletion

value: Untreated

tag: genotype

value: 2A1 Expt. 1


title: 7 NIH/3T3 ctrl1

tag: cell type

value: fibroblast


title: 11 NIH/3T3 OSM2

value: 10 ng/mL of OSM


title: Sample_165_Subject_21_AlcoholUseDisorder

description:
miRNA transcriptome data
PUT_802_S48_L002

value: AlcoholUseDisorder

tag: alcoholdailyuse (gram/day)

tag: Sex


title: 1B1

description: RiboZero bacterial rRNA depletion

source_name: F. tularensis LVS

tag: agent

value: Treated with Menadione

value: wildtype

value: 1B1 Expt. 1


title: 1B2

description: RiboZero bacterial rRNA depletion

value: 1B2 Expt. 2


title: Sample_162_Subject_18_AlcoholUseDisorder

description:
miRNA transcriptome data
PUT_779_S47_L002

tag: aud status

value: Right

value: Hepatic

value: Steatosis


title: Sample_156_Subject_12_AlcoholUseDisorder

description:
miRNA transcriptome data
654_PUT_077_116_S42_L001

value: Male

value: Left

value: Normal


title: 9 NIH/3T3 ctrl3

tag: cell line


title: Subject_8_Control

description:
Sample_176
miRNA transcriptome data

value: Control

tag: alcoholdailyuse(gram/day)

tag: batch

value: Cardiac

value: Never


title: Sample_157_Subject_13_Control

description:
miRNA transcriptome data
PUT_675_S44_L002

tag: brainweight


title: 6 OP9 OSM3

value: stroma


title: 2B3

description: RiboZero bacterial rRNA depletion

value: osrR Mutant

tag: experiment

value: 2B3 Expt. 3


title: 1A3

description: RiboZero bacterial rRNA depletion

value: Untreated

value: 1A3 Expt. 3


title: 5 OP9 OSM2

value: 10 ng/mL of OSM


title: 1A2

description: RiboZero bacterial rRNA depletion

value: wildtype

value: 1A2 Expt. 2


title: 2A2

description: RiboZero bacterial rRNA depletion

value: 2A2 Expt. 2


title: Sample_154_Subject_10_Control

description:
miRNA transcriptome data
635_PUT_006_187_S40_L001

tag: brainph

tag: pmi

value: Current

value: Congestion


title: Sample_158_Subject_14_AlcoholUseDisorder

description:
miRNA transcriptome data
715_PUT_155_038_S43_L001

value: AlcoholUseDisorder

value: Female

tag: leftrightbrain

tag: causeofdeathcategory

value: Toxicity

value: Cirrhosis


title: Sample_153_Subject_9_AlcoholUseDisorder

description:
miRNA transcriptome data
PUT_628_S43_L002

value: Male

value: Right

tag: smoking

tag: liverclass

value: Steatosis


title: Sample_149_Subject_5_AlcoholUseDisorder

description:
miRNA transcriptome data
PUT_577_S40_L002

tag: rin

value: Respiratory


title: ko-Tterm-rep4

city: Charlestown

first: Aleksandra

last: Ozga

address: 149 13th Street

institute: Massachusetts General Hospital and Harvard Medical School

description: BV605, APC, BUV395, PERCPCy5.5

hyb_protocol: RNA was incubated at 65oC with Reporter Code Set, Hybridization Buffer and Capture ProbeSet for 17 hours (nCounter ® Mouse Immunology Panel gene expression CodeSet). Once the hybridization reaction was terminated, samples were injected into loading ports on the cartridge and sealed.

scan_protocol: RNA levels were assayed by direct digital detection following the manufacturer’s instructions (NanoString Technologies, Seattle, WA).

data_processing:
Data were processed and analyzed with nSolver 4.0. In brief, data were controlled for any imaging and binding quality control issues, positive control linearity and limit of detection parameters. The counts for each sample were normalized based on housekeeping gene expression. Analysis of differentially expressed genes was performed, accounting for multiple comparison corrections with Benjamini-Yekutieli False Discovery Rate method.
The counts for each sample were normalized based on housekeeping gene expression with the use of nSolver software. Analysis of differentially expressed genes was performed, accounting for multiple comparison corrections with Benjamini-Yekutieli False Discovery Rate method.

label: NanoString

source_name: spleen, Cxcl10-/-

label_protocol: The sorting was based on following markers: stem-like T cells (PD1+Ly108+CX3CR1–CD101– CD8+ T cells); CX3CR1+ stem-like T cells (PD1+Ly108+CX3CR1+CD101– CD8+ T cells); effector-like T cells (PD1+Ly108–CX3CR1+CD101– CD8+ T cells); and terminally differentiated T cells (PD1+Ly108–CX3CR1+CD101+  CD8+ T cells).

growth_protocol: mice were housed under specific-pathogen-free conditions

extract_protocol: cells were sorted on FACSAria Fusion Cell Sorter, BSL2+, with 70μ nozzle and a 4oC circulating cool-down system. Post sorting cells were spun down and lysed using TRIZOL reagent (ThermoFisher Scientific). Total RNA was chloroform-extracted, precipitated overnight at -20oC with isopropanol in the presence of 3μg of RNA grade glycogen (ThermoFisher Scientific), washed two times with 75% ethanol, and dissolved in water. 50ng of RNA was used for downstream preparation according to manufacturer’s recommendation.

treatment_protocol: WT or Cxcl10-/- mice were infected with LCMV CL13, and spleens harvested on d24 pi

tag: infection

value: LCMV d24

tag: strain


title: 2 OP9 ctrl2

tag: cell type

value: stroma


title: Sample_146_Subject_2_Control

description:
miRNA transcriptome data
PUT_460_S38_L002

value: Control

tag: Sex

value: Cardiac

value: Unknown

value: Normal


title: Sample_151_Subject_7_AlcoholUseDisorder

description:
miRNA transcriptome data
PUT_596_S41_L002

tag: aud status

tag: alcoholdailyuse (gram/day)


title: Sample_152_Subject_8_Control

description:
miRNA transcriptome data
PUT_600_S42_L002

value: Left

value: Never


title: 2A3

description: RiboZero bacterial rRNA depletion

tag: agent

value: Untreated

tag: genotype

value: osrR Mutant

value: 2A3 Expt. 3


title: 1B3

description: RiboZero bacterial rRNA depletion

value: Treated with Menadione

value: wildtype

value: 1B3 Expt. 3


title: Sample_147_Subject_3_Control

description:
miRNA transcriptome data
477_PUT_167_026_S38_L001

value: Female

tag: batch

tag: brainweight

value: Current


title: Sample_148_Subject_4_AlcoholUseDisorder

description:
miRNA transcriptome data
PUT_530_S39_L002

value: AlcoholUseDisorder

tag: brainph

value: Right

value: Toxicity


title: Sample_150_Subject_6_AlcoholUseDisorder

description:
miRNA transcriptome data
584_PUT_018_175_S39_L001

tag: pmi

value: Respiratory


title: BM_untreated_rep3

city: Melbourne

first: Rachel

middle: M

last: Koldej

address: 305 Grattan St

institute: Melbourne Health

hyb_protocol: as per manufacturers instructions

scan_protocol: as per manufacturers instructions

data_processing: Analysed using nCounter Advanced Analysis (version 2.0.115; NanoString Technologies) as per manufacturers instructions

label: Nanostring ncounter probes

source_name: C57BL/6 mouse BM untreated mouse

label_protocol: as per manufacturers instructions

extract_protocol: RNA extracted using Qiagen Rneasy kit

tag: tissue

value: bone marrow

tag: gender

tag: age

value: 6-8 weeks

tag: treatment

value: untreated

tag: days post drug treatment

value: not applicable


title: BM_Rux_D7_rep3

source_name: C57BL/6 mouse BM 7 day post treatment with ruxolitinib

value: Ruxolitinib


title: CD8SP long-read [CD8SP_CCS]

city: Fitzroy

first: Mark

last: Chong

state: Victoria

address: 9 Princes Street

institute: St Vincent's Institute of Medical Research

data_processing:
PacBio circular consensus sequencing data were processed using Iso-Seq SMRT Link (version 5.0.1.9585) to identify high-quality full-length sequences.
High-quality full-length sequences were mapped to mouse genome by GMAP (version2016-11-07). Cupcake ToFU (v9.0.2) was used to collapse redundant sequences and unify the CD4SP and CD8SP libraries.
SQANTI2 (version3.6) was used to perfom isoform quality assessment and annotation.
Filtered high-quality full-length PacBio transcripts were served as a reference.
FastQC was used to check Illumina short reads quality and Trimmomatic was used to trim and remove low quality reads.
RSEM (version 1.3.1) was used to align processed Illumina short reads to previously contructed full-length transcript reference.
SUPPA2 (version2.3) was used to identify alternative splicing patterns in full-length transcript reference and percentage of spliced-in (PSI) values were quantified using processed Illumina short reads.
Identifying splicing isoforms based on only Illumina data: Illumina short reads quaility was checked by FastQC and filtered and trimmed by Trimmomatic. Processed short reads were aligned to mouse reference by TopHat  (v2.0.14) and then assembled by Cufflinks (v2.1.1). Two assemblies of CD4SP and CD8SP were compared by Cuffcompare.
Genome_build: GRCm38.97
Supplementary_files_format_and_content: PacBio long-read annotation information and normalised read counts. GTF files from Illumina short reads assemblies (including FPKM values)

source_name: CD8SP thymocytes

growth_protocol: C57BL/6 mice at 6-8-week of age were euthanised by asphyxiation with CO2 and the thymi were excised and placed in RPMI 1640 medium. Thymi were passed through a 100µm stainless steel mesh to produce single cell suspensions of thymocytes.

extract_protocol:
Total RNA was then extracted from the sorted cells with on GenElute Total RNA Purification columns (Sigma).
PacBio libraries were constructed following the IsoSeq Express Template Preparation for Sequel Systems protocol (www.pacb.com). For this procedure, first strand cDNA synthesis was performed using SMARTer PCR cDNA Synthesis Kit (Clontech), which also add necessary adaptor sequences for subsequent PCR amplification. PCR amplification of the cDNA was then performed using PrimerSTAR GXL DNA Polymerase (Clontech) and purified using AMPure PB magnetic beads (PacBio). The purified cDNAs were then end-repaired and ligated using the Template Prep Kit (PacBio) to generate the circular SMRTbell libraries. Each library was then sequenced on individual PacBio SMRT cells. For Illumina libraries, the RNA concentration and integrity of samples were first determined with a LabChip GX (Perkin Elmer). Paired-end RNA-seq libraries were then constructed with the TruSeq total RNA sample preparation kit with rRNA-depletion (Illumina) and sequenced on an Illumina NextSeq at the Ramaciotti Centre for Genomics, University of New South Wales.

treatment_protocol: Two or three thymi were pooled for each sample and then depleted of CD4 expression cells (DP and CD4SP) or CD8 expressing cells (DP and CD8SP) using anti-CD4 or CD8 MACS magnetic beads (Miltenyi). The depleted samples were then sorted for mature CD4SP (CD4+CD8-TCRß+CD24-) or CD8SP (CD8+CD4-TCRß+CD24-) thymocytes on a FACS Aria Fusion (BD).

value: thymus

value: Sorted for mature CD8SP (CD8+CD4-TCRbeta+CD24-) from CD4 depleted samples


title: ko-Tterm-rep3

description: BV605, APC, BUV395, PERCPCy5.5

tag: infection

value: LCMV d24


title: Subject_12_AlcoholUseDisorder

description:
Sample_180
miRNA transcriptome data

tag: alcoholdailyuse(gram/day)

value: Male

tag: rin

tag: leftrightbrain

value: Left

tag: causeofdeathcategory

value: Cardiac

tag: smoking

tag: liverclass

value: Normal


title: CD4SP long-read [CD4SP_CCS]

source_name: CD4SP thymocytes

tag: strain

tag: cell type

value: Sorted for mature CD4SP (CD4+CD8-TCRbeta+CD24-) from CD8 depleted samples


title: 1A1

description: RiboZero bacterial rRNA depletion

tag: agent

value: Untreated

tag: genotype

value: wildtype

tag: experiment

value: 1A1 Expt. 1


title: 1 OP9 ctrl1

tag: cell line

value: stroma


title: BM_Rux_D7_rep2

tag: tissue

value: bone marrow

tag: gender

value: Female


title: BM_Rux_Vehicle_D7_rep1

source_name: C57BL/6 mouse BM 7 day post treatment with ruxolitinib vehicle

tag: age

value: 6-8 weeks

tag: treatment

value: Ruxolitinib vehicle


title: Subject_24_AlcoholUseDisorder [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_120

source_name: Human postmortem nucleus accumbens

tag: aud status

value: AlcoholUseDisorder

tag: Sex

tag: batch

tag: brainweight

tag: brainph

tag: pmi

value: Cardiovascular

value: Current

value: Steatosis


title: BM_Rux_D7_rep1

value: Ruxolitinib

tag: days post drug treatment


title: ko-Teff-l-rep4

description: BV605, APC, BUV395, PERCPCy5.5

tag: infection

value: LCMV d24

tag: strain


title: ko-Tterm-rep1

description: BV605, APC, BUV395, PERCPCy5.5


title: BM_Ven_D7_rep3

source_name: C57BL/6 mouse BM 7 day post treatment with venetoclax

value: Venetoclax


title: Subject_23_AlcoholUseDisorder [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_119

tag: alcoholdailyuse(gram/day)

tag: rin

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Toxicity

tag: smoking

value: Never

tag: liverclass


title: Sample_145_Subject_1_Control

description:
miRNA transcriptome data
453_PUT_179_014_S37_L001

value: Control

tag: alcoholdailyuse (gram/day)

value: Male

value: Left

value: Cardiac

value: MildSteatosis


title: BM_Rux_Vehicle_D7_rep2

tag: tissue

value: bone marrow

tag: gender

value: Female

tag: age

value: 6-8 weeks

tag: treatment


title: Subject_21_AlcoholUseDisorder [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_117

tag: aud status

value: AlcoholUseDisorder

tag: Sex

tag: batch

tag: brainweight

value: Cirrhosis


title: ko-Tterm-rep2

description: BV605, APC, BUV395, PERCPCy5.5

tag: infection


title: Subject_22_Control [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_118

tag: brainph

tag: pmi

value: Normal


title: BM_Ven_D7_rep1

tag: strain

tag: days post drug treatment


title: ko-Teff-l-rep3

description: BV605, APC, BUV395, PERCPCy5.5


title: ko-Teff-l-rep2

description: BV605, APC, BUV395, PERCPCy5.5


title: ko-Teff-l-rep1

description: BV605, APC, BUV395, PERCPCy5.5


title: BM_Ven_Vehicle_D7_rep1

source_name: C57BL/6 mouse BM 7 day post treatment with venetoclax vehicle

value: Venetoclax vehicle


title: Subject_20_Control [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_116

tag: alcoholdailyuse(gram/day)

tag: rin

tag: leftrightbrain

tag: causeofdeathcategory

value: Unknown

value: Congestion


title: Subject_19_Control [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_115

value: Right

tag: smoking

value: Current

tag: liverclass


title: BM_Ven_Vehicle_D7_rep2

tag: tissue

tag: gender

tag: age


title: ko-Tstem-l-rep3

description: BV605, APC, BUV395, PERCPCy5.5

value: LCMV d24


title: ko-Tstem-l-rep4

description: BV605, APC, BUV395, PERCPCy5.5


title: Subject_18_AlcoholUseDisorder [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_114

tag: aud status

tag: Sex

value: Hepatic

value: Steatosis


title: Subject_17_Control  [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_113

value: Control

value: Male

tag: batch

tag: brainweight

value: Vascular


title: BM_Ven_D7_rep2

value: bone marrow

tag: treatment

value: Venetoclax


title: BM_untreated_rep2

value: Female

value: 6-8 weeks

value: untreated

value: not applicable


title: BM_Rux_D3_rep3

source_name: C57BL/6 mouse BM 3 day post treatment with ruxolitinib

value: Ruxolitinib


title: US-1675329_edlMusc__lean

city: Seattle

first: Sara

middle: A

last: Murray

state: WA

address: 530 Fairview Ave N

department: Obesity Research Group

institute: Novo Nordisk Research Center Seattle, Inc.

data_processing:
fastqc sequencing quality assessment
STAR alignment of sequenced reads
HTseq read counting
QC using DESeq2 guidelines: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html
Low expression filter: genes that had a total count of >= 10 across all samples within a tissue type were included in the analysis
Count normalization with 'normTransform' (DESeq2)
Differential gene expression between DIO and Lean mice within each tissue type was run with DESeq2 'results'
Genome_build: Mmusculus_GRCm38r90
Supplementary_files_format_and_content: Normalized read counts

source_name: EDL muscle

growth_protocol: Adult wild-type male C57BL/6J mice aged 6-12 weeks were obtained from Jackson Laboratories (Stock # 000664). Mice were housed 4-8 per cage with ad libitum access to water and food (Type IV Scanbur Cages; 1800 cm2 floor area). Mice were acclimated to housing for one week and then marked with 2D barcode ear tags. Animal holding rooms temperature ranged from 20-26 °C and humidity ranged from 30-70%. Lighting was on an automated light/dark cycle with lights on between 6:00 AM and 6:00 PM. Mice were provided with Alpha Dri bedding material to just cover the bottoms of cages cage, one Nestlet square, and two 8g Bed-r’Nest “pucks” or similar. Environmental enrichment included a plastic hut, a paper hut, one wood gnawing block, and a tunnel suspended from the top of cages. Mice received a hydrogel cup upon arrival until familiarized with the automatic water system which supplied reverse osmosis purified water via the Scantainer rack system. Standard rodent chow diet [PicoLab Rodent Diet 20 Lab Diet #5R53 (24.5% Protein, 13.1% Fat, 62.4% Carbohydrate)] was provided to the mice upon arrival until diet was switched from chow to high fat.

extract_protocol:
Mice were sacrificed and tissues of interest were extracted and kept at -80 °C until RNA extraction.  RNA isolated from frozen tissue chunks using RNAeasy kit (Qiagen).
Isolated RNA was sent for RNA-sequencing at the Covance Genomics Lab, Redmond, WA. cDNA libraries were prepared with Illumina TruSeq stranded mRNA kit and sequenced on an Illumina HiSeq. 2000 using paired-end, 100 nucleotide reads with an average depth of 20 million reads per sample.

treatment_protocol: At 4 weeks of age mice were placed on a 60% high fat diet (High-Fat Diet #D12492 (20.0% Protein, 60% Fat, 20% Carbohydrate) during 10 weeks and they reached dietary induced obese status (DIO). After this point, mice were moved from group housing to 2 mice per Type IV Scanbur cage, separated by an opaque cage divider. Food and water were provided ad lib.  Transcriptomic profile from 19 tissues, comparing control chow diet and HFD diet interventions were carried out.

tag: status

value: Lean


title: US-1675330_edlMusc__lean


title: US-1675327_edlMusc_DIO

value: DIO


title: US-1675328_edlMusc_DIO


title: Subject_16_AlcoholUseDisorder [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_112

value: AlcoholUseDisorder

tag: brainph

tag: pmi

value: Left

value: Cirrhosis


title: ko-CX3CR1+Tstem-l-rep4

description: BV605, APC, BUV395, PERCPCy5.5

tag: infection

value: LCMV d24

tag: strain


title: BM_Rux_D3_rep2

tag: days post drug treatment


title: US-1675331_edlMusc__lean


title: Subject_14_AlcoholUseDisorder [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_110

tag: alcoholdailyuse(gram/day)

tag: rin

tag: leftrightbrain

tag: causeofdeathcategory

value: Toxicity

value: Current


title: US-1675332_edlMusc__lean


title: US-1675326_edlMusc_DIO


title: BM_Rux_Vehicle_D3_rep2

source_name: C57BL/6 mouse BM 3 day post treatment with ruxolitinib vehicle

tag: tissue

tag: gender

value: Ruxolitinib vehicle


title: BM_Rux_D3_rep1

tag: age


title: ko-CX3CR1+Tstem-l-rep3

description: BV605, APC, BUV395, PERCPCy5.5


title: BM_Rux_Vehicle_D3_rep1


title: ko-CX3CR1+Tstem-l-rep2

description:
excluded due to normalization flag
BV605, APC, BUV395, PERCPCy5.5


title: US-1675325_edlMusc_DIO


title: BM_Ven_D3_rep3

source_name: C57BL/6 mouse BM 3 day post treatment with venetoclax


title: ko-CX3CR1+Tstem-l-rep1

description: BV605, APC, BUV395, PERCPCy5.5


title: Subject_13_Control  [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_109

tag: aud status

value: Control

tag: Sex

value: Male

value: Cardiac

tag: smoking

value: Never

tag: liverclass

value: Normal


title: Subject_15_Control [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_111

value: Female

tag: batch

tag: brainweight


title: BM_Ven_D3_rep2

value: bone marrow

value: 6-8 weeks

tag: treatment

value: Venetoclax


title: Subject_10_Control  [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_106

tag: brainph

tag: pmi

value: Congestion


title: BM_Ven_Vehicle_D3_rep2

source_name: C57BL/6 mouse BM 3 day post treatment with venetoclax vehicle

tag: strain

value: Venetoclax vehicle

tag: days post drug treatment


title: Subject_11_Control  [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_107

tag: alcoholdailyuse(gram/day)

tag: rin

value: Left


title: ko-Tstem-l-rep1

description: BV605, APC, BUV395, PERCPCy5.5

tag: infection


title: US-1675323_edlMusc_DIO

tag: status

value: DIO


title: BM_Ven_Vehicle_D3_rep1

tag: tissue

tag: gender


title: BM_untreated_rep1

tag: age

value: untreated

value: not applicable


title: wt-Teff-l-rep3

description: BV605, APC, BUV395, PERCPCy5.5

source_name: spleen,wt

value: LCMV d24


title: US-1675322_retroFat__lean

source_name: Retro FAT

value: Lean


title: BM_Rux_D1_rep3

source_name: C57BL/6 mouse BM 1 day post treatment with ruxolitinib

value: Ruxolitinib


title: ko-Tstem-l-rep2

source_name: spleen, Cxcl10-/-


title: Subject_8_Control [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_104

tag: aud status

value: Control

tag: Sex

value: Male

tag: leftrightbrain

tag: causeofdeathcategory

value: Steatosis


title: Subject_7_AlcoholUseDisorder [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_103

value: AlcoholUseDisorder

tag: batch

tag: brainweight

value: Right

value: Cardiac

tag: smoking

value: Current

tag: liverclass

value: Cirrhosis


title: US-1675320_retroFat__lean


title: Subject_9_AlcoholUseDisorder [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_105

tag: brainph

tag: pmi

value: Toxicity


title: BM_Ven_D3_rep1

tag: strain

value: bone marrow

value: Female

value: 6-8 weeks

tag: treatment

value: Venetoclax

tag: days post drug treatment


title: wt-Tterm-rep4

description: BV605, APC, BUV395, PERCPCy5.5

tag: infection


title: US-1675317_retroFat__lean

tag: status


title: US-1675314_retroFat_DIO

value: DIO


title: wt-Teff-l-rep1

description: BV605, APC, BUV395, PERCPCy5.5

value: LCMV d24


title: Subject_4_AlcoholUseDisorder [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_100

tag: alcoholdailyuse(gram/day)

tag: rin

value: Normal


title: US-1675313_retroFat_DIO


title: wt-Tstem-l-rep4

description: BV605, APC, BUV395, PERCPCy5.5


title: wt-Tterm-rep1

description: BV605, APC, BUV395, PERCPCy5.5


title: Subject_12_AlcoholUseDisorder [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_108

tag: aud status

value: Left


title: Subject_3_Control  [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_99

value: Control

tag: Sex


title: US-1675312_retroFat_DIO


title: wt-Tterm-rep2

description: BV605, APC, BUV395, PERCPCy5.5


title: wt-Tstem-l-rep3

description: BV605, APC, BUV395, PERCPCy5.5


title: wt-Tterm-rep3

description: BV605, APC, BUV395, PERCPCy5.5


title: US-1675316_retroFat_DIO


title: Subject_6_AlcoholUseDisorder [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_102

tag: leftrightbrain

value: Respiratory


title: US-1675318_retroFat__lean

value: Lean


title: BM_Ven_D1_rep3

source_name: C57BL/6 mouse BM 1 day post treatment with venetoclax

tag: tissue

tag: gender

tag: age


title: Subject_1_Control  [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_97

value: Male

tag: batch

tag: brainweight

tag: causeofdeathcategory

tag: smoking

value: Never

value: MildSteatosis


title: US-1675310_eWAT__lean

source_name: eWAT


title: Subject_5_AlcoholUseDisorder [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_101

value: AlcoholUseDisorder

tag: brainph

tag: pmi

value: Right

value: Current

tag: liverclass


title: US-1675319_retroFat__lean


title: wt-CX3CR1+Tstem-l-rep4

description: BV605, APC, BUV395, PERCPCy5.5

tag: infection

tag: strain


title: BM_Rux_D1_rep1

value: bone marrow

tag: treatment

value: Ruxolitinib

tag: days post drug treatment


title: Subject_24_AlcoholUseDisorder [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_144

source_name: Human postmortem prefrontal cortex

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: rin

value: Cardiovascular

value: Steatosis


title: Subject_2_Control  [Human postmortem nucleus accumbens]

description:
mRNA transcriptome data
Sample_98

tag: Sex

value: Female

tag: leftrightbrain

value: Cardiac

value: Unknown


title: Subject_22_Control [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_142

value: Left

value: Normal


title: Subject_21_AlcoholUseDisorder [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_141

value: Cirrhosis


title: wt-CX3CR1+Tstem-l-rep1

description: BV605, APC, BUV395, PERCPCy5.5

value: LCMV d24


title: BM_Rux_D1_rep2

tag: tissue

tag: gender

tag: age

value: 6-8 weeks


title: Subject_20_Control [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_140

value: Control

tag: batch

tag: brainweight

tag: causeofdeathcategory

value: Toxicity

value: Congestion


title: Human chimpanzee embryoids at 48h

city: Syracuse

first: Yi

last: Zheng

address: 900 S Crouse Ave

department: Biomedical and Chemical Engineering

institute: Syracuse University

data_processing:
see the associated publication
Genome_build: GRCh38.p13 and Pan_tro_3.0
Supplementary_files_format_and_content: .Rd files are the output of R Studio containing the data anlaysis ressults. The .Rd files can be loaded into RStudio using "load ("file_name.Rd")", and analyzed using the Seurat R package (https://satijalab.org/seurat/). In case of difficulties accessing the data, please contact Dr. Yi Zheng (zhengum@umich.edu)

organism: Pan troglodytes

source_name: microfluidic embryoids

growth_protocol: see the associated publication

extract_protocol:
see the associated publication
10x genomics

treatment_protocol: see the associated publication

tag: genotype

value: wildtype


title: BM_Ven_D1_rep2

value: Venetoclax


title: US-1675305_eWAT_DIO

tag: status

value: DIO


title: Subject_23_AlcoholUseDisorder [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_143

value: AlcoholUseDisorder

tag: brainph

tag: pmi

value: Right

tag: smoking

value: Never

tag: liverclass


title: US-1675311_retroFat_DIO


title: BM_Ven_D1_rep1

tag: strain

value: bone marrow

value: Female

tag: treatment

tag: days post drug treatment


title: US-1675308_eWAT__lean

value: Lean


title: BM_Rux_Vehicle_D1_rep1

source_name: C57BL/6 mouse BM 1 day post treatment with ruxolitinib vehicle

value: Ruxolitinib vehicle


title: BM_Rux_Vehicle_D1_rep2


title: wt-Tstem-l-rep1

description: BV605, APC, BUV395, PERCPCy5.5

tag: infection


title: wt-Teff-l-rep2

description: BV605, APC, BUV395, PERCPCy5.5


title: BM_Ven_Vehicle_D1_rep2

source_name: C57BL/6 mouse BM 1 day post treatment with venetoclax vehicle

value: Venetoclax vehicle


title: US-1675309_eWAT__lean


title: US-1675304_eWAT_DIO


title: wt-CX3CR1+Tstem-l-rep3

description: BV605, APC, BUV395, PERCPCy5.5


title: wt-CX3CR1+Tstem-l-rep2

description: BV605, APC, BUV395, PERCPCy5.5


title: wt-Tstem-l-rep2

description: BV605, APC, BUV395, PERCPCy5.5


title: Galac_F

city: Merelbeke

first: Yu

last: Wang

address: Salisburylaan 133, D5

country: Belgium

institute: Ghent University

data_processing:
Quality control: Raw data (raw reads) of FASTQ format were firstly processed through fastp. In this step, clean data (clean reads) were obtained by removing reads containing adapter and poly-N sequences and reads with low quality from raw data. At the same time, Q20, Q30 and GC content of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Mapping to reference genome: Reference genome and gene model annotation files were downloaded from genome website browser (NCBI/UCSC/Ensembl) directly. Paired-end clean reads were mapped to the reference genome using HISAT2 software.
Quantification: Featurecounts was used to count the read numbers mapped of each gene, including known and novel genes. And then RPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis: (For DESeq2 with biological replicates) Differential expression analysis between two conditions/groups (three biological replicates per condition) was performed using DESeq2 R package. The resulting P values were adjusted using the Benjamini and Hochberg’s approach for controlling the False Discovery Rate (FDR). Genes with an adjusted P value < 0.05 found by DESeq2 were assigned as differentially expressed.
Genome_build: GCA_002006685.1
Supplementary_files_format_and_content: readcount_genename.txt

organism: Batrachochytrium salamandrivorans

source_name: Batrachochytrium salamandrivorans (AMFP 13/01)

growth_protocol: Bsal type strain (AMFP 13/01) (Martel et al., 2013) was grown in tryptone-gelatin hydrolysate-lactose (TGhL) broth and incubated for 5-7 days at 15 °C. Zoospores were harvested from 175 cm2 cell culture flasks by replacing the TGhL broth with distilled water, which was filtered using a sterile mesh filter with pore size 10 µm (Pluristrainer, PluriSelect).

extract_protocol:
RNA was extracted using the RNeasy mini kit (Qiagen). The RNA was treated with Turbo™ DNase (Ambion), following the manufacturer's instructions. RNA degradation and contamination was monitored on 1% agarose gels. The RNA purity was checked using the NanoPhotometer® spectrophotometer (IMPLEN, CA, USA). Finally, the RNA integrity and quantitation were assessed using the RNA Nano 6000 assay kit of the Bioanalyzer 2100 system (Agilent Technologie, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Six independent pools containing 4 x 10e7 zoospores were obtained (biological replicates). Per pool, the spores were divided in 4 eppendorfs (107 zoospores/eppendorf) which were treated for 1 hour at 15°C with H2O (control), 50 mM α-D-galactose, 50 mM α-D-glucose or 50 mM α-D-mannose. After 1 hour, the zoospores were centrifuged for 5 min at 3000 rpm at 15°C to remove the supernatant, after which RNA was extracted.

tag: sample type

value: zoospores

tag: zoospore pool/biological replicate

value: pool F

value: Galactose treated (50 mM)

tag: duration treatment

value: 1 hour


title: BM_Ven_Vehicle_D1_rep1

tag: tissue

tag: gender

tag: age

value: 6-8 weeks


title: Subject_18_AlcoholUseDisorder [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_138

tag: aud status

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Male

tag: batch

tag: rin

tag: brainweight

tag: leftrightbrain

tag: causeofdeathcategory

value: Hepatic

value: Current

value: Steatosis


title: Gluc_F

tag: strain

tag: treatment

value: Glucose treated (50 mM)


title: HEPM_10_c: circRNA-SAG-2

city: Huddinge

first: Ani

last: Azatyan

state: Stockholm

address: Hälsovägen 7C

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

data_processing:
Illumina bcl2fastq (v2.20.0) was used for basecalling and demultiplexing.
Read quality was checked for each sample using FastQC (v0.11.8).
Reads were aligned to Ensemble GRCh38 reference genome using TopHat (v2.1.0).
Read summarization to gene counts was performed using featureCounts (v1.5.1).
Normalized counts were generated using DESeq2 (v1.22.2).
Genome_build: GRCh38/hg38.
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample.

growth_protocol: The Daoy medulloblastoma and HEPM (CRL-1486) human embryonic palatal mesenchyme cells were cultured in EMEM medium with L-glutamine (Lonza, Switzerland) and UW-228 cells in DMEM/F12 (1:1) medium with L-glutamine (11320033, Gibco, USA), supplemented with 10 % fetal bovine serum (FBS) (A31608-02, Gibco) and 100 IU/ml penicillin/streptomycin (15140-122, Gibco) and maintained in 5 % CO2 humidified incubator at 37˚C.

extract_protocol:
Total RNA from cell lines or the medulloblastoma tumor sample was isolated with E.Z.N.A total RNA kit I (R6834-02) or total RNA midi kit (R6664-02) (Omega Bio-tek, USA) according to the manufacturer’s instructions. On-column DNA digestion was performed with 40 KU (R6834-02 kit) and 60 KU (R6664-02 kit) of DNase (79254, Qiagen, Germany).
a) Poly(A) enriched fraction: ≈ 100 ng of total RNA was used to generate stranded mRNA libraries with the TruSeq®Stranded mRNA Low Throughput Sample Preparation kit according to the manufacturer’s instructions (15031047, Illumina, USA). This protocol involves a poly(A) selection/enrichment and ribosomal RNA depletion step.
b) circRNA enriched fraction: 5 μg of total RNA was used. First, ribosomal RNA was depleted using the RiboMinusTM Eukaryote System V2 (Ambion) (A15026, ThermoFisher USA), followed by digestion with 5U RNase R for 1 hr to degrade linear RNAs and purification with the RNeasy MinElute Cleanup Kit (74204, Qiagen). The concentration and quality of the enriched circRNA RiboMinus/RNase R preparations were assessed with an Agilent 2100 Bioanalyzer (Agilent Technologies, USA). 4.4 ng (for Daoy cells) or 1 ng (for HEPM cells) of RiboMinus/RNase R treated RNA was used for cDNA library generation. Random hexamer primers and Superscript III reverse transcriptase (18080055, Invitrogen, USA) were used for 1st strand synthesis and stranded mRNA library was generated according to the TruSeq®Stranded mRNA Low Throughput Sample Preparation protocol (15031047, Illumina, USA) as described above. The concentration and quality of the cDNA libraries were assessed with Qubit (Life Technologies, USA) and TapeStation, respectively. The cDNA libraries were normalized and pooled for sequencing on the Illumina NextSeq 550 platform using the Illumina NextSeq 500/550 High Output v2 kit (75 cycles; single read).

treatment_protocol: The Smoothened agonist (SAG, 566660) was purchased from Merck (Germany) and the recombinant human Sonic Hedgehog N-terminus ligand (SHH-C24II, 185-SH) was purchased from R&D Systems (USA). SAG was dissolved and diluted in DMSO, and SHH was dissolved and diluted in PBS with 0.1 % BSA. Daoy cells were seeded in 6-well plates at ≈ 30 % confluency in complete medium, then starved in Optimem medium (11058-021, Gibco) for 24 hr and treated with either 200 nM SAG in EMEM medium supplemented with 0.5 % FBS for 72 hr or with 400 ng/ml SHH in Optimem for 72 hr. From each treatment condition two separate wells were combined and processed further for RNA isolation. Similarly, for the control (Ctr) treatments, cells were either starved in Optimem for 24 hr and mock-treated with SAG solvent (DMSO) in EMEM medium supplemented with 0.5 % FBS for 72 hr (SAG_Ctr) or with SHH solvent (0.1 % BSA in PBS) in Optimem for 72 hr (SHH_Ctr). HEPM cells were seeded in 10 cm cell culture dishes at ≈ 40 % confluency in complete medium, then starved in Optimem for 24 hr and treated with either 200 nM SAG or 400 ng/ml SHH in Optimem medium for 72 hr or with DMSO + 0.1 % BSA in PBS as the control treatment.

tag: organ

value: embryonic palatal mesenchyme

tag: tissue type

value: palatal mesenchyme, epithelial morphology

tag: cell line

value: HEPM

tag: molecule

value: circRNA / (poly(A-) / RNaseR+)

value: SAG-200 nM


title: HEPM_12_c: circRNA-SAG-4

source_name: HEPM (CRL-1486) human embryonic palatal mesenchyme cells


title: Subject_19_Control [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_139

value: Control

value: Female

tag: brainph

tag: pmi

value: Right

value: Cardiac

tag: smoking

tag: liverclass

value: Congestion


title: US-1675302_eWAT_DIO

tag: status

value: DIO


title: Subject_16_AlcoholUseDisorder [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_136

tag: aud status

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

tag: Sex

value: Left

value: Cirrhosis


title: Galac_E

tag: sample type

value: zoospores

tag: zoospore pool/biological replicate

value: pool E

value: Galactose treated (50 mM)

tag: duration treatment

value: 1 hour


title: US-1675306_eWAT__lean

value: Lean


title: US-1675307_eWAT__lean


title: HEPM_11_c: circRNA-SAG-3

value: embryonic palatal mesenchyme

value: palatal mesenchyme, epithelial morphology

value: HEPM


title: US-1675300_eWAT_DIO


title: H2O_E

tag: strain

value: H2O treated


title: H2O_F

value: pool F

tag: treatment


title: HEPM_8_c: circRNA-SHH-4

tag: organ

value: circRNA / (poly(A-) / RNaseR+)

value: SHH-400 ng/ml


title: Subject_17_Control  [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_137

value: Control

value: Male

tag: batch

tag: rin

tag: brainweight

tag: leftrightbrain

value: Right

tag: causeofdeathcategory

value: Vascular

value: Normal


title: HEPM_7_c: circRNA-SHH-3

tag: tissue type

tag: cell line

tag: molecule


title: Man_F

value: zoospores

value: Mannose treated (50 mM)


title: US-1675303_eWAT_DIO

tag: status

value: DIO


title: US-1675299_colon__lean

source_name: Colon


title: Man_E

value: pool E

value: 1 hour


title: US-1675298_colon__lean

value: Lean


title: HEPM_9_c: circRNA-SAG-1

value: embryonic palatal mesenchyme

value: palatal mesenchyme, epithelial morphology

value: SAG-200 nM


title: HEPM_5_c: circRNA-SHH-1

value: HEPM


title: Subject_14_AlcoholUseDisorder [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_134

tag: aud status

value: AlcoholUseDisorder

tag: alcoholdailyuse(gram/day)

value: Female

tag: brainph

tag: pmi

value: Left

value: Toxicity

tag: smoking

value: Current

tag: liverclass

value: Cirrhosis


title: Subject_13_Control  [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_133

value: Control

tag: Sex

value: Male

value: Cardiac

value: Never

value: Normal


title: Subject_12_AlcoholUseDisorder [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_132


title: Gluc_D

tag: strain

tag: sample type

value: zoospores

tag: zoospore pool/biological replicate

value: pool D

tag: treatment

value: Glucose treated (50 mM)

tag: duration treatment

value: 1 hour


title: Gluc_E

value: pool E


title: HEPM_3_c: circRNA-DMSO/PB-3

tag: organ

value: embryonic palatal mesenchyme

value: palatal mesenchyme, epithelial morphology

value: HEPM

value: circRNA / (poly(A-) / RNaseR+)

value: Control-DMSO-PBS/BSA


title: Subject_10_Control  [Human postmortem prefrontal cortex]

description:
mRNA transcriptome data
Sample_130

tag: batch

tag: rin

tag: brainweight

tag: leftrightbrain

value: Left

tag: causeofdeathcategory

value: Current

value: Congestion


title: HEPM_4_c: circRNA-DMSO/PB-4

tag: tissue type

tag: cell line

tag: molecule


title: H2O_D

value: H2O treated


title: HEPM_6_c: circRNA-SHH-2

value: SHH-400 ng/ml


title: HEPM_2_c: circRNA-DMSO/PB-2


title: US-1675295_colon__lean

tag: status

value: Lean


title: Man_D

value: Mannose treated (50 mM)


title: US-1675286_colon__lean