title: 29007_S154_priod2

city: NANTES

first: Isabelle

last: Girault

state: PAYS-DE-LA-LOIRE

address: 22 BOULEVARD BENONI GOULIN

country: France

institute: OSE IMMUNOTHERAPEUTICS

data_processing:
The raw files fastq were evaluated for the quality of sequencing by fastQC bioinformatic tool
Reads were pseudo-aligned to CRGh38/hg38 using bioinformatic tool salmon with the index preparation option –genecode, and raw count table and normalized TPM table for reads number for each gene were generated using bioinformatic tool salmon with the option --geneMap
Pseudo mapping quality reads were evaluated using fastQC bioinformatic tool, with an average of 20 to 30M reads with more than 90% bases >= 30for all the samples
Assembly: CRGh38/hg38
Supplementary files format and content: csv files for raw count values for each sample
Supplementary files format and content: csv files for TPM count values for each sample

source_name: blood

extract_protocol:
blood collected in Paxgen tubes and RNA extracted with Paxgen Blood RNA kit
total RNA with rRNA and globin depletion
150-base pair-end sequenced on an Illumina HiSeq by Genewiz company

value: blood

tag: dose

value: 10 mg/kg


title: 29007_S154_priod1

status: Public on Feb 01 2023

type: SRA

library_source: transcriptomic

molecule: total RNA

organism: Homo sapiens

tag: tissue

tag: time

tag: treatment


title: 29006_S149_priod2


title: 29006_S149_priod1


title: proliferating ctrl R2 2018

city: Stuttgart

first: Stefan

last: Legewie

address: Allmandring 30E

department: Institute of Biomedical Genetics, Systems Biology

country: Germany

institute: University of Stuttgart

description:
DEseq_proliferating_6h_TGFB_vs_proliferating_ctrl.csv
rpkm_proliferating_ctrl.csv

data_processing:
Samples were demultiplexed (bcl2fastq v.2.19.1.403, Illumina) and FastQ files were generated.
Raw sequence reads were assessed with FastQC (v.0.11.5, Babraham Bioinformatics) and aligned to the human reference genome GRCh38.p7 (GTF annotation file from Gencode human release 25) using STAR aligner v.2.5.2b (3).
Mapped data were summarized on the gene level using the featureCounts software (v.1.6.2, Subread) (4). Further data evaluation, normalization and pairwise differential expression analyses were carried out in R (v.3.5.0) using the Bioconductor package DESeq2 (v.1.20.0) following the recommended analysis workflow (5).
To calculate the robust reads per kilobase of transcript per million mapped reads (RPKMs) for each gene, the Bioconductor
packages GenomicRanges (v.1.32.1) and (v.1.40.6) with the above mentioned GTF annotation file and robust fragments per million (FPM) data computed by DESeq2 were used (6, 7).
To calculate fold changes, this package uses a maximum likelihood model with the assumption of a negative binomial distribution of reads fitted to the read counts of all samples available for a given combination of conditions.
Additionally, based on those models, p-values were calculated for each fold change that refer to the differential expression compared to a reference condition
Assembly: human reference genome GRCh38.p7 (GTF annotation file from Gencode human release 25)
Supplementary files format and content: csv files include RPKM values for each Sample or fold-changes and BH adjusted p-Values

growth_protocol: MCF10A cell lines were cultured in DMEM/F12 growth-medium.  When required, the medium was supplemented with selective antibiotics to maintain transgene expression (400 μg/ml geneticin disulphate (G418, ROTH), 50 μg/ml hygromycin B (Thermo Fisher Scientific) or 5 μg/ml blasticidin S hydrochloride (ROTH))

extract_protocol:
Total RNA was isolated from the cells using the High Pure RNA Isolation Kit by Roche according to the manufacturer‘s instruction.
TruSeq stranded mRNA LT Sample Prep Kit (Illumina) was used according to the manufacturer’s instructions. Libraries were prepared with a starting amount of 500 ng RNA, amplified in 11 PCR cycles, and profiled using a DNA 1000 kit and a 2100 Bioanalyzer (both Agilent)
Afterwards, the libraries were quantified in a Qubit 2.0 Fluorometer using the dsDNA HS Assay Kit (both Thermo Fisher). All libraries were pooled in equimolar ratios and sequenced on the NextSeq 500 sequencing system (Illumina)

tag: cell line

tag: cell type

value: epithelial cell

tag: cell state

value: proliferating


title: 29005_S156_priod2


title: proliferating 3h TGFB R2 2018

description:
DEseq_proliferating_3h_TGFB_vs_proliferating_ctrl.csv
rpkm_proliferating_TGFB.csv

value: 100 pM TGFb


title: Damage-seq of BPDE-dG: 2 uM BPDE exposed genomic DNA from BEAS-2B cells rep 3

city: Zürich

first: Shana

last: Sturla

state: No

address: Schmelzbergstrasse 9

department: Department of Health Sciences and Technology

country: Switzerland

institute: ETH Zürich

description:
NGS9666
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.

library_source: genomic

data_processing:
Filteration of common adaptor contaminations and non-specific reads using BBMap v38.9.
The paired-end reads were mapped to the reference human genome hg38 using Burrows-Wheeler Aligner v0.7.17.
Deduplication using Picard tools v2.25.3.
Identify damage sites using customized scripts.
Normalization of damage level using size factor calculated by DESeq2 (Bioconductor 3.1.2).
Assembly: hg38
Supplementary files format and content: bigwig, normalized damage level along genome.
Supplementary files format and content: bigwig, mean of normalized damage level along genome calculated from biological triplicates.
Library strategy: Damage-seq

molecule: genomic DNA

growth_protocol: BEAS-2B cells were cultured in BEGM Bronchial Epithelial Cell Growth Medium Bullet Kit (Lonza, Basel, Switzerland) at 37 °C in a humidified atmosphere with 5% CO2.

extract_protocol:
Genomic DNA was extracted using the QIAamp DNA Mini kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.
Genomic DNA extracted from BEAS-2B cells was fragmented and ligated with customized adapter 1 using NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched using an anti-BPDE antibody and the damage site was marked by polymerase stalling using NEBNext Ultra II Q5 polymerase. Non-specific DNA fragments were removed using subtractive hybridization and the resulting DNA product was subjected to adapter 2 ligation. The ligation product were indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.

treatment_protocol: BEAS-2B cells grown in 10 cm dishes were exposed to (+)-anti-BPDE (0.25–2 μM) for 24 h. Negative control cells were exposed to 0.1% solvent (anhydrous tetrahydrofuran/5% triethylamine).

value: lung cell line

tag: genotype

value: wild type

value: exposed to 2 uM BPDE


title: 29005_S156_priod1


title: Damage-seq of BPDE-dG: 1 uM BPDE exposed BEAS-2B cells rep 2

description:
NGS10097
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.

value: exposed to 1 uM BPDE


title: Damage-seq of BPDE-dG: 2 uM BPDE exposed BEAS-2B cells rep 1

description:
NGS10099
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.


title: Placenta, Atp11a, HOM, 1e

city: Calgary

first: Myriam

last: Hemberger

state: Alberta

address: 3330 Hospital Dr NW

country: Canada

institute: University of Calgary

data_processing:
Libraries were sequenced on the Illumina NovaSeq 6000 to obtain ~33M reads per sample.
Library quality was assessed with FASTQC and visualized in Seqmonk.
Reads were then aligned with STAR using the GrCM38/mm10 build.
Count tables were assembled with htseq-count using the reverse strand and intersection-nonempty settings
Assembly: mm10
Supplementary files format and content: Tab delimited raw counts are provided for all samples

organism: Mus musculus

source_name: Placenta

growth_protocol: Whole placentas were dissected at E14.5, frozen in liquid nitrogen and stored at -80 until sample processing.

extract_protocol:
Total RNA was isolated from E14.5 frozen placentas with the mirVana™ miRNA Isolation Kit according to the manufacturer's protocol.
Libraries were constructed with the NEB Ultra II Directional RNA Library Prep, using poly-A capture for mRNA enrichment.

treatment_protocol: 6-11 placentas per genotype (WT,HET,KO)  in each mutant mouse line were selected for RNAseq analysis

value: Placenta

tag: mouse line

tag: age

value: KO

tag: litter


title: Placenta, Atp11a, HOM, 1d


title: proliferating ctrl R1 2018


title: Damage-seq of BPDE-dG: 1 uM BPDE exposed BEAS-2B cells rep 3

description:
NGS10098
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.


title: Placenta, Atp11a, HOM, 3d


title: 29004_S153_priod2

value: PLACEBO

value: 0 mg/kg


title: Placenta, Atp11a, HOM, 7e


title: Damage-seq of BPDE-dG: 1 uM BPDE exposed BEAS-2B cells rep 1

description:
NGS10096
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.


title: Placenta, Atp11a, HOM, 1c


title: proliferating 3h TGFB R1 2018


title: proliferating 3h TGFB R3 2018


title: Damage-seq of BPDE-dG: 0.5 uM BPDE exposed BEAS-2B cells rep 3

description:
NGS10095
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.

value: exposed to 0.5 uM BPDE


title: 29004_S153_priod1


title: proliferating 3h GDF11 R2 2020

description:
DEseq_proliferating_3h_GDF11_vs_proliferating_ctrl.csv
rpkm_proliferating_GDF11.csv

value: 10 nM GDF11


title: 29003_S151_priod2


title: Placenta, Atp11a, HOM, 1b


title: Placenta, Atp11a, HET, 7c

value: HET


title: Damage-seq of BPDE-dG: 0.5 uM BPDE exposed BEAS-2B cells rep 2

description:
NGS10094
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.


title: proliferating 3h GDF11 R1 2020


title: 29003_S151_priod1


title: Damage-seq of BPDE-dG: 0.5 uM BPDE exposed BEAS-2B cells rep 1

description:
NGS10093
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.


title: proliferating ctrl R2 2020

description:
DEseq_quiescent_ctrl_vs_proliferating_ctrl.csv
rpkm_proliferating_ctrl.csv


title: 29002_S147_priod2


title: Placenta, Atp11a, HET, 4c


title: proliferating 6h GDF11 R2 2020

description:
DEseq_proliferating_6h_GDF11_vs_proliferating_ctrl.csv
rpkm_proliferating_GDF11.csv


title: Damage-seq of BPDE-dG: 0.25 uM BPDE exposed BEAS-2B cells rep 3

description:
NGS10092
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.

value: exposed to 0.25 uM BPDE


title: Damage-seq of BPDE-dG: 0.25 uM BPDE exposed BEAS-2B cells rep 2

description:
NGS10091
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.


title: proliferating ctrl R1 2020


title: Placenta, Atp11a, HET, 4b


title: 29002_S147_priod1

value: blood


title: Damage-seq of BPDE-dG: 0.25 uM BPDE exposed BEAS-2B cells rep 1

description:
NGS10090
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.


title: proliferating 6h GDF11 R1 2020


title: Placenta, Atp11a, HET, 3b


title: 29001_S145_priod1

value: 10 mg/kg


title: Placenta, Atp11a, HET, 1i


title: Damage-seq of BPDE-dG: unexposed BEAS-2B cells rep 2

description:
NGS10088
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.

value: unexposed


title: 28004_S132_priod2


title: Placenta, Atp11a, HET, 1g


title: 28004_S132_priod1


title: Placenta, Atp11a, HET, 10a


title: NonAE_liver_nuclei_12

city: Edinburgh

first: John

middle: Roger

last: Wilson-Kanamori

address: 47 Little France Crescent

department: Centre for Inflammation Research

country: United Kingdom

institute: University of Edinburgh

description: 10x Genomics single nuclei 3' gene expression v3

library_source: transcriptomic single cell

data_processing:
Demultiplexing, alignment (to a modified version of the GRCh38 reference counting intronic reads in addition to those aligned to exons), and estimation of cell-containing partitions and associated UMIs using Cell Ranger 3.1.0
Quality control, normalisation, data integration, and downstream analysis using Seurat 4.1.1
Assembly: GRCh38 (Ensembl 93)
Supplementary files format and content: fastq: fastq files of individual samples; mtx: count matrix in sparse matrix format; barcodes: barcode ids per sample; features: feature ids per sample

source_name: NonAE liver explant

extract_protocol:
Tris-Salt-Tween based nuclei isolation
10x Genomics single nuclei 3’ gene expression v3
snRNA-seq (10x)

value: NonAE liver explant


title: Placenta, Atp11a, HET, 6d


title: GSC08, KDM1A, V, rep1

city: San Antonio

first: Zhenqing

last: Ye

state: TX

address: 8403 Floyd Curl Dr

department: 6Department of Population Health Sciences

country: USA

institute: UT Health San Antonio

data_processing:
Cut&Run-seq reads were trimmed from 3' end by discarding low quality bases, and aligned to reference genome, as well as subsequential processing by the pipeline nf-core/cutandrun
Basically, reads were aligned to the UCSC hg38 genome using Bowtie version 2.4.2. Only uniquely mapping reads with at most two mismatches were retained.
Peaks were called uing seacr v1.3 in the above nf-core pipeline with the significance cut-off q-value <=0.01, and the final peak set were merged from the consensus peaks
bigWig files were generated using the deeptools Python package. Score represents the normalized coverage of DNA fragments at a given genomic coordinate.
Assembly: hg38
Supplementary files format and content: bigWig, sicer peak
Library strategy: CUT&Tag

source_name: patient derived glioma stem cells

growth_protocol: patient derived GSCs were cultured as neurospheres in neurobasal medium (Invitrogen, Carlsbad, CA) supplemented with B27 serum-free supplement, EGF (20 ng/mL), bFGF (20 ng/mL), LIF (10 ng/mL) and heparin (5 µg/mL)

extract_protocol:
GSC082209 (GSC08) cells were treated with vehicle or NCD38 (5 μM) for 24 h and 250,000 cells per condition were used.
Libraries were amplified using barcoded primers using NEBNext HiFi 2x PCR Master mix. Post PCR cleanup was performed, and the eluted DNA was subjected to 38 bp paired-end sequencing using the Illumina NextSeq 500 system.

value: patient derived glioma stem cells

value: glioblastoma

tag: chip antibody

value: LSD1/KDM1A rabbit, (Abcam, Cat# ab17721)


title: GSC08, KDM1A, V, rep2


title: GSC08, IgG, V, Rb

value: Rabbit anti-mouse IgG (Abcam ab46540)


title: Placenta, Ssr2, WT, 7j

value: WT


title: 28001_S129_priod1


title: 28001_S129_priod2


title: BA9_miRNA_UTHBC0099

city: Houston

first: Consuelo

last: Walss-Bass

state: Texas

address: 1941 East Road Rm. 3110

department: Louis A. Faillace Department of Psychiatry and Behavioral Sciences

institute: University of Texas Health Science Center at Houston

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0099

data_processing:
Low quality sequences were trimmed using trim_galore v0.4.4
Data was mapped to the human genome build UCSC hg38 using star v2.7.3a, allowing up to 20 matches
MicroRNA expression was quantified using feature counts with the miRBASE v22 reference, accounting for multiple mappings
Assembly: hg38
Supplementary files format and content: eature counts

source_name: Brain

extract_protocol:
RNA was isolated using the 125 miRNAeasy Mini Kit (Qiagen) and total RNA, including miRNA, was bound to a miRNeasy spin column and washed three times before subsequent elution.
miRNA libraries were prepared with the QIAseq miRNA library kit (Qiagen) using 5uL of the extracted total RNA sample. Libraries were produced by sequentially ligating adapters to the 3' and 5' ends of miRNAs. This was followed by reverse transcription into cDNA and subsequent ligation of sample indexes and sequencing adapters. The size selection for libraries was performed using QIAseq beads (Qiagen). Library purity was analyzed using the DNA HS1000 tape on a Tapestation 4200 (Agilent) and quantified with Qubit Fluorometer (Thermo Fisher).

tag: uthbc subject_id

value: Brain

tag: ethnicity

value: White

tag: gender

value: Male

tag: pmi (hours)

tag: rin

tag: ph

tag: group

value: OUD


title: NonAE_liver_nuclei_11

tag: tissue


title: BA9_miRNA_UTHBC0098

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0098

value: Hispanic

value: control


title: 29001_S145_priod2

tag: time

tag: treatment

tag: dose


title: NonAE_liver_nuclei_10


title: 16008_S113_D15


title: BA9_miRNA_UTHBC0097

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0097

value: Female


title: 16008_S113_D1


title: BA9_miRNA_UTHBC0096

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0096


title: Damage-seq of BPDE-dG: unexposed BEAS-2B cells rep 3

description:
NGS10089
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.

tag: cell line

tag: cell type

value: lung cell line

value: wild type


title: Placenta, Ssr2, HOM, 8c

value: Placenta

tag: mouse line

tag: genotype

value: KO


title: NonAE_liver_nuclei_08

value: NonAE liver explant


title: Placenta, Ssr2, HOM, 16f

tag: age

tag: litter


title: 16007_S112_D15

value: blood

value: 10 mg/kg


title: NonAE_liver_nuclei_07


title: 16007_S112_D1


title: BA9_miRNA_UTHBC0094

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0094

tag: uthbc subject_id

value: Black


title: 16006_S109_D57


title: NonAE_liver_nuclei_06


title: Damage-seq of BPDE-dG: unexposed BEAS-2B cells rep 1

description:
NGS10087
Genomic DNA extracted from BEAS-2B cells was fragmented by sonication and purified using size-selective beads to yield an average length of 500 bp. The DNA was then ligated with adapter 1 following the instructions for the NEBNext Ultra II DNA Library Prep Kit for Illumina. The DNA fragments containing BPDE-dG were enriched by magnetic bead-based immunoprecipitation using an anti-BPDE antibody. After the enriched DNA was eluted from beads, NEBNext Ultra II Q5 polymerase was used to perform primer extension until the damage sites. We use subtractive hybridization to remove non-specific DNA fragments, and the resulting DNA product was subjected to adapter 2 ligation, then indexed and amplified to the desired concentration for sequencing on an Illumina NovaSeq6000 sequencer.

value: unexposed


title: Placenta, Ssr2, HET, 4c

value: HET


title: NonAE_liver_nuclei_05


title: Placenta, Ssr2, WT, 11i

value: WT


title: NonAE_liver_nuclei_04


title: 16006_S109_D15


title: BA9_miRNA_UTHBC0087

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0087

value: Brain

tag: ethnicity

value: White


title: Placenta, Ssr2, HET, 3g


title: 16006_S109_D1


title: BA9_miRNA_UTHBC0093

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0093

tag: gender


title: Placenta, Ssr2, HET, 9g


title: Placenta, Ssr2, HET, 16g


title: BA9_miRNA_UTHBC0084

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0084

tag: pmi (hours)

value: OUD


title: NonAE_liver_nuclei_03


title: NonAE_liver_nuclei_09


title: BA9_miRNA_UTHBC0081

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0081

tag: rin


title: NonAE_liver_nuclei_02


title: BA9_miRNA_UTHBC0089

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0089

value: Male

tag: ph


title: Placenta, Ssr2, WT, 9f


title: BA9_miRNA_UTHBC0080

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0080

tag: group


title: Placenta, Ssr2, HET, 8e

tag: tissue


title: Healthy_liver_nuclei_09

source_name: Healthy liver explant

value: Healthy liver explant


title: NonAE_liver_nuclei_01


title: Placenta, Ssr2, WT, 8f


title: 16004_S111_D57

tag: time


title: BA9_miRNA_UTHBC0077

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0077

value: Female

value: control


title: Placenta, Ssr2, HOM, 13f


title: Healthy_liver_nuclei_08


title: Placenta, Ssr2, HOM, 8a


title: 16005_S119_D1

tag: treatment


title: Placenta, Ssr2, WT, 9b


title: Healthy_liver_nuclei_06


title: 16003_S104_D1

value: PLACEBO

tag: dose

value: 0 mg/kg


title: BA9_miRNA_UTHBC0076

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0076


title: 16004_S111_D1


title: Placenta, Ssr2, WT, 7g

value: Placenta


title: 16004_S111_D15


title: 16005_S119_D57


title: Placenta, Ssr2, HOM, 7b

value: KO


title: 16003_S104_D15

value: blood


title: Healthy_liver_nuclei_07


title: BA9_miRNA_UTHBC0075

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0075


title: BA9_miRNA_UTHBC0070

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0070


title: Healthy_liver_nuclei_05

description: 10x Genomics single nuclei 3' gene expression v3


title: BA9_miRNA_UTHBC0065

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0065

value: Asian


title: 16002_S105_D57

value: 10 mg/kg


title: Placenta, Ssr2, HET, 7f


title: Placenta, Ssr2, HOM, 7a


title: BA9_miRNA_UTHBC0062

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0062

value: Black


title: 16002_S105_D1


title: BA9_miRNA_UTHBC0061

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0061


title: Healthy_liver_nuclei_02


title: Placenta, Ssr2, HET, 3e

value: HET


title: Placenta, Ssr2, HET, 20f


title: Healthy_liver_nuclei_03


title: 16001_S102_D1


title: 16001_S102_D15


title: BA9_miRNA_UTHBC0053

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0053


title: Healthy_liver_nuclei_01


title: BA9_miRNA_UTHBC0056

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0056


title: Placenta, Ssr2, WT, 20b

value: WT


title: APAP_liver_nuclei_10

source_name: APAP liver explant

value: APAP liver explant


title: APAP_liver_nuclei_09_B


title: 15005_S088_D15


title: 15005_S088_D1


title: Placenta, Ssr2, WT, 1a


title: Healthy_liver_nuclei_04


title: APAP_liver_nuclei_09_A


title: Placenta, Ssr2, HOM, 20a


title: 16005_S119_D15


title: 16002_S105_D15


title: BA9_miRNA_UTHBC0059

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0059

value: Brain

value: White


title: 15002_S083_D15


title: BA9_miRNA_UTHBC0046

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0046

value: Male


title: Placenta, Ssr2, HOM, 20c


title: APAP_liver_nuclei_08


title: BA9_miRNA_UTHBC0044

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0044

value: OUD


title: APAP_liver_nuclei_07


title: BA9_miRNA_UTHBC0079

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0079

value: Female


title: 15002_S083_D1


title: BA9_miRNA_UTHBC0047

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0047


title: BA9_miRNA_UTHBC0039

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0039


title: Placenta, Ssr2, HOM, 19d


title: APAP_liver_nuclei_06


title: 14005_S049_D15


title: APAP_liver_nuclei_05


title: Placenta, Ssr2, WT, 13i


title: BA9_miRNA_UTHBC0041

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0041

value: control


title: Placenta, Ssr2, HET, 13d


title: 14001_S055_D15

value: PLACEBO


title: APAP_liver_nuclei_04


title: 14005_S049_D1

value: 0 mg/kg


title: BA9_miRNA_UTHBC0035

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0035


title: APAP_liver_nuclei_03


title: Placenta, Ssr2, HOM, 13c

value: Placenta


title: 14001_S055_D1


title: Placenta, Ssr2, HET, 12d


title: Placenta, Ssr2, HET, 19e


title: APAP_liver_nuclei_02


title: Placenta, Ssr2, HOM, 12b

value: KO


title: BA9_miRNA_UTHBC0028

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0028


title: APAP_liver_nuclei_01


title: BA9_miRNA_UTHBC0036

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0036


title: BA9_miRNA_UTHBC0027

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0027

value: Hispanic


title: Placenta, Smg9, WT, 7b


title: BA9_miRNA_UTHBC0017

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0017


title: Placenta, Smg9, WT, .4i


title: Placenta, Smg9, WT, 6b


title: Placenta, Smg9, WT, 8b


title: 732 S1-1 CD4+PD-1+

city: Oxford

first: Nicholas

last: Lim

state: Oxfordshire

address: 26 Bullingdon Road

department: Paediatrics

institute: University of Oxford

data_processing:
Reads aligned and pre-processed according to the Smart-Seq 2 Computational Protocol v2.0 (https://cumulus.readthedocs.io/en/0.14.0/smart_seq_2.html)
Assembly: hg38
Supplementary files format and content: Processed data is a tab or comma delimited text file containing a digital gene expression matrix with the number of UMIs for each gene (rows) and cell barcode (columns)

source_name: PBMCs

extract_protocol:
Full-length RNA-seq from single cells using Smart-seq2 (Picelli et al., Nature Protocols 2014)
Nextera XT DNA Library Prep Kit

tag: Sex

tag: clinical hiv outcome

value: Progressor


title: 732 S3-2 CD8+PD-1+

tag: cell type


title: 732 S3-1 CD8+PD-1+


title: 732 S4-2 CD8+PD-1-


title: 732 S2-2 CD4+PD-1-


title: BA9_miRNA_UTHBC0016

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0016


title: Placenta, Smg9, WT, 9c

tag: mouse line

tag: genotype


title: 380 S4-3 CD8+PD-1-

value: Slow-Progressor


title: 380 S3-3 CD8+PD-1+


title: Placenta, Smg9, WT, 4h

tag: age

tag: litter


title: BA9_miRNA_UTHBC0023

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0023

tag: uthbc subject_id

tag: ethnicity


title: 380 S1-3 CD4+PD-1+


title: BA9_miRNA_UTHBC0010

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0010

value: Black

tag: gender

tag: pmi (hours)


title: BA9_miRNA_UTHBC0034

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0034

tag: rin

tag: ph


title: BA9_miRNA_UTHBC0008

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0008

tag: tissue

tag: group


title: BA9_miRNA_UTHBC0030

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0030


title: Placenta, Smg9, WT, 10e


title: Placenta, Smg9, WT, 2f


title: BA9_miRNA_UTHBC0001

description:
microRNAs.BA9_OUD.int.04192021.csv
BA9_UTHBC0001


title: 380 S2-2 CD4+PD-1-


title: Blood_miRNA_UTHBC0081

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0081

source_name: Blood Plasma

value: Blood Plasma


title: 380 S2-1 CD4+PD-1-


title: Placenta, Smg9, HOM, 9a


title: Blood_miRNA_UTHBC0080

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0080


title: 675 S4-3 CD8+PD-1-


title: 675 S3-3 CD8+PD-1+


title: Placenta, Smg9, HOM, 8g


title: Blood_miRNA_UTHBC0075

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0075


title: HDFB_POLYIC_1

city: Innsbruck

first: Can

last: Gollmann-Tepeköylü

address: Anichstraße 35

department: Department for Cardiac Surgery

country: Austria

institute: Medical University of Innsbruck

data_processing:
Samples were sequenced by llumina NovaSseq 6000 with paired-end 150bp reads (on average 32.67 million reads per sample) by Novogene Inc. Base-calling was performed by Novogene Inc. with the latest Illumina software and trimming adapters.
Reads were mapped to the human reference genome (hg38) using splice aware aligner STAR 2.7.1a
Quantifications on NCBI gene models (hg38refGene) were performed using featureCounts v2.0.0
Transcript per million (TPM) were calculated for each gene based on the NCBI gene models
Differentially expressed genes were idintified using DESeq2
Assembly: hg38
Supplementary files format and content: Raw counts and TPMs for all samples are summarized as separated tab delimited txt file

source_name: Human dermal fibroblasts  in medium + Poly(I:C) for 72h

growth_protocol: Valvular interstitial cells from patients undergoing aortic valve replacement or cardiac transplantation were isolated via collagen digestion as described previously. Valves were rinsed in EBSS and subsequently subjected to collagenase digestion (Sigma, St. Louis, MO; 2.5 mg/mL in M199) for 30 minutes at 37°C. Thereafter, tissue samples were vortexed and supernatant containing endothelial cells was removed. Again, collagenase was added to the remaining valve tissue (1 mg/mL) for 3h at 37°C. For mechanical disintegration of the tissue, vortexing and repeated aspiration via pipette was performed. The supernatant was transferred into a new tube and subjected to centrifugation (1100 g for 8 minutes at 4°C). Subsequently, cells were resuspended in M199 medium containing 10% fetal calve serum, penicillin, streptomycin, glutamate and amphotericin B (2.5 mg/L). Human osteoblasts were purchased (Promocell, Heidelberg, Germany) and cultivated in in DMEM with 4.5 g/L glucose (Lonza, Basel, Switzerland), 10% FCS (Sigma, St. Louis, MO), penicillin, streptomycin, glutamate and amphotericin B (2.5 mg/L). Human dermal fibroblasts were cultured in DMEM supplemented with 4.5 g/l glucose (Lonza, Basel, Switzerland), 10% FCS (Sigma, St. Louis, MO), penicillin, streptomycin and L-glutamine.

extract_protocol:
Total RNA was isolated using  RNeasy Mini Kit 50 (Qiagen) according to the manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols by Novogene Inc.

treatment_protocol: Polyinosinic:polycytidylic acid (Poly (I:C); Invivogen, San Diego, CA) was used to stimulate cells at a concentration of 20 µg/mL for 72h

value: Fibroblasts

tag: treatment

value: Medium+Poly (I:C)

tag: time

value: Skin


title: HDFB_CTR_3

source_name: Human dermal fibroblasts cultured in medium for 72h

value: Medium


title: Blood_miRNA_UTHBC0065

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0065

value: Asian

value: Male


title: HDFB_POLYIC_2


title: Placenta, Smg9, HOM, 7f


title: Blood_miRNA_UTHBC0070

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0070

value: OUD


title: HDFB_POLYIC_3


title: 675 S2-3 CD4+PD-1-

tag: Sex

value: Female


title: Placenta, Smg9, HOM, 6f


title: Placenta, Smg9, HOM, 4f


title: 559 S4-3 CD8+PD-1-

tag: clinical hiv outcome


title: 675 S1-3 CD4+PD-1+

tag: cell type


title: HDFB_CTR_1


title: Placenta, Smg9, HOM, 2d

tag: mouse line


title: Blood_miRNA_UTHBC0062

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0062


title: 559 S3-3 CD8+PD-1+


title: Placenta, Smg9, HOM, 10h

tag: genotype


title: Blood_miRNA_UTHBC0061

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0061

value: White

tag: age


title: 559 S2-3 CD4+PD-1-


title: Blood_miRNA_UTHBC0059

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0059


title: HOB_3

source_name: Human osteoblasts cultured in medium

value: Osteoblasts

value: Bone


title: 559 S1-3 CD4+PD-1+


title: Placenta, Smg9, HET, 9i

value: Placenta

value: HET

tag: litter


title: HOB_2


title: Placenta, Smg9, HET, 8d


title: Blood_miRNA_UTHBC0056

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0056

tag: uthbc subject_id


title: HDFB_CTR_2


title: HOB_1


title: 559 S2-2 CD4+PD-1-


title: Placenta, Smg9, HET, 7c


title: Blood_miRNA_UTHBC0053

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0053

tag: ethnicity


title: Placenta, Smg9, HET, 6a


title: VIC_POLYIC_2

source_name: Valvular interstitial cells cultured in medium + Poly(I:C) for 72h

value: Valvular interstitial cells

value: Cardiac valves


title: Blood_miRNA_UTHBC0046

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0046

value: Black

tag: gender

value: control


title: VIC_POLYIC_3


title: 675 S4-1 CD8+PD-1-

value: Progressor


title: Blood_miRNA_UTHBC0047

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0047

value: Blood Plasma

tag: pmi (hours)


title: 675 S3-1 CD8+PD-1+


title: 675 S2-1 CD4+PD-1-


title: Blood_miRNA_UTHBC0041

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0041

tag: rin


title: VIC_CTR_3

source_name: Valvular interstitial cells cultured in medium for 72h


title: Placenta, Smg9, HET, 2b


title: VIC_CTR_2


title: 559 S3-1 CD8+PD-1+

value: Slow-Progressor


title: VIC_CTR_1

value: Medium


title: Blood_miRNA_UTHBC0036

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0036

tag: ph


title: Placenta, Smg9, HET, 10a

tag: tissue


title: Hippocampus-TfamAKO-5

city: Tucson

first: Fei

last: Yin

state: Arizona

address: 1230 N Cherry Ave BSRL 471

institute: University of Arizona

data_processing:
Transcripts were mapped to mouse cDNA (ensembl release 95) using Salmon.
Tximport V1.15.0 was used to generate a counts table from salmon output.
DESeq2 V1.26.0 was used to calculate normalized read counts for each gene to perform expression analysis.
Assembly: Mouse Ensembl Release 95
Supplementary files format and content: csv files of normalized counts and unnormalized counts.

source_name: Hippocampus

extract_protocol:
Total RNA from hippocampus were isolated using PureLink RNA Mini Kit (Thermo Fisher) following the manufacter’s instructions.
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA-Seq library prep kit following manufacturer's protocols.

value: Hippocampus

value: Tfam AKO


title: 559 S1-1 CD4+PD-1+

value: Male


title: Blood_miRNA_UTHBC0035

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0035

tag: group


title: Blood_miRNA_UTHBC0034

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0034

value: Female

value: OUD


title: Placenta, Smg9, HET, 4d


title: Hippocampus-TfamAKO-4


title: VIC_POLYIC_1

tag: treatment

value: Medium+Poly (I:C)


title: Placenta, Smg9, HET, 4b


title: MCF7_968_day4_bruseq0h

city: Ann Arbor

first: Karan

last: Bedi

state: MI

address: 1600 Huron Pkwy

department: Biostatistics

institute: University of Michigan

description: Bru labeling for 30 mins (0.5 hours). cRNA incubation time is 4 days

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

growth_protocol: Cells were cultured in RPMI1640 medium with 10% fetal bovine serum, 25 U/mL penicillin and 25 µg/mL streptomycin in the incubator (37°C, 5% CO2).

extract_protocol:
Cells were lysed directly in TRIzol followed by isolation of total RNA. The isolated total RNA was further treated with DNAse (TURBO DNA-free Kit; Invitrogen) and a spike-in cocktail of Bru-labeled and unlabeled RNA was mixed in with total RNA. Bru-labeled RNA was immunocaptured using anti-BrdU antibodies (BD Biosciences).
A spike-in cocktail of Bru-labeled and unlabeled RNA was mixed in with total RNA prior to Bru-RNA IP.  Ribosomal RNA was reduced via QiaSeq FastSelect (Qiagen) prior to first strand synthesis. These strand-specific libraries were made using a universal ligation adapter and dual-index, barcoded primers for PCR. Size selection for all libraries was via agarose gel excision.

treatment_protocol: Cells expressing doxycycline-inducible Cas9 and control non-targeting sgRNAs or GRHL2-specific sgRNAs were exposed to 1 µg/ml doxycycline. At different timepoints after doxycycline-induced deletion of GRHL2, cells were incubated with a final concentration of 2 mM bromouridine at 37°C for 30 minutes.

tag: cell line

value: Breast cancer cell line

value: cRNA targeting GRHL2

value: 0.5 hours

tag: time

value: 4 days


title: Blood_miRNA_UTHBC0030

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0030

value: White


title: Hippocampus-TfamAKO-3


title: Hippocampus-TfamAKO-2


title: MCF7_968_day2_bruseq0h

description: Bru labeling for 30 mins (0.5 hours). cRNA incubation time is 2 days

value: 2 days


title: 021 S3-3 CD8+PD-1+

tag: Sex

tag: clinical hiv outcome


title: Blood_miRNA_UTHBC0028

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0028

value: Black


title: 021 S4-3 CD8+PD-1-

tag: cell type


title: MCF7_968_day16_bruseq0h

description: Bru labeling for 30 mins (0.5 hours). cRNA incubation time is 16 days

tag: genotype

value: 16 days


title: MCF7_968_day8_bruseq0h

description: Bru labeling for 30 mins (0.5 hours). cRNA incubation time is 8 days

value: 8 days


title: Hippocampus-TfamAKO-1


title: 559 S2-1 CD4+PD-1-

value: Slow-Progressor


title: 435 S2-3 CD4+PD-1-

value: Progressor


title: MCF7_966_day8_bruseq0h


title: Blood_miRNA_UTHBC0027

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0027

value: Blood Plasma

value: Hispanic

tag: age

value: control


title: 435 S1-3 CD4+PD-1+

value: Female


title: Hippocampus-WT-5

value: Hippocampus

value: Wild Type


title: Hippocampus-WT-4


title: 021 S4-2 CD8+PD-1-


title: Blood_miRNA_UTHBC0017

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0017

value: Male

value: OUD


title: Blood_miRNA_UTHBC0016

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0016


title: MCF7_966_day4_bruseq0h

value: Breast cancer cell line

value: cRNA targeting GRHL2

value: 0.5 hours


title: Hippocampus-WT-3


title: Blood_miRNA_UTHBC0044

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0044

value: White


title: 021 S3-2 CD8+PD-1+


title: MCF7_966_day2_bruseq0h

value: 2 days


title: 435 S3-3 CD8+PD-1+


title: MCF7_966_day16_bruseq0h

value: 16 days


title: Blood_miRNA_UTHBC0010

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0010

value: Black


title: MCF7_968_bruseq0h

description: Bru labeling for 30 mins (0.5 hours). cRNA incubation time is 0 days

value: control cRNA

value: 0 days


title: 021 S1-2 CD4+PD-1+

value: Slow-Progressor


title: Hippocampus-WT-1


title: MCF7_966_bruseq0h


title: 675 S1-1 CD4+PD-1+

value: Progressor


title: 435 S4-2 CD8+PD-1-


title: Blood_miRNA_UTHBC0023

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0023

value: Blood Plasma


title: Blood_miRNA_UTHBC0001

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0001

value: control


title: Blood_miRNA_UTHBC0008

description:
miRNA.Plasma_OUD.featureCounts.04192021.csv
P_UTHBC0008


title: 435 S3-2 CD8+PD-1+

value: Female


title: 3-Parenchyma-PBS (X204)

city: Crawley, Perth

first: Emma

last: de Jong

state: WA

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

description: RNAseq (3 week PBS parenchyma)

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.6.0  and Real Time Analysis (RTA) v3.4.4, running on the instrument computer. RTA performs  real-time base calling on the NovaSeq instrument computer.
Then the Illumina bcl2fastq  2.20.0.422 pipeline was used to generate the sequence data.
Read libraries were mapped to the mouse genome using STAR (v2.5.1b), followed by gene quantitation with RSEM (v1.2.31) and Kallisto (v0.44.0).
Assembly: mm10
Supplementary files format and content: raw gene counts comma separated

source_name: Parenchyma

extract_protocol:
RNA was prepared using TRizol (Invitrogen) extraction method following the manufacturer's recommendations. RNA was quantified using a NanoDrop-1000 Spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol:
Experimental asthma: Some mice were sensitized and challenged intranasally with house dust mite (HDM) extract 5 days per week for 3 weeks. In other mice, this was HDM treatment 3 times/week from weeks 4-11. Controls received phosphate buffered saline (PBS).
Experimental chronic obstructive pulmonary disease (COPD): Mice were exposed to cigarette smoke (CS) twice per day, 5 days per week for 8 weeks. Control mice were exposed to normal air (AIR).
Experimental asthma-COPD overlap (ACO): Mice were sensitized and challenged intranasally with HDM or PBS. From weeks 4-11, mice were also exposed to CS or AIR.
Treatment with dexamethasone (DEX): Separate groups of mice were treated with DEX during week 11.

value: Parenchyma

tag: strain

value: Balb/C

value: 18-20 weeks

tag: exposure

value: PBS


title: 3-Airway-PBS (X203)

description: RNAseq (3 week PBS airway)

source_name: Airway

value: Airway


title: MCF7_965_day8_bruseq0h

value: Breast cancer cell line

value: cRNA targeting GRHL2

value: 0.5 hours

value: 8 days


title: 435 S2-2 CD4+PD-1-


title: MCF7_965_day4_bruseq0h

value: 4 days


title: 3-Parenchyma-PBS (X202)

description: RNAseq (3 week PBS parenchyma)


title: 40-5859-Month-3

city: Lebanon

first: Timothy

last: Sullivan

state: Grafton

address: 1 Medical Center Dr.

department: Biomedical Data Science

institute: Dartmouth College

data_processing:
First, we applied the cutadapt (version 1.15) to remove the adapter sequence (in our case it is “AGATCGGAAGAGC”) for the FASTQ files. Then, STAR (version 2.5.3a) was applied to align the reads to the hg19 human genome(17). Next, gene abundance was quantified using RSEM (version 3.3.9)(18). Lastly, normalized RPKM was calculated using TMM function (edgeR package)(19).
Supplementary files format and content: RNA-seq_20180810_normalizedRPKM_GeneSymbol_labelled_fixed.csv contains normalized RPKM values for all samples in the study.

source_name: Skin

extract_protocol:
Samples were stored in RNAlater and subsequently homogenized using a Qiagen Tissuelyser II.  RNA was purified using Qiagen’s RNeasy Fibrous Tissue minikit. Quality and concentration of RNA was assessed on a TapeStation 4400 (Agilent)
100ng of total RNA was used for library preparation using the TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA). Libraries were prepared manually or automated on an epMotion 5075t (Eppendorf, Hauppauge, NY). Libraries were assessed for size and concentration using the TapeStation 4400. Sequencing libraries were quantified on a Qubit fluorometer 3.0 (Thermo Fisher Scientific, Waltham, MA) prior to normalization for equimolar pooling.
Single-index paired-end sequencing was performed on Illumina’s NextSeq 500 to achieve >40 million reads per sample.

value: Skin

value: Placebo

tag: timepoint

tag: patient

tag: escape

value: N

tag: intrinsic subtype


title: 40-5859-Month-6


title: MCF7_965_day2_bruseq0h

value: 2 days


title: 435 S1-2 CD4+PD-1+

value: Progressor


title: Hippocampus-WT-2

value: Hippocampus

value: Wild Type


title: 40-5859-Baseline

value: Baseline


title: 021 S4-1 CD8+PD-1-

value: Female

value: Slow-Progressor


title: 40-5856-Month-3

value: Abatacept


title: 11-Parenchyma-HDM.CS.DEX (X200)

description: RNAseq (11 week HDM.CS.DEX parenchyma)

value: Parenchyma

value: Balb/C

value: 18-20 weeks


title: 11-Airway-HDM.CS.DEX (X199)

description: RNAseq (11 week HDM.CS.DEX airway)

value: Airway


title: 021 S3-1 CD8+PD-1+


title: 40-5856-Baseline


title: MCF7_965_bruseq0h

value: Breast cancer cell line

value: control cRNA

value: 0.5 hours

value: 0 days


title: MCF7_965_day16_bruseq0h

value: cRNA targeting GRHL2

value: 16 days


title: 40-5853-Month-3

value: Skin

value: Placebo

value: N

value: Inflammatory


title: 40-5853-Month-6


title: 435 S4-1 CD8+PD-1-

value: Female

value: Progressor


title: 11-Parenchyma-HDM.CS (X198)

description: RNAseq (11 week HDM.CS parenchyma)


title: 435 S3-1 CD8+PD-1+


title: 40-5853-Baseline

value: Baseline


title: CTMS29_mFOL1-GEX

city: New York

first: Zachary

last: Sethna

state: NY

address: 417 E 68th Street

institute: Memorial Sloan Kettering Cancer Center

description:
10x Genomics
Sample5-GEX

data_processing:
10x Genomics Cell Ranger Single Cell Software suite (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger was used to perform sample) was used for demultiplexing, alignment (hg19), filtering, UMI counting, single-cell 5’end gene counting, TCR assembly, annotation of paired VDJ and performing quality control using the manufacturer parameters.
Assembly: hg19
Supplementary files format and content: h5 files for gene expression matrices
Supplementary files format and content: csv files for barcoded TCR sequences and annotation

source_name: Blood

extract_protocol:
Single-cell RNA-seq libraries were prepared according to 10x Genomics specifications (Chromium Single Cell V(D)J User Guide PN-1000006, 10x Genomics, Pleasanton, CA, USA). Each cellular suspension (>90% viability) at a concentration between 700-1000 cells/µl, were loaded onto to the 10x Genomics Chromium platform to generate Gel Beads-in-Emulsion (GEM), targeting about 10000 single cells per sample. After GEM generation, polyA cDNA barcoded at the 5’end by the addition of a template switch oligo (TSO) linked to a cell barcode and Unique Molecular Identifiers (UMIs), was generated by an incubation at 53 °C for 45 min in a C1000 Touch Thermal cycler with 96-Deep Well Reaction Module (Bio-Rad, Hercules). GEMs were broken and the single-strand cDNA was cleaned up with DynaBeads MyOne Silane Beads (Thermo Fisher Scientific, Waltham, MA). The cDNA was amplified for 13 cycles (98 °C for 45 sec; 98 °C for 20 s, 67 °C for 30 s, 72 °C for 1h).  Quality and quantity of the cDNA was assessed using an Agilent Bioanalyzer 2100 (Santa Clara, CA), obtaining a product of about 1600bp.
For generation of 5P expression libraries, an aliquot of the cDNA (about 50ng) was enzymatically fragmented, end repaired, A-tailed, subjected to a double-sided size selection with SPRI select beads (Beckman Coulter, IN, USA) and ligated to adaptors provided in the kit. A unique sample index for each library was introduced through 14 cycles of PCR amplification using the indexes provided in the kit (98 °C for 45 s; 98 °C for 20 s, 54 °C for 30 s, and 72 °C for 20 s x 14 cycles; 72 °C for 1 min; held at 4 °C). Indexed libraries were subjected to a second double-sided size selection, and libraries were then quantified using Qubit fluorometric quantification (Thermo Fisher Scientific, Waltham, MA). The quality was assessed on an Agilent Bioanalyzer 2100, obtaining an average library size of 430bp. For generation of full-length T-Cell-Receptor VDJ regions, an aliquot of the cDNA (about 5ng) was subjected to nested PCR amplification with specific VDJ outer and inner primer pairs (98 °C for 45 s; 98 °C for 20 s, 67 °C for 30 s, and 72 °C for 20 s x 8 cycles; 72 °C for 1 min; held at 4 °C), and one-sided size selection using SPRI select beads. Quality and quantity of the VDJ region was assessed using an Agilent Bioanalyzer 2100 (Santa Clara, CA). Average library size was 620bp.

value: Blood

value: T cells

value: personalized cancer vaccine


title: 11-Parenchyma-PBS.CS.DEX (X196)

description: RNAseq (11 week PBS.CS.DEX parenchyma)

value: Parenchyma

value: Balb/C

value: 18-20 weeks


title: 11-Airway-HDM.CS (X197)

description: RNAseq (11 week HDM.CS airway)

value: Airway


title: CTMS29_mFOL1-TCR

description:
10x Genomics
Sample5-TCR


title: 435 S2-1 CD4+PD-1-


title: CTMS11_mFOL1-TCR

description:
10x Genomics
Sample4-TCR


title: 31-4524-Month-6

value: Proliferative


title: 3-Airway-PBS (X201)

description: RNAseq (3 week PBS airway)

value: PBS


title: 435 S1-1 CD4+PD-1+


title: CTMS11_mFOL1-GEX

description:
10x Genomics
Sample4-GEX


title: CTMS10_mFOL1-TCR

description:
10x Genomics
Sample3-TCR


title: 11-Parenchyma-PBS.CS (X194)

description: RNAseq (11 week PBS.CS parenchyma)


title: 31-4524-Month-3


title: 11-Airway-PBS.CS.DEX (X195)

description: RNAseq (11 week PBS.CS.DEX airway)


title: circRNA Muscle_ALS4

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

data_processing:
BCL files were de-multiplexed and converted to standard FASTQ files using bcl2fastq program (v2.20.0.422).
FASTQ files were trimmed for adapter sequences using Cutadapt version v1.18 and aligned to human genome hg19 Ensembl v82 using STAR software v2.4.0j.
featureCounts (v1.6.4) were used to create gene counts from the samples.
Circular RNAs were identified using CIRCexplorer v1.1.10
Assembly: hg19
Supplementary files format and content: text files containing counts and circRNA annotation

source_name: muscle

extract_protocol:
Tissue samples were homogenized in TRIzol reagent and RNA was isolated with the RNAspin Mini Columns (GE Healthcare)
Prior to library preparation, 2 μg of RNA were treated with 20 U of RNase R for 1 h at 37°C, after which RNA was isolated using Direct-zol RNA kit following the manufacturer’s instructions; the isolated RNA was polyadenylated using a poly(A) tailing kit and then selected using Oligo(dT)25 Dynabeads following the manufacturer’s instructions.  From the supernatant, which contained the enriched circRNA pool, RNA was isolated using Direct-zol RNA kit following the manufacturer’s instructions; using the entire material, sequencing libraries were prepared, omitting the rRNA depletion steps, using Illumina TruSeq Stranded Total RNA Library prep kit following the manufacturer’s instructions.

value: muscle

value: M

tag: age (years)

tag: disease state

value: ALS


title: 31-4524-Baseline

tag: tissue

value: Skin

value: Placebo

value: N


title: 11-Airway-PBS.CS (X193)

description: RNAseq (11 week PBS.CS airway)

value: Female


title: CTMS1_followup4-TCR

description:
10x Genomics
Sample2-TCR

tag: treatment


title: circRNA Muscle_ALS3

value: F


title: 11-Parenchyma-HDM.AIR.DEX (X192)

description: RNAseq (11 week HDM.AIR.DEX parenchyma)


title: 31-4521-Month-3

value: Abatacept


title: CTMS1_followup4-GEX

description:
10x Genomics
Sample2-GEX

value: Blood

value: T cells


title: 31-4518-Baseline

value: Baseline

value: Inflammatory


title: circRNA Muscle_ALS2


title: 31-4515-Month-6


title: circRNA Muscle_ALS1


title: 31-4515-Month-3


title: circRNA Muscle_CTR5

value: Healthy


title: 11-Parenchyma-HDM.AIR (X190)

description: RNAseq (11 week HDM.AIR parenchyma)

value: Parenchyma

value: Balb/C

value: 18-20 weeks


title: CTMS1_mFOL1-GEX

description:
10x Genomics
Sample1-GEX

value: personalized cancer vaccine


title: CTMS1_mFOL1-TCR

description:
10x Genomics
Sample1-TCR


title: 31-4515-Baseline


title: CTMS10_mFOL1-GEX

description:
10x Genomics
Sample3-GEX


title: circRNA Muscle_CTR3

value: muscle

value: M


title: Mut2

city: Shanghai

first: Le

last: Bu

state: Please Select

address: Tenth People's Hospital of Shanghai,301 Yanchang Road, Jing'an District, Shanghai

country: China

institute: Shanghai Tenth People's Hospital

data_processing:
Raw reads generated during high-throughput sequencing were fastq format sequences
Trimmomatic software was first used for adpter removing, And then low-quality bases and N-bases or low-quality reads were filtered out
Using hisat2 to align clean reads to the reference genome of the experimental specie, the sample should be assessed by genomic and gene alignment
Using the estimateSizeFactors function of the DESeq (2012) R package to normalize the counts
Assembly: hg19
Supplementary files format and content: tab-delimited text files includes FPKM value and counts value for each sample

source_name: leukocyte

extract_protocol:
Total RNA was extracted using the mirVana miRNA Isolation Kit (Ambion) following the manufacturer's protocol. RNA integrity was evaluated using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA). The samples with RNA Integrity Number (RIN) ≥ 7 were subjected to the subsequent analysis
The libraries were constructed using TruSeq Stranded Total RNA with Ribo-Zero Gold according to the manufacturer’s instructions.

value: leukocyte

value: heterozygote p. R21Afs MEN1 mutation

tag: condition

value: multiple endocrine neoplasia type 1 (MEN1)


title: Mut3


title: 11-Airway-PBS.AIR.DEX (X187)

description: RNAseq (11 week PBS.AIR.DEX airway)

value: Airway

value: Female


title: circRNA Muscle_ALS5

value: F

value: ALS


title: 11-Parenchyma-PBS.AIR.DEX (X188)

description: RNAseq (11 week PBS.AIR.DEX parenchyma)


title: 31-4152-Baseline

value: Skin

value: Abatacept

value: N


title: 11-Airway-HDM.AIR.DEX (X191)

description: RNAseq (11 week HDM.AIR.DEX airway)


title: Mut1


title: circRNA Muscle_CTR2

value: Healthy


title: 11-Airway-HDM.AIR (X189)

description: RNAseq (11 week HDM.AIR airway)


title: 31-4512-Month-6

value: Inflammatory


title: 11-Airway-PBS.AIR (X185)

description: RNAseq (11 week PBS.AIR airway)

value: Balb/C


title: circRNA Muscle_CTR4


title: WT2

value: WT

value: unaffected relative


title: 31-4512-Month-3


title: 31-4509-Month-3

value: Placebo

value: Y; 6mo

value: Proliferative


title: WT1

value: leukocyte


title: 31-4509-Baseline

value: Baseline


title: 3-Airway-HDM (X183)

description: RNAseq (3 week HDM airway)

value: Airway

value: 18-20 weeks

value: HDM


title: 11-Parenchyma-PBS.AIR (X186)

description: RNAseq (11 week PBS.AIR parenchyma)

value: Parenchyma

value: Female


title: 3-Parenchyma-PBS (X182)

description: RNAseq (3 week PBS parenchyma)

value: PBS


title: 3-Airway-PBS (X181)

description: RNAseq (3 week PBS airway)


title: U87 cells,siRNA-2

city: shenyang

first: jialing

middle: jia

last: bai

state: liaoning

address: Culture Road No. 103

institute: shenyang pharmaceutical university

data_processing:
the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene
Assembly: hg38
Supplementary files format and content: tab-delimited text files include count and FPKM values for each Sample

source_name: glioma cell

growth_protocol: U87 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted by Trizol isolution RNA Extraction Kit
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

treatment_protocol: U87 cells were transfected with siRNA(100pmol) using lipofectamine 3000 (Invitrogen, USA) and Opti-MEM, according to the manufacturer’s instructions.

value: glioma cell

tag: cell line


title: 31-4506-Month-6

value: Skin

value: Abatacept

value: N


title: U87 cells,siRNA-3


title: WT3

value: WT


title: U87 cells,siRNA-1


title: U87 cells,control-3

value: no


title: 31-4506-Month-3


title: U87 cells,control-2


title: 581076_IL-13_2

city: San Diego

last: Walker

state: CA

address: 10675 John Jay Hopkins Dr

institute: NIBR

data_processing:
Reads were generated from a NovaSeq instrument with bcl2fastq from Illumina, v 2.20.0.422-2 and were aligned to a genome and annotation from ensembl, assembly GRCh38.p13, release version 104
Gene counts were assessed with RSEM v1.3
Differential gene expression was assessed with DESeq2 v.1.28.1, in R version 4.2.0
Assembly: ensembl, assembly GRCh38.p13, release version 104
Supplementary files format and content: a single Excel file includes DESEQ2-derived expression values for each Sample

source_name: hBSMCs

growth_protocol: Microtissues treated with control, TGF-b1 (10ng/mL), or IL-13 (10ng/mL) for 7 days were lysed in the 96-well plate with Quagen buffer RLT

extract_protocol:
RNA was isolated using Qiagen RNEasy kit
RNA libraries for RNA-seq were prepared using the TruSeq Stranded mRNA Prep Kit (Illumina 20020595) following manufacturer's protocols.

value: hBSMCs

value: Human Bronchial Smooth Muscle Cells

tag: time

value: 7 days


title: U87 cells,control-1


title: 11-Parenchyma-HDM.CS.DEX (X180)

description: RNAseq (11 week HDM.CS.DEX parenchyma)

value: Balb/C

tag: Sex


title: 581076_TGFb1_2

tag: cell type


title: 581076_IL-13_3


title: 3-Parenchyma-HDM (X184)

description: RNAseq (3 week HDM parenchyma)


title: 11-Airway-HDM.CS.DEX (X179)

description: RNAseq (11 week HDM.CS.DEX airway)


title: 31-4506-Baseline

value: Baseline


title: 581076_TGFb1_1


title: 581076_IL-13_1


title: 11-Parenchyma-HDM.CS (X178)

description: RNAseq (11 week HDM.CS parenchyma)


title: 31-4503-Month-6


title: 31-4503-Month-3


title: 581076_Control_3

value: Control


title: 31-4503-Baseline


title: 581076_Control_2


title: 11-Airway-HDM.CS (X177)

description: RNAseq (11 week HDM.CS airway)

value: Airway

value: 18-20 weeks


title: 11-Airway-PBS.CS.DEX (X175)

description: RNAseq (11 week PBS.CS.DEX airway)


title: B7M

city: Changsha

first: Zaiye

last: Li

state: Hunan

address: Xiangya load 87. Changsha, China

institute: Xiangya hospital of Central South University

description: mRNA_Expression_FPKM; lncRNA_Expression_FPKM

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample

source_name: oral cancer

extract_protocol:
Total RNA was isolated from a total of 10 samples.  The quality of RNA was evaluated by Qubit, Nanodrop and Agilent 2100 Bioanalyzer.
RNA sequencing libraries were prepared using TruSeq Stranded Total RNA Library Prep Kit according to manufacturer’s specifications. Before cDNA synthesis, we deleted rRNAs, purify and fragment total RNA.

tag: tumor stage

value: primary tumor

value: bucal


title: B17M


title: T8M

value: tongue


title: T11M


title: 11-Parenchyma-PBS.CS.DEX (X176)

description: RNAseq (11 week PBS.CS.DEX parenchyma)

value: Parenchyma

tag: age

value: Female


title: 581076_Control_1


title: 138668_TGFb1_3


title: 30-4359-Month-3

value: Skin

value: Abatacept

value: Inflammatory


title: 11-Airway-PBS.CS (X174)

description: RNAseq (11 week PBS.CS airway)

tag: strain


title: 30-4359-Baseline

value: N


title: B4M


title: 138668_TGFb1_2

value: hBSMCs


title: 11-Parenchyma-PBS.CS (X173)

description: RNAseq (11 week PBS.CS parenchyma)

tag: exposure


title: LLP


title: TC


title: 11-Parenchyma-HDM.AIR.DEX (X172)

description: RNAseq (11 week HDM.AIR.DEX parenchyma)


title: 30-4356-Month-6

tag: timepoint


title: 138668_TGFb1_1

value: Human Bronchial Smooth Muscle Cells


title: 138668_IL-13_3

value: 7 days


title: 11-Airway-HDM.AIR.DEX (X171)

description: RNAseq (11 week HDM.AIR.DEX airway)

value: Balb/C


title: 30-4359-Month-6

tag: patient


title: 30-4356-Month-3

tag: escape


title: 138668_IL-13_2


title: TM2


title: 11-Parenchyma-HDM.AIR (X170)

description: RNAseq (11 week HDM.AIR parenchyma)


title: 138668_IL-13_1


title: 30-4353-Month-6

tag: intrinsic subtype


title: 30-4356-Baseline

value: Baseline


title: TM1


title: 11-Parenchyma-PBS.AIR.DEX (X168)

description: RNAseq (11 week PBS.AIR.DEX parenchyma)


title: 138668_Control_3

value: Control


title: 30-4353-Baseline


title: 26-3759-Month-3


title: 11-Airway-PBS.AIR.DEX (X167)

description: RNAseq (11 week PBS.AIR.DEX airway)

value: Airway


title: 138668_Control_1


title: H1299sh

city: Dalian

first: Yang

last: Wang

address: No.9 West section, South Lv Road

institute: Dalian Medical University

data_processing:
Base-calling performed with CASAVA 1.8.2 software
Alignment performed with Tophat software, aligning to Human Genome Consortium Reference Human Genome hg38
Relative abundances calculated using Cufflinks software
Genome_build: hg38

growth_protocol: H1299 and A549 cells were cultured in RPMI-1640 or F12K medium containing 10% FBS separately.

extract_protocol:
RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: lung cancer cells

tag: knockdown

value: knockdown of RBM4


title: H1299control

value: control


title: T3M

value: primary tumor

value: tongue


title: A549sh


title: 11-Parenchyma-PBS.AIR (X166)

description: RNAseq (11 week PBS.AIR parenchyma)

value: Parenchyma

value: 18-20 weeks

value: Female


title: 127528_TGFb1_3


title: A549control


title: 26-3759-Month-6

value: Skin

value: Abatacept

value: Proliferative


title: 11-Airway-PBS.AIR (X165)

description: RNAseq (11 week PBS.AIR airway)


title: 127528_TGFb1_2

value: hBSMCs

value: Human Bronchial Smooth Muscle Cells


title: 11-Airway-HDM.AIR (X169)

description: RNAseq (11 week HDM.AIR airway)

value: Balb/C


title: 26-3759-Baseline

value: Baseline

value: N


title: 127528_TGFb1_1

value: 7 days


title: 26-3756-Month-3

value: Placebo


title: 30-4353-Month-3


title: 127528_IL-13_3


title: 138668_Control_2

value: Control


title: 26-3756-Month-6


title: 3-Parenchyma-PBS (X162)

description: RNAseq (3 week PBS parenchyma)

value: PBS


title: 127528_IL-13_2


title: 26-3756-Baseline


title: 3-Airway-PBS (X161)

description: RNAseq (3 week PBS airway)

value: Airway


title: 3-Parenchyma-HDM (X164)

description: RNAseq (3 week HDM parenchyma)

value: HDM


title: 127528_IL-13_1


title: 26-3753-Month-3


title: AETC_1500 µg/ml_3

type: RNA

city: Delhi

first: Bhavana

last: Prasher

state: Delhi

address: Sukhdev Vihar

country: India

institute: IGIB

description: Gene expression data from AETC treated Th17 cells

hyb_protocol: 5.2 µg of fragmented and labelled ss cDNA were hybridized on Affymetrix MTA 1.0 Cartridge arrays for 16hrs at 45°C at 60rpm in Affymetrix hybridization oven. Arraya were stained and washed in the Affymetrix Fluidics Station 450

scan_protocol: The stained chips were then scanned using GeneChip™ Scanner 3000

data_processing: CEL files were processed using SST Robust multi-array (RMA) normalization in Transcriptome Analysis Console (TAC) .

label: biotin

source_name: in vitro cultured Th17 cells

label_protocol: Fragmented and biotin labelled Second cycle single stranded cDNA were prepared from 250ng total RNA following the manufacturers protocol (GeneChip WT plus reagent kit user manual)

growth_protocol: CD4+ T cells were isolated ex vivo from spleens and lymph nodes of mice by enrichment with Dynal Mouse CD4 Negative Isolation Kit (Life Technologies, USA). The isolated CD4+ T cells were incubated with anti-CD25 PE antibody to isolate CD4+CD25− T cells. CD4+CD25− T cells were isolated using the MACS column as mentioned above. The purity of CD4+CD25− T cells was >90%. TexMACSTM RPMI 1640 GlutaMAX (Miltenyibiotech, Germany) the medium was used for CD4, iTreg, and Th1 cell cultures and IMDM (Gibco, USA) for Th17 cell cultures. The medium was supplemented with 10% heat-inactivated FCS (Gibco, USA), 500U penicillin-streptomycin (Life Technologies, USA), and 50 µM β-mercaptoethanol (Life technologies, USA). For Th17 cell induction, 1-1.5 × 105 CD4+CD25- T cells were cultured for 4 d with plate-bound anti-CD3ε (10 µg/ mL, clone 145-2C11; Bio X Cell), anti-CD28 (1 µg/mL, clone 37.51; Bio X Cell), anti-IFN-γ (5 µg/mL, clone XMG1.2; Bio X Cell), anti-IL-4 (5 µg/ mL, clone 11B11; Bio X Cell), rhTGF-β1 (2 ng/ mL Peprotech), rmIL-6 (5 ng/ mL; Peprotech) and rmIL-1β (50 ng/ mL; Peprotech).

extract_protocol: Extraction of total RNA was performed according to the RNeasy Mini Kit (Qiagen) manufacturer's instructions.

treatment_protocol: AETC was added at day0 at 500, 1000 and 1500 µg/ml.

value: in vitro cultured Th17 cells

tag: time point

value: Day 4

value: 1500µg/ml AETC


title: 11-Parenchyma-HDM.CS.DEX (X160)

description: RNAseq (11 week HDM.CS.DEX parenchyma)

tag: tissue

value: Parenchyma

value: 18-20 weeks

value: Female


title: 127528_Control_2

value: hBSMCs

tag: treatment


title: 11-Airway-HDM.CS.DEX (X159)

description: RNAseq (11 week HDM.CS.DEX airway)


title: AETC_1500 µg/ml_2


title: 3-Airway-HDM (X163)

description: RNAseq (3 week HDM airway)


title: 11-Parenchyma-HDM.CS (X158)

description: RNAseq (11 week HDM.CS parenchyma)


title: 127528_Control_3

value: Human Bronchial Smooth Muscle Cells


title: 25-3615-Month-6

value: Skin

value: Abatacept

value: Proliferative


title: 31-4509-Month-6

value: Y; 6mo


title: 11-Airway-HDM.CS (X157)

description: RNAseq (11 week HDM.CS airway)

value: Balb/C


title: 26-3753-Month-6

value: N


title: 104462_TGFb1_3

value: 7 days


title: AETC_1000 µg/ml_3

value: 1000µg/ml AETC


title: 25-3615-Month-3


title: AETC_1000 µg/ml_2


title: 11-Parenchyma-PBS.CS.DEX (X156)

description: RNAseq (11 week PBS.CS.DEX parenchyma)


title: AETC_500 µg/ml_3

value: 500µg/ml AETC


title: AETC_1500 µg/ml_1

value: in vitro cultured Th17 cells


title: AETC_500 µg/ml_2

value: Day 4


title: AETC_1000 µg/ml_1


title: 104462_TGFb1_2


title: 26-3753-Baseline

value: Baseline


title: 25-3615-Baseline


title: 11-Airway-PBS.CS.DEX (X155)

description: RNAseq (11 week PBS.CS.DEX airway)

value: Airway


title: 104462_TGFb1_1


title: 127528_Control_1

value: Control


title: AETC_500 µg/ml_1


title: 25-3609-Month-6

value: Placebo

value: Y; 12mo- still can use!

value: Inflammatory


title: 25-3609-Month-3

value: Skin


title: 104462_IL-13_3

value: hBSMCs

value: Human Bronchial Smooth Muscle Cells


title: 11-Parenchyma-PBS.CS (X154)

description: RNAseq (11 week PBS.CS parenchyma)

value: Parenchyma

value: 18-20 weeks

value: Female


title: 11-Parenchyma-HDM.AIR.DEX (X152)

description: RNAseq (11 week HDM.AIR.DEX parenchyma)

value: Balb/C


title: 11-Airway-PBS.CS (X153)

description: RNAseq (11 week PBS.CS airway)


title: 25-3609-Baseline


title: 104462_IL-13_1

value: 7 days


title: 11-Airway-HDM.AIR.DEX (X151)

description: RNAseq (11 week HDM.AIR.DEX airway)


title: 104462_IL-13_2


title: circRNA Muscle_CTR1

value: muscle

value: M

tag: age (years)

tag: disease state

value: Healthy


title: 104462_Control_3

tag: cell line

tag: time


title: 25-3606-Month-6

value: Y; 6mo


title: 25-3606-Month-3


title: 11-Parenchyma-HDM.AIR (X150)

description: RNAseq (11 week HDM.AIR parenchyma)

tag: Sex


title: 104462_Control_1

tag: cell type


title: 25-3606-Baseline

value: Baseline


title: AETC_Control_3

value: in vitro cultured Th17 cells

value: Day 4

value: Control


title: 11-Parenchyma-PBS.AIR.DEX (X148)

description: RNAseq (11 week PBS.AIR.DEX parenchyma)

tag: age


title: THP-1_Vit C+INH_IN_96 h_Rep 4

city: Bangalore

first: Genotypic

last: technology

state: Karnataka

address: 259, Apoorva 4th cross,80 feet Road,RMV 2ND STAGE

institute: Genotypic Technology

description: Gene expression of PMA-differentiated Vit C and INH-treated Mtb infected-THP-1 cells at 96 h

hyb_protocol: Labeled cRNA were hybridized on the array using the Gene Expression Hybridization kit (Part Number 5190-0404; Agilent) in Sure hybridization Chambers (Agilent) at 65º C for 16 hours. Hybridized slides were washed using Agilent Gene Expression wash buffers (Part No: 5188-5327).

scan_protocol: Scanned on an Agilent  scanner G2505C

data_processing: Images were quantified using Agilent Feature Extraction Software (Version-10.7, Agilent). Feature extracted raw data was analyzed using Limma R Bioconductor package . Normalization of the data was done using Quantile normalization.

source_name: THP-1, Vit C+INH-treated, Mtb infected, 96 h, Replicate 4

label_protocol: The samples were labeled using Agilent Quick Amp Kit (Part number: 5190-0442). 500ng of total RNA was reverse transcribed using oligodT primer tagged to T7 promoter sequence. cDNA thus obtained was converted to double stranded cDNA in the same reaction. Further the cDNA was converted to cRNA in the in-vitro transcription step using T7 RNA polymerase enzyme and Cy3 dye was added into the reaction mix. During cRNA synthesis Cy3 dye was incorporated into the newly synthesized strands. cRNA obtained was cleaned up using Qiagen RNeasy columns(Qiagen, Cat No: 74106). Concentration and amount of dye incorporated was determined using Nanodrop. Samples that pass the QC for specific activity were taken for hybridization.

growth_protocol: THP-1 cells were maintained in RPMI 1640 supplemented with 2 mM glutamine, HEPES and sodium bicarbonate with 10% fetal bovine serum and 1× Penicillin-Streptomycin solution. The cells were passaged at nearly 80% confluency. The experiment was performed at ~99% cell viability as determined by trypan blue exclusion method.

extract_protocol: RNA was prepared using the TRIzol following the manufacturer's recommendations. RNA was quantified using NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Nearly, 10 ×10^6 THP-1 cells were seeded in T-175 cm2 flasks in RPMI with 10% FBS. The cells were then differentiated with 30 nM PMA for 16-18 h. Following differentiation, the cells were allowed resting for 2-3 h. The cells were infected with Mtb H37Rv at a multiplicity of infection (MOI) of ~10:1 (Bacteria: THP-1 cells) for 4 h and then treated with 0.1 mM Vitamin C (Vit C). After 24 h of Vit C treatment, the cells were treated with 4 µg/ ml isoniazid (INH). THP-1 RNA was isolated from Mtb infected-untreated flasks, -Vit C treated flasks and -Vit C + INH treated flasks at different time-points (2 h, 24 h, 96 h) post-Vit C addition. A parallel set of uninfected and untreated THP-1 cells served as uninfected control samples.

value: PMA-differentiated THP-1 cells

value: Vit C and INH- treated

tag: infection

value: Mtb infected


title: AETC_Control_2

tag: strain


title: 20-2853-Month-6

value: Skin

value: Abatacept

tag: timepoint

value: N

value: Inflammatory


title: AETC_Control_1


title: 20-2853-Month-3

tag: patient


title: THP-1_Vit C+INH_IN_96 h_Rep 3

source_name: THP-1, Vit C+INH-treated, Mtb infected, 96 h, Replicate 3


title: LvNC-3

city: changsha

first: wei

last: qin

state: State...

address: xiangya

institute: xiangya

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
STAR is used to align clean reads to reference genome.
HTSeq v0.6.0 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
We applied DESeq2 algorithm to filter the differentially expressed genes, after the significant analysis and FDR analysis under the following criteria: i) |log2FC| > 1 ; ii) Pvalue < 0.05.
GO and KEGG enrichment analysis of differentially expressed genes
Assembly: hg38
Supplementary files format and content: Raw_gene_counts_matrix.txt

source_name: cell line

extract_protocol:
sgSLC12A5,sgNC,LvSLC12A5 and LvNC RBE cells were collected and the RNA was extracted using Trizol (Thermo Fisher Scientific,15596018).
The sequencing library was conducted by NEBNext UltraTM RNA Library Prep Kit（NEB #E7490）, and purified by AMPure XP system, according to the standard Illumina protocols.

value: cell line

value: RBE

tag: genotype

value: SLC12A5-overexpression control


title: LvNC-1


title: LvNC-2


title: 11-Airway-PBS.AIR.DEX (X147)

description: RNAseq (11 week PBS.AIR.DEX airway)

value: Airway

value: Balb/C

value: 18-20 weeks

value: Female

tag: exposure


title: 20-2853-Baseline

value: Baseline

tag: escape

tag: intrinsic subtype


title: THP-1_Vit C+INH_IN_96 h_Rep 1

source_name: THP-1, Vit C+INH-treated, Mtb infected, 96 h, Replicate 1


title: 11-Parenchyma-PBS.AIR (X146)

description: RNAseq (11 week PBS.AIR parenchyma)

tag: tissue

value: Parenchyma


title: 11-Airway-PBS.AIR (X145)

description: RNAseq (11 week PBS.AIR airway)


title: LvSLC12A5-3

tag: treatment


title: 19-2709-Baseline


title: LvSLC12A5-2


title: 11-Airway-HDM.AIR (X149)

description: RNAseq (11 week HDM.AIR airway)


title: 19-2706-Month-6

value: Placebo

value: Y; 9mo


title: 3-Parenchyma-HDM (X144)

description: RNAseq (3 week HDM parenchyma)

value: HDM


title: LvSLC12A5-1


title: THP-1_Vit C_IN_96 h_Rep 2

description: Gene expression of PMA-differentiated Vit C-treated Mtb infected-THP-1 cells at 96 h

source_name: THP-1, Vit C-treated, Mtb infected, 96 h, Replicate 2

value: PMA-differentiated THP-1 cells

value: Vit C-treated

value: Mtb infected


title: THP-1_Vit C_IN_96 h_Rep 3

source_name: THP-1, Vit C-treated, Mtb infected, 96 h, Replicate 3


title: THP-1_Vit C_IN_24 h_Rep 2

description: Gene expression of PMA-differentiated Vit C-treated Mtb infected-THP-1 cells at 24 h

source_name: THP-1, Vit C-treated, Mtb infected, 24 h, Replicate 2


title: THP-1_Vit C_IN_24 h_Rep 3

source_name: THP-1, Vit C-treated, Mtb infected, 24 h, Replicate 3


title: THP-1_Vit C+INH_IN_96 h_Rep 2

source_name: THP-1, Vit C+INH-treated, Mtb infected, 96 h, Replicate 2

value: Vit C and INH- treated


title: THP-1_Vit C_IN_96 h_Rep 1

source_name: THP-1, Vit C-treated, Mtb infected, 96 h, Replicate 1


title: 19-2706-Month-3

source_name: Skin

value: Skin


title: 3-Airway-HDM (X143)

description: RNAseq (3 week HDM airway)

source_name: Airway


title: sgNC-3

value: cell line

value: SLC12A5-knockdown control


title: 19-2706-Baseline


title: 3-Parenchyma-PBS (X142)

description: RNAseq (3 week PBS parenchyma)

source_name: Parenchyma

value: PBS


title: 3-Airway-PBS (X141)

description: RNAseq (3 week PBS airway)

value: Airway


title: 19-2703-Month-6

value: Y; 6mo

value: Proliferative


title: 19-2703-Month-3


title: THP-1_Vit C_IN_24 h_Rep 1

source_name: THP-1, Vit C-treated, Mtb infected, 24 h, Replicate 1


title: 11-Parenchyma-HDM.CS.DEX (X140)

description: RNAseq (11 week HDM.CS.DEX parenchyma)

value: Balb/C

value: 18-20 weeks

value: Female


title: sgSLC12A5-3

value: RBE


title: sgNC-2


title: 11-Airway-HDM.CS.DEX (X139)

description: RNAseq (11 week HDM.CS.DEX airway)


title: sgNC-1


title: 19-2703-Baseline

value: Placebo

value: Baseline


title: 11-Parenchyma-HDM.CS (X138)

description: RNAseq (11 week HDM.CS parenchyma)

value: Parenchyma


title: sgSLC12A5-1


title: 11-Airway-HDM.CS (X137)

description: RNAseq (11 week HDM.CS airway)


title: sgSLC12A5-2


title: 18-2553-Month-6

value: Y; 12mo- still can use!

value: Inflammatory


title: 18-2556-Baseline

value: N


title: patient5

city: Wuhan

first: AnYi

last: Liang

address: 1037 Luoyu Road, Wuchang, Wuhan

institute: Huazhong University of Science and Technology

description: HCC

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trim Galore
Trimmed sequence reads were mapped to GRCh37 using STAR
Read count extraction were performed using hitseq
Assembly: GRCh37
Supplementary files format and content: raw_matrix.txt
Supplementary files format and content: raw counts

source_name: liver

extract_protocol:
Total RNA was isolated from FFPE liver cancer tissue from cases and controls using the RNeasy FFPE kit (Qiagen)according to the manufacturer's instructions with a minor modification.
The Trio RNA-Seg Library Preparation Kit (Nugen; Redwood City, CA) was used togenerate sequencing libraries as per the manufacturer's instructions, with 1to 5 ng RNA used as input

value: liver


title: 11-Parenchyma-PBS.CS.DEX (X136)

description: RNAseq (11 week PBS.CS.DEX parenchyma)


title: THP-1_Vit C_IN_2 h_Rep 1

description: Gene expression of PMA-differentiated Vit C-treated Mtb infected-THP-1 cells at 2 h

source_name: THP-1, Vit C-treated, Mtb infected, 2 h, Replicate 1

value: PMA-differentiated THP-1 cells

value: Vit C-treated

value: Mtb infected

value: 2 h


title: THP-1_Vit C_IN_2 h_Rep 2

source_name: THP-1, Vit C-treated, Mtb infected, 2 h, Replicate 2


title: THP-1_UT_IN_96 h_Rep 2

description: Gene expression of PMA-differentiated untreated Mtb infected-THP-1 cells at 96 h

source_name: THP-1, Untreated, Mtb infected, 96 h, Replicate 2

value: Untreated


title: THP-1_Vit C_IN_2 h_Rep 3

source_name: THP-1, Vit C-treated, Mtb infected, 2 h, Replicate 3


title: THP-1_UT_IN_96 h_Rep 1

source_name: THP-1, Untreated, Mtb infected, 96 h, Replicate 1


title: patient4

description: HCC


title: THP-1_UT_IN_24 h_Rep 1

description: Gene expression of PMA-differentiated untreated Mtb infected-THP-1 cells at 24 h

source_name: THP-1, Untreated, Mtb infected, 24 h, Replicate 1


title: 11-Airway-PBS.CS.DEX (X135)

description: RNAseq (11 week PBS.CS.DEX airway)

value: Airway


title: THP-1_UT_IN_24 h_Rep 2

source_name: THP-1, Untreated, Mtb infected, 24 h, Replicate 2


title: patient2

description: HCC


title: 11-Airway-PBS.CS (X133)

description: RNAseq (11 week PBS.CS airway)

value: Balb/C


title: 17-2421-Month-6

value: Skin


title: 17-2421-Month-3


title: 17-2415-Month-6

value: Abatacept


title: 11-Airway-HDM.AIR.DEX (X131)

description: RNAseq (11 week HDM.AIR.DEX airway)

value: 18-20 weeks

value: Female


title: patient1

description: HCC


title: THP-1_UT_IN_2 h_Rep 2

description: Gene expression of PMA-differentiated untreated Mtb infected-THP-1 cells at 2 h

source_name: THP-1, Untreated, Mtb infected, 2 h, Replicate 2


title: 18-2553-Month-3

value: Placebo


title: 10x snRNA-seq on in vitro birthdated 39d old cortical neurons (271ba0)

city: Leuven

first: Emir

last: Erkol

address: ON5 Herestraat 49

department: Department of Neuroscience

country: Belgium

institute: KU Leuven-VIB

library_source: genomic single cell

data_processing:
10x Genomics single cell samples were demultiplexed using the 10x Genomics Cell Ranger  v3.0.2 mkfastq command. A custom, multi-species Cell Ranger index was generated from the  UCSC hg38 and UCSC mm10 genomes, as well as the WPRE element present in these cells  using the mkref command, and this index was used to map reads and generate gene  expression matrices using the count command.
Filtered gene expression matrices were processed using the Scanpy (1.7.2) package. Cells with 95% counts assigned to human genes were kept for downstream analysis. Cells with less than 1000 genes or more than 15% of counts present in mitochondrial genes were excluded, counts were log-normalized and counts per cell were scaled to a total of 10,000. Highly variable genes were selected with pp.highly_variable_genes using default settings and principal component analysis (PCA) was performed with the selected genes. The top 28 PCs were selected and used to compute a neighbourhood graph. UMAP was computed using default Scanpy parameters. Clusters identified as excitatory neurons were used for downstream analysis.
Assembly: hg38
Supplementary files format and content: scrna_counts.tsv.gz: tab seperated flat text file containing cells as rows, genes as columns and counts for each gene in each cell as values.

source_name: in vitro

extract_protocol:
Human cortical cells (frozen at day 25) were thawed and plated on Matrigel-coated plates using DDM/B27+Nb/B27 medium at 37˚C with 5% CO 2 . Seven days after thawing (day 32), the cells were dissociated using Accutase and plated on Matrigel-coated plate at high confluency (450,000-700,000 cells/cm 2 ) with LV-NeuroD1 promoter-CreERT2-WPRE and LV-CAG-DIO-EGFP-T2A-tCD8-WPRE. Four days later (day 36), the medium was changed to DDM/B27+Nb/B27 medium with 1µM 4-OHT and 10µM DAPT (Abcam, Cat#ab120633). Two days after 4-OHT/DAPT induction (day 38), the medium was changed to fresh DDM/B27+Nb/B27 medium. At day 40, cortical cells were dissociated using NeuroCult Enzymatic Dissociation Kit for Adult CNS Tissue (STEMCELL technologies, Cat#05715) following the manufacturer’s instructions. For CD8+ magnetic cell sorting (MACS), dissociated cells were incubated with magnetic beads conjugated anti-human CD8 (Miltenyi Biotec, Cat#130-045-201) in MACS buffer, mixture of autoMACS Rinsing Solution (Miltenyi Biotec, Cat#130-091-222) and MACS BSA Stock Solution (Miltenyi Biotec, Cat#130-091-376), at 4˚C for 10 min. CD8 positive selection was carried out with MS or LS columns (Miltenyi Biotec, Cat# 130-042- 201 or 130-042-401) according to the manufacturer’s instructions. The sorted cells were plated on mouse astrocyte-coated plates at intermediate confluency (160,000 cells/cm 2 ). The culture medium was changed two times a week. At indicated time points, cortical neurons were dissociated using NeuroCult Enzymatic Dissociation Kit following the manufacturer’s instructions and resuspended in PBS containing 1%BSA. The cell suspension was passed through a cell strainer (Merk, Cat#BAH136800040) and counted using a LUNA dual fluorescence cell counter (Logos Biosystems) after Acridine Orange/Propidium Iodide staining (Logos Biosystems, Cat#F23001). Library preparations for the scRNA-seq was performed using 10X Genomics  Chromium Single Cell 3’ Kit, v3.1 NextGEM chemistry (10X Genomics, Pleasanton, CA, USA). The cell count and the viability of the samples were accessed using LUNA dual  florescence cell counter and a targeted cell recovery of 10,000 cells was aimed for each of the samples. Following cell count and QC, the samples were immediately loaded onto the Chromium Controller. Single cell RNAseq libraries were prepared using manufacturer’s recommendations (Single cell 3’ reagent kits v3.1 user guide; CG000204 Rev D), and at different check points the library quality was assessed using Qubit (Thermo Fisher Scientific)  and Bioanalyzer (Agilent). With a sequencing saturation targeted for ~ 40-60%, single cell libraries were sequenced on Illumina’s NovaSeq 6000 platform using paired-end sequencing workflow and with recommended 10X; v3.1 read parameters (28-8-0-91 cycles).
Single-nuclei libraries were generated using the 10x Chromium Single-Cell Instrument and Chromium Single Cell 3’ Reagent v3 Kits (10x Genomics) according to the manufacturer’s protocol. In brief, the single mouse liver nuclei suspension was loaded in the Chromium chip B for partitioning into nanoliter-scale Gel Beads-in-emulsion (GEMs). After GEMs generation, the obtained emulsion was incubated in a C1000 Touch Thermal Cycler (Bio-Rad) under the following program: 53°C for 45 min, 85°C for 5 min and hold at 4°C. Incubation of the GEMs produced barcoded, full-length cDNA from poly-adenylated mRNA. After incubation, single-cell droplets were dissolved, and full-length cDNA were isolated using Cleanup Mix containing Silane Dynabeads. To generate sufficient mass for library construction, the cDNA was amplified via PCR: 98°C for 3 min; 12 cycles of 98°C for 15 s, 63°C for 20 s, 72°C for 1 min; 72°C for 1 min; and hold at 4°C. Subsequently, the amplified cDNA was fragmented, end- repaired, A-tailed and index adaptor ligated, with SPRIselect cleanup in between steps. The final gene expression library was amplified by PCR: 98°C for 45 s; 10-12 cycles of 98°C for 20 s, 54°C for 30 s, 72°C for 20 s. 72°C for 1 min; and hold at 4°C. The sequencing-ready libraries were cleaned up with SPRIselect beads. Before sequencing, the fragment size of every library was analyzed using the Bioanalyzer high-sensitivity chip and were sequenced on HiSeq2500 or NovaSeq6000 instruments with the following sequencing parameters: 28 bp read 1 – 10 bp index 1 (i7) – 10 bp index 2 (i5) – 75 bp read 2.
Single-cell RNA-seq (10X Genomics)

value: in vitro

tag: sample status

value: Fresh

tag: sample type


title: 10x snRNA-seq on in vitro birthdated 24d old cortical neurons (0fdbfb)


title: 11-Parenchyma-HDM.AIR (X130)

description: RNAseq (11 week HDM.AIR parenchyma)

value: Parenchyma


title: patient3

description: HCC


title: 11-Airway-HDM.AIR (X129)

description: RNAseq (11 week HDM.AIR airway)


title: 10x snRNA-seq on in vitro birthdated 9d old cortical neurons (1bd629)


title: THP-1_UT_UI_96 h_Rep 3

description: Gene expression of PMA-differentiated untreated unifected-THP-1 cells at 96 h

source_name: THP-1, Untreated, Uninfected, 96 h, Replicate 3

value: Uninfected


title: 11-Parenchyma-PBS.CS (X134)

description: RNAseq (11 week PBS.CS parenchyma)


title: BLCa98 parental tumor

city: Bern

first: Daniel

middle: Walter

last: Hanhart

state: Bern

address: Murtenstrasse 24

department: Department for BioMedical Research (DBMR)

institute: UroGenus

data_processing:
Raw reads were mapped to the human reference genome GRCh38 (version 3.0.0 provided by 10X Genomics) using Cell Ranger (version 6.0.1).
The resulting gene count matrices were used to create a Seurat (version 4.1.1) object.
Cells with less than one detected feature and features found in less than one cell, were removed.
Heterotypic doublets were identified and removed with scDblFinder (version 1.6.0).
Low quality cells were removed using a median absolute deviation (MAD) threshold of 3 on the log10 transformed Feature and RNA counts per cell. Cells with above 50% mitochondrial reads were removed.
RNA expression was normalized using the NormalizeData function from Seurat with default parameters.
Assembly: GRCh38
Supplementary files format and content: data.matrix.h5, HDF5 feature-barcode matrix with normalized count (LogNormalized)

source_name: bladder

extract_protocol:
Organoids were collected in Basis medium (100g, 5min) and dissociated into single cells with 1ml TrypLE Express at 37°C for 10 min. Single-cell suspension was counted and cryopreserved in FBS/10%DMSO before scRNA sequencing. To obtain single cells from tumor tissue, tissues were digested as explained in the protocol for organoid derivation, and then cells were counted and cryopreserved in FBS/10%DMSO before analysis.  Slow-frozen single cell suspensions were shipped to the Genomics Facility Basel for scRNA-seq processing.
Cryovials were thawed and content transferred into 10 mL Basis medium and incubated for 10 min at room temperature to ensure complete removal of DMSO from the cells. Cells were collected (350g, 5 min), resuspended in 1 mL washing buffer consisting of PBS (Ca2+/Mg2+-free, Gibco, 10010-015) and 1% BSA (Sigma-Aldrich, A7906) and sequentially filtered through 100 µm (Falcon, 352360) and 40 µm cell strainers (Falcon, 352340). Apoptotic cells were removed by immunomagnetic cell separation using the Annexin Dead Cell Removal Kit (StemCell Technologies, 17899) and EasySepTM Magnet (StemCell Technologies, 18000). Whenever possible and required, repeat dead cell removal was performed to increase cell viability. Next, cells were washed with a resuspension buffer (PBS with 0.05% BSA), spin down and resuspended in a resuspension buffer. Cell numbers and viability were assessed at each step on a Cellometer K2 Image Cytometer (Nexcelom Bioscience, Cellometer K2) using ViaStain AOPI Staining Solution (Nexcelom Bioscience, CS2-0106-5mL) and PD100 cell counting slides (Nexcelom Bioscience, CHT4-PD100-003). Optimal cell concentrations were set according to 10x Genomics protocols (700-1200 cells/µL). Cells were loaded and processed using the 10x Genomics Chromium platform with the Next GEM Single Cell 3’ Reagent Kit v3.1 on 10x Genomics Chromium Single Cell Controller (10x Genomics, PN-120263). 4’000 cells were targeted per sample. Gene expression (GEX) libraries were amplified, pooled and sequenced on the Illumina NovaSeq 6000 platform with addition of 1% PhiX at recommended sequencing depth (20,000-50,000 reads/cell).

value: bladder

value: primary tissue

tag: tumor stage

value: male

value: naive


title: 17-2415-Month-3

value: N


title: 17-2415-Baseline

value: Baseline


title: 17-2421-Baseline

value: Inflammatory


title: 11-Parenchyma-PBS.AIR.DEX (X128)

description: RNAseq (11 week PBS.AIR.DEX parenchyma)

value: Balb/C


title: THP-1_UT_UI_96 h_Rep 2

source_name: THP-1, Untreated, Uninfected, 96 h, Replicate 2

value: PMA-differentiated THP-1 cells

value: Untreated

tag: time


title: 11-Parenchyma-HDM.AIR.DEX (X132)

description: RNAseq (11 week HDM.AIR.DEX parenchyma)

value: 18-20 weeks

tag: Sex


title: 17-2412-Baseline

source_name: Skin

value: Skin

value: Abatacept

value: Y; 9mo


title: THP-1_UT_IN_2 h_Rep 1

source_name: THP-1, Untreated, Mtb infected, 2 h, Replicate 1

tag: cell type

value: Mtb infected

value: 2 h


title: 11-Airway-PBS.AIR.DEX (X127)

description: RNAseq (11 week PBS.AIR.DEX airway)

source_name: Airway

value: Airway

tag: age

value: Female


title: BLCa98 organoids

value: bladder

value: organoids from primary tissue


title: 17-2406-Month-3

value: Y; 6mo

value: Proliferative


title: BLCa86 parental tumor

value: primary tissue

value: male

value: naive


title: THP-1_UT_UI_24 h_Rep 3

description: Gene expression of PMA-differentiated untreated unifected-THP-1 cells at 24 h

source_name: THP-1, Untreated, Uninfected, 24 h, Replicate 3

value: PMA-differentiated THP-1 cells

tag: infection

value: Uninfected


title: THP-1_UT_UI_96 h_Rep 1

source_name: THP-1, Untreated, Uninfected, 96 h, Replicate 1

value: Untreated


title: 17-2406-Baseline

value: Skin

value: Baseline