title: Vv_ONT_Yeast_12h

description:
MinION
Vv_ONT_FlairQuantify_gene_tpm_ECstress12h.txt
Vv_ONT_bedtools_TE_counts_ECstress12h.txt

source_name: Embryogenic callus

tag: clone

value: Pinot noir UCD7

tag: tissue

value: embryogenic callus

tag: time-point

tag: genotype

value: wild type

tag: treatment

value: yeast


title: fetal lung tissue, Sample295

status: Public on May 05 2022

type: SRA

city: Aurora

first: Sunita

last: Sharma

address: 13199 East Montview Blvd

department: Medicine-Pulmonary Sciences & Critical Care

country: USA

institute: University of Colorado Hospital

library_source: transcriptomic

data_processing:
Trimming for low-quality base calls and adpator sequeiencs was completed using cutadapt v.2.7. FastQC v0.11.8 was applied to each trimmed .fastq file to assess adaptor removal. Then reads were mapped to counts of known miRNAs using miR-MaGiC with reference to the Homo sapiens miRbase v22.1 database with collapsed functional groups (repo verision 7147b7a).
Samples passing quality-control (≥1x10^5 mapped reads, having available phenotypic information, and being within the 7 - 17 week pseudoglandular period) and autosomal miRNAs passing pre-filtering criteria (non-zero counts in at least 25% of samples; passes DESeq2 independent filtering algorithm;and not mapped to X or Y chromosome) were tested for differences by sex.
Using RUV-Seq v1.22.0, we also obtained four RUVr factors representing unmeasured miRNA expression heterogeneity for inclusion in regression models.
Assembly: Homo sapiens miRBase database v22.1
Supplementary files format and content: Matrix table with raw miRNA counts for every miRNA and every sample

molecule: total RNA

organism: Homo sapiens

source_name: fetal lung tissue

extract_protocol:
Total RNA was extracted from 30mg of homogenized prenatal lung tissue with the miRNeasy Mini Kit per manufacturer instructions.
Samples were block-randomized by age, sex, and smoke exposure status to four batches of miRNA library preparation (Small RNA Sequencing Kit v3 for Illumina Platforms; Bio Scientific) and sequencing (HiSeq2500; Illumina; San Diego, CA, USA).

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

value: female

tag: smokebinary

value: <7.5 ng cotinine/g placenta

tag: run


title: Patient sample 252A

city: Los Angeles

first: Matthew

middle: A

last: Fischer

state: CA

address: 650 Charles Young Dr

department: Anesthesiology and Perioperative Medicine

institute: University of California, Los Angeles

library_source: genomic

data_processing:
BSBolt (PMID 33966074) was used to align to human reference genome hg38.
We removed from analysis CpGs with less than 10x coverage. Additionally, CpGs were removed from the cohort if they were located at SNPs with minor allele frequency greater than 1% in humans (dbSNP build 150 common SNPs: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/snp150Common.txt.gz) or not present in at least 50% of the cohort after filtering for coverage.
Genome_build: hg38
Supplementary_files_format_and_content: Each patient's methylation call file contains the chromosome and base pair location of each CpG and each CpG's coverage and percent methylation data.

molecule: genomic DNA

source_name: Whole blood

extract_protocol:
Genomic DNA was isolated (PureLink Genomic DNA Kit, K1820-01) from whole blood (separately we biobanked buffy coat containing leukocytes and platelets at -80ºC), subjected to enzymatic digestion with MspI (NEB, R0106S) and bisulfite converted (EpiTect Fast. DNA Bisulfite Kit, Qiagen, 59824).
Samples underwent library preparation involving unique adaptor ligation and were subsequently pooled to be individually sequenced together. Single stranded DNA was then isolated and hybridized with 120 bp biotinylated DNA probes from Integrated DNA Technologies (Coralville, IA). Following probe pull down with streptavidin magnetic coated beads, the pooled samples underwent bisulfite conversion, PCR amplification and sequencing on NovaSeq 6000 instrunments.
Bisulfite-seq (targeted)

value: Male

tag: age

tag: paroxysmal atrial fibrillation

value: No

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: post-operative atrial fibrillation

value: Yes


title: fetal lung tissue, Sample292

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary

value: >=7.5 ng cotinine/g placenta


title: Patient sample 254A

tag: age

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension


title: Patient sample 247A

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery


title: Vv_ONT_Mock_12h

city: Lincoln

first: Christopher

last: Winefield

state: Canterbury

address: Ellesmere Junction Road/Springs Road

country: New Zealand

institute: Lincoln University

data_processing:
For short-read sequencing:
Illumina Casava v1.8.2 used for basecalling.
Sequenced reads were trimmed for adaptor sequence following removal of low-quality sequence and tRNA and rRNA reads, then mapped to V. vinifera 12X PN40024 reference genome using HISAT2 v2.1.0 with parameters --rna-strandness RF --dta -k 100.
Raw read counts for genes were calculated using htseq-count v0.10.0 with parameters -f bam -t exon -i transcript_id -s reverse -m intersection-nonempty.
Gene FPKM was calculated by dividing gene's raw read counts per kb gene transcript length with per million mapped reads.
For TEFingerprint analysis, sequenced reads were trimmed for adaptor sequence following removal of low-quality sequence and tRNA and rRNA reads, then mapped to TE sequences extraced from all annotated TE loci using bwa mem (with default setting).
Read counts for TE loci were calculated by htseq-count v0.10.0 (-f bam -t exon -i transcript_id -s reverse -m intersection-nonempty), bedtools v2.27.0 (bedtools coverage), and TEFingerprint v0.1.4 (tef preprocess --exclude-tails and then tef compare -m 11 -e 600 -q 30 -t 8).
Average read depth of each TE locus was calculated by dividing the sum of read bases overlapping with a TE locus (obtained from bedtools intersect v2.27.0) with the read-covered bases of the TE locus (obtained from bedtools coverage v2.27.0).
Read counts for TE families were calculated by TEtranscripts with parameters --mode multi --stranded reverse.
TE family FPKM was calculated by dividing TE familiy's read counts per kb TE length with per million mapped reads.
For long-read sequencing:
Oxford Nanopore Technology Guppy v3.1.5 used for basecalling.
The resulting fastq files were processed by Pychopper2 (v2.0.1) to capture full-length reads and remove adapter sequences.
The full-length reads were mapped to the 12X PN40024 V. vinifera reference genome using minimap2 v2.17 with the option -ax splice for long-read splice alignment. For TE loci analysis, the minimap2 parameters -N 100  -ax splice  were used instead. For TE family analysis, reads were mapped to V. vinifera canonical TE sequences (Repbase) with the option -ax splice.
Gene TPM was calculated using FLAIR pipeline (v1.4).
Read counts for TE loci and TE families were calculated by bedtools v2.27.0 (bedtools coverage).
TE family TPM was calculated by dividing read counts of TE families with per million mapped reads.
Genome_build: 12X PN40024
Supplementary_files_format_and_content: Tab-delimited table with raw counts for every gene and every Illumina RNA-seq library.
Supplementary_files_format_and_content: Tab-delimited table with FPKM values for every genes and every Illumina RNA-seq library.
Supplementary_files_format_and_content: Tab-delimited table with raw count values (htseq-count) for every TE loci and every Illumina RNA-seq library.
Supplementary_files_format_and_content: Tab-delimited table with raw count values (bedtools) for every TE loci and every Illumina RNA-seq library.
Supplementary_files_format_and_content: Tab-delimited table with TE's average read depth of mapped region for every TE loci and every Illumina RNA-seq library.
Supplementary_files_format_and_content: Tab-delimited table for raw count values (TEFingerprint) for every TE loci and every Illumina RNA-seq library.
Supplementary_files_format_and_content: Tab-delimited text files include gene TPM values for each ONT cDNA-seq library.
Supplementary_files_format_and_content: Tab-delimited text files include TE loci read count values (bedtools) for each ONT cDNA-seq library.

molecule: polyA RNA

organism: Vitis vinifera

growth_protocol: Embryogenic callus (EC) cultures were established from Vitis vinifera cv Pinor noir clone UCD5 and maintained in C1P medium which contains half strength MS medium, half strength MS micro elements, 0.1 % (w/v) casein hydrolysate, 3 % (w/v) sucrose, 0.5 % (w/v) gelrite, 250 μg myo-inositol, 5 μg nicotinic acid, 5 μg pyridoxine-HCl, 5 μg thiamine-HCl, 5 μg Ca-pantothenoate, 50 μg D-biotin, 1 μM BAP and 5 μM 2,4-D.

extract_protocol:
For short-read RNA-seq, total RNA of harvested embryogenic callus were isolated according to the manufacturer’s instructions of Spectrum Plant Total RNA Kit (Sigma). Each purified RNA sample was treated with DNase I following the TURBO DNA-free kit protocol (Ambion) to remove contaminating genomic DNA. For long-read sequencing, Total RNA was extracted and separated using NORGEN Plant microRNA purification kit (Norgen Biotek) according to the manufacturer’s instruction. Genomic DNA contamination was removed with the standard protocol of the TURBO DNA-free kit (Thermo Fisher).
For short-read RNA-seq, RNA libraries were prepared using standard Illumina protocols. For long-read cDNA-seq, the libraries were prepared following the protocol of Oxford Nanopore cDNA-PCR kit (SQK-PCS109).

treatment_protocol: For mock treatment, the embryogenic callus cultures were subjected to vigorous shaking in hormone-free C1P liquid medium to break the lumps of callus apart. For the yeast treatment, the embryogenic callus cultures were firstly subjected to mock treatment and then exposed to live H. uvarum cultures. For both mock and yeast treatments, samples were harvested at 1, 3, 6, and 12 hours. A common untreated 0 hour time point  for mock and the biotic treatment was taken prior to any treatment.

tag: clone

value: Pinot noir UCD6

tag: tissue

tag: time-point

tag: genotype

tag: treatment

value: mock


title: fetal lung tissue, Sample287

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

value: male

tag: run


title: Patient sample 251A

tag: Sex

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: post-operative atrial fibrillation


title: Patient sample 246A

tag: age

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery


title: Patient sample 248A


title: fetal lung tissue, Sample286

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run


title: Patient sample 245A

tag: Sex

value: Female

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian


title: fetal lung tissue, Sample293


title: fetal lung tissue, Sample284


title: fetal lung tissue, Sample288


title: fetal lung tissue, Sample285


title: Patient sample 244A

tag: age

tag: paroxysmal atrial fibrillation

tag: black

tag: hispanic

tag: post-operative atrial fibrillation


title: Patient sample 249A

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure


title: fetal lung tissue, Sample40

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary


title: Patient sample 242A

tag: Sex

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index


title: fetal lung tissue, Sample282

tag: run


title: Patient sample 216A

data_processing:
BS-Seeker2 (PMID 24206606) was used to align the reads to hg38, allowing for up to 10 mismatches, and methylation was called for CpGs and then processed using MethylKit in R as described in previous publications (PMIDs 29566149 and 26838786)
We removed from analysis CpGs with less than 10x coverage. Additionally, CpGs were removed from the cohort if they were located at SNPs with minor allele frequency greater than 1% in humans (dbSNP build 150 common SNPs: http://hgdownload.cse.ucsc.edu/goldenpath/hg38/database/snp150Common.txt.gz) or not present in at least 50% of the cohort after filtering for coverage.
Genome_build: hg38
Supplementary_files_format_and_content: Each patient's methylation call file contains the chromosome and base pair location of each CpG and each CpG's coverage and percent methylation data.

extract_protocol:
Genomic DNA was isolated (PureLink Genomic DNA Kit, K1820-01) from whole blood (separately we biobanked buffy coat containing leukocytes and platelets at -80ºC), subjected to enzymatic digestion with MspI (NEB, R0106S) and bisulfite converted (EpiTect Fast. DNA Bisulfite Kit, Qiagen, 59824).
Libraries were prepared using Illumina TruSeq kit, size-selected for 330 bp with AMPure XP beads and subjected to 100 bp, single-end sequencing on HiSeq instruments.

tag: age

tag: paroxysmal atrial fibrillation

tag: current smoker

tag: asian

tag: black

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition


title: fetal lung tissue, Sample29

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary


title: Patient sample 243A

tag: Sex

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: hispanic

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample283

tag: run


title: fetal lung tissue, Sample280


title: fetal lung tissue, Sample281


title: fetal lung tissue, Sample28


title: Patient sample 240A

tag: age

tag: paroxysmal atrial fibrillation

tag: current smoker

tag: asian

tag: black


title: fetal lung tissue, Sample279

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary


title: Patient sample 241A

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure


title: Patient sample 237A

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: hispanic

tag: post-operative atrial fibrillation


title: Patient sample 236A

tag: age

tag: paroxysmal atrial fibrillation

tag: current smoker

tag: asian


title: Patient sample 239A

tag: black


title: fetal lung tissue, Sample277

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: run


title: fetal lung tissue, Sample278

tag: smokebinary


title: UMUC3 HLA-

type: RNA

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: UM-UC3 - (HLA-ABC-)

hyb_protocol: The labelled RNA samples were hybridized at 65°C for at least 16 hours but not more than 48 hours in a thermal cycler.

scan_protocol: Each individual lane were scanned 194 Fields of View (FOV). The system images these FOVs separately, and sums the barcode counts of all FOVs from a single lane to form the final raw data count for each unique barcode target. Finally, the system reports the number of FOVs successfully imaged as FOV Counted.

data_processing: The raw data were processed using NanoString nSolver. The raw data were normalized using positive control and housekeeping genes control.

label: biotin

source_name: Bladder Cancer Cell line

label_protocol: 100ng of unamplified total RNA were labelled with nanoString Reporter CodeSet and Capture ProbeSet, procedure as per MAN-10023-11_nCounter_XT_Assay_User_Manual.

growth_protocol: All cell-lines were maintained in culture with antibiotic-free media RPMI 1640 following the addition of 10% heat-inactivated fetal bovine serum (GE Healthcare) at 37 °C in a humid atmosphere containing 5% CO2.

extract_protocol: RNA was extracted using the Direct-zol RNA MiniPrep Kit (Zymo Research).

treatment_protocol: BCG treatment for 24 hours for HLA+ samples.

tag: cell line

tag: phenotype

value: HLA-

tag: treatment

value: Pre-BCG


title: UMUC3 HLA+

description: UM-UC3+ (HLA-ABC+)

value: HLA+

value: Post-BCG


title: RT4 HLA-

description: RT4 - (HLA ABC -)


title: fetal lung tissue, Sample276


title: 5637 HLA+

description: 5637 + (HLA-ABC+)


title: Patient sample 233A

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index


title: Patient sample 210A

tag: age

tag: paroxysmal atrial fibrillation

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: RT4 HLA+

description: RT4 + (HLA-ABC+)

tag: cell line

tag: phenotype

tag: treatment


title: Patient sample 235A

tag: Sex

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index


title: Patient sample 238A

tag: age

tag: paroxysmal atrial fibrillation

tag: current smoker

tag: asian

tag: black

tag: hispanic


title: Patient sample 234A

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample275

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run


title: exp_SSCF-1

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

country: China

institute: Qingdao Agricultural University

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m
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.
Genome_build: mm10
Supplementary_files_format_and_content: include gene expression

organism: Mus musculus

source_name: spleen

extract_protocol:
Spleen were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used to abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain

value: ICR

tag: tissue

value: spleen

value: 10 weeks

tag: treatment

value: STZ+control-FMT


title: Patient sample 231A

tag: Sex

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time


title: Patient sample 192A

tag: age

tag: paroxysmal atrial fibrillation

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample272

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary

value: <7.5 ng cotinine/g placenta

tag: run


title: exp_SSAF-3

tag: strain

tag: tissue

tag: age

tag: treatment


title: Patient sample 203A

value: Male

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: b cells composition


title: fetal lung tissue, Sample274

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary

tag: run


title: Patient sample 232A

tag: age

tag: paroxysmal atrial fibrillation

value: No

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: post-operative atrial fibrillation


title: exp_SSCF-2

tag: strain

tag: tissue

tag: treatment


title: fetal lung tissue, Sample273


title: Patient sample 229A

value: Yes

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic


title: fetal lung tissue, Sample271

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

value: female

tag: smokebinary

value: >=7.5 ng cotinine/g placenta

tag: run


title: exp_SSAF-2

tag: strain

tag: tissue

tag: age


title: exp_SSA-2

tag: treatment


title: fetal lung tissue, Sample270


title: Patient sample 151A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 228A

tag: Sex

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic


title: Patient sample 230A

tag: age

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation


title: 5637 HLA-

description: 5637- (HLA-ABC-)

tag: cell line

tag: phenotype

tag: treatment


title: exp_SSCF-3

tag: strain

tag: tissue


title: fetal lung tissue, Sample27

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary

tag: run


title: exp_SSA-3

tag: age


title: Patient sample 150A

tag: paroxysmal atrial fibrillation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample269

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary

tag: run


title: exp_SSAF-1

tag: strain

tag: tissue

tag: age

tag: treatment


title: Patient sample 225A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic


title: exp_SSA-1

tag: strain


title: fetal lung tissue, Sample267

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary

tag: run


title: Patient sample 226A

tag: age

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample266


title: exp_SS-3

tag: tissue

tag: treatment

value: STZ


title: Patient sample 224A

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: exp_SS-2

tag: strain


title: exp_SS-1

tag: age


title: fetal lung tissue, Sample268

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

value: male

tag: smokebinary

tag: run


title: Patient sample 147A

value: Female

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: Patient sample 148A

tag: age

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black


title: Patient sample 227A

tag: Sex

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: hispanic


title: Patient sample 222A


title: Patient sample 133A

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition


title: fetal lung tissue, Sample262

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: smokebinary

tag: run


title: Patient sample 223A

tag: Sex

tag: age

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample263


title: Kasumi-1 treated with I13_3

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

data_processing:
Raw reads were processed using Trimmomatic. The reads containing ploy-N and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to reference genome using hisat 2.
FPKM value of each gene was calculated using cufflinks, and the read counts of each gene were obtained by htseq-count.
Genome_build: hg38
Supplementary_files_format_and_content: FPKM value

source_name: Kasumi-1 cell line treated with I13 3

extract_protocol:
Total RNA was extracted using using Trizol reagent following the manufacturer's protocol.
The libraries were constructed using TruSeq Stranded mRNA LTSample Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's instructions.

tag: cell line

tag: protocol

value: incubating with I13 for 48 h

tag: agent


title: exp_Scon-3

tag: strain

tag: tissue

tag: treatment

value: control


title: fetal lung tissue, Sample260

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary

tag: run


title: fetal lung tissue, Sample265


title: fetal lung tissue, Sample264


title: exp_SA-2

tag: age

value: AOS 10mg/kg


title: exp_SA-1


title: Kasumi-1 treated with control_2

source_name: Kasumi-1 cell line treated with control 2

value: incubating with control for 48 h

value: Control


title: fetal lung tissue, Sample258


title: fetal lung tissue, Sample257


title: fetal lung tissue, Sample259


title: exp_LSCF3

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 mm10 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m
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.
Genome_build: mm10
Supplementary_files_format_and_content: includ gene expression

source_name: Liver

extract_protocol:
Liver were removed, quikly frozen in luquid nitrogen, and RNA was harvested using Trizol reagent. PurelinkTM RNA Mini Kit (Cat#12183018A) was used tp abtain 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: ICR

value: liver


title: exp_Scon-2

value: spleen

value: 10 weeks


title: Patient sample 221A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: hispanic


title: Older_8

city: Salt Lake City

first: Jingtao

last: Guo

state: UT

address: 2000 Circle of Hope

department: Department of Surgery Division of Urology

institute: University of Utah School of Medicine

description:
18489X2_201113_A00421_0256_BHLY3JDSXY_S3
processed data file: Older_Group2_matrix.txt.gz

data_processing:
Samples were sequenced as paired end sequencing. Raw data were firstly demultiplexed using mkfastq application (Cell Ranger v2.2.0). Fastq files were then run with count application (Cell Ranger v2.2.0) using default settings, which performs alignment (using STAR aligner), filtering and UMI counting. The UMI count table was used for further analysis.
Genome_build: hg38
Supplementary_files_format_and_content: tab-delimited text files include UMI numbers for all genes and single cells that passed filtering

source_name: Human testicular tissue_older

extract_protocol:
Testicular tissues were firstly minced into small pieces mechanically, and subject to collagenase IV and trypsin digestion for ~5 min at 37 C, respectively. The reaction was terminated by addition of FBS. Then, cell suspension was centrifuged and resuspended in cold PBS buffer with 0.4% of BSA at the concentration of ~1000/ul, which then was loaded onto the 10X Chromium Controller using Chromium Single Cell 3’ v3.1 reagents.
Sequencing library was prepared following the manufacturer’s instructions (10X Genomics), with 13 cycles used for cDNA amplification and 12 cycles for library amplification, which was then sequenced on a 2 X 150 cycle paired-end run via a Illumina Novaseq 6000 instrument. Each sample was sequenced in one separate sequencing lane.
10X Genomics single cell RNA sequencing

tag: tissue

value: Testicle

value: older adults (>60 years old)


title: Older_7

description:
18489X3_201113_A00421_0256_BHLY3JDSXY_S4
processed data file: Older_Group2_matrix.txt.gz


title: fetal lung tissue, Sample256

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

value: <7.5 ng cotinine/g placenta


title: exp_LSAF3

tag: strain

tag: treatment


title: exp_Scon-1

tag: age


title: Kasumi-1 treated with I13_2

source_name: Kasumi-1 cell line treated with I13 2

tag: cell line

tag: protocol

tag: agent


title: fetal lung tissue, Sample261

tag: Sex

tag: smokebinary

tag: run


title: Kasumi-1 treated with I13_1

source_name: Kasumi-1 cell line treated with I13 1


title: exp_SA-3


title: Older_4

description:
18434X4_201016_A00421_0249_BHKN3JDSXY_S4
processed data file: Older_Group1_matrix.txt.gz


title: fetal lung tissue, Sample254

value: female


title: exp_LSAF1


title: fetal lung tissue, Sample26


title: exp_LSCF2

value: STZ+control-FMT


title: Kasumi-1 treated with control_3

source_name: Kasumi-1 cell line treated with control 3


title: exp_LSA3


title: fetal lung tissue, Sample253


title: fetal lung tissue, Sample252


title: Kasumi-1 treated with control_1

source_name: Kasumi-1 cell line treated with control 1


title: exp_LSCF1


title: fetal lung tissue, Sample255

value: >=7.5 ng cotinine/g placenta


title: fetal lung tissue, Sample250

value: male


title: fetal lung tissue, Sample249


title: fetal lung tissue, Sample25


title: exp_LS1

value: STZ


title: exp_LSAF2


title: Older_6

description:
18489X1_201113_A00421_0256_BHLY3JDSXY_S2
processed data file: Older_Group2_matrix.txt.gz


title: Older_5

description:
18434X5_201016_A00421_0249_BHKN3JDSXY_S5
processed data file: Older_Group1_matrix.txt.gz


title: Older_2

description:
18434X3_201016_A00421_0249_BHKN3JDSXY_S3
processed data file: Older_Group1_matrix.txt.gz


title: Older_1

description:
18434X2_201016_A00421_0249_BHKN3JDSXY_S2
processed data file: Older_Group1_matrix.txt.gz


title: exp_LSA1


title: exp_LSA2


title: fetal lung tissue, Sample246


title: exp_Lcon2


title: fetal lung tissue, Sample248


title: exp_Lcon3


title: Older_3

description:
18434X6_201016_A00421_0249_BHKN3JDSXY_S6
processed data file: Older_Group1_matrix.txt.gz


title: fetal lung tissue, Sample245


title: exp_LS3


title: fetal lung tissue, Sample244


title: exp_LS2


title: fetal lung tissue, Sample247


title: COV168, small RNA

city: Xian

first: chengsheng

last: zhang

state: Shaanxi

address: 277 West Yanta Road, Xi'an, Shaanxi, P.R.China

department: precision medicine center

institute: First Affiliated Hospital of Xi 'an Jiaotong University

data_processing:
Raw sequencing data was firstly filtered by fastx_toolkit (version: 0.0.13.2, http://hannonlab.cshl.edu/fastx_toolkit/) for discarding the low-quality reads and adaptor sequences were trimmed by cutadapt (version: 1.15) (version: 1.15)
Clean Reads were further treated to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with 100% sequence identity were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-cluster.
Then, the reads were subjected to an in-house program, ACGT101-miR (LC Sciences, Houston, Texas, USA), to remove common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats. Subsequently, unique sequences with length in 18-26 nucleotide were mapped to human precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3’and 5’ends and one mismatch inside of the sequence were allowed in the alignment. The unique sequences mapping to human mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known human precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p- derived miRNA candidates. For novel miRNAs, the criterion is that the total expression level in 233 samples were >100.The unmapped sequences were BLASTed against the human genomes (ftp://ftp.ensembl.org/pub/release-96/fasta/homo_sapiens/dna/), and the hairpin RNA structures containing sequences were predicated from the flank 80 nt sequences using RNAfold software (http://rna.tbi.univie.ac.at/cgi-bin/RNAfold.cgi).  The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (<=12); (2) number of base pairs in the stem region of the predicted hairpin (>=16); (3) cutoff of free energy (kCal/mol <=﹣15); (4) length of hairpin (up and down stems + terminal loop >=50); (5) length of hairpin loop (<=20); (6) number of nucleotides in one bulge in mature region (<=8); (7) number of biased errors in one bulge in mature region(<=4); (8) number of biased bulges in mature region (<=2); (9) number of errors in mature region (<=7); (10) number of base pairs in the mature region of the predicted hairpin (>=12); (11) percent of mature in stem (>=80).
Student’t test and paired t-test were used to calculate the differentially expressed miRNAs in different compared groups. P<0.05 and fold changes >1.50 or < 0.67 were selected as the significant level. Low expression of miRNAs was excluded.
Genome_build: GRCh38_v96
Supplementary_files_format_and_content: normalized counts

source_name: Peripheral blood

extract_protocol:
The peripheral blood was collected into standard EDTA blood tubes and stored on ice until processed. The time of centrifugation should be as fast as possible. The upper plasma was separated after centrifuged at 2500 rpm with 20 minutes and frozen in the -80 refrigerator for standby procession. After all plasma samples were collected, the samples were randomly divided into three groups, and RNA was extracted within 3 days. The volume of plasma for RNA extraction was 2-3 ml by Norgen Plasma/Serum Circulating and Exosomal RNA Purification Kit (Slurry Format) (Cat. 42800) kit in a biosafety level 2 (BSL 2) laboratory at the department of inspection, east Hospital, people's Hospital of Wuhan University. 3 μL total RNA was used as input for miRNA library preparation by using NEBNext® Multiplex Small RNA Library Prep Set for Illumina® (Catalog NO. E7300, New England Biolabs) following the manufacturer’s instruction with modification, which labeled the pre-amplified small RNA molecules with unique molecular identifier (UMI)（LC-Bio Technology Co., LTD）. UMI reduces duplication bias in PCR and sequencing steps. The DNA library was purified by using 6 % PAGE gel, quantified by using QubitTM3 fluorometer (Invitrogen™, Cat. No. Q33216) with Qubit™ dsDNA HS Assay Kit (Invitrogen™, Cat. No. Q32854), examined by using Qsep100TM bio-fragment analyzer (Bioptic Inc., Taiwan, China), and finally sequenced on Novaseq 6000 sequencer (Illumina) with PE150 model.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: gender

value: Male

tag: infection

tag: disease symptom

value: Symptomatic

tag: disease state

value: Moderate

tag: disease duration

value: Long-term nucleic acid test positive

value: Peripheral blood


title: COV167, small RNA

tag: tissue


title: exp_Lcon1

value: ICR

value: control


title: exp_LA1

value: liver

value: AOS 10mg/kg


title: fetal lung tissue, Sample251

tag: age (days post coitum)

tag: age orthogonal polynomial linear term


title: exp_LA3

tag: strain

value: 10 weeks


title: COV166, small RNA

value: Female


title: exp_LA2

tag: treatment


title: fetal lung tissue, Sample242

tag: age orthogonal polynomial quadratic term

value: <7.5 ng cotinine/g placenta


title: fetal lung tissue, Sample243


title: COV165, small RNA

tag: age

value: Severe


title: COV164, small RNA


title: COV163, small RNA


title: fetal lung tissue, Sample241

value: female


title: COV161, small RNA


title: fetal lung tissue, Sample240

value: >=7.5 ng cotinine/g placenta


title: COV160, small RNA


title: fetal lung tissue, Sample239

value: male


title: COV162, small RNA


title: COV159, small RNA


title: COV158, small RNA


title: fetal lung tissue, Sample238


title: fetal lung tissue, Sample236


title: COV156, small RNA


title: COV157, small RNA


title: fetal lung tissue, Sample237


title: fetal lung tissue, Sample235


title: fetal lung tissue, Sample233


title: fetal lung tissue, Sample234


title: COV154, small RNA

value: Asymptomatic

value: Asymptomatic infection


title: COV155, small RNA


title: Patient sample 100A

value: Male

tag: paroxysmal atrial fibrillation

value: No

tag: diabetes mellitus

tag: hypertension

value: Yes

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: COV153, small RNA

tag: age

tag: gender

tag: infection

tag: disease symptom

tag: disease state

tag: tissue

value: Peripheral blood


title: COV152, small RNA

value: Symptomatic

value: Moderate

tag: disease duration

value: Short-term nucleic acid test positive


title: fetal lung tissue, Sample232

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary

tag: run


title: fetal lung tissue, Sample231


title: Patient sample 092A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition


title: fetal lung tissue, Sample24

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary

tag: run


title: fetal lung tissue, Sample230


title: fetal lung tissue, Sample23


title: COV149, small RNA

tag: age

tag: gender

tag: infection

tag: disease symptom

tag: disease state

tag: tissue


title: COV148, small RNA


title: COV151, small RNA


title: Patient sample 087A

tag: paroxysmal atrial fibrillation

tag: diabetes mellitus

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: natural killer cell composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample229

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary

tag: run


title: fetal lung tissue, Sample228


title: COV147, small RNA

tag: age

tag: gender

tag: infection

tag: disease symptom

tag: disease state

tag: tissue


title: COV146, small RNA


title: fetal lung tissue, Sample227


title: COV150, small RNA


title: fetal lung tissue, Sample226


title: nonBPD cord blood of sample 4010_1

type: genomic

city: Research Triangle Park

first: Xuting

last: Wang

state: NC

address: 111 TW Alexander Dr

institute: NIEHS/NIH

description: nonBPD cord blood sample

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation450 and MethylationEPIC Beadchips using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: Beta (processed using minfi preprocessNoob)

label: Cy5 and Cy3

source_name: nonBPD cord blood

label_protocol: 250 ng of DNA was bisulfite converted using the EZ-DNA Methylation kit (Zymo Research)

extract_protocol: Umbilical cord blood samples were collected at birth in PAXgene reagent (Qiagen Inc., Valencia, CA) and snap frozen at -80°C. Samples were processed with PAXgene Blood miRNA Kit (PreAnalytix/Qiagen).  For DNA isolation, the isopropanol precipitants were loaded into the DNeasy Mini spin columns (DNeasy Blood & Tissue Kit, Qiagen). All extraction steps followed the manufacturer’s procedure.

tag: disease status

value: nonBPD

value: cord blood


title: COV145, small RNA

value: Female

tag: disease duration


title: fetal lung tissue, Sample225

value: <7.5 ng cotinine/g placenta


title: nonBPD cord blood of sample 4015_1

description: nonBPD cord blood sample


title: COV144, small RNA


title: nonBPD cord blood of sample 4014_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample223


title: nonBPD cord blood of sample 1002_1

description: nonBPD cord blood sample


title: COV142, small RNA


title: COV143, small RNA


title: nonBPD cord blood of sample 4011_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 4012_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 4013_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 4009_1

description: nonBPD cord blood sample


title: COV140, small RNA


title: fetal lung tissue, Sample221


title: nonBPD cord blood of sample 4006_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 4003_2

description: nonBPD cord blood sample


title: COV141, small RNA


title: nonBPD cord blood of sample 4003_1

description: nonBPD cord blood sample


title: COV139, small RNA


title: fetal lung tissue, Sample22


title: nonBPD cord blood of sample 4007_1

description: nonBPD cord blood sample


title: COV138, small RNA


title: fetal lung tissue, Sample220


title: fetal lung tissue, Sample219


title: fetal lung tissue, Sample222


title: nonBPD cord blood of sample 4008_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 3019_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 3018_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 4002_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 4006_2

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 4010_2

description: nonBPD cord blood sample


title: COV137, small RNA

value: Severe-repeated

value: Short-term nucleic acid test positive-repeated


title: nonBPD cord blood of sample 3016_1

description: nonBPD cord blood sample


title: COV136, small RNA

value: Long-term nucleic acid test positive-repeated


title: fetal lung tissue, Sample218

value: female


title: nonBPD cord blood of sample 3014_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample216

value: male


title: fetal lung tissue, Sample217

value: >=7.5 ng cotinine/g placenta


title: COV135, small RNA

value: Male


title: COV134, small RNA

value: Moderate-repeated


title: fetal lung tissue, Sample215


title: nonBPD cord blood of sample 3011_2

description: nonBPD cord blood sample


title: COV132, small RNA


title: nonBPD cord blood of sample 3015_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample224


title: fetal lung tissue, Sample214


title: COV131, small RNA

value: Long-term nucleic acid test positive


title: COV133, small RNA

value: Peripheral blood


title: fetal lung tissue, Sample211


title: COV130, small RNA

value: Symptomatic


title: nonBPD cord blood of sample 3011_1

description: nonBPD cord blood sample


title: COV129, small RNA


title: fetal lung tissue, Sample213


title: nonBPD cord blood of sample 3010_2

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 3009_3

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 3009_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample21


title: COV127, small RNA


title: COV128, small RNA

value: Moderate


title: nonBPD cord blood of sample 3010_1

description: nonBPD cord blood sample


title: Patient sample 073A

tag: paroxysmal atrial fibrillation

value: No

tag: diabetes mellitus

value: Yes

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: natural killer cell composition


title: fetal lung tissue, Sample210

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary

tag: run


title: fetal lung tissue, Sample209


title: COV126, small RNA

tag: age

tag: gender

tag: infection

tag: disease symptom

tag: disease state

tag: disease duration

tag: tissue


title: fetal lung tissue, Sample208


title: COV125, small RNA


title: fetal lung tissue, Sample206


title: COV124, small RNA


title: nonBPD cord blood of sample 3008_1

description: nonBPD cord blood sample

tag: disease status

value: nonBPD

value: cord blood


title: fetal lung tissue, Sample212


title: fetal lung tissue, Sample207


title: nonBPD cord blood of sample 3006_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample205

value: <7.5 ng cotinine/g placenta


title: COV123, small RNA

value: Severe-repeated


title: nonBPD cord blood of sample 3003_1

description: nonBPD cord blood sample


title: COV121, small RNA

value: Female


title: fetal lung tissue, Sample203


title: COV122, small RNA

value: Short-term nucleic acid test positive-repeated


title: fetal lung tissue, Sample204

value: female


title: nonBPD cord blood of sample 3004_1

description: nonBPD cord blood sample


title: COV119, small RNA

value: Severe

value: Short-term nucleic acid test positive

tag: repeated samples


title: nonBPD cord blood of sample 3001_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 3007_1

description: nonBPD cord blood sample


title: COV118, small RNA


title: fetal lung tissue, Sample202


title: fetal lung tissue, Sample201

value: >=7.5 ng cotinine/g placenta


title: nonBPD cord blood of sample 3005_1

description: nonBPD cord blood sample


title: COV120, small RNA

value: Male

value: Moderate-repeated


title: COV117, small RNA

value: Peripheral blood


title: fetal lung tissue, Sample2

value: male


title: COV116, small RNA

value: Symptomatic


title: fetal lung tissue, Sample200


title: nonBPD cord blood of sample 2027_1

description: nonBPD cord blood sample


title: COV115, small RNA

value: Long-term nucleic acid test positive-repeated


title: COV114, small RNA


title: nonBPD cord blood of sample 2026_2

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 2026_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 3002_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample199


title: fetal lung tissue, Sample20


title: nonBPD cord blood of sample 2024_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample197


title: nonBPD cord blood of sample 2025_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 2023_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample198


title: Patient sample 041A

tag: paroxysmal atrial fibrillation

value: Yes

tag: diabetes mellitus

value: No

tag: hypertension

tag: congestive heart failure

tag: pulmonary vein isolation

tag: maze procedure

tag: combined surgery

tag: cardiopulmonary bypass time

tag: body mass index

tag: current smoker

tag: asian

tag: black

tag: hispanic

tag: b cells composition

tag: cd4+ t cell composition

tag: cd8+ t cell composition

tag: monocyte composition

tag: neutrophil composition

tag: post-operative atrial fibrillation


title: fetal lung tissue, Sample195

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

tag: smokebinary

tag: run


title: COV112, small RNA

tag: age

tag: gender

tag: infection

tag: disease symptom

tag: disease state

tag: tissue


title: nonBPD cord blood of sample 2022_2

description: nonBPD cord blood sample

tag: disease status

value: nonBPD

value: cord blood


title: nonBPD cord blood of sample 2020_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 2021_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 2021_2

description: nonBPD cord blood sample


title: fetal lung tissue, Sample196

value: <7.5 ng cotinine/g placenta


title: nonBPD cord blood of sample 2022_1

description: nonBPD cord blood sample


title: COV111, small RNA

value: Severe-repeated

tag: disease duration


title: fetal lung tissue, Sample193


title: COV113, small RNA

value: Female


title: fetal lung tissue, Sample194

value: female


title: nonBPD cord blood of sample 2018_1

description: nonBPD cord blood sample


title: COV109, small RNA


title: nonBPD cord blood of sample 2016_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 2019_1

description: nonBPD cord blood sample


title: COV110, small RNA


title: COV104, small RNA


title: COV108, small RNA

value: Short-term nucleic acid test positive-repeated


title: COV106, small RNA


title: COV107, small RNA


title: COV102, small RNA

value: Moderate


title: fetal lung tissue, Sample190


title: fetal lung tissue, Sample192


title: COV105, small RNA


title: nonBPD cord blood of sample 2015_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample189

value: >=7.5 ng cotinine/g placenta


title: fetal lung tissue, Sample19


title: COV103, small RNA


title: nonBPD cord blood of sample 2006_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 2005_2

description: nonBPD cord blood sample


title: fetal lung tissue, Sample188


title: nonBPD cord blood of sample 2013_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 2008_1

description: nonBPD cord blood sample


title: LNCaP_siTRIM33#2-10nM DHT

city: Macau

first: Edwin

middle: Chong Wing

last: CHEUNG

state: Macau

address: Avenida da Universidade, Taipa

department: Faculty of Health Sciences

institute: University of Macau

description:
siTRIM33_2_DHT
genes-fpkm-matrix.tsv

data_processing:
Basecalls performed using CASAVA-1.8.2.
The raw reads of every sample were first trimmed to 75bp and then mapped as paired-end sequencing reads against UCSC hg19 and the gene annotation reference GRCh37 using HISAT2.
The FPKM (Fragments Per Kilobase of exon model per Million mapped fragments) expression values were calculated from the BAM file generated by HISAT2 and SAMtools using the StringTie package.
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: genes-fpkm-matrix.tsv: Tab-separated text file includes FPKM values for each Sample.

source_name: prostate cancer cell line

extract_protocol:
The total RNA of each sample was extracted using the RNeasy Mini Kit (QIAGEN) according to the manufacturer’s protocol.
Library preparations were constructed using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina® according to the manufacturer’s protocol.

tag: cell line

value: LNCaP

tag: sirna

value: siTRIM33 #2

tag: treatment

value: DHT for 12 h


title: fetal lung tissue, Sample187

tag: age (days post coitum)

value: male


title: LNCaP_siTRIM33#2-EtOH

description:
siTRIM33_2_ETOH
genes-fpkm-matrix.tsv

value: EtOH for 12 h


title: nonBPD cord blood of sample 2005_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 2009_1

description: nonBPD cord blood sample


title: COV101, small RNA

value: Symptomatic

value: Long-term nucleic acid test positive

value: Peripheral blood


title: fetal lung tissue, Sample183

tag: age orthogonal polynomial linear term


title: fetal lung tissue, Sample191

tag: age orthogonal polynomial quadratic term


title: LNCaP_siTRIM33#1-10nM DHT

description:
siTRIM33_1_DHT
genes-fpkm-matrix.tsv

value: siTRIM33 #1


title: COV097, small RNA

value: Male

value: Short-term nucleic acid test positive


title: fetal lung tissue, Sample184

tag: Sex

value: <7.5 ng cotinine/g placenta


title: COV100, small RNA

value: Female


title: nonBPD cord blood of sample 2004_1

description: nonBPD cord blood sample

value: nonBPD

value: cord blood


title: LNCaP_siTRIM33#1-EtOH

description:
siTRIM33_1_ETOH
genes-fpkm-matrix.tsv


title: nonBPD cord blood of sample 2003_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample185

tag: smokebinary


title: LNCaP Input

data_processing:
Basecalls performed using CASAVA-1.8.2.
ChIP-seq reads were aligned to the hg19 genome assembly using Bowtie v0.12.9 with default parameters.
SAM to BAM conversion and sorting was performed using samtools v1.9.0.
The duplicated reads were marked using Picard MarkDuplicates v2.20.0 utility.
Peak calling was performed using MACS1.4 with pvalue < 1e-4.
The alignment coverage was calculated and converted into bigwig format using deeptools v3.4.3 bamCoverage utility and visualized into IGV v2.7.2 (Genome Build: hg19).
Genome_build: hg19 (GRCh37)
Supplementary_files_format_and_content: .bed files representing the peaks in text format.
Supplementary_files_format_and_content: .bw files store alignment coverage in binary format.

extract_protocol:
Lysates were clarified from sonicated nuclei and interested protein-DNA complexes were isolated with antibody.
Library preparations were constructed using NEBNext® Ultra™ DNA Library Prep Kit for Illumina® according to the manufacturer’s protocol.

value: Untreated

tag: chip antibody


title: fetal lung tissue, Sample182

value: >=7.5 ng cotinine/g placenta

tag: run


title: COV099, small RNA

tag: age

tag: gender

value: Moderate


title: LNCaP_NC-10nM DHT

description:
NC_DHT
genes-fpkm-matrix.tsv

value: LNCaP

value: NC


title: nonBPD cord blood of sample 1040_1

description: nonBPD cord blood sample


title: COV098, small RNA

tag: infection

tag: disease symptom


title: LNCaP_NC-EtOH

description:
NC_ETOH
genes-fpkm-matrix.tsv


title: fetal lung tissue, Sample181

value: female


title: nonBPD cord blood of sample 1034_2

description: nonBPD cord blood sample

tag: tissue


title: LNCaP AR_siTRIM33#2-100nM DHT

value: siTRIM33 #2

value: DHT for 2 h

value: AR (Santa Cruz, sc-H280)


title: nonBPD cord blood of sample 1039_1

description: nonBPD cord blood sample

tag: disease status


title: COV096, small RNA

value: Symptomatic

tag: disease state

tag: disease duration

value: Peripheral blood


title: fetal lung tissue, Sample186

value: male


title: LNCaP AR_siTRIM33#2-EtOH

tag: cell line

tag: sirna

value: EtOH for 2 h


title: nonBPD cord blood of sample 1033_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 1038_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 1035_1

description: nonBPD cord blood sample


title: LNCaP AR_NC-EtOH rep2

tag: treatment


title: COV095, small RNA

value: Long-term nucleic acid test positive


title: fetal lung tissue, Sample180

tag: age (days post coitum)

tag: age orthogonal polynomial linear term


title: fetal lung tissue, Sample18

tag: age orthogonal polynomial quadratic term

tag: Sex

value: <7.5 ng cotinine/g placenta


title: fetal lung tissue, Sample178

tag: smokebinary


title: COV093, small RNA

value: Female

value: Moderate-repeated


title: LNCaP AR_NC-100nM DHT rep2

tag: chip antibody


title: fetal lung tissue, Sample179

tag: run


title: COV094, small RNA

tag: age

tag: gender

value: Male

value: Short-term nucleic acid test positive


title: COV092, small RNA

tag: infection

tag: disease symptom

value: Moderate


title: LNCaP AR_siTRIM33#1-100nM DHT

value: LNCaP

value: siTRIM33 #1


title: COV091, small RNA

tag: tissue


title: fetal lung tissue, Sample177

value: female


title: LNCaP AR_NC-100nM DHT rep1

value: NC


title: COV090, small RNA

value: Suspected


title: fetal lung tissue, Sample176


title: LNCaP AR_siTRIM33#1-EtOH

value: AR (Santa Cruz, sc-H280)


title: COV089, small RNA

value: Symptomatic

tag: disease state


title: LNCaP AR_NC-EtOH rep1


title: nonBPD cord blood of sample 1030_2

description: nonBPD cord blood sample

tag: disease status

value: nonBPD

value: cord blood


title: COV088, small RNA

value: Peripheral blood


title: nonBPD cord blood of sample 1031_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample173

value: male

value: >=7.5 ng cotinine/g placenta


title: nonBPD cord blood of sample 1032_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample175

value: <7.5 ng cotinine/g placenta


title: LNCaP TRIM33-EtOH

tag: cell line

value: EtOH for 2 h

value: TRIM33 (Bethyl Laboratories, A301-060A))


title: fetal lung tissue, Sample174


title: LNCaP TRIM33-100nM DHT

value: DHT for 2 h


title: COV086, small RNA

value: Female

value: Moderate

tag: disease duration

value: Short-term nucleic acid test positive


title: COV087, small RNA

value: Male


title: nonBPD cord blood of sample 1029_2

description: nonBPD cord blood sample


title: COV085, small RNA


title: nonBPD cord blood of sample 1030_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample171


title: MEL624_H3K27ac_shFTO1 ChIP-seq

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

data_processing:
Sequencing reads were trimmed of low quality nucleotides by trim_galore.
High-quality reads were then mapped to mm9/hg19 reference genome by bowtie2 with uniquely mapped reads retained for the following analyses.
For ATAC-Seq, reads mapped to chrM were removed before normalization.
Normalization were performed by Deeptools with duplication removed.
Peak calling was performed with macs2.
Genome_build: mm9, hg19
Supplementary_files_format_and_content: peaks

growth_protocol: mESCs were maintained in DMEM (Invitrogen) supplemented with 15% FBS, 1% nucleosides (100×),1 mM L-glutamine,1% nonessential amino acid, 0.1 mM 2-mercaptoethanol, 1,000 U/ml LIF, 3 μM CHIR99021 and 1 μM PD0325901 and Melanoma cells were maintained in DMEM supplemented with 10% FBS and 0.5 ug/ml puromycin at 37 °C in 5% CO2.

extract_protocol:
For ChIP-seq,  Mel624 cells were resuspended in growth media with a concentration of 10e6 ml-1 and cross-linked by adding 1% formaldehyde directly to the media, slow shaked 10 min at room temperature. Cross-linking was stopped by adding glycine to a final concentration of 0.125 M and incubating for 5 min at room temperature with slowly shaking. The media was removed and the cells were washed twice with ice-cold PBS; For ATAC-seq, cells were harvested and proceeded to  transposition reaction and purifications.
ChIP was performedusing Auto iDeal ChIP-seq kit for Histone following the manufacturer’s protocols. Library preparation was performed by using NEBnext ultra II DNA lib prep according to the manufacturer’s protocols. ATAC-seq was performed by using Illumina Nextera DNA Flex Library Prep Kit following the manufacturer's protocols.

tag: cell type

tag: genotype/variation

value: FTO KD


title: fetal lung tissue, Sample172

tag: age (days post coitum)

tag: age orthogonal polynomial linear term


title: nonBPD cord blood of sample 1029_1

description: nonBPD cord blood sample


title: MEL624_H3K27ac_shFTO2 ChIP-seq


title: COV083, small RNA

value: Severe-repeated


title: nonBPD cord blood of sample 1027_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample17

tag: age orthogonal polynomial quadratic term

tag: Sex


title: MEL624_Input_shFTO ChIP-seq


title: COV084, small RNA

tag: repeated samples


title: fetal lung tissue, Sample168

tag: smokebinary

tag: run


title: fetal lung tissue, Sample169


title: fetal lung tissue, Sample170


title: COV082, small RNA

tag: age

tag: gender

value: Short-term nucleic acid test positive-repeated


title: MEL624_H3K27ac_shNC1 ChIP-seq

value: WT


title: MEL624_H3K27ac_shNC2 ChIP-seq


title: COV080, small RNA

tag: infection

tag: disease symptom

value: Symptomatic

value: Long-term nucleic acid test positive


title: fetal lung tissue, Sample167


title: nonBPD cord blood of sample 1028_1

description: nonBPD cord blood sample

value: nonBPD

tag: tissue

value: cord blood


title: nonBPD cord blood of sample 1026_1

description: nonBPD cord blood sample

tag: disease status


title: COV081, small RNA

tag: disease state

value: Peripheral blood


title: nonBPD cord blood of sample 2011_1

description: nonBPD cord blood sample


title: COV078, small RNA


title: MEL624_KD1 ATAC-seq


title: fetal lung tissue, Sample165

value: female

value: >=7.5 ng cotinine/g placenta


title: nonBPD cord blood of sample 1021_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 1025_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample164

value: <7.5 ng cotinine/g placenta


title: MEL624_WT2 ATAC-seq


title: MEL624_WT1 ATAC-seq


title: fetal lung tissue, Sample163

value: male


title: LNCaP_EnzR_H3K9me3

city: Cleveland

first: Vladimir

last: Makarov

state: OH

address: 9500 Euclid Ave

institute: CLEVELAND CLINIC LERNER COM-CWRU

data_processing:
After a final PCR amplification step, the resulting DNA libraries were quantified and sequenced on Illumina’s NextSeq 500 (75 nt reads, single end).
Reads were aligned consecutively to the human genome (hg38).
Duplicate reads were removed, and only uniquely mapped reads (mapping quality ≥ 25) were used for further analysis.
The resulting histograms (genomic “signal maps”) were stored in BigWig files. Peak locations were identified using the SICER algorithm.
Assembly: hg38
Supplementary files format and content: bigWig

source_name: LNCaP

growth_protocol: RMPI-1640, 10% fetal bovine serum, 2mM L-glutamine, 1% penicillin/streptomycin. Cells were cultured at 37 °C at 5% CO2.

extract_protocol:
Cells were fixed with 1% formaldehyde for 15 minutes. After quenching and cell lysis, chromatin was sonicated using Bioruptor from Diagenode.
Illumina sequencing libraries were prepared from input and ChIP DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation.

tag: cell line

value: LNCaP

value: Prostate cancer

tag: treatment

value: Enzalutamide

tag: time

value: 1 year


title: MEL624_KD2 ATAC-seq

tag: cell type

tag: genotype/variation

value: FTO KD


title: COV075, small RNA

value: Male

value: Moderate

tag: disease duration

value: Short-term nucleic acid test positive


title: nonBPD cord blood of sample 1024_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample166

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex


title: nonBPD cord blood of sample 1022_1

description: nonBPD cord blood sample


title: COV074, small RNA

tag: age

value: Symptomatic


title: fetal lung tissue, Sample162

tag: smokebinary

tag: run


title: nonBPD cord blood of sample 1023_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 1018_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 1020_1

description: nonBPD cord blood sample


title: nonBPD cord blood of sample 1019_1

description: nonBPD cord blood sample


title: LNCaP_EnzR_H3K9me2


title: LNCaP_Enz_120hrs_H3K9me3

value: 120 hours


title: fetal lung tissue, Sample160


title: COV073, small RNA

tag: gender

value: Female

tag: infection

tag: disease symptom

value: Long-term nucleic acid test positive


title: fetal lung tissue, Sample161


title: COV072, small RNA

tag: disease state

tag: tissue

value: Peripheral blood


title: fetal lung tissue, Sample16

value: female


title: nonBPD cord blood of sample 1017_1

description: nonBPD cord blood sample

tag: disease status

value: nonBPD

value: cord blood


title: COV071, small RNA


title: LNCaP_Enz_120hrs_H3K9me2

tag: cell line

tag: treatment

tag: time


title: LNCaP_Parental_H3K9me3

tag: cell type

value: DMSO


title: nonBPD cord blood of sample 1016_1

description: nonBPD cord blood sample


title: fetal lung tissue, Sample159

tag: age (days post coitum)

value: >=7.5 ng cotinine/g placenta


title: LNCaP_Parental_H3K9me2

value: LNCaP

value: Prostate cancer


title: fetal lung tissue, Sample158

tag: age orthogonal polynomial linear term


title: nonBPD cord blood of sample 1015_1

description: nonBPD cord blood sample


title: MEL624_Input_shNC ChIP-seq

tag: genotype/variation

value: WT


title: COV070, small RNA

value: Severe

tag: disease duration


title: fetal lung tissue, Sample157

tag: age orthogonal polynomial quadratic term

tag: Sex

value: male

value: <7.5 ng cotinine/g placenta


title: LNCaP_Pooled_Input_2


title: COV077, small RNA

tag: age

value: Male

value: Severe--repeated


title: COV069, small RNA

tag: gender

value: Symptomatic


title: COV068, small RNA

value: Female

tag: infection

value: Moderate-repeated


title: fetal lung tissue, Sample156

tag: smokebinary

tag: run


title: LNCaP_Pooled_Input_1

value: 120 hours


title: nonBPD cord blood of sample 1005_1

description: nonBPD cord blood sample

tag: tissue


title: nonBPD cord blood of sample 1011_1

description: nonBPD cord blood sample

tag: disease status


title: nonBPD cord blood of sample 1006_1

description: nonBPD cord blood sample


title: COV067, small RNA

tag: disease symptom

tag: disease state

value: Severe-repeated

value: Short-term nucleic acid test positive-repeated

value: Peripheral blood


title: fetal lung tissue, Sample155


title: Patient 3, Term in labor

first: Ariel

last: Dotts

address: 303 E Superior Street

data_processing:
Sequence reads were trimmed using Cutadapt by TrimGalore
Trimmed reads were aligned using STAR aligner (v2.6.3) with default settings.
Reads count per gene was performed using HTSeq
Assembly: hg38
Supplementary files format and content: tab delimited text files with counts per gene

source_name: myometrium

extract_protocol:
0.35 grams to 0.5 grams of tissue was used for RNA extraction with the mini-Rneasy kit (74101, Qiagen)
Libraries were constructed using the KAPA RNA Hyper Prep Kit (KAPA Biosystems)

value: myometrium

tag: status

value: term pregnant in-active-labor (TIL)


title: Patient 4, Term in labor


title: fetal lung tissue, Sample154

source_name: fetal lung tissue

value: female


title: Patient 2, Term in labor


title: nonBPD cord blood of sample 1010_1

description: nonBPD cord blood sample

value: nonBPD

value: cord blood


title: COV079, small RNA

value: Long-term nucleic acid test positive-repeated


title: fetal lung tissue, Sample153

value: male


title: COV066, small RNA


title: COV064, small RNA

value: Moderate


title: nonBPD cord blood of sample 1001_1

description: nonBPD cord blood sample


title: COV065, small RNA

tag: repeated samples


title: nonBPD cord blood of sample 1004_1

description: nonBPD cord blood sample


title: COV063, small RNA

value: Male


title: Patient 1, Term in labor


title: fetal lung tissue, Sample150

tag: age (days post coitum)

value: <7.5 ng cotinine/g placenta


title: Patient 7, Term not in labor

value: term pregnant not-in-labor (TNIL)


title: Patient 6, Term not in labor


title: Patient 5, Term not in labor


title: fetal lung tissue, Sample151

tag: age orthogonal polynomial linear term

value: >=7.5 ng cotinine/g placenta


title: fetal lung tissue, Sample152


title: BPD cord blood of sample 4005_1

description: BPD cord blood sample

source_name: BPD cord blood

value: BPD


title: nonBPD cord blood of sample 1009_1

description: nonBPD cord blood sample


title: COV076, small RNA

value: Female

value: Symptomatic


title: fetal lung tissue, Sample15


title: Patient 4, Term not in labor


title: COV061, small RNA

value: Short-term nucleic acid test positive


title: COV062, small RNA

value: Severe

value: Peripheral blood


title: nonBPD cord blood of sample 1003_1

description: nonBPD cord blood sample


title: COV060, small RNA


title: Patient 3, Term not in labor

value: myometrium


title: BPD cord blood of sample 2014_1

description: BPD cord blood sample


title: fetal lung tissue, Sample148


title: COV059, small RNA


title: COV057, small RNA


title: COV058, small RNA


title: fetal lung tissue, Sample146


title: fetal lung tissue, Sample149


title: Patient 1, Term not in labor


title: BPD cord blood of sample 2003_2

description: BPD cord blood sample


title: BPD cord blood of sample 3013_1

description: BPD cord blood sample


title: fetal lung tissue, Sample147


title: BPD cord blood of sample 3017_1

description: BPD cord blood sample


title: Patient 3, Term in Labor, Histone Input

data_processing:
Sequence reads were trimmed using Cutadapt by TrimGalore
Trimmed reads were aligned to hg38 using Bowtie2 leading to BAM files
Peak calling was performed using HOMER with findPeaks (-factor) for PGR and findPeaks (-histone) for histone modifications
bedgraph files were generated from BAM using bedtools genomecov
Assembly: hg38
Supplementary files format and content: bedgraph files

extract_protocol:
Tissues were fixed with 1% formaldehyde, cut into small pieces, and incubated for 15 minutes. After quenching and cell lysis, chromatin was sonicated.
Libraries were constructed by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. Steps were performed on an automated system (Apollo 342, Wafergen Biosystems/Takara)

value: term pregnant in-active-labor (TIL)


title: BPD cord blood of sample 2017_1

description: BPD cord blood sample


title: WTg_MEF9

city: Suita

first: Shotaro

last: Tatekawa

state: Osaka

address: 2-2(D10), Yamadaoka, Suita-city

department: Departments of Radiation Oncology,

country: Japan

institute: The University of Osaka Graduate School of Medicine

data_processing:
After checking the quality of sequencing using FastQC(v0.11.9) , and reads were aligned to human reference genomes and transcriptomes using STAR(v2.7.10) . We calculated the reads using RSEM(v1.3.3).
After the read count step, we performed expression analysis with iDEP and GSEA.
Assembly: GRCm38
Supplementary files format and content: Processed_Data.csv

source_name: pancreas

growth_protocol: All cell lines were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
ISOGEN (NIPPON GENE)
RNA libraries were constructed following manufacturer instructions using the TruSeq stranded mRNA Library Prep Kit (Illumina, USA).

treatment_protocol: NMS-P937 for 24hr at 80 nM

value: pancreas

tag: cell line

value: primary cells from tumors

tag: cell type

value: fibroblasts

tag: genotype

value: WTg (EL1-Luc/EL1-Tag x CAG-Mettl3)

tag: treatment


title: Patient 2, Term not in labor


title: WTg_MEF8


title: Patient 2, Term in Labor, Histone Input


title: fetal lung tissue, Sample145

data_processing:
Trimming for low-quality base calls and adpator sequeiencs was completed using cutadapt v.2.7. FastQC v0.11.8 was applied to each trimmed .fastq file to assess adaptor removal. Then reads were mapped to counts of known miRNAs using miR-MaGiC with reference to the Homo sapiens miRbase v22.1 database with collapsed functional groups (repo verision 7147b7a).
Samples passing quality-control (≥1x10^5 mapped reads, having available phenotypic information, and being within the 7 - 17 week pseudoglandular period) and autosomal miRNAs passing pre-filtering criteria (non-zero counts in at least 25% of samples; passes DESeq2 independent filtering algorithm;and not mapped to X or Y chromosome) were tested for differences by sex.
Using RUV-Seq v1.22.0, we also obtained four RUVr factors representing unmeasured miRNA expression heterogeneity for inclusion in regression models.
Assembly: Homo sapiens miRBase database v22.1
Supplementary files format and content: Matrix table with raw miRNA counts for every miRNA and every sample

extract_protocol:
Total RNA was extracted from 30mg of homogenized prenatal lung tissue with the miRNeasy Mini Kit per manufacturer instructions.
Samples were block-randomized by age, sex, and smoke exposure status to four batches of miRNA library preparation (Small RNA Sequencing Kit v3 for Illumina Platforms; Bio Scientific) and sequencing (HiSeq2500; Illumina; San Diego, CA, USA).

tag: age orthogonal polynomial quadratic term

tag: Sex

value: female


title: COV056, small RNA

tag: age

tag: gender

tag: infection

value: Severe-repeated


title: WTg_MEF7

tag: tissue


title: BPD cord blood of sample 1013_1

description: BPD cord blood sample

tag: disease status

value: cord blood


title: fetal lung tissue, Sample143

tag: smokebinary

value: <7.5 ng cotinine/g placenta

tag: run


title: COV054, small RNA

tag: disease symptom

tag: disease state

value: Moderate

tag: disease duration


title: Patient 2, Term in Labor, H3K27ac IP

tag: status


title: fetal lung tissue, Sample142

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

value: >=7.5 ng cotinine/g placenta


title: BPD cord blood of sample 2002_1

description: BPD cord blood sample

value: BPD


title: COV055, small RNA

value: Male

value: Symptomatic

tag: repeated samples


title: fetal lung tissue, Sample144


title: COV052, small RNA

value: Female


title: fetal lung tissue, Sample141


title: Patient 2, Term in Labor, H3K4me3 IP


title: WTg_MEF4

tag: cell line

tag: cell type

tag: genotype

tag: treatment


title: BPD cord blood of sample 1014_1

description: BPD cord blood sample


title: WTg_MEF6


title: fetal lung tissue, Sample140

tag: age orthogonal polynomial quadratic term

tag: Sex

value: male


title: COV051, small RNA

tag: age

tag: gender

tag: infection

value: Severe

value: Short-term nucleic acid test positive

tag: tissue

value: Peripheral blood


title: WTg_MEF3

value: pancreas

value: primary cells from tumors


title: Patient 6, Term in labor, PGR Input

value: myometrium

value: term pregnant in-active-labor (TIL)


title: BPD cord blood of sample 1037_1

description: BPD cord blood sample

tag: disease status


title: COV050, small RNA

tag: disease symptom

tag: disease state


title: fetal lung tissue, Sample14

tag: smokebinary

tag: run


title: BPD cord blood of sample 1009_2

description: BPD cord blood sample


title: BPD cord blood of sample 2012_1

description: BPD cord blood sample


title: WTg_MEF2

value: fibroblasts

value: WTg (EL1-Luc/EL1-Tag x CAG-Mettl3)


title: Patient 2, Term in labor, PGR Input

tag: status


title: COV048, small RNA

tag: repeated samples


title: fetal lung tissue, Sample139

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

value: female

value: <7.5 ng cotinine/g placenta


title: WTg_MEF1

tag: cell line

tag: cell type

tag: genotype


title: fetal lung tissue, Sample138

tag: age orthogonal polynomial quadratic term

tag: Sex

value: >=7.5 ng cotinine/g placenta


title: COV049, small RNA

tag: age

tag: gender


title: BPD cord blood of sample 1007_1

description: BPD cord blood sample

value: BPD

tag: tissue

value: cord blood


title: fetal lung tissue, Sample137


title: Patient 2, Term in labor, PGR IP


title: MAC050721_023

first: Leonid

last: Feferman

state: Illinois

address: 1737 West Polk St

department: Research Resources Center

institute: University of Illinois at Chicago

data_processing:
Raw reads were aligned to the reference genome using STAR.
ENSEMBL gene expression was quantified using FeatureCounts.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: genes.txt: Tab-delimited text table

source_name: small intestine (ileum)

extract_protocol:
Whole ileum was flushed with PBS, the Peyer’s patches removed, opened longitudinally, and cut into 1 cm pieces. Three consecutive washes were performed with HBSS supplemented with 10% bovine calf serum, 15 mM HEPES, 5mM EDTA and 1.25 mM DTT at room temperature for 20 min under continuous rotation followed by 20 seconds of vortexing in PBS, pH 7.4, to dissociate intestinal epithelial cells (IECs) and intraepithelial lymphocytes (IELs). The remaining lamina propria (LP) pieces were transferred to 15 ml RPMI 1640 supplemented with 10% FBS, 50 U/ml penicillin, 50 ug/ml streptomycin and 2 mM L-glutamine with 0.5 mg/ml Collagenase VIII (Sigma Aldrich) warmed to 37oC. Samples were shaken vigorously by hand and placed in a shaking incubator at 220 rpm and 37oC for 15 min with additional manual shaking at 10 min. After 15 min, 35 ml ice-cold complete media was added to stop enzymatic digestion. Samples were washed twice with FACS buffer (PBS pH 7.4 plus 1% FBS and 2 mM EDTA) and filtered with 100 um and 70 um strainers. 50% of the IEC fraction was combined with the LP fraction. Cells were stained with Zombie NIR viability dye and AF488 anti-CD45 antibody. Live, CD45+ and CD45- singlets were sorted on a MoFlo Astrios Cell Sorter (Beckman Coulter) into RLT buffer containing 1% beta-mercaptoethanol, flash frozen on dry ice and stored at -80oC. RNA extraction was performed using an RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s instructions.
RNA samples were checked for purity using NanoDrop™ One Spectrophotometer (Thermo Scientific) and analyzed for integrity using 4200 TapeStation (Agilent). Relative levels of remaining DNA were checked by dual RNA/DNA measurements using Qubit fluorometer (Invitrogen). DNA amounts did not exceed 10% of the total amount of nucleic acid. Libraries for Illumina sequencing were prepared using 10-20 ng of total RNA per sample. Library preparation was performed with the Universal Plus mRNA-Seq library preparation kit (Tecan/NuGen, 0520-A01), as written in the product manual (NuGen, M01485 v5). In brief, RNA underwent poly-A selection, enzymatic fragmentation, and generation of double-stranded cDNA using a mixture of oligo(dT) and random priming. The cDNA underwent end repair, ligation of dual-index adaptors, strand selection, and 16 cycles of PCR amplification. The number of cycles was determined by qPCR on a small aliquot of the unamplified libraries. All intermediate purification steps, and final library purification was carried out using Agencourt AMPure XP Beads (Beckman Coulter A63881). Final amplified libraries were measured with the Qubit 1X dsDNA HS Assay Kit (Invitrogen, Q33231), and fragment size distribution was confirmed to be approximately 360 bp using the D5000 ScreenTape assay (Agilent, 5067-5588, 5067-5589). Concentration of the final library pool was confirmed by qPCR and subjected to test sequencing in order to check sequencing efficiencies and adjust accordingly proportions of individual libraries. The pool was purified with the Agencourt AMPure XP Beads (Beckman Coulter A63881), quantified by qPCR using KAPA Library Quantification Kit and sequenced on a NovaSeq 6000 S4 flow cell, 2x150 bp, approximately 30 M clusters per sample, at the University of Illinois Roy J. Carver Biotechnology Center High-Throughput Sequencing and Genotyping Unit.

value: small intestine (ileum)

value: CD45 negative

tag: strain

value: 9.9 weeks


title: fetal lung tissue, Sample136

value: male


title: MAC050721_024

value: CD45 positive

value: 9.1 weeks


title: COV046, small RNA

value: Male

tag: infection

tag: disease symptom

value: Symptomatic

value: Moderate

value: Peripheral blood


title: COV053, small RNA

value: Female

tag: disease state

value: Severe


title: BPD cord blood of sample 1012_1

description: BPD cord blood sample

tag: disease status


title: MAC050721_022

value: 9.0 weeks


title: Patient 5, Term in labor, PGR IP

value: myometrium

tag: status

value: term pregnant in-active-labor (TIL)


title: Patient 5, Term in labor, PGR Input


title: fetal lung tissue, Sample135

tag: smokebinary

value: <7.5 ng cotinine/g placenta

tag: run


title: MAC050721_021

value: 9.7 weeks


title: Patient 6, Term in labor, PGR IP


title: COV044, small RNA

tag: repeated samples


title: COV047, small RNA

tag: disease duration

value: Short-term nucleic acid test positive


title: fetal lung tissue, Sample134

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

value: female

value: >=7.5 ng cotinine/g placenta


title: Patient 4, Term not in labor, Histone Input

value: term pregnant not-in-labor (TNIL)


title: MAC050721_019

value: small intestine (ileum)

tag: cell type

value: CD45 positive

tag: genotype


title: Patient 1, Term not in labor, Histone Input


title: fetal lung tissue, Sample133

tag: age orthogonal polynomial quadratic term

tag: Sex

value: male


title: COV043, small RNA

tag: age

tag: gender

value: Symptomatic

value: Moderate-repeated

tag: tissue


title: Patient 7, Term not in labor, H3K27ac IP


title: COV045, small RNA

tag: infection

tag: disease symptom

value: Long-term nucleic acid test positive

value: Peripheral blood


title: MAC050721_018

tag: strain

value: 9.9 weeks


title: fetal lung tissue, Sample131


title: Patient 7, Term not in labor, Histone Input

tag: status


title: fetal lung tissue, Sample130

tag: smokebinary


title: MAC050721_017

value: 9.6 weeks


title: Patient 1, Term not in labor, H3K27ac IP

value: myometrium


title: MAC050721_016


title: Patient 4, Term not in labor, H3K27ac IP


title: COV039, small RNA

value: Male

tag: disease state

value: Severe-repeated

value: Long-term nucleic acid test positive-repeated


title: COV038, small RNA

value: Female

value: Severe


title: Patient 7, Term not in labor, H3K4me3 IP


title: MAC050721_020

value: 9.7 weeks


title: COV040, small RNA


title: MAC050721_015

value: 9.4 weeks


title: fetal lung tissue, Sample132

value: >=7.5 ng cotinine/g placenta

tag: run


title: fetal lung tissue, Sample13

value: female

value: <7.5 ng cotinine/g placenta


title: Patient 4, Term not in labor, H3K4me3 IP

value: term pregnant not-in-labor (TNIL)


title: COV042, small RNA

value: Symptomatic


title: fetal lung tissue, Sample129


title: COV037, small RNA


title: COV041, small RNA


title: MAC050721_013

value: small intestine (ileum)

value: CD45 positive

value: 9.0 weeks


title: COV036, small RNA

value: Moderate

tag: disease duration

value: Short-term nucleic acid test positive

value: Peripheral blood


title: fetal lung tissue, Sample127

tag: age (days post coitum)

value: male


title: MAC050721_012

value: 9.1 weeks


title: Patient 8, Term not in labor, PGR Input

value: myometrium


title: fetal lung tissue, Sample126

tag: age orthogonal polynomial linear term


title: COV035, small RNA

value: Female

tag: repeated samples


title: MAC050721_011

tag: cell type

value: CD45 negative

tag: genotype


title: COV033, small RNA

value: Male

value: Severe


title: Patient 4, Term not in labor, PGR Input


title: fetal lung tissue, Sample125

tag: age orthogonal polynomial quadratic term

tag: Sex

value: female

value: >=7.5 ng cotinine/g placenta


title: MAC050721_010

tag: age

value: 9.7 weeks


title: MAC050721_014

tag: tissue

value: 9.9 weeks


title: COV032, small RNA

tag: gender

tag: infection

value: Symptomatic


title: fetal lung tissue, Sample124


title: Patient 1, Term not in labor, H3K4me3 IP

value: term pregnant not-in-labor (TNIL)


title: MAC050721_009

value: small intestine (ileum)

tag: strain


title: MAC050721_008


title: fetal lung tissue, Sample128


title: fetal lung tissue, Sample123


title: Patient 3, Term in Labor, H3K27ac IP

tag: status

value: term pregnant in-active-labor (TIL)


title: Patient 6, Term not in labor, PGR IP


title: COV030, small RNA

tag: disease symptom


title: Patient 8, Term not in labor, PGR IP


title: COV031, small RNA

tag: disease state

value: Severe--repeated


title: COV029, small RNA

value: Long-term nucleic acid test positive

value: Peripheral blood


title: Patient 3, Term in Labor, H3K4me3 IP


title: MAC050721_007

value: 9.0 weeks


title: fetal lung tissue, Sample121

value: male

tag: smokebinary

value: <7.5 ng cotinine/g placenta

tag: run


title: Patient 6, Term not in labor, PGR Input

value: myometrium


title: fadu-fcabs-untargeted-ctr-1 [rbs-ctr-1]

city: Heidelberg

first: Sylvain

last: Delaunay

address: Im Neuenheimer Feld 280

department: Tumor BIology

country: Germany

institute: German Cancer Research Center (DKFZ)

description:
Untargeted fCABseq (Mitochondrial tRNA) FaDu rep1
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt

data_processing:
Raw sequencing fastq files were trimmed with ‘TrimGalore !’
Reads were aligned to the GRCh38 (hg38) reference genome using Bismark
mtRNA genomic coordinates for the GRCh38 reference genome were obtained from the ENSEMBL database
Original targeted sequencing reads and their multiple sequence alignments on mtRNAs were extracted from sorted Bismark alignment (bam) files using the R packages RSamtools and GenomicAlignments
Assembly: hg38
Supplementary files format and content: Table Delaunay_MT_TM.meth_Kerats_FaDu.txt is a tab delimited text file which contains the calculated total number of reads to the mt-tRNA methionine and the number of Cytosine in position 34 of the targeted tRNA.
Supplementary files format and content: Table Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt is tab delimited text and contains the calculated methylation levels of Cs and coverage on the mitochondrial genome (fragments >20nt)

source_name: FaDu cell line

growth_protocol: NHEK cells were maintained in KSFM medium with antibiotics, FaDu cells were maintained in EMEM madium supplement with fetal bovin serum albumin (FBS) 10% with antibiotics, in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was extracted with Trizol kit, according to manufacturers' protocol. tRNA were isolated using Mirvana kit.
for the untargeted samples, the library was created with the Il TruSeq Small RNA kit. For the targeted apporach, the NEBNext Ultra II DNA library prep kit was used.

tag: cell line

value: FaDu cell line

value: Pharynx squamous cell carcinoma

value: WT

tag: sample type

value: Untargeted fCABseq


title: MAC050721_005

value: CD45 negative

value: 9.1 weeks


title: COV027, small RNA

value: Female

value: Symptomatic

value: Severe

tag: disease duration


title: fadu-fcabs-untargeted-ctr-2 [rbs-ctr-2]

description:
Untargeted fCABseq (Mitochondrial tRNA) FaDu rep2
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt

tag: cell type


title: MAC050721_004

value: small intestine (ileum)

tag: genotype

value: 9.6 weeks


title: fetal lung tissue, Sample120

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term


title: fetal lung tissue, Sample12

tag: Sex

value: female

value: >=7.5 ng cotinine/g placenta


title: fadu-fcabs-untargeted-ctr-3 [rbs-ctr-3]

description:
Untargeted fCABseq (Mitochondrial tRNA) FaDu rep3
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt


title: COV026, small RNA

tag: age

tag: gender

value: Male

tag: tissue

value: Peripheral blood


title: Patient 4, Term not in labor, PGR IP

tag: status

value: term pregnant not-in-labor (TNIL)


title: fetal lung tissue, Sample119

value: <7.5 ng cotinine/g placenta


title: COV025, small RNA

tag: infection

tag: disease symptom


title: fadu-fcabs-untargeted-ctr-4 [rbs-ctr-4]

description:
Untargeted fCABseq (Mitochondrial tRNA) FaDu rep4
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt

value: FaDu cell line


title: MAC050721_006

tag: strain

value: 10.3 weeks


title: fadu-fcabs-untargeted-ctr-5 [rbs-ctr-5]

description:
Untargeted fCABseq (Mitochondrial tRNA) FaDu rep5
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt

value: Pharynx squamous cell carcinoma

value: WT


title: MAC050721_003

value: CD45 negative


title: fetal lung tissue, Sample118

value: male

tag: smokebinary

tag: run


title: nhek2-fcabs-untargeted-ctr-1 [rbs-wt1-1]

description:
Untargeted fCABseq (Mitochondrial tRNA) NHEK batch2 rep1
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt

source_name: NHEK

tag: cell line

value: NHEK

value: Keratinocyte

tag: sample type

value: Untargeted fCABseq


title: MAC050721_001

value: small intestine (ileum)

tag: cell type

value: 9.4 weeks


title: fetal lung tissue, Sample116


title: MAC050721_002

tag: genotype


title: COV024, small RNA

value: Symptomatic

tag: disease state

value: Severe

tag: disease duration

value: Short-term nucleic acid test positive


title: COV023, small RNA

value: Male

value: Long-term nucleic acid test positive

value: Peripheral blood


title: COV028, small RNA

value: Female


title: fetal lung tissue, Sample122

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

value: female

value: <7.5 ng cotinine/g placenta


title: MR_DKO_rep2

first: Chuan

last: He

address: 929 E 57th Street

department: Chemistry

institute: University of Chicago

data_processing:
Base-calling was performed using CASAVA.
sequencing data were sent to trimmomatic to remove low quality bases and adaptor sequence contaminants under default parameters except for “–length 50”
Remaining reads were then aligned to the mouse transcriptome annotation based on mm10 assembly using hisat2 aligner (v2.1.0), default parameters were used,except for "-k 30"
reads count were called by featureCounts for each samples
Genome_build: mm10
Supplementary_files_format_and_content: csv; reads count

source_name: Morula

growth_protocol: Cells were maintained in DMEM (Invitrogen) supplemented with 15% FBS, 1% nucleosides (100×),1 mM L-glutamine,1% nonessential amino acid, 0.1 mM 2-mercaptoethanol, 1,000 U/ml LIF, 3 μM CHIR99021 and 1 μM PD0325901 37 °C in 5% CO2. Embryos were cultured in G1 plus medium (Vitrolife) at 37°C under 5% CO2 in air.

extract_protocol:
Embryos at GV, MII and morula stages were transferred to 500 μl Trizol Reagent and then mixed well with 100 μl chloroform added. The mixture was transferred Qiagen MaXtract High Density tubes (129046). After centrifuge, upper and aqueous phase was removed. RNA was precipitated by adding equal volume isopropanol and washing by 75% ethanol. Then purified RNA were analyzed by RT-qPCR or subjected to library generation using SMARTer Stranded Total RNASeq Kit (Takara Bio) following manufacturer’s protocol.
Library preparation was performed by using SMARTer Stranded Total RNA-Seq Kit v2 (Takara) according to the manufacturer’s protocols.

treatment_protocol:
mESCs cells were cross-linked by adding 1% formaldehyde directly to the media for 10 min at RT. Cross-linking was stopped by adding glycine to a final concentration of 0.125 M and incubating for 5 min at RT. The media was removed and the cells were washed twice with ice-cold PBS.
actinomycin D protocol: Four 6-cm plates of WT and Fto-/- mESCs were seeded and controlled to afford the same number of cells, respectively. After 48 h, actinomycin D was added to 5 μg/mL at 6 h and 0 h before trypsinization collection.
EU protocol: Six 6-cm plates of WT and Fto-/- mESCs were seeded and controlled to afford the same number of cells, respectively. After 48 h, 5-Ethynyl Uridine (EU) was added to 0.5 mM at 60 min, 30 min, and 10 min before trypsinization collection.

value: Morula

value: Fto Knockout

tag: molecule subtype

value: totalRNA


title: nhek2-fcabs-untargeted-ctr-2 [rbs-wt1-2]

description:
Untargeted fCABseq (Mitochondrial tRNA) NHEK batch2 rep2
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt

value: NHEK

value: WT


title: nhek2-fcabs-untargeted-ctr-4 [rbs-wt1-4]

description:
Untargeted fCABseq (Mitochondrial tRNA) NHEK batch2 rep4
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt

value: Keratinocyte

value: Untargeted fCABseq


title: fetal lung tissue, Sample117

first: Sunita

last: Sharma

address: 13199 East Montview Blvd

tag: Sex

value: >=7.5 ng cotinine/g placenta


title: fetal lung tissue, Sample115

value: male


title: fetal lung tissue, Sample113


title: COV021, small RNA

tag: age

tag: gender

value: Symptomatic

value: Severe

tag: tissue


title: COV022, small RNA

value: Male

tag: infection

tag: disease symptom

value: Moderate


title: COV019, small RNA

value: Short-term nucleic acid test positive

value: Peripheral blood


title: MII_KO_rep2

source_name: MII

value: MII


title: nhek2-fcabs-untargeted-ctr-3 [rbs-wt1-3]

description:
Untargeted fCABseq (Mitochondrial tRNA) NHEK batch2 rep3
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt


title: fetal lung tissue, Sample114

tag: smokebinary

value: <7.5 ng cotinine/g placenta

tag: run


title: MR_WT_rep2

value: Morula

value: wild type


title: fetal lung tissue, Sample112


title: COV020, small RNA

value: Female


title: MR_DKO_rep1

value: Fto Knockout

value: totalRNA


title: WTg_MEF5

value: pancreas

tag: cell line

value: primary cells from tumors

value: fibroblasts

value: WTg (EL1-Luc/EL1-Tag x CAG-Mettl3)

tag: treatment


title: fetal lung tissue, Sample111

value: male

value: >=7.5 ng cotinine/g placenta


title: nhek-fcabs-untargeted-ctr-2 [rbs-wt2-2]

description:
Untargeted fCABseq (Mitochondrial tRNA) NHEK batch1 rep2
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt

value: NHEK

tag: cell type

value: Keratinocyte

tag: genotype

value: WT

tag: sample type

value: Untargeted fCABseq


title: nhek2-fcabs-untargeted-ctr-5 [rbs-wt1-5]

description:
Untargeted fCABseq (Mitochondrial tRNA) NHEK batch2 rep5
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt


title: COV017, small RNA

value: Male

value: Symptomatic

tag: disease state

value: Moderate

tag: disease duration

value: Short-term nucleic acid test positive

tag: repeated samples

value: Peripheral blood


title: nhek-fcabs-untargeted-ctr-1 [rbs-wt2-1]

description:
Untargeted fCABseq (Mitochondrial tRNA) NHEK batch1 rep1
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt


title: MR_WT_rep1

value: Morula

value: wild type

tag: molecule subtype


title: COV018, small RNA

value: Severe

value: Long-term nucleic acid test positive


title: nhek-fcabs-untargeted-ctr-4 [rbs-wt2-4]

description:
Untargeted fCABseq (Mitochondrial tRNA) NHEK batch1 rep4
Delaunay_UntargetedfCABseq_20nt_meth.table_MitoGenome.txt


title: fetal lung tissue, Sample110

tag: age (days post coitum)

tag: age orthogonal polynomial linear term

tag: age orthogonal polynomial quadratic term

tag: Sex

value: female


title: fetal lung tissue, Sample11


title: MII_KO_rep1

value: MII

value: Fto Knockout

value: totalRNA


title: MII_WT_rep1