title: Patient_89, Serum, iMCD, Cycle1_Day1, Rep 1


title: Patient_90, Serum, iMCD, Cycle4_Day1

status: Public on Nov 04 2022

type: protein

city: Philadelphia

first: David

last: Fajgenbaum

state: PA

address: 3535 Market St, 717

department: Medicine

country: USA

institute: University of Pennsylvania

description:
JRD16.xlsx
2.15 JRD_16-166.hybNorm.medNorm.calibrate.20160923.adat

hyb_protocol: Hybridization protocol done in accordance with SomaLogic standard operating procedures and best practices.

scan_protocol: Scan protocol done in accordance with SomaLogic standard operating procedures and best practices.

data_processing: SomaLogic SOMAscan pre-processing was performed, and 1,178 analytes passed quality control. Data were log2 transformed and capped at 2.5th and 97.5th percentiles. Batches were bridged together by the average log ratio of technical replicates for each analyte. Following quality control sample exclusion, pretreatment samples available for analysis included 88 iMCD patients, 42 healthy donors, and 20 each of RA, HL, and HHV8-MCD. Longitudinal samples available for analysis included samples from day 8 and day 64 of treatment from 73 iMCD patients.

molecule: protein

organism: Homo sapiens

source_name: Serum

label_protocol: Label protocol done in accordance with SomaLogic standard operating procedures and best practices.

extract_protocol: Protein extracted from serum in accordance with SomaLogic standard operating procedures and best practices.

tag: patient label

tag: disease state

value: iMCD

tag: batch

tag: Sex

value: F

tag: age

value: TRUE

value: Siltuximab + BSC


title: Patient_83, Serum, iMCD, Cycle4_Day1

value: FALSE


title: Patient_89, Serum, iMCD, Cycle1_Day1, Rep 2

description:
JRD17.xlsx
2.5 PX-17-116.HybMedNormCal.Premium.adat
Technical replicate used for batch normalizing

value: M

value: Placebo + BSC


title: Patient_76, Serum, iMCD, Cycle1_Day8


title: SV3-YB-01-b

type: SRA

city: Galveston

first: Juquan

last: Song

state: TX

address: 301 University Blvd.

institute: University of Texas Medical Branch at Galveston

library_source: transcriptomic

data_processing:
Base calling was using Illumina's bcl2fastq2-v2.20 converter
A genome index was built with STAR (v2.7.5c) using the mouse GRCm38 genome .
RNA-Seq reads were aligned to the mouse reference using the STAR software version 2.7.5c with the parameters recommended for the ENCODE consortium.
Gene read counts obtained from the STAR quantMode GeneCounts feature using the Gencode vM25 annotation file.
miRNA read 1 adapter trimming with the mapper.pl function of miRDeep2.0.0.8 using the command mapper.pl input.fastq -e -v -u -h -k AGATCGGAAGAGCACACGTCT -l 18 -m
miRNA read1 aligned to mouse reference using STAR version 2.7.5c with parameters "--runThreadN 10 --outSAMtype BAM SortedByCoordinate  --alignIntronMax 1 --outFilterMismatchNoverLmax 0.04 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outMultimapperOrder Random"
featureCounts v2.0.1 used to count miRNA reads with the mirBase v22 annotation file and parameters "-T12 -s 1 -t miRNA_primary_transcript  -f -M --primary -g Name -a mmu.gff3"
Assembly: GRCm38
Supplementary files format and content: Tab delimited tables of raw gene read counts per sample and miRNA read counts per sample

molecule: total RNA

organism: Mus musculus

source_name: Gastrocnemius muscle

extract_protocol:
Poly-A plus RNA was enriched from ~0.1ug of total RNA and used to generate libraries using New England Biolabs NEBNext Ultra II Kit.
Qiagen RNeasy Mini Kit following manufacturer's protocol

tag: tissue

value: Gastrocnemius muscle

tag: strain

value: male

value: Young

tag: treatment

value: Burn


title: Patient_79, Serum, iMCD, Cycle1_Day1


title: Patient_79, Serum, iMCD, Cycle1_Day8


title: SV3-AS-02-b

value: Adult

value: Sham burn


title: SV3-AS-03-b


title: SV3-AS-01-b


title: SV3-AB-02-b


title: SV3-AB-03-b


title: Patient_87, Serum, iMCD, Cycle4_Day1


title: SV3-AB-01-b


title: Patient_86, Serum, iMCD, Cycle1_Day1


title: Patient_84, Serum, iMCD, Cycle4_Day1


title: SD_WD_ly14_scRNA

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: single cell sample from unsorted whole mammary gland from young SD rats, collected at Day 0 (when treatment was stopped) from a drug-treated animal

library_source: transcriptomic single cell

data_processing:
single cell: Sequenced reads from the whole mammary glandwere aligned to the rat reference genome rn6 using 10x Genomics Cell Ranger 7.0.0 with include-introns set to off.
single cell: The filtered reads assigned to cell barcodes were analyzed with the R package Seurat, version 4.1.1 (111,567). In an initial quality control step, only genes expressed in at least 10 cells and only cells expressing at least 100 genes were retained. In a second step, cells with more than 15% mitochondrial genes were removed.
after quality control, a total of 103,524 cells were analyzed (40,828 control and 62,696 treated), and assigned to cell types as follows: 28,623 epithelial cells (9,891 basal, 11,242 luminal progenitor, 7,490 alveolar); 46,061 immune cells (8,527 T cells, 1,975 NK cells, 4,547 NK cells or T cells, 23,917 B cells, 4,532 macrophages, 2,563 monocyte-macrophages;); 27,480 stroma cells (6,094 vascular smooth muscle cells, 5,442 fibroblasts, 2,776 FAP+ fibroblasts, 4,524 endothelium, 6,129 TIE1+ endothelium, 2,794 stroma-progenitor, 279 vein cells), and 1,081 nerve-myelin cells. The data were normalized separately for each rat strain using SCTransform and decomposed using PCA. UMAP embeddings were then computed using the first 30 PCA dimensions as input.
Assembly: rn6
Supplementary files format and content: expression text files

organism: Rattus norvegicus

source_name: normal mammary gland

extract_protocol:
single cell: mammary gland single-cell suspensions were stained with Live/Dead aqua stain and RNA was extracted using the AllPrep DNA/RNA mini kit (Qiagen)  Total RNA was extracted using the RNeasy Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Rats were treated with vehicle or 75mg/kg of LY22157299 by oral gavage twice daily (8-16 hours between doses) for 10 consecutive days.

tag: experiment

value: single cell normal SD

value: SD

value: breast

tag: cell type

value: whole mammary gland (unsorted)

value: drug

tag: day

tag: animal

tag: tumor status

tag: parity

value: virgin

tag: estradiol pellet


title: SV3-YB-03-b


title: Patient_86, Serum, iMCD, Cycle1_Day8

value: iMCD

value: F

value: TRUE


title: Patient_83, Serum, iMCD, Cycle1_Day1

value: Siltuximab + BSC

value: FALSE


title: SD_WD_ly11_scRNA


title: Patient_85, Serum, iMCD, Cycle4_Day1

value: M


title: Patient_81, Serum, iMCD, Cycle4_Day1


title: SD_WD_ly6_scRNA


title: SD_WD_veh4_scRNA

description: single cell sample from unsorted whole mammary gland from young SD rats, collected at Day 0 (when treatment was stopped) from a control animal

value: control


title: SD_WD_ly4_scRNA


title: SD_WD_ly1_scRNA


title: Patient_82, Serum, iMCD, Cycle4_Day1


title: SD_WD_ly2_scRNA


title: Patient_80, Serum, iMCD, Cycle4_Day1

value: Placebo + BSC


title: Patient_77, Serum, iMCD, Cycle1_Day1


title: SD_WD_veh1_scRNA


title: Patient_76, Serum, iMCD, Cycle1_Day1


title: Patient_77, Serum, iMCD, Cycle4_Day1


title: Patient_78, Serum, iMCD, Cycle4_Day1


title: Patient_68, Serum, iMCD, Cycle4_Day1


title: Patient_67, Serum, iMCD, Cycle4_Day1


title: Patient_75, Serum, iMCD, Cycle4_Day1


title: WT_ND4

city: Tsukuba

first: Yuri

last: Fujikura

state: Ibaraki

address: 1-1-1 Higashi

country: Japan

institute: National Institute of Advanced Industrial Science and Technology

data_processing:
Reference genome and gene model annotation files were downloaded from genome website directly.Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5 with parameters "hisat2 -x genome  -p 4 --dta -t --phred33 -1 R1.fq.gz -2 R2.fq.gz".
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Assembly: mRatBN7.2
Supplementary files format and content: comma-delimited text files include RPKM values for each Sample

source_name: skeletal muscle

extract_protocol:
Total RNA was extracted from frozen tibialis anterior (TA) muscles  using RNAisoPlus according to the manufacturer’s recommendation (Takara Bio Inc. Kusatsu, Japan).
Messenger RNAwas purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNAwas synthesized using random hexamer primers,followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.

treatment_protocol: DMD rats were fed MCTKD or normal diet (ND) from weaning to 9 months, and wild-type rats were fed with the ND.

value: skeletal muscle

tag: strain background

value: Wistar-Imamichi

tag: genotype

value: WT

value: fed ND from weaning to 9months


title: DMD_ND11

value: Dmd


title: WT_ND9


title: WT_ND3


title: WT_ND1


title: Patient_79, Serum, iMCD, Cycle4_Day1

tag: patient label


title: Patient_57, Serum, iMCD, Cycle1_Day8

tag: disease state


title: Patient_55, Serum, iMCD, Cycle1_Day8

tag: batch


title: DMD_ND9


title: Patient_56, Serum, iMCD, Cycle1_Day8

tag: Sex


title: Patient_74, Serum, iMCD, Cycle4_Day1

tag: age


title: DMD_ND5

tag: tissue


title: SD_WD_veh2_scRNA

value: single cell normal SD

tag: strain

value: SD

value: breast


title: Patient_58, Serum, iMCD, Cycle1_Day8


title: DMD_ND3

tag: treatment


title: Patient_55, Serum, iMCD, Cycle1_Day1


title: Patient_68, Serum, iMCD, Cycle1_Day8


title: Patient_72, Serum, iMCD, Cycle4_Day1


title: DMD_KD10

value: fed MCTKD from weaning to 9months


title: Patient_71, Serum, iMCD, Cycle4_Day1

value: iMCD


title: DMD_KD7


title: Patient_70, Serum, iMCD, Cycle4_Day1


title: DMD_KD3


title: Patient_73, Serum, iMCD, Cycle4_Day1


title: DMD_ND7


title: Patient_72, Serum, iMCD, Cycle1_Day8

value: F


title: DMD_ND6


title: Ctr3

first: Ming

last: Zhai

state: Massachusetts

address: Avenue Louis Pasteur

department: Cardiovascular Division, Department of Medicine

institute: Brigham and Women's Hospital

data_processing: The trimmed reads were aligned to the rat reference genome NCBI Rnor6.0 with TopHat v2.1.1 with default parameter settings.The aligned bam files were then processed using Cufflinks v2.2.1 for gene quantification.The gene expression profiles (Fragments Per Kilo base per Million or FPKM) were used as the input for differential expression gene (DEG) analysis by using Cuffdiff.

source_name: RASMC

extract_protocol:
Cultivated SMCs was washed after H3cit combined with dsDNA stimulied and was collected in the triZol, after the cells were
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Smooth muscle cells (SMC)


title: DMD_KD1

extract_protocol:
Total RNA was extracted from frozen tibialis anterior (TA) muscles  using RNAisoPlus according to the manufacturer’s recommendation (Takara Bio Inc. Kusatsu, Japan).
Messenger RNA was purified from total RNA using poly-T oligo-attached magnetic beads. After fragmentation, the first strand cDNAwas synthesized using random hexamer primers,followed by the second strand cDNA synthesis using either dUTP for directional library or dTTP for non-directional library.


title: Ctr2


title: Patient_70, Serum, iMCD, Cycle1_Day8

value: TRUE


title: CitH3+dsDNA_3


title: CitH3+dsDNA_2


title: Ctr1


title: Patient_74, Serum, iMCD, Cycle1_Day8

value: Siltuximab + BSC


title: Patient_71, Serum, iMCD, Cycle1_Day8

value: FALSE


title: CitH3+dsDNA_1


title: DMD_KD9


title: Patient_73, Serum, iMCD, Cycle1_Day8

value: M


title: Patient_74, Serum, iMCD, Cycle1_Day1


title: DMD_KD5


title: Patient_72, Serum, iMCD, Cycle1_Day1


title: Patient_70, Serum, iMCD, Cycle1_Day1

value: Placebo + BSC


title: Patient_66, Serum, iMCD, Cycle4_Day1


title: Patient_73, Serum, iMCD, Cycle1_Day1


title: NTERT-TXN1 KO3

city: New York

first: Daniel

middle: Parker

last: Ball

state: New York

department: Chemical Biology

institute: Memorial Sloan Kettering Cancer Center

description: WT-vs-TXN1_KO_Differential_expression_analysis_table.csv

data_processing:
Sequencing libraries were multiplexed and clustered onto a flowcell and loaded onto the Illumina HiSeq 4000 instrument according to manufacturer’s instructions and sequenced using a 2x150 bp Paired End configuration. Image analysis and base calling were conducted by the Illumina Control Software. Raw sequencing data (.bcl files) were converted to fastq and de-multiplexed using Illumina bcl2fastq 2.20 software. One mismatch was allowed for index sequence identification.
Sequence reads were trimmed using Trimmomatic v.0.36 and mapped to the Homo sapiens GRCh38 reference genomes (ENSEMBL) using the STAR aligner v.2.5.2b. Unique gene hit counts were summarized and reported using the gene_id feature in the annotation file. Only unique reads within exon regions were counted.
Gene hit count tables were used for downstream differential expression analysis. DESeq2 was used for comparative gene expression analysis between sample groups.
The Wald test was used to generate p-values and log2FC. Genes with an adjusted p-value < 0.05 and absolute log2FC > 1 were defined as differentially expressed genes for each comparison. Gene ontology analysis was performed on the statistically significant set of genes using GeneSCF v.1.1-p2 software.
Assembly: GRCh38 - hg38
Supplementary files format and content: Log2FC, p-value, p-adjusted, and RPKM values for the differential expression measured for the indicated gene.

source_name: Skin

extract_protocol:
Total RNA content was collected and purified using the Rneasy kit (Qiagen) following the manufacturer's directions
Library preparation, polyA selection, and sequencing were performed as follows. Briefly, RNA samples were quantified using a Qubit 2.0 fluorometer (ThermoFisher Scientific) and RNA integrity assessed with a 4200 TapeStation (agilent Technologies). Samples were then normalized using the ERCC RNA Spike-In Mix kit (ThermoFisher Scientific) following the manufacturer’s recommendations. The RNA sequencing library was prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following the manufacturer’s recommendations.

value: Skin

tag: cell line

value: keratinocyte

value: +hTERT, lack p16INK4 expression

value: Male

value: Electroporation of TXN1 RNP


title: NTERT-WT-ctrl2

tag: cell type

value: Electroporation of control RNP


title: NTERT-WT-ctrl3


title: NTERT-TXN1 KO2


title: NTERT-TXN1 KO1


title: Patient_69, Serum, iMCD, Cycle1_Day1


title: Patient_69, Serum, iMCD, Cycle1_Day8


title: NTERT-WT-ctrl1


title: Patient_65, Serum, iMCD, Cycle4_Day1, Rep 2

description:
JRD16.xlsx
2.15 JRD_16-166.hybNorm.medNorm.calibrate.20160923.adat
Technical replicate; not included in final analysis


title: Patient_64, Serum, iMCD, Cycle4_Day1


title: Sample_10006600658728

city: Trondheim

first: Pål

last: Sætrom

address: Erling Skjalgsons gate 1

department: Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology, NTNU

data_processing:
Sequence reads were demultiplexed and converted from BCL to fastq file format using bcl2fastq2 conversion software V2.20.0422 (Illumina, Inc. San Diego, CA, USA).
Adapters from the 3’end of the raw sequences were trimmed using cutadapt-1.2.1.
Trimmed sequence were collapsed into single unique reads along with their total read count using the fastx collapser tool (http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the human (hg38) genome and the known calibrator sequences using bowtie2, allowing for up to 10 alignments per read to account for reads from duplicated miRNA loci.
Reads overlapping with mature miRNA loci were identified using htseq-count from the HTseq python package. These reads were further filtered to identify those with perfect alignment to the genome, and the total read counts for mature miRNAs were then computed by summing the total read count per sequence (isomiR) overlapping each miRNA locus. Mature miRNAs were annotated using miRBase (Release 22).
The calibrator counts were used to compute normalization factors per sample (calcNormFactors from edgeR). MicroRNA read counts were then normalized by using the calibrator RNA normalization factors (norm.factors in DGEList from edgeR), followed by reads per million (RPM) normalization and log2 transformation (voom from limma). MicroRNAs with average RPM < 1 were excluded from further analyses.
Genome_build: GRCh38

extract_protocol:
Inclusion criteria were: (i) patients with suspected LC that will during routine examination have a biopsy or blood samples taken, (ii) patients with relapse of LC, (iii) patients aged 18 years or more, (iv) written informed consent, (v) sampling does not imply significant delay of treatment, and (vi) sampling does not imply a significantly increased risk compared to routine diagnostic sampling. The recruited participants included individuals that were symptomatic of lung cancer, but not all were diagnosed with a confirmed lung cancer diagnosis and for those that were confirmed, the study sample comprised patients of any histological subtype and stage. Symptomatic persons with a CT scan which indicated LC but who during diagnostic follow-up were not diagnosed with lung cancer are hereafter referred to as FalsePos (“false positives”). During diagnostic workup of patients with suspected LC, blood samples were collected together with phenotype data. None of the patients had started cancer treatment at the time of sampling. Phenotype data were collected from questionnaires and electronic health records from the hospital. Serum were collected and stored at -80°C.    The miRNeasy Serum/Plasma Kit (Cat No./ID: 217184, Qiagen, Hilden, Germany) in combination with an automated Qiacube system, was used to purify total RNA, including miRNA, from 100 µl serum.
For assessment of extracted RNA quality and relative size, selected samples were measured using the Agilent Eukaryote Total RNA Pico assay and an Agilent 2100 Bioanalyzer (Waldbronn, Germany). The sequencing libraries were prepared using extracted RNA samples eluted in 14 µl water, a pool of 10 synthetic calibrator RNAs, and the NEXTflex small RNA-seq kit v3 (Bioo Scientific, Austin, TX, USA). Double-stranded cDNA was prepared by PCR amplification (22 cycles) and fragments/libraries were run on Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) or LabChip GX DNA High Sensitivity (Perkin Elmer, Waltham, MA, US) for quality control and quantitation. Individual libraries were normalized to 10 nM and pooled. The library pool was purified with the QIAquick PCR Purification Kit (Qiagen AB, Sweden) according to instructions. Automated size selection was performed using the Blue Pippin (Sage Science, Beverly, MA, USA), with a range of 135 to 175 bp to select the ~152 bp fragments. Following size selection, the pool was evaluated on Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using the High Sensitivity DNA kit. The pool of libraries was quantified with the KAPA Library Quantification Kit (Roche, Pleasanton, CA, USA). Quantitated libraries were further diluted and normalized to 2.4 nM before clustering on the cBot (Illumina, Inc., San Diego, CA, USA). Single read sequencing was performed for 51 cycles on a HiSeq4000 flowcell, according to the manufacturer's instructions (Illumina, Inc., San Diego, CA, USA). One in-house pooled reference sample consisting of plasma from ten random healthy individuals was included in each sample preparation batch.

tag: lane

value: FalsePos

tag: histology

tag: agescaled

tag: smokingstatus

value: Former

tag: survival


title: Sample_10006600658491


title: Sample_10006600658504

value: Female


title: Patient_199, Serum, iMCD, Cycle4_Day1

description:
JRD16.xlsx
2.15 JRD_16-166.hybNorm.medNorm.calibrate.20160923.adat
Failed QA; removed from processed data

value: iMCD


title: Patient_65, Serum, iMCD, Cycle4_Day1, Rep 1


title: Patient_71, Serum, iMCD, Cycle1_Day1

value: F


title: Sample_10006600658155

value: Late

value: Other


title: Patient_199, Serum, iMCD, Cycle1_Day8

value: TRUE

value: Siltuximab + BSC


title: Sample_10006600657829

value: AD


title: Sample_10006600657717

value: Current


title: Sample_10006600657592

value: Never


title: Patient_64, Serum, iMCD, Cycle1_Day8

value: M

value: Placebo + BSC

value: FALSE


title: Sample_10006600657368

value: Middle

value: SQ


title: Patient_66, Serum, iMCD, Cycle1_Day8


title: Patient_69, Serum, iMCD, Cycle4_Day1


title: Patient_67, Serum, iMCD, Cycle1_Day8


title: Patient_68, Serum, iMCD, Cycle1_Day1


title: Sample_10006600656818


title: Patient_58, Serum, iMCD, Cycle1_Day1


title: Sample_10006600656693

value: Male


title: Patient_57, Serum, iMCD, Cycle1_Day1


title: Sample_10006600658379

value: FalsePos


title: Sample_10006600655807

value: Female


title: Patient_56, Serum, iMCD, Cycle1_Day1

value: iMCD


title: Patient_66, Serum, iMCD, Cycle1_Day1


title: Patient_67, Serum, iMCD, Cycle1_Day1


title: Patient_65, Serum, iMCD, Cycle1_Day8


title: Patient_199, Serum, iMCD, Cycle1_Day1

value: F


title: Sample_10006600654447

value: Late

value: SCLC


title: Sample_10006600654671

value: Former


title: Sample_10006600654098


title: Sample_10006600653884


title: Patient_65, Serum, iMCD, Cycle1_Day1

value: TRUE

value: Siltuximab + BSC


title: Sample_10006600464900

value: Current


title: Sample_10006600465114


title: Sample_10006600656469


title: Patient_62, Serum, Healthy

description:
JRD17.xlsx
2.5 PX-17-116.HybMedNormCal.Premium.adat

value: Healthy


title: Sample_10006600464775

value: Early


title: Patient_61, Serum, Healthy

value: M


title: Sample_10006600464327


title: Sample_10006600656245

value: AD

value: Never


title: Patient_60, Serum, Healthy


title: Sample_10006600655458

value: SQ


title: Sample_10006600464103

value: Other


title: Patient_59, Serum, Healthy


title: Patient_58, Serum, iMCD, Cycle4_Day1

value: FALSE


title: Sample_10006600463764

value: Female

value: Middle


title: Patient_64, Serum, iMCD, Cycle1_Day1

value: iMCD

value: Placebo + BSC


title: Sample_10006600463540


title: Patient_63, Serum, Healthy


title: Patient_57, Serum, iMCD, Cycle4_Day1

value: F


title: Sample_10006600463204

value: Male

value: Former


title: Patient_56, Serum, iMCD, Cycle4_Day1

value: TRUE

value: Siltuximab + BSC


title: Sample_10006600463079


title: Patient_55, Serum, iMCD, Cycle4_Day1


title: Patient_54, Serum, Healthy

value: Healthy


title: Patient_53, Serum, Healthy


title: Patient_52, Serum, Healthy


title: Sample_10006600462641

value: Early

value: Current


title: Sample_10006600462068

value: Late


title: Sample_10006600461630

value: SCLC


title: Patient_51, Serum, Healthy

value: M


title: Sample_10006600462865

value: Other


title: Sample_10006600461406

value: FalsePos


title: Patient_50, Serum, Healthy


title: Patient_49, Serum, iMCD, Cycle1_Day1

value: FALSE


title: Patient_48, Serum, iMCD, Cycle1_Day1


title: Sample_10006600461281

value: SQ


title: Patient_200, Serum, iMCD

description:
JRD17.xlsx
2.5 PX-17-116.HybMedNormCal.Premium.adat
Failed QA; removed from processed data

value: iMCD


title: Sample_10006600460843

value: Female

value: Middle

value: AD


title: Patient_47, Serum, iMCD, Cycle4_Day1


title: Sample_10006600460494

value: Former


title: A98

type: genomic

city: Heidelberg

first: Martin

last: Sill

address: Im Neuenheimer Feld 280

department: Division of Pediatric Neurooncology

country: Germany

institute: DKFZ

hyb_protocol: Illumina

scan_protocol: Illumina iScan System

data_processing:
Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.
Raw signal intensities were obtained from IDAT-files using the minfi Bioconductor package. Signal intensities were normalized per sample by performing a background correction (shifting of mean negative control probe intensity to 0) and a dye-bias correction (scaling of mean normalization control probe intensity to 10,000). Standard beta-values were calculated.

label: biotin/DNP

molecule: genomic DNA

source_name: CNS tumor

label_protocol: Illumina

extract_protocol:
Extraction of high molecular weight DNA from fresh frozen or FFPE tumor samples was carried out using the Maxwell RSC Tissue DNA kit or the Maxwell RSC DNA FFPE kit, respectively.
Extraction of high molecular weight DNA from frozen tumor samples was carried out using a Qiagen Blood & Cell Culture DNA Midi Kit (Qiagen, Hilden, Germany) after milling of the frozen sample in a Micro-Dismembrator S (B. Braun, Melsungen, Germany).

value: male

tag: location

value: brainstem

tag: tumor subgroup


title: Sample_10006600460270


title: Patient_46, Serum, iMCD, Cycle1_Day1

tag: patient label


title: A100

value: infratentorial, midline


title: Blood_Control_patient-50_visit-V2

city: Columbia

first: Rene

middle: Gabriel

last: Cortese

state: MO

address: 1 Hospital Dr. MA104E

department: Child health Research Institute

institute: University of Missouri

description:
50_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

hyb_protocol: Bisulphite converted DNA was amplified, fragmented and hybridized to Illumina Infinium Human Methylation450 Beadchip using standard Illumina protocol.

scan_protocol: Arrays were imaged using High Scan SQ using standard recommended Illumina scanner setting.

data_processing: Microarray data was processed using the minfi package version 1.38.0 (Arye et al. 2014).

label: Cy3, Cy5

source_name: Peripheral blood lymphocytes at visit 2

label_protocol: Standard Illumina labelling protocol.

extract_protocol: Genomic DNA was isolated from the stored blood samples using the Illustra blood genomic Prep Midi Flow Kit (GE Healthcare, UK) following the manufacturer’s instructions.

value: Peripheral blood lymphocytes

value: Male

tag: disease

value: Control

tag: visit

value: Visit 2

tag: patient


title: A102

tag: Sex

tag: age

value: cerebellum


title: Blood_Control_patient-30_visit-V2

description:
30_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

tag: tissue


title: A106

value: female

value: hemispheric


title: Blood_Control_patient-50_visit-v1

description:
50_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

source_name: Peripheral blood lymphocytes at visit 1

value: Visit 1


title: Blood_Control_patient-34_visit-V2

description:
34_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: A101


title: A94

value: ventricles


title: Sample_10006600460046

value: FalsePos


title: A97


title: Blood_Control_patient-36_visit-V2

description:
36_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

value: Female


title: Blood_Control_patient-4_visit-V2

description:
4_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_Control_patient-14_visit-V2

description:
14_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_Control_patient-31_visit-V2

description:
31_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: A96


title: Blood_Control_patient-10_visit-V2

description:
10_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Patient_44, Serum, iMCD, Cycle1_Day1

tag: disease state

value: iMCD

tag: batch

value: M

value: FALSE


title: Blood_Control_patient-30_visit-v1

description:
30_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_Control_patient-14_visit-v1

description:
14_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_Control_patient-10_visit-v1

description:
10_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Sample_10006600459833

value: Never


title: Blood_OSA_patient-66_visit-V2

description:
66_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

value: OSA


title: A99


title: Sample_10006600459609


title: Blood_OSA_patient-57_visit-V2

description:
57_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Sample_10006600459484


title: Blood_Control_patient-4_visit-v1

description:
4_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Patient_42, Serum, RA

description:
JRD17.xlsx
2.5 PX-17-116.HybMedNormCal.Premium.adat

value: RA

value: F


title: A93


title: Sample_10006600459260


title: Blood_Control_patient-31_visit-v1

description:
31_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

value: Peripheral blood lymphocytes

value: Male


title: Blood_Control_patient-36_visit-v1

description:
36_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

value: Control


title: Blood_OSA_patient-29_visit-V2

description:
29_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls

value: Visit 2


title: Patient_41, Serum, RA


title: Patient_40, Serum, RA


title: Sample_10006600459036

value: Early

value: SQ

value: Current


title: Sample_10006600458822

value: Former


title: Patient_43, Serum, RA


title: Patient_39, Serum, RA


title: Blood_OSA_patient-9_visit-V2

description:
9_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Sample_10006600458585

value: FalsePos


title: Patient_45, Serum, iMCD, Cycle1_Day1


title: Patient_38, Serum, RA


title: Blood_Control_patient-34_visit-v1

description:
34_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

value: Visit 1


title: Blood_OSA_patient-21_visit-V2

description:
21_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Patient_37, Serum, RA


title: Sample_10006600458137

value: Middle

value: Other


title: Sample_10006600457923


title: Patient_36, Serum, RA

value: M


title: Blood_OSA_patient-5_visit-V2

description:
5_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Sample_10006600457798

value: Late

value: AD

value: Never


title: Patient_35, Serum, RA

value: RA

value: F


title: Sample_10006600457574

value: Female


title: Blood_OSA_patient-8_visit-V2

description:
8_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

value: Peripheral blood lymphocytes

value: Male

value: OSA


title: Sample_10006600457126


title: Blood_OSA_patient-39_visit-V2

description:
39_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls

value: Visit 2


title: Blood_OSA_patient-46_visit-V2

description:
46_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_OSA_patient-6_visit-V2

description:
6_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_OSA_patient-12_visit-V2

description:
12_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Sample_10006600456912

value: SQ


title: Blood_OSA_patient-45_visit-V2

description:
45_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_OSA_patient-18_visit-V2

description:
18_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Patient_32, Serum, RA


title: Patient_31, Serum, RA


title: HPL mBG _p4/p5_4_883

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

country: Austria

data_processing:
Quality control was conducted using FASTQC (version 0.11.7 - Bioinformatics Group at the Babraham Institute).
Trimming and removal of residual adapters was done with AdapterRemova
Reads were then mapped to the Ensembl GRCh38 human genome using Tophat2
The number of mapped reads/gene (counts) was then calculated using HTseq
Genome_build: Human GRCh38
Supplementary_files_format_and_content: Norm_counts_RNAseq_hPL_vs_FBS.csv
Supplementary_files_format_and_content: DESeq2 nromalized counts

source_name: Bone marrow

growth_protocol: For human bone marrow mononuclear cell isolation, approval was obtained from the Institutional Review Board of the Medical University of Graz (protocol 19–252, 21–060). Samples were collected in accordance with the Declaration of Helsinki after written informed consent from healthy volunteers. Cells were cultured in alpha-modified minimum essentials Eagle’s medium, α-MEM (Sigma-Aldrich, St. Louis, MO, USA) supplemented with 5 mM N(2)-L-alanyl-L-glutamin (Dipeptiven, Fresenius Kabi, Austria), 100 U/mL penicillin and 0.1 mg/mL streptomycin (both Sigma-Aldrich). We supplemented this BMSC expansion medium additionally with 10% of either hPL O/AB (JOVE 2009) or pooled hPL mixed blood group (mBG) in the presence of 2 IU/mL preservative-free heparin (Biochrom, Germany) (https://www.mdpi.com/1422-0067/22/10/5178) as indicated. For comparison, an optimized concentration of 16.5% heat inactivated FBS (FBS Superior, Sigma-Aldrich) was used.

extract_protocol:
RNA was isolated using Macherey&Nagel RNA isolation kit according to the manufacturers protocol. The quality of total RNA isolates was analyzed using the Agilent RNA 6000 Nano Kit.   Poly-(A)-selection was performed utilizing the NEBNext Poly(A)mRNA Magnetic Isolation Module (NEB) according to the manufacturer’s requirements.
mRNA libraries were prepared with the NEBNext Ultra RNA Library Prep Kit for Illumina (NEB). All libraries were analyzed with the Agilent DNA 1000 Kit and quantified using the Qubit® dsDNA BR Assay Kit (ThermoFisher). After equimolar pooling all samples were sequenced on an Illumina HiSeq 1500 system with High Output chemistry v4 (50 cycles, single-read).

treatment_protocol: Bone marrow aspirations were divided 50/50 and stromal cells were isolated and expanded either under animal serum-free conditions with BMSC expansion media containing hPL O/AB or with media containing FBS as previously described (Schallmoser et al Transfusion 2007) (Figure 1). We cyro-preserved BMSC passage 0 (i.e., at the end of primary culture, P°) for later analysis. For large-scale expansion, we seeded the cells directly into in four-layered cell factories (CF-4) in BMSC expansion medium supplemented with either hPL O/AB or FBS upon thawing. Expanded BMSCs from passage 1 (P1) were either analyzed or further continued to be cultured in these media until passage 4 - 5 (P4 - 5). An aliquot of BMSCs cultured in hPL O/AB was transferred to BMSC expansion medium containing hPL mBG and also cultured until P5. BMSCs from P1 and P4 were further analyzed as indicated. In selected experiments, due to different cell growth of the different samples we used samples P4 +/- one passage. BMSC population doublings (PD) for all passages were calculated using the formula LN(fold increase cell number)/LN(2). We derived cumulative PD by addition of PD of all passages. Cumulative cell numbers were calculated by assuming that all cells were further expanded and therefor by multiplying the totally harvested cells of P1 with the fold-increase of the following passages P2 - 3 in smaller culture vessels.

tag: cell type

value: Mesenchymal stromal cells

tag: treatment

value: HPL mBG

tag: passage

tag: donor


title: Patient_34, Serum, RA


title: Sample_10006600456675

tag: lane

tag: histology

tag: agescaled

tag: smokingstatus

value: Former


title: Blood_OSA_patient-2_visit-V2

description:
2_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Patient_30, Serum, RA

tag: patient label


title: Blood_OSA_patient-66_visit-v1

description:
66_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

tag: disease

value: Visit 1


title: Blood_OSA_patient-57_visit-v1

description:
57_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

tag: visit


title: HPL mBG _p4/p5_2_881


title: Patient_29, Serum, RA

description:
JRD17.xlsx
2.5 PX-17-116.HybMedNormCal.Premium.adat


title: Blood_OSA_patient-6_visit-v1

description:
6_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

tag: patient


title: Blood_OSA_patient-29_visit-v1

description:
29_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

tag: Sex


title: Blood_OSA_patient-21_visit-v1

description:
21_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

tag: age


title: Sample_10006600455888

value: FalsePos

tag: survival


title: Sample_10006600455776

value: Middle

value: Other


title: Blood_OSA_patient-8_visit-v1

description:
8_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

tag: tissue


title: HPL mBG _p4/p5_1_880


title: Blood_OSA_patient-18_visit-v1

description:
18_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: YRM1, Sort-seq

city: St. Louis

first: Pamela

last: Recio

address: 4523 Clayton Avenue

department: Genetics

institute: Washington University in St Louis

description: Sort-seq experiment to measure Transcription Factor expression in vivo

library_source: genomic

data_processing:
Sort-seq: We use our python analysis source code for data processing. The code is available on Gitlab.
Assembly: Sort-seq: Not applicable
Supplementary files format and content: Sort-seq: The processed data files is in CSV format each row as a synthetic promoter sequence. Columns contain read count, YFP FITC-A Mean from FACS, and relative expression information.

organism: Saccharomyces cerevisiae

source_name: Synthetic library designed based on yeast promoters

extract_protocol:
Sort-seq: After measuring expression of library sequences with Sort-seq, plasmid DNA is extracted from yeast cells using EZ Yeast Plasmid Prep kit. Desired regions of the Sort-see library are amplified using PCR.
Sort-Seq library was constructed using similar methods described in Lui et al., 2020. To prepare the vector plasmid pRM1806 for cloning, the plasmid was liberalized with high fidelity restriction enzymes KpnI and ApaI. We then purified the digest and   used a molar ratio of 3:1 plasmid to library DNA in a Gibson assembly reaction, following manufactures instructions. The Gibson assembly product was filtered by drop dialysis with a Nitrocellulose membrane (0.025 µm), following the Millipore Sigma protocol. The library product was electroporated into 7 0.1 cm (about 0.04 in) cuvette tubes, each containing 25 µl of E. coli electrocompetent cells and cells were then plated onto 28 15-cm Kanamycin containing plates. After 16 hours, plates containing 50,000 colonies each were scraped, and the plasmid DNA extracted using a Qiagen Maxiprep kit.

tag: strain

tag: genotype


title: Blood_OSA_patient-45_visit-v1

description:
45_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_OSA_patient-46_visit-v1

description:
46_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_OSA_patient-67_visit-v1

description:
67_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_OSA_patient-12_visit-v1

description:
12_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_OSA_patient-7_visit-V2

description:
7_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_OSA_patient-9_visit-v1

description:
9_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_OSA_patient-39_visit-v1

description:
39_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_OSA_patient-5_visit-v1

description:
5_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: Blood_OSA_patient-7_visit-v1

description:
7_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.


title: △Leu3, Sort-seq, -Leucine

value: Synthetic library designed based on yeast promoters


title: Sample_10006600454877

value: Late

value: AD

value: Current


title: Sample_10006600455091

value: SCLC


title: LEU3, Sort-seq, -Leucine


title: HPL 0/AB _p4/p5_1_876

tag: cell type

tag: treatment

value: HPL 0/AB


title: Patient_26, Serum, Healthy

tag: disease state

value: Healthy

tag: batch

value: M


title: Patient_201, Serum, Healthy

description:
JRD17.xlsx
2.5 PX-17-116.HybMedNormCal.Premium.adat
Failed QA; removed from processed data


title: Sample_10006600455104

tag: lane

value: Male

tag: histology


title: HPL 0/AB _p4/p5_2_877

tag: passage

tag: donor


title: Patient_25, Serum, iMCD, Cycle4_Day1

description:
JRD17.xlsx
2.5 PX-17-116.HybMedNormCal.Premium.adat

tag: patient label

value: iMCD

value: FALSE


title: Sample_10006600454765

tag: agescaled

tag: smokingstatus


title: Blood_OSA_patient-2_visit-v1

description:
2_v1
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

value: Peripheral blood lymphocytes

tag: Sex

tag: disease

value: OSA

tag: visit

tag: patient


title: Patient_27, Serum, RA

value: RA

tag: age


title: HPL 0/AB _p4/p5_3_878

value: Mesenchymal stromal cells


title: HPL 0/AB _p4/p5_4_879


title: HPL 0/AB _p1_4_875


title: TEA1, Sort-seq

tag: strain

tag: tissue

tag: genotype


title: LEU3, Sort-seq, +Leucine


title: Patient_24, Serum, iMCD, Cycle1_Day1

tag: disease state


title: △GAL4, Sort-seq, -Galactose


title: Sample_10006600454080

value: Female

value: FalsePos

value: Former

tag: survival


title: Patient_23, Serum, iMCD, Cycle1_Day1

tag: batch


title: GAL4, Sort-seq, -Galactose

value: Synthetic library designed based on yeast promoters


title: HPL 0/AB _p1_3_874

tag: cell type

tag: treatment


title: Sample_10006600453293

tag: lane

value: Middle

tag: histology

value: Other


title: HPL 0/AB _p1_2_873

tag: passage

tag: donor


title: HPL 0/AB _p1_1_872


title: Sample_10006600452855

tag: Sex

value: Late

value: SCLC

tag: agescaled

tag: smokingstatus

value: Current


title: Blood_OSA_patient-67_visit-V2

description:
67_V2
Genomic DNA isolated from peripheral blood lymphocytes from OSA patients and controls.

tag: disease

tag: visit

value: Visit 2

tag: patient


title: GAL4, △YRM1, Calling Card Assay

description: "Calling Card" Assay for in vivo Transcription Factor Binding: a retrotransposon is directed into the genome at loci bound by a given transcription factor

data_processing:
Calling Card Assay: Paired end sequence reads were first filtered for read 1 sequences containing the correct 17 bp Ty5 3’LTR sequence and verified experiment-specific barcodes on both Read 1 (5 bp) and Read 2 (8 bp) matched. Once filtered, the 17bp LTR and Read1 barcodes were removed from the 5’ end and 80 bp of Read 1 genomic sequence were aligned to the Saccharomyces cerevisiae reference genome sacCer2 (R-61-1-1) via Novoalign with default parameter settings. Promoters were defined as all intergenic regions spanning 150 bp into the ORF of the upstream and downstream gene that were smaller than 5kb in length. To measure TF binding at a given promoter, the number insertions into each intergenic region were normalized so that the total number of insertions recovered for each experiment was equal to 100,000 and assigned a Transposons per Hundred Thousand (TPH) value to the TF binding at each promoter. Statistically significant binding was determined by first calculating the expected number of insertions at each promoter under the null. Poisson statistics was then used to calculate the p-value for each promoter and significant binding was defined as those promoters having a p-value <1e-5.
Assembly: Calling Card Assay: 2008 S. cerevisiae reference genome (R-61-1-1) Supplementary_files_format_and_content: .sig.txt - a table indicating genomic position (chromosome, chromosomecoordinate) of the retrotransposon insertion and number of reads aligning to that position
Supplementary files format and content: Calling Card Assay: sig.txt - Significantly bound intergenic regions file giving S. cerevisiae intergenic region, flanking ORFs (standard and systematic names), number of detected retrotransposon "calling card" insertions, normalized number of insertions (TPH), hyper-geometric p-value.

extract_protocol:
“Calling Cards” Assay: After TF directed transposition induction and selection, genomic DNA was extracted using a standard glass bead-beating, phenol chloroform isoamyl alcohol purification, and NH4Ac ethanol protocol. Genomic DNA was then divided into 3 separate enzyme digest reactions consisting of either HpaII, HinP1I, or Taqα1  Digested DNA was then, self-ligated using T4 DNA ligase, and Ty5 calling cards were recovered from genomic DNA in the self-ligated template by inverse PCR.
The desired yeast strain for each experiment is created by co-transforming two plasmids, one plasmid contains a Sir4p-tagged TF regulated by the ADH1 promoter with a LEU2 and URA3 auxotrophic marker, and the second contains a Ty5 transposon driven by the inducible GAL1/10 promoter with a HIS3 auxotrophic marker.

tag: strain

value: sir4D gal4D yrm1D


title: FBS _p4/p5_4_871

value: FBS


title: Patient_28, Serum, RA

tag: patient label

value: F

tag: age


title: Sample_10006600452631

value: Male

value: AD

tag: survival


title: Sample_10006600456451


title: Patient_202, Serum, Healthy

tag: disease state

value: Healthy

tag: batch


title: FBS _p4/p5_3_870

tag: cell type

value: Mesenchymal stromal cells

tag: treatment


title: Sample_10006600454429

tag: lane

tag: histology

value: SQ


title: △TEA1, Sort-seq

tag: tissue

tag: genotype


title: Patient_20, Serum, HIV/HHV-8+

tag: Sex

value: M


title: GAL4, △LEU3, Calling Card Assay

value: sir4D gal4D leu3D


title: Sample_10006600452407

value: Female

tag: agescaled

tag: smokingstatus


title: Patient_22, Serum, iMCD, Cycle1_Day1

value: iMCD

value: FALSE


title: FBS _p4/p5_2_869

tag: passage

tag: donor


title: Patient_19, Serum, HIV/HHV-8+


title: GAL4, Sort-seq, +Galactose

tag: strain

value: Synthetic library designed based on yeast promoters


title: HPL mBG _p4/p5_3_882

value: HPL mBG


title: GAL4, △HMO1, Calling Card Assay

value: sir4D gal4D hmoD


title: FBS _p4/p5_1_868


title: GAL4, △SEF1, Calling Card Assay

value: sir4D gal4D sef1D


title: Sample_10006600452170

value: Late

value: SCLC

value: Former


title: ARO80, Calling Card Assay

value: sir4D aro80D


title: FBS _p1_4_867

value: FBS


title: Sample_10006600452394

value: Male

value: Middle

value: AD


title: Patient_18, Serum, HIV/HHV-8+

tag: patient label

value: M


title: Patient_17, Serum, HIV/HHV-8+

tag: age


title: HAL9, Calling Card Assay

value: sir4D hal9D


title: Sample_10006600451956

value: Female

value: Early

value: SQ

value: Current

tag: survival


title: FBS _p1_3_866

value: Mesenchymal stromal cells


title: Sample_10006600451508


title: URC2, Calling Card Assay

value: sir4D urc2D


title: PUT3, Calling Card Assay

value: sir4D put3D


title: FBS _p1_2_865


title: Sample_10006600448812

value: FalsePos

value: Never


title: Sample_10006600449026

value: Late

value: Former


title: FBS _p1_1_864

value: FBS


title: CHA4, Calling Card Assay

value: sir4D cha4D


title: CAT8, Calling Card Assay

value: sir4D cat8D


title: Patient_13, Serum, HIV/HHV-8+

tag: disease state


title: Patient_15, Serum, HIV/HHV-8+

tag: batch


title: Patient_16, Serum, HIV/HHV-8+


title: HPL_P4_4_mBG_1108

data_processing:
Sequence images were transformed to BCL files with the Illumina BaseCaller software and samples were demultiplexed to FASTQ files with bcl2fastq v2.17.1.14
Trimming and removal of residual adapters was done with AdapterRemova
Reads were then mapped to the Ensembl GRCh38 human genome using Bowtie2
Differentially methylated regions were identified using QSEA R package
Genome_build: Human GRCh38
Supplementary_files_format_and_content: Counts_QSEA_hPL_vs_FBS.csv
Supplementary_files_format_and_content: counts from QSEA (500 nt windows)

extract_protocol:
isolated DNA was sheared using a Bioruptor device (Diagenode). Subsequently, methylated DNA was isolated and eluted in high salt elution buffer using the MethylCap kit (Diagenode) according to the manufacturer´s instructions .
Methylated DNA samples were prepared for next generation sequencing using the NEBNext ChIP-Seq Library Prep Master Mix Set for Illumina according to the manufacturer´s instructions. Amplified libraries were analyzed using the Bioanalyzer 2100 device and DNA 1000 Kit (Agilent) and concentrations were determined by means of Qubit 3.0 fluorometer device and the dsDNA BR assay (ThermoFisher). Samples were sequenced using the Illumina HiSeq 1500 system (50 bp single reads) in three independent rounds.

tag: cell type

value: HPL mBG


title: Patient_14, Serum, HIV/HHV-8+

value: M


title: Patient_12, Serum, HIV/HHV-8+


title: Sample_10006600448687

value: Middle

value: Other


title: Sample_10006600448463

value: Male


title: TEA1, Calling Card Assay

value: sir4D tea1D


title: HPL_P4_2_mBG_1106

tag: treatment


title: LYS14, Calling Card Assay

value: sir4D lys14D


title: Patient_33, Serum, RA

value: RA

value: F


title: Sample_10006600451047

tag: lane

value: AD


title: Patient_11, Serum, HIV/HHV-8+


title: Patient_10, Serum, HIV/HHV-8+


title: Sample_10006600448239

tag: histology

value: SCLC

value: Current


title: HPL_P4_4_O/AB_1104

value: Mesenchymal stromal cells


title: YRR1, Calling Card Assay

value: sir4D yrr1D


title: YRM1, Calling Card Assay

value: sir4D yrm1D


title: Sample_10006600448015

value: Late

value: Former


title: Sample_10006600447788

value: Female

value: SQ


title: LEU3, Calling Card Assay

value: sir4D leu3D


title: Sample_10006600447676

value: Middle

value: Other


title: HPL_P4_3_mBG_1107

value: HPL mBG


title: GAL4, Calling Card Assay

value: sir4D gal4D


title: Patient_8, Serum, HIV/HHV-8+

value: M


title: Patient_9, Serum, HIV/HHV-8+


title: HPL_P4_1_O/AB_1101

value: FBS


title: HPL_P4_2_O/AB_1102


title: Patient_7, Serum, HIV/HHV-8+


title: Sample_10006600447452

value: Male

value: AD


title: Sample_10006600447228

value: FalsePos

value: Current


title: tumor, recurrent after DMAG+STV,  rep2

city: Buffalo

first: Andrei

last: Gudkov

state: NY

address: Elm and Carlton Streets

department: Department of Cell Stress Biology

institute: Roswell Park Comprehensive Cancer Center

data_processing:
Illumina bcl2fastq2/2.20 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and then mapped to mouse reference genome (UCSC mm10/GRCm38) using  STAR RNA-seq aligner v2.6.0 using annotation from the same source with default parameters. Reads were counted per gene using featureCounts as part of Subread package, version 1.6.2 with parameters -Q 10 -t exon -g gene_id.
Assembly: mm10
Supplementary files format and content: Matrix tab-delimited table with raw gene counts for every gene and every sample

source_name: recurrent tumor that regrew following 17-DMAG+stavudine treatment

extract_protocol:
10-50 mg of frozen tissue samples, with the addition of 700 ml of Qiazol reagent, are first homogenized using Navy Rhino tubes in a Bullet Blender Homogenizer (Next Advance) for 5 minutes.  The homogenate is then removed and incubated in a new tube at room temperature.  After addition of chloroform, the homogenate is then separated into aqueous and organic phases by centrifugation. RNA partitions to the upper, aqueous phase, while DNA partitions to the interphase and proteins to the lower, organic phase or the interphase.  The upper, aqueous phase is extracted, and ethanol is added to provide appropriate binding conditions for all RNA molecules from 18 nucleotides upwards. The sample is then applied to the miRNeasy Mini spin column, where the total RNA binds to the membrane and phenol and other contaminants are efficiently washed away.  On-column DNAse digestion is also performed to remove any residual genomic DNA contamination followed by additional washes.  High quality RNA is then eluted in 60 ml of RNase-free water.
Sequencing libraries were prepared with the RNA HyperPrep Kit with RiboErase (HMR) kit (Roche Sequencing Solutions) from 500ng total RNA.  Following the manufacturer’s instructions, the first step depletes rRNA from total RNA.  The remaining RNA is DNase-digested to remove any genomic DNA contamination. Samples are then purified, fragmented, and primed for cDNA synthesis.  Fragmented RNA is then reverse transcribed into first strand cDNA using random primers.  The next step removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA.  Pure Beads (KAPA Biosystems) are used to separate the ds cDNA from the second strand reaction mix resulting in blunt-ended cDNA.  A single ‘A’ nucleotide is then added to the 3’ ends of the blunt fragments.  Multiple indexing adapters, containing a single ‘T’ nucleotide on the 3’ end of the adapter, are ligated to the ends of the double-dtranded cDNA, preparing them for hybridization onto a flow cell.   Adapter-ligated libraries are amplified by PCR, purified using Pure Beads, and validated for appropriate size on a 4200 TapeStation using D1000 Screentape (Agilent Technologies, Inc.). The DNA libraries are quantitated using the KAPA Biosystems qPCR kit (Sigma) and are pooled together in an equimolar fashion, following experimental design criteria. NovaSeq Standard- Each pool is denatured and diluted to 350pM with 1% PhiX control library (Illumina) added.  The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge (Illumina), as determined by the number of sequencing cycles desired, and sequenced on a NovaSeq6000 instrument (Illumina) following the manufacturer’s recommended protocol.

treatment_protocol: Stavudine (STV) was provided in non-acidic drinking water to MMTV transgenic mice ad libitum starting at two months of age or after prime tumors appearance.  STV provided in non-acidified sterile water, pH 7, at 1mg/mL results in a dose ~ 200 mg/kg/day, estimated by assuming consumption of 4 mL/mouse per day. As a control, mice were provided with non-acidified sterile water. 17-DMAG (20 mg/kg) dissolved in DPBS buffer was administered to tumor-bearing mice as IP injections three times per week, treated in the presence or absence of STV in drinking water. See also Materials and Methods section of Novototskaya-Valsova et al., PNAS 2022.

tag: tissue

value: tumor

value: FVB/N-TgN (MMTV-HER2/neu) 202Mul/J

value: Wild type

value: DMAG+STV


title: tumor, recurrent after DMAG+STV,  rep1

tag: genotype


title: HPL_P1_4_1100

value: Mesenchymal stromal cells


title: HPL_P1_3_1099


title: Patient_4, Serum, HIV/HHV-8+

tag: Sex


title: HPL_P4_1_mBG_1105


title: Sample_10006600447004

value: Early

value: SQ

tag: agescaled

value: Former


title: tumor, primary STV,  rep3

source_name: primary tumor from stavudine-treated mouse

value: STV


title: HPL_P4_3_O/AB_1103


title: Patient_3, Serum, HIV/HHV-8+


title: tumor, primary STV,  rep2


title: HPL_P1_1_1097


title: HPL_P1_2_1098


title: Sample_10006600446329

tag: smokingstatus


title: tumor, primary STV,  rep1


title: Sample_10006600446889


title: tumor, recurrent after DMAG,  rep3

source_name: recurrent tumor that regrew following 17-DMAG treatment

value: DMAG


title: Sample_10006600446092


title: Patient_2, Serum, HIV/HHV-8+


title: Sample_10006600446105

value: Female

value: Late

value: SCLC


title: Mammary gland macrophages replicate 3 [RNA-seq]

first: Joschka

last: Hey

state: Deutschland

department: Cancer epigenomics

data_processing:
Illumina bcl2fastq software used for base calling.
Sample barcodes were extracted from read 2 and concatenated to the fastq header of read 1. Barcode is of size 7 followed by UMI of size 8
aligment: STAR v2.4.2a parameters: –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No
We used the 3’ end (1000bp) of the transcripts for counting the number of reads per gene. Counting (UMI counts) was done after marking duplicates (in-house script) using HTSeq-count (DOI: 10.1093/bioinformatics/btu638) in union mode.
Further analysis was done for genes having minimum 5 reads in at least one sample
Genome_build: mm10
Supplementary_files_format_and_content: tab delimited text files include mRNA molecule count values for each sample

molecule: polyA RNA

source_name: Normal mammary fat pad

growth_protocol: 8 to 13 weeks-old mice housed at the Weizmann Institute animal facility under specific pathogen-free conditions.

extract_protocol:
Normal mammary fat pad: Tissue was minced using scissors and placed and disrupted for 25 min at 37oC in a gentleMACS C tube using gentleMACS dissociator, in the presence of enzymatic digestion solution containing 1 mg ml-1 collagenase II, 1 mg ml-1collagenase IV and 70 unit ml-1 DNase. Primary tumor: Tissue was minced using scissors and treated with enzymatic digestion solution containing 3 mg ml-1 collagenase A and 70 unit ml-1 DNase in RPMI 1640 for 20 min at 37oC, with pipetting every 3 min. Foe BMDM extraction the Tibia and Femur leg bones were dissected Bones were flushed with MACS buffer using a 5 ml syringe with a 25 G needle. The flushed cells from the bone marrow were centrifuged at 500 g for 5 min and resuspended in red blood cell lysis buffer  cells were washed with PBS and resuspended in macs buffer.
3' end mRNA libraries were prepared for sequencing using a method developed at Dr. Ido Amit's lab, Weizmann Institute of Science
3' RNA-seq for digital gene expression quantitation; Single end protocol R2 used for 7N barcode + 8N UMI concatenated to R1 header

treatment_protocol: 8 weeks old BALB/c females were injected under anaesthesia with 100,000 4T1-luc cells suspended in PBS, directly into the lower left mammary fat pad. To obtain TAMs from primary tumors, mice were sacrificed and tumors were immediately excised post mortem.

value: BALB/c

value: Normal mammary fat pad

value: Mammary gland macrophages

tag: selection marker

tag: mouse age

value: 12 weeks

value: batch 2


title: Patient_1, Serum, HIV/HHV-8+

value: M


title: Patient_5, Serum, HIV/HHV-8+


title: FBS_P4_3_1095

value: HPL O/AB

tag: passage

tag: donor


title: △YRM11, Sort-seq

tag: strain

value: Synthetic library designed based on yeast promoters


title: Patient_6, Serum, HIV/HHV-8+

tag: patient label

tag: age


title: FBS_P4_4_1096

value: Mesenchymal stromal cells


title: Mammary gland macrophages replicate 2 [RNA-seq]

tag: batch


title: tumor, recurrent after DMAG,  rep1

value: tumor

value: FVB/N-TgN (MMTV-HER2/neu) 202Mul/J

value: Wild type


title: Sample_10006600445878

value: FalsePos

value: Current

tag: survival


title: tumor, recurrent after DMAG,  rep2

tag: treatment

value: DMAG


title: FBS_P4_2_1094

tag: cell type


title: Sample_10006600445430

tag: lane

value: Female

value: Early

tag: histology

value: AD


title: FBS_P4_1_1093


title: Tumor-associated macophages replicate 3 [RNA-seq]

source_name: Tumor microenvironment of breast cancer

value: BALB/c

tag: tissue

value: breast cancer

value: Tumor-associated macrophages

value: Orthotopic injection of 4T1-luc cells into the mammary fat pad

value: 8 weeks

value: batch 1


title: mammary gland, rep2

source_name: mammary gland from untreated mouse

value: mammary gland

tag: genotype

value: untreated


title: Tumor-associated macophages replicate 2 [RNA-seq]


title: Sample_10006600445318

source_name: Serum

tag: Sex

value: Middle

value: SCLC

tag: agescaled


title: FBS_P1_4_1092

value: Mesenchymal stromal cells

value: HPL


title: mammary gland, rep1

value: FVB/N-TgN (MMTV-HER2/neu) 202Mul/J

value: Wild type


title: FBS_P1_3_1091


title: Sample_10006600445193

value: Female

value: Late

tag: smokingstatus

value: Current


title: Sample_10006600444531

value: Male

value: Other

value: Former


title: tumor, primary untreated,  rep2

source_name: primary tumor from untreated mouse

value: tumor


title: Sample_10006600444307

value: AD


title: Sample_10006600444182


title: tumor, primary untreated,  rep1


title: Bone marrow-derived monocytes from healthy mice replicate 7 [RNA-seq]

source_name: Bone marrow of healthy mice

value: BALB/c

value: Bone marrow

value: Bone marrow-derived monocytes

tag: selection marker

value: CD11b+ Gr+ F4/80low

tag: mouse age

value: 12 weeks

value: batch 2


title: FBS_P1_1_1089

value: Mesenchymal stromal cells

value: HPL

tag: passage

tag: donor


title: Bone marrow-derived monocytes from healthy mice replicate 6 [RNA-seq]

tag: strain


title: 4T1 cells, Doxycycline-treated, rep3

source_name: 4T1-tetL1(GLucAI) cells following 48h exposure to 400ng/mL Doxycycline

growth_protocol: DMEM medium with 10% fetal bovine serum, 37 degrees Celsium, 5% CO2

extract_protocol:
10-50 mg of freshly collected cell pellets are lysed with 700 ml of Qiazol reagent.  After addition of chloroform, the homogenate is then separated into aqueous and organic phases by centrifugation. RNA partitions to the upper, aqueous phase, while DNA partitions to the interphase and proteins to the lower, organic phase or the interphase.  The upper, aqueous phase is extracted, and ethanol is added to provide appropriate binding conditions for all RNA molecules from 18 nucleotides upwards. The sample is then applied to the miRNeasy Mini spin column, where the total RNA binds to the membrane and phenol and other contaminants are efficiently washed away.  On-column DNAse digestion is also performed to remove any residual genomic DNA contamination followed by additional washes.  High quality RNA is then eluted in 60 ml of RNase-free water.
Sequencing libraries were prepared with the RNA HyperPrep Kit with RiboErase (HMR) kit (Roche Sequencing Solutions) from 500ng total RNA.  Following the manufacturer’s instructions, the first step depletes rRNA from total RNA.  The remaining RNA is DNase-digested to remove any genomic DNA contamination. Samples are then purified, fragmented, and primed for cDNA synthesis.  Fragmented RNA is then reverse transcribed into first strand cDNA using random primers.  The next step removes the RNA template and synthesizes a replacement strand, incorporating dUTP in place of dTTP to generate ds cDNA.  Pure Beads (KAPA Biosystems) are used to separate the ds cDNA from the second strand reaction mix resulting in blunt-ended cDNA.  A single ‘A’ nucleotide is then added to the 3’ ends of the blunt fragments.  Multiple indexing adapters, containing a single ‘T’ nucleotide on the 3’ end of the adapter, are ligated to the ends of the double-dtranded cDNA, preparing them for hybridization onto a flow cell.   Adapter-ligated libraries are amplified by PCR, purified using Pure Beads, and validated for appropriate size on a 4200 TapeStation using D1000 Screentape (Agilent Technologies, Inc.). The DNA libraries are quantitated using the KAPA Biosystems qPCR kit (Sigma) and are pooled together in an equimolar fashion, following experimental design criteria. NovaSeq Standard- Each pool is denatured and diluted to 350pM with 1% PhiX control library (Illumina) added.  The resulting pool is then loaded into the appropriate NovaSeq Reagent cartridge (Illumina), as determined by the number of sequencing cycles desired, and sequenced on a NovaSeq6000 instrument (Illumina) following the manufacturer’s recommended protocol.

treatment_protocol: 4T1-tetL1(GLucAI) cells were either untreated or exposed to 400ng/mL doxycycline (Doxy)  for 48h. See also Materials and Methods section of Novototskaya-Valsova et al., PNAS 2022.

tag: cell line

value: Breast carcinoma-derived cells

value: Transduced with DOX-inducible LINE-1 retrotransposition reporter cassette

value: Doxycycline


title: Sample_10006600443744

value: FalsePos


title: Bone marrow-derived monocytes from healthy mice replicate 4 [RNA-seq]

tag: batch

value: batch 1


title: Bone marrow-derived monocytes from healthy mice replicate 5 [RNA-seq]


title: 4T1 cells, Doxycycline-treated, rep2


title: 4T1 cells, Doxycycline-treated, rep1


title: Sample_10006600443632

value: Male

value: Late

value: SCLC

value: Current

tag: survival


title: tumor, primary untreated,  rep3

value: tumor

value: FVB/N-TgN (MMTV-HER2/neu) 202Mul/J

value: Wild type

tag: treatment

value: untreated


title: Sample_10006600443408

value: Female

value: Middle

value: Other

value: Former


title: 4T1 cells, untreated, rep3.

source_name: 4T1-tetL1(GLucAI) cells

tag: cell type

value: Breast carcinoma-derived cells

value: Vehicle


title: Tumor-associated macophages replicate 1 [RNA-seq]

value: BALB/c

value: Breast cancer

value: Tumor-associated macrophages

value: Orthotopic injection of 4T1-luc cells into the mammary fat pad

value: 8 weeks


title: Bone marrow-derived monocytes from healthy mice replicate 8 [RNA-seq]

value: Bone marrow

value: Bone marrow-derived monocytes

value: CD11b+ Gr+ F4/80low

value: 12 weeks

value: batch 2


title: FBS_P1_2_1090

value: Mesenchymal stromal cells

value: HPL


title: Sample_10006600442733

tag: lane

value: Male

value: Late

value: SCLC

value: Current


title: Bone marrow-derived monocytes from healthy mice replicate 2 [RNA-seq]

value: batch 1


title: Bone marrow-derived monocytes from healthy mice replicate 1 [RNA-seq]

value: BALB/c


title: Sample_10006600442621

tag: histology

value: AD

value: Former


title: Bone marrow-derived monocytes from tumor-bearing mice replicate 4 [RNA-seq]

source_name: Bone marrow of tumor bearing mice

tag: tissue

value: Orthotopic injection of 4T1-luc cells into the mammary fat pad


title: Sample_10006600442509


title: Bone marrow-derived monocytes from healthy mice replicate 3 [RNA-seq]


title: Patient_21, Serum, Healthy

extract_protocol: Protein extracted from serum in accordance with SomaLogic standard operating procedures and best practices.

tag: patient label

tag: disease state

value: Healthy

value: M

tag: age


title: Bone marrow-derived monocytes from tumor-bearing mice replicate 3 [RNA-seq]

value: Bone marrow

value: Bone marrow-derived monocytes

value: 8 weeks


title: Sample_10006600442384

tag: Sex

value: FalsePos

tag: agescaled

tag: smokingstatus


title: 4T1R2 cells, DMAG-treated, rep2

source_name: 17-DMAG-resistant selected cell population 4T1R2 treated for 48h with 1.5 μM 17-DMAG

treatment_protocol: 4T1 cells resistant to 17-DMAG were generated by passing 4T1 cells through three rounds of exposure to 1.5 μM 17-DMAG for 48h and two populations (4T1R1 and 4T1R2) were used for further experiments. Before RNA extraction, 4T1, 4T1R1, 4T1R2 cells were either untreated or exposed to 1.5 μM 17-DMAG for 48h. See also Materials and Methods section of Novototskaya-Valsova et al., PNAS 2022.

value: Breast carcinoma-derived cells

tag: genotype

value: Wild type


title: 4T1 cells, untreated, rep2.

value: Transduced with DOX-inducible LINE-1 retrotransposition reporter cassette

value: Vehicle


title: Bone marrow-derived monocytes from tumor-bearing mice replicate 2 [RNA-seq]

tag: selection marker

value: CD11b+ Gr+ F4/80low

tag: mouse age


title: 4T1 cells, untreated, rep1.

tag: strain

tag: cell line


title: Sample_10006600442272

value: Female

value: Late

tag: survival


title: Bone marrow-derived monocytes from tumor-bearing mice replicate 1 [RNA-seq]

value: BALB/c

tag: treatment

tag: batch

value: batch 1


title: Sample_10006600442048

tag: lane

value: Male

value: Early

value: AD

value: Never


title: 4T1R2 cells, DMAG-treated, rep3

tag: cell type


title: 4T1 cells, DMAG-treated, rep3

source_name: control/parental cell population 4T1 treated for 48h with 1.5 μM 17-DMAG


title: Sample_10006600441610

tag: histology

value: SQ

value: Current


title: 4T1R2 cells, DMAG-treated, rep1


title: 4T1 cells, DMAG-treated, rep2


title: PGF2a (PGF) I.M., in vivo, 12 hr, ovaryectomy [12H-7475]

city: Omaha

first: John S

last: Davis

state: NE

address: 983255 Nebraska Medical Cente

department: Departments of Obstetrics and Gynecology and Biochemistry and Molecular Biology

institute: University of Nebraska Medical Center

data_processing:
The original fastq format reads were trimmed by fqtirm tool to remove adapters, terminal unknown bases (Ns) and low quality 3’ regions (Phred score < 30)
The reads were mapped to ARS-UCD1.2 cow reference genome using Star 2.5 and the transripts were quanified using strand specific protocol in RSEM 1.3.
Assembly: ARS-UCD1.2
Supplementary files format and content: tab-delimited text files include expected_count,TPM, FPKM values for each Sample.

organism: Bos taurus

source_name: corpus luteum

growth_protocol: Estrous cycles of cows were synchonized to provide cows at mid luteal phase (day 10)

extract_protocol: Trizol

treatment_protocol: Saline or luteolytic dose of PGF2a was injected i.m.

tag: tissue

value: corpus luteum

tag: time point

value: Day 10 luteal phase

value: mixed breed

value: PGF, I.M., 12 hr


title: Sample_10006600441485


title: PGF2a (PGF) I.M., in vivo, 12 hr, ovaryectomy [12H-7382]


title: 4T1 cells, DMAG-treated, rep1

value: Breast carcinoma-derived cells

value: Wild type


title: PGF2a (PGF) I.M., in vivo, 12 hr, ovaryectomy [12H-6314]


title: Sample_10006600441373


title: PGF2a (PGF) I.M., in vivo, 12 hr, ovaryectomy [12H-5266]


title: 4T1R2 cells, untreated, rep3

source_name: 17-DMAG-resistant selected cell population 4T1R2

value: untreated


title: Sample_10006600440698

value: Other

value: Former


title: 4T1R2 cells, untreated, rep2


title: PGF2a (PGF) I.M., in vivo, 4 hr, ovaryectomy [4H-6456]

value: PGF, I.M., 4 hr


title: Sample_10006600440474

value: Female

value: Middle


title: 4T1R2 cells, untreated, rep1


title: A389

source_name: CNS tumor

value: male

tag: age

tag: location

tag: tumor subgroup


title: A118

tag: Sex

value: female

value: hemispheric


title: Sample_10006600439925

value: Late

value: AD

tag: agescaled

tag: smokingstatus


title: PGF2a (PGF) I.M., in vivo, 4 hr, ovaryectomy [4H-6455]

value: corpus luteum

tag: genotype


title: PGF2a (PGF) I.M., in vivo, 4 hr, ovaryectomy [4H-5341]

value: Day 10 luteal phase


title: 4T1 cells, untreated, rep3

source_name: control/parental cell population 4T1

tag: strain


title: Sample_10006600439701

value: Male

value: FalsePos


title: 4T1 cells, untreated, rep2

tag: cell line

value: Breast carcinoma-derived cells


title: Sample_10006600439576

value: SQ

tag: survival


title: 4T1 cells, untreated, rep1

value: Wild type

tag: treatment

value: untreated


title: A386

value: no PLAGL1/2 amplification


title: A104

value: cerebellum


title: Sample_10006600439352

value: Other

value: Current


title: A379

value: male


title: Control, saline injection, in vivo, ovaryectomy [C-7514]

value: mixed breed

value: saline


title: A136

value: hemispheric


title: A381

value: infratentorial, midline


title: Control, saline injection, in vivo, ovaryectomy [C-6464]

value: corpus luteum


title: PGF2a (PGF) I.M., in vivo, 4 hr, ovaryectomy [4H-4291]

value: Day 10 luteal phase

value: PGF, I.M., 4 hr


title: Control, saline injection, in vivo, ovaryectomy [C-7367]


title: Sample_10006600438914

value: Male

value: FalsePos


title: 4T1R1 cells, DMAG-treated, rep1

source_name: 17-DMAG-resistant selected cell population 4T1R1 treated for 48h with 1.5 μM 17-DMAG

value: Breast carcinoma-derived cells


title: Control, saline injection, in vivo, ovaryectomy [C-4285]


title: 4T1R1 cells, DMAG-treated, rep3

value: Wild type


title: Sample_10006600438789

value: Late

value: AD


title: Sample_10006600439128

value: Former


title: A141


title: Mouse lung, infected, P. aeruginosa mPA08-31, rep4

city: Birmingham

first: Melissa

middle: Skye

last: McDaniel

state: AL

address: 845 19th St S BBRB 744

department: Microbiology

institute: University of Alabama at Birmingham

data_processing:
Raw reads were trimmed using Trim Galore! (v. 0.4.4) and Cutadapt (v. 1.9.1) and were evaluated for quality with FastQC
Reads were aligned to the published genome of S. maltophilia K279a or the Mus musculus genome build GRCm39/mm39 using the STAR aligner (v. 2.7.3a)
Read counts were obtained via Subread FeatureCounts
Differential expression analysis was performed with DESeq2
Assembly: GRCm39/mm39
Supplementary files format and content: tab-delimited text files include gene counts from FeatureCounts and differential expression values as calculated using DESeq2

source_name: Lung

extract_protocol:
For RNA isolation from the lung, BALB/cJ mice (8-10 weeks old) were obtained from Jackson laboratories (Bar Harbor, ME).  Mice were anesthetized with isoflurane and intratracheally infected with either S. maltophilia, P. aeruginosa, or both (~107 CFU each in 100 µL PBS). Mice were euthanized 24 hours post-infection, and lungs were inflated with RNA-later to preserve RNA integrity. Whole lungs were homogenized, and cells were lysed by bead beating (0.1 mm silica) in Trizol reagent (Invitrogen), and a full lung RNA extraction was performing using a standard protocol (50). Extracted RNA samples were sent to GENEWIZ (South Plainfield, NJ) for DNase treatment, host and bacterial rRNA depletion (Ribo-Zero Gold rRNA Removal Kit (Epidemiology), Illumina), and library preparation using standard protocols. For bacterial RNA-seq, single-end directional samples were DNase treated (DNase I, NEB) using a standard protocol, before being run through a second Trizol extraction to purify the sample of enzyme.
Sequencing libraries were constructed using the directional RNA Library Prep Kit (NEB) and tagged for multiplexing via the NE Next Multiplex Oligos for Illumina (NEB).
For in vivo bacterial samples, a pathogen-specific probe list for S. maltophilia was generated using previously published methods (28). Briefly, 100 bp probes were generated to cover annotated coding sequences of S. maltophilia, with 15 bp spacer sequences added on either end to allow for amplification of the probe library.   5’ SPACER : ATCGCACCAGCGTGT  3’ SPACER: CACTGCGGCTCCTCA  Probes completely covered the sense strand of each gene and were also generated to tile every other 100 bp of the antisense strand for a total of 68,704 probe sequences Figure S1). Probes with significant homology to the mouse genome or to bacterial non-coding RNAs (P <0.05 with BLAST analysis) were manually removed from the list. The resulting oligo pool was synthesized by Genscript (Piscataway, NJ). Before hybridization, DNA oligos were amplified and then transcribed (MEGAshortscript T7 Transcription Kit, Ambion), with added biotin-16-UTP (Roche) to generate biotinylated RNA probes.   Prepared cDNA libraries were hybridized to the generated pathogen-specific RNA probes using previously described methods (28) with a few modifications. Briefly, the synthesized probes and the prepared cDNA library were incubated in hybridization buffer for 24 hours at 68°C. Blocking primers were modified for compatibility with NEB multiplexing primers and a 3’ ddc’ modification was added to maintain barcoding.   Hybridization primer FWD:   AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT/3ddC/  Hybridization primer REV:  CAAGCAGAAGACGGCATACGAGATNNNNNNNNGTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT/3ddC/  Hybridized cDNA was isolated via streptavidin beads and then eluted. Enriched samples were amplified using universal primers that maintained sample barcoding before sequencing.

value: Lung

value: WT

value: P. aeruginosa mPA08-31


title: Mouse lung, infected, P. aeruginosa mPA08-31, rep5


title: Sample_10006600438565

value: SQ


title: A112

value: female

value: ventricles


title: 4T1R1 cells, untreated, rep3

source_name: 17-DMAG-resistant selected cell population 4T1R1

value: untreated


title: Sample_10006600438341

value: Female

value: Current


title: A109

value: male

value: supratentorial, midline


title: A140


title: Mouse lung, infected, P. aeruginosa mPA08-31, rep2


title: A110

value: cerebellum


title: 4T1R1 cells, untreated, rep1

value: Breast carcinoma-derived cells


title: Mouse lung, infected, P. aeruginosa mPA08-31, rep1


title: 330156 control_normal gland

city: Frederick

first: Ludmila

last: Szabova

state: MD

address: 1050 Boyles Street

department: CAPR

institute: Frederick National Laboratory for Cancer Research

data_processing:
18 mRNA-Seq samples were pooled and sequenced on NovaSeq 6000 SP using Illumina Stranded mRNA Prep and paired-end sequencing. The sequencing quality of the reads was assessed per sample using FastQC (version 0.11.5), Preseq (version 2.0.3), Picard tools (version 1.119) and RSeQC (version 2.6.4). Sequencing reads were trimmed of low-quality bases and adapter sequences were removed using Cutadapt (version 1.18). The trimmed reads were aligned using the GRCh38 (GENCODE hg38, version 30). Gene expression levels are quantified using RSEM (version 1.3.0 DEseq2 (version 1.28.1). Raw read counts (expected counts from RSEM) were imported into the NIH Integrated Data Analysis Platform for downstream analysis (https://nidap.nih.gov/).
Assembly: Mouse_mm10
Supplementary files format and content: tab-delimited text files include RPM values for each Sample

source_name: normal mammary glalnd

growth_protocol: mouse mammary tumors developed in vivo

extract_protocol: total RNA extracted with RNAeasy tissue Qiagen kit

value: normal mammary glalnd

value: wild type


title: Sample_10006600437778

value: Middle


title: A390


title: A380


title: Breast Cancer BC2232

type: RNA

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

institute: Toray Industries, Inc.

hyb_protocol: Hybridized for 16 h at 32 ºC with rotary shaker (250 rpm). Hybridization buffer and washing protocol was attached in the 3D-Gene® miRNA oligo chip kit.

scan_protocol: 3D-Gene® Scanner (Toray Industries, Inc.) was used for scanning. Images were quantified using Extraction version 2.0.0.6 (Toray Industries, Inc.).

data_processing: The presence of miRNA was determined based on a corresponding microarray signal of greater than [the mean + 2 × standard deviation] of the negative controls signal, of which the top and bottom ranked ones by signal intensity were removed. Once a miRNA was considered present, the mean signal of the negative controls of which the top and bottom 5% ranked by signal intensity were removed was subtracted from the miRNA signal. When the signal value was negative (or undetEsophageal Cancerted) after background subtraction, the value was replaced by 0.1 on a base 2 logarithm scale.

label_protocol: miRNA was labeled using 3D-Gene® miRNA Labeling kit in accordance with the manufacturer's instructions.

extract_protocol: Total RNA was extracted each from 300uL serum samples using 3D-Gene® RNA extraction reagent from liquid sample kit (Toray Industries, Inc.).

tag: er (allread)

tag: pgr (allread)

tag: response

value: PR


title: 4T1R1 cells, untreated, rep2

tag: cell type

value: Wild type


title: Mouse lung, infected, Dual species, rep5

tag: tissue

value: Lung

value: WT

value: S. maltophilia K279a, P. aeruginosa mPA08-31


title: Sample_10006600438117

tag: lane

value: Late

tag: histology

value: Other

value: Former


title: Sample_10006600435980

value: Female

value: Early

value: AD


title: A388

value: female

tag: age

tag: location

value: hemispheric


title: Breast Cancer BC2234

tag: Sex

value: CR


title: A387

tag: tumor subgroup


title: Breast Cancer BC2231


title: Mouse lung, infected, P. aeruginosa mPA08-31, rep3

value: P. aeruginosa mPA08-31


title: Breast Cancer BC2233


title: A105

value: male

value: cerebellum


title: A108


title: Sample_10006600433497

value: Male

tag: agescaled

tag: smokingstatus


title: 330154 control_normal gland

value: normal mammary glalnd

tag: strain

tag: genotype

value: wild type


title: 290845 tumor: Rbf, p53

source_name: mammary tumor

value: mammary tumor


title: 287822 tumor: Rbf, p53


title: Sample_10006600432947

source_name: Serum

value: FalsePos

value: Current

tag: survival


title: Mouse lung, infected, Dual species, rep3

value: Lung

value: WT

tag: treatment

value: S. maltophilia K279a, P. aeruginosa mPA08-31


title: Sample_10006600432723

value: Late

value: SQ

value: Former


title: Breast Cancer BC2229

value: female

tag: er (allread)


title: 290860 tumor: Rbf, p53


title: Breast Cancer BC2230

tag: pgr (allread)

value: SD


title: Sample_10006600432374

value: Middle

value: SCLC


title: 287845 tumor: Rbf, p53


title: Breast Cancer BC2228

tag: response

value: PR


title: Mouse lung, infected, Dual species, rep1


title: 287842 tumor: Rbf, p53


title: A117

value: male

value: brainstem


title: Mouse lung, infected, Dual species, rep2


title: 248662 tumor: Brca1, p53


title: Breast Cancer BC2235


title: A103

value: cerebellum


title: Mouse lung, infected, S. maltophilia K279a, rep4

value: S. maltophilia K279a


title: 4T1R1 cells, DMAG-treated, rep2

tag: cell line

tag: cell type

value: Breast carcinoma-derived cells

value: Wild type


title: Breast Cancer BC2227


title: Breast Cancer BC2226


title: Sample_10006600431712

tag: lane

value: Female

value: AD


title: Mouse lung, infected, S. maltophilia K279a, rep3

tag: tissue

value: Lung

value: WT


title: Breast Cancer BC2225

tag: age


title: A115

tag: location


title: Mouse lung, infected, S. maltophilia K279a, rep5


title: 255232 tumor: Brca1, p53

value: mammary tumor

tag: Sex


title: Sample_10006600431936

value: Male

value: FalsePos

tag: histology

value: Never


title: Mouse lung, infected, S. maltophilia K279a, rep2


title: Breast Cancer BC2224

value: female

value: CR


title: Sample_10006600431475

value: Middle

value: SQ

tag: agescaled

value: Former


title: Breast Cancer BC2223

value: PR


title: Mouse lung, infected, S. maltophilia K279a, rep1

value: S. maltophilia K279a


title: 225070 tumor: Brca1, p53


title: 246361 tumor: Brca1, p53


title: Sample_10006600431251

tag: smokingstatus


title: HSCs, Per2_KO

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

description: Per2-deficient mouse

data_processing:
Image processing, base calling, quality scoring (Phred), and sample demultiplexing were executed by HiSeq Control Software with Real Time Analysis (HCS 1.5/RTA 1.13) and CASAVA 1.8 software (Illumina; San Diego, CA).
RNA-Seq sequence reads (FASTQ format) were aligned to the reference mousenome assembly (Dec. 2011, GRCm38/mm10) using TopHat software, which performs splice junction mapping after read alignment with Bowtie2. Gene- and transcript-level expression were comprehensively quantified with Cufflinks software, which performed 1) transcript assembly, 2) identification of splice variants, and 3) quantification of normalized expression as FPKM (fragments per kilobase of transcript per million mapped reads) values.
Processed data are Cufflinks output files and contain Gene_Symbol, FPKM values, and FPKM status.
Genome_build: Dec. 2011, GRCm38/mm10
Supplementary_files_format_and_content: Tab-delimited text files include Gene Symbol, FPKM values, and FPKM status for each transcript and were prepared from the Cufflinks gene-level output files.

source_name: Bone marrow hematopoietic stem cells (HSCs)

growth_protocol: Both Per2def and Per2wt mice were housed 5 mice per cage at an ambient temperature of 22 ± 2°C and provided regular chow and filtered tap water ad libitum. Before each experiment, both mice were maintained under a 12:12 light/dark cycle for at least 2 weeks.

extract_protocol:
Total cellular RNA was isolated using the TRIzol reagent (Life Technologies) and a modified protocol that incorporates an additional extraction with phenol/chloroform/isoamyl alcohol (25:24:1, pH 4.3).
Indexed RNA-seq libraries were prepared using the NEBNext Ultra Directional RNA Library Prep Kit (New England BioLabs, Ipswich, MA), according to the manufacturer’s standard protocol. Briefly, poly-adenylated mRNA was purified from total RNA (100 ng) and rRNA removed by binding to magnetic oligo(dT)25 beads, which was followed by RNA fragmentation. Double-stranded cDNA was then generated by random-primed first-strand synthesis and subsequent second strand synthesis in the presence of dUTP for strand marking. The double-stranded cDNA was then end repaired, 3’-dA tailed, and an Illumina-compatible NEBNext adaptor was ligated. Uridine excision was performed with the USER (Uracil-Specific Excision Reagent) enzyme, and the libraries were then indexed and enriched by high-fidelity PCR amplification (15 cycles) with Q5 High-Fidelity DNA Polymerase and NEBNext multiplex primers.

treatment_protocol: Mice were untreated prior to collection of bone marrow HMCs.

tag: strain

tag: mouse model

value: Per2def (C57BL/6)


title: Sample_10006600431027

value: Current

tag: survival


title: 225068 tumor: Brca1, p53

tag: genotype


title: Breast Cancer BC2221

tag: er (allread)

value: SD


title: 210906 tumor: Brca1, Rbf, p53


title: HSCs, Per2_WT

description: Per2 wild-type mouse

value: Bone marrow hematopoietic stem cells (HSCs)

value: Per2wt (C57BL/6)


title: Breast Cancer BC2222

tag: pgr (allread)


title: Sample_10006600430701

value: Late

value: SCLC


title: 209490 tumor: Brca1, Rbf, p53

value: mammary tumor


title: Sample_10006600430576

value: Male


title: 208863 tumor: Brca1, Rbf, p53


title: Breast Cancer BC2220

tag: response


title: Sample_10006600429454

value: Female


title: Sample_10006600432150

value: FalsePos


title: Sample_10006600430128


title: 208857 tumor: Brca1, Rbf, p53

value: female


title: Breast Cancer BC2219

value: CR


title: 208855 tumor: Brca1, Rbf, p53


title: Sample_10006600429230


title: Sample_10006600428891

value: Middle

value: AD


title: Sample_10006600428667

value: Former


title: HD_VglutCer_tot_R2

city: Linköping

first: Susanne

last: Bauer

address: BKV, Cellbiologi Pl 10

department: BKV

country: Sweden

institute: Linköpings universitet

data_processing:
RNAseq data was analyzed with nf-core/rnaseq 3.0 pipeline, using default parameters. STAR/Salmon were used for alignment and quantification
Assembly: Gencode M25 (GRCm38.p6)
Supplementary files format and content: raw transcript counts obtained from salmon are provided in raw_count.csv.

source_name: Cerebrum

extract_protocol:
Flash frozen brain hemispheres were homogenized and total RNA ("Input") was isolated from tissue homogenate using Trizol and purified using the Qiagen Rneasy Mini kit. For "RiboTag IP" samples, 12CA5 monoclonal anti-HA antibody (Roche) was coupled to protein G-coated dynabeads (Invitrogen) and incubated with tissue homogenate for 90 min to immunoprecipitate HA-tagged ribosomes and their attached mRNAs. Ribosome-bound mRNAs were isolated using Qiazol and purified using the Qiagen miRNeasy kit.
Libraries were prepared according to protovol using the Illumina TruSeq stranded mRNA kit

tag: source

value: mRNA from flash frozen brain tissue

value: HD

tag: celltype

tag: preparation

value: Input

value: Cerebrum


title: HD_VglutCer_tot_R3

tag: tissue


title: HD_VglutCer_tot_R1


title: Breast Cancer BC2217

tag: age

value: PR


title: Breast Cancer BC2216


title: Breast Cancer BC2215


title: E18.5 Organs of Corti, Sox2-Tbx2LOF vs control, rep 3

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried-out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Protocol V5.7’ (Agilent), except that 3000ng of each labelled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file: GE2_107_Sep09.xml.  Measurements of on-chip replicates (quadruplicates) were averaged using the geometric mean of ‘ProcessedSignal’ (PS) values to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:   normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed to 15. All of those normalized PS values that fell below this intensity border were substituted by the respective surrogate value of 15.

source_name: control 3

label_protocol: 1000ng of total RNA were used as input. Synthesis of Cy3- or Cy5-labeled cRNA was performed with the ‘Quick Amp Labeling kit, two color’ (#5190-0444, Agilent Technologies) according to the manufacturer’s recommendations, except for a twofold downscaling of all reaction volumes.

extract_protocol: Extraction of total RNA was performed using peqGOLD RNAPure (VWR Peqlab) according to the manufacturer’s recommendations.

treatment_protocol: To induce recombination, 4 mg of tamoxifen were orally applied to timed pregnant dams in a single pulse at E16.5. Organs of Corti (basal halves) were then mechanically dissected from E18.5 embryos.

value: NMRI

value: male

tag: developmental stage

value: Organ of Corti

source_name: Sox2-Tbx2LOF, 3


title: Breast Cancer BC2218

tag: Sex


title: E18.5 Organs of Corti, Sox2-Tbx2LOF vs control, rep 4

source_name: control 4

source_name: Sox2-Tbx2LOF, 4


title: E18.5 Organs of Corti, Sox2-Tbx2LOF vs control, rep 2

source_name: control 2

source_name: Sox2-Tbx2LOF, 2


title: Breast Cancer BC2213


title: Breast Cancer BC2214


title: Sample_10006600428219

extract_protocol:
Inclusion criteria were: (i) patients with suspected LC that will during routine examination have a biopsy or blood samples taken, (ii) patients with relapse of LC, (iii) patients aged 18 years or more, (iv) written informed consent, (v) sampling does not imply significant delay of treatment, and (vi) sampling does not imply a significantly increased risk compared to routine diagnostic sampling. The recruited participants included individuals that were symptomatic of lung cancer, but not all were diagnosed with a confirmed lung cancer diagnosis and for those that were confirmed, the study sample comprised patients of any histological subtype and stage. Symptomatic persons with a CT scan which indicated LC but who during diagnostic follow-up were not diagnosed with lung cancer are hereafter referred to as FalsePos (“false positives”). During diagnostic workup of patients with suspected LC, blood samples were collected together with phenotype data. None of the patients had started cancer treatment at the time of sampling. Phenotype data were collected from questionnaires and electronic health records from the hospital. Serum were collected and stored at -80°C.    The miRNeasy Serum/Plasma Kit (Cat No./ID: 217184, Qiagen, Hilden, Germany) in combination with an automated Qiacube system, was used to purify total RNA, including miRNA, from 100 µl serum.
For assessment of extracted RNA quality and relative size, selected samples were measured using the Agilent Eukaryote Total RNA Pico assay and an Agilent 2100 Bioanalyzer (Waldbronn, Germany). The sequencing libraries were prepared using extracted RNA samples eluted in 14 µl water, a pool of 10 synthetic calibrator RNAs, and the NEXTflex small RNA-seq kit v3 (Bioo Scientific, Austin, TX, USA). Double-stranded cDNA was prepared by PCR amplification (22 cycles) and fragments/libraries were run on Agilent 2100 Bioanalyzer (Agilent Technologies, Waldbronn, Germany) or LabChip GX DNA High Sensitivity (Perkin Elmer, Waltham, MA, US) for quality control and quantitation. Individual libraries were normalized to 10 nM and pooled. The library pool was purified with the QIAquick PCR Purification Kit (Qiagen AB, Sweden) according to instructions. Automated size selection was performed using the Blue Pippin (Sage Science, Beverly, MA, USA), with a range of 135 to 175 bp to select the ~152 bp fragments. Following size selection, the pool was evaluated on Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) using the High Sensitivity DNA kit. The pool of libraries was quantified with the KAPA Library Quantification Kit (Roche, Pleasanton, CA, USA). Quantitated libraries were further diluted and normalized to 2.4 nM before clustering on the cBot (Illumina, Inc., San Diego, CA, USA). Single read sequencing was performed for 51 cycles on a HiSeq4000 flowcell, according to the manufacturer's instructions (Illumina, Inc., San Diego, CA, USA). One in-house pooled reference sample consisting of plasma from ten random healthy individuals was included in each sample preparation batch.

tag: lane

value: Late

tag: histology


title: Breast Cancer BC2212


title: HD_VglutCer_re_R1

value: RiboTag IP


title: E18.5 Organs of Corti, Sox2-Tbx2LOF vs control, rep 1

source_name: control 1

source_name: Sox2-Tbx2LOF, 1


title: Sample_10006600428443

value: Male

tag: agescaled

tag: smokingstatus


title: Bud31

city: jinan

first: Junchao

last: Qin

address: 44 Wenhua Xi Road

country: China

institute: Shandong University

data_processing:
Sequenced reads were generated by base calling using the Illumina standard pipeline
Adaptor and low-quality bases were trimmed with Trimmomatictools(version:0.36)
the clean reads underwent rRNA deleting through RNAcentralto get effective reads
Genomic alignment (version from UCSC genome browser) was using Tophat(version:2.0.13)to get uniquely mapping reads
RIPseekre(version 1.18.0) was employed to perform peak calling,then Hommer(version:4.8) to annotate the peaks
Genome_build: mm10
Supplementary_files_format_and_content: Convert BCL files into recognizable sequence files

source_name: Mouse testicular germ cell

extract_protocol: Primary germ cells P14 mouse testis tissue through a two-step enzymatic digestion method

tag: strain

value: Testis

tag: treatment

value: Enzymatic digestion into single cells

value: post natal day 14


title: Sample_10006600429006

data_processing:
Sequence reads were demultiplexed and converted from BCL to fastq file format using bcl2fastq2 conversion software V2.20.0422 (Illumina, Inc. San Diego, CA, USA).
Adapters from the 3’end of the raw sequences were trimmed using cutadapt-1.2.1.
Trimmed sequence were collapsed into single unique reads along with their total read count using the fastx collapser tool (http://hannonlab.cshl.edu/fastx_toolkit/) and mapped to the human (hg38) genome and the known calibrator sequences using bowtie2, allowing for up to 10 alignments per read to account for reads from duplicated miRNA loci.
Reads overlapping with mature miRNA loci were identified using htseq-count from the HTseq python package. These reads were further filtered to identify those with perfect alignment to the genome, and the total read counts for mature miRNAs were then computed by summing the total read count per sequence (isomiR) overlapping each miRNA locus. Mature miRNAs were annotated using miRBase (Release 22).
The calibrator counts were used to compute normalization factors per sample (calcNormFactors from edgeR). MicroRNA read counts were then normalized by using the calibrator RNA normalization factors (norm.factors in DGEList from edgeR), followed by reads per million (RPM) normalization and log2 transformation (voom from limma). MicroRNAs with average RPM < 1 were excluded from further analyses.
Genome_build: GRCh38

value: Female

value: FalsePos

value: Current

tag: survival


title: E14.5 cochlear ducts, Sox2-Tbx2LOF vs control, rep 4

treatment_protocol: To induce recombination, 4 mg of tamoxifen were orally applied to timed pregnant dams in a single pulse at E12.5. Cochlear ducts were then mechanically dissected from E14.5 embryos.

tag: genotype

value: cochlear duct


title: Breast Cancer BC2210

value: female

tag: er (allread)

tag: pgr (allread)

value: SD


title: HD_VglutCer_R4

tag: source

value: mRNA from flash frozen brain tissue

value: HD

value: Cerebrum


title: Sample_10006600428094

value: Early

value: Other


title: HD_VglutCer_R5

tag: celltype


title: S. maltophilia K279a, dual species infection, rep3

organism: Stenotrophomonas maltophilia

value: Lung

value: WT

value: Dual-species murine pulmonary infection with P. aeruginosa


title: Input

value: Testis


title: HD_VglutCer_R3

tag: preparation

value: RiboTag IP


title: Sample_10006600427880

value: Late

value: Former


title: Sample_10006600427656

value: Female

value: FalsePos


title: HD_VglutCer_R2

tag: tissue


title: S. maltophilia K279a, dual species infection, rep2