title: Sample_27-474275_S51_L006

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

value: OA

value: GBM

tag: progressed tumor grade

value: IV

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNASET2HippocampusControl5000nucleiSakib_C2_L002

status: Public on Sep 30 2021

type: SRA

city: Göttingen

first: Andre

last: Fischer

state: NDS

address: Von-Siebold-Str. 3a

department: Epigenetics and Systems Medicine in Neurodegenerative Diseases

country: Germany

institute: DZNE Göttingen

description:
Sample Title format: sample_sequencing run_lane
Processed data file: RNASET2HippocampusControl5000nucleiSakib_processed_data_files.tar.gz

library_source: transcriptomic

data_processing:
Cellranger-4.0.0 mkfastq was used for adapter trimming and converting the base calls
Cellranger-4.0.0 counts was used to align the reads on the pre-mRNA and create the read count matrices
Genome_build: mm10
Supplementary_files_format_and_content: count matrices, barcode tables, feature tables (in a tar.gz archive)

molecule: total RNA

organism: Mus musculus

source_name: Hippocampus, tissue from adult mice brain

extract_protocol:
10X Chromium v3.1 kit (NextGEM) and 5000 nuclei out of 300000 sorted nuclei were barcoded
Mice were deeply anesthetized with ketamine and medetomidine and transcardially perfused with phosphate buffered saline (PBS, pH 7.4). After cervical dislocation, the whole brain was removed from the skull and the preparation of the hippocampus and caudate putamen was performed in a petri dish filled with ice cold PBS buffer under a binocular. Tissue sample from two hemispheres of different mice were pooled and immediately frozen on liquid nitrogen and stored at -80°C until further processing. Nuclei from frozen mouse brain tissues were isolated according to previously published protocol with modifications.65 Isolated total nuclei were stained with 7AAD (Invitrogen, Cat: 00-6993-50) and single nuclei were sorted using BD FACS Aria III sorter. Sorted nuclei were counted in Countess II FL Automated Counter.
Around 5000 single nuclei per sample were used for GEM generation, barcoding, and cDNA libraries according to 10X Chromium Next GEM Single Cell 3′ Reagent v3.1 protocol. Pooled libraries were sequenced in Illumina NextSeq 550 in order to achieve >50,000 reads/nuclei.
10X genomics single-cell seq

tag: strain

tag: genotype

value: WT

tag: age

tag: developmental stage

value: adult

value: Hippocampus


title: Sample_23-728542_S47_L005

city: Houston

first: Akdes

last: Serin Harmanci

state: TX

address: One Baylor Plaza

country: USA

institute: Baylor College of Medicine

data_processing:
Raw reads from the RNA-seq data were processed using an in-house pipeline that uses STAR for read alignment; FastQC and RSeQC (for read and alignment quality assessment) and FeatureCount for expression count. Samples with degraded RNA or unique mapping rates lower than 30% were excluded. The reads were aligned to GRCh38 Human reference genome and mapping to the human transcriptome according to UCSC gene annotations. We then normalized the RNA-seq read counts for genes, applied a variance stabilizing transformation, and identified differentially expressed genes using the DESeq2 package. Differential gene expression determined by a false discovery rate cutoff of 0.05.
Genome_build: hg38
Supplementary_files_format_and_content: raw counts

organism: Homo sapiens

source_name: Glioma

extract_protocol:
Total RNA was isolated from formalin-fixed, paraffin-embedded (FFPE) glioma tissue using MasterPure kit (Epicentre).
RNA libraries were prepared for sequencing using standard Illumina protocols.Paired-end RNA sequencing was performed.

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

value: HGG

value: Mutant

tag: gender

value: F

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

value: AA

value: III

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade


title: RNASET2HippocampusControl5000nucleiSakib_C2_L001


title: GC071392_AGCTAGAA-TAAGGCGA

city: Leuven

first: Vincent

last: Pasque

address: Herestraat 49 bus 804

department: Development and Regeneration

country: Belgium

institute: KU Leuven

description: smart-seq2 protocol

data_processing:
For non-allele resulotion analyses, reads were mapped to the mouse reference genome (mm10) using STAR 2.5.3a (Dobin et al. 2013) and GENCODE vM16 annotation file. Alignment was performed with default parameters and --sjdbOverhang set to 74 and output to sorted BAM files. Uniquely aligned reads were quantified using the featureCounts function from the R Bioconductor package “Rsubread” (version 1.5.2) (Liao et al. 2019).
For allele resolution analyses, reads processed as previously described in (Janiszewski, talon et al). Briefly, reads were mapped to the same reference genome release in which SNP positions were substituted by N base (referred to as N-masked mm10). N-masking was performed with SNPsplit software (Version 0.3.2 released (29-03-2017)) (Krueger and Andrews 2016) supplied with the list of strain-specific SNPs (129S1_SvImJ and CAST_EiJ) from Sanger Mouse Genomes project database (mgp.v5.merged.snps_all.dbSNP142.vcf.gz). N-masking was done in dual hybrid mode and resulted in the identification throughout the entire genome of 20,563,466 SNP positions unique for either strain, of which 634,730 on the X Chromosome. Next, reads were aligned to the N-masked mm10 genome using STAR 2.5.3a with parameters disabling soft-clipping of incompletely aligned reads (--alignEndsType EndToEnd --outSAMattributes NH HI NM MD). Reads aligned to the N-masked reference genome were then split into two BAM files containing only strain-specific reads (on average 10.95% for Mus and 10.25% for Cast of total mapped reads) using SNPsplit (version 0.3.4). Unclassified reads were not used for subsequent allele-specific analysis. Using the allelic BAM files, variant calling files (VCF) were generated using samtools’ mpilup command (version 1.7) (ref), and merged using bcftools (ref)(version 1.5). An allelic count matrix was created by retaining counts from SNP positions and annotating these positions with their respective genes, where only genes covered by 4 SNPs or more are kept. Allelic data was size factor normalised by dividing allele-specific gene counts by total counts of that cell, this was then multiplied by 10000 and log transformed.
Genome_build: mm10
Supplementary_files_format_and_content: smartseq_norm_counts.csv: text file containing normalized read counts
Supplementary_files_format_and_content: smartseq_annotation.xlsx: spreadsheet containing additional metadata information
Supplementary_files_format_and_content: loom_XCR_5runs.loom: loom file containing both expression and gene regulatory network data together with tSNE embeddings

molecule: polyA RNA

source_name: MEF to iPSC reprogramming timecourse

growth_protocol: MEFs were cultured in MEF medium [DMEM (Gibco, 41966-554 052) supplemented with 10% (v/v) fetal bovine serum (FBS, Gibco, 10270-106), 1% (v/v) penicillin/streptomycin (P/S, Gibco, 15140-122), 1% (v/v) GlutaMAX (Gibco, 35050-061), 1% (v/v) non-essential amino acids (NEAA, Gibco, 11140-050), and 0.008% (v/v) beta-mercaptoethanol (Sigma-Aldrich, M7522)].   Cells undergoing reprogramming, and iPSCs were cultured in mouse ESC medium [KnockOut DMEM (Gibco, 10829-018) supplemented with 15% FBS, 1% P/S 10,000 U/mL, 1% GlutaMAX 100×, 1% NEAA 100×, 0.008% (v/v) beta-mercaptoethanol, and mouse LIF] in the presence of ascorbic acid (50 μg/ml final).

extract_protocol:
For the isolation of Day 0 time point of single-cell transcriptome analysis, 96 Xi-GFP cells were sorted into a 96-well multiwell plate with 2 µl lysis buffer, followed by initial steps of smart-seq2 protocol (see below). Remaining cells were plated for reprogramming directly after sorting, 50.000 cells per one well of a 12 well plate. Reprogramming was induced by doxycycline (2 μg/ml final) in mouse ESC medium in the presence of ascorbic acid (50 μg/ml final). The medium together with doxycycline and ascorbic acid was replaced every two days and maintained throughout entire reprogramming experiments. To derive iPSCs from picked colonies, the same conditions were used with dox and AA withdrawal after picking. Next, FUT4+ reprogramming intermediates were sorted into single wells, each with 2 µl of the lysis buffer [0,2% Triton X100, 1:20 RRI (Recombinant RNase Inhibitor Takara)] and snap-frozen in -80°C until cells from all timepoints were collected.
All samples were processed following the smart-seq2 protocol (Picelli et al). cDNA synthesis was done starting from 500 pg of input RNA, followed by library preparation from 80 pg of cDNA using the Nextera XT kit (Illumina, FC-131-1096). Indexing was performed with the Nextera XT index Kit V2 (Illumina, FC-131-2003). The quality of cDNA and individual libraries was assessed using an Agilent 2100 Bioanalyzer system.

treatment_protocol: Reprogramming experiments, unless stated otherwise, were performed by conditional induction of lentivirally delivered reprogramming factors. First, passage 1 MEFs at around 70% confluency were transduced with concentrated lentiviral supernatants. Lentiviruses were generated using HEK cells separately for two constructs: tetO-FUW-OSKM, Addgene cat. 20321 (Carey et al. 2009) and FUW-M2rtTA, Addgene cat. 20342 (Hockemeyer et al. 2008) with the calcium precipitation method. Supernatants with lentiviral particles were concentrated using lenti-X-concentrator (Takara, 631231) in 1:100 ratios. Infection with a pool of equal volumes of both constructs was carried out overnight, followed by 12 hours culture in MEF medium and 1:6 split. Cells were then sorted using FACS (described below) in order to isolate homogeneous population with regard to allelic inactivation of the X-GFP transgene (either Xi-GFP or Xa-GFP).

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNA-SEQ_A10-171-3_15-008/030_buffy coat

city: Bethesda

first: Adam

middle: G.

last: Sowalsky

state: MD

address: 37 Convent Drive Building 37 Room 1062B

department: Genitourinary Malignancies Branch

institute: National Cancer Institute

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-3
processed_counts.txt
processed_TPM.txt

data_processing:
Base-calling was performed with CASAVA 1.9
FASTQ files were pre-processed to remove sequencing adaptors with Trimmomatic v0.36.
Paired-end trimmed FASTQ files were aligned to hg19 using STAR.
RSEM was used to estimate read counts for each genomic feature.
Genome_build: hg19
Supplementary_files_format_and_content: tab separated values, gene symbol, description, transcripts-per-million (TPM) or count

extract_protocol:
RNA was extracted from FFPE prostate tissues using the Qiagen RNeasy FFPE kit or from frozen buffy coats using the Macharay-Nagel NucleoSpin RNA Blood  kit.
Libraries were prepared with the NEBNext Globin and rRNA depletiion library construction kit and the Illumina TruSeq stranded total RNA with ribo-zero globin kit.

treatment_protocol: Patients with prostate cancer underwent radical prostatectomy with no prior therapy. Blood was drawn into EDTA tubes prior to surgery. Prostate tissues were grossed, accessioned, fixed in formalin, and embedded in paraffin.

tag: disease state

value: prostate cancer

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

value: buffy coat


title: RNA-SEQ_A10-183-6_15-008/030_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-6
processed_counts.txt
processed_TPM.txt

tag: gender

tag: age

tag: tissue

value: prostate tissue


title: GC071392_AGCTAGAA-GTAGAGGA

description: smart-seq2 protocol


title: Sample_21-473295_S45_L005

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_22-824338_S56_L006

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

value: LGG

value: WT

tag: age

tag: gender

tag: second progression date

tag: second progressed tumor pathology

value: GBM

tag: second progressed tumor grade

value: IV


title: RNASET2HippocampusControl5000nucleiSakib_C1_L004

tag: strain

tag: genotype

tag: developmental stage

value: adult

value: Hippocampus


title: GC071392_AGCTAGAA-GGAGCTAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_AGCTAGAA-GCTCATGA

description: smart-seq2 protocol


title: Sample_20-474126_S44_L005

tag: grade

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

value: F

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

value: AA

tag: progressed tumor grade

value: III

tag: percentage of total mapped reads


title: RNASET2HippocampusControl5000nucleiSakib_C1_L003

tag: strain

tag: genotype

tag: age

tag: tissue


title: RNASET2HippocampusControl5000nucleiSakib_C1_L002

tag: developmental stage


title: RNA-SEQ_A10-183-3_15-008/028_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-3
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: unknown

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: cancer


title: RNASET2PutamenKO5000nucleiSakib_K4_L004

description:
Sample Title format: sample_sequencing run_lane
Processed data file: RNASET2PutamenKO5000nucleiSakib_processed_data_files.tar.gz

source_name: Putamen, tissue from adult mice brain

value: RNT2AB KO

value: Putamen


title: RNA-SEQ_A10-183-5_15-008/029_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-5
processed_counts.txt
processed_TPM.txt

value: white

value: prostate tissue


title: GC071392_AGCTAGAA-GCGTAGTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-171-2_15-008/029_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-2
processed_counts.txt
processed_TPM.txt

value: normal

value: buffy coat


title: Sample_24-86073_S48_L005

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNASET2HippocampusControl5000nucleiSakib_C1_L001

tag: strain

tag: genotype

value: WT

tag: age

tag: developmental stage

value: adult

tag: tissue

value: Hippocampus


title: Sample_20-643629_S58_L007

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: gender

value: II

value: AA

value: III

tag: second progression date

tag: second progressed tumor pathology

value: GBM

tag: second progressed tumor grade

value: IV


title: Sample_2-490697_S43_L005

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: OA

tag: progression date

tag: progressed tumor pathology

value: AOA

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-183-2_15-008/028_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-2
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: unknown

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue

value: prostate tissue


title: RNA-SEQ_A10-171-1_15-008/028_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-171-1
processed_counts.txt
processed_TPM.txt

tag: gender

value: buffy coat


title: GC071392_AGCTAGAA-CGGAGCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNA-SEQ_A10-183-1_15-008/026_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-183-1
processed_counts.txt
processed_TPM.txt

value: white

value: cancer


title: GC071392_AGCTAGAA-GGACTCCT

description: smart-seq2 protocol


title: GC071392_AGCTAGAA-CTCTCTAC

description: smart-seq2 protocol


title: RNA-SEQ_A10-183-4_15-008/029_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-183-4
processed_counts.txt
processed_TPM.txt


title: Sample_2-663713_S26_L003

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: A

tag: percentage of total mapped reads


title: RNASET2PutamenKO5000nucleiSakib_K4_L003

tag: strain

tag: genotype

value: RNT2AB KO

tag: age

tag: developmental stage

value: adult

value: Putamen


title: RNA-SEQ_A10-182-39_15-008/026_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-39
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

tag: sample type

tag: tissue


title: GC071392_AGCTAGAA-CGATCAGT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNASET2PutamenKO5000nucleiSakib_K4_L001


title: RNASET2PutamenKO5000nucleiSakib_K4_L002


title: RNA-SEQ_A10-182-38_15-008/025_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-38
processed_counts.txt
processed_TPM.txt

value: remission


title: Sample_21-765076_S59_L007

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: WT

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

value: III

tag: initial tumor pathology

value: AA

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: second progression date

tag: second progressed tumor pathology

value: GBM

tag: second progressed tumor grade

value: IV

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_19-473907_S43_L005

tag: tissue

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: age

tag: gender

value: F


title: Sample_19-84436_S46_L005

value: LGG

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology


title: RNASET2PutamenKO5000nucleiSakib_K3_L004

tag: strain

tag: genotype

value: RNT2AB KO

tag: developmental stage


title: Sample_18-280601_S42_L005

tag: tissue

tag: unique sample id

tag: patient id

value: II

value: O

value: AO

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-182-36_15-008/023_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-36
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

value: cancer

value: prostate tissue


title: GC071392_AGCTAGAA-CGTACTAG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Sample_17-329452_S41_L005

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

value: GBM

tag: progressed tumor grade


title: RNASET2PutamenKO5000nucleiSakib_K3_L002

tag: strain

tag: genotype

tag: age

tag: developmental stage

value: adult

value: Putamen


title: RNA-SEQ_A10-182-37_15-008/025_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-37
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue


title: GC071392_AGCTAGAA-CCTAAGAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_18-276429_S44_L005

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: III

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

value: AOA

tag: progressed tumor grade

tag: second progression date

tag: second progressed tumor pathology

value: GBM (anaplastic mixed oligoastrocytoma grade IV)

tag: second progressed tumor grade

value: IV

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_AGCTAGAA-CGAGGCTG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-182-34_15-008/021_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-34
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: unknown

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

value: cancer

tag: tissue

value: prostate tissue


title: RNASET2PutamenKO5000nucleiSakib_K2_L003

tag: strain

tag: genotype

value: RNT2AB KO

tag: developmental stage

value: adult


title: Sample_15-51787_S62_L007

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

value: F

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: AA

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-182-35_15-008/023_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-35
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: normal

tag: tissue


title: RNA-SEQ_A10-182-33_15-008/021_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-33
processed_counts.txt
processed_TPM.txt


title: RNASET2PutamenKO5000nucleiSakib_K3_L003

tag: strain

tag: genotype

tag: developmental stage

value: Putamen


title: RNASET2PutamenKO5000nucleiSakib_K2_L002


title: GC071392_AGCTAGAA-ATGCGCAG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNA-SEQ_A10-182-32_15-008/020_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-32
processed_counts.txt
processed_TPM.txt


title: Sample_16-647051_S49_L005

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

value: III

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNASET2PutamenKO5000nucleiSakib_K2_L001

tag: strain

tag: genotype

tag: age

tag: developmental stage

tag: tissue


title: GC071392_AGCTAGAA-ACTCGCTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_14-474996_S48_L005

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

tag: diagnosis date

value: II

value: A


title: GC071392_AGCTAGAA-ATCTCAGG

description: smart-seq2 protocol


title: RNASET2PutamenKO5000nucleiSakib_K3_L001

tag: strain


title: Sample_13-480248_S37_L004

tag: patient initial tumor grade

tag: initial tumor pathology

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_AGCTAGAA-AGGCAGAA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_AGCTAGAA-AAGAGGCA

description: smart-seq2 protocol


title: GC071392_AGAGGATA-TCGACGTC

description: smart-seq2 protocol


title: Sample_13-474997_S55_L006

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: age

tag: date of birth


title: Sample_15-49530_S39_L004

tag: vital status

tag: death censoring

tag: gender

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

tag: progression date

value: GBM

value: IV


title: RNASET2PutamenKO5000nucleiSakib_K2_L004

tag: strain

tag: genotype

value: RNT2AB KO

tag: developmental stage

value: adult


title: GC071392_AGAGGATA-TAGGCATG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-182-28_15-008/018_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-28
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

tag: sample type

value: cancer

tag: tissue

value: prostate tissue


title: RNASET2PutamenKO5000nucleiSakib_K1_L004

tag: age

value: Putamen


title: Sample_12-780771_S36_L004

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

tag: gender

value: M

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

tag: progressed tumor pathology

value: AA

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-182-26_15-008/017_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-26
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

tag: tissue


title: GC071392_AGAGGATA-TCCTGAGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNASET2PutamenKO5000nucleiSakib_K1_L003

description:
Sample Title format: sample_sequencing run_lane
Processed data file: RNASET2PutamenKO5000nucleiSakib_processed_data_files.tar.gz

tag: strain

tag: genotype

tag: developmental stage


title: RNASET2PutamenControl5000nucleiSakib_C4_L003

description:
Sample Title format: sample_sequencing run_lane
Processed data file: RNASET2PutamenControl5000nucleiSakib_processed_data_files.tar.gz

value: WT


title: GC071392_AGAGGATA-TGCAGCTA

description: smart-seq2 protocol


title: RNA-SEQ_A10-182-29_15-008/019_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-29
processed_counts.txt
processed_TPM.txt

tag: gender

value: normal


title: Sample_11-493155_S35_L004

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

value: F

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: O

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNASET2PutamenControl5000nucleiSakib_C4_L002

tag: strain

tag: genotype

tag: age

tag: developmental stage

value: adult

tag: tissue


title: RNA-SEQ_A10-182-27_15-008/018_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-27
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

tag: sample type


title: GC071392_AGAGGATA-TACGCTGC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: Sample_17-276430_S51_L006

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

value: III

tag: initial tumor pathology

value: AO

tag: progression date

tag: progressed tumor pathology

value: AOA

tag: progressed tumor grade

tag: second progression date

tag: second progressed tumor pathology

value: GBM (anaplastic mixed oligoastrocytoma grade IV)

tag: second progressed tumor grade

value: IV

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: Sample_14-133900_S38_L004

tag: tissue

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: age

tag: gender

value: M

value: GBM


title: GC071392_AGAGGATA-TAAGGCGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: GC071392_AGCTAGAA-ACTGAGCG

description: smart-seq2 protocol


title: RNASET2PutamenKO5000nucleiSakib_K1_L002

tag: strain

tag: genotype

value: RNT2AB KO

tag: developmental stage

value: Putamen


title: RNASET2PutamenControl5000nucleiSakib_C3_L002

value: WT


title: GC071392_AGAGGATA-GGAGCTAC

description: smart-seq2 protocol


title: RNA-SEQ_A10-182-31_15-008/020_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-31
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

value: prostate tissue


title: GC071392_AGAGGATA-GGACTCCT

description: smart-seq2 protocol


title: RNASET2PutamenControl5000nucleiSakib_C3_L001

value: adult

tag: tissue


title: Sample_12-856277_S47_L005

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

value: F

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: OA

tag: progression date

tag: progressed tumor pathology

tag: progressed tumor grade

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-182-25_15-008/017_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-25
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

tag: tissue


title: RNA-SEQ_A10-182-21_15-008/014_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-21
processed_counts.txt
processed_TPM.txt


title: GC071392_AGAGGATA-TAGCGCTC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: Sample_10-840737_S57_L007

tag: unique sample id

tag: patient id

tag: grade

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: III

tag: initial tumor pathology

value: AA

tag: progression date

tag: progressed tumor pathology

value: AO

tag: progressed tumor grade

tag: second progression date

tag: second progressed tumor pathology

tag: second progressed tumor grade

tag: percentage of total mapped reads


title: RNA-SEQ_A10-182-30_15-008/019_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-30
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

value: remission

tag: sample type

value: cancer

tag: tissue


title: RNASET2PutamenControl5000nucleiSakib_C2_L004

tag: strain

tag: genotype

value: WT

tag: developmental stage

value: adult

value: Putamen


title: GC071392_AGAGGATA-GCTCATGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNASET2PutamenControl5000nucleiSakib_C4_L001


title: RNA-SEQ_A10-182-24_15-008/015_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-24
processed_counts.txt
processed_TPM.txt

value: recurrence

value: prostate tissue


title: RNA-SEQ_A10-182-23_15-008/015_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-23
processed_counts.txt
processed_TPM.txt

value: normal


title: RNASET2PutamenControl5000nucleiSakib_C4_L004


title: Sample_11-474221_S52_L006

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

value: F

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

value: OA

tag: progression date

tag: progressed tumor pathology

value: GBM

tag: progressed tumor grade

value: IV

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNA-SEQ_A10-172-4_15-008/015_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-172-4
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: age

tag: 5-year disease status

tag: sample type

tag: tissue

value: buffy coat


title: Sample_10-130792_S34_L004

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: A

tag: progression date

tag: progressed tumor pathology

value: AOA

value: III

tag: second progression date

tag: second progressed tumor pathology

value: AO

tag: second progressed tumor grade


title: RNASET2PutamenControl5000nucleiSakib_C3_L003

tag: strain

tag: genotype

value: WT

tag: age

tag: developmental stage

value: adult

tag: tissue

value: Putamen


title: GC071392_AGAGGATA-GTAGAGGA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: RNASET2PutamenControl5000nucleiSakib_C2_L003


title: GC071392_AGAGGATA-CTCTCTAC

description: smart-seq2 protocol


title: MH_S_Lcor_inf_1

city: Jena

first: Patricia

last: Sieber

address: Adolf-Reichwein-Straße 23

institute: HKI

description: NG-7587_MH_S_Lcor_inf_1_lib62845_3472_5_1

data_processing:
Read quality was checked using Fastqc. Trimming and Adapter clippling was applied using Trimmomatic-0.32 (parameters: windowsize=15, qualcut=25, phred="-phred33",leading=3,trailing=3,minlen=30,adapters=”adapters/TruSeq3-SE.fa”)
Trimmed reads were mapped to reference genome of Lichtheimia_corymbifera_v1.genome.fasta and of Mus_musculus.GRCm38.dna.primary_assembly using tophat2 with following parameters: -p 10 -g 1 --no-mixed --no-discordant --b2-very-sensitive --max-intron-length 100000 –no-coverage-search -o OUTDIR -G ANNOTATION INDEX FASTQFILE > OUTFILE
Mapped reads were counted using featureCounts version and DeSeq2 were used for differential expression filtering.
Genome_build: Lichtheimia corymbifera JMRC:FSU:09682 (NCBI WGS accession CBTN000000000); Mus_musculus.GRCm38.79 primaryAssembly
Supplementary_files_format_and_content: text files include counts for each gene per sample

organism:
Mus musculus
Lichtheimia corymbifera

growth_protocol: Spores from Lichtheimia corymbifera JMRC:SF:09682 harvested from cultures grown  in KK1 medium (Kraibooj et al. 2014) at 37 °C for 7 days. Murine alveolar MH-S macrophages (ATCC: CRL-2019) were cultivated in RPMI-1640 supplemented with 10% heat inactivated fetal bovine serum at 37 °C in 5 % CO2. Macrophages were seeded in 6 well plates at 10^6 cells per well to adhere overnight.

extract_protocol:
Fungal RNA was isolated using RiboPure Yeast Kit (Thermo Fisher) and macrophage RNA was isolated with the RNeasy Mini kit (Qiagen), according to the manufacturers’ instructions. The concentration and purity of RNA samples were assessed using a NanoDrop spectrophotometer and Agilent 2100 bioanalyzer. Pooling ratio: L. corymbifera : MH-S = 1 : 3.9
Random-primed cDNA library per samples, Isolation of poly(A)+ RNA mRNA-Fragmentation, Random-primed cDNA synthesis adapter-ligation and PCR amplification
Illumina HiSeq 2500, Sequence Mode: HSHOv4 SR50

treatment_protocol: Macrophages were infected with spores at a MOI (Multiplicity of Infection) of 5. After 3 hr of co-incubation with MH-S, extracellular spores were removed by at least 3 washing steps with pre-warmed RPMI-1640 (PAA Laboratories) and incubated for 13 hr in prior to the RNA extraction procedure. Controls in these experiments were fungus grown for 16 hours without macrophages and macrophages without fungal spores.

tag: genotype/variation

tag: cocultured with

value: murine alveolar macrophage cell line MH-S

tag: time point


title: MH_S_Lcor_inf_2

description: NG-7587_MH_S_Lcor_inf_2_lib62846_3505_7_1


title: RNASET2PutamenKO5000nucleiSakib_K1_L001

value: RNT2AB KO


title: RNA-SEQ_A10-182-19_15-008/013_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-19
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: normal

value: prostate tissue


title: RNASET2PutamenControl5000nucleiSakib_C3_L004

tag: strain

tag: genotype

tag: age


title: GC071392_AGAGGATA-CGTACTAG

description: smart-seq2 protocol

tag: timepoint


title: MH_S_Lcor_3


title: RNASET2PutamenControl5000nucleiSakib_C1_L004

tag: developmental stage

tag: tissue


title: MH_S_Lcor_2

tag: genotype/variation


title: GC071392_AGAGGATA-CGATCAGT

description: smart-seq2 protocol

tag: initially inactive x allele


title: MH_S_Lcor_inf_3

description: NG-7587_MH_S_Lcor_inf_3_lib62847_3472_5_1

tag: cocultured with

tag: time point


title: RNA-SEQ_A10-182-20_15-008/013_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-20
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

value: male

value: cancer


title: Sample_1-854739_S25_L003

value: Glioma

tag: unique sample id

tag: patient id

tag: grade

value: LGG

tag: batch

tag: idh status prediction

value: Mutant

tag: date of birth

tag: vital status

tag: death censoring

value: M

tag: diagnosis date

tag: patient initial tumor grade

value: II

tag: initial tumor pathology

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: GC071392_AGAGGATA-CGGAGCCT

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNASET2PutamenControl5000nucleiSakib_C2_L002

tag: strain

tag: genotype

value: WT

tag: age

tag: developmental stage

tag: tissue


title: RNA-SEQ_A10-182-14_15-008/009_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-14
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: 5-year disease status

tag: sample type


title: Sample_1-490698_S42_L005

tag: unique sample id

tag: patient id

tag: grade

value: HGG

tag: batch

tag: idh status prediction

tag: date of birth

tag: vital status

tag: death censoring

tag: diagnosis date

tag: patient initial tumor grade

tag: initial tumor pathology

value: OA

tag: progression date

tag: progressed tumor pathology

value: AOA

tag: progressed tumor grade

value: III

tag: percentage of total mapped reads

tag: percentage of uniquely mapped reads

tag: progress free survival (months)

tag: overall survival (months)


title: RNASET2PutamenControl5000nucleiSakib_C1_L001

tag: strain

tag: genotype

tag: age

tag: developmental stage

value: adult

tag: tissue

value: Putamen


title: RNA-SEQ_A10-182-22_15-008/014_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-22
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: patientid

tag: gender

tag: preoperative psa

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

value: remission

tag: sample type

value: prostate tissue


title: RNASET2PutamenControl5000nucleiSakib_C1_L003

description:
Sample Title format: sample_sequencing run_lane
Processed data file: RNASET2PutamenControl5000nucleiSakib_processed_data_files.tar.gz


title: GC071392_AGAGGATA-GCGTAGTA

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele

value: Mus


title: MH_S_Lcor_1

tag: genotype/variation

tag: time point


title: GC071392_AGAGGATA-ATCTCAGG

description: smart-seq2 protocol


title: grafted on S. lycopersicum var Emperador RNA-Seq rep1

city: Birmingham

first: Marco

last: Catoni

address: Edgbaston

department: School of Biosciences

country: United Kingdom

institute: University of Birmingham

library_source: genomic

data_processing:
Reads were mapped with TopHat (Trapnell et al., 2009) on the eggplant genome (Barchi et al., 2019), using parameters–max-multihits 1–read-realign-edit-dist 0–no-mixed.
Mapped reads were subsequently counted using htseq-count (Anders et al., 2015) with parameters–order name–type = exon–stranded = reverse. As most of plant genomes are composed of transposable elements and LTRs are the most abundant, we used the LTRpred R tool (https://github.com/HajkD/LTRpred) to generate a new retrotransposon annotation file which was used as input for htseq-count.
Differential expression was assessed with DEseq (Anders and Huber, 2010), using as thresholds 1 Log2 fold change and a Benjamini-Hochberg’s FDR < 0.05.
Genome_build: 67/3 genome assembly, available at http://www.eggplantgenome.org/
Supplementary_files_format_and_content: For each genotype, the bigwig coverage file is provided, generated with samtools depth (Li et al 2009, Bioinformatics) from the the aligned reads.

molecule: genomic DNA

organism: Solanum virginianum

source_name: scion leaves

growth_protocol: Grafted plants were grown in in the experimental greenhouse of Carmagnola, Italy (44°53′N; 7°41′E) during the 2017 eggplant growing season.

extract_protocol:
Total RNA was extracted using the Spectrum Plant Total RNA Kit (Sigma, Saint Loius, USA) method according to the manufacturer’s instructions.
Libraries for RNA expression analysis were prepared in duplicates from 2 µg of total RNA using the TrueSeq Stranded mRNA Sample Prep Kit (Illumina, San Diego, CA) following the manufacturer’s instructions. Libraries quality and fragment sizes were checked with a TapeStation 2200 (Agilent technologies, Santa Clara, CA) instrument.

treatment_protocol: Grafting was performed using the cleft methods (Lee et al., 1994, Gisbert et al., 2011)

tag: ecotype

value: Ecavi

value: leaves

value: 5 months

tag: rootstock

value: Solanum lycopersicum Var. Emperador RZ


title: DNA_oncoscan_prostatecancer_15-492/005

type: genomic

description: OncoScan CNV for prostate cancer sample from patient 15-492/005

hyb_protocol: Labeled libraries were hybridized to Affymetrix OncoScan CNV arrays according to the manufacturer's instructions.

scan_protocol: Arrays were scanned on an Affymetrix GeneChip Scanner according to the manufacturer's instructions.

data_processing:
CEL files were processed with the Affymetrix OncoScan console to generate OSCHP files. OSCHP files were processed with Biodiscovery Nexus Copy Number software using default settings for the OSCHP-TuScan algorithm.
Regions of LOH and/or copy number change were reported for each genomic interval, with a listing of gene symbols in each interval.

label: biotin

source_name: prostate cancer tissue

label_protocol: Libraries were labeled with biotin according to the manufacturer's instructions.

extract_protocol: Genomic DNA was purifed from ribbons of FFPE tissues using the QIAamp DNA FFPE Tissue Kit according to the manufacturer's instructions.

treatment_protocol: Patients with prostate cancer underwent radical prostatectomy with no prior therapy. Prostate tissues were grossed, accessioned, fixed in formalin, and embedded in paraffin.

value: male

tag: age

value: recurrence

value: prostate cancer tissue


title: RNASET2PutamenControl5000nucleiSakib_C1_L002

tag: strain

tag: genotype

value: WT

tag: developmental stage

tag: tissue


title: GC071392_AGAGGATA-CCTAAGAC

description: smart-seq2 protocol


title: RNA-SEQ_A10-182-18_15-008/012_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-18
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: patientid

tag: gender

tag: preoperative psa

value: unknown

value: cancer


title: RNA-SEQ_A10-182-12_15-008/008_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-12
processed_counts.txt
processed_TPM.txt

tag: gleason score

tag: race

value: white

tag: pathologic stage

tag: 5-year disease status


title: RNA-SEQ_A10-182-16_15-008/010_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-16
processed_counts.txt
processed_TPM.txt

tag: sample type


title: RNA-SEQ_A10-172-3_15-008/014_buffy coat

description:
Paired-end RNA-seq for buffy coat normal sample from patient A10-172-3
processed_counts.txt
processed_TPM.txt

value: normal

value: buffy coat


title: GC071392_AGAGGATA-ACTGAGCG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: RNA-SEQ_A10-182-11_15-008/008_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-11
processed_counts.txt
processed_TPM.txt

value: remission


title: DNA_oncoscan_prostatecancer_15-492/006

description: OncoScan CNV for prostate cancer sample from patient 15-492/006


title: DNA_oncoscan_prostatecancer_15-492/001

description: OncoScan CNV for prostate cancer sample from patient 15-492/001


title: RNA-SEQ_A10-182-9_15-008/007_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-9
processed_counts.txt
processed_TPM.txt

value: prostate tissue


title: grafted on S. lycopersicum var Emperador RNA-Seq rep2

tag: ecotype

tag: rootstock


title: GC071392_AGAGGATA-ATGCGCAG

description: smart-seq2 protocol

value: Mus


title: DNA_oncoscan_prostatecancer_15-492/002

description: OncoScan CNV for prostate cancer sample from patient 15-492/002

value: black

tag: age


title: DNA_oncoscan_prostatecancer_15-008/U47

description: OncoScan CNV for prostate cancer sample from patient 15-008/U47


title: RNA-SEQ_A10-182-17_15-008/012_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-17
processed_counts.txt
processed_TPM.txt


title: RNA-SEQ_A10-182-8_15-008/006_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-8
processed_counts.txt
processed_TPM.txt


title: DNA_oncoscan_prostatecancer_15-492/003

description: OncoScan CNV for prostate cancer sample from patient 15-492/003


title: GC071392_ACTCTAGG-TGCAGCTA

description: smart-seq2 protocol


title: RNA-SEQ_A10-182-7_15-008/006_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-7
processed_counts.txt
processed_TPM.txt


title: GC071392_AGAGGATA-CGAGGCTG

description: smart-seq2 protocol


title: self-grafted RNA-Seq rep1

description: self-grafted

value: Ecavi

value: leaves

value: Solanum melongena


title: grafted on S. torvum RNA-Seq rep1

description: grafted on S. torvum

value: 5 months

value: Solanum torvum


title: DNA_oncoscan_prostatecancer_15-492/004

description: OncoScan CNV for prostate cancer sample from patient 15-492/004

value: male

value: prostate cancer tissue


title: wild type RNA-Seq rep1

description: wild type

value: not grafted


title: RNA-SEQ_A10-182-15_15-008/010_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-15
processed_counts.txt
processed_TPM.txt

value: prostate cancer


title: self-grafted RNA-Seq rep2

description: self-grafted


title: RNA-SEQ_A10-182-6_15-008/005_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-6
processed_counts.txt
processed_TPM.txt

value: cancer


title: GC071392_AGAGGATA-ACTCGCTA

description: smart-seq2 protocol


title: RNA-SEQ_A10-182-5_15-008/005_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-5
processed_counts.txt
processed_TPM.txt

value: white


title: DNA_oncoscan_prostatecancer_15-008/U46

description: OncoScan CNV for prostate cancer sample from patient 15-008/U46


title: GC071392_AGAGGATA-AGGCAGAA

description: smart-seq2 protocol


title: GC071392_ACTCTAGG-TAGGCATG

description: smart-seq2 protocol


title: RNASET2PutamenControl5000nucleiSakib_C2_L001

description:
Sample Title format: sample_sequencing run_lane
Processed data file: RNASET2PutamenControl5000nucleiSakib_processed_data_files.tar.gz

tag: strain

tag: genotype

value: WT

value: adult

value: Putamen


title: grafted on S. lycopersicum var Emperador BS-Seq rep1

data_processing:
Whole genome bisulfite sequencing (WGBS) and RNA-seq raw reads were trimmed using Trimmomatic (Bolger et al., 2014) to remove adapter sequences
High-quality trimmed sequences (on average 90,7 % of raw reads) were aligned against the eggplant genome (Barchi et al., 2019) using Bismark (Krueger & Andrews, 2011). Duplicated reads were collapsed into one read.
Not repeated chloroplast sequences (mappability = 1) retrieved from Ding et al., 2016 were used to estimate the bisulfite conversion. The mappability was computed on eggplant genome, with the gem‐mappability tool from the Gem library (Derrien et al., 2012), with a k-mer size of 75 bp and allowing a maximum of one mismatch.
To account for non-converted DNA, we applied a correction according to (Catoni et al. 2017, EMBO Journal). Briefly, the number of methylated reads were decreased as: m*= max(0, m – nc) (where m* is the corrected number of methylated reads, m is the raw number of methylated reads, n is the total number of reads and c is the conversion rate).
Genome_build: 67/3 genome assembly, available at http://www.eggplantgenome.org/
Supplementary_files_format_and_content: For each genotype, the CX_Report generated by Bismark is reported (Krueger et al. 2011, Bioinformatics), after correction for non-converted DNA has been applied.

extract_protocol:
Genomic DNA was extracted using the Qiagen Plant DNeasy kit (Qiagen).
Libraries were constructed starting from 120 ng of genomic DNA bisulfite-converted using the EZ DNA Methylation-Gold Kit (Zymo Research, Irvine, CA). Converted samples were immediately used to prepare bisulfite libraries employing the TrueSeq DNA Methylation Kit (Illumina, San Diego, CA) accordingly to the protocol’s instruction

tag: tissue

value: Solanum lycopersicum Var. Emperador RZ


title: RNA-SEQ_A10-182-10_15-008/007_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-10
processed_counts.txt
processed_TPM.txt

tag: disease state

value: remission

value: prostate tissue


title: DNA_oncoscan_prostatecancer_15-008/U42

description: OncoScan CNV for prostate cancer sample from patient 15-008/U42

tag: patientid


title: DNA_oncoscan_prostatecancer_15-008/U41

description: OncoScan CNV for prostate cancer sample from patient 15-008/U41

tag: gender


title: DNA_oncoscan_prostatecancer_15-008/U44

description: OncoScan CNV for prostate cancer sample from patient 15-008/U44

tag: preoperative psa

value: unknown


title: GC071392_ACTCTAGG-TCGACGTC

description: smart-seq2 protocol

value: Mus


title: DNA_oncoscan_prostatecancer_15-008/U45

description: OncoScan CNV for prostate cancer sample from patient 15-008/U45

tag: gleason score


title: RNA-SEQ_A10-182-13_15-008/009_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-13
processed_counts.txt
processed_TPM.txt

tag: race

value: normal


title: GC071392_AGAGGATA-AAGAGGCA

description: smart-seq2 protocol


title: DNA_oncoscan_prostatecancer_15-008/U39

description: OncoScan CNV for prostate cancer sample from patient 15-008/U39

tag: pathologic stage


title: grafted on S. lycopersicum var Emperador BS-Seq rep2

value: Ecavi

value: leaves

value: 5 months


title: wild type RNA-Seq rep2

description: wild type


title: GC071392_ACTCTAGG-TCCTGAGC

description: smart-seq2 protocol


title: DNA_oncoscan_prostatecancer_15-008/U38

description: OncoScan CNV for prostate cancer sample from patient 15-008/U38

value: male

tag: 5-year disease status

value: prostate cancer tissue


title: GC071392_ACTCTAGG-GTAGAGGA

description: smart-seq2 protocol


title: RNA-SEQ_A12-2-1_15-008/003_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A12-2-1
processed_counts.txt
processed_TPM.txt

value: prostate cancer

tag: sample type


title: grafted on S. torvum RNA-Seq rep2

description: grafted on S. torvum

value: Solanum torvum


title: RNA-SEQ_A10-182-4_15-008/004_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-4
processed_counts.txt
processed_TPM.txt

value: white

value: cancer


title: grafted on S. torvum BS-Seq rep2

description: grafted on S. torvum


title: grafted on S. torvum BS-Seq rep1

description: grafted on S. torvum


title: self-grafted BS-Seq rep2

description: self-grafted

value: Solanum melongena


title: RNA-SEQ_A10-182-2_15-008/001_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A10-182-2
processed_counts.txt
processed_TPM.txt


title: GC071392_ACTCTAGG-TAGCGCTC

description: smart-seq2 protocol

tag: timepoint


title: self-grafted BS-Seq rep1

description: self-grafted


title: RNA-SEQ_A12-2-2_15-008/003_prostate tissue

description:
Paired-end RNA-seq for prostate tissue cancer sample from patient A12-2-2
processed_counts.txt
processed_TPM.txt


title: wild type BS-Seq rep2

description: wild type

value: not grafted


title: DNA_oncoscan_prostatecancer_15-008/U43

description: OncoScan CNV for prostate cancer sample from patient 15-008/U43

value: recurrence


title: GC071392_ACTCTAGG-GGACTCCT

description: smart-seq2 protocol

tag: initially inactive x allele


title: GC071392_ACTCTAGG-TACGCTGC

description: smart-seq2 protocol


title: DNA_oncoscan_prostatecancer_15-008/U40

description: OncoScan CNV for prostate cancer sample from patient 15-008/U40

value: remission


title: CD19+/CD20+ B cells 3, scRNA-seq

city: Stanford

first: Aaron

middle: M

last: Newman

state: CA

address: 265 Campus Drive

department: Department of Biomedical Data Science

institute: Stanford University

description: Sample was prepared using the Next GEM Single Cell 5’ kit v1.1, sequenced using NovaSeq, and aligned using Cell Ranger v5.0

data_processing:
The resulting scRNA-seq data were processed with CellRanger (version 2.1, 3.0, and 5.0, 10x Genomics) and mapped to the hg38 reference genome.
Seurat (versions 3.0 and 4.0) was used to process the cell types.
After pre-processing, cell types were annotated in all four samples together (B cells and non-B cell samples for DLBCL007 and DLBCL111), with a clustering resolution parameter of 1.2 and 20 PCA dimensions. This step was repeated for two additional DLBCL samples that were analyzed in a separate batch (DLBCL002 and DLBCL008). Canonical marker genes were used to annotate B cells (MS4A1 and CD79B) and T cells (CD3D and CD3E), with T cells further divided into CD8 T cells (CD8A, CD8B) and CD4 T cells (CD4). Among the latter, follicular helper T cells were defined as the cluster showing highest expression of CXCL13 and regulatory T cells by the highest expression of FOXP3. Myeloid cells were defined by high expression of CD14, FCER1A, and/or FCGR3A and NKs by high expression of GLNY and NKG7 but not CD3D/E. FL and tonsil specimens were analyzed for each sample individually and annotated using the same set of genes listed above.
Genome_build: hg38
Supplementary_files_format_and_content: Matrix with raw gene counts for every gene and every cell
Supplementary_files_format_and_content: Tab-delimited text file including the cell annotations

source_name: Diffuse large B cell lymphoma

extract_protocol:
Chromium Single Cell 5’ Library & Gel Bead Kit, Chromium Next GEM Single Cell 5’ Library & Gel Bead Kit v1.1, following manufacturer’s protocol
Chromium Single Cell 5’ Library Construction Kit following manufacturer’s protocol
Chromium Single Cell 5' Feature Barcode Library Kit, Chromium Single Cell A Chip Kit, Chromium i7 Multiplex Kit, following manufacturer's protocol

tag: patient

value: DLBCL

tag: cell type

value: B cells

tag: diagnosis

value: ABC DLBCL

tag: coo

value: ABC

tag: Sex

value: M


title: Viral genomic RNA sequencing of a recombinant virus: GFP-inserted WK-521with D614G/P681R

city: Minato-ku

first: Kei

last: Sato

state: Tokyo

address: 4-6-1 Shiroganedai

department: Department of Microbiology and Immunology

country: Japan

institute: The Institute of Medical Science, The University of Tokyo

data_processing:
Sequencing reads were trimmed using fastp (ver. 0.21.0).
Sequencing reads were mapped to the viral genome sequences of WK-521 strain or a GFP-inserted WK-521 using BWA-MEM (ver. 0.7.17).
Variant calling and filtering were performed using SAMtools (ver. 1.9).
Variant annotation was performed using snpEff (ver. 5.0e).
For clinical isolate viruses, only variants that are not present in the original isolates are reported.
Genome_build: WK-521 strain (EPI_ISL_408667)
Supplementary_files_format_and_content: Variant information  (tsv)

organism: Severe acute respiratory syndrome coronavirus 2

source_name: Viral genomic RNA of a recombinant virus: GFP-inserted WK-521with D614G/P681R

extract_protocol:
QIAamp viral RNA mini kit (Qiagen)
NEB Next Ultra RNA Library Prep Kit for Illumina (New England Biolabs)

tag: isolate

value: Viral genomic RNA of a recombinant virus:GFP-inserted WK-521with D614G/P681R


title: RNA-SEQ_A10-182-3_15-008/004_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-3
processed_counts.txt
processed_TPM.txt

tag: disease state

tag: age

value: normal

tag: tissue

value: prostate tissue


title: DNA_oncoscan_prostatecancer_15-008/U37

description: OncoScan CNV for prostate cancer sample from patient 15-008/U37

tag: patientid

tag: gender

value: male

tag: preoperative psa

value: unknown

value: prostate cancer tissue


title: wild type BS-Seq rep1

description: wild type

tag: ecotype

value: Ecavi

value: leaves

value: 5 months

tag: rootstock


title: Viral genomic RNA sequencing of a recombinant virus: GFP-inserted WK-521 with D614G

source_name: Viral genomic RNA of a recombinant virus: GFP-inserted WK-521 with D614G

value: Viral genomic RNA of a recombinant virus:GFP-inserted WK-521 with D614G


title: GC071392_ACTCTAGG-GGAGCTAC

description: smart-seq2 protocol

value: Mus


title: GC071392_ACTCTAGG-TAAGGCGA

description: smart-seq2 protocol


title: CD19-/CD20- non-B cells 1, scRNA-seq

value: non-B cells

value: F


title: GC071392_ACTCTAGG-GCGTAGTA

description: smart-seq2 protocol


title: DNA_oncoscan_prostatecancer_15-008/U33

description: OncoScan CNV for prostate cancer sample from patient 15-008/U33

tag: gleason score

tag: race

tag: pathologic stage

tag: 5-year disease status

value: remission


title: DNA_oncoscan_prostatecancer_15-008/U36

description: OncoScan CNV for prostate cancer sample from patient 15-008/U36

value: white


title: DNA_oncoscan_prostatecancer_15-008/U35

description: OncoScan CNV for prostate cancer sample from patient 15-008/U35


title: CD19-/CD20- non-B cells 3, scRNA-seq

tag: patient

value: DLBCL

tag: cell type

value: ABC DLBCL

value: ABC


title: DNA_oncoscan_prostatecancer_15-008/U34

description: OncoScan CNV for prostate cancer sample from patient 15-008/U34


title: GC071392_ACTCTAGG-CTCTCTAC

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_ACTCTAGG-GCTCATGA

description: smart-seq2 protocol


title: DNA_oncoscan_prostatecancer_15-008/U31

description: OncoScan CNV for prostate cancer sample from patient 15-008/U31


title: DNA_oncoscan_prostatecancer_15-008/U32

description: OncoScan CNV for prostate cancer sample from patient 15-008/U32


title: Viral genomic RNA sequencing of a D614G-bearing B.1.1 isolate

source_name: Viral genomic RNA of a D614G-bearing B.1.1 isolate

tag: isolate


title: Viral genomic RNA sequencing of a recombinant virus: WK-521 with D614G

source_name: Viral genomic RNA of a recombinant virus: WK-521 with D614G

value: Viral genomic RNA of a recombinant virus:WK-521 with D614G


title: Viral genomic RNA sequencing of a recombinant virus: WK-521with D614G/P681R

source_name: Viral genomic RNA of a recombinant virus: WK-521with D614G/P681R

value: Viral genomic RNA of a recombinant virus:WK-521with D614G/P681R


title: GC071392_ACTCTAGG-CCTAAGAC

description: smart-seq2 protocol


title: GC071392_ACTCTAGG-CGAGGCTG

description: smart-seq2 protocol


title: GC071392_ACTCTAGG-CGGAGCCT

description: smart-seq2 protocol


title: DNA_oncoscan_prostatecancer_15-008/U28

description: OncoScan CNV for prostate cancer sample from patient 15-008/U28

value: male

value: black

value: recurrence


title: Viral genomic RNA sequencing of a B.1.617.2/Delta isolate

source_name: Viral genomic RNA of a B.1.617.2/Delta isolate


title: CD19+/CD20+ B cells 1, scRNA-seq

value: B cells

tag: diagnosis

tag: coo

tag: Sex


title: GC071392_ACTCTAGG-ATCTCAGG

description: smart-seq2 protocol


title: DNA_oncoscan_prostatecancer_15-008/U27

description: OncoScan CNV for prostate cancer sample from patient 15-008/U27

tag: patientid

value: unknown

tag: age

tag: tissue

value: prostate cancer tissue


title: RNA-SEQ_A10-182-1_15-008/001_prostate tissue

description:
Paired-end RNA-seq for prostate tissue normal sample from patient A10-182-1
processed_counts.txt
processed_TPM.txt

tag: disease state

value: prostate cancer

tag: gender

tag: preoperative psa

tag: sample type

value: normal

value: prostate tissue


title: DNA_oncoscan_prostatecancer_15-008/U29

description: OncoScan CNV for prostate cancer sample from patient 15-008/U29

tag: gleason score

tag: race

tag: pathologic stage


title: GC071392_ACTCTAGG-AGGCAGAA

description: smart-seq2 protocol

value: Mus


title: GC071392_ACTCTAGG-CGATCAGT

description: smart-seq2 protocol


title: DNA_oncoscan_prostatecancer_15-008/U30

description: OncoScan CNV for prostate cancer sample from patient 15-008/U30

tag: 5-year disease status


title: H1.core.sham.rat.2

type: RNA

city: San Bartolomeo in Galdo

first: Antonio

last: Vinciguerra

state: Benevento

address: via Pasquale Circelli 130

country: Italy

institute: Università Politecnica delle Marche

hyb_protocol: Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://miRBase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate. The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry. The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 uL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.

scan_protocol: The hybridization melting temperatures were balanced by chemical modifications of the detection probes. Hybridization used 100 mL 6xSSPE buffer (0.90 M NaCl, 60 mM Na2HPO4, 6 mM EDTA, pH 6.8) containing 25% formamide at 34 °C.  After RNA hybridization, tag-conjugating Alexa Fluor®546 dye was circulated through the microfluidic chip for dye staining.  Fluorescence images were collected using a laser scanner (GenePix 4000B, Molecular Device) and digitized using Array-Pro image analysis software (Media Cybernetics).

data_processing: Data were analyzed by first subtracting the background and then normalizing the signals using a LOWESS filter (Locally-weighted Regression) (2). (2) Bolstad, B. M., Irizarry, R. A., Astrandand, M., Speed, T. P. (2003) A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinfo. 19, 185-193.

organism: Rattus rattus

label_protocol: Microarray assay was performed using a service provider (LC Sciences).  Total RNA sample (2 µg) were 3’-extended with a poly(A) tail using poly(A) polymerase.  An oligonucleotide tag was then ligated to the poly(A) tail for later fluorescent dye staining.  Hybridization was performed overnight on a µParaflo microfluidic chip using a micro-circulation pump (Atactic Technologies) (1). On the microfluidic chip, each detection probe consisted of a chemically modified nucleotide coding segment complementary to target microRNA (from miRBase, http://mirbase.org) or other RNA (control or customer defined sequences) and a spacer segment of polyethylene glycol to extend the coding segment away from the substrate.  The detection probes were made by in situ synthesis using PGR (photogenerated reagent) chemistry.  (1) (a) Gao, X., Gulari, E., and Zhou, X. (2004) In situ synthesis of oligonucleotide microarrays. Biopolymers 73, 579-596; (b) Zhu, Q., Hong, A., Sheng, N., Zhang, X., Jun, K.-Y., Srivannavit, O., Gulari, E., Gao, X., and Zhou, X. (2007) Microfluidic biochip for nucleic acid and protein analysis. in Methods Mol. Biol. Ed. Rampal, J. B. 382:287-312.

extract_protocol: Qiagen miRNeasy kit was used for total RNA extraction following manufacturer's protocol.

tag: strain background

value: Sprague Dawley

tag: sample group

value: controls (Sham)

value: temporo-parietal cortex


title: GC071392_ACTCTAGG-ACTGAGCG

description: smart-seq2 protocol

tag: timepoint

tag: initially inactive x allele


title: GC071392_ACTCTAGG-ATGCGCAG

description: smart-seq2 protocol


title: GC071392_ACTCTAGG-CGTACTAG

description: smart-seq2 protocol


title: DNA_oncoscan_prostatecancer_15-008/U24

description: OncoScan CNV for prostate cancer sample from patient 15-008/U24

value: white

value: remission


title: GC071392_ACTCTAGG-ACTCGCTA

description: smart-seq2 protocol


title: G2.peri.sham.rat.1

value: Striatum


title: DNA_oncoscan_prostatecancer_15-008/058

description: OncoScan CNV for prostate cancer sample from patient 15-008/058


title: ATAC_XCR_GFPneg_Day12

data_processing:
Paired-end ATAC-seq raw data were analyzed using the ATAC-seq pipeline from the Kundaje laboratory (v1.1.5) with default parameters as described previously (Lee, 2016). Reads were aligned to the ENCODE mouse reference genome GRCm38/mm10 (ENCSR425FOI). Differential chromatin accessibility analysis was performed using the DiffBind (v3.8) package after which quantification occurred using the DESEQ2 (v1.21.22) in R (Love et al., 2014). Counts were normalized by size-factor and log2 transformation.
Genome_build: mm10
Supplementary_files_format_and_content: normalized accessibility values in txt file

source_name: iPSC reprogramming intermediate

extract_protocol:
For the isolation of Day 0 time point of ATAC-seq analysis, 20,000 cells were sorted into a 1,5 ml centrifuge tube, followed by initial steps of Omni-ATAC-seq protocol. Remaining cells were plated for reprogramming directly after sorting, 50.000 cells per one well of a 12 well plate. Reprogramming was induced by doxycycline (2 μg/ml final) in mouse ESC medium in the presence of ascorbic acid (50 μg/ml final). The medium together with doxycycline and ascorbic acid was replaced every two days and maintained throughout entire reprogramming experiments. To derive iPSCs from picked colonies, the same conditions were used with dox and AA withdrawal after picking.
Assay for transposase accessible chromatin (ATAC) followed by sequencing was performed using the Omni-ATAC protocol (Corces et al., 2017). Briefly, 20,000 sorted Day 0 (Xi-GFP),  FUT4+/Xi-GFP Day 8, 9, 10, 12 reprogramming intermediates, and iPSC were pelleted at 500 RCF at 4°C for 5 min in a fixed-angle centrifuge, and then the cells were gently washed once with 50 µl of cold PBS. Next, the cell pellets were resuspended in 50 µl of ATAC-lysis buffer (10mM Tris HCl pH7.4, 10mM NaCl, 3mM MgCl2, 0.1% Tween-20, 0.1% NP40, and 0.01% Digitonin) and incubated on ice for 3 min. Wash out lysis with 1 ml of cold ATAC-lysis buffer containing 0.1% Tween-20 but No NP40 or digitonin and invert tube 3 times to mix. Nuclei were pelleted at 500 RCF for 10 min at 4°C in a fixed-angle centrifuge. After discarding all supernatant, nuclei were resuspended in 50 µl of transposition mixture (25 ul 2x TD buffer, 2.5 ul transposase (100 nM final), 16.5 ul PBS, 0.5 ul 1% digitonin, 0.5 ul 10% Tween-20, and 5 ul H2O) (Nextera DNA Sample Preparation Kit, Illumina, FC-121-1030). The reaction was performed at 37°C for 30 minutes in a thermomixer with 1000 RPM mixing. The transposed DNA was purified using a Zymo DNA Clean and Concentrator-5 Kit (D4014). DNA libraries were PCR amplified using NEBNext HighFidelity 2x PCR Master Mix (Bioke, M0541), and size selected for 200 to 800 bp using homemade Serapure beads (Rohland and Reich, 2012). Library concentrations were quantified with the KAPA Library Quantification Kit (KK4854), and equimolar amounts were pooled for paired-end sequencing on an Illumina NextSeq 500 instrument (Illumina) to yield ~100 million of 75 bp long reads per sample.

tag: cell type

value: iPSC reprogramming intermediate


title: L2.peri.sham.rat.3


title: DNA_oncoscan_prostatecancer_15-008/U26

description: OncoScan CNV for prostate cancer sample from patient 15-008/U26

value: male


title: ATAC_XCR_GFPneg_Day10


title: H2.peri.sham.rat.2


title: ATAC_XCR_GFPneg_Day9


title: GC071392_ACTCTAGG-AAGAGGCA

description: smart-seq2 protocol


title: DNA_oncoscan_prostatecancer_15-008/056

description: OncoScan CNV for prostate cancer sample from patient 15-008/056


title: F1.core.postC.rat.3

value: Remote limb postconditioning (PostC)


title: L1.core.sham.rat.3


title: DNA_oncoscan_prostatecancer_15-008/059

description: OncoScan CNV for prostate cancer sample from patient 15-008/059

value: black


title: DNA_oncoscan_prostatecancer_15-008/055

description: OncoScan CNV for prostate cancer sample from patient 15-008/055


title: E2.peri.postC.rat.2


title: D2.peri.postC.rat.1


title: ATAC_XCR_GFPneg_iPSC

source_name: iPSCs

value: iPSC

value: iPSCs


title: F2.peri.postC.rat.3


title: G1.core.sham.rat.1


title: DNA_oncoscan_prostatecancer_15-008/060

description: OncoScan CNV for prostate cancer sample from patient 15-008/060

value: prostate cancer tissue


title: DNA_oncoscan_prostatecancer_15-008/057

description: OncoScan CNV for prostate cancer sample from patient 15-008/057


title: DNA_oncoscan_prostatecancer_15-008/053

description: OncoScan CNV for prostate cancer sample from patient 15-008/053


title: DNA_oncoscan_prostatecancer_15-008/054

description: OncoScan CNV for prostate cancer sample from patient 15-008/054


title: DNA_oncoscan_prostatecancer_15-008/U25

description: OncoScan CNV for prostate cancer sample from patient 15-008/U25


title: D1.core.postC.rat.1


title: ATAC_XCR_GFPneg_Day8


title: DNA_oncoscan_prostatecancer_15-008/052

description: OncoScan CNV for prostate cancer sample from patient 15-008/052


title: C2.periischemic.rat.3

source_name: periischemic

value: transient middle cerebral artery occlusion (tMCAO)


title: ATAC_XCR_GFPneg_Day0

source_name: mouse embryonic fibroblasts

value: mouse embryonic fibroblasts


title: E1.core.postC.rat.2


title: MUSC-HN012-Post-Tumor

city: LOS ANGELES

first: Sixue

last: Liu

state: California

address: 10833 Le Conte Avenue

department: Medicine

institute: UCLA

data_processing:
The reads are first mapped to Grch37 using HISAT2
Gene level raw read counts are quantified using htseq-count
Ensemble ID to HUGO gene mapping using biomaRt R package
Using log2 counts per million (CPM) as normalized gene expression values
Genome_build: GRCh37
Supplementary_files_format_and_content: Gene level normalized expression matrix

source_name: Human OCSCC

extract_protocol:
QIAGEN All Prep DNA/RNA Mini Kit and Ambion mirVana miRNA Isolation Kit
NuGEN Universal Plus mRNA-Seq with NuQuant Library Preparation Kit

tag: phenotype

value: Post-treatment


title: MUSC-HN014-Post-Tumor


title: C1.stroke.core.rat.3


title: MUSC-HN010-Post-Tumor


title: DNA_oncoscan_prostatecancer_15-008/051

description: OncoScan CNV for prostate cancer sample from patient 15-008/051

tag: patientid

value: unknown


title: GR18

city: Utrecht

first: Guy

last: Roukens

address: Uppsalalaan 8

country: Netherlands

institute: UMCU

data_processing:
Bulk: Reads were aligned to the mouse reference genome NCBIM37 mm9 using STAR version2.4.2a
Single cell: Sequencing reads were mapped against the mouse reference genome (NCBIM37 mm9 ) as described before in  doi:10.1016/j.cels.2016.09.002
Bulk: Read groups were added to the compressed binary version of the sequence alignment file (*.bam) files using Picard?s ?AddOrReplaceReadGroups? tool (v1.98)
Single cell: Reads were counted using STAR and then further processed in Rstudio (version 1.2.5019, Rstudio Team, 2019) and R (version 3.6.1, R Core Team, 2019) using the Seurat package version 3.157. Only cells in which less than 2% of the UMI counts mapped to mitochondrial genes, and at least 1000 genes were expressed, passed the quality control.
Bulk: The bam files were sorted with Sambamba v0.4.5, and transcript abundances were quantified with HTSeq-count version 0.6.1p117 using the union mode.
Single cell: Data where normalized and scaled with the SCTransform method.
Reads per kilobase of transcript per million reads sequenced were calculated with edgeR?s rpkm() function
Differentially expressed genes in the transcriptome data were identified using the DESeq. 2 package with standard settings
Genome_build: NCBIM37 mm9
Supplementary_files_format_and_content: Tab-delimited text files containing FPKM normalized values
Supplementary_files_format_and_content: Tab-delimited text files containing barcode counts

source_name: Mouse mammary tumor PyMT organoids

growth_protocol: Organoids were grown for 4 days after splitting as single cells in DMEM/F12 + HEPES + pen/strep, +B27 + FGF2 (12,5 ng/ml)

extract_protocol:
total RNA-isolation with RNAeasy kit (Qiagen)

Bulk sequencing: Sequencing libraries were made using the Rapid Directional RNA-Seq Kit (NEXTflex)
Single cell sequencing: Libraries were generated by Single Cell Discoveries as described before in doi:10.1016/j.cels.2016.09.002

tag: control or knockout

value: SOX4 knockout

tag: bulk or single-cell

value: Single-cell

value: Mammary tumor cells


title: MUSC-HN010-Pre-Tumor

value: Pre-treatment


title: MUSC-HN012-Pre-Tumor


title: H4

value: Bulk


title: DNA_oncoscan_prostatecancer_15-008/050

description: OncoScan CNV for prostate cancer sample from patient 15-008/050

tag: age

value: remission

tag: tissue


title: GR17

value: Control


title: MUSC-HN014-Pre-Tumor


title: DNA_oncoscan_prostatecancer_15-008/049

description: OncoScan CNV for prostate cancer sample from patient 15-008/049

tag: gender

value: male

tag: preoperative psa

value: white


title: MUSC-HN009-Pre-Tumor


title: B2.periischemic.rat.2

value: Sprague Dawley

value: Striatum


title: B1.stroke.core.rat.2

value: temporo-parietal cortex


title: M4


title: DNA_oncoscan_prostatecancer_15-008/048

description: OncoScan CNV for prostate cancer sample from patient 15-008/048

tag: gleason score

value: recurrence

value: prostate cancer tissue


title: GR19


title: A2.periischemic.rat.1

value: transient middle cerebral artery occlusion (tMCAO)


title: NC38: 21 dpi SARS-CoV-2

city: Covington

first: Joseph

middle: C

last: Mudd

state: LA

address: 18703 Three Rivers rd

institute: Tulane University

data_processing:
Sequencing reads were demultiplexed and adapter-trimmed with Trim Galore (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/).  The –hardtrim  option was used to clip the first 6 basepairs of mate R2 that exhibited low quality scores.  Because reads were derived from 2 separate species with different genomes and different genome annotations, these were treated as different datasets from alignment to gene correlation steps.  In brief, lanes were concatenated and mapped with STAR aligner to their respective species genomes, Mmul_10 (GCF_003339764.) for RM and ChlSabl.1 (GCF_000409795.2) for AGM (49).  Parameters were modified from the default run option that gave the highest percentage of uniquely mapped reads:  --outFilterScoreMinOverLread 0   --outFilterMatchNmin 0   --outFilterMatchNminOverLread 0   --outFilterMismatchNmax 2.  Counts were generated by the STAR option –quantMode geneCounts and an n  n matrix was prepared as input for the R package DESeq2 (50).  Data was fitted to a generalized linear model in accordance with the DEseqdataset function.  Samples that received an RNA concentration step during the isolation process were found to strongly influence fitted values of the model.  Thus a revised analysis was performed incorporating the effect of RNA clean-up into the generalized linear model.  Hidden variables were further incorporated with the R package SVA and the object was post-filtered to remove genes with at least 4 samples having normalized counts < 10.
Genome_build: Mmul_8.0.1 (for rhesus samples), ChlSabl.1 (for AGM samples
Supplementary_files_format_and_content: tab delimited text files correspond to transcript read counts calculated by Htseq-count

organism: Chlorocebus sabaeus

source_name: PAXgene

extract_protocol:
collection protocol: Whole venous blood was collected from nonhuman primates using a BD Vacutainer Safety-Lok Blood Collection Set (BD catg#367281) and BD Vacutainer one use needle holder (BD catg# 364815). Blood was added to the PAXgene Blood RNA reagent tube (PreAnalytiX catg#762165) in the same ratio as the manufacturer’s guidelines. Post collection, PAXgene blood tubes were stored upright for a minimum of two hours and then placed into the -20C freezer until further processing.
Samples were processed in accordance with the PreAnalytiX PAXgene Blood RNA Kit (PreAnalytiX catg#762165). The RNA Clean & Concentrator-5 kit (Zymo, Catg#R1015) was used to purify and increase RNA samples with low yields. Procedures were followed per manufacturer’s guidelines. For AGM NC33, Paxgene tubes were not collected at 1 and 3 dpi due to blood being prioritized for other assays.
Total RNA samples were quantitated using Qubit RNA HS Assay kit (Invitrogen Q32855). A RIN for each sample was determined by running 1ul on an Agilent 4150 TapeStation using RNA Screen Tapes (Agilent 5067-5576). 1-2 ug of each sample were treated with Baseline Zero DNase (Epicentre, DB0711K) for 30 minutes at 37°C. DNase was inactivated by adding 2ul 10X Stop solution and following a 10 minute incubation at 65°C. The Total RNAs were then purified using Agencourt RNAClean XP magnetic beads by following the manufactory recommendation (Beckman Coulter Life Sciences). 10 ng of each sample were used to make SMART-Seq libraries following the SMART-Seq Stranded Kit User Manual (Takara Bio). Briefly, cDNAs were first generated from all total RNA fragments after RNA fragmentation. Addition of Illumina adapters and indexes and then library purification were followed. Final library amplification and purification were performed after enzymatically removing ribosomal fragments originating from rRNA molecules by using probes specific to mammalian rRNA.
Libraries were quantitated using Qubit DNA HS Assay kit (Molecular Probes Life Technologies, Q32854). Average size of each library was determined by running each sample on Agilent 4150 TapeStation using D1000 Screen Tapes. (Agilent 5067-5582). Each library was diluted to 4nM in DNase RNase free ultrapure water (Invitrogen 10977-015). All libraries were pooled at a concentration of 4nM before denaturing with 0.2 N NaOH for 5 min at RT. The libraries were neutralized using 0.2 N Tris-HCl, pH 7 before being diluted to 20pM in HT1 buffer (Illumina).
Finally, denatured libraries were loaded into an Illumina NextSeq 550 v2 High-Output reagent cartridge at a final concentration of 1.2pM in HT1 buffer. Denatured PhiX control library was also included at 1% concentration. Dual indexes and paired end 75bp sequencing was performed on a High-Output flow cell yielding about 18M read pairs per sample.

tag: treatment

value: Blood

tag: time


title: DNA_oncoscan_prostatecancer_15-008/046

description: OncoScan CNV for prostate cancer sample from patient 15-008/046

tag: race

tag: pathologic stage

tag: 5-year disease status


title: MUSC-HN009-Post-Tumor

value: Post-treatment


title: A1.stroke.core.rat.1

tag: strain background

tag: sample group


title: NC33: 21 dpi SARS-CoV-2


title: H7

value: SOX4 knockout

tag: cell type


title: DNA_oncoscan_prostatecancer_15-008/047

description: OncoScan CNV for prostate cancer sample from patient 15-008/047


title: NC40: 21 dpi SARS-CoV-2


title: MUSC-HN007-Pre-Tumor

tag: phenotype


title: MUSC-HN008-Post-Tumor


title: NC33: 14 dpi SARS-CoV-2


title: Zmroot_sc_read1/2_rep7

city: New York

first: Kenneth

middle: David

last: Birnbaum

state: NY

address: 12 Waverly Place

department: Biology

institute: New York University

description: barcode read single cell run3 (4 primers combined)

data_processing:
Raw base calls were demultiplexed using Illumina's bcl2fastq.
Alignment, barcode and UMI quantification were performed with Chromium 10x Cell Ranger software package. Samples were normalized, and cell clusters determined using Seurat.
Differential gene expression analyses between cell clusters was perfomed using the VST algorithm from Seurat.
Genome_build: Zea mays ssp mays B73 v4
Supplementary_files_format_and_content: Matrix table with raw counts for every cell (column) and gene (rows). The nine replicates were combined.

organism: Zea mays

source_name: Maize root meristem

growth_protocol: Growth chamber: 26 oC, 16h light/8 h dark. Plantlets were grown on germination paper to avoid the presence of substrate.

extract_protocol:
Root tips from maize seminal and principal roots were cut and collected (3-4 mm lenght). Root tip were incubated in a enzymatic solution to digest cell walls and produce protoplasts. Protoplasts were filtered using a cell strainer and used as input for the 10x Chromium Single Cell 3' V2 pipeline.
Libraries were prepared using Chromium Single Cell 3' Reagent Kit V2 and V3

tag: cultivar

tag: genotype

value: wild type

value: 7 DAG


title: Zmroot_sc_read1/2_rep9


title: DNA_oncoscan_prostatecancer_15-008/044

description: OncoScan CNV for prostate cancer sample from patient 15-008/044

tag: patientid

value: Hawaiian/Pacific Islander


title: DNA_oncoscan_prostatecancer_15-008/045

description: OncoScan CNV for prostate cancer sample from patient 15-008/045

tag: age


title: NC40: 7 dpi SARS-CoV-2

tag: tissue


title: Zmroot_sc_read1/2_rep8


title: MUSC-HN005-Post-Tumor


title: NC33: 7 dpi SARS-CoV-2


title: MUSC-HN007-Post-Tumor


title: DNA_oncoscan_prostatecancer_15-008/041

description: OncoScan CNV for prostate cancer sample from patient 15-008/041

tag: gender

value: unknown


title: WT1

tag: control or knockout

tag: bulk or single-cell

value: Bulk

value: Mammary tumor cells


title: MUSC-HN004-Pre-Tumor

value: Pre-treatment


title: MUSC-HN005-Pre-Tumor


title: WT3

value: Control


title: DNA_oncoscan_prostatecancer_15-008/040

description: OncoScan CNV for prostate cancer sample from patient 15-008/040

value: male

tag: preoperative psa

tag: gleason score

value: black

value: remission


title: NC34: 7 dpi SARS-CoV-2

tag: treatment

tag: time


title: DNA_oncoscan_prostatecancer_15-008/043

description: OncoScan CNV for prostate cancer sample from patient 15-008/043

tag: race

value: white

tag: pathologic stage

tag: 5-year disease status

value: recurrence


title: MUSC-HN003-Post-Tumor


title: NC40: 4 dpi SARS-CoV-2


title: MUSC-HN002-Pre-Tumor


title: NC38:14 dpi SARS-CoV-2


title: MUSC-HN008-Pre-Tumor


title: MUSC-HN004-Post-Tumor


title: NC40: 1 dpi SARS-CoV-2


title: Zmroot_sc_read1/2_rep6


title: DNA_oncoscan_prostatecancer_15-008/035

description: OncoScan CNV for prostate cancer sample from patient 15-008/035

value: prostate cancer tissue


title: THP-1 whith H37RV△1759c infection rep1

city: ChangSha

first: Yongwei

last: Zhu

state: Hunan

address: No.87,  Xiangya Street

country: China

institute: CSU Xiangya hospital

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCh38 whole genome using bowtie2 v2.3.5 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Fragments Per Kilobase of exon model per Million mapped fragments (FPKM) were calculated using a protocol from Trapnell C et al., Nat Biotechnol, 2010.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab-delimited text files include TMP values for each Sample

growth_protocol: THP-1 human monocyte macrophages were grown in RPMI-1640 medium supplemented with 10% fetal bovine serum, and HEK293T cells were grown in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% FBS, which were both cultured at 37°C with 5% CO2. H37Rv and H37Rv△1759c were cultured in Middlebrook 7H9 medium (Becton Dickinson, Difco, 271310) supplemented with 10% oleic acid, albumin, dextrose (OADC) (Becton Dickinson, Difco, 212352), 0.5% (v/v) glycerol (Sigma Aldrich, G5516), and 0.05% (v/v) Tween 80 (Sigma Aldrich, P8074).

extract_protocol:
Total miRNA of the 9 samples was isolated by using an RNeasy minikit (Qiagen, 217004) .
RNA libraries were prepared for sequencing using standard Illumina protocols
Hiseq Single-End RNA-Seq

treatment_protocol: THP-1 cells were differentiated with 100 ng/mL phorbol myristate acetate (PMA) for 48 h and incubated with 1640 medium for another 8 h. Cells were infected with H37Rv or  H37Rv△1759c  at an MOI of 1 . At 4 h postinfection (4 hpi), cells were washed three times with phosphate-buffered saline (PBS) and incubated at 37°C with fresh medium. Cells were collected with TRIzol reagent  at  24 h postinfection ( 24 hpi).

value: treatment group


title: THP-1 whith H37RV infection rep3

value: positive control


title: DNA_oncoscan_prostatecancer_15-008/034

description: OncoScan CNV for prostate cancer sample from patient 15-008/034


title: NC40: 14 dpi SARS-CoV-2

value: Blood


title: NC38: 7 dpi SARS-CoV-2


title: MUSC-HN003-Pre-Tumor


title: NC38:1 dpi SARS-CoV-2


title: MUSC-HN001-Pre-Tumor


title: DNA_oncoscan_prostatecancer_15-008/039

description: OncoScan CNV for prostate cancer sample from patient 15-008/039


title: DNA_oncoscan_prostatecancer_15-008/037

description: OncoScan CNV for prostate cancer sample from patient 15-008/037


title: DNA_oncoscan_prostatecancer_15-008/042

description: OncoScan CNV for prostate cancer sample from patient 15-008/042


title: THP-1 without infection rep3

value: negative control


title: THP-1 whith H37RV△1759c infection rep2


title: MUSC-HN001-Recur-Tumor

value: Recurrent tumor


title: Zmroot_sc_read1/2_rep5

value: wild type

value: 7 DAG


title: DNA_oncoscan_prostatecancer_15-008/031

description: OncoScan CNV for prostate cancer sample from patient 15-008/031


title: DNA_oncoscan_prostatecancer_15-008/036

description: OncoScan CNV for prostate cancer sample from patient 15-008/036


title: MUSC-HN002-Post-Tumor

value: Post-treatment


title: Zmroot_sc_read1/2_rep4


title: THP-1 without infection rep1


title: NC38: Pre-infection

value: uninfected

value: PRE


title: DNA_oncoscan_prostatecancer_15-008/030

description: OncoScan CNV for prostate cancer sample from patient 15-008/030


title: NC34: pre-infection


title: THP-1 whith H37RV infection rep2


title: DNA_oncoscan_prostatecancer_15-008/038

description: OncoScan CNV for prostate cancer sample from patient 15-008/038


title: THP-1 whith H37RV△1759c infection rep3


title: NC38:3 dpi SARS-CoV-2


title: NC33: pre-infection


title: kidney, sample 2, scATAC-seq

city: Nanjing

first: Jingping

last: Yang

state: Jiangsu

address: 22 Hankou Road

department: Medical School

institute: Nanjing University

description:
peaks_and_bigwigs.tar
master_peak.bed
scATAC_SparseMatrix.rds
scATAC_barcodes.csv

data_processing:
For each read, we first appended the barcode which was in the whitelist to the read name. Then adapter sequences were trimmed  using trimmomatic (0.32). Bowtie2 (2.3.0) was used to align reads to the hg38 reference genome with ‘-X 2000 -3 1’ as options. Read pairs that did not map uniquely to autosomes or sex chromosomes with a mapping quality of at least 30 were filtered out using samtools (1.3.1).
High quality cells were identified as log10(unique fragments) > 3.4, ratio of fragments in TSS region > 0.15 and a log-transformed nucleosomal periodicity score > -1.75.
Harmony was used for batch correction and Louvain was used for clustering by SnapATAC package.
MACS2 was used for peak calling for each cluster with the following parameters:’ --nomodel --keep-dup all --extsize 200 --shift 100 –nolambda -q 0.001’.  Peaks overlapping ENCODE blacklisted regions (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists) were removed for each cluster to generate clean peaks and  a master peak list  was generated by taking clean peaks identified in any cluster and merged them with the bedtools.
Genome_build: hg38
Supplementary_files_format_and_content: bed file represents master peak list
Supplementary_files_format_and_content: csv file represents information of barcodes
Supplementary_files_format_and_content: tar file includes narrowpeaks and bigwig files for each cluster
Supplementary_files_format_and_content: rds Matrix table with raw counts for each peak in each cell

source_name: kidney paracancerous tissue

extract_protocol:
Kidney paracancerous tissues was stored in PBS on ice and then cut into 1mm3 segments for nuclei isolation. Samples were homogenized using a Dounce homogenizer  in 1ml chilled Lysis Buffer on ice. Following lysis, 9 ml chilled Wash Buffer was added and the resulting solution was filtered through a 30-µm cell strainer. Nuclei were centrifuged (500g for 5 min at 4 °C) and the supernatant removed without disrupting the nuclei pellet. Nuclei were resuspended in chilled Diluted Nuclei Buffer at approximately 3,000–4,000 nuclei per µl.
10X Chromium libraries were prepared according to manufacturer protocol.

value: kidney

tag: Sex

value: female


title: NC34: 3 dpi SARS-CoV-2


title: MUSC-HN001-Post-Tumor

tag: phenotype


title: hDMCs-BMP4 Dorsomorphin rep2

city: FuZhou

first: XIAOXIAO

last: HU

address: Qishan Branch

institute: Fujian Normal University

description: Normalized_counts_file_BMP4 Dorsomorphin.txt

data_processing:
Illumilla HiSeq X Ten was used to perform sequencing
Reads were mapped to genome with HISAT2
counted in genomic features with featureCounts software
DEseq2 was used to differ differential expressions
Genome_build: hg38
Supplementary_files_format_and_content: TXT

source_name: human dental mesenchymal cells

extract_protocol:
Total RNA of cultured hDMCs was extracted using RNeasy Mini Kit (Qiagen, 74104).
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: BMP4 protein (R&D Systems, 314-BP-050) was added to the medium at the final concentration of 100ng/ml. For small molecule inhibition experiments, dorsomorphin (Sigma, P5499), SB203580 (CST, 5633), U0126 (CST, 9903), and SP600125 (Abcam, ab120065) were added into the medium at the final concentration of 20uM. DMSO (Sigma, 76314) was used as negative control.

value: molar tooth germ

value: BMP4 Dorsomorphin