title: LN-511-d18-3

city: Guangzhou

first: Jinyan

address: 7th Jinsui Road

institute: Zhongshan Ophthalmic Centre

data_processing:
The reads were filtered by fastp (version 0.18.0)
Short reads alignment tool Bowtie2 (version 2.2.8) was used for mapping reads to ribosome  RNA (rRNA) database. The rRNA mapped reads then will be removed.
Paired-end clean reads were mapped to the reference genome using HISAT2. 2.4
A FPKM (fragment per kilobase of transcript per million mapped reads) value was calculated to quantify its expression abundance and variations, using RSEM software.
Assembly: Homo sapiens (Ensembl_release104) reference genome
Supplementary files format and content: Tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: Tab-delimited text file includes FPKM  for each Sample

source_name: HES H9

extract_protocol:
Total RNA was extracted using TRIzol Reagent (Invitrogen) following the manufacturer’s instructions. 1.5 μg of total RNA was used for the construction of sequencing libraries. RNA quality was assessed on an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA, USA) and checked using RNase free agarose gel electrophoresis.
RNA libraries for RNA-seq were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina following manufacture’s protocols. The ligation reaction was purified with the AMPure XP Beads(1.0X).

tag: culture

tag: time point

value: HES H9

value: human embryonic stem cell


title: ML cells H3K9me2 biol rep 2 [ML_H3K9me2_2]

status: Public on Sep 08 2023

type: SRA

city: Parkville

first: Gordon

middle: K

last: Smyth

state: Vic

address: 1G Royal Pde

department: Bioinformatics

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

library_source: genomic

data_processing:
Libraries were sequenced on an Illumina NextSeq 500, generating 80 bp paired-end reads.
Reads were aligned to the mouse genome mm10 by Bowtie2 with duplicates removed with Picard tools MarkDuplicates command.
Bam files for technical replicates were merged using samtools post-mapping.
BigWig files were generated with BamCoverage from Deeptools with bamCoverage --normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: *.bw: BigWig, a coverage track generated from the mapped read fragments. The coverage is calculated as the number of reads per 50 bp bin. Coverage was normalization by reads Per Kilobase per Million mapped reads (RPKM).
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: Mammary epithelial cells

extract_protocol:
Whole cells were captured on ConA beads and genomic DNA treated with pA-Tn5 followed by overnight antibody incubation.
Libraries were constructed as per Kaya-Okur et al. 2019.

tag: tissue

value: Mammary epithelial cells

tag: cell type

value: mature luminal

tag: strain

value: FVB/N mice

tag: developmental stage

value: adult (9-10 weeks of age)

tag: Sex

value: female

tag: antibody

value: H3K9me2 (abcam Cat#1220)

tag: mouse pool


title: genomic DNA from Sperm [FD99018]

type: genomic

city: Provo

first: Timothy

middle: G

last: Jenkins

state: UT

address: 4005 Life Sciences Building

department: Cell Biology and Physiology

country: USA

institute: Brigham Young University

description: Tissue Specific Aging Between Tissue Types

hyb_protocol: bisulphite converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human Methylation850K Beadchip using standard Illumina protocol

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

data_processing: Data was processed using the minfi R package, and normalized using SWAN normalization.

label: Cy5 and Cy3

organism: Homo sapiens

label_protocol: Standard Illumina Protocol

extract_protocol: not provided

tag: gender

value: Male

tag: sample type

value: Sperm

tag: disease state

value: Normozoospermia


title: ML cells H3K9me2 biol rep 1 [ML_H3K9me2_1]


title: genomic DNA from Sperm [28AS014]


title: genomic DNA from Whole Blood [EX8V009]

value: Blood


title: genomic DNA from Whole Blood [V0IJ022]


title: LN-511-d18-2

last: Li

country: China

library_source: transcriptomic

molecule: polyA RNA

tag: cell line


title: genomic DNA from Sperm [V0IJ022]


title: genomic DNA from Sperm [EX8V009]


title: LN-511-d12-2


title: genomic DNA from Whole Blood [0T3J012]


title: genomic DNA from Sperm [0T3J012]


title: ML cells H3K9ac biol rep 1 [ML_H3K9ac_1]

value: H3K9ac (abcam Cat#4441)


title: genomic DNA from Whole Blood [56B]

description: Aerobic Continuous Training Whole Blood

value: Female

tag: disease

value: Polycystic Ovary Syndrome

value: Whole Blood

tag: group

value: Aerobic Continuous Training


title: ML cells H3K9me3 biol rep 1 [ML_H3K9me3_1]

value: H3K9me3 (abcam Cat#8898)


title: LN-511-d12-1

value: HES H9

value: human embryonic stem cell


title: genomic DNA from Whole Blood [56A]

description: Aerobic Continuous Training Whole Blood


title: genomic DNA from Whole Blood [55A]

description: Aerobic Continuous Training Whole Blood


title: genomic DNA from Whole Blood [55B]

description: Aerobic Continuous Training Whole Blood


title: genomic DNA from Whole Blood [54A]

description: Aerobic Continuous Training Whole Blood


title: LN-511-d18-1


title: genomic DNA from Whole Blood [53A]

description: Aerobic Continuous Training Whole Blood


title: genomic DNA from Whole Blood [54B]

description: Aerobic Continuous Training Whole Blood


title: LN-511-d12-3


title: ML cells H2AK119ub biol rep 1 [ML_H2AK119ub_1]

value: Mammary epithelial cells

value: mature luminal

value: H2AK119ub (CST Cat#8240)


title: genomic DNA from Whole Blood [52A]

description: Aerobic Continuous Training Whole Blood


title: Ctrl-d18-1

value: ctrl


title: genomic DNA from Whole Blood [53B]

description: Aerobic Continuous Training Whole Blood


title: ML cells H3K36me3 biol rep 1 [ML_H3K36me3_1]

value: FVB/N mice

value: adult (9-10 weeks of age)

value: female

value: H3K36me3 (Active Motif Cat#61021)


title: Ctrl-d18-2


title: Ctrl-d12-3


title: genomic DNA from Whole Blood [51A]

description: Aerobic Continuous Training Whole Blood


title: ML cells H3K4me3 biol rep 2 [ML_H3K4me3_2]

value: H3K4me3 (Merck Cat#07-473)


title: genomic DNA from Whole Blood [52B]

description: Aerobic Continuous Training Whole Blood


title: ML cells H3K9ac biol rep 2 [ML_H3K9ac_2]

value: H3K9ac (abcam Cat#4441)


title: Ctrl-d12-2


title: genomic DNA from Whole Blood [51B]

description: Aerobic Continuous Training Whole Blood

value: Female


title: ML cells H2AK119ub biol rep 2 [ML_H2AK119ub_2]


title: Ctrl-d12-1


title: genomic DNA from Whole Blood [50A]

description: Aerobic Continuous Training Whole Blood

value: Polycystic Ovary Syndrome


title: genomic DNA from Whole Blood [50B]

description: Aerobic Continuous Training Whole Blood

value: Whole Blood


title: ML cells H3K36me3 biol rep 2 [ML_H3K36me3_2]


title: ML cells H3K4me1 biol rep 2 [ML_H3K4me1_2]

value: H3K4me1 (abcam Cat#8895)


title: Ctrl-d18-3


title: ML cells H3K4me1 biol rep 1 [ML_H3K4me1_1]


title: ML cells H3K4me3 biol rep 1 [ML_H3K4me3_1]


title: genomic DNA from Whole Blood [49A]

description: Aerobic Continuous Training Whole Blood

value: Aerobic Continuous Training


title: genomic DNA from Whole Blood [49B]

description: Aerobic Continuous Training Whole Blood


title: Prostate cancer tissue PCa56413

city: Toronto

first: Mathieu

last: Lupien

state: Ontario

address: 101 College Street

country: Canada

institute: University Health Network

description: For this ChIP-seq sample (patient data) we need controlled access for the raw fastq files, hence only processed data is being submitted for this sample.

data_processing:
For Cut&Run, data is first trimmed for adapters with trimmomatic-0.36 then mapped with bowtie2 with following parameter " -q -I 10 -X 700  --local --very-sensitive-local --no-mixed --no-discordant --no-unal --phred33". Peak calling is done with SEACR q <= 0.05
For ChIP-Seq data, ENCODE ChIP-Seq pipeline was followed with default parameters with bowtie2 aligner, macs2 peak caller.
Assembly: hg38
Supplementary files format and content: narrowPeak, bedgraphs

source_name: Prostate cancer tissue

growth_protocol: DU145 cells were cultivated in DMEM 10% FBS and 1x penicillin/streptomycin, while CRISPRi 22Rv1 clonal cell lines were grown in RPMI 10% FBS, 1x penicillin/streptomycin, Blasticidin 6ug/ml

extract_protocol:
For ChIP-seq cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the Diagenode Bioruptor 300. For Cut&Run cells were incubated with concanavalinA beads, followed by incubation with antibody with digitonin-containing buffer. After washing, samples were incubated with G-protein coupled with MNase and exposed DNA was digested by activating MNase with CaCl2 for 30 min in ice bath.
ChIP-seq and Cut&Run libraries were prepared using the Takara Thruplex Library Preparation Kit. 10 ul of  eluted DNA was used as starting material for input and/or IP samples. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

value: Prostate cancer tissue

value: prostate cancer

tag: chip antibody


title: ML cells H3K27me3, biol rep 2 [ML_H3K27me3_2]

value: Mammary epithelial cells


title: genomic DNA from Whole Blood [48A]

description: Aerobic Continuous Training Whole Blood


title: genomic DNA from Whole Blood [47A]

description: Aerobic Continuous Training Whole Blood


title: Prostate cancer tissue PCa3023


title: genomic DNA from Whole Blood [46A]

description: Aerobic Continuous Training Whole Blood


title: genomic DNA from Whole Blood [47B]

description: Aerobic Continuous Training Whole Blood


title: ML cells H3K27me3, biol rep 1 [ML_H3K27me3_1]

value: mature luminal


title: genomic DNA from Whole Blood [46B]

description: Aerobic Continuous Training Whole Blood


title: Prostate cancer tissue PCa13848


title: genomic DNA from Whole Blood [48B]

description: Aerobic Continuous Training Whole Blood


title: genomic DNA from Whole Blood [45A]

description: Aerobic Continuous Training Whole Blood


title: Prostate_tumor_RIB0011803

city: Leipzig

first: Michael

last: Rade

address: Perlickstr. 1

country: Germany

institute: Fraunhofer Institute for Cell Therapy and Immunology

description: Gene expression of prostate biopsy prior to RP (FFPE)

data_processing:
Processing of primary sequencing data was done using the workflow management software UAP (https://github.com/fraunhofer-izi/uap).
Demultiplexing of Illumina raw files was performed with the Illumina bcl2fastq software v2.19.
Paired-end FASTQ reads were trimmed and filtered using AdaptorRemoval v2.2.1 with additional parameters to trim ambiguous bases (N) at 5’/3’ termini (–trimns), remove low-quality bases (–trimqualities, –minquality 20) and keep reads with a minimum read length of 30bp (–minlength 30).
Trimmed reads were mapped to the human reference genome version GRCh38/hg38 by HISAT2 v2.1.0 by specifying a reverse stranded library.
Gene level quantification was performed using HTSeq v0.11.2 with following parameters: –mode intersection-strict, –stranded reverse and –type exon. To ensure that the putative novel intergenic genes from the ProstaTrend signature (DOI: 10.1016/j.eururo.2020.06.001) are also represented in the FFPE_Bx cohort, we extended the human reference gene annotation GENCODE (release 36 GRCh38.p12) used for HTSeq as follows: we used the annotation of expression quality filtered novel transcripts classified as “u”(unknown intergenic) of the cohort FF_seq_RP as described previously (DOI: 10.1016/j.eururo.2020.06.001). Since these annotations are based on GRCh37/hg19, we updating the annotation using UCSC liftOver tool to GRCh38/hg38 (Chain file: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz. After converting the coordinates all prognostic genes from the ProstaTrend signature (classified as unknown intergenic and FDR <0.05) could be retained.
179 samples passed the quality filter, 3 samples were excluded because time to BCR was not recorded. In total, we analyzed transcriptome data from 176 patients.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Matrix table (HTSeq output) with raw gene counts for each sample as a separate file. The gene IDs consist of Ensembl IDs (GENCODE v36, GRCh38.p12) and prognostic putative novel genes (prefix XLOC) classified as “u” (unknown intergenic)
Supplementary files format and content: Comma-delimited text file with rawcounts for each gene and sample. The gene IDs consist of Ensembl IDs (GENCODE v36, GRCh38.p12) and prognostic putative novel genes (prefix XLOC) classified as “u” (unknown intergenic)
Supplementary files format and content: Comma-delimited text file with variance stabilizing transformation (VST) counts for each gene and sample. The gene IDs consist of Ensembl IDs (GENCODE v36, GRCh38.p12) and prognostic putative novel genes (prefix XLOC) classified as “u” (unknown intergenic)

molecule: total RNA

source_name: FFPE PCa biopsy

extract_protocol:
From up to five FFPE tissue slices of 10 μm we isolated RNA using Deparaffinization Solution (Qiagen) according to the miRNEASY protocol. A pathologist evaluated HE-stained flanking tissue slices and tumor content was assessed, ranging between 5% and 100% (mean= 41%). After subsequent proteinase K digestion and formalin-de-crosslinking, we transferred the samples onto RNeasy MinElute spin columns. We used the miRNeasy FFPE kit on the QIAcube (Qiagen) following the manufacturer’s instruction for the final RNA purification. To eliminate all traces of genomic DNA, we performed DNAse-digestion (TURBO DNA free Kit, Thermo Fisher) twice in each sample. The RNA was concentrated using a standard precipitation protocol if necessary. Finally, we quantified extracted RNA using a Qubit RNA-Kit and the Qubit 2.0 instrument (Thermo Fisher). We analyzed the quality of RNA on a Bioanalyzer 2100 instrument (Agilent Technologies) and calculated the DV200 values (the percentage of fragments >200 nucleotides), ranging between 5% and 63% (mean=37%). Because of the well-known quality issues of old FFPE specimens, we decided to include all samples in further analysis.
For RNA-sequencing of FFPE specimens, we used 200 ng RNA per sample (when available). We prepared RNA libraries using TruSeq-Stranded Total RNA Sample Prep kit (Illumina), including an rRNA depletion step according to manufacturers’ protocol, i.e., Ribo-Zero Gold rRNA Removal Kit. Following Illumina's recommendation, we skipped the fragmentation step for all samples. We analyzed the quality and quantity of each prepared library with the Denovix instrument (Qubit DNA-Kit) and with the Bioanalyzer 2100, calculated the molarity of each library and pooled equal amounts, which were used for subsequent sequencing (12 pM). We sequenced 2 x 126-bp paired-end reads using SBS V4 chemistry with a HiSeq 2500 (Illumina) on four eight-lane flow cells: the first one with 32 and the others with 51 libraries each (185 in total).

value: FFPE PCa biopsy

tag: alternative sample_id

tag: tumor type

value: Primary tumor

tag: biochemical relapse_(bcr)

value: no

tag: gleason score

tag: pathological t_stage

tag: pathological n_stage

tag: total psa_(ng/ml,_pre-biopsy)

tag: tumor cell_content_(%)


title: genomic DNA from Whole Blood [45B]

description: Aerobic Continuous Training Whole Blood

tag: tissue


title: Prostate_tumor_RIB0011850


title: LP cells PolII biol rep 1 [LP_PolII_1]

tag: cell type

value: luminal progenitor

tag: strain

value: FVB/N mice

tag: developmental stage

value: adult (9-10 weeks of age)

tag: Sex

tag: antibody

value: PolII (Merck Cat#05-623)

tag: mouse pool


title: LP cells PolII biol rep 2 [LP_PolII_2]

value: female


title: Prostate_tumor_RIB0011717


title: genomic DNA from Whole Blood [44A]

description: Aerobic Continuous Training Whole Blood

tag: gender

value: Female

tag: disease

tag: group


title: genomic DNA from Whole Blood [44B]

description: Aerobic Continuous Training Whole Blood

value: Polycystic Ovary Syndrome


title: Prostate_tumor_RIB0011873

tag: alternative sample_id

tag: tumor type


title: genomic DNA from Whole Blood [43A]

description: Aerobic Continuous Training Whole Blood

value: Whole Blood


title: genomic DNA from Whole Blood [43B]

description: Aerobic Continuous Training Whole Blood


title: LP cells IgG biol rep 1 [LP_muIgG_1]

value: IgG (Merck Cat#12-371)


title: LP cells IgG biol rep 2 [LP_muIgG_2]


title: genomic DNA from Whole Blood [42B]

description: Aerobic Continuous Training Whole Blood

value: Aerobic Continuous Training


title: genomic DNA from Whole Blood [42A]

description: Aerobic Continuous Training Whole Blood


title: Prostate_tumor_RIB0011853

tag: biochemical relapse_(bcr)

tag: gleason score


title: Prostate_tumor_RIB0011835

tag: pathological t_stage

tag: pathological n_stage

value: pNA


title: LP cells H3K27ac biol rep 1 [LP_H3K27ac_1]

value: H3K27ac (abcam Cat#4729)


title: Prostate_tumor_RIB0011834

tag: total psa_(ng/ml,_pre-biopsy)

tag: tumor cell_content_(%)


title: LP cells H3K27ac biol rep 2 [LP_H3K27ac_2]

tag: tissue

value: Mammary epithelial cells

tag: cell type


title: genomic DNA from Whole Blood [41B]

description: Aerobic Continuous Training Whole Blood


title: genomic DNA from Whole Blood [39B]

description: Aerobic Continuous Training Whole Blood


title: genomic DNA from Whole Blood [40B]

description: Aerobic Continuous Training Whole Blood


title: Prostate_tumor_RIB0011802


title: genomic DNA from Whole Blood [40A]

description: Aerobic Continuous Training Whole Blood


title: LP cells H3K9me3 biol rep 1 [LP_H3K9me3_1]

tag: strain

tag: developmental stage

value: H3K9me3 (abcam Cat#8898)


title: Prostate_tumor_RIB0011895

value: FFPE PCa biopsy


title: LP cells H3K9me2 biol rep 2 [LP_H3K9me2_2]

tag: Sex

tag: antibody

value: H3K9me2 (abcam Cat#1220)


title: genomic DNA from Whole Blood [39A]

description: Aerobic Continuous Training Whole Blood

tag: gender


title: genomic DNA from Whole Blood [38B]

description: Aerobic Continuous Training Whole Blood

tag: disease


title: genomic DNA from Whole Blood [37A]

description: Aerobic Continuous Training Whole Blood

tag: group


title: LP cells H3K9me2 biol rep 1 [LP_H3K9me2_1]

tag: mouse pool


title: genomic DNA from Whole Blood [36A]

description: Aerobic Continuous Training Whole Blood


title: Prostate_tumor_RIB0011826

tag: alternative sample_id

tag: tumor type

value: Primary tumor

value: no


title: genomic DNA from Whole Blood [37B]

description: Aerobic Continuous Training Whole Blood


title: LP cells H3K9ac biol rep 2 [LP_H3K9ac_2]

value: luminal progenitor

value: FVB/N mice

value: H3K9ac (abcam Cat#4441)


title: genomic DNA from Whole Blood [41A]

description: Aerobic Continuous Training Whole Blood


title: genomic DNA from Whole Blood [35A]

description: Aerobic Continuous Training Whole Blood


title: LP cells H3K9ac biol rep 1 [LP_H3K9ac_1]

value: adult (9-10 weeks of age)

value: female


title: genomic DNA from Whole Blood [35B]

description: Aerobic Continuous Training Whole Blood

value: Female

value: Polycystic Ovary Syndrome


title: LP cells H3K9me3 biol rep 2 [LP_H3K9me3_2]


title: Prostate_tumor_RIB0011832

tag: biochemical relapse_(bcr)

tag: gleason score


title: genomic DNA from Whole Blood [34A]

description: Aerobic Continuous Training Whole Blood

value: Whole Blood


title: genomic DNA from Whole Blood [33A]

description: Aerobic Continuous Training Whole Blood

value: Aerobic Continuous Training


title: Prostate_tumor_RIB0020778

tag: pathological t_stage

tag: pathological n_stage


title: genomic DNA from Whole Blood [34B]

description: Aerobic Continuous Training Whole Blood


title: LP cells H2AK119ub biol rep 2 [LP_H2AK119ub_2]

value: H2AK119ub (CST Cat#8240)


title: genomic DNA from Whole Blood [33B]

description: Aerobic Continuous Training Whole Blood


title: Prostate_tumor_RIB0011815

tag: total psa_(ng/ml,_pre-biopsy)

tag: tumor cell_content_(%)


title: Prostate_tumor_RIB0020748

tag: tissue


title: genomic DNA from Whole Blood [36B]

description: Aerobic Continuous Training Whole Blood


title: Prostate_tumor_RIB0020755


title: genomic DNA from Whole Blood [38A]

description: Aerobic Continuous Training Whole Blood


title: LP cells H2AK119ub biol rep 1 [LP_H2AK119ub_1]

tag: cell type

tag: strain


title: genomic DNA from Whole Blood [32B]

description: Aerobic Continuous Training Whole Blood


title: LP cells H3K36me3 biol rep 1 [LP_H3K36me3_1]

tag: developmental stage

tag: Sex

value: H3K36me3 (Active Motif Cat#61021)


title: Prostate_tumor_RIB0020741


title: LP cells H3K36me3 biol rep 2 [LP_H3K36me3_2]

value: Mammary epithelial cells

tag: antibody


title: genomic DNA from Whole Blood [31A]

description: Aerobic Continuous Training Whole Blood

tag: gender

tag: disease


title: genomic DNA from Whole Blood [31B]

description: Aerobic Continuous Training Whole Blood

tag: group


title: genomic DNA from Whole Blood [30A]

description: Resistance Training Whole Blood

value: Resistance Training


title: Prostate_tumor_RIB0020759

value: FFPE PCa biopsy

tag: alternative sample_id


title: genomic DNA from Whole Blood [30B]

description: Resistance Training Whole Blood


title: Prostate_tumor_RIB0011896

tag: tumor type


title: LP cells H3K4me3 biol rep 2 [LP_H3K4me3_2]

value: H3K4me3 (Merck Cat#07-473)

tag: mouse pool


title: LP cells H3K4me3 biol rep 1 [LP_H3K4me3_1]


title: genomic DNA from Whole Blood [28A]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [32A]

description: Aerobic Continuous Training Whole Blood


title: genomic DNA from Whole Blood [29B]

description: Resistance Training Whole Blood


title: Prostate_tumor_RIB0020775

value: Primary tumor

tag: biochemical relapse_(bcr)

tag: gleason score


title: Prostate_tumor_RIB0020725

value: no

tag: pathological t_stage

tag: pathological n_stage


title: genomic DNA from Whole Blood [27A]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [29A]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [27B]

description: Resistance Training Whole Blood


title: LP cells H3K4me1 biol rep 2 [LP_H3K4me1_2]

value: luminal progenitor

value: H3K4me1 (abcam Cat#8895)


title: LP cells H3K4me1 biol rep 1 [LP_H3K4me1_1]

value: FVB/N mice


title: genomic DNA from Whole Blood [25A]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [26B]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [25B]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [26A]

description: Resistance Training Whole Blood


title: Prostate_tumor_RIB0020787

tag: total psa_(ng/ml,_pre-biopsy)

tag: tumor cell_content_(%)


title: Prostate_tumor_RIB0020721

tag: tissue


title: LP cells H3K27me3, biol rep 2 [LP_H3K27me3_2]

tag: cell type

tag: strain

value: adult (9-10 weeks of age)


title: Prostate_tumor_RIB0011824


title: Basal cells PolII biol rep 2 [Ba_PolII_2]

value: myoepithelial

tag: developmental stage

tag: Sex

value: female

value: PolII (Merck Cat#05-623)


title: genomic DNA from Whole Blood [24A]

description: Resistance Training Whole Blood

tag: gender

value: Female

value: Polycystic Ovary Syndrome

value: Whole Blood


title: Prostate_tumor_RIB0020772


title: genomic DNA from Whole Blood [23A]

description: Resistance Training Whole Blood

tag: disease


title: genomic DNA from Whole Blood [23B]

description: Resistance Training Whole Blood

tag: group


title: Prostate_tumor_RIB0020701

tag: alternative sample_id


title: genomic DNA from Whole Blood [22A]

description: Resistance Training Whole Blood


title: Basal cells PolII biol rep 1 [Ba_PolII_1]

tag: antibody


title: genomic DNA from Whole Blood [28B]

description: Resistance Training Whole Blood


title: Basal cells IgG biol rep 2 [Ba_muIgG_2]

value: IgG (Merck Cat#12-371)

tag: mouse pool


title: Prostate_tumor_RIB0020733

tag: tumor type

tag: biochemical relapse_(bcr)


title: Prostate_tumor_RIB0020714

tag: gleason score

tag: pathological t_stage


title: Basal cells IgG biol rep 1 [Ba_muIgG_1]

value: Mammary epithelial cells


title: LP cells H3K27me3, biol rep 1 [LP_H3K27me3_1]


title: Basal cells H3K27ac biol rep 2 [Ba_H3K27ac_2]

value: H3K27ac (abcam Cat#4729)


title: genomic DNA from Whole Blood [22B]

description: Resistance Training Whole Blood

value: Resistance Training


title: genomic DNA from Whole Blood [21B]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [20A]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [19A]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [20B]

description: Resistance Training Whole Blood


title: Prostate_tumor_RIB0020771

value: FFPE PCa biopsy

tag: pathological n_stage

tag: total psa_(ng/ml,_pre-biopsy)


title: genomic DNA from Whole Blood [19B]

description: Resistance Training Whole Blood

tag: tissue


title: Basal cells H3K27ac biol rep 1 [Ba_H3K27ac_1]

tag: cell type


title: Basal cells H3K9me3 biol rep 2 [Ba_H3K9me3_2]

tag: strain

value: H3K9me3 (abcam Cat#8898)


title: genomic DNA from Whole Blood [18B]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [24B]

description: Resistance Training Whole Blood


title: Prostate_tumor_RIB0015736

value: Primary tumor

value: yes

tag: tumor cell_content_(%)


title: genomic DNA from Whole Blood [17A]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [17B]

description: Resistance Training Whole Blood


title: Basal cells H3K9me3 biol rep 1 [Ba_H3K9me3_1]

tag: developmental stage

tag: Sex


title: Prostate_tumor_RIB0015797


title: genomic DNA from Whole Blood [16A]

description: Resistance Training Whole Blood

tag: gender

tag: disease


title: genomic DNA from Whole Blood [16B]

description: Resistance Training Whole Blood

tag: group


title: Prostate_tumor_RIB0015787

tag: alternative sample_id

value: no


title: genomic DNA from Whole Blood [21A]

description: Resistance Training Whole Blood


title: Basal cells H3K9me2 biol rep 2 [Ba_H3K9me2_2]

value: FVB/N mice

tag: antibody

value: H3K9me2 (abcam Cat#1220)

tag: mouse pool


title: genomic DNA from Whole Blood [15A]

description: Resistance Training Whole Blood


title: Basal cells H3K9me2 biol rep 1 [Ba_H3K9me2_1]

value: myoepithelial

value: adult (9-10 weeks of age)


title: Prostate_tumor_RIB0020703

tag: tumor type

tag: biochemical relapse_(bcr)


title: Prostate_tumor_RIB0015812

tag: gleason score

tag: pathological t_stage


title: genomic DNA from Whole Blood [18A]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [15B]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [13A]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [14A]

description: Resistance Training Whole Blood


title: Basal cells H3K9ac biol rep 1 [Ba_H3K9ac_1]

value: female

value: H3K9ac (abcam Cat#4441)


title: Prostate_tumor_RIB0015832

tag: pathological n_stage

tag: total psa_(ng/ml,_pre-biopsy)


title: Basal cells H3K9ac biol rep 2 [Ba_H3K9ac_2]

tag: tissue

tag: cell type


title: genomic DNA from Whole Blood [12A]

description: Resistance Training Whole Blood

value: Female

value: Polycystic Ovary Syndrome


title: genomic DNA from Whole Blood [13B]

description: Resistance Training Whole Blood

value: Whole Blood


title: genomic DNA from Whole Blood [11A]

description: Resistance Training Whole Blood


title: Basal cells H2AK119ub biol rep 2 [Ba_H2AK119ub_2]

value: Mammary epithelial cells

tag: strain

value: H2AK119ub (CST Cat#8240)


title: Prostate_tumor_RIB0015775

tag: tumor cell_content_(%)


title: Prostate_tumor_RIB0015807


title: Basal cells H2AK119ub biol rep 1 [Ba_H2AK119ub_1]

tag: developmental stage

tag: Sex


title: genomic DNA from Whole Blood [12B]

description: Resistance Training Whole Blood

tag: gender

tag: disease

value: Resistance Training


title: genomic DNA from Whole Blood [10A]

description: Resistance Training Whole Blood

tag: group


title: Basal cells H3K36me3 biol rep 2 [Ba_H3K36me3_2]

tag: antibody

value: H3K36me3 (Active Motif Cat#61021)


title: genomic DNA from Whole Blood [10B]

description: Resistance Training Whole Blood


title: Prostate_tumor_RIB0015804

value: FFPE PCa biopsy

tag: alternative sample_id


title: Prostate_tumor_RIB0018104

tag: tumor type

value: Primary tumor


title: genomic DNA from Whole Blood [9A]

description: Resistance Training Whole Blood


title: Basal cells H3K36me3 biol rep 1 [Ba_H3K36me3_1]

tag: mouse pool


title: Prostate_tumor_RIB0025310

tag: biochemical relapse_(bcr)

value: yes

tag: gleason score


title: genomic DNA from Whole Blood [9B]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [8A]

description: Resistance Training Whole Blood


title: Basal cells H3K4me3 biol rep 2 [Ba_H3K4me3_2]

value: H3K4me3 (Merck Cat#07-473)


title: genomic DNA from Whole Blood [8B]

description: Resistance Training Whole Blood


title: Prostate_tumor_RIB0025403

tag: pathological t_stage

tag: pathological n_stage


title: Prostate_tumor_RIB0025284

tag: tissue

tag: total psa_(ng/ml,_pre-biopsy)


title: genomic DNA from Whole Blood [7A]

description: Resistance Training Whole Blood


title: Basal cells H3K4me3 biol rep 1 [Ba_H3K4me3_1]

tag: cell type

tag: strain

value: FVB/N mice


title: genomic DNA from Whole Blood [6A]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [7B]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [14B]

description: Resistance Training Whole Blood


title: Basal cells H3K4me1 biol rep 2 [Ba_H3K4me1_2]

tag: developmental stage

value: H3K4me1 (abcam Cat#8895)


title: Prostate_tumor_RIB0025281

tag: tumor cell_content_(%)


title: genomic DNA from Whole Blood [11B]

description: Resistance Training Whole Blood

tag: gender


title: genomic DNA from Whole Blood [6B]

description: Resistance Training Whole Blood

tag: disease


title: genomic DNA from Whole Blood [5A]

description: Resistance Training Whole Blood

tag: group


title: genomic DNA from Whole Blood [4B]

description: Resistance Training Whole Blood


title: genomic DNA from Whole Blood [3B]

description: Resistance Training Whole Blood


title: Basal cells H3K27me3, biol rep 2 [Ba_H3K27me3_2]

value: myoepithelial

tag: Sex

tag: antibody


title: Prostate_tumor_RIB0025247

tag: alternative sample_id

tag: tumor type


title: Basal cells H3K4me1 biol rep 1 [Ba_H3K4me1_1]

value: adult (9-10 weeks of age)

tag: mouse pool


title: genomic DNA from Whole Blood [3A]

description: Resistance Training Whole Blood


title: Prostate_tumor_RIB0025285

tag: biochemical relapse_(bcr)

tag: gleason score


title: Basal cells H3K27me3, biol rep 1 [Ba_H3K27me3_1]

value: female


title: genomic DNA from Whole Blood [2B]

description: Resistance Training Whole Blood


title: ML cells, biol rep 2 [ML_ATAC_2]

data_processing:
Libraries were sequenced on an Illumina NextSeq 500, generating 80 bp paired-end reads.
Fastq files for technical replicates were merged and reads were aligned to the mouse genome mm10 by Bowtie2 with duplicates removed with Picard tools MarkDuplicates command and mitochondrial reads excluded.
BigWig files were generated with BamCoverage from Deeptools with bamCoverage --normalizeUsing RPKM.
Assembly: mm10
Supplementary files format and content: *.bw: BigWig, a coverage track generated from the mapped read fragments. The coverage is calculated as the number of reads per 50 bp bin. Coverage was normalization by reads Per Kilobase per Million mapped reads (RPKM).

extract_protocol: Transposed genomic DNA was extracted and amplified for sequencing as per Buenrostro et al. 2015.

value: mature luminal


title: genomic DNA from Whole Blood [1B]

description: Resistance Training Whole Blood

value: Female


title: genomic DNA from Whole Blood [1A]

description: Resistance Training Whole Blood

value: Polycystic Ovary Syndrome


title: ML cells, biol rep 1 [ML_ATAC_1]


title: LP cells, biol rep 3 [LP_ATAC_3]

value: luminal progenitor


title: genomic DNA from Whole Blood [5B]

description: Resistance Training Whole Blood

value: Whole Blood


title: VNLG152_MDA_MB231_rep3

city: Baltimore

first: Carrie

last: McCracken

state: MD

address: 670 W. Baltimore St

department: Institute for Genome Sciences

institute: Institute of Genome

data_processing:
Raw data were analyzed using the Hisat aligner with stand-specific settings.
Differential gene expression was analyzed using the DESeq R package (Bioconductor) and the negative binomial model
Criteria for significant differences in gene expression were (1) false discovery rate (FDR) <0.05, (2) expression level >10th percentile, and (3) ≥ 2-fold change.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: htseq output with gene counts for each sample

source_name: Cell line drived from breast cancer tissue

growth_protocol: Standard (ATCC)

extract_protocol:
Qiagen RNeasy Micro Kit (50), Cat. No. / ID: 74004
PolyA-enriched, strand-specific RNA libraries were constructed and 100bp paired-end reads were sequenced on an Illumina NovaSeq 6000 platform

tag: cell line

value: Cancer cell, adherent

tag: treatment

value: VNLG-152R 10 µM 24hrs


title: Prostate_tumor_RIB0025361

tag: tissue

tag: pathological t_stage

tag: pathological n_stage

tag: total psa_(ng/ml,_pre-biopsy)


title: VNLG152_MDA_MB231_rep2

value: Cell line drived from breast cancer tissue

tag: cell type


title: Prostate_tumor_RIB0025271

value: FFPE PCa biopsy

tag: tumor cell_content_(%)


title: Prostate_tumor_RIB0018137

value: Primary tumor


title: genomic DNA from Whole Blood [4A]

description: Resistance Training Whole Blood

tag: gender

tag: disease

value: Resistance Training


title: Prostate_tumor_RIB0027342

value: yes


title: Prostate_tumor_RIB0025324


title: Control_MDA_MB231_rep3

value: DMSO 24hrs


title: Control_MDA_MB231_rep2


title: Control_MDA_MB231_rep1


title: LP cells, biol rep 1 [LP_ATAC_1]

value: Mammary epithelial cells

tag: strain

value: FVB/N mice

tag: developmental stage

tag: Sex


title: LP cells, biol rep 2 [LP_ATAC_2]

value: adult (9-10 weeks of age)


title: ML cells, biol rep 3 [ML_ATAC_3]

value: female


title: Prostate_tumor_RIB0025302

tag: alternative sample_id

tag: tumor type


title: Basal cells, biol rep 3 [Ba_ATAC_3]

value: myoepithelial

tag: mouse pool


title: VNLG152_MDA_MB231_rep1


title: genomic DNA from Whole Blood [2A]

description: Resistance Training Whole Blood

value: Female

tag: group


title: Tspan8+ Basal cells, biol rep 3

first: Yunshun

last: Chen

state: VIC

address: 1G Royal Parade

department: ACRF Cancer Biology and Stem Cells

data_processing:
Libraries were sequenced on an Illumina NextSeq 500, generating 80 bp paired-end reads.
Reads were aligned to the mouse genome mm10 by the align function of the Rsubread software tool version 2.6.4.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

extract_protocol:
Total RNA was extracted using Qiagen's miRNeasy kit and DNase treated.
100ng of total RNA was used to construct libraries following Illumina's recommended protocol for TruSeq RNA Library Prep Kit v2.

value: Tspan8+ myoepithelial (quiescent basal, QBa)


title: Prostate_tumor_RIB0015770

tag: biochemical relapse_(bcr)

tag: gleason score


title: Basal cells, biol rep 2 [Ba_ATAC_2]

tag: tissue


title: Tspan8- Basal cells, biol rep 3

value: Tspan8- myoepithelial (active basal, ABa)


title: Prostate_tumor_RIB0025382

tag: pathological t_stage


title: Prostate_tumor_RIB0025356

tag: pathological n_stage


title: Prostate_tumor_RIB0025346

tag: total psa_(ng/ml,_pre-biopsy)


title: Basal cells, biol rep 1 [Ba_ATAC_1]

tag: cell type


title: Prostate_tumor_RIB0025308

tag: tumor cell_content_(%)


title: Prostate_tumor_RIB0018135


title: Tspan8+ Basal cells, biol rep 2


title: Tspan8- Basal cells, biol rep 1


title: Prostate_tumor_RIB0025301


title: ML cells, biol rep 3

data_processing:
Libraries were sequenced on an Illumina NextSeq 500, generating 80 bp paired-end reads.
Reads were aligned to the mouse genome mm10 by the subjunc function of the Rsubread software tool version 1.34.4.
Read counts were summarized by Entrez Gene ID using the Rsubread featureCounts function and Rsubread's inbuilt RefSeq annotation.
Assembly: mm10
Supplementary files format and content: Tab-delimited text files; columns represent Entrez Gene ID, gene length (total base count of all exons) and the number of reads mapped to that gene.

value: mature luminal


title: Tspan8+ Basal cells, biol rep 1


title: Prostate_tumor_RIB0025358


title: Prostate_tumor_RIB0025331


title: Prostate_tumor_RIB0025357


title: Prostate_tumor_RIB0018152


title: Prostate_tumor_RIB0025348


title: Prostate_tumor_RIB0025349


title: ML cells, biol rep 1


title: LP cells, biol rep 3

value: luminal progenitor


title: ML cells, biol rep 2


title: Tspan8- Basal cells, biol rep 2


title: Prostate_tumor_RIB0007090


title: LP cells, biol rep 2


title: LP cells, biol rep 1


title: Prostate_tumor_RIB0025456


title: Prostate_tumor_RIB0018198


title: Basal cells, biol rep 3


title: Basal cells, biol rep 1


title: Prostate_tumor_RIB0018156


title: Basal cells, biol rep 2


title: CPI and FMT treated replicate 2

city: London

first: Nick

last: Powell

address: Du Cane Road

department: Department of Metabolism, Digestion and Reproduction

country: United Kingdom

institute: Imperial College London

library_source: transcriptomic single cell

data_processing:
Raw single-cell RNA-seq data were processed using 10X Genomics Cell Ranger (v3.0.1)
The raw 10X Genomics sequencing libraries were processed using the Cell Ranger suite v.3.0.1.
Base call files were demultiplexed with the "cellranger mkfastq" pipeline.
Single-cell feature counts for each library were calculated with the "cellranger count" pipeline using the pre-built mouse (mm10 v. 3.0.0) reference data.
Assembly: mm10
Supplementary files format and content: For each sample, the compressed UMI count matrix in sparse matrix format (.mtx.gz), the compressed gene name information in tab-separated value format (tsv.gz), and the compressed cell barcode identifiers in tab-separated value format (.tsv.gz)

source_name: colon

extract_protocol:
2cm distal colon segments were taken from mice after confirmation of death, and placed into 1 ml of RNA later. RNA was extracted with Qiazol reagent (Invitrogen). Distilled solutions of RNA were purified using chloroform and isopropanol and eluted with ethanol before being resuspended in RNAse free water. RNA was cleaned up using the Qiagen RNeasy Microkit according to the manufacturer’s guidelines.
Libraries were prepared using 10x Chromium Single Cell 3' Reagent Kits (v3)

treatment_protocol: Faecal content extracted from the caecum of TRUC mice was spun down and reconstituted in sterile PBS with 25% glycerol and then 200µl was orally gavaged into mice at the beginning of the experiment only. Mice treated with immune checkpoint blockade drugs were intraperitoneally administered anti-CTLA-4 (9H10, BioXCell) using doses of 200μg and anti-PD-1 (RMP1-14, BioXCell) at a dose of 250μg once per week for 3 weeks.

value: Balb/C

value: colon

tag: treatment

value: Combination CTLA-4 and PD-1 therapy and faecal microbiota transplant


title: CPI and FMT treated replicate 3


title: CPI and FMT treated replicate 1


title: Prostate_tumor_RIB0018200

value: FFPE PCa biopsy

value: Primary tumor


title: Prostate_tumor_RIB0018167

value: yes


title: PC3, input, bio rep 2

description: PC3_3_H3K9me3_R1__files_to_merge.txt_merged.srt.nodup_x_ctl.pooled.200M.peaks.sorted.qval0.05.bed

data_processing:
ChIP-Seq mapped with Encode ChIP pipeline with default settings.
Cut&Run  data mapped with Bowtie2 and peak called with SEACR
RNA-seq mapped with Kallisto to v38 transcripts
Assembly: hg38
Supplementary files format and content: Peaks bed, RNA abundance

growth_protocol: naïve DU145, PC3 and VCaP cells were cultivated in DMEM 10% FBS and 1x penicillin/streptomycin, naïve 22Rv1 and LNCaP in RPM1 10% FBS and 1x penicillin/streptomycin, PWR1E and RWPE1 were cultivated in keratinocyte SFM with 1x penicillin/streptomycin, while CRISPRi 22Rv1 clonal cell lines were grown in RPMI 10% FBS, 1x penicillin/streptomycin, Blasticidin 6ug/ml

extract_protocol:
For ChIP-seq cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using the Diagenode Bioruptor 300. For Cut&Run cells were incubated with concanavalinA beads, followed by incubation with antibody with digitonin-containing buffer. After washing, samples were incubated with G-protein coupled with MNase and exposed DNA was digested by activating MNase with CaCl2 for 30 min in ice bath. For RNA-seq, whole RNA was extracted using Qiagen RNeasy extraction kit
ChIP-seq and Cut&Run libraries were prepared using the Takara Thruplex Library Preparation Kit. 10 ul of  eluted DNA was used as starting material for input and/or IP samples. Post amplification libraries were size selected at 250-450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.

tag: cell line

tag: disease

value: prostate cancer

tag: chip antibody


title: Prostate_tumor_RIB0018171


title: Control replicate 2

tag: strain


title: Prostate_tumor_RIB0018142

tag: alternative sample_id


title: AD, ReN cells, multiple treatments

city: Charlestown

first: Joseph

last: Park

state: MA

address: 114 16th Street

department: Neurology

institute: Massachusetts General Hospital/Harvard Medical School

description:
InDrop
AD (A5) PBS + IgG 01, seurat.list.matrix_a5_01_a.csv
AD (A5) PBS + IgG 02, seurat.list.matrix_a5_01_b.csv
AD (A5) Irisin + IgG 01, seurat.list.matrix_a5_02_a.csv
AD (A5) Irisin + IgG 02, seurat.list.matrix_a5_02_b.csv
AD (A5) Irisin + anti Integrin aV/B5 01, seurat.list.matrix_a5_03_a.csv
AD (A5) Irisin + anti Integrin aV/B5 02, seurat.list.matrix_a5_03_b.csv
AD (H10) PBS + IgG 01, seurat.list.matrix_h10_01_a.csv
AD (H10) PBS + IgG 02, seurat.list.matrix_h10_01_b.csv
AD (H10) Irisin + IgG 02, seurat.list.matrix_h10_02_b.csv
AD (10) Irisin + anti Integrin aV/B5 01, seurat.list.matrix_h10_03_a.csv
AD (10) Irisin + anti Integrin aV/B5 02, seurat.list.matrix_h10_03_b.csv

data_processing:
Demultiplexing, barcode processing, and gene count matrix files genereated.
Assembly: hg38
Supplementary files format and content: gene name and count matrix file

source_name: ReN cells

extract_protocol:
Cells treated with Accutase at room termperature for 10mins and then dissociated to disperse into single cells. Shorlty after that Live/cell dead assay performed to count live cells and then loaded into InDrop in-house equipment for the capturing of the single cells.
After generating barcoded cDNA from single cells, the droplets are broken and cDNA is processed for next-gen sequencing (Nature Protocol, ; doi:10.1038/nprot.2016.154). Briefly, purification of the cDNA library and second-strand synthesis, followed by in vitro transcription (IVT) using T7 RNA polymerase. The amplified antisense RNA is fragmented using zinc-ion-mediated cleavage, and converted into a DNA library ready for Illumina sequencing by a second RT reaction and a few cycles of PCR. This library preparation step takes ~2 d and includes two quality control (QC) steps. As detailed in Figure 3, a library index is added during the final PCR to allow pooling of multiple libraries for sequencing in a single run. Our protocol is designed to work with all Illumina sequencing platforms and can possibly be adapted to work with different sequencers.

tag: disease state

value: AD

value: ReN cells

value: Brain cells (Neuron, astrocyte)

tag: genotype

value: no, Irisin, Irisin + Anti Integrin aV/B5


title: Control replicate 3


title: Control replicate 1


title: PC3, H3K9me3, bio rep 2


title: PC3, input, bio rep 1

description: PC3_2_H3K9me3_R1__files_to_merge.txt_merged.srt.nodup_x_ctl.pooled.200M.peaks.sorted.qval0.05.bed


title: PC3, H3K9me3, bio rep 1


title: PWR1E, H3K9me3, bio rep 2

description: PWR1E__3_-_H3K9me3_S18_L002_R1_001.merged.srt.nodup_x_ctl.pooled.peaks.sorted.qval0.05.bed


title: PWR1E, H3K9me3, bio rep 1

description: PWR1E__2_-_H3K9me3_S17_L001_R1_001.merged.srt.nodup_x_ctl.pooled.peaks.sorted.qval0.05.bed


title: Prostate_tumor_RIB0025328

tag: tumor type


title: Prostate_tumor_RIB0025333

tag: biochemical relapse_(bcr)


title: PWR1E, input, bio rep 2


title: PWR1E, input, bio rep 1


title: Prostate_tumor_RIB0007043

tag: gleason score


title: Prostate_tumor_RIB0018164

tag: tissue


title: Prostate_tumor_RIB0015779

tag: pathological t_stage


title: OLG,  Flag-tagged Sp7

city: Chicago

first: Benayahu

last: Elbaz

state: Illinois

address: 303 E. Chicago Ave. Ward 7-641. Chicago, IL 60611

institute: Northwestern University

data_processing:
First, reads with low-quality base calls are trimmed off from the 3' end of the reads. Second, reads were trimmed from 3' end with a phred score > 20, using Trim Galore v0.6.7.
ChIP-seq reads were aligned to the UCSC mm10 genome using Bowtie2 version 2.4.5. Alignments with MAPQ smaller than 5 were filtered and only uniquely/primary mapping reads were retained using SAMtools v1.14. PCR duplicates were removed using Picard v2.26.10.
Peak detection was carried out with HOMER version 4.11, findPeaks command were used with factor style for the chip compred to the input file. findMotifs.pl command were used to identify enriched motifs within the alled peak list.
BigWig files were generated using  deepTools package version 3.5.1. with the help of the bamCoverage command. The resulting BigWig files were normalised using the RPKM option. Other options applied were ‘--binSize 20’, ‘--extendReads’ and ‘--centerReads’ for highest resolution. The computeMatrix command was used together with the mm10 blacklist to exclude problematic regions. Heat maps were generated with plotHeatmap command.
Assembly: mm10
Supplementary files format and content: BigWig, Called peaks

source_name: Primary cultured oligodendrocytes derived from the brain of WT mice

growth_protocol: Primary oligodendrocyte progenitor cells were isolated and maintained in Sato serum-free Dulbecco's modified Eagle medium with the addition of B27 supplement. platelet-derived growth factor-AA (PDGF-AA; 10 ng/ml), neurotrophin-3 (1 ng/ml), forskolin (0.01 mM), and ciliary neurotrophic factor (CNTF; 10 ng/ml) were added.

extract_protocol:
The cells were washed with PBS (to remove cell debris), fixed in 1% PFA for 10 min, incubated with glycine, and then were flash frozen.  After quenching and cell lysis, chromatin was sonicated using aBioruptor, Diagenode with high power with 40 cycles of 30 sec “on”, 45 sec “off”. chromatin was incubated over night with 4.5ug antibody, washes was done acording to: Hojo H, Ohba S, He X, Lai LP, McMahon AP. Sp7/Osterix Is Restricted to Bone-Forming Vertebrates where It Acts as a Dlx Co-factor in Osteoblast Specification. Dev Cell. 2016 May 9;37(3):238-53. doi: 10.1016/j.devcel.2016.04.002. Epub 2016 Apr 28. PMID: 27134141; PMCID: PMC4964983.
ChIP-seq libraries were prepared  essentially as described in PMID: 23429716.  Libraries were amplified using 14 cycles on the thermocycler.  Libraries were validated using tape station and Qubit.

treatment_protocol: To stimulate differentiation, the platelet-derived growth factor-AA (PDGF-AA) was removed and triiodothyronine (40 ng/ml) was added. Media was changed every other day and differentiated cells were collected after 5 days in differentiation media.

value: Anti-Flag (Sigma F1804)


title: VCaP, input, bio rep 2

description: VCaP_2_H3K9me3_R1__files_to_merge.txt_merged.srt.nodup_x_ctl.pooled.peaks.sorted.qval0.05.bed

source_name: VCaP

value: VCaP


title: Prostate_tumor_RIB0018117

tag: pathological n_stage


title: RWPE1, H3K9me3, bio rep 2

description: RWPE1_2_H3K9me3_R1__files_to_merge.txt_merged.srt.nodup_x_ctl.pooled.peaks.sorted.qval0.05.bed


title: Prostate_tumor_RIB0025443

value: no

tag: total psa_(ng/ml,_pre-biopsy)


title: VCaP, H3K9me3, bio rep 2


title: RWPE1, input, bio rep 1

description: RWPE1_1_H3K9me3_R1__files_to_merge.txt_merged.srt.nodup_x_ctl.pooled.peaks.sorted.qval0.05.bed


title: RWPE1, input, bio rep 2


title: OLG, matureSP7KO, Rep1

data_processing:
First, reads with low-quality base calls are trimmed off from the 3' end of the reads. Second, reads were trimmed from 3' end with a phred score > 20, using Trim Galore v0.6.7.
ATAC-seq reads were aligned to the UCSC mm10 genome using Bowtie2 version 2.4.5. Alignments with MAPQ smaller than 5 were filtered and only uniquely mapping reads with at most two mismatches were retained using SAMtools v1.14.
Peak detection was carried out with MACS2 version 2.2.7.1, callpeak command were used with mm as the genome and both treatment and control specified. To identify differential regions we used MACS2 sub commands: predictd, callpeak, and bdgdiff. This results in three sets of regions, either specific to one or the other sample, or common to both.
BigWig files were generated using  deepTools package version 3.5.1. with the help of the bamCoverage command. The resulting BigWig files were normalised using the RPKM option. The ATAC-seq replicate samples were combined in order to produce the processed data files.
Assembly: mm10
Supplementary files format and content: BigWig

source_name: Primary cultured mature oligodendrocytes derived from the brain of the Sp7-ablated mice

growth_protocol: Primary cultured oligodendrocyte derived from brain of the Sp7fl/fl; Olig2-Cre mice and Cre negative Sp7fl/fl mice (used as control) were cultured in proliferation media, platelet-derived growth factor-AA (PDGF-AA; 10 ng/ml, PeproTech #100-13A), neurotrophin-3 (1 ng/ml, PeproTech #450-03), forskolin (Sigma Aldrich [0.01 mM]), and ciliary neurotrophic factor (CNTF; 10 ng/ml, PeproTech #450-13) were added. To stimulate differentiation, PDGF-AA was removed and triiodothyronine (40 ng/ml, Sigma # T6397) was added. Oligodendrocyte progenitor cells that were grown in differentiation for three days in differentiation media were used for pre-mature oligodendrocytes, and oligodendrocyte progenitor cells that were grown for five days in differentiation media were used for mature oligodendrocyte.

extract_protocol:
libraries preparation was performed using the ATAC-seq Kit (Active Motif cat#53150) according to manufacturer instructions
libraries was performed using the ATAC-seq Kit (Active Motif cat#53150) according to manufacturer instructions

treatment_protocol: To stimulate differentiation, the platelet-derived growth factor-AA (PDGF-AA) was removed and triiodothyronine (40 ng/ml) was added.

tag: cell type

value: oligodendrocytes


title: VCaP, H3K9me3, bio rep 1

description: VCaP_1_H3K9me3_R1__files_to_merge.txt_merged.srt.nodup_x_ctl.pooled.peaks.sorted.qval0.05.bed


title: OLG, SP7, WT

value: Primary cultured oligodendrocytes derived from the brain of WT mice

value: Anti-Sp7 (Abcam, ab22552)


title: Prostate_tumor_RIB0025440

tag: tumor cell_content_(%)


title: RWPE1, H3K9me3, bio rep 1


title: Prostate_tumor_RIB0025413

value: pNA


title: OLG matureWT, Rep2

source_name: Primary cultured mature oligodendrocytes derived from the brain of WT mice

value: WT


title: OLG, matureWT, Rep1


title: OLG, matureSP7KO, Rep2


title: OLG, Input

value: none (input)


title: Microglia, 000

city: Clayton

first: Jan

last: Schroeder

address: Building 75 Innovation Walk

department: Anatomy & Developmental Biology

institute: Monash University

description: Microglia, 000

data_processing:
Demultiplexed FASTQ files are single-end reads per sample with UMI barcode are added to the read name.
We used STAR (v2.5.2b) to align the reads to  the mm10 Ensembl reference genome (v93). Read deduplication based on UMIs was performed with je markdupes (v1.2).
and transcript read counts calculated with featureCounts (v1.5.2) against mm10 Ensembl transcripts annotation.
Genome_build: GRCm38
Supplementary_files_format_and_content: Transcript counts for all samples. Gene meta data columns at the start. Tab separated file format.

source_name: Microglia

extract_protocol:
RNA extraction from  microglia was performed on QIAcube (Qiagen) using the RNeasy Micro Kit (Qiagen, #74004).
RNA libraries were prepared for sequencing using standard Illumina protocols

value: Microglia

tag: diet

value: HAMSAB

tag: Sex

value: F


title: Prostate_tumor_RIB0025499

value: FFPE PCa biopsy

value: Primary tumor


title: DU145, input, bio rep 2

description: DU145_2_H3K9me3_R1__files_to_merge.txt_merged.srt.nodup_x_ctl.pooled.peaks.sorted.qval0.05.bed

tag: cell line

tag: disease

value: prostate cancer


title: Prostate_tumor_RIB0025479


title: LNCaP, input, bio rep 2

description: LNCaP_2_H3K9me3_R1__files_to_merge.txt_merged.srt.nodup_x_ctl.pooled.peaks.sorted.qval0.05.bed

source_name: LNCaP

value: LNCaP

tag: chip antibody


title: LNCaP, H3K9me3, bio rep 1

description: LNCaP_1_H3K9me3_R1__files_to_merge.txt_merged.srt.nodup_x_ctl.pooled.peaks.sorted.qval0.05.bed


title: LNCaP, H3K9me3, bio rep 2


title: Prostate_tumor_RIB0025424

tag: alternative sample_id


title: Microglia, 3012

description: Microglia, 3012

value: Control

value: M


title: VCaP, input, bio rep 1

value: VCaP


title: DU145, input, bio rep 1

description: DU145_1_H3K9me3_R1__files_to_merge.txt_merged.srt.nodup_x_ctl.pooled.peaks.sorted.qval0.05.bed


title: DU145, H3K9me3, bio rep 2


title: Microglia, 3011

description: Microglia, 3011


title: Prostate_tumor_RIB0025416

value: no


title: DU145, H3K9me3, bio rep 1


title: Microglia, 3009

description: Microglia, 3009

value: AD


title: 22Rv1, input, bio rep 1

description: 22Rv1_1_H3K9me3_R1__files_to_merge.txt_merged.srt.nodup_x_ctl.pooled.peaks.sorted.qval0.05.bed


title: LNCaP, input, bio rep 1


title: Prostate_tumor_RIB0025427


title: Prostate_tumor_RIB0025419


title: 22Rv1, input, bio rep 2

description: 22Rv1_2_H3K9me3_R1__files_to_merge.txt_merged.srt.nodup_x_ctl.pooled.peaks.sorted.qval0.05.bed


title: 22Rv1, H3K9me3, bio rep 2


title: Prostate_tumor_RIB0025461

value: yes


title: Microglia, 3006

description: Microglia, 3006


title: CRISPRi 22Rv1 clone3, dCas9, bio rep 1 [clone3_Ctrl_2]

source_name: CRISPRi 22Rv1

value: CRISPRi 22Rv1

tag: treatment

value: nucleofection Ctrl guides combo


title: CRISPRi 22Rv1 clone3, dCas9, bio rep 1 [clone3_Tigger3a_1]

value: nucleofection Tigger3a guides combo


title: CRISPRi 22Rv1 clone3, dCas9, bio rep 1 [clone3_Tigger3a_2]


title: CRISPRi 22Rv1 clone3, dCas9, bio rep 1 [clone3_Ctrl_1]


title: Microglia, 3007

description: Microglia, 3007

tag: genotype


title: Prostate_tumor_RIB0025497

tag: tumor type


title: CRISPRi 22Rv1 clone2, dCas9, bio rep 1 [clone2_Tigger3a_1]


title: Prostate_tumor_RIB0025404

tag: biochemical relapse_(bcr)


title: Microglia, 3005

description: Microglia, 3005

value: WT


title: Microglia, 3000

description: Microglia, 3000

value: Microglia

value: zero fiber


title: CRISPRi 22Rv1 clone2, dCas9, bio rep 1 [clone2_Ctrl_2]


title: CRISPRi 22Rv1 clone2, dCas9, bio rep 1 [clone2_Ctrl_1]


title: Prostate_tumor_RIB0025444

tag: gleason score


title: Microglia, 2993

description: Microglia, 2993

value: F


title: CRISPRi 22Rv1 clone1, dCas9, bio rep 1 [clone1_Tigger3a_2]


title: 22Rv1, H3K9me3, bio rep 1


title: CRISPRi 22Rv1 clone1, dCas9, bio rep 1 [clone1_Tigger3a_1]


title: Prostate_tumor_RIB0025463

tag: tissue

value: FFPE PCa biopsy


title: Microglia, 2992

description: Microglia, 2992


title: CRISPRi 22Rv1 clone3, dCas9, bio rep 1 [Jun_9th_Clone_6_Tiggr2]

description: Jun_9th_Clone_6_Tiggr2_seacr_top0.05.peaks.stringent.bed

data_processing:
ChIP-Seq mapped with Encode ChIP pipeline with default settings.
Cut&Run  data mapped with Bowtie2 and peak called with SEACR
RNA-seq mapped with Kallisto to v38 transcripts
Assembly: hg38
Supplementary files format and content: Peaks bed, RNA abundance
Library strategy: Cut & Run

value: AR

value: nucleofection Tigger3a/Ctrl guides combo


title: CRISPRi 22Rv1 clone1, dCas9, bio rep 1 [clone1_Ctrl_2]

value: prostate cancer


title: Microglia, 2991

description: Microglia, 2991


title: CRISPRi 22Rv1 clone1, dCas9, bio rep 1 [clone1_Ctrl_1]


title: Prostate_tumor_RIB0025412

description: Gene expression of prostate biopsy prior to RP (FFPE)

value: Primary tumor

tag: pathological t_stage


title: CRISPRi 22Rv1 clone3, dCas9, bio rep 1 [Jun_9th_Clone_6_Tiggr1]

description: Jun_9th_Clone_6_Tiggr1_seacr_top0.05.peaks.stringent.bed


title: CRISPRi 22Rv1 clone2, dCas9, bio rep 1 [clone2_Tigger3a_2]


title: Microglia, 2990

description: Microglia, 2990


title: CRISPRi 22Rv1 clone3, dCas9, bio rep 1 [Jun_9th_Clone_6_Neg1]

description: Jun_9th_Clone_6_Neg1_seacr_top0.05.peaks.stringent.bed


title: CRISPRi 22Rv1 clone2, dCas9, bio rep 1 [July_3rd_Clone_5_Neg2]

description: July_3rd_Clone_5_Neg2_seacr_top0.05.peaks.stringent.bed


title: CRISPRi 22Rv1 clone3, dCas9, bio rep 1 [Jun_9th_Clone_6_Neg2]

description: Jun_9th_Clone_6_Neg2_seacr_top0.05.peaks.stringent.bed


title: Microglia, 2986

description: Microglia, 2986

value: HAMSAB

value: M


title: CRISPRi 22Rv1 clone2, dCas9, bio rep 1 [July_3rd_Clone_5_Neg1]

description: July_3rd_Clone_5_Neg1_seacr_top0.05.peaks.stringent.bed


title: Prostate_tumor_RIB0025472

value: no

tag: pathological n_stage


title: CRISPRi 22Rv1 clone2, dCas9, bio rep 1 [July_3rd__Clone_5_Tiggr2]

description: July_3rd__Clone_5_Tiggr2_seacr_top0.05.peaks.stringent.bed


title: Prostate_tumor_RIB0025484

tag: total psa_(ng/ml,_pre-biopsy)


title: Microglia, 2989

description: Microglia, 2989

tag: cell type

value: AD


title: Prostate_tumor_RIB0025476

tag: tumor cell_content_(%)


title: CRISPRi 22Rv1 clone1, dCas9, bio rep 1 [July_3rd_Clone_1_Neg3]

description: July_3rd_Clone_1_Neg3_seacr_top0.05.peaks.stringent.bed


title: CRISPRi 22Rv1 clone1, dCas9, bio rep 1 [July_3rd_Clone_1_Neg1]

description: July_3rd_Clone_1_Neg1_seacr_top0.05.peaks.stringent.bed


title: Prostate_tumor_RIB0025490

value: yes


title: CRISPRi 22Rv1 clone2, dCas9, bio rep 1 [July_3rd__Clone_5_Tiggr1]

description: July_3rd__Clone_5_Tiggr1_seacr_top0.05.peaks.stringent.bed

value: CRISPRi 22Rv1


title: Microglia, 2979

description: Microglia, 2979

tag: diet

value: Control


title: Prostate_tumor_RIB0025425


title: Microglia, 2976

description: Microglia, 2976

tag: Sex


title: Prostate_tumor_RIB0025437


title: CRISPRi 22Rv1 clone1, dCas9, bio rep 1 [July_3rd__Clone_1_Tiggr1]

description: July_3rd__Clone_1_Tiggr1_seacr_top0.05.peaks.stringent.bed

tag: cell line


title: CRISPRi 22Rv1 clone1, dCas9, bio rep 1 [July_3rd__Clone_1_Tiggr3]

description: July_3rd__Clone_1_Tiggr3_seacr_top0.05.peaks.stringent.bed

tag: disease


title: Microglia, 2975

description: Microglia, 2975


title: Microglia, 2974

description: Microglia, 2974


title: NYU994-N (RNA-seq)

city: New York

first: Aristotelis

last: Tsirigos

address: 435 E 30th St

institute: NYU School of Medicine

data_processing:
Base calling and demultiplexing was performed using Illumina bcl2fastq software.
The sequencing reads were adapter- and quality-trimmed with Trimmomatic.
The sequencing reads were aligned to the human genome (build hg38/GRCh38) using the splice-aware STAR aligner.
The featureCounts program was utilized to generate counts for each gene.
The raw counts were normalized using the DESeq2 R package.
Assembly: hg38
Supplementary files format and content: CSV files contain raw and normalized counts for all genes and samples

source_name: Lung adjacent normal

extract_protocol:
DNase treatment to remove genomic DNA, cDNA synthesis from the input RNA, single primer isothermal amplification (SPIA) of the resultant cDNAs, enzymatic fragmentation and construction of unique barcoded libraries, PCR library amplification and a final step to remove rRNA transcripts.
1 ng of total RNA was used to prepare libraries using Trio RNA-Seq library prep kit (Tecan Genomics) following the manufacturer's instructions. The Agencourt AMPure XP bead (Beckman Coulter) purified libraries were quantified using qPCR and the size distribution was checked using Agilent TapeStation 2200.

tag: patient

value: Lung adjacent normal

tag: progression type

value: No Progression (>5y)

tag: progression

tag: recurrence


title: Prostate_tumor_RIB0025441

tag: alternative sample_id

tag: tumor type


title: NYU965-T (RNA-seq)

source_name: Tumor

value: Tumor


title: NYU994-T (RNA-seq)


title: Prostate_tumor_RIB0007044

tag: biochemical relapse_(bcr)

tag: gleason score


title: NYU965-N (RNA-seq)

tag: tissue


title: NYU955-T (RNA-seq)


title: Microglia, 2972

description: Microglia, 2972

value: Microglia

tag: genotype

value: WT


title: Prostate_tumor_RIB0015796

value: FFPE PCa biopsy

tag: pathological t_stage

tag: pathological n_stage

tag: total psa_(ng/ml,_pre-biopsy)


title: NYU947-N (RNA-seq)


title: NYU875-T (RNA-seq)


title: Microglia, 2965

description: Microglia, 2965

tag: cell type

tag: diet

value: F


title: NYU875-N (RNA-seq)


title: NYU867-N (RNA-seq)

value: Second Primary

value: Progression


title: Microglia, 2966

description: Microglia, 2966

tag: Sex


title: NYU947-T (RNA-seq)


title: Prostate_tumor_RIB0007018

value: Primary tumor

tag: tumor cell_content_(%)


title: Prostate_tumor_RIB0025323


title: NYU848-T (RNA-seq)

tag: patient


title: NYU848-N (RNA-seq)

tag: progression type


title: NYU831-T (RNA-seq)

tag: progression


title: Microglia, 2964

description: Microglia, 2964

value: HAMSAB


title: Microglia, 2861

description: Microglia, 2861


title: Prostate_tumor_RIB0007086


title: NYU831-N (RNA-seq)

tag: recurrence


title: NYU822-N (RNA-seq)


title: NYU822-T (RNA-seq)


title: NYU784-T (RNA-seq)


title: Prostate_tumor_RIB0025352

tag: alternative sample_id


title: Prostate_tumor_RIB0018049

tag: tumor type


title: Prostate_tumor_RIB0007083

tag: biochemical relapse_(bcr)


title: NYU955-N (RNA-seq)


title: Microglia, 2859

description: Microglia, 2859

value: M


title: Microglia, 2857

description: Microglia, 2857


title: Prostate_tumor_RIB0007088

value: no

tag: gleason score


title: NYU867-T (RNA-seq)

tag: tissue


title: Microglia, 2858

description: Microglia, 2858

tag: genotype

value: AD


title: Prostate_tumor_RIB0007028

value: yes

tag: pathological t_stage


title: NYU784-N (RNA-seq)


title: Microglia, 2854

description: Microglia, 2854


title: Prostate_tumor_RIB0015718

tag: pathological n_stage


title: NYU779-T (RNA-seq)

value: Locoregional

value: Recurrence


title: Microglia, 2851

description: Microglia, 2851

value: Control


title: NYU779-N (RNA-seq)

value: Lung adjacent normal


title: NYU741-T (RNA-seq)

value: Tumor


title: Microglia, 2963

description: Microglia, 2963

value: Microglia


title: NYU780-N (RNA-seq)

value: No Progression (>5y)


title: NYU780-T (RNA-seq)


title: Prostate_tumor_RIB0007020

value: FFPE PCa biopsy

tag: total psa_(ng/ml,_pre-biopsy)


title: NYU741-N (RNA-seq)


title: Prostate_tumor_RIB0007001


title: Microglia, 2850

description: Microglia, 2850

tag: cell type


title: Microglia, 2849

description: Microglia, 2849

tag: diet

value: F


title: NYU713-N (RNA-seq)


title: NYU706-T (RNA-seq)


title: NYU704-N (RNA-seq)

value: Systemic


title: NYU706-N (RNA-seq)


title: Microglia, 2848

description: Microglia, 2848

tag: Sex


title: NYU689-N (RNA-seq)


title: Microglia, 2742

description: Microglia, 2742

value: zero fiber


title: Prostate_tumor_RIB0007026

value: Primary tumor

tag: tumor cell_content_(%)


title: NYU704-T (RNA-seq)

tag: patient

value: Progression


title: Prostate_tumor_RIB0007048


title: Prostate_tumor_RIB0007062


title: NYU689-T (RNA-seq)

tag: progression type


title: Microglia, 2844

description: Microglia, 2844

value: WT


title: NYU675-N (RNA-seq)

tag: progression


title: Prostate_tumor_RIB0007025

value: no


title: NYU669-T (RNA-seq)

tag: recurrence


title: NYU669-N (RNA-seq)


title: NYU713-T (RNA-seq)


title: NYU62-T (RNA-seq)


title: Microglia, 2840

description: Microglia, 2840

value: HAMSAB

value: M

value: AD


title: Microglia, 2841

description: Microglia, 2841


title: Prostate_tumor_RIB0007072

tag: alternative sample_id


title: Prostate_tumor_RIB0025319

tag: tumor type

value: pNA


title: NYU608-N (RNA-seq)

value: Recurrence


title: NYU608-T (RNA-seq)


title: Microglia, 2836

description: Microglia, 2836


title: Prostate_tumor_RIB0007011

tag: biochemical relapse_(bcr)


title: NYU565-T (RNA-seq)


title: Microglia, 2837

description: Microglia, 2837


title: NYU565-N (RNA-seq)

value: Lung adjacent normal


title: NYU539-T (RNA-seq)

value: Tumor


title: NYU675-T (RNA-seq)

value: Locoregional


title: NYU539-N (RNA-seq)


title: NYU502-T (RNA-seq)

value: Second Primary


title: Microglia, 2833

description: Microglia, 2833

value: Microglia


title: Prostate_tumor_RIB0025369

value: FFPE PCa biopsy

tag: gleason score


title: Prostate_tumor_RIB0025343

tag: tissue


title: Prostate_tumor_RIB0007063


title: Microglia, 2831

description: Microglia, 2831

tag: genotype


title: NYU502-N (RNA-seq)


title: NYU50-N (RNA-seq)

value: No Progression (>5y)


title: NYU457-T (RNA-seq)


title: Prostate_tumor_RIB0025332

tag: pathological t_stage


title: NYU62-N (RNA-seq)


title: NYU457-N (RNA-seq)


title: Prostate_tumor_RIB0007059

tag: pathological n_stage


title: Microglia, 2830

description: Microglia, 2830

value: zero fiber


title: NYU454-T (RNA-seq)

value: Systemic


title: Prostate_tumor_RIB0025336

value: Primary tumor

value: yes

tag: total psa_(ng/ml,_pre-biopsy)


title: NYU454-N (RNA-seq)

value: Progression


title: NYU373-T (RNA-seq)


title: NYU373-N (RNA-seq)


title: Microglia, 2828

description: Microglia, 2828

tag: cell type

value: WT


title: NYU359-T (RNA-seq)


title: Microglia, 2827

description: Microglia, 2827

tag: diet

value: F


title: Microglia, 2829

description: Microglia, 2829

tag: Sex


title: NYU50-T (RNA-seq)


title: NYU346-T (RNA-seq)


title: Prostate_tumor_RIB0025388

value: no

tag: tumor cell_content_(%)


title: Microglia, 2832

description: Microglia, 2832

value: M

value: AD


title: Prostate_tumor_RIB0025344


title: Prostate_tumor_RIB0018090


title: NYU359-N (RNA-seq)

tag: patient

value: Lung adjacent normal


title: Prostate_tumor_RIB0025368


title: NYU330-N (RNA-seq)

tag: progression type

value: Recurrence


title: NYU346-N (RNA-seq)

tag: progression


title: NYU32-T (RNA-seq)

value: Tumor

tag: recurrence


title: NYU330-T (RNA-seq)


title: NYU32-N (RNA-seq)


title: Prostate_tumor_RIB0027099

tag: alternative sample_id


title: D1_Prmt5_n2

city: Farmington

first: Sabriya

last: Syed

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

data_processing:
Illumina NextSeq High Output instrument
Fastq files were aligned to the mm10 reference genome with bowtie2. Reads with a mapq score of 20 or greater were retained using Samtools. PCR duplicates were filtered out using picard.
Bam files were converted to bigWig using the package deepTools.
Genome_build: mm10

growth_protocol: Mouse 3T3-L1 cells (obtained from ATCC) were grown in Dulbecco’s Modified Eagle’s Medium (DMEM, #11965118, Gibco) supplemented with 10% calf serum (#26140079, Gibco) and 1% pen/strep (#15140163, Gibco).

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed on fixed and fragmented DNA isolated from 3T3-L1 cultures using anti-Prmt5 antibody (Epigentek, #A3005100).
Sequencing libraries were prepared using the ThruPLEX DNA-seq kits (Rubicon Genomics).

treatment_protocol: Cells were induced to differentiate two days post confluency by addition of growth media (DMEM supplemented with 10% fetal bovine serum and 1% pen/strep) supplemented with 1 μg/ml insulin (Sigma-Aldrich, I9278), 250 ng/ml dexamethasone (Sigma-Aldrich, D4902) and 0.5 mM 3-Isobutyl-1-methylxanthine (Sigma-Aldrich, I5879). Two days after induction of differentiation, fresh growth media supplemented with 1 μg/ml insulin were added.

value: mouse fibroblast-derived preadipocyte line


title: D2_Prmt5_n2


title: D2_input_n2


title: NYU318-T (RNA-seq)


title: NYU307-T (RNA-seq)

value: Second Primary


title: NYU307-N (RNA-seq)


title: NYU318-N (RNA-seq)


title: D1_input_n2


title: Prostate_tumor_RIB0027067

value: FFPE PCa biopsy

tag: tumor type


title: NYU300-N (RNA-seq)

value: Locoregional


title: NYU300-2-T (RNA-seq)


title: D0_input_n2


title: Prostate_tumor_RIB0027085

tag: biochemical relapse_(bcr)

value: pNA


title: NYU279-T (RNA-seq)

value: No Progression (>5y)


title: NYU294-T (RNA-seq)


title: D2_Prmt5_n1


title: Prostate_tumor_RIB0027058

value: Primary tumor

tag: gleason score


title: NYU294-N (RNA-seq)

tag: tissue


title: Prostate_tumor_RIB0007074


title: Prostate_tumor_RIB0027062


title: NYU278-T (RNA-seq)


title: Prostate_tumor_RIB0027090


title: NYU278-N (RNA-seq)


title: NYU268-T (RNA-seq)


title: D1_Prmt5_n1


title: Prostate_tumor_RIB0025488


title: Prostate_tumor_RIB0025483


title: NYU252-T (RNA-seq)


title: NYU268-N (RNA-seq)


title: D0_Prmt5_n2


title: NYU20S-T (RNA-seq)

value: Systemic


title: D0_Prmt5_n1


title: Prostate_tumor_RIB0025414

value: yes


title: NYU20S-N (RNA-seq)

value: Progression


title: NYU279-N (RNA-seq)


title: NYU2005A-T (RNA-seq)


title: Prostate_tumor_RIB0025434


title: Prostate_tumor_RIB0025482


title: NYU1999-T (RNA-seq)


title: NYU2002-N (RNA-seq)

value: Short Follow Up (<5y)


title: NYU2002-T (RNA-seq)


title: Microglia, 2835

description: Microglia, 2835

value: Microglia

value: HAMSAB

tag: genotype

value: WT


title: D2_input_n1


title: human renal proximal tubule epithelial cells [hPTC_CTL]

city: Firenze

first: Roberto

last: Semeraro

address: Viale Pieraccini, 6

department: Medicina Sperimentale e Clinica

country: Italy

institute: Università degli studi di Firenze

data_processing:
Basecall performed with cellranger mkfastq v3.0.1.
Single cell feature counts performed with cellranger count v.3.0.1.
Assembly: GRCh38
Supplementary files format and content: matrix.mtx (filtered count matrix), barcodes.tsv, and features.tsv files generated through cellranger count.

growth_protocol: Primary hPTC cultures (ATCC-PCS-400-010) at passage 3 were put in culture and maintained in REGM (Lonza, CC-3190).

extract_protocol:
The single cell suspension with over 97% viability was run on a 10x Chromium Single Cell instrument (10x Genomics, Pleasanton, CA) following Manufacturer’s instructions
3’ gene expression libraries were constructed following 10x Genomics's instructions
Libraries were sequenced on an Illumina NextSeq500 (Illumina Inc., San Diego, CA).

treatment_protocol: hPTC were seeded at a density of 100,000 cells/6-well. 48h after plating the cells were harvested. A full 6-well plate was employed for each experiment.

value: kidney

value: primary cell culture

tag: developmental stage

value: adult

tag: passage

tag: treatment

value: vehicle


title: human renal proximal tubule epithelial cells [hPTC_TGF]

tag: cell type


title: Prostate_tumor_RIB0025496

value: no

tag: pathological t_stage

tag: pathological n_stage

tag: total psa_(ng/ml,_pre-biopsy)


title: NYU1999-N (RNA-seq)

tag: patient

value: Lung adjacent normal


title: NYU1997A-T (RNA-seq)

value: Tumor

tag: progression type


title: D1_input_n1

value: mouse fibroblast-derived preadipocyte line


title: Prostate_tumor_RIB0025421

value: FFPE PCa biopsy

tag: tumor cell_content_(%)


title: NYU1997-N (RNA-seq)

value: No Progression (>5y)

tag: progression

tag: recurrence


title: breast cancer, R3-S5

city: Tomsk

first: Tashireva

last: Liubov

address: 5 Kooperativny Street, Tomsk

department: Cancer Research Institute

country: Russia

institute: Tomsk National Research Medical Center

description:
Sample info for slides with two samples: One sample
FFPE sample

data_processing:
Raw sequencing data were processed using the 10x Genomix Space Ranger pipeline to generate FASTQ files
Sequences were aligned to hg38 genome to gene expression count using Space Ranger`s default setting
Gene expression level of Refseq coding genes were quantified using Space Ranger`s default setting
Assembly: hg38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: hires_image.png: hi-res image of tissue
Supplementary files format and content: lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcodes and the coordinates specifyng spots
Library strategy: Spatial transcriptomics

source_name: Breast cancer

extract_protocol:
FFPE were prepared according to standard operating procedure and 10 µm sections were cut with microtome
Spatial transcriptome sequensing libraries were preparied with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer`s construction

value: Breast cancer

value: anthracyclines, taxanes


title: NYU252-N (RNA-seq)


title: Prostate_tumor_RIB0025405

tag: alternative sample_id

tag: tumor type

value: Primary tumor

value: yes


title: NYU1986A-T (RNA-seq)

value: Second Primary

value: Progression


title: breast cancer, R3-S4


title: D0_input_n1


title: NYU1986-N (RNA-seq)


title: NYU1982A-T (RNA-seq)

value: Short Follow Up (<5y)


title: breast cancer, R3-S3


title: Prostate_tumor_RIB0025374

tag: biochemical relapse_(bcr)

tag: gleason score


title: NYU1982-N (RNA-seq)

tag: tissue


title: breast cancer, R3-S2

description:
Sample info for slides with two samples: R3-S21 - upper; R3-S22 - lower
FFPE sample


title: Prostate_tumor_RIB0025394


title: NYU1970A-T (RNA-seq)


title: NYU2005-N (RNA-seq)


title: NYU1970-N (RNA-seq)


title: NYU1967A-T (RNA-seq)


title: NYU1967-N (RNA-seq)


title: NYU1953-T (RNA-seq)


title: breast cancer, R3-S1


title: NYU1953-N (RNA-seq)


title: Prostate_tumor_RIB0025378

value: pNA


title: NYU1951-T (RNA-seq)


title: Prostate_tumor_RIB0025393


title: Prostate_tumor_RIB0025389


title: NYU1951-N (RNA-seq)


title: NYU1949-CH-T (RNA-seq)


title: NYU1940A-T (RNA-seq)


title: breast cancer, R2-S3


title: breast cancer, R2-S2


title: NYU1949-CH-N (RNA-seq)


title: NYU1940-N (RNA-seq)


title: Prostate_tumor_RIB0025439


title: breast cancer, R2-S1


title: NYU1932A-T (RNA-seq)

value: Systemic

value: Recurrence


title: NYU1932-N (RNA-seq)


title: breast cancer, R1-S6


title: NYU1923-N (RNA-seq)


title: NYU1923-T (RNA-seq)


title: NYU1906-T (RNA-seq)


title: NYU1906-N (RNA-seq)


title: Prostate_tumor_RIB0025500


title: breast cancer, R2-S5

description:
Sample info for slides with two samples: R2-S51 - upper; R2-S52 - lower
FFPE sample


title: Prostate_tumor_RIB0025489


title: breast cancer, R1-S5

description:
Sample info for slides with two samples: R1-S51 - upper; R1-S52 - lower
FFPE sample


title: breast cancer, R1-S4


title: NYU1900-N (RNA-seq)


title: breast cancer, R1-S3

description:
Sample info for slides with two samples: R1-S31 - upper; R1-S32 - lower
FFPE sample


title: NYU1898-N (RNA-seq)

value: Locoregional


title: Prostate_tumor_RIB0025371

description: Gene expression of prostate biopsy prior to RP (FFPE)

value: no


title: Prostate_tumor_RIB0015792


title: Prostate_tumor_RIB0025447


title: NYU1897-T (RNA-seq)


title: breast cancer, R1-S2


title: NYU1897-N (RNA-seq)

value: Lung adjacent normal


title: NYU1891-T (RNA-seq)

value: Tumor


title: Prostate_tumor_RIB0018085


title: NYU1891-N (RNA-seq)


title: Prostate_tumor_RIB0025481


title: NYU1884-T (RNA-seq)


title: breast cancer, R1-S1


title: NYU1884-N (RNA-seq)


title: NYU1883-T (RNA-seq)


title: Prostate_tumor_RIB0002506


title: NYU1900-T (RNA-seq)


title: NYU1883-N (RNA-seq)


title: NYU1873-T (RNA-seq)


title: HZ_9-1Y_S13

city: Antwerp

first: Pieter

last: Meysman

address: Middelheimlaan 1

department: Computer Science

country: Belgium

institute: University of Antwerp

description: Herpes Zoster resolved (1Y)

data_processing:
Sequencing reads from fastq files were checked for quality using FastQC, trimmed for polyA-tails and further read processing using Trimmomatic v0.36. The reads were then aligned against the human reference genome (GRCh38 from Ensembl) using HISAT2 v2.0.4, and the read count table was assembled using HTSeq. Subsequent expression analysis was performed using the DESeq2 v1.32.0 R package.
Assembly: GRCh38 from Ensembl
Supplementary files format and content: Processed read counts in tabular format

source_name: Whole blood

extract_protocol:
RNA extraction from whole blood collected in PAXGene tubes was performed via a column-based RNA extraction using the PaxGene blood RNA extraction kit (Cat. No./ID: 762174, Qiagen) following the manufacturer’s instructions. Subsequently, RNA was concentrated using the RNA clean & concentrator-5 kit (R1013, Zymo research). RNA concentration was measured using the Qubit™ RNA BR Assay Kit (Cat n°: Q10211, Thermo Fisher) on a Qubit 4 fluorometer (Invitrogen).
All RNA samples were prepared with the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD  for Illumina (Lexogen   GmbH) following the standard protocol for long fragments. Resulting cDNA libraries were equimolarly pooled, up to 40 samples for one NextSeq 500/550 sequencing run (high output v2.5 kit, 150 cycles, single read, Illumina)

value: Whole blood

tag: Sex

value: M

tag: disease state

value: Herpes Zoster resolved (1Y)


title: HZ_8_S5

description: Herpes Zoster

value: Herpes Zoster


title: NYU1873-N (RNA-seq)


title: NYU1898-T (RNA-seq)


title: Prostate_tumor_RIB0002521

data_processing:
Processing of primary sequencing data was done using the workflow management software UAP (https://github.com/fraunhofer-izi/uap).
Demultiplexing of Illumina raw files was performed with the Illumina bcl2fastq software v2.19.
Paired-end FASTQ reads were trimmed and filtered using AdaptorRemoval v2.2.1 with additional parameters to trim ambiguous bases (N) at 5’/3’ termini (–trimns), remove low-quality bases (–trimqualities, –minquality 20) and keep reads with a minimum read length of 30bp (–minlength 30).
Trimmed reads were mapped to the human reference genome version GRCh38/hg38 by HISAT2 v2.1.0 by specifying a reverse stranded library.
Gene level quantification was performed using HTSeq v0.11.2 with following parameters: –mode intersection-strict, –stranded reverse and –type exon. To ensure that the putative novel intergenic genes from the ProstaTrend signature (DOI: 10.1016/j.eururo.2020.06.001) are also represented in the FFPE_Bx cohort, we extended the human reference gene annotation GENCODE (release 36 GRCh38.p12) used for HTSeq as follows: we used the annotation of expression quality filtered novel transcripts classified as “u”(unknown intergenic) of the cohort FF_seq_RP as described previously (DOI: 10.1016/j.eururo.2020.06.001). Since these annotations are based on GRCh37/hg19, we updating the annotation using UCSC liftOver tool to GRCh38/hg38 (Chain file: http://hgdownload.soe.ucsc.edu/goldenPath/hg19/liftOver/hg19ToHg38.over.chain.gz. After converting the coordinates all prognostic genes from the ProstaTrend signature (classified as unknown intergenic and FDR <0.05) could be retained.
179 samples passed the quality filter, 3 samples were excluded because time to BCR was not recorded. In total, we analyzed transcriptome data from 176 patients.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Matrix table (HTSeq output) with raw gene counts for each sample as a separate file. The gene IDs consist of Ensembl IDs (GENCODE v36, GRCh38.p12) and prognostic putative novel genes (prefix XLOC) classified as “u” (unknown intergenic)
Supplementary files format and content: Comma-delimited text file with rawcounts for each gene and sample. The gene IDs consist of Ensembl IDs (GENCODE v36, GRCh38.p12) and prognostic putative novel genes (prefix XLOC) classified as “u” (unknown intergenic)
Supplementary files format and content: Comma-delimited text file with variance stabilizing transformation (VST) counts for each gene and sample. The gene IDs consist of Ensembl IDs (GENCODE v36, GRCh38.p12) and prognostic putative novel genes (prefix XLOC) classified as “u” (unknown intergenic)

value: FFPE PCa biopsy


title: NYU1871-N (RNA-seq)


title: Prostate_tumor_RIB0002577

value: Primary tumor


title: NYU1854-T (RNA-seq)

value: No Progression (>5y)


title: HZ_6-1Y_S38

description: Herpes Zoster resolved (1Y)


title: Prostate_tumor_RIB0002507


title: NYU1854-N (RNA-seq)


title: NYU1845-T (RNA-seq)

value: Second Primary


title: HZ_9_S12

description: Herpes Zoster


title: Prostate_tumor_RIB0025491


title: HZ_5_S3

description: Herpes Zoster


title: NYU1845-N (RNA-seq)

value: Progression


title: HZ_5-1Y_S4

description: Herpes Zoster resolved (1Y)


title: Prostate_tumor_RIB0015774


title: Prostate_tumor_RIB0007100


title: HZ_4_S1

description: Herpes Zoster


title: NYU1837-N (RNA-seq)


title: NYU1808-N (RNA-seq)


title: NYU1808-T (RNA-seq)


title: HZ_4-1Y_S2

description: Herpes Zoster resolved (1Y)


title: NYU1795-N (RNA-seq)

value: Short Follow Up (<5y)


title: Prostate_tumor_RIB0015798


title: HZ_6_S37

description: Herpes Zoster


title: NYU1871-T (RNA-seq)


title: NYU1795-T (RNA-seq)


title: Prostate_tumor_RIB0015745


title: Prostate_tumor_RIB0002549


title: HZ_3_S5

description: Herpes Zoster

value: F


title: NYU1787-T (RNA-seq)


title: NYU1787-N (RNA-seq)


title: HZ_38_S34

description: Herpes Zoster


title: NYU178-T (RNA-seq)


title: Prostate_tumor_RIB0002892

value: yes


title: Prostate_tumor_RIB0002824


title: NYU1769-T (RNA-seq)


title: NYU1769-N (RNA-seq)


title: HZ_38-1Y_S35

description: Herpes Zoster resolved (1Y)


title: NYU1837-T (RNA-seq)


title: HZ_36_S32

description: Herpes Zoster


title: Prostate_tumor_RIB0002861


title: NYU1767-T (RNA-seq)

value: Recurrence


title: NYU1767-N (RNA-seq)

value: Locoregional


title: HZ_36-1Y_S33

description: Herpes Zoster resolved (1Y)


title: NYU175-T (RNA-seq)


title: HZ_34_S30

description: Herpes Zoster


title: Prostate_tumor_RIB0002853


title: NYU175-N (RNA-seq)


title: NYU1749-T (RNA-seq)


title: Prostate_tumor_RIB0002829


title: NYU1749-N (RNA-seq)


title: male DN mice, female BTBRob/ob mice 2, 14 weeks

city: Ya'an

first: Jianning

state: Sichuan

address: 46, Xinkang Road

institute: Sichuan Agricultural University

data_processing:
SOAPnuke ( v1.5.2)
Sequence reads were trimmed for adaptor sequence/low-quality sequence using SOAPnuke ( v1.5.2).
HISAT (v2.0.4) was used to align clean reads to the reference genome.
Bowtie2 (v2.2.5) was used to align clean reads to reference gene sequence, and RSEM (v1.2.12) was used to calculate gene and transcript expression levels.
Assembly: mm10
Supplementary files format and content: The excel file we provide in xlsx format contains the RPKM value for each Sample.

source_name: mesenchymal stem cells

extract_protocol:
Total RNA from these kidney samples was separately isolated with Trizol reagent (Invitrogen, Carlsbad, CA, USA) and purified using the RNeasy Animal Mini Kit (Qiagen, Valencia, CA). RNA quality was then assessed using an Agilent 2100 Bioanalyzer (Agilent Technologies, PaloAlto, Calif)
RNA libraries for RNA-seq were prepared using BGISEQ-500RS High-throughput Sequenciing Set Kit following manufacturer's protocols.

treatment_protocol:
Adequate food, water, and bedding were provided.
Mice were sacrificed by carbon dioxide asphyxiation, and death was confirmed by cervical dislocation.

value: male

value: mesenchymal stem cells

tag: genotype

value: BTRTob/ob

tag: treatment

value: It is under temperature, light and humidity control.  Adequate food, water, and bedding were provided.

tag: time

value: 14 weeks


title: NYU1738-T (RNA-seq)

value: Tumor


title: HZ_34-1Y_S31

description: Herpes Zoster resolved (1Y)

value: Whole blood

value: Herpes Zoster resolved (1Y)


title: Prostate_tumor_RIB0002858

value: FFPE PCa biopsy

value: Primary tumor

value: no

tag: pathological t_stage

tag: pathological n_stage


title: NYU178-N (RNA-seq)

tag: patient

value: Lung adjacent normal

value: No Progression (>5y)


title: Prostate_tumor_RIB0002830

tag: total psa_(ng/ml,_pre-biopsy)


title: female DN mice, female BTBRob/ob mice 2, 14 weeks

growth_protocol: It is under temperature, light and humidity control.

value: female

tag: cell type


title: HZ_30_S18

description: Herpes Zoster

value: F

value: Herpes Zoster


title: HZ_31_S25

description: Herpes Zoster

value: M


title: male DN mice, male BTBRob/ob mice 1, 14 weeks

value: male


title: HZ_3-1Y_S6

description: Herpes Zoster resolved (1Y)


title: female DN mice, female BTBRob/ob mice 1, 14 weeks

value: mesenchymal stem cells


title: NYU1707-T (RNA-seq)

tag: progression type

tag: progression


title: NYU1738-N (RNA-seq)

value: Second Primary

value: Progression

tag: recurrence


title: GR6-35d-1uM

city: Taichung

first: Pei-Chih

last: Lee

address: No. 91, Hsueh-Shih Road

department: Graduate Institute of Biomedical Science

country: Taiwan

institute: China Medical University

data_processing:
The bases with low quality and sequences from adapters in raw data were removed using program Trimmomatic (version 0.39)
The filtered reads were aligned to the reference genomes using Bowtie2 (version 2.3.4.1)
A user-friendly software RSEM (version 1.2.28) was applied for the quantification of the transcript abundance
Differentially expressed genes (DEGs) were identified by EBSeq (version 1.16.0)
Assembly: hg18

source_name: GR6 cells

growth_protocol: GR6 cells were maintained in RPMI supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using  TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) following manufacturer's protocols.

treatment_protocol: GR6 cells were treated with 1 uM curcumin and 35d for 24h.

tag: cell line

value: GR6 cells

value: lung cancer cells

value: WT


title: Prostate_tumor_RIB0002854

source_name: FFPE PCa biopsy

extract_protocol:
From up to five FFPE tissue slices of 10 μm we isolated RNA using Deparaffinization Solution (Qiagen) according to the miRNEASY protocol. A pathologist evaluated HE-stained flanking tissue slices and tumor content was assessed, ranging between 5% and 100% (mean= 41%). After subsequent proteinase K digestion and formalin-de-crosslinking, we transferred the samples onto RNeasy MinElute spin columns. We used the miRNeasy FFPE kit on the QIAcube (Qiagen) following the manufacturer’s instruction for the final RNA purification. To eliminate all traces of genomic DNA, we performed DNAse-digestion (TURBO DNA free Kit, Thermo Fisher) twice in each sample. The RNA was concentrated using a standard precipitation protocol if necessary. Finally, we quantified extracted RNA using a Qubit RNA-Kit and the Qubit 2.0 instrument (Thermo Fisher). We analyzed the quality of RNA on a Bioanalyzer 2100 instrument (Agilent Technologies) and calculated the DV200 values (the percentage of fragments >200 nucleotides), ranging between 5% and 63% (mean=37%). Because of the well-known quality issues of old FFPE specimens, we decided to include all samples in further analysis.
For RNA-sequencing of FFPE specimens, we used 200 ng RNA per sample (when available). We prepared RNA libraries using TruSeq-Stranded Total RNA Sample Prep kit (Illumina), including an rRNA depletion step according to manufacturers’ protocol, i.e., Ribo-Zero Gold rRNA Removal Kit. Following Illumina's recommendation, we skipped the fragmentation step for all samples. We analyzed the quality and quantity of each prepared library with the Denovix instrument (Qubit DNA-Kit) and with the Bioanalyzer 2100, calculated the molarity of each library and pooled equal amounts, which were used for subsequent sequencing (12 pM). We sequenced 2 x 126-bp paired-end reads using SBS V4 chemistry with a HiSeq 2500 (Illumina) on four eight-lane flow cells: the first one with 32 and the others with 51 libraries each (185 in total).

tag: alternative sample_id

tag: tumor type

tag: biochemical relapse_(bcr)

tag: tumor cell_content_(%)


title: male normal control mice, male control 2, 14 weeks

tag: Sex

value: It is under temperature, light and humidity control.  Adequate food, water, and bedding were provided.

value: 14 weeks


title: HZ_2_S3

description: Herpes Zoster

tag: tissue

value: Whole blood

tag: disease state


title: NYU1707-N (RNA-seq)


title: GR6-Curcumin-1uM

tag: genotype

tag: treatment

value: 24h Curcumin


title: HZ_29_S23

description: Herpes Zoster


title: GR6-Control

value: 0 h


title: female normal control mice, female control 2, 14 weeks

tag: time


title: male normal control mice, male control 1, 14 weeks


title: NYU1682-N (RNA-seq)

tag: patient

value: Lung adjacent normal

value: No Progression (>5y)


title: NYU1678-T (RNA-seq)

value: Tumor


title: D0_3T3L1_siRNA_Prmt5Oligo3_2

data_processing:
Basecalling performed by BGI
Sequenced reads were processed using the SOAPnuke software.  Reads were trimmed for the adaptor sequence and filtered for low quality reads and stored in FASTQ format.
HISAT2 was used for genome mapping to mm10 after which a complete reference transcriptome was generated using StringTie, Cufflinks and CPC.
The SOAPnuke output was then mapped to the reference transcriptome using Bowtie2 and RSEM was used to calculate gene expression levels.
Differential gene expression was calculated using DESeq2
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

extract_protocol:
Total RNA was harvested from 3T3-L1 cells transfected with siRNA at day 0 with TRIzol
RNA libraries were prepared by the Beijing Genomics Institute (BGI) for sequencing on a BGISEQ-500

treatment_protocol: Cells were transfected at 60–70% confluence using the Lipofectamine 2000 (Invitrogen) reagent with 24 nM siRNA (scrambled or Prmt5 siRNA oligo3). Cells were incubated with siRNA in DMEM (Invitrogen) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin for 6 hours, after which media was replaced. Cells were harvested two days after reaching confluency.

value: mouse fibroblast-derived preadipocyte line

tag: genotype/variation


title: female normal control mice, female control 1, 14 weeks

value: female

tag: cell type


title: HZ_28_S21

description: Herpes Zoster

value: F

value: Herpes Zoster


title: NYU1678-N (RNA-seq)

tag: progression type


title: HZ_28-1Y_S22

description: Herpes Zoster resolved (1Y)

value: Herpes Zoster resolved (1Y)


title: HZ_29-1Y_S24

description: Herpes Zoster resolved (1Y)

value: M


title: WT_WCE (input DNA)

city: Quebec

last: Schwab

state: Québec

address: 2725 Chemin Ste-Foy

institute: CRIUCPQ / Hopital Laval

data_processing:
Analysis of raw sequencing reads was performed using the MUGQIC ChIP-Seq pipeline (Bourgey et al., 2019).
Reads were trimmed for adaptor sequences using Trimmomatic (Bolger et al., 2014).
High-quality reads were aligned to the human reference genome (GRCH38/hg38) with the BWA aligner (Li and Durbin, 2009).
Narrow peaks were called using MACS2 (Zhang et al., 2008), using the corresponding input DNA as background.
Differential binding between SHP1-KO and WT was assessed using csaw (Lun and Smyth, 2016)
Genome_build: GRCH38/hg38
Supplementary_files_format_and_content: Annotated narrowPeak files for peak calling
Supplementary_files_format_and_content: Csaw text file of differential binding

source_name: Hepatoma cells

growth_protocol: HepG2 cells (WT or SHP-1-KO) were cultured in 150 mm dishes.

extract_protocol:
Cells were washed 3 times with PBS and 5x107 cells for each ChIP-seq fixed with 1% formaldehyde for 10 min. Cross-linked cells were quenched using glycine for 5 min at room temperature. Cells were washed twice with ice-cold PBS and harvested using a silicon scraper. Cells were transferred to 50 ml falcon and centrifuged at 1350 g for 5 min. Pellets obtained were washed again with ice-cold PBS. Cell pellets were suspended in LB1 buffer (50 mM Hepes-KOH, pH7.5, 140 mM NaCl, 1 mM EDTA, 10 % glycerol, 0.5% IGEPAL, 0.25% Triton X-100, PMSF and protease inhibitor cocktail) and incubated at 4°C for 10 min with rotation. Pellets were obtained using centrifugation. The cell pellet was suspended in LB2 buffer (10 mM Tris-HCl, pH8.0, 200 mM NaCl, 1mM EDTA, and 0.5 mM EGTA supplemented with protease inhibitors) and incubated for 10 min at room temperature with rotation. Lysates were centrifuged at 1350 g for 5 min and pellets were suspended in sonication buffer (20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA pH8.0, 0.1 % SDS, and 1% Triton X-100 supplemented with proteinase inhibitors). Lysates were sonicated using Bioruptor instrument (Diagenode) for a total of 6 min (high intensity, 12 cycles of 30 sec ON and 30 sec OFF) at 4°C to obtain a chromatin fragmentation of 200-900 bp. Protein G dynabeads pre-blocked in blocking solution (0.5% BSA in PBS) were incubated with antibodies (RPB1 and pSer2-RPB1) at 4°C for 6 h. Protein G Dynabead-antibody complexes were washed 3 times with 1 ml blocking solution, then added to chromatin preparations and incubated overnight at 4°C. Some portions of the chromatin were left untreated and used as whole-cell extract (WCE) control.  Beads were washed once with Wash buffer B (20 mM Tris-HCl pH8.0, 150 mM NaCl, 2 mM EDTA pH8.0, 0.1% SDS, 1% Triton X-100 and protease inhibitors), followed by wash buffer C (20 mM Tris-HCl pH8.0, 500 mM NaCl, 2 mM EDTA pH8.0, 0.1% SDS, 1% Triton X-100 and protease inhibitors), and Wash Buffer D (10 mM Tris-HCl pH8.0, 250 mM LiCl, 1 mM EDTA pH8.0, 1% NP40 and protease inhibitor) and TE buffer (10 mM Tris pH8.0, 1 mM EDTA, 50 mM NaCl and protease inhibitors). Complexes were eluted off the beads using elution buffer containing 50 mM Tris-HCl pH 8.0, 1 mM EDTA pH 8.0, and 50 mM NaCl. Beads were collected and incubated at 65°C overnight to reverse cross-linked. In parallel, WCE were also reverse cross-linked.  Samples were subsequently treated with RNase A (Ambion) at 37°C for 2 hours followed by Proteinase K (InVitrogen) treatment at 55°C for 30 min. DNA was purified using the phenol-chloroform method.
Libraries were constructed from ChIP- and WCE-samples using NEBNext Ultra II DNA library prep kit (New England Biolabs) according to the manufacturer’s instructions and single-end sequenced (50 bp) on an Illumina HiSeq 2500 instrument at the Next-Generation Sequencing Platform of the CHU de Québec-Université Laval Research Center (CRCHUQ).

treatment_protocol: untreated

value: SHP-1-WT (CRISPR control)

tag: chip antibody


title: HZ_26_S19

description: Herpes Zoster


title: SHP-1-KO_WCE (input DNA)

value: SHP-1-KO (CRISPR knockout)


title: WT_Rpb1-Ser2-IP

value: anti-Rpb1-pSer2 (anti-RNAPII-CTD-pSer2), abcam (ab5095)


title: D0_3T3L1_siRNA_scrmb_2


title: D0_3T3L1_siRNA_Prmt5Oligo3_1


title: NYU1636-N (RNA-seq)

value: Second Primary

tag: progression

value: Progression

tag: recurrence


title: D0_3T3L1_siRNA_scrmb_1

tag: cell line


title: SHP-1-KO_Rpb1-IP

value: anti-Rpb1 (anti-RNAPII-CTD), abcam (ab817)


title: HZ_24_S31

description: Herpes Zoster

value: Whole blood


title: NYU1630-T (RNA-seq)


title: NYU1682-T (RNA-seq)


title: WT_Rpb1-IP


title: HZ_24-1Y_S32

description: Herpes Zoster resolved (1Y)


title: AM_TFI_21, biol rep3

city: Barcelona

first: Lucas

middle: Esteban

last: Wange

address: Dr. Aiguader 88

department: Institut de Biologia Evolutiva

country: Spain

institute: Universitat Pompeu Fabra

description: CTTAACCAGTCA

data_processing:
demultiplexing, deML
adapter trimming, cutadapt, version 3.4
mapping and counting, zUMIs, version 2.9.7c
normalisation and differential expression analysis, DESeq2
Assembly: hg38
Supplementary files format and content: raw count matrix as generated by zUMIs

source_name: Bone Marrow

growth_protocol: healthy donor derived human adapter CAR-T cells

extract_protocol:
prime-seq bead extraction
prime-seq RNA-sequencing

treatment_protocol: time course

value: Bone Marrow

value: AM

value: TFI


title: NYU1630-N (RNA-seq)

value: Lung adjacent normal


title: SHP-1-KO_Rpb1-Ser2-IP


title: hLSEC

description: single cell RNA seq

data_processing:
Alignment and transcript counting using cellranger (v3.1)
Replicates are counted at the same time for each sample
Genome_build: hg38
Supplementary_files_format_and_content: h5 filtered counts matrixes containing transcript counts and cell barcodes

source_name: human liver sinusoidal endothelial cells

extract_protocol:
10X Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 used for GEM generation and barcoding
10X Chromium™ Single Cell 3’ Library & Gel Bead Kit v2 used for library construcion. Libraries sequenced using a HiSeq 2500 System.

treatment_protocol: FACS isolation of cells, resuspended in HBSS with bovine serum albumin. Cell viability confirmed prior to proceeding with GEM generation and barcoding.

tag: fluorescent tag

tag: tissue origin

value: Liver


title: NYU1609-T (RNA-seq)

value: Tumor

value: Locoregional

value: Recurrence


title: HZ_22_S29

description: Herpes Zoster

value: Herpes Zoster


title: iEC 4 weeks, 2

description: single cell RNA seq

source_name: hiPSC-endothelial cells

value: TdTom+


title: A_CONT_21, biol rep1

description: TGACACTCACCA

value: A

value: healthy donor derived human adapter CAR-T cells

value: CONT


title: NYU1636-T (RNA-seq)

value: Second Primary


title: S_TFI_21, biol rep2

description: GATCAGCTTACA

value: S