title: FTD hTau sciATAC Drosophila Exp 210624

status: Public on Jul 31 2026

type: SRA

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

country: USA

institute: Oregon Health & Science University

description:
Library name: FTD_hTau_sciATAC_210624
sciATAC-seq of day 5 and 30 frozen whole heads

library_source: genomic single cell

data_processing:
sciATAC-seq The NextSeq 550 was used for all sequencing runs using custom chemistry (Thornton et al., 2021). The “scitools” software (github.com/adeylab/scitools) was used to process the sequencing runs. The following “scitools” commands were used to process the runs: fastq file creation (Nextseq2fastq -R, wrapper for bcl2fastq (Illumina Inc., v2.19.0)), index assignment (fastqdump, hamming distance of 2), alignment (fastq-align -r 10 -n -t 25 to dm6), merged bams by age (samtools merge -n), remove PCR duplicates (bam-rmdup –n –t 10), check for sequencing saturation and quality (plot-complexity), merged ages (5 and 30 day), and filtered bam for cells with at least 1000 reads (scitools bam-filter –N 1000). MACS3 callpeak was used for peak calling with the following settings: --call-summits --shift -100 --extsize 200 --nomodel --keep-dup all (Cusanovich et al., 2018). The peaks file was subtracted from the dm6 TSS file (utilized ensemble dm6 tss bed files) to create a background file for TSS enrichment. All cells with TSS lower than 2 were removed for downstream analysis (scitools filter-bam). Peaks were called using macs3 callpeak with the filtered bam and read groups were added to assign reads to strain, age, and experiment indicators (scitools bam-addrg). Bams were split by experiment (scitools bam-filter) for doublet removal in ArchR (Granja et al., 2021). ArchR was utilized for all downstream analysis with the following used to create a custom genome:BSgenome.Dmelanogaster.UCSC.dm6,TxDb.Dmelanogaster.UCSC.dm6.ensGene(Granja et al., 2021). ArrowFiles were created for each experiment date with the following parameters and excluding mitochondrial DNA and sex chromosomes:minFrags=0,maxFrags=10000000,minTSS=0,gsubExpression=":.*",addTileMat=T,addGeneScoreMat=T, nChunk = 20, cleanTmp = T, force=T. R version 4.0.4 and 4.1.2 were used for following analyses depending on the package compatibility. ArchR was used for all downstream analyses (Granja et al., 2021). For dimensionality reduction, addIterativeLSI, addClusters, and addUMAP were used with the following settings: excludeChr=c(“X”,”Y”), iterations=3,useMatrix="TileMatrix",varFeatures=25000,totalFeatures=200000,resolution=2,sampleCells=10000,maxClusters=9,nNeighbors=30. addCellColData was used to add annotations for experiment date, age, and strain. MAC3 peakset was added using addPeakSet.  snRNA-seq R version 4.0.4 and 4.1.2 were used for the following analyses. The snRNA-seq data was pre-processed using the 10x Genomics Cell Ranger v6.1.2 software suite. The Ensembl Drosophila_melanogaster.BDGP6.28.dna.*.fa.gz version was used to create the genome assembly. The Adey Lab unidex was used to demultiplex the sequencing runs (github.com/adeylab/unidex). Count matrices were created using cellranger count --expect-cells=10000 --include-introns --chemistry=SC3Pv3 for each sample. To reduce noise, cellranger reanalyze --force-cells 10000 was used prior to running Scrublet for doublet detection and removal with the expected doublet rate of 7.6% based on the 10x protocol (Wolock et al., 2019). Reanalyze was used to filter out doublets prior to running SoupX to remove ambient RNA (Young et al., 2020). All downstream analysis was done using Seurat 4.1.0 (Hao et al., 2021). The dataset was filter with the following: nFeature_RNA > 200, nFeature_RNA < 4000 and percent.mt < 5. FindMarkers with the Wilcoxon test was used for differential expression analysis.
Assembly: dm6
Supplementary files format and content: ArchR project, Seurat Object

molecule: genomic DNA

organism: Drosophila melanogaster

source_name: whole adult head

extract_protocol:
sciATAC-seq Flies (5-7 days and 30 days old) were frozen at -80°C and the heads collected using a sieve on dry ice (20-60 heads). The heads were gently sheared open using a Teflon homogenizing stick in 150µl cold Nuclei Isolation Buffer (NIB) (10 mM HEPES-KOH, pH 7.2 [Fisher, Cat. BP310-1], 10 mM NaCl [Fisher, Cat. M-11624], 3 mM MgCl2 [Sigma, Cat. M8226], 0.1% IGEPAL [v/v; Sigma, I8896], 0.1% Tween-20 [v/v, Sigma, Cat. P7949], and 1x protease inhibitor [Roche, Cat. 11836170001]). All contents were transferred to a 1mL Dounce-homogenizer with 300µl of cold NIB and left for 5 minutes. The A (loose) pestle was used 3-4 times to achieve a turbid solution then left to incubate for 15 minutes on ice. The B (tight) pestle was then used 3-4 times until the heads were sheared and left to incubate for 15 minutes on ice. The solution was strained using a 35 µM cell strainer and the nuclei concentration was determined using a hemacytometer.  snRNA-seq Fly heads (from 5-7 day old) were removed and collected into 1xPBS (phosphate-buffered saline) on ice (~20 heads) and gently homogenized using a Teflon homogenizing stick in 150µl of cold Nuclei Isolation Buffer (NIB) (10 mM Tris HCl, pH 7.4, 10 mM NaCl [Fisher, Cat. M-11624], 3 mM MgCl2 [Sigma, Cat. M8226], 0.1% IGEPAL [v/v; Sigma, I8896], 0.5% RNase Inhibitor Murine NEB [M0314S]). The contents were transferred to a 1mL Dounce-homogenizer with 350 µl of cold NIB and left for 5 minutes. The A (loose) pestle was used 4 times to achieve a turbid solution then left to incubate for 15 minutes on ice. The B (tight) pestle was then used 4 times until the heads were sheared and left to incubate for 15 minutes on ice. The solution was strained using a 35 µM cell strainer and spun at 500 rcf at 4°C for 10 minutes. The nuclei were washed twice with 400µl of the NIB without IGEPAL. The nuclei concentration was determined using a hemacytometer.
sciATAC-seq Single cells were uniquely labeled using two rounds of combinatorial indexing. The first round utilized transposase to introduce an index into open regions of chromatin. Each 96 well plate used had a unique index oligo pre-loaded into the Tn5. Fresh 4X TAPS buffer was diluted with cold NIB to 1X and used to dilute nuclei to desired concentration of 200 nuclei/µl (132 mM TAPS (N-[Tris(hydroxymethyl)methyl]-3-aminopropanesulfonic acid) pH=8.5, 264 mM potassium acetate, 40 mM magnesium acetate, and 64% dimethylformamide). 10 µl of nuclei solution and 1.5 µl 8µM uniquely indexed transposase was added to each well on ice (Picelli et al., 2014). The 96-well tagmentation plates were then incubated on a thermomixer at 55°C with gentle shaking at 300 rpm for 15 minutes. Once completed, the plates were immediately returned to ice to prevent over-transposition and nuclei lysis. All wells for each strain or experimental condition were pooled on ice. Each condition was pooled separately to limit sorting bias. Nuclei were stained with DAPI (5mg/mL) prior to sorting with the BD FACS Diva software (v8.0.1) on a Sony SH800 FACS machine. Sorting 96-well plates with Transposase Neutralization Buffer (8.5 µl/well) were prepared in advance and placed on ice (0.25 µl BSA [NEB, Cat. B9000S], 0.5 µl 1% SDS, 7.75 µl dH20 per well). Indexed PCR primers were added prior to sorting (2.5 µl of 10 µM i5 indexed PCR Primer and 2.5 µl of 10 µM i7 indexed PCR Primer. For each condition, 15 events per 96-well plate were sorted per PCR plate. After sorting, the transposase was denatured, and nuclei were lysed at 55°C for 20 minutes in SDS Transposase Neutralization Buffer. The plates were spun down and frozen at -20°C. The second index was added via PCR on the BioRad CFX real-time cycler running CFX Manager (v3.1) software. 11.5 µl of PCR Master Mix was added to each well of the 96-well nuclei sorted plates (5 µl 5x KAPA HiFi Buffer (GC Buffer), 0.75 µl 10mM KAPA dNTP mix, 0.5 1U/µL KAPA HiFi DNA Polymerase, 0.25 µl 100X SYBR Green I, 5µl dH2O). The real time PCR was performed with the following setup: 72°C 5min, 15-21 cycles of 98°C 30sec, 63°C 30sec, 72°C 1min, Plate Read, 72°C 20sec. The libraries were stored at -20°C after spin down. 10µl from each PCR reaction was pooled and DNA was concentrated using the Nucleospin Gel and PCR Clean-up kit and size selection using 1X SPRI beads (DNA >200 bp). The DNA concentration was quantified using the Qubit 2.0 fluorometer High-Sensitivity kit and then diluted to 1ng/µl for library fragment size and concentration measures using the Agilent Tapestation.  snRNA-seq The Chromium Single Cell 3ʹ v3 protocol was used for index introduction, library construction and sequencing (Zheng et al., 2017).

tag: tissue

value: whole adult head

tag: genotype

value: Canton-S (CS), hTauWildtype(WT)/CS, dTaudel, hTauK369I/CS, hTauK369I/hTauK369I, hTauP301L/CS, hTauV337M/CS

tag: age

value: 5 days and 30 days old

tag: Sex

value: pooled male and female


title: FTD hTau sciATAC Drosophila Exp 210622

description:
Library name: FTD_hTau_sciATAC_210622
sciATAC-seq of day 5 and 30 frozen whole heads


title: FTD hTau sciATAC Drosophila Exp 201202

description:
Library name: FTD_hTau_sciATAC_201202
sciATAC-seq of day 5 and 30 frozen whole heads


title: FTD hTau sciATAC Drosophila Exp 201023

description:
Library name: FTD_hTau_sciATAC_201023
sciATAC-seq of day 5 and 30 frozen whole heads


title: FTD hTau sciATAC Drosophila Exp 200224

description:
Library name: FTD_hTau_sciATAC_200224
sciATAC-seq of day 5 and 30 frozen whole heads


title: FTD hTau snRNA Drosophila KICS S1

description:
Library name: FTD_hTau_snRNA_KICS_S1
snRNA-seq of day 5 fresh whole heads

library_source: transcriptomic single cell

molecule: polyA RNA

value: Canton-S (CS), hTauWildtype(WT)/CS, dTaudel, hTauK369I/CS

value: 5 days old


title: FTD hTau snRNA Drosophila KICS 2 S1

description:
Library name: FTD_hTau_snRNA_KICS_2_S1
snRNA-seq of day 5 fresh whole heads


title: FTD hTau snRNA Drosophila dTauDel S1

description:
Library name: FTD_hTau_snRNA_dTauDel_S1
snRNA-seq of day 5 fresh whole heads


title: FTD hTau snRNA Drosophila dTauDel 2 S1

description:
Library name: FTD_hTau_snRNA_dTauDel_2_S1
snRNA-seq of day 5 fresh whole heads


title: FTD hTau snRNA Drosophila WTCS S1

description:
Library name: FTD_hTau_snRNA_WTCS_S1
snRNA-seq of day 5 fresh whole heads


title: FTD hTau snRNA Drosophila CS S1

description:
Library name: FTD_hTau_snRNA_CS_S1
snRNA-seq of day 5 fresh whole heads


title: FTD hTau snRNA Drosophila WTCS 2 S1

description:
Library name: FTD_hTau_snRNA_WTCS_2_S1
snRNA-seq of day 5 fresh whole heads


title: FTD hTau snRNA Drosophila CS 2 S1

description:
Library name: FTD_hTau_snRNA_CS_2_S1
snRNA-seq of day 5 fresh whole heads


title: HT-29 Combo replicate 3

type: RNA

city: miami

first: RIMPI

last: KHURANA

state: FL

address: Room 6112B, Rosenstiel Medical Science Building (RMSB),1600 NW 10th Avenue

institute: University of miami

description: HT-29 xenograft, combination treated

hyb_protocol: RNA hybridized with nCounter Human Tumor Signaling 360 panel according to manufacturer protocol.

scan_protocol: Samples scanned on nCounter Digital Analyzer using standard settings.

data_processing: RCC files processed using nSolver 4.0 Advanced Analysis module with standard normalization and Benjamini–Hochberg correction.

molecule: total RNA

organism: Homo sapiens

label_protocol: n/a (NanoString uses direct detection, no labeling required)

growth_protocol: HT-29 xenografts were established in NSG mice (5-6 weeks old, male and female). Cells implanted subcutaneously in flank.

extract_protocol: RNA extracted from tumor tissue using NanoString protocols. RCC files generated for each sample.

treatment_protocol: Mice treated with vehicle (Control), MV-CD46-muPA (3 doses, i.v.), Minnelide (0.21 mg/kg, i.p., 21 days), or combination. Three biological replicates per treatment.

tag: tag

value: MV-CD46-muPA + Minnelide


title: HT-29 Combo replicate 2

description: HT-29 xenograft, combination treated


title: HT-29 Combo replicate 1

description: HT-29 xenograft, combination treated


title: HT-29 Minnelide replicate 3

description: HT-29 xenograft, Minnelide treated

value: Minnelide


title: HT-29 Minnelide replicate 2

description: HT-29 xenograft, Minnelide treated


title: HT-29 Minnelide replicate 1

description: HT-29 xenograft, Minnelide treated


title: HT-29 MV-CD46-muPA replicate 3

description: HT-29 xenograft, virus treated


title: HT-29 MV-CD46-muPA replicate 2

description: HT-29 xenograft, virus treated


title: HT-29 MV-CD46-muPA replicate 1

description: HT-29 xenograft, virus treated


title: HT-29 Ctrl replicate 3

description: HT-29 xenograft, vehicle treated

value: Ctrl


title: HT-29 Ctrl replicate 2

description: HT-29 xenograft, vehicle treated


title: HT-29 Ctrl replicate 1

description: HT-29 xenograft, vehicle treated


title: 200uM genipin, rep4

city: Singapore

first: Weihan

last: Huai

address: 10 Medical Dr

country: Singapore

institute: NUS

description: Library name: G4

library_source: transcriptomic

data_processing:
Sequence data was subjected to quality control FastQC
then trimmed using Trimmomatics v0.32 to remove adaptors.
Processed/cleaned reads were then mapped with STAR (2.7.11b)
and counted via RSEM 1.3.3
The raw count was then imported into R using the R package tximport 1.26.1
Assembly: WBcel235
Supplementary files format and content: csv files with raw counts for each sample

organism: Caenorhabditis elegans

source_name: whole tissue

growth_protocol: Hermaphrodites C. elegans strain wild-type N2 was obtained from Caenorhabditis Genetic Center. Worms were cultured at 20°C on nematode growth medium (NGM) agar plates seeded with OP50-1 strain Escherichia coli with 200ug/mL streptomycin.

extract_protocol:
Clean worm pellets were then frozen and later used for RNA extraction. Total RNA was isolated using Qiagen RNeasy micro kit (Qiagen, Hilden, Germany) following the standard protocol. Afterward, RNA was quantified photometrically with NanoDrop 2000 and stored at -80oC until use.
Libraries were sequenced using Illumina HiSeq4000 sequencing platform (Illumina, San Diego, CA, USA) in a paired end read approach at a read length of 150 nucleotides.

treatment_protocol: Synchronized young adult worms are transferred into plates supplemented with drugs dissolved in DMSO for 2 days, and collected for RNA extraction. For maintaining synchronized populations, FUDR was added to NGM media.

value: whole tissue

tag: strain

tag: time

value: 48 hours after young adult

tag: batch


title: 200uM genipin, rep3

description: Library name: G3


title: 200uM genipin, rep2

description: Library name: G2


title: 200uM genipin, rep1

description: Library name: G1


title: DMSO, rep4

description: Library name: C4


title: DMSO, rep2

description: Library name: C2


title: DMSO, rep3

description: Library name: C3


title: 100uM bromhexine rep4

description: Library name: B4


title: DMSO, rep1

description: Library name: C1


title: 100uM bromhexine rep3

description: Library name: B3


title: 100uM bromhexine rep2

description: Library name: B2


title: 100uM bromhexine rep1

description: Library name: B1


title: CF1038 Day 6, rep20

description:
Library name: CF1038_D6_20
CF1038_20_trim_noZero_alignedAlt

growth_protocol: Hermaphrodites C. elegans strains wild-type N2, CF1038: daf-16(mu86) were obtained from Caenorhabditis Genetic Center. Worms were cultured at 20°C on nematode growth medium (NGM) agar plates seeded with OP50-1 strain Escherichia coli with 200ug/mL streptomycin.

treatment_protocol: Freshly prepared bacteria (OP50-1 E. coli) were spotted on 94 cm NGM agar plates on the previous evening and allowed to dry. Synchronized, young adult worms were transferred to fresh plates. For maintaining synchronized populations, FUDR was added to NGM media. Worms are transferred every two days into fresh plates to avoid food exhaustion. Worms are harvested at day 6, 8, 11, 14, and 18 and were washed off the plates into 15 ml tubes and then washed several times with fresh buffer until a clear solution was obtained.

value: Day 6


title: CF1038 Day 6, rep19

description:
Library name: CF1038_D6_19
CF1038_19_trim_noZero_alignedAlt


title: CF1038 Day 6, rep18

description:
Library name: CF1038_D6_18
CF1038_18_trim_noZero_alignedAlt


title: CF1038 Day 6, rep17

description:
Library name: CF1038_D6_17
CF1038_17_trim_noZero_alignedAlt


title: CF1038 Day 6, rep16

description:
Library name: CF1038_D6_16
CF1038_16_trim_noZero_alignedAlt


title: CF1038 Day 6, rep13

description:
Library name: CF1038_D6_13
CF1038_13_trim_noZero_alignedAlt


title: CF1038 Day 6, rep14

description:
Library name: CF1038_D6_14
CF1038_14_trim_noZero_alignedAlt


title: CF1038 Day 6, rep12

description:
Library name: CF1038_D6_12
CF1038_12_trim_noZero_alignedAlt


title: CF1038 Day 6, rep11

description:
Library name: CF1038_D6_11
CF1038_11_trim_noZero_alignedAlt


title: CF1038 Day 6, rep10

description:
Library name: CF1038_D6_10
CF1038_10_trim_noZero_alignedAlt


title: CF1038 Day 6, rep15

description:
Library name: CF1038_D6_15
CF1038_15_trim_noZero_alignedAlt


title: CF1038 Day 6, rep9

description:
Library name: CF1038_D6_9
CF1038_9_trim_noZero_alignedAlt


title: CF1038 Day 6, rep8

description:
Library name: CF1038_D6_8
CF1038_8_trim_noZero_alignedAlt


title: CF1038 Day 6, rep7

description:
Library name: CF1038_D6_7
CF1038_7_trim_noZero_alignedAlt


title: CF1038 Day 6, rep6

description:
Library name: CF1038_D6_6
CF1038_6_trim_noZero_alignedAlt


title: CF1038 Day 6, rep5

description:
Library name: CF1038_D6_5
CF1038_5_trim_noZero_alignedAlt


title: CF1038 Day 6, rep3

description:
Library name: CF1038_D6_3
CF1038_3_trim_noZero_alignedAlt


title: CF1038 Day 6, rep2

description:
Library name: CF1038_D6_2
CF1038_2_trim_noZero_alignedAlt


title: CF1038 Day 6, rep4

description:
Library name: CF1038_D6_4
CF1038_4_trim_noZero_alignedAlt


title: CF1038 Day 6, rep1

description:
Library name: CF1038_D6_1
CF1038_1_trim_noZero_alignedAlt


title: N2, Day 6, rep35

description:
Library name: N2_29
N2_29_trim_noZero_alignedAlt


title: N2, Day 6, rep34

description:
Library name: N2_28
N2_28_trim_noZero_alignedAlt


title: N2, Day 6, rep32

description:
Library name: N2_26
N2_26_trim_noZero_alignedAlt


title: N2, Day 6, rep31

description:
Library name: N2_25
N2_25_trim_noZero_alignedAlt


title: N2, Day 6, rep33

description:
Library name: N2_27
N2_27_trim_noZero_alignedAlt


title: N2, Day 6, rep30

description:
Library name: N2_24
N2_24_trim_noZero_alignedAlt


title: N2, Day 6, rep28

description:
Library name: N2_22
N2_22_trim_noZero_alignedAlt


title: N2, Day 6, rep29

description:
Library name: N2_23
N2_23_trim_noZero_alignedAlt


title: N2, Day 6, rep27

description:
Library name: N2_21
N2_21_trim_noZero_alignedAlt


title: N2, Day 6, rep26

description:
Library name: N2_20
N2_20_trim_noZero_alignedAlt


title: N2, Day 6, rep25

description:
Library name: N2_19
N2_19_trim_noZero_alignedAlt


title: N2, Day 6, rep24

description:
Library name: N2_18
N2_18_trim_noZero_alignedAlt


title: N2, Day 6, rep23

description:
Library name: N2_17
N2_17_trim_noZero_alignedAlt


title: N2, Day 6, rep36

description:
Library name: N2_30
N2_30_trim_noZero_alignedAlt


title: N2, Day 6, rep20

description:
Library name: N2_14
N2_14_trim_noZero_alignedAlt


title: N2, Day 6, rep22

description:
Library name: N2_16
N2_16_trim_noZero_alignedAlt


title: N2, Day 6, rep21

description:
Library name: N2_15
N2_15_trim_noZero_alignedAlt


title: N2, Day 6, rep19

description:
Library name: N2_13
N2_13_trim_noZero_alignedAlt


title: N2, Day 6, rep17

description:
Library name: N2_11
N2_11_trim_noZero_alignedAlt


title: N2, Day 6, rep15

description:
Library name: N2_9
N2_9_trim_noZero_alignedAlt


title: N2, Day 6, rep16

description:
Library name: N2_10
N2_10_trim_noZero_alignedAlt


title: N2, Day 6, rep12

description:
Library name: N2_6
N2_6_trim_noZero_alignedAlt


title: N2, Day 6, rep18

description:
Library name: N2_12
N2_12_trim_noZero_alignedAlt


title: N2, Day 6, rep14

description:
Library name: N2_8
N2_8_trim_noZero_alignedAlt


title: N2, Day 6, rep10

description:
Library name: N2_4
N2_4_trim_noZero_alignedAlt


title: N2, Day 6, rep9

description:
Library name: N2_3
N2_3_trim_noZero_alignedAlt


title: N2, Day 6, rep11

description:
Library name: N2_5
N2_5_trim_noZero_alignedAlt


title: N2, Day 6, rep13

description:
Library name: N2_7
N2_7_trim_noZero_alignedAlt


title: N2, Day 6, rep7

description:
Library name: N2_1
N2_1_trim_noZero_alignedAlt


title: N2, Day18, rep6

description:
Library name: N2_D18_6
N2_D18_6_trim_noZero_alignedAlt

value: Day 18


title: N2, Day18, rep5

description:
Library name: N2_D18_5
N2_D18_5_trim_noZero_alignedAlt


title: N2, Day 6, rep8

description:
Library name: N2_2
N2_2_trim_noZero_alignedAlt


title: N2, Day18, rep4

description:
Library name: N2_D18_4
N2_D18_4_trim_noZero_alignedAlt


title: N2, Day18, rep3

description:
Library name: N2_D18_3
N2_D18_3_trim_noZero_alignedAlt


title: N2, Day18, rep2

description:
Library name: N2_D18_2
N2_D18_2_trim_noZero_alignedAlt


title: N2, Day18, rep1

description:
Library name: N2_D18_1
N2_D18_1_trim_noZero_alignedAlt


title: N2, Day14, rep2

description:
Library name: N2_D14_2
N2_D14_2_trim_noZero_alignedAlt

value: Day 14


title: N2, Day14, rep5

description:
Library name: N2_D14_5
N2_D14_5_trim_noZero_alignedAlt


title: N2, Day14, rep4

description:
Library name: N2_D14_4
N2_D14_4_trim_noZero_alignedAlt


title: N2, Day14, rep6

description:
Library name: N2_D14_6
N2_D14_6_trim_noZero_alignedAlt


title: N2, Day14, rep1

description:
Library name: N2_D14_1
N2_D14_1_trim_noZero_alignedAlt


title: N2, Day11, rep3

description:
Library name: N2_D11_3
N2_D11_3_trim_noZero_alignedAlt

value: Day 11


title: N2, Day14, rep3

description:
Library name: N2_D14_3
N2_D14_3_trim_noZero_alignedAlt


title: N2, Day11, rep4

description:
Library name: N2_D11_4
N2_D11_4_trim_noZero_alignedAlt


title: N2, Day11, rep5

description:
Library name: N2_D11_5
N2_D11_5_trim_noZero_alignedAlt


title: N2, Day11, rep6

description:
Library name: N2_D11_6
N2_D11_6_trim_noZero_alignedAlt


title: N2, Day11, rep2

description:
Library name: N2_D11_2
N2_D11_2_trim_noZero_alignedAlt


title: N2, Day11, rep1

description:
Library name: N2_D11_1
N2_D11_1_trim_noZero_alignedAlt


title: N2, Day 8, rep5

description:
Library name: N2_D8_5
N2_D8_5_trim_noZero_alignedAlt

value: Day 8


title: N2, Day 8, rep6

description:
Library name: N2_D8_6
N2_D8_6_trim_noZero_alignedAlt


title: N2, Day 8, rep4

description:
Library name: N2_D8_4
N2_D8_4_trim_noZero_alignedAlt


title: N2, Day 8, rep2

description:
Library name: N2_D8_2
N2_D8_2_trim_noZero_alignedAlt


title: N2, Day 6, rep6

description:
Library name: N2_D6_6
N2_D6_6_trim_noZero_alignedAlt


title: N2, Day 8, rep3

description:
Library name: N2_D8_3
N2_D8_3_trim_noZero_alignedAlt


title: N2, Day 6, rep4

description:
Library name: N2_D6_4
N2_D6_4_trim_noZero_alignedAlt


title: N2, Day 6, rep5

description:
Library name: N2_D6_5
N2_D6_5_trim_noZero_alignedAlt


title: N2, Day 8, rep1

description:
Library name: N2_D8_1
N2_D8_1_trim_noZero_alignedAlt


title: N2, Day 6, rep2

description:
Library name: N2_D6_2
N2_D6_2_trim_noZero_alignedAlt


title: N2, Day 6, rep3

description:
Library name: N2_D6_3
N2_D6_3_trim_noZero_alignedAlt


title: N2, Day 6, rep1

description:
Library name: N2_D6_1
N2_D6_1_trim_noZero_alignedAlt


title: COMBO 3

type: protein

description:
Combined treatment
Jaime_R_Merchan__Valery_Chavez_12

hyb_protocol: RPPA performed following standard Core Facility protocols (details at MD Anderson RPPA Core website).

scan_protocol: RPPA slides scanned using Core Facility instrumentation; data output provided in normalized log2 scale.

data_processing: Normalization and log2 transformation performed by Core; differential analysis done using limma R package (v3.26.9), p < 0.05, FDR < 0.2.

molecule: protein

label_protocol: Not applicable (RPPA uses antibody binding detection).

growth_protocol: HT-29 cells cultured in McCoy’s 5A with 10% FBS, penicillin, streptomycin at 37°C, 5% CO2. Cells used at passages 1–6.

extract_protocol: Cells lysed for protein collection, processed for RPPA at MD Anderson RPPA Core Facility.

treatment_protocol: Cells treated for 48 hours with vehicle, MV-GFP (MOI 0.5), Triptolide (6.25 nM), or combination.

tag: cell line

tag: treatment

value: MV-GFP + TRP


title: TRP3

description:
TRP treatment
Jaime_R_Merchan__Valery_Chavez_9

value: TRP treatment


title: COMBO 2

description:
Combined treatment
Jaime_R_Merchan__Valery_Chavez_11


title: COMBO 1

description:
Combined treatment
Jaime_R_Merchan__Valery_Chavez_10


title: TRP2

description:
TRP treatment
Jaime_R_Merchan__Valery_Chavez_8


title: GFP 2

description:
MV-GFP treatment
Jaime_R_Merchan__Valery_Chavez_5

value: MV-GFP


title: NES (Nuclear Export Signal) in vivo 4SU label biol rep 1

city: Shanghai

first: Jiapeng

last: Liu

address: Yueyang Road 320

department: SIBCB

country: China

institute: CEMCS, CAS

description:
Library name: Sample 19
Ribosomal RNA Depletion

library_source: other

data_processing:
Quantification of gene expression level. Reference genome and gene model annotation files (v44) were downloaded from genome website directly. Index of the reference genome was built using STAR-2.7.9a and paired-end clean reads were aligned to the reference genome using STAR-2.7.9a.
FeatureCounts was used to count the read numbers mapped to each gene.
Differential expression analysis. Differential expression analysis of two groups (two biological replicates per condition) was performed using the DESeq2 R package (1.42.0).
Assembly: GRCh38

molecule: other

source_name: whole organism

extract_protocol:
RNA was harvested using VeZol Reagent (R411, Vazyme).
RNA libraries for RNA-seq were prepared using Ribo-MagOff rRNA Depletion Kit (N420, Vazyme) and VAHTS Universal V10 RNA-seq Library Prep Kit (NR616, Vazyme) fllowing manufacturer's protocols.

treatment_protocol: PRADA metabolic labeling in living cells. Cells stably expressing the indicated PRADA construct were grown to approximately 90% confluency. Cells were then incubated in fresh media containing 100 µM s4U for 5 hrs at 37°C. The media were then replaced with fresh media containing 0.5 mM alkyne phenol and 100 µM s4U for another 30 minutes. To initiate PRADA labeling, a final concentration of 10 mM D-amino acid was added for 30 minutes. The cells were then rinsed with quench solution three times to terminate the labeling reaction. Cells omitting D-amino acid treatment were used as the unlabeled control group. PRADA labeling in mice. 1 × 10^7 HEK-PRADA stable cells in 100 μL PBS were subcutaneously implanted into the hind leg regions of B-NDG mouse. Tumour sizes were measured with calliper and tumour volumes were calculated according to the standard formula (length × width × Height × π/6). For s4U metabolic labeling, s4U was dissolved in 2 mL saline solution and injected intraperitoneally at a dose of 430 mg/kg body weight. 5 hours after injection, tumor-bearing B-NDG mice were anesthetized and intratumorally injected with 1 mL saline solution containing 30 mM alkyne phenol, 100 mM D-Ala, and 100 mM D-Phe. The solution was prepared using non-contact ultrasound-assisted dissolution (<45°C). After 30 minutes, another 1 mL of the solution was injected. After an additional 30 min, the mice were euthanized, and the tissues were collected for subsequent experiments. Mice receiving only 30 mM alkyne phenol in saline solution were used as unlabeled negative controls.

value: whole organism

tag: cell type

value: mixed cell types


title: CTRL 1

description:
Human Cell Line
Jaime_R_Merchan__Valery_Chavez_1

value: Control


title: NES (Nuclear Export Signal) in vivo 4SU label biol rep 2

description:
Library name: Sample 20
Ribosomal RNA Depletion


title: GFP 3

description:
MV-GFP treament
Jaime_R_Merchan__Valery_Chavez_6


title: CTRL 2

description:
Human Cell Line
Jaime_R_Merchan__Valery_Chavez_2


title: CTRL 3

description:
Human Cell Line
Jaime_R_Merchan__Valery_Chavez_3


title: GFP 1

description:
MV-GFP treatment
Jaime_R_Merchan__Valery_Chavez_4


title: NLS (Nuclear Localization Signal) in vivo 4SU label biol rep 2

description:
Library name: Sample 18
Ribosomal RNA Depletion


title: TRP1

description:
TRP treatment
Jaime_R_Merchan__Valery_Chavez_7


title: NLS (Nuclear Localization Signal) in vivo 4SU label biol rep 1

description:
Library name: Sample 17
Ribosomal RNA Depletion


title: pol-iv_meiocytes_BS-seq_rep1

city: Klosterneuburg

first: Xiaoqi

last: Feng

address: Am Campus 1

department: Cell Biology

country: Austria

institute: Institute of Science and Technology Austria

description:
Library name: pol-iv_meiocytes_BS-seq_rep1
Bisulfite-Seq

library_source: genomic

data_processing:
Bisulfite-Seq: We used Perl scripts to convert all the Cs in the reads (and in the scaffolds) to Ts, and aligned the converted reads to the converted reference scaffold, allowing up to two mismatches per read. 76 base reads were divided into the first 45 and the last 31 bases, 100 base reads and 150 base reads were divided in half. Each half of the read was aligned independently using bowtie, allowing up to two mismatches. The coordinates of the two halves were subsequently correlated; the second half was discarded if it did not match the first.
Single_C: We used Perl scripts to recover the original sequence of each mapped read and, for each C (on either strand), count the number of times it was sequenced as a C or a T.
50bp_window: We used a Perl script to calculate fractional methylation (#C/(#C+#T)) within a 50 bp sliding window for each sequence context (CG, CHG, CHH).
RNA-Seq: TE transcript annotation was created using four biological replicates of pollen RNA-seq data. Hisat was used to align the RNA-seq reads to the TAIR10 genome
RIPseq: Bowtie2 was used to align the smRNA-seq reads to the TAIR10 genome
Assembly: TAIR10
Supplementary files format and content: bigWig signal tracks (*.bw): RNA-seq RPKM-normalized coverage, RIP-seq 24 nt RPM-normalized sRNA signal, and BS-seq CG/CHG/CHH methylation tracks with w50 smoothing.

organism: Arabidopsis thaliana

source_name: meiocyte

growth_protocol: A. thaliana plants of Col-0 ecotype were grown under 16h light/ 8h dark in a growth chamber.

extract_protocol:
Stage 9 flower buds were collected and gently squeezed between a glass slide and coverslip. The released meiocytes (of meiotic prophase I) were examined carefully under a microscope. Clean meiocytes free from any somatic cell debris were transferred to a new slide using capillary glass pipettes, washed by 1 x PBS buffer 3 times, and frozen in liquid nitrogen. Sperm cells and vegetative cell nuclei were isolated by Fluorescence-activated cell sorting (FACS) Single-end bisulfite sequencing libraries for Illumina sequencing were constructed using the Ovation Ultralow Methyl-Seq Library Systems (Nugen, #0336) and EpiTect Fast Bisulfite Conversion (Qiagen, #59802) kits according to the kit protocols, except the incorporation of two rounds of bisulfite conversion.Strand-specific RNA sequencing libraries were prepared using ScriptSeq v2 RNA-Seq (Illumina, #SSV21106) Library Preparation and Ovation RNA-Seq Systems for Model Organisms Arabidopsis (Nugen, #0351) kits
Sequencing libraries were prepared for RNA-seq, whole genome bisulfite sequencing, or RIP-seq according to the corresponding assay workflow and sequenced on an Illumina NextSeq 1000 instrument.

treatment_protocol: No external treatment was applied; samples represent wild type and mutant/genotype comparisons.

value: meiocyte

value: pol-iv


title: pol-iv_meiocytes_BS-seq_rep2

description:
Library name: pol-iv_meiocytes_BS-seq_rep2
Bisulfite-Seq


title: ago4,6,9_meiocytes_BS-seq_rep2

description:
Library name: ago4,6,9_meiocytes_BS-seq_rep2
Bisulfite-Seq


title: ago4,6,9_meiocytes_BS-seq_rep1

description:
Library name: ago4,6,9_meiocytes_BS-seq_rep1
Bisulfite-Seq


title: ago6,9_meiocytes_BS-seq_rep1

description:
Library name: ago6,9_meiocytes_BS-seq_rep1
Bisulfite-Seq


title: ago4,6_meiocytes_BS-seq_rep1

description:
Library name: ago4,6_meiocytes_BS-seq_rep1
Bisulfite-Seq


title: ago9_meiocytes_BS-seq_rep2

description:
Library name: ago9_meiocytes_BS-seq_rep2
Bisulfite-Seq


title: ago6_meiocytes_BS-seq_rep2

description:
Library name: ago6_meiocytes_BS-seq_rep2
Bisulfite-Seq


title: ago9_meiocytes_BS-seq_rep1

description:
Library name: ago9_meiocytes_BS-seq_rep1
Bisulfite-Seq


title: ago6,9_meiocytes_BS-seq_rep2

description:
Library name: ago6,9_meiocytes_BS-seq_rep2
Bisulfite-Seq


title: ago6_meiocytes_BS-seq_rep1

description:
Library name: ago6_meiocytes_BS-seq_rep1
Bisulfite-Seq


title: ago4,6_meiocytes_BS-seq_rep2

description:
Library name: ago4,6_meiocytes_BS-seq_rep2
Bisulfite-Seq


title: ago4_meiocytes_BS-seq_rep2

description:
Library name: ago4_meiocytes_BS-seq_rep2
Bisulfite-Seq


title: ago4_meiocytes_BS-seq_rep1

description:
Library name: ago4_meiocytes_BS-seq_rep1
Bisulfite-Seq


title: WT_meiocytes_BS-seq_rep2

description:
Library name: WT_meiocytes_BS-seq_rep2
Bisulfite-Seq

value: WT


title: ago5_meiocytes_BS-seq_rep2

description:
Library name: ago5_meiocytes_BS-seq_rep2
Bisulfite-Seq


description:
Library name: GFP_RIP-seq_in_WT_floral_buds_(35S-GFP)_rep1
miRNA-Seq


title: AGO5_RIP-seq_in_pol-iv_floral_buds_rep2

description:
Library name: AGO5_RIP-seq_in_pol-iv_floral_buds_rep2
miRNA-Seq


title: WT_meiocytes_BS-seq_rep1_

description:
Library name: WT_meiocytes_BS-seq_rep1_
Bisulfite-Seq


title: ago5_meiocytes_BS-seq_rep1

description:
Library name: ago5_meiocytes_BS-seq_rep1
Bisulfite-Seq


title: AGO5_RIP-seq_in_pol-iv_floral_buds_rep1

description:
Library name: AGO5_RIP-seq_in_pol-iv_floral_buds_rep1
miRNA-Seq


description:
Library name: AGO5_RIP-seq_in_clsy3,4_floral_buds_rep2
miRNA-Seq


description:
Library name: AGO5_RIP-seq_in_clsy3,4_floral_buds_rep1
miRNA-Seq


title: AGO5_RIP-seq_in_clsy4_floral_buds_rep1

description:
Library name: AGO5_RIP-seq_in_clsy4_floral_buds_rep1
miRNA-Seq


description:
Library name: GFP_RIP-seq_in_WT_floral_buds_(35S-GFP)_rep2
miRNA-Seq


title: AGO5_RIP-seq_in_clsy4_floral_buds_rep2

description:
Library name: AGO5_RIP-seq_in_clsy4_floral_buds_rep2
miRNA-Seq


title: AGO5_RIP-seq_in_clsy3_floral_buds_rep2

description:
Library name: AGO5_RIP-seq_in_clsy3_floral_buds_rep2
miRNA-Seq


title: AGO5_RIP-seq_in_clsy3_floral_buds_rep1

description:
Library name: AGO5_RIP-seq_in_clsy3_floral_buds_rep1
miRNA-Seq


description:
Library name: AGO5_RIP-seq_in_clsy1,2_floral_buds_rep1
miRNA-Seq


description:
Library name: AGO5_RIP-seq_in_clsy1,2_floral_buds_rep2
miRNA-Seq


title: AGO4_RIP-seq_in_WT_floral_buds_rep2

description:
Library name: AGO4_RIP-seq_in_WT_floral_buds_rep2
miRNA-Seq


title: AGO6_RIP-seq_in_WT_floral_buds_rep1

description:
Library name: AGO6_RIP-seq_in_WT_floral_buds_rep1
miRNA-Seq


title: AGO9_RIP-seq_in_WT_floral_buds_rep2

description:
Library name: AGO9_RIP-seq_in_WT_floral_buds_rep2
miRNA-Seq


title: AGO5_RIP-seq_in_WT_floral_buds_rep1

description:
Library name: AGO5_RIP-seq_in_WT_floral_buds_rep1
miRNA-Seq


title: AGO4_RIP-seq_in_WT_floral_buds_rep1

description:
Library name: AGO4_RIP-seq_in_WT_floral_buds_rep1
miRNA-Seq


title: AGO5_RIP-seq_in_WT_floral_buds_rep2

description:
Library name: AGO5_RIP-seq_in_WT_floral_buds_rep2
miRNA-Seq


title: AGO9_RIP-seq_in_WT_floral_buds_rep1

description:
Library name: AGO9_RIP-seq_in_WT_floral_buds_rep1
miRNA-Seq


title: AGO6_RIP-seq_in_WT_floral_buds_rep2

description:
Library name: AGO6_RIP-seq_in_WT_floral_buds_rep2
miRNA-Seq


title: pol-iv_meiocytes_RNA-seq_rep1

description:
Library name: pol-iv_meiocytes_RNA-seq_rep1
RNA-Seq

data_processing:
Reads were mapped to Arabidopsis reference transcriptome (TAIR10) using Hisat2
FeatureCounts was used to calculate the number of raw counts for individual TEs or genes
Assembly: TAIR10
Supplementary files format and content: bigWig signal tracks (*.bw): RNA-seq RPKM-normalized coverage


title: pol-iv_meiocytes_RNA-seq_rep3

description:
Library name: pol-iv_meiocytes_RNA-seq_rep3
RNA-Seq


title: pol-iv_meiocytes_RNA-seq_rep2

description:
Library name: pol-iv_meiocytes_RNA-seq_rep2
RNA-Seq


title: ago4,6,9_meiocytes_RNA-seq_rep3

description:
Library name: ago4,6,9_meiocytes_RNA-seq_rep3
RNA-Seq


title: ago4,6,9_meiocytes_RNA-seq_rep2

description:
Library name: ago4,6,9_meiocytes_RNA-seq_rep2
RNA-Seq


title: ago5_meiocytes_RNA-seq_rep2

description:
Library name: ago5_meiocytes_RNA-seq_rep2
RNA-Seq


title: ago5_meiocytes_RNA-seq_rep3

description:
Library name: ago5_meiocytes_RNA-seq_rep3
RNA-Seq


title: ago5_meiocytes_RNA-seq_rep1

description:
Library name: ago5_meiocytes_RNA-seq_rep1
RNA-Seq


title: Stomach,desert_type,ZSP

city: Fuzhou

first: Guangtan

last: Lin

state: Fujian

address: No. 29 Xinquan Road

department: Department of Gastric Surgery

institute: Fujian Medical University Union Hospital

description:
Library name: ZSP_scRNA_GC
10x Genomics

data_processing:
Raw sequencing data were processed using Cell Ranger v7.0 (10x Genomics) with alignment to the human reference genome. Downstream analyses, including quality control, normalization, dimensionality reduction, clustering, and cell-type annotation, were performed using Seurat v5.3.0.
Assembly: GRCh38 (hg38)
Supplementary files format and content: Processed data files include barcodes.tsv.gz (cell barcodes), features.tsv.gz (gene features), and matrix.mtx.gz (count matrix) generated by Cell Ranger, containing single-cell gene expression data.

source_name: Stomach

extract_protocol:
Human GC tissues were washed with PBS, cleared of blood and adjacent non-tumor tissue, minced, and enzymatically dissociated into single-cell suspensions. Total RNA was extracted from single cells using the 10x Genomics Chromium Single Cell 3' Reagent Kit v3 according to the manufacturer’s instructions.
Single-cell RNA-seq libraries were prepared using the 10x Genomics Chromium Single Cell 3' Reagent Kit v3 according to the manufacturer’s instructions. Briefly, single-cell suspensions were loaded onto the 10x Genomics Chromium platform for cell capture and barcoding, followed by reverse transcription, cDNA amplification, and library construction.

value: Stomach

tag: immune phenotype

value: Desert


title: WT_meiocytes_RNA-seq_rep3

description:
Library name: WT_meiocytes_RNA-seq_rep3
RNA-Seq


title: Stomach,inflamed_type,XZB

description:
Library name: XZB_scRNA_GC
10x Genomics

value: Inflamed


title: Stomach,desert_type,WYZ

description:
Library name: WYZ_scRNA_GC
10x Genomics


title: WT_meiocytes_RNA-seq_rep1

description:
Library name: WT_meiocytes_RNA-seq_rep1
RNA-Seq


title: WT_meiocytes_RNA-seq_rep2

description:
Library name: WT_meiocytes_RNA-seq_rep2
RNA-Seq


title: Stomach,desert_type,YWM

description:
Library name: YWM_scRNA_GC
10x Genomics


title: Stomach,desert_type,ZWG

description:
Library name: ZWG_scRNA_GC
10x Genomics


title: Stomach,desert_type,WHJ

description:
Library name: WHJ_scRNA_GC
10x Genomics


title: ago4,6,9_meiocytes_RNA-seq_rep1

description:
Library name: ago4,6,9_meiocytes_RNA-seq_rep1
RNA-Seq


title: Stomach,desert_type,MWX

description:
Library name: MWX_scRNA_GC
10x Genomics


title: Stomach,inflamed_type,LZJ

description:
Library name: LZJ_scRNA_GC
10x Genomics


title: Stomach,inflamed_type,LZX

description:
Library name: LZX_scRNA_GC
10x Genomics


title: Stomach,inflamed_type,LYF

description:
Library name: LYF_scRNA_GC
10x Genomics


title: Stomach,desert_type,LGL

description:
Library name: LGL_scRNA_GC
10x Genomics


title: Stomach,inflamed_type,LSB

description:
Library name: LSB_scRNA_GC
10x Genomics


title: Stomach,inflamed_type,LNQ

description:
Library name: LNQ_scRNA_GC
10x Genomics


title: Stomach,inflamed_type,HHG

description:
Library name: HHG_scRNA_GC
10x Genomics


title: Stomach,desert_type,ZRZ

description:
Library name: ZRZ_ST_GC
FFPE human gastric cancer Spatial transcriptome sequencing

data_processing:
Raw sequencing reads were mapped to GRCh38 via Space Ranger v2.0.0 for initial matrix generation. Low-quality spots were filtered based on detected gene counts and mitochondrial transcript percentage. Seurat v5.3.0 was used for SCTransform normalization, PCA/UMAP dimensionality reduction, unsupervised clustering and Robust Cell Type Decomposition (RCTD) cell deconvolution. Functional pathway enrichment was analyzed using MSigDB Hallmark collection gene sets.
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz：list of all spatial spot barcodes
Supplementary files format and content: features.tsv.gz：gene ID annotation list
Supplementary files format and content: matrix.mtx.gz：raw UMI count matrix in Matrix Market format
Supplementary files format and content: aligned_fiducials.jpg：aligned fiducial marker image of histology slide
Supplementary files format and content: aligned_tissue_image.jpg：aligned tissue histology image
Supplementary files format and content: cytassist_image.tiff：original cytassist scanning image of FFPE section
Supplementary files format and content: detected_tissue_image.jpg：image with auto-detected tissue area and spot layout
Supplementary files format and content: scalefactors_json.json：JSON-formatted scaling coefficients for image alignment
Supplementary files format and content: tissue_hires_image.png：high-resolution H&E histology image
Supplementary files format and content: tissue_lowres_image.png：low-resolution H&E histology image
Supplementary files format and content: tissue_positions.csv：spatial coordinate table linking barcode and spot position
Library strategy: Spatial Transcriptomics

extract_protocol:
FFPE gastric cancer sections were permeabilized following the official 10x Genomics Visium FFPE protocol to release intact mRNA for spatial capture.
Spatially barcoded cDNA libraries were generated on Visium slides following tissue permeabilization, followed by end repair, adapter ligation and PCR amplification. Final libraries were sequenced on an Illumina NovaSeq 6000 platform.


title: Stomach,desert_type,CHJ

description:
Library name: CHJ_scRNA_GC
10x Genomics


title: Stomach,inflamed_type,CYY

description:
Library name: CYY_scRNA_GC
10x Genomics


title: Stomach,desert_type,MWX

description:
Library name: MWX_ST_GC
FFPE human gastric cancer Spatial transcriptome sequencing


title: Stomach,inflamed_type,LZX

description:
Library name: LZX_ST_GC
FFPE human gastric cancer Spatial transcriptome sequencing


title: Stomach,inflamed_type,LZJ

description:
Library name: LZJ_ST_GC
FFPE human gastric cancer Spatial transcriptome sequencing


title: Stomach,desert_type,YWM

description:
Library name: YWM_ST_GC
FFPE human gastric cancer Spatial transcriptome sequencing


title: hTERT_MSC_Whole_Cell_3

city: La Jolla

first: Richard

middle: L.

last: Klemke

state: CA

address: 3120 Biomedical Sciences Wy

department: Pathology

institute: University of California, San Diego

description:
Library name: Sample9
column name in all_samples_featureCounts.txt: Wholecell3

data_processing:
Raw gene counts were converted to TPM by first normalizing counts to gene length in kilobases to calculate reads per kilobase (RPK), followed by scaling each sample by the total RPK per million. For downstream differential expression filtering, genes with low average expression were removed by retaining only genes with a DESeq2 baseMean ≥ 10.
Assembly: Homo sapiens GRCh38
Supplementary files format and content: tab-delimited text fiile includes raw counts for each Sample
Supplementary files format and content: pooled csv file with TPM value for each Sample

source_name: Adipose

growth_protocol: hTERT-MSCs (ATCC (#SCRC-4000) were cultured in alpha MEM (Gibco #12561) supplemented with 16.5% premium fetal bovine serum (FBS; Atlanta Biologics #S1150), 1% HEPES (Gibco #15630), 1% GlutaMAX 100x (Gibco #35050), 1% Anti-Anti 100x (Gibco #15240) and incubated at 37°C, 5% CO₂.

extract_protocol:
Inserts were washed in phosphate-buffered saline (PBS Invitrogen #AM9625), and cell protrusions were harvested using a sharp cell scraper (Corning #3010). The lower side of the membrane was scraped first, and the cell scraper was thoroughly washed in 0.5 mL TRIzol Reagent (ThermoFisher #15596026) for RNA isolation. Care was taken to ensure that the cell scraper was used only once on the membrane to avoid cell lysis by TRIzol Reagent or loading buffer. Cells on the upper side of the membrane were subsequently scraped and transferred to TRIzol Reagent or loading buffer for further analysis. RNA was precipitated using 1 µg glycogen as a carrier.
NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina (E6420S)

treatment_protocol: 6-well cell culture inserts with 3 µm pore-size polycarbonate membranes and a 3.14 cm² insert culture area were used (Thermo Fisher #140642). Well inserts (Thermo Fished #140675) were placed into wells without ECM coating. Cells were serumstarved overnight and detached using 0.5% Trypsin-EDTA and inactivated in alpha MEM containing 16.5% FBS. Cells were pelleted by centrifugation and resuspended in serum-free medium, and 2 × 10⁶ cells were transferred to each membrane insert. After 2 hours, the insert was transferred to a well containing serum-free medium supplemented with 50 ng/mL PDGF-BB (Gibco, #PHG0134). Cell protrusions were allowed to grow through the membrane for 1 hour before protein and RNA purification

value: Adipose

value: mesenchymal stem cell

value: hTERT-MSC

value: Whole Cell

value: PDGF-BB


title: Stomach,inflamed_type,CYY

description:
Library name: CYY_ST_GC
FFPE human gastric cancer Spatial transcriptome sequencing


title: hTERT_MSC_Whole_Cell_2

description:
Library name: Sample8
column name in all_samples_featureCounts.txt: Wholecell2


title: hTERT_MSC_Whole_Cell_1

description:
Library name: Sample7
column name in all_samples_featureCounts.txt: Wholecell1


title: hTERT_MSC_CB_3

description:
Library name: Sample6
column name in all_samples_featureCounts.txt: CellBody3

value: Cell Body Fraction


title: hTERT_MSC_CB_2

description:
Library name: Sample5
column name in all_samples_featureCounts.txt: CellBody2


title: hTERT_MSC_PD_1

description:
Library name: Sample1
column name in all_samples_featureCounts.txt: Protrusion1

value: Pseudopodia Fraction


title: hTERT_MSC_PD_2

description:
Library name: Sample2
column name in all_samples_featureCounts.txt: Protrusion2


title: hTERT_MSC_PD_3

description:
Library name: Sample3
column name in all_samples_featureCounts.txt: Protrusion3


title: hTERT_MSC_CB_1

description:
Library name: Sample4
column name in all_samples_featureCounts.txt: CellBody1


title: CRC_N08

city: 广西

first: 晓倩

last: 赵

address: 南宁

institute: 广西中医药大学

description:
Library name: CRC_N08
Primary colorectal adenocarcinoma tissue from paired discovery cohort.

data_processing:
Raw reads were processed using fastx v0.0.13 to remove adapter sequences, trim low-quality bases from the 3' end, and discard reads shorter than 10 nt.
Clean reads within the 18-40 nt small RNA size range were retained for downstream small RNA annotation and miRNA analysis.
Filtered clean reads were aligned to the human reference genome GRCh38 using Bowtie, allowing one mismatch.
Known miRNAs were annotated according to miRBase, and novel miRNAs were predicted using the small RNA sequencing analysis pipeline.
miRNA read counts were calculated for each sample, normalized using the TMM method, and converted to TPM values. Differential expression analysis between colorectal cancer tissues and matched adjacent non-tumor tissues was performed using edgeR.
Assembly: GRCh38
Supplementary files format and content: miRNA_expression_matrix.txt is a tab-delimited text matrix containing miRNA identifiers, raw read counts and TPM-normalized expression values for all 16 miRNA-seq samples.
Supplementary files format and content: Rows represent miRNAs, and columns represent individual samples. The original expression table was generated from miRNA_expression.xls.

source_name: adjacent normal tissue

growth_protocol: Not applicable. Human colorectal tissue samples were collected from surgical specimens.

extract_protocol:
Total RNA was extracted from human tissue samples using TM miRNA extraction kit #TR205-200 according to the manufacturer's instructions. RNA quality and quantity were assessed before library construction.
Small RNA libraries were constructed for microRNA sequencing according to the manufacturer's protocol. Qualified libraries were sequenced on the Illumina NovaSeq 6000 platform to generate single-end 50 bp reads.

treatment_protocol: No experimental treatment was applied. Fresh colorectal cancer and matched adjacent non-tumor tissue samples were collected during surgical resection.

value: adjacent normal tissue

tag: pair

value: wild type


title: CRC_T06

description:
Library name: CRC_T06
Primary colorectal adenocarcinoma tissue from paired discovery cohort.

source_name: colorectal cancer tissue

value: colorectal cancer tissue


title: CRC_T08

description:
Library name: CRC_T08
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: CRC_N07

description:
Library name: CRC_N07
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: CRC_T07

description:
Library name: CRC_T07
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: CRC_N06

description:
Library name: CRC_N06
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: CRC_T05

description:
Library name: CRC_T05
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: CRC_N05

description:
Library name: CRC_N05
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: CRC_T03

description:
Library name: CRC_T03
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: CRC_N03

description:
Library name: CRC_N03
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: CRC_T04

description:
Library name: CRC_T04
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: CRC_N04

description:
Library name: CRC_N04
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: CRC_T01

description:
Library name: CRC_T01
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: WTC11 hiPSC, Passage 63, Day 113 hPSC-CMs, Well Replicate 4

city: Madison

first: Sean

middle: P.

last: Palecek

state: Wisconsin

address: 1415 Engineering Drive

department: Chemical and Biological Engineering

institute: University of Wisconsin-Madison

description:
Library name: D4
column name in both processed data files: D113-4

data_processing:
Raw FASTQ files were mapped to the human genome (hg38+decoy) using STAR v2.5.3a
Gene-level transcript abundances were calculated using featureCounts v2.0.3
Assembly: Assembly: hg38+decoy
Supplementary files format and content: csv files starting with featureCounts include gene-level counts for each sample and gene, csv files starting with TPM include transcipts per million values for each sample and gene

source_name: WTC11 hiPSC line

growth_protocol: hPSCs were differentiated using the GiWi protocol as described previously. On Day -2, hPSCs were detached and singularized with Accutase (Innovative Cell Technology AT104) for 5 min prior to quenching 1:1 v/v in DMEM/F12 (ThermoFisher 11330032). Subsequently, hPSCs were counted and resuspended at an optimal cell density for cardiomyocyte differentiation for the WTC11 hiPSC line. hPSCs were resuspended in mTeSR1 with 5 μM Y-27632 (Tocris 1254) and seeded onto Matrigel-coated 12-well plates in 2 mL of media. To facilitate even cell attachment on Day -2, plates were left at room temperature for 30 min prior to maintenance in a cell culture incubator. On Day -1, medium was replaced with mTeSR1. On Day 0, differentiation was induced with CHIR99021 (Selleckchem S1263) at a concentration between 6-12 μM, optimized for cardiomyocyte differentiation for the WTC11 hiPSC line. CHIR99021 was added to RPMI1640 medium (Life Technologies 11875119) with 2% v/v B27 minus insulin (B27-). Media was replaced with B27- and 5 μM IWP2 (Tocris 3533) on Day 2 and on Day 4 with B27-. On Days 6, 8, 10, and 13, media was replaced with RPMI1640 with 2% v/v B27 with insulin (B27+, Life Technologies 17504044) until collection for flow cytometry to confirm high purity cardiomyocyte differentiation on Day 16. Parallel wells for multi-omic collection were maintained in B27+ medium, which was replaced every 2-3 days.

extract_protocol:
RNA was harvested from Trizol-collected samples by tri-phasic extraction followed by purification and concentration with Zymo Direct-zol MiniPrep Plus columns (including on-column DNAase treatment). 500ng of total RNA per sample was used for the construction of sequencing libraries.
Poly(A)-selected mRNA-seq libraries were prepared by Novogene from total RNA using poly-T oligo-attached magnetic beads, followed by RNA fragmentation, random-hexamer-primed cDNA synthesis, adapter ligation, size selection, PCR amplification, and purification. Libraries were sequenced on an Illumina NovaSeq 6000 platform using paired-end 150-bp reads.

treatment_protocol: After hPSC-CM differentiation was completed and flow cytometry was performed to quantify hPSC-CM differentiation purity (%cTnT+ cells), wells were cultured long-term to promote hPSC-CM maturation. Wells were collected on Day 30, Day 60, and Day 113 to assess the long-term hPSC-CM maturation time course. Subsequently, temporally trizol-collected hPSC-CM long-term maturation samples were further processed for RNA sequencing.

value: WTC11 hiPSC line

value: Day 113 hPSC-CMs

tag: passage number

value: Passage 63


title: CRC_N02

description:
Library name: CRC_N02
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: WTC11 hiPSC, Passage 63, Day 113 hPSC-CMs, Well Replicate 2

description:
Library name: D2
column name in both processed data files: D113-2


title: CRC_N01

description:
Library name: CRC_N01
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: WTC11 hiPSC, Passage 63, Day 113 hPSC-CMs, Well Replicate 3

description:
Library name: D3
column name in both processed data files: D113-3


title: WTC11 hiPSC, Passage 63, Day 113 hPSC-CMs, Well Replicate 1

description:
Library name: D1
column name in both processed data files: D113-1


title: CRC_T02

description:
Library name: CRC_T02
Primary colorectal adenocarcinoma tissue from paired discovery cohort.


title: WTC11 hiPSC, Passage 63, Day 60 hPSC-CMs, Well Replicate 2

description:
Library name: C2
column name in both processed data files: D060-2

value: Day 60 hPSC-CMs


title: WTC11 hiPSC, Passage 63, Day 60 hPSC-CMs, Well Replicate 1

description:
Library name: C1
column name in both processed data files: D060-1


title: WTC11 hiPSC, Passage 63, Day 30 hPSC-CMs, Well Replicate 1

description:
Library name: B1
column name in both processed data files: D030-1

value: Day 30 hPSC-CMs


title: WTC11 hiPSC, Passage 63, Day 30 hPSC-CMs, Well Replicate 4

description:
Library name: B4
column name in both processed data files: D030-4


title: WTC11 hiPSC, Passage 63, Day 30 hPSC-CMs, Well Replicate 3

description:
Library name: B3
column name in both processed data files: D030-3


title: WTC11 hiPSC, Passage 63, Day 60 hPSC-CMs, Well Replicate 3

description:
Library name: C3
column name in both processed data files: D060-3


title: Control-2

city: Tianjin

first: Shu-Lin

address: No.94 of Weijin Road

institute: Nankai University

description: Library name: Control-2

data_processing:
Raw image files generated by the Illumina sequencing platform were converted to FASTQ format using CASAVA (Base Calling). Quality control was performed to generate clean reads by removing: Reads shorter than 100 bp after adapter trimming and low-quality base removal; Reads containing more than 10 ambiguous nucleotides (N); Reads in which low-quality bases (Q ≤ 30) accounted for more than 40% of the read length. Clean reads were aligned to the Homo sapiens reference genome GRCh38.112 using HISAT2 with default parameters. Alignment statistics, read distribution, sequencing saturation, and transcript coverage analyses were subsequently performed. Transcript assembly and gene expression quantification were carried out using StringTie, and expression levels were normalized as FPKM and TPM values. Differential expression analysis was performed using DESeq2. Genes with a P-value < 0.05 and |log2FoldChange| ≥ 2 were considered significantly differentially expressed. Variant detection, including SNP and INDEL identification, was performed using GATK.Software versions were those implemented in the commercial transcriptome analysis pipeline provided by Qingke Biotechnology. Default parameters were used unless otherwise specified.
Assembly: GRCh38
Supplementary files format and content: Microsoft Excel file containing normalized gene expression values for all detected genes across the nine RNA-seq samples (Clu-1, Clu-2, Clu-3, Con-1, Con-2, Con-3, MAR-1, MAR-2, and MAR-3). Rows represent genes and columns represent samples. Gene identifiers, gene symbols, and normalized expression values (FPKM) generated using StringTie are included.

extract_protocol:
MCF-7 cells cultured in 6-well plates were harvested by centrifugation, and RNA was extracted using the Trizol RNA extraction method. The purity and concentration of the extracted RNA were then measured using an ELISA reader. The RNA samples were flash-frozen in liquid nitrogen and stored at −80°C for subsequent analysis.
Total RNA was extracted from samples and subjected to mRNA enrichment using poly(A) selection. Purified mRNA was fragmented into short fragments and reverse-transcribed into first-strand cDNA using random primers, followed by second-strand cDNA synthesis. The resulting cDNA fragments were end-repaired, A-tailed, and ligated to Illumina sequencing adapters. After PCR amplification and library quality assessment, the libraries were sequenced on an Illumina platform using paired-end 150 bp reads (PE150).

value: cell line

tag: sample group

value: Control


title: Control-1

description: Library name: Control-1


title: WTC11 hiPSC, Passage 63, Day 30 hPSC-CMs, Well Replicate 2

description:
Library name: B2
column name in both processed data files: D030-2


title: MARRS-3

description: Library name: MARRS-3

value: MARRS


title: MARRS-2

description: Library name: MARRS-2


title: CLUSTER-3

description: Library name: CLUSTER-3

value: CLUSTER


title: CLUSTER-2

description: Library name: CLUSTER-2


title: MARRS-1

description: Library name: MARRS-1


title: Control-3

description: Library name: Control-3


title: Lung tissue37,LCME group

city: Chongqing

first: Yuhao

last: Wu

address: No. 136, Zhongshan Second Road

institute: Children’s Hospital of Chongqing Medical University

description: Library name: L37

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Homo sapiens reference genome using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: GRCh38
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: Lung

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

treatment_protocol: Patients were assigned into LCME and HCME groups based on the MNP levels in the lung tissues

value: Lung


title: CLUSTER-1

description: Library name: CLUSTER-1


title: Lung tissue25,LCME group

description: Library name: L25


title: Lung tissue20,LCME group

description: Library name: L20


title: Lung tissue31,HCME group

description: Library name: H31


title: Lung tissue27,HCME group

description: Library name: H27


title: Lung tissue17,HCME group

description: Library name: H17


title: umbilical cord plasma, Gen3G, PubM2491

city: Sherbrooke

first: Luigi

last: Bouchard

country: Canada

institute: Université de Shebrooke

description: Library name: Gen3G_UCP_PubM2491

data_processing:
The extra-cellular RNA processing toolkit (exceRpt) pipeline version 4.6.3 (PMID : 30956140) was used to process miRNA sequencing data from fastq files.
Low quality reads (Phred score < 20 for more than  80% of the read) and adapters sequences were removed with the FASTX-Toolkit integrated in the exceRpt pipeline. High quality sequences were mapped to the human genome (GRCh37) and miRBase version 21 using the STAR alignment algorithm version 2.4.2a.
Read count extraction was performed using the Rscript provided for processing exceRpt output for multiple samples (PMID : 30956140).
Assembly: GRCh37
Supplementary files format and content: Comma-seperated value file, include non-normalized read counts for each microRNA detected in each samples.

source_name: umilical cord plasma

extract_protocol:
Total RNA was extracted using the mirVana PARIS kit and protocol (Thermo Fisher Scientific, catalogue # AM1556), in a randomized order, from up to 500 μL of UCP (130 µL to 500 µL, based on availability) kept at -80 °C until extraction. Prior to extraction, a volume of miRNeasy Serum/Plasma  Caenorhabditis elegans cel-miR-39-3p mimic Spike-In Control (Qiagen, catalog # 219610) was added to each sample, folowing a 1 μL for each 250 μL of plasma ratio. Elution of total RNA was performed in 75 µL of nuclease-free water, and 70 µL of this RNA eluate was then precipitated, dried and resuspended in 5 μL of nuclease-free water as previously described (PMID: 35246451). The whole volume was used for library preparation.
Samples were randomized before library preparation. The libraries were created using the the Truseq Small RNA Sample Prep kit (Illumina, BC, Canada; catalogue # RS-200- 0012) following  the standard procedure adapted to samples of low RNA concentration by Burgos et al (PMID: 23525801). To maintain an optimal reaction ratio, half of the reagents volumes were used for RNA ligation with adapters at 3′ and 5′ ends, reverse transcription, barcoding (index 1-48: one index per sample) and PCR amplification (15 cycles). Libraries were purified by migration in a Novex polyacrylamide TBE Gel, 6% (ThermoFisher Scientific, Waltham, United States, catalog #EC265BOX). Fragments between 145 and 160 bp were excised and eluted from the gel with 300 µL of nuclease-free water at room temperature, during an overnight incubation at 500 RPM on a microplate shaker (VWR, ON, Canada, catalog #12620-930). Libraries were concentrated by precipitation following manufacturer's instructions, briefly with a 30 minutes incubation at -80°C, and resuspended in 25 µL of 10 mM Tris-HCl pH 8.5 buffer. Libraries sequencing, including quality control and sample pooling, was performed at the Centre d’expertise et de services Génome Québec (Montréal, Canada). The Kapa Illumina GA with Revised Primers-SYBR Fast Universal kit (Kapa Biosystems) was used to assess the quality of each library (i.e., concentration, library length and primer dimers absence).  Librairies were pooled equimolarly (200 pM final molarity; 48 libraries with different indexes per lane), denatured and clustered on an Illumina NovaSeq S1 flowcell following the Xp protocol from manufacturer’s recommendations. The sequencing run was performed for 100 cycles in single-end mode, on a NovaSeq 6000 platform.

value: umilical cord plasma

tag: fetal sex

value: male

tag: gestational age_at_birth_(weeks)

tag: delivery type

value: vaginal

tag: birth weight_(g)

tag: z-score birth_weight

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: umbilical cord plasma, Gen3G, PubM2871

description: Library name: Gen3G_UCP_PubM2871

tag: tissue


title: umbilical cord plasma, Gen3G, PubM2551

description: Library name: Gen3G_UCP_PubM2551

value: female


title: umbilical cord plasma, Gen3G, PubM2748

description: Library name: Gen3G_UCP_PubM2748


title: umbilical cord plasma, Gen3G, PubM2345

description: Library name: Gen3G_UCP_PubM2345


title: umbilical cord plasma, Gen3G, PubM2172

description: Library name: Gen3G_UCP_PubM2172


title: umbilical cord plasma, Gen3G, PubM2350

description: Library name: Gen3G_UCP_PubM2350


title: umbilical cord plasma, Gen3G, PubM2846

description: Library name: Gen3G_UCP_PubM2846

value: cesarean


title: umbilical cord plasma, Gen3G, PubM2700

description: Library name: Gen3G_UCP_PubM2700


title: umbilical cord plasma, Gen3G, PubM2582

description: Library name: Gen3G_UCP_PubM2582


title: umbilical cord plasma, Gen3G, PubM2843

description: Library name: Gen3G_UCP_PubM2843


title: umbilical cord plasma, Gen3G, PubM2577

description: Library name: Gen3G_UCP_PubM2577


title: umbilical cord plasma, Gen3G, PubM2634

description: Library name: Gen3G_UCP_PubM2634


title: umbilical cord plasma, Gen3G, PubM2448

description: Library name: Gen3G_UCP_PubM2448


title: umbilical cord plasma, Gen3G, PubM2364

description: Library name: Gen3G_UCP_PubM2364


title: umbilical cord plasma, Gen3G, PubM2344

description: Library name: Gen3G_UCP_PubM2344


title: umbilical cord plasma, Gen3G, PubM2468

description: Library name: Gen3G_UCP_PubM2468


title: umbilical cord plasma, Gen3G, PubM2765

description: Library name: Gen3G_UCP_PubM2765


title: umbilical cord plasma, Gen3G, PubM2298

description: Library name: Gen3G_UCP_PubM2298


title: umbilical cord plasma, Gen3G, PubM2197

description: Library name: Gen3G_UCP_PubM2197


title: umbilical cord plasma, Gen3G, PubM2592

description: Library name: Gen3G_UCP_PubM2592


title: umbilical cord plasma, Gen3G, PubM2052

description: Library name: Gen3G_UCP_PubM2052


title: umbilical cord plasma, Gen3G, PubM2319

description: Library name: Gen3G_UCP_PubM2319


title: umbilical cord plasma, Gen3G, PubM2728

description: Library name: Gen3G_UCP_PubM2728


title: umbilical cord plasma, Gen3G, PubM2229

description: Library name: Gen3G_UCP_PubM2229


title: umbilical cord plasma, Gen3G, PubM2080

description: Library name: Gen3G_UCP_PubM2080


title: umbilical cord plasma, Gen3G, PubM2616

description: Library name: Gen3G_UCP_PubM2616


title: umbilical cord plasma, Gen3G, PubM2716

description: Library name: Gen3G_UCP_PubM2716


title: umbilical cord plasma, Gen3G, PubM2246

description: Library name: Gen3G_UCP_PubM2246


title: umbilical cord plasma, Gen3G, PubM2811

description: Library name: Gen3G_UCP_PubM2811


title: umbilical cord plasma, Gen3G, PubM2383

description: Library name: Gen3G_UCP_PubM2383


title: umbilical cord plasma, Gen3G, PubM2363

description: Library name: Gen3G_UCP_PubM2363


title: umbilical cord plasma, Gen3G, PubM2380

description: Library name: Gen3G_UCP_PubM2380


title: umbilical cord plasma, Gen3G, PubM2116

description: Library name: Gen3G_UCP_PubM2116


title: umbilical cord plasma, Gen3G, PubM2847

description: Library name: Gen3G_UCP_PubM2847


title: umbilical cord plasma, Gen3G, PubM2207

description: Library name: Gen3G_UCP_PubM2207


title: umbilical cord plasma, Gen3G, PubM2546

description: Library name: Gen3G_UCP_PubM2546


title: umbilical cord plasma, Gen3G, PubM2664

description: Library name: Gen3G_UCP_PubM2664


title: umbilical cord plasma, Gen3G, PubM2234

description: Library name: Gen3G_UCP_PubM2234


title: umbilical cord plasma, Gen3G, PubM2713

description: Library name: Gen3G_UCP_PubM2713


title: umbilical cord plasma, Gen3G, PubM2750

description: Library name: Gen3G_UCP_PubM2750


title: umbilical cord plasma, Gen3G, PubM2446

description: Library name: Gen3G_UCP_PubM2446


title: umbilical cord plasma, Gen3G, PubM2074

description: Library name: Gen3G_UCP_PubM2074


title: umbilical cord plasma, Gen3G, PubM2740

description: Library name: Gen3G_UCP_PubM2740


title: umbilical cord plasma, Gen3G, PubM2578

description: Library name: Gen3G_UCP_PubM2578


title: umbilical cord plasma, Gen3G, PubM2747

description: Library name: Gen3G_UCP_PubM2747


title: umbilical cord plasma, Gen3G, PubM2657

description: Library name: Gen3G_UCP_PubM2657


title: umbilical cord plasma, Gen3G, PubM2307

description: Library name: Gen3G_UCP_PubM2307


title: umbilical cord plasma, Gen3G, PubM2418

description: Library name: Gen3G_UCP_PubM2418


title: umbilical cord plasma, Gen3G, PubM2240

description: Library name: Gen3G_UCP_PubM2240


title: umbilical cord plasma, Gen3G, PubM2670

description: Library name: Gen3G_UCP_PubM2670


title: umbilical cord plasma, Gen3G, PubM2648

description: Library name: Gen3G_UCP_PubM2648


title: umbilical cord plasma, Gen3G, PubM2119

description: Library name: Gen3G_UCP_PubM2119


title: umbilical cord plasma, Gen3G, PubM2394

description: Library name: Gen3G_UCP_PubM2394


title: umbilical cord plasma, Gen3G, PubM2554

description: Library name: Gen3G_UCP_PubM2554


title: umbilical cord plasma, Gen3G, PubM2233

description: Library name: Gen3G_UCP_PubM2233


title: umbilical cord plasma, Gen3G, PubM2039

description: Library name: Gen3G_UCP_PubM2039


title: umbilical cord plasma, Gen3G, PubM2600

description: Library name: Gen3G_UCP_PubM2600


title: umbilical cord plasma, Gen3G, PubM2729

description: Library name: Gen3G_UCP_PubM2729


title: umbilical cord plasma, Gen3G, PubM2012

description: Library name: Gen3G_UCP_PubM2012


title: umbilical cord plasma, Gen3G, PubM2046

description: Library name: Gen3G_UCP_PubM2046


title: umbilical cord plasma, Gen3G, PubM2610

description: Library name: Gen3G_UCP_PubM2610


title: umbilical cord plasma, Gen3G, PubM2175

description: Library name: Gen3G_UCP_PubM2175


title: umbilical cord plasma, Gen3G, PubM2760

description: Library name: Gen3G_UCP_PubM2760


title: umbilical cord plasma, Gen3G, PubM2770

description: Library name: Gen3G_UCP_PubM2770


title: umbilical cord plasma, Gen3G, PubM2263

description: Library name: Gen3G_UCP_PubM2263


title: umbilical cord plasma, Gen3G, PubM2674

description: Library name: Gen3G_UCP_PubM2674


title: umbilical cord plasma, Gen3G, PubM2790

description: Library name: Gen3G_UCP_PubM2790


title: umbilical cord plasma, Gen3G, PubM2313

description: Library name: Gen3G_UCP_PubM2313


title: umbilical cord plasma, Gen3G, PubM2308

description: Library name: Gen3G_UCP_PubM2308


title: umbilical cord plasma, Gen3G, PubM2723

description: Library name: Gen3G_UCP_PubM2723


title: umbilical cord plasma, Gen3G, PubM2034

description: Library name: Gen3G_UCP_PubM2034


title: umbilical cord plasma, Gen3G, PubM2386

description: Library name: Gen3G_UCP_PubM2386


title: umbilical cord plasma, Gen3G, PubM2635

description: Library name: Gen3G_UCP_PubM2635


title: umbilical cord plasma, Gen3G, PubM2812

description: Library name: Gen3G_UCP_PubM2812


title: umbilical cord plasma, Gen3G, PubM2737

description: Library name: Gen3G_UCP_PubM2737


title: umbilical cord plasma, Gen3G, PubM2286

description: Library name: Gen3G_UCP_PubM2286


title: umbilical cord plasma, Gen3G, PubM2325

description: Library name: Gen3G_UCP_PubM2325


title: umbilical cord plasma, Gen3G, PubM2225

description: Library name: Gen3G_UCP_PubM2225


title: umbilical cord plasma, Gen3G, PubM2845

description: Library name: Gen3G_UCP_PubM2845


title: umbilical cord plasma, Gen3G, PubM2092

description: Library name: Gen3G_UCP_PubM2092


title: umbilical cord plasma, Gen3G, PubM2184

description: Library name: Gen3G_UCP_PubM2184


title: umbilical cord plasma, Gen3G, PubM2409

description: Library name: Gen3G_UCP_PubM2409


title: umbilical cord plasma, Gen3G, PubM2715

description: Library name: Gen3G_UCP_PubM2715


title: umbilical cord plasma, Gen3G, PubM2112

description: Library name: Gen3G_UCP_PubM2112


title: umbilical cord plasma, Gen3G, PubM2542

description: Library name: Gen3G_UCP_PubM2542


title: umbilical cord plasma, Gen3G, PubM2376

description: Library name: Gen3G_UCP_PubM2376


title: umbilical cord plasma, Gen3G, PubM2396

description: Library name: Gen3G_UCP_PubM2396


title: umbilical cord plasma, Gen3G, PubM2333

description: Library name: Gen3G_UCP_PubM2333


title: umbilical cord plasma, Gen3G, PubM2219

description: Library name: Gen3G_UCP_PubM2219


title: umbilical cord plasma, Gen3G, PubM2603

description: Library name: Gen3G_UCP_PubM2603


title: umbilical cord plasma, Gen3G, PubM2178

description: Library name: Gen3G_UCP_PubM2178


title: umbilical cord plasma, Gen3G, PubM2681

description: Library name: Gen3G_UCP_PubM2681


title: umbilical cord plasma, Gen3G, PubM2822

description: Library name: Gen3G_UCP_PubM2822


title: umbilical cord plasma, Gen3G, PubM2793

description: Library name: Gen3G_UCP_PubM2793


title: umbilical cord plasma, Gen3G, PubM2252

description: Library name: Gen3G_UCP_PubM2252


title: umbilical cord plasma, Gen3G, PubM2734

description: Library name: Gen3G_UCP_PubM2734


title: umbilical cord plasma, Gen3G, PubM2016

description: Library name: Gen3G_UCP_PubM2016


title: umbilical cord plasma, Gen3G, PubM2118

description: Library name: Gen3G_UCP_PubM2118


title: umbilical cord plasma, Gen3G, PubM2653

description: Library name: Gen3G_UCP_PubM2653


title: umbilical cord plasma, Gen3G, PubM2605

description: Library name: Gen3G_UCP_PubM2605


title: umbilical cord plasma, Gen3G, PubM2431

description: Library name: Gen3G_UCP_PubM2431


title: umbilical cord plasma, Gen3G, PubM2521

description: Library name: Gen3G_UCP_PubM2521


title: umbilical cord plasma, Gen3G, PubM2033

description: Library name: Gen3G_UCP_PubM2033


title: umbilical cord plasma, Gen3G, PubM2028

description: Library name: Gen3G_UCP_PubM2028


title: umbilical cord plasma, Gen3G, PubM2369

description: Library name: Gen3G_UCP_PubM2369


title: umbilical cord plasma, Gen3G, PubM2844

description: Library name: Gen3G_UCP_PubM2844


title: umbilical cord plasma, Gen3G, PubM2048

description: Library name: Gen3G_UCP_PubM2048


title: umbilical cord plasma, Gen3G, PubM2198

description: Library name: Gen3G_UCP_PubM2198


title: umbilical cord plasma, Gen3G, PubM2253

description: Library name: Gen3G_UCP_PubM2253


title: umbilical cord plasma, Gen3G, PubM2500

description: Library name: Gen3G_UCP_PubM2500


title: umbilical cord plasma, Gen3G, PubM2025

description: Library name: Gen3G_UCP_PubM2025


title: umbilical cord plasma, Gen3G, PubM2355

description: Library name: Gen3G_UCP_PubM2355


title: umbilical cord plasma, Gen3G, PubM2301

description: Library name: Gen3G_UCP_PubM2301


title: umbilical cord plasma, Gen3G, PubM2602

description: Library name: Gen3G_UCP_PubM2602


title: umbilical cord plasma, Gen3G, PubM2211

description: Library name: Gen3G_UCP_PubM2211


title: umbilical cord plasma, Gen3G, PubM2788

description: Library name: Gen3G_UCP_PubM2788


title: umbilical cord plasma, Gen3G, PubM2216

description: Library name: Gen3G_UCP_PubM2216


title: umbilical cord plasma, Gen3G, PubM2745

description: Library name: Gen3G_UCP_PubM2745


title: umbilical cord plasma, Gen3G, PubM2220

description: Library name: Gen3G_UCP_PubM2220


title: umbilical cord plasma, Gen3G, PubM2604

description: Library name: Gen3G_UCP_PubM2604


title: umbilical cord plasma, Gen3G, PubM2404

description: Library name: Gen3G_UCP_PubM2404


title: umbilical cord plasma, Gen3G, PubM2503

description: Library name: Gen3G_UCP_PubM2503


title: umbilical cord plasma, Gen3G, PubM2480

description: Library name: Gen3G_UCP_PubM2480


title: umbilical cord plasma, Gen3G, PubM2526

description: Library name: Gen3G_UCP_PubM2526


title: umbilical cord plasma, Gen3G, PubM2120

description: Library name: Gen3G_UCP_PubM2120


title: umbilical cord plasma, Gen3G, PubM2538

description: Library name: Gen3G_UCP_PubM2538


title: umbilical cord plasma, Gen3G, PubM2192

description: Library name: Gen3G_UCP_PubM2192


title: umbilical cord plasma, Gen3G, PubM2179

description: Library name: Gen3G_UCP_PubM2179


title: umbilical cord plasma, Gen3G, PubM2107

description: Library name: Gen3G_UCP_PubM2107


title: umbilical cord plasma, Gen3G, PubM2062

description: Library name: Gen3G_UCP_PubM2062


title: umbilical cord plasma, Gen3G, PubM2459

description: Library name: Gen3G_UCP_PubM2459


title: umbilical cord plasma, Gen3G, PubM2673

description: Library name: Gen3G_UCP_PubM2673


title: umbilical cord plasma, Gen3G, PubM2411

description: Library name: Gen3G_UCP_PubM2411


title: umbilical cord plasma, Gen3G, PubM2302

description: Library name: Gen3G_UCP_PubM2302


title: umbilical cord plasma, Gen3G, PubM2083

description: Library name: Gen3G_UCP_PubM2083


title: umbilical cord plasma, Gen3G, PubM2416

description: Library name: Gen3G_UCP_PubM2416


title: umbilical cord plasma, Gen3G, PubM2407

description: Library name: Gen3G_UCP_PubM2407


title: umbilical cord plasma, Gen3G, PubM2828

description: Library name: Gen3G_UCP_PubM2828


title: umbilical cord plasma, Gen3G, PubM2801

description: Library name: Gen3G_UCP_PubM2801


title: umbilical cord plasma, Gen3G, PubM2875

description: Library name: Gen3G_UCP_PubM2875


title: umbilical cord plasma, Gen3G, PubM2223

description: Library name: Gen3G_UCP_PubM2223


title: umbilical cord plasma, Gen3G, PubM2455

description: Library name: Gen3G_UCP_PubM2455


title: umbilical cord plasma, Gen3G, PubM2342

description: Library name: Gen3G_UCP_PubM2342


title: umbilical cord plasma, Gen3G, PubM2561

description: Library name: Gen3G_UCP_PubM2561


title: umbilical cord plasma, Gen3G, PubM2876

description: Library name: Gen3G_UCP_PubM2876


title: umbilical cord plasma, Gen3G, PubM2248

description: Library name: Gen3G_UCP_PubM2248


title: umbilical cord plasma, Gen3G, PubM2638

description: Library name: Gen3G_UCP_PubM2638


title: umbilical cord plasma, Gen3G, PubM2714

description: Library name: Gen3G_UCP_PubM2714


title: umbilical cord plasma, Gen3G, PubM2505

description: Library name: Gen3G_UCP_PubM2505


title: umbilical cord plasma, Gen3G, PubM2607

description: Library name: Gen3G_UCP_PubM2607


title: umbilical cord plasma, Gen3G, PubM2454

description: Library name: Gen3G_UCP_PubM2454


title: umbilical cord plasma, Gen3G, PubM2135

description: Library name: Gen3G_UCP_PubM2135


title: umbilical cord plasma, Gen3G, PubM2166

description: Library name: Gen3G_UCP_PubM2166


title: umbilical cord plasma, Gen3G, PubM2081

description: Library name: Gen3G_UCP_PubM2081


title: umbilical cord plasma, Gen3G, PubM2267

description: Library name: Gen3G_UCP_PubM2267


title: umbilical cord plasma, Gen3G, PubM2511

description: Library name: Gen3G_UCP_PubM2511


title: umbilical cord plasma, Gen3G, PubM2389

description: Library name: Gen3G_UCP_PubM2389


title: umbilical cord plasma, Gen3G, PubM2167

description: Library name: Gen3G_UCP_PubM2167


title: umbilical cord plasma, Gen3G, PubM2032

description: Library name: Gen3G_UCP_PubM2032


title: umbilical cord plasma, Gen3G, PubM2646

description: Library name: Gen3G_UCP_PubM2646


title: umbilical cord plasma, Gen3G, PubM2322

description: Library name: Gen3G_UCP_PubM2322


title: umbilical cord plasma, Gen3G, PubM2518

description: Library name: Gen3G_UCP_PubM2518


title: umbilical cord plasma, Gen3G, PubM2391

description: Library name: Gen3G_UCP_PubM2391


title: umbilical cord plasma, Gen3G, PubM2467

description: Library name: Gen3G_UCP_PubM2467


title: umbilical cord plasma, Gen3G, PubM2710

description: Library name: Gen3G_UCP_PubM2710


title: umbilical cord plasma, Gen3G, PubM2465

description: Library name: Gen3G_UCP_PubM2465


title: umbilical cord plasma, Gen3G, PubM2280

description: Library name: Gen3G_UCP_PubM2280


title: umbilical cord plasma, Gen3G, PubM2481

description: Library name: Gen3G_UCP_PubM2481


title: umbilical cord plasma, Gen3G, PubM2236

description: Library name: Gen3G_UCP_PubM2236


title: umbilical cord plasma, Gen3G, PubM2105

description: Library name: Gen3G_UCP_PubM2105


title: umbilical cord plasma, Gen3G, PubM2101

description: Library name: Gen3G_UCP_PubM2101


title: umbilical cord plasma, Gen3G, PubM2872

description: Library name: Gen3G_UCP_PubM2872


title: umbilical cord plasma, Gen3G, PubM2649

description: Library name: Gen3G_UCP_PubM2649


title: umbilical cord plasma, Gen3G, PubM2469

description: Library name: Gen3G_UCP_PubM2469


title: umbilical cord plasma, Gen3G, PubM2161

description: Library name: Gen3G_UCP_PubM2161


title: umbilical cord plasma, Gen3G, PubM2484

description: Library name: Gen3G_UCP_PubM2484


title: umbilical cord plasma, Gen3G, PubM2585

description: Library name: Gen3G_UCP_PubM2585


title: umbilical cord plasma, Gen3G, PubM2861

description: Library name: Gen3G_UCP_PubM2861


title: umbilical cord plasma, Gen3G, PubM2540

description: Library name: Gen3G_UCP_PubM2540


title: umbilical cord plasma, Gen3G, PubM2190

description: Library name: Gen3G_UCP_PubM2190


title: umbilical cord plasma, Gen3G, PubM2367

description: Library name: Gen3G_UCP_PubM2367


title: umbilical cord plasma, Gen3G, PubM2774

description: Library name: Gen3G_UCP_PubM2774


title: umbilical cord plasma, Gen3G, PubM2021

description: Library name: Gen3G_UCP_PubM2021


title: umbilical cord plasma, Gen3G, PubM2850

description: Library name: Gen3G_UCP_PubM2850


title: umbilical cord plasma, Gen3G, PubM2040

description: Library name: Gen3G_UCP_PubM2040


title: umbilical cord plasma, Gen3G, PubM2661

description: Library name: Gen3G_UCP_PubM2661


title: umbilical cord plasma, Gen3G, PubM2769

description: Library name: Gen3G_UCP_PubM2769


title: umbilical cord plasma, Gen3G, PubM2581

description: Library name: Gen3G_UCP_PubM2581


title: umbilical cord plasma, Gen3G, PubM2688

description: Library name: Gen3G_UCP_PubM2688


title: umbilical cord plasma, Gen3G, PubM2601

description: Library name: Gen3G_UCP_PubM2601


title: umbilical cord plasma, Gen3G, PubM2030

description: Library name: Gen3G_UCP_PubM2030


title: umbilical cord plasma, Gen3G, PubM2736

description: Library name: Gen3G_UCP_PubM2736


title: umbilical cord plasma, Gen3G, PubM2100

description: Library name: Gen3G_UCP_PubM2100


title: umbilical cord plasma, Gen3G, PubM2388

description: Library name: Gen3G_UCP_PubM2388


title: umbilical cord plasma, Gen3G, PubM2706

description: Library name: Gen3G_UCP_PubM2706


title: umbilical cord plasma, Gen3G, PubM2384

description: Library name: Gen3G_UCP_PubM2384


title: umbilical cord plasma, Gen3G, PubM2102

description: Library name: Gen3G_UCP_PubM2102


title: umbilical cord plasma, Gen3G, PubM2496

description: Library name: Gen3G_UCP_PubM2496


title: umbilical cord plasma, Gen3G, PubM2157

description: Library name: Gen3G_UCP_PubM2157


title: umbilical cord plasma, Gen3G, PubM2382

description: Library name: Gen3G_UCP_PubM2382


title: umbilical cord plasma, Gen3G, PubM2003

description: Library name: Gen3G_UCP_PubM2003


title: umbilical cord plasma, Gen3G, PubM2335

description: Library name: Gen3G_UCP_PubM2335


title: umbilical cord plasma, Gen3G, PubM2804

description: Library name: Gen3G_UCP_PubM2804


title: umbilical cord plasma, Gen3G, PubM2749

description: Library name: Gen3G_UCP_PubM2749


title: umbilical cord plasma, Gen3G, PubM2006

description: Library name: Gen3G_UCP_PubM2006


title: umbilical cord plasma, Gen3G, PubM2515

description: Library name: Gen3G_UCP_PubM2515


title: umbilical cord plasma, Gen3G, PubM2687

description: Library name: Gen3G_UCP_PubM2687


title: umbilical cord plasma, Gen3G, PubM2709

description: Library name: Gen3G_UCP_PubM2709


title: Primary PCa, patient with no bone metastasis, donor RC_27

city: Melbourne

first: xin

last: liu

address: 305 Graattan St

country: Australia

institute: Peter mac

description: Library name: RC_27_RARP

data_processing:
RNA-seq analysis was performed in R (v4.1.0). Clean reads (no adapter contamination, < 20% undecided bases, > 50% high quality bases) were aligned using the RSubread package (v2.8.1). An index was built using the Ensembl Homo sapiens GRCh38 primary assembly genome file and alignment was performed using subjunc with default settings.
Gene counts were obtained using featureCounts using the Ensembl Homo sapiens GRCm38 version 105 GTF annotation file, with isPairedEnd = TRUE, useMetaFeatures = TRUE and strandSpecific = 0.
Ensembl gene IDs were annotated using the biomaRt package (v2.50.1) and a DGEList object was created with the counts and gene annotation using the edgeR package (v3.36.0). A design matrix was constructed incorporating the sample group (NBmRC, BmRC, LN or Bone met).
Lowly expressed genes were removed using the filterByExpr function and normalisation factors were calculated using the TMM method. Counts were transformed using the voom method and a linear model was fit using the edgeR voomLmFit function, incorporating sample weights and using donor as a blocking factor.
Differential gene expression analyses were performed using the limma (v3.50.0) package. Groups were compared using the contrasts.fit function and moderated t-statistics were calculated using the treat function with a 1.2-fold cut-off. Differentially expressed genes were determined using a false discovery rate-adjusted (FDR) p-value < 0.05.
Assembly: hg38
Supplementary files format and content: PCa_Met_processed.xlsx contains processed counts (tab 1) and voom-transformed expression values (tab 2).

source_name: Primary adenocarcinoma

extract_protocol:
Total RNA was extracted from fresh frozen tissue (n = 50) using the AllPrep DNA/RNA Mini kit (Qiagen, Maryland U.S.A) according to manufacturer’s instructions. RNA yield was quantified using the Qubit RNA High Sensitivity Assay (Invitrogen) with the Qubit 2.0 Fluorometer. RNA quality was assessed using the RNA 6000 Pico Kit on the Agilent 2100 Bioanalyzer.
One microgram of total RNA (RIN > 6.5) was used as input into the TruSeq RNA Sample Preparation Kit v2 (Illumina). cDNA fragments were end repaired, adenylated, adaptors-ligated, purified and PCR enriched. Two samples did not pass pre-sequencing QC (RC_02_RARP, RC_17_RARP). Sequencing (n = 48) was performed on the Illumina HiSeq3000 (PE-150, 20 million paired reads per sample) by Novogene Bioinformatics (Hong Kong).

value: Primary adenocarcinoma

tag: donor

tag: cancer type

value: Prostate cancer

tag: group

value: NBmRC

tag: group description

value: NBmRC denotes non-metastatic primary tumor tissue

tag: age at_diagnosis

tag: path ggs

tag: clinical tumor_stage


title: umbilical cord plasma, Gen3G, PubM2245

description: Library name: Gen3G_UCP_PubM2245

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: birth weight_(g)

tag: z-score birth_weight

tag: birth lenght_(cm)


title: umbilical cord plasma, Gen3G, PubM2237

description: Library name: Gen3G_UCP_PubM2237

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))


title: Primary PCa, patient with no bone metastasis, donor RC_26

description: Library name: RC_26_RARP

tag: tissue

tag: donor

tag: cancer type

tag: group


title: umbilical cord plasma, Gen3G, PubM2560

description: Library name: Gen3G_UCP_PubM2560

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: PCa lymph node metastases, donor RC_27

description: Library name: RC_27_LN

source_name: Lymph node metastases

value: Lymph node metastases

value: LN

tag: group description

value: LN denotes tissue from PCa lymph node metastases

tag: age at_diagnosis

tag: path ggs

tag: clinical tumor_stage


title: umbilical cord plasma, Gen3G, PubM2724

description: Library name: Gen3G_UCP_PubM2724

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: birth weight_(g)

tag: z-score birth_weight

tag: birth lenght_(cm)


title: umbilical cord plasma, Gen3G, PubM2117

description: Library name: Gen3G_UCP_PubM2117

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))


title: umbilical cord plasma, Gen3G, PubM2257

description: Library name: Gen3G_UCP_PubM2257

tag: tissue

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: umbilical cord plasma, Gen3G, PubM2827

description: Library name: Gen3G_UCP_PubM2827


title: PCa lymph node metastases, donor RC_26

description: Library name: RC_26_LN

tag: donor

tag: cancer type

tag: group

tag: group description

tag: age at_diagnosis

tag: path ggs


title: umbilical cord plasma, Gen3G, PubM2071

description: Library name: Gen3G_UCP_PubM2071

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: birth weight_(g)

tag: z-score birth_weight


title: Primary PCa, patient with bone-metastatic disease, donor RC_25

description: Library name: RC_25_RARP

value: BmRC

value: BmRC denotes primary tumor tissue from patient with bone-metastatic PCa

tag: clinical tumor_stage


title: Primary PCa, patient with bone-metastatic disease, donor RC_24

description: Library name: RC_24_RARP


title: umbilical cord plasma, Gen3G, PubM2741

description: Library name: Gen3G_UCP_PubM2741

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)


title: umbilical cord plasma, Gen3G, PubM2477

description: Library name: Gen3G_UCP_PubM2477

tag: tissue

tag: sample leptinemia_(pg/ml))

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: umbilical cord plasma, Gen3G, PubM2108

description: Library name: Gen3G_UCP_PubM2108


title: Primary PCa, patient with bone-metastatic disease, donor RC_23

description: Library name: RC_23_RARP

tag: donor

tag: cancer type

tag: group

tag: group description

tag: age at_diagnosis

tag: path ggs


title: umbilical cord plasma, Gen3G, PubM2495

description: Library name: Gen3G_UCP_PubM2495

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: birth weight_(g)

tag: z-score birth_weight


title: Primary PCa, patient with bone-metastatic disease, donor RC_21

description: Library name: RC_21_RARP

tag: clinical tumor_stage


title: umbilical cord plasma, Gen3G, PubM2434

description: Library name: Gen3G_UCP_PubM2434

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)


title: umbilical cord plasma, Gen3G, PubM2264

description: Library name: Gen3G_UCP_PubM2264

tag: tissue

tag: sample leptinemia_(pg/ml))

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: Primary PCa, patient with no bone metastasis, donor RC_19

description: Library name: RC_19_RARP

tag: donor

tag: cancer type

tag: group

tag: group description

tag: age at_diagnosis

tag: path ggs


title: umbilical cord plasma, Gen3G, PubM2502

description: Library name: Gen3G_UCP_PubM2502

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: birth weight_(g)

tag: z-score birth_weight


title: Primary PCa, patient with bone-metastatic disease, donor RC_22

description: Library name: RC_22_RARP

tag: clinical tumor_stage


title: Primary PCa, patient with bone-metastatic disease, donor RC_16

description: Library name: RC_16_RARP


title: Primary PCa, patient with no bone metastasis, donor RC_18

description: Library name: RC_18_RARP


title: umbilical cord plasma, Gen3G, PubM2400

description: Library name: Gen3G_UCP_PubM2400

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)


title: umbilical cord plasma, Gen3G, PubM2121

description: Library name: Gen3G_UCP_PubM2121

tag: tissue

tag: sample leptinemia_(pg/ml))

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: umbilical cord plasma, Gen3G, PubM2022

description: Library name: Gen3G_UCP_PubM2022


title: PCa bone metastases, donor RC_15

description: Library name: RC_15_MET

source_name: Bone metastases

value: Bone metastases

tag: donor

tag: cancer type

tag: group

tag: group description

value: Bone met denotes tissue from PCa bone metastases

tag: age at_diagnosis

tag: path ggs


title: PCa lymph node metastases, donor RC_18

description: Library name: RC_16_LN

value: LN denotes tissue from PCa lymph node metastases from patient RC_18 incorrectly named in RC_16 in "library")

tag: clinical tumor_stage


title: umbilical cord plasma, Gen3G, PubM2381

description: Library name: Gen3G_UCP_PubM2381

value: umilical cord plasma

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: birth weight_(g)

tag: z-score birth_weight

tag: birth lenght_(cm)


title: Primary PCa, patient with bone-metastatic disease, donor RC_20

description: Library name: RC_20_RARP

tag: tissue


title: umbilical cord plasma, Gen3G, PubM2862

description: Library name: Gen3G_UCP_PubM2862

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))


title: Primary PCa, patient with bone-metastatic disease, donor RC_15

description: Library name: RC_15_RARP

tag: donor

tag: cancer type

tag: group

tag: group description


title: PCa lymph node metastases, donor RC_15

description: Library name: RC_15_LN

tag: age at_diagnosis

tag: path ggs

tag: clinical tumor_stage


title: umbilical cord plasma, Gen3G, PubM2262

description: Library name: Gen3G_UCP_PubM2262

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: birth weight_(g)

tag: sample glycemia_(mmol/l)

tag: batch (run_and_region)


title: PCa bone metastases, donor RC_13

description: Library name: RC_13_MET

tag: tissue


title: PCa bone metastases, donor RC_12

description: Library name: RC_12_MET


title: umbilical cord plasma, Gen3G, PubM2294

description: Library name: Gen3G_UCP_PubM2294

tag: z-score birth_weight

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: maternal parity


title: umbilical cord plasma, Gen3G, PubM2173

description: Library name: Gen3G_UCP_PubM2173

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))


title: umbilical cord plasma, Gen3G, PubM2217

description: Library name: Gen3G_UCP_PubM2217


title: umbilical cord plasma, Gen3G, PubM2510

description: Library name: Gen3G_UCP_PubM2510

value: male


title: PCa bone metastases, donor RC_06

description: Library name: RC_06_MET

tag: donor

tag: cancer type

tag: group

tag: group description

tag: age at_diagnosis

tag: path ggs


title: umbilical cord plasma, Gen3G, PubM2685

description: Library name: Gen3G_UCP_PubM2685

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: birth weight_(g)

tag: sample glycemia_(mmol/l)


title: Primary PCa, patient with bone-metastatic disease, donor RC

description: Library name: RC_06_RARP

tag: tissue

tag: clinical tumor_stage


title: PCa bone metastases, donor RC_05

description: Library name: RC_05_MET


title: umbilical cord plasma, Gen3G, PubM2078

description: Library name: Gen3G_UCP_PubM2078

tag: z-score birth_weight

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: gestationnal weight_gain_(kg)

tag: batch (run_and_region)


title: Primary PCa, patient with bone-metastatic disease, donor RC_05

description: Library name: RC_05_RARP

tag: donor

tag: cancer type

tag: group


title: PCa bone metastases, donor RC_08

description: Library name: RC_08_MET

tag: group description

tag: age at_diagnosis


title: Primary PCa, patient with bone-metastatic disease, donor RC_04

description: Library name: RC_04_RARP

tag: path ggs

value: Poorly differentiated


title: umbilical cord plasma, Gen3G, PubM2583

description: Library name: Gen3G_UCP_PubM2583

tag: fetal sex

value: female

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))


title: PCa bone metastases, donor RC_03

description: Library name: RC_03_MET

tag: tissue

tag: clinical tumor_stage


title: Primary PCa, patient with no bone metastasis, donor NR_15

description: Library name: NR_15_RARP


title: umbilical cord plasma, Gen3G, PubM2131

description: Library name: Gen3G_UCP_PubM2131

value: vaginal

tag: birth weight_(g)

tag: z-score birth_weight

tag: birth lenght_(cm)

tag: maternal age_at_first_trimester_(years)

tag: maternal bmi_(kg/m2)

tag: sample glycemia_(mmol/l)


title: umbilical cord plasma, Gen3G, PubM2863

description: Library name: Gen3G_UCP_PubM2863

tag: gestationnal weight_gain_(kg)

tag: batch (run_and_region)


title: Primary PCa, patient with no bone metastasis, donor NR_14

description: Library name: NR_14_RARP

value: Primary adenocarcinoma

tag: donor

tag: cancer type

tag: group

tag: group description

tag: age at_diagnosis

tag: path ggs


title: umbilical cord plasma, Gen3G, PubM2026

description: Library name: Gen3G_UCP_PubM2026

tag: fetal sex

tag: gestational age_at_birth_(weeks)

tag: delivery type

tag: maternal parity

tag: sample hemolysis_(from_0_to_5)

tag: sample leptinemia_(pg/ml))